diff --git a/vcell-core/src/main/java/cbit/vcell/xml/XmlReader.java b/vcell-core/src/main/java/cbit/vcell/xml/XmlReader.java index 50cfb68af6..2a5f9ef551 100644 --- a/vcell-core/src/main/java/cbit/vcell/xml/XmlReader.java +++ b/vcell-core/src/main/java/cbit/vcell/xml/XmlReader.java @@ -1,8413 +1,8535 @@ -/* - * Copyright (C) 1999-2011 University of Connecticut Health Center - * - * Licensed under the MIT License (the "License"). - * You may not use this file except in compliance with the License. - * You may obtain a copy of the License at: - * - * http://www.opensource.org/licenses/mit-license.php - */ - -package cbit.vcell.xml; - -import java.beans.PropertyVetoException; -import java.math.BigInteger; -import java.text.SimpleDateFormat; -import java.util.*; -import java.util.function.Consumer; - -import cbit.vcell.mapping.*; -import cbit.vcell.model.*; -import cbit.vcell.solver.*; -import org.jdom2.Attribute; -import org.jdom2.DataConversionException; -import org.jdom2.Element; -import org.jdom2.Namespace; -import org.vcell.chombo.ChomboSolverSpec; -import org.vcell.chombo.RefinementRoi; -import org.vcell.chombo.RefinementRoi.RoiType; -import org.vcell.chombo.TimeInterval; -import org.vcell.model.rbm.*; -import org.vcell.model.rbm.MolecularComponentPattern.BondType; -import org.vcell.model.rbm.SpeciesPattern.Bond; -import org.vcell.pathway.PathwayModel; -import org.vcell.pathway.persistence.PathwayReaderBiopax3; -import org.vcell.pathway.persistence.RDFXMLContext; -import org.vcell.relationship.RelationshipModel; -import org.vcell.relationship.persistence.RelationshipReader; -import org.vcell.util.BeanUtils; -import org.vcell.util.Commented; -import org.vcell.util.Coordinate; -import org.vcell.util.Extent; -import org.vcell.util.GenericUtils; -import org.vcell.util.Hex; -import org.vcell.util.ISize; -import org.vcell.util.Origin; -import org.vcell.util.Pair; -import org.vcell.util.document.ExternalDataIdentifier; -import org.vcell.util.document.GroupAccess; -import org.vcell.util.document.GroupAccessAll; -import org.vcell.util.document.GroupAccessNone; -import org.vcell.util.document.GroupAccessSome; -import org.vcell.util.document.KeyValue; -import org.vcell.util.document.SimulationVersion; -import org.vcell.util.document.User; -import org.vcell.util.document.VCellSoftwareVersion; -import org.vcell.util.document.Version; -import org.vcell.util.document.VersionFlag; -import org.vcell.util.springsalad.Colors; -import org.vcell.util.springsalad.NamedColor; - -import cbit.image.ImageException; -import cbit.image.VCImage; -import cbit.image.VCImageCompressed; -import cbit.image.VCPixelClass; -import cbit.vcell.biomodel.BioModel; -import cbit.vcell.biomodel.meta.VCMetaData; -import cbit.vcell.biomodel.meta.xml.XMLMetaData; -import cbit.vcell.biomodel.meta.xml.XMLMetaDataReader; -import cbit.vcell.biomodel.meta.xml.rdf.XMLRDF; -import cbit.vcell.data.DataContext; -import cbit.vcell.data.DataSymbol; -import cbit.vcell.data.DataSymbol.DataSymbolType; -import cbit.vcell.data.FieldDataSymbol; -import cbit.vcell.dictionary.BoundCompound; -import cbit.vcell.dictionary.BoundEnzyme; -import cbit.vcell.dictionary.BoundProtein; -import cbit.vcell.dictionary.CompoundInfo; -import cbit.vcell.dictionary.EnzymeInfo; -import cbit.vcell.dictionary.EnzymeRef; -import cbit.vcell.dictionary.FormalCompound; -import cbit.vcell.dictionary.FormalEnzyme; -import cbit.vcell.dictionary.FormalProtein; -import cbit.vcell.dictionary.ProteinInfo; -import cbit.vcell.geometry.AnalyticSubVolume; -import cbit.vcell.geometry.CSGHomogeneousTransformation; -import cbit.vcell.geometry.CSGNode; -import cbit.vcell.geometry.CSGObject; -import cbit.vcell.geometry.CSGPrimitive; -import cbit.vcell.geometry.CSGPrimitive.PrimitiveType; -import cbit.vcell.geometry.CSGPseudoPrimitive; -import cbit.vcell.geometry.CSGRotation; -import cbit.vcell.geometry.CSGScale; -import cbit.vcell.geometry.CSGSetOperator; -import cbit.vcell.geometry.CSGSetOperator.OperatorType; -import cbit.vcell.geometry.CSGTranslation; -import cbit.vcell.geometry.CompartmentSubVolume; -import cbit.vcell.geometry.ControlPointCurve; -import cbit.vcell.geometry.Geometry; -import cbit.vcell.geometry.GeometryClass; -import cbit.vcell.geometry.GeometryException; -import cbit.vcell.geometry.GeometryThumbnailImageFactoryAWT; -import cbit.vcell.geometry.GeometryUnitSystem; -import cbit.vcell.geometry.ImageSubVolume; -import cbit.vcell.geometry.Line; -import cbit.vcell.geometry.SampledCurve; -import cbit.vcell.geometry.Spline; -import cbit.vcell.geometry.SubVolume; -import cbit.vcell.geometry.SurfaceClass; -import cbit.vcell.geometry.surface.GeometricRegion; -import cbit.vcell.geometry.surface.GeometrySurfaceDescription; -import cbit.vcell.geometry.surface.SurfaceGeometricRegion; -import cbit.vcell.geometry.surface.VolumeGeometricRegion; -import cbit.vcell.mapping.BioEvent.BioEventParameterType; -import cbit.vcell.mapping.BioEvent.TriggerType; -import cbit.vcell.mapping.MicroscopeMeasurement.ConvolutionKernel; -import cbit.vcell.mapping.MicroscopeMeasurement.GaussianConvolutionKernel; -import cbit.vcell.mapping.MicroscopeMeasurement.ProjectionZKernel; -import cbit.vcell.mapping.ParameterContext.LocalParameter; -import cbit.vcell.mapping.ParameterContext.ParameterRoleEnum; -import cbit.vcell.mapping.ReactionRuleSpec.ReactionRuleMappingType; -import cbit.vcell.mapping.ReactionRuleSpec.Subtype; -import cbit.vcell.mapping.ReactionRuleSpec.TransitionCondition; -import cbit.vcell.mapping.SimulationContext.Application; -import cbit.vcell.mapping.SimulationContext.SimulationContextParameter; -import cbit.vcell.mapping.spatial.PointObject; -import cbit.vcell.mapping.spatial.SpatialObject; -import cbit.vcell.mapping.spatial.SpatialObject.QuantityCategory; -import cbit.vcell.mapping.spatial.SurfaceRegionObject; -import cbit.vcell.mapping.spatial.VolumeRegionObject; -import cbit.vcell.mapping.spatial.processes.PointKinematics; -import cbit.vcell.mapping.spatial.processes.PointLocation; -import cbit.vcell.mapping.spatial.processes.SpatialProcess; -import cbit.vcell.mapping.spatial.processes.SpatialProcess.SpatialProcessParameterType; -import cbit.vcell.mapping.spatial.processes.SurfaceKinematics; -import cbit.vcell.mapping.spatial.processes.VolumeKinematics; -import cbit.vcell.math.Action; -import cbit.vcell.math.BoundaryConditionType; -import cbit.vcell.math.CompartmentSubDomain; -import cbit.vcell.math.ComputeCentroidComponentEquation; -import cbit.vcell.math.ComputeCentroidComponentEquation.CentroidComponent; -import cbit.vcell.math.ComputeMembraneMetricEquation; -import cbit.vcell.math.ComputeMembraneMetricEquation.MembraneMetricComponent; -import cbit.vcell.math.ComputeNormalComponentEquation; -import cbit.vcell.math.ComputeNormalComponentEquation.NormalComponent; -import cbit.vcell.math.Constant; -import cbit.vcell.math.ConvolutionDataGenerator; -import cbit.vcell.math.ConvolutionDataGenerator.ConvolutionDataGeneratorKernel; -import cbit.vcell.math.ConvolutionDataGenerator.GaussianConvolutionDataGeneratorKernel; -import cbit.vcell.math.Distribution; -import cbit.vcell.math.Event; -import cbit.vcell.math.Event.Delay; -import cbit.vcell.math.Event.EventAssignment; -import cbit.vcell.math.ExplicitDataGenerator; -import cbit.vcell.math.FastInvariant; -import cbit.vcell.math.FastRate; -import cbit.vcell.math.FastSystem; -import cbit.vcell.math.FilamentRegionVariable; -import cbit.vcell.math.FilamentSubDomain; -import cbit.vcell.math.FilamentVariable; -import cbit.vcell.math.Function; -import cbit.vcell.math.GaussianDistribution; -import cbit.vcell.math.InsideVariable; -import cbit.vcell.math.InteractionRadius; -import cbit.vcell.math.JumpCondition; -import cbit.vcell.math.JumpProcess; -import cbit.vcell.math.JumpProcessRateDefinition; -import cbit.vcell.math.LangevinParticleJumpProcess; -import cbit.vcell.math.LangevinParticleMolecularComponent; -import cbit.vcell.math.LangevinParticleMolecularType; -import cbit.vcell.math.MacroscopicRateConstant; -import cbit.vcell.math.MathDescription; -import cbit.vcell.math.MathException; -import cbit.vcell.math.MathFormatException; -import cbit.vcell.math.MemVariable; -import cbit.vcell.math.MembraneParticleVariable; -import cbit.vcell.math.MembraneRandomVariable; -import cbit.vcell.math.MembraneRegionEquation; -import cbit.vcell.math.MembraneRegionVariable; -import cbit.vcell.math.MembraneSubDomain; -import cbit.vcell.math.OdeEquation; -import cbit.vcell.math.OutsideVariable; -import cbit.vcell.math.ParticleComponentStateDefinition; -import cbit.vcell.math.ParticleComponentStatePattern; -import cbit.vcell.math.ParticleJumpProcess; -import cbit.vcell.math.ParticleJumpProcess.ProcessSymmetryFactor; -import cbit.vcell.math.ParticleMolecularComponent; -import cbit.vcell.math.ParticleMolecularComponentPattern; -import cbit.vcell.math.ParticleMolecularComponentPattern.ParticleBondType; -import cbit.vcell.math.ParticleMolecularType; -import cbit.vcell.math.ParticleMolecularTypePattern; -import cbit.vcell.math.ParticleObservable.ObservableType; -import cbit.vcell.math.ParticleObservable.Sequence; -import cbit.vcell.math.ParticleProperties; -import cbit.vcell.math.ParticleProperties.ParticleInitialCondition; -import cbit.vcell.math.ParticleProperties.ParticleInitialConditionConcentration; -import cbit.vcell.math.ParticleProperties.ParticleInitialConditionCount; -import cbit.vcell.math.ParticleSpeciesPattern; -import cbit.vcell.math.ParticleVariable; -import cbit.vcell.math.PdeEquation; -import cbit.vcell.math.PdeEquation.BoundaryConditionValue; -import cbit.vcell.math.PointSubDomain; -import cbit.vcell.math.PointVariable; -import cbit.vcell.math.ProjectionDataGenerator; -import cbit.vcell.math.RandomVariable; -import cbit.vcell.math.StochVolVariable; -import cbit.vcell.math.SubDomain.BoundaryConditionSpec; -import cbit.vcell.math.UniformDistribution; -import cbit.vcell.math.VarIniCondition; -import cbit.vcell.math.VarIniCount; -import cbit.vcell.math.VarIniPoissonExpectedCount; -import cbit.vcell.math.Variable; -import cbit.vcell.math.Variable.Domain; -import cbit.vcell.math.VariableHash; -import cbit.vcell.math.VariableType; -import cbit.vcell.math.VolVariable; -import cbit.vcell.math.VolumeParticleObservable; -import cbit.vcell.math.VolumeParticleSpeciesPattern; -import cbit.vcell.math.VolumeParticleVariable; -import cbit.vcell.math.VolumeRandomVariable; -import cbit.vcell.math.VolumeRegionEquation; -import cbit.vcell.math.VolumeRegionVariable; -import cbit.vcell.mathmodel.MathModel; -import cbit.vcell.model.Kinetics.KineticsParameter; -import cbit.vcell.model.Model.ModelParameter; -import cbit.vcell.model.Model.RbmModelContainer; -import cbit.vcell.model.Model.ReservedSymbol; -import cbit.vcell.model.Model.StructureTopology; -import cbit.vcell.model.NodeReference.Mode; -import cbit.vcell.model.RbmKineticLaw.RateLawType; -import cbit.vcell.model.RbmKineticLaw.RbmKineticLawParameterType; -import cbit.vcell.modelopt.AnalysisTask; -import cbit.vcell.modelopt.ParameterEstimationTask; -import cbit.vcell.modelopt.ParameterEstimationTaskXMLPersistence; -import cbit.vcell.parser.Expression; -import cbit.vcell.parser.ExpressionBindingException; -import cbit.vcell.parser.ExpressionException; -import cbit.vcell.parser.SymbolTableEntry; -import cbit.vcell.render.Vect3d; -import cbit.vcell.solver.AnnotatedFunction.FunctionCategory; -import cbit.vcell.solvers.mb.MovingBoundarySolverOptions; -import cbit.vcell.solvers.mb.MovingBoundarySolverOptions.ExtrapolationMethod; -import cbit.vcell.solvers.mb.MovingBoundarySolverOptions.RedistributionMode; -import cbit.vcell.solvers.mb.MovingBoundarySolverOptions.RedistributionVersion; -import cbit.vcell.units.VCUnitDefinition; - - -/** - * This class implements the translation of XML data into Java Vcell objects.. - * Creation date: (7/17/2000 12:22:50 PM) - * - * @author: - */ - -public class XmlReader extends XmlBase { - - //The following parameter specifies if the keys should be read. - //By default the value is FALSE to not affect of the current software. - private boolean readKeysFlag = false; - private Namespace vcNamespace = Namespace.getNamespace(XMLTags.VCML_NS_BLANK); // default - blank namespace - private ModelUnitSystem forcedModelUnitSystem = null; - - /** - * This constructor takes a parameter to specify if the KeyValue should be ignored - * Creation date: (3/13/2001 12:16:30 PM) - */ - public XmlReader(boolean readKeys){ - super(); - this.readKeysFlag = readKeys; - } - - public XmlReader(boolean readKeys, Namespace argNS){ - super(); - this.readKeysFlag = readKeys; - this.vcNamespace = argNS; - } - - public void setForcedModelUnitSystem(ModelUnitSystem newModelUnitSystem){ - forcedModelUnitSystem = newModelUnitSystem; - } - - /** - * This method returns a Action object from a XML element. - * Creation date: (7/24/2006 5:56:36 PM) - * - * @param param Element - * @return cbit.vcell.math.Action - * @throws cbit.vcell.xml.XmlParseException The exception description. - */ - private Action getAction(Element param, MathDescription md) throws XmlParseException, MathException, ExpressionException{ - //retrieve values - String operation = unMangle(param.getAttributeValue(XMLTags.OperationAttrTag)); - String operand = param.getText(); - Expression exp = null; - if(operand != null && operand.length() != 0){ - exp = unMangleExpression(operand); - } - String name = unMangle(param.getAttributeValue(XMLTags.VarNameAttrTag)); - - Variable var = md.getVariable(name); - if(var == null){ - throw new MathFormatException("variable " + name + " not defined"); - } - if(!(var instanceof StochVolVariable) && !(var instanceof ParticleVariable)){ - throw new MathFormatException("variable " + name + " not a Stochastic Volume Variable"); - } - try { - Action action = new Action(var, operation, exp); - return action; - } catch(Exception e){ - lg.error(e.getMessage(), e); - } - - return null; - } - - private VolumeGeometricRegion getAdjacentVolumeRegion(ArrayList regions, String regionName){ - for(int i = 0; i < regions.size(); i++){ - GeometricRegion rvl = regions.get(i); - if(rvl instanceof VolumeGeometricRegion && rvl.getName().equals(regionName)){ - return (VolumeGeometricRegion) rvl; - } - } - - return null; - } - - - /** - * This method returns an AnalyticSubVolume object from a XML representation. - * Creation date: (5/1/2001 5:26:17 PM) - * - * @param param Element - * @return cbit.vcell.geometry.AnalyticSubVolume - */ - private AnalyticSubVolume getAnalyticSubVolume(Element param) throws XmlParseException{ - //retrieve the attributes - String name = param.getAttributeValue(XMLTags.NameAttrTag); - int handle = Integer.parseInt(param.getAttributeValue(XMLTags.HandleAttrTag)); - - //process the key - KeyValue key = null; - String temp = param.getAttributeValue(XMLTags.KeyValueAttrTag); - - if(temp != null && temp.length() > 0 && this.readKeysFlag){ - key = new KeyValue(temp); - } - - //Retrieve the expression - temp = param.getChildText(XMLTags.AnalyticExpressionTag, vcNamespace); - if(temp == null){ - throw new XmlParseException("A Problem occured while retrieving the analytic expression of the AnalyticSubvolume " + name); - } - Expression newexpression = unMangleExpression(temp); - - //Create the AnalyticCompartment - AnalyticSubVolume newsubvolume = null; - try { - newsubvolume = new AnalyticSubVolume(key, name, newexpression, handle); - } catch(ExpressionException e){ - throw new XmlParseException("An ExpressionException occured when creating the new AnalyticSubvolume " + name, e); - } - - return newsubvolume; - } - - private VCellSoftwareVersion docVCellSoftwareVersion = null; - - /** - * This method returns a Biomodel object from a XML Element. - * Creation date: (3/13/2001 12:35:00 PM) - * - * @param param Element - * @return cbit.vcell.biomodel.BioModel - */ - public BioModel getBioModel(Element param, VCellSoftwareVersion docVcellSoftwareVersion) throws XmlParseException{ - this.docVCellSoftwareVersion = docVcellSoftwareVersion; -//long l1 = System.currentTimeMillis(); - //Get metadata information Version (if available) - Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace)); - - //Create new biomodel - BioModel biomodel = new BioModel(version); - - //Set name - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - try { - biomodel.setName(name); -// String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag); - -// if (annotation!=null) { -// biomodel.setDescription(unMangle(annotation)); -// } - //get annotation - String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace); - if(annotationText != null && annotationText.length() > 0){ - biomodel.setDescription(unMangle(annotationText)); - } - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException(e); - } -//long l2 = System.currentTimeMillis(); -//System.out.println("biomodel-------- "+((double)(l2-l1))/1000); - - //***Add biomodel to the dictionnary*** - //dictionnary.put(simcontext.getClass().getName()+":"+simcontext.getName(), simcontext); - //Set model - Model newmodel = getModel(param.getChild(XMLTags.ModelTag, vcNamespace)); - biomodel.setModel(newmodel); - //Set simulation contexts - java.util.List children = param.getChildren(XMLTags.SimulationSpecTag, vcNamespace); - java.util.Iterator iterator = children.iterator(); -//long l3 = System.currentTimeMillis(); -//System.out.println("model-------- "+((double)(l3-l2))/1000); - if(biomodel.getVersion() != null && biomodel.getVersion().getVersionKey() != null){ - Long lpcBMKey = Long.valueOf(biomodel.getVersion().getVersionKey().toString()); - MathDescription.originalHasLowPrecisionConstants.remove(lpcBMKey); - } - while (iterator.hasNext()) { -//long l4 = System.currentTimeMillis(); - Element tempElement = iterator.next(); - SimulationContext simContext = getSimulationContext(tempElement, biomodel); - try { - biomodel.addSimulationContext(simContext); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("An error occurred while trying to add the SimContext " + simContext.getName() + " to the BioModel Object!", e); - } - //process the simulations within this Simspec - Iterator simIterator = tempElement.getChildren(XMLTags.SimulationTag, vcNamespace).iterator(); -//long l5 = System.currentTimeMillis(); -//System.out.println("simcontext-------- "+((double)(l5-l4))/1000); - while (simIterator.hasNext()) { - try { - biomodel.addSimulation(getSimulation((Element) simIterator.next(), simContext.getMathDescription(), simContext)); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A PropertyVetoException occurred when adding a Simulation entity to the BioModel " + name, e); - } - } -//long l6 = System.currentTimeMillis(); -//System.out.println("sims-------- "+((double)(l6-l5))/1000); - } - - // biomodel.getVCMetaData().setAnnotation(biomodel, param); - // biomodel.getVCMetaData().setNotes(biomodel, param); - boolean bMetaDataPopulated = false; - List elementsMetaData = param.getChildren(XMLMetaData.VCMETADATA_TAG, VCMetaData.nsVCML); - if(elementsMetaData != null && elementsMetaData.size() > 0){ - for(Element elementMetaData : elementsMetaData){ - XMLMetaDataReader.readFromElement(biomodel.getVCMetaData(), biomodel, elementMetaData); - } - bMetaDataPopulated = true; - } else { - // no metadata was found, populate vcMetaData from biomodel (mainly free text annotation for identifiables) - if(!bMetaDataPopulated){ - biomodel.populateVCMetadata(bMetaDataPopulated); - } - } - Element pathwayElement = param.getChild(XMLTags.PathwayModelTag, vcNamespace); - if(pathwayElement != null){ - Element rdfElement = pathwayElement.getChild(XMLRDF.tagRDF, XMLRDF.nsRDF); - if(rdfElement != null){ - PathwayReaderBiopax3 pathwayReader = new PathwayReaderBiopax3(new RDFXMLContext()); - PathwayModel pathwayModel = pathwayReader.parse(rdfElement, false); - pathwayModel.reconcileReferences(null); // ??? is this needed ??? - // we keep as lvl 1 only the objects which we want to show in the diagram - pathwayModel.filterDiagramObjects(); - biomodel.getPathwayModel().merge(pathwayModel); - } else { - throw new XmlParseException("expecting RDF element as child of pathwayModel within VCML document"); - } - } - - Element relationshipElement = param.getChild(XMLTags.RelationshipModelTag, vcNamespace); - if(relationshipElement != null){ - Element rmnsElement = relationshipElement.getChild("RMNS", vcNamespace); - if(rmnsElement != null){ - RelationshipReader relationshipReader = new RelationshipReader(); - RelationshipModel relationshipModel = relationshipReader.parse(rmnsElement, biomodel); - biomodel.getRelationshipModel().merge(relationshipModel); - } else { -// throw new XmlParseException("expecting RMNS element as child of pathwayModel within VCML document"); - } - } - - return biomodel; - } - - - /** - * This method returns a Catalyst object from a XML representation. - * Creation date: (5/4/2001 2:22:56 PM) - * - * @param param Element - * @return cbit.vcell.model.Product - * @throws cbit.vcell.xml.XmlParseException The exception description. - */ - private Catalyst getCatalyst(Element param, ReactionStep reaction, Model model) throws XmlParseException{ - //retrieve the key if there is one - KeyValue key = null; - String keystring = param.getAttributeValue(XMLTags.KeyValueAttrTag); - if(keystring != null && keystring.length() > 0 && this.readKeysFlag){ - key = new KeyValue(keystring); - } - - String speccontref = unMangle(param.getAttributeValue(XMLTags.SpeciesContextRefAttrTag)); - SpeciesContext speccont = model.getSpeciesContext(speccontref); - if(speccont == null){ - throw new XmlParseException( - "The reference to the SpecieContext " + speccontref - + " for a Catalyst could not be resolved!"); - } - - return new Catalyst(key, reaction, speccont); - } - - - /** - * This method returns a CompartmentSubDomain objecy from a XML element. - * Creation date: (5/17/2001 11:59:45 AM) - * - * @param param Element - * @return cbit.vcell.math.CompartmentSubDomain - * @throws cbit.vcell.xml.XmlParseException The exception description. - */ - private CompartmentSubDomain getCompartmentSubDomain(Element param, MathDescription mathDesc) throws XmlParseException{ - //get attributes - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - int priority = -1; - String temp = param.getAttributeValue(XMLTags.PriorityAttrTag); - if(temp != null){ - priority = Integer.parseInt(temp); - } - //--- create new CompartmentSubDomain --- - CompartmentSubDomain subDomain = new CompartmentSubDomain(name, priority); - transcribeComments(param, subDomain); - - //Process BoundaryConditions - Iterator iterator = param.getChildren(XMLTags.BoundaryTypeTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - - //create BoundaryConditionType - temp = tempelement.getAttributeValue(XMLTags.BoundaryTypeAttrTag); - BoundaryConditionType bType = new BoundaryConditionType(temp); - - //check where it goes - //Process Xm - if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueXm)){ - subDomain.setBoundaryConditionXm(bType); - } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueXp)){ - //Process Xp - subDomain.setBoundaryConditionXp(bType); - } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueYm)){ - //Process Ym - subDomain.setBoundaryConditionYm(bType); - } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueYp)){ - //Process Yp - subDomain.setBoundaryConditionYp(bType); - } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueZm)){ - //Process Zm - subDomain.setBoundaryConditionZm(bType); - } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueZp)){ - //Process Zp - subDomain.setBoundaryConditionZp(bType); - } else { - // If not indentified throw an exception!! - throw new XmlParseException("Unknown BoundaryConditionType: " + tempelement.getAttributeValue(XMLTags.BoundaryAttrTag)); - } - } - - //process BoundaryConditionSpecs - iterator = param.getChildren(XMLTags.BoundaryConditionSpecTag, vcNamespace).iterator(); - if(iterator != null){ - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - try { - subDomain.addBoundaryConditionSpec(getBoundaryConditionSpec(tempelement)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding a BoundaryConditionSpec to the compartmentSubDomain " + name, e); - } - } - } - - - //process OdeEquations - iterator = param.getChildren(XMLTags.OdeEquationTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - - try { - subDomain.addEquation(getOdeEquation(tempelement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding an OdeEquation to the compartmentSubDomain " + name, e); - } - } - - //process PdeEquations - iterator = param.getChildren(XMLTags.PdeEquationTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - - try { - subDomain.addEquation(getPdeEquation(tempelement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding an PdeEquation to the compartmentSubDomain " + name, e); - } - } - - //Process VolumeRegionEquation - iterator = param.getChildren(XMLTags.VolumeRegionEquationTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - - try { - subDomain.addEquation(getVolumeRegionEquation(tempelement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding a VolumeRegionEquation to the compartmentSubDomain " + name, e); - } - } - - //Process Variable initial conditions (added for stochastic algos) - iterator = param.getChildren(XMLTags.VarIniCount_OldTag, vcNamespace).iterator(); - if(iterator != null){ - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - try { - subDomain.addVarIniCondition(getVarIniCount(tempelement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding a variable initial condition to the compartmentSubDomain " + name, e); - } catch(ExpressionException e){ - lg.error(e); - } - } - } - - iterator = param.getChildren(XMLTags.VarIniCountTag, vcNamespace).iterator(); - if(iterator != null){ - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - try { - subDomain.addVarIniCondition(getVarIniCount(tempelement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding a variable initial condition to the compartmentSubDomain " + name, e); - } catch(ExpressionException e){ - lg.error(e); - } - } - } - - iterator = param.getChildren(XMLTags.VarIniPoissonExpectedCountTag, vcNamespace).iterator(); - if(iterator != null){ - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - try { - subDomain.addVarIniCondition(getVarIniPoissonExpectedCount(tempelement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding a variable initial condition to the compartmentSubDomain " + name, e); - } catch(ExpressionException e){ - lg.error(e); - } - } - } - // - //Process JumpProcesses (added for stochastic algos) - iterator = param.getChildren(XMLTags.JumpProcessTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - try { - subDomain.addJumpProcess(getJumpProcess(tempelement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding a jump process to the compartmentSubDomain " + name, e); - } - } - - iterator = param.getChildren(XMLTags.ParticleJumpProcessTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - try { - subDomain.addParticleJumpProcess(getParticleJumpProcess(tempelement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding a jump process to the compartmentSubDomain " + name, e); - } - } - iterator = param.getChildren(XMLTags.LangevinParticleJumpProcessTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - try { - subDomain.addParticleJumpProcess(getParticleJumpProcess(tempelement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding a jump process to the compartmentSubDomain " + name, e); - } - } - - iterator = param.getChildren(XMLTags.ParticlePropertiesTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - try { - subDomain.addParticleProperties(getParticleProperties(tempelement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding a jump process to the compartmentSubDomain " + name, e); - } - } - - //process ComputeCentroid "equations" - iterator = param.getChildren(XMLTags.ComputeCentroidTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - - try { - subDomain.addEquation(getComputeCentroid(tempelement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding an ComputeCentroid 'equation' to the compartmentSubDomain " + name, e); - } - } - - //process ComputeMembraneMetric "equations" - iterator = param.getChildren(XMLTags.ComputeMembraneMetricTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - - try { - subDomain.addEquation(getComputeMembraneMetric(tempelement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding an ComputeMembraneMetric 'equation' to the compartmentSubDomain " + name, e); - } - } - - //Process the FastSystem (if thre is) - Element tempelement = param.getChild(XMLTags.FastSystemTag, vcNamespace); - if(tempelement != null){ - subDomain.setFastSystem(getFastSystem(tempelement, mathDesc)); - } - return subDomain; - } - - - /** - * This method returns a CompartmentSubVolume object from a XML representation. - * Creation date: (5/1/2001 5:26:17 PM) - * - * @param param Element - * @return cbit.vcell.geometry.CompartmentSubVolume - */ - private CompartmentSubVolume getCompartmentSubVolume(Element param) throws XmlParseException{ - //retrieve the attributes - String name = param.getAttributeValue(XMLTags.NameAttrTag); - int handle = Integer.parseInt(param.getAttributeValue(XMLTags.HandleAttrTag)); - - //process the key - KeyValue key = null; - String temp = param.getAttributeValue(XMLTags.KeyValueAttrTag); - if(temp != null && temp.length() > 0 && this.readKeysFlag){ - key = new KeyValue(temp); - } - - //Create the CompartmentVolume - CompartmentSubVolume newcompartment = new CompartmentSubVolume(key, handle); - - //set the name - try { - newcompartment.setName(name); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A propertyVetoException was fired when setting the name to the compartmentSubVolume " + name, e); - } - - return newcompartment; - } - - private void transcribeComments(Element source, Object destination){ - String before = source.getAttributeValue(XMLTags.BEFORE_COMMENT_ATTR_TAG); - String after = source.getAttributeValue(XMLTags.AFTER_COMMENT_ATTR_TAG); - if(before != null || after != null){ - if(!(destination instanceof Commented)){ - throw new UnsupportedOperationException("Can't add comments, " + destination.getClass().toString() + " does not implement " + Commented.class.toString()); - - } - Commented c = (Commented) destination; - c.setBeforeComment(before); - c.setAfterComment(after); - } - } - - /** - * This method returns a Constant object from a XML element. - * Creation date: (5/16/2001 1:50:07 PM) - * - * @param param Element - * @return cbit.vcell.math.Constant - * @throws cbit.vcell.xml.XmlParseException The exception description. - */ - private Constant getConstant(Element param) throws XmlParseException{ - //retrieve values - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - Expression exp = unMangleExpression(param.getText()); - - //-- create new constant object --- - Constant newconstant = new Constant(name, exp); - transcribeComments(param, newconstant); - - return newconstant; - } - - - /** - * This method returns a ControlPointcurve object from a XML element. - * Creation date: (5/22/2001 5:20:39 PM) - * - * @param param Element - * @return cbit.vcell.geometry.ControlPointCurve - */ - private ControlPointCurve getControlPointCurve(Element param){ - ControlPointCurve curve = null; - //get Attributes - String type = param.getAttributeValue(XMLTags.TypeAttrTag); - boolean closed = Boolean.valueOf(param.getAttributeValue(XMLTags.ClosedAttrTag)).booleanValue(); - List coordList = param.getChildren(); - - //Upon de type, decide which Curve type to create - if(type.equalsIgnoreCase(XMLTags.PolyLineTypeTag)){ - if(coordList.size() == 2){ //I have a Line - Coordinate begin = getCoordinate(coordList.get(0)); - Coordinate end = getCoordinate(coordList.get(1)); - // ****create new Line **** - curve = new Line(begin, end); - } else { - //If it it is not a Line, then it is a SampledCurve - Coordinate[] coords = new Coordinate[coordList.size()]; - for(int i = 0; i < coordList.size(); i++){ - coords[i] = getCoordinate(coordList.get(i)); - } - //****create new SampledCurve **** - curve = new SampledCurve(coords); - } - } else if(type.equalsIgnoreCase(XMLTags.SplineTypeTag)){ - Coordinate[] coords = new Coordinate[coordList.size()]; - for(int i = 0; i < coordList.size(); i++){ - coords[i] = getCoordinate(coordList.get(i)); - } - //****create new Spline **** - curve = new Spline(coords); - } - - //set Atributes - curve.setClosed(closed); - - return curve; - } - - - /** - * This method returns a Coordinate object from a XML Element. - * Creation date: (5/22/2001 5:53:05 PM) - * - * @param param Element - * @return cbit.vcell.geometry.Coordinate - */ - public Coordinate getCoordinate(Element param){ - //get attributes - double x = Double.parseDouble(param.getAttributeValue(XMLTags.XAttrTag)); - double y = Double.parseDouble(param.getAttributeValue(XMLTags.YAttrTag)); - double z = Double.parseDouble(param.getAttributeValue(XMLTags.ZAttrTag)); - - //**** create coordinate *** - Coordinate coord = new Coordinate(x, y, z); - - return coord; - } - - - /** - * This method returns a DBFormalSpecies from a XML representation. - * Creation date: (6/3/2003 8:46:44 PM) - * - * @param formalSpeciesElement Element - * @return cbit.vcell.dictionary.DBFormalSpecies - */ - private DBFormalSpecies getDBFormalSpecies(Element formalSpeciesElement) throws XmlParseException{ - //read key - String keystring = formalSpeciesElement.getAttributeValue(XMLTags.KeyValueAttrTag); - KeyValue key = new KeyValue(keystring); - //read type - String typestring = formalSpeciesElement.getAttributeValue(XMLTags.TypeAttrTag); - //read the FormalSpeciesInfo - Element speciesInfoElement = formalSpeciesElement.getChild(XMLTags.FormalSpeciesInfoTag, vcNamespace); - - //create the DBFormalSpecies upon the type - DBFormalSpecies formalSpecies = null; - - if(typestring.equalsIgnoreCase(XMLTags.CompoundTypeTag)){ - formalSpecies = new FormalCompound(key, (CompoundInfo) getFormalSpeciesInfo(speciesInfoElement)); - } else if(typestring.equalsIgnoreCase(XMLTags.EnzymeTypeTag)){ - formalSpecies = new FormalEnzyme(key, (EnzymeInfo) getFormalSpeciesInfo(speciesInfoElement)); - } else if(typestring.equalsIgnoreCase(XMLTags.ProteinTypeTag)){ - formalSpecies = new FormalProtein(key, (ProteinInfo) getFormalSpeciesInfo(speciesInfoElement)); - } else { - throw new XmlParseException("DBFormalSpecies type:" + typestring + ", not supported yet!"); - } - - return formalSpecies; - } - - - /** - * This method reads a DBSpecies from a XML representation. - * Creation date: (6/3/2003 8:20:54 PM) - * - * @param dbSpeciesElement Element - * @return cbit.vcell.dictionary.DBSpecies - */ - private DBSpecies getDBSpecies(Element dbSpeciesElement) throws XmlParseException{ - //Read the key - String keystring = dbSpeciesElement.getAttributeValue(XMLTags.KeyValueAttrTag); - KeyValue key = new KeyValue(keystring); - DBSpecies dbSpecies = null; - - //read the type - String type = dbSpeciesElement.getAttributeValue(XMLTags.TypeAttrTag); - //Read the DBFormalSpecies - Element formalSpeciesElement = dbSpeciesElement.getChild(XMLTags.DBFormalSpeciesTag, vcNamespace); - - if(type.equalsIgnoreCase(XMLTags.CompoundTypeTag)){ - //Create a BoundCompound - dbSpecies = new BoundCompound(key, (FormalCompound) getDBFormalSpecies(formalSpeciesElement)); - } else if(type.equalsIgnoreCase(XMLTags.EnzymeTypeTag)){ - //Create a BoundEnzyme - dbSpecies = new BoundEnzyme(key, (FormalEnzyme) getDBFormalSpecies(formalSpeciesElement)); - } else if(type.equalsIgnoreCase(XMLTags.ProteinTypeTag)){ - //Create a BoundProtein - dbSpecies = new BoundProtein(key, (FormalProtein) getDBFormalSpecies(formalSpeciesElement)); - } else { - throw new XmlParseException("DBSpecies type: " + type + ", not supported yet!"); - } - - return dbSpecies; - } - - - /** - * This method returns a Diagram object from a XML element. - * Creation date: (4/4/2001 4:20:52 PM) - * - * @param param Element - * @return cbit.vcell.model.Diagram - */ - private Diagram getDiagram(Element param, Model model) throws XmlParseException{ - //get Attibutes - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String structureName = unMangle(param.getAttributeValue(XMLTags.StructureAttrTag)); - Structure structureref = model.getStructure(structureName); - if(structureref == null){ - throw new XmlParseException("The structure " + structureName + "could not be resolved!"); - } - //try to create the new Diagram - Diagram newdiagram = new Diagram(structureref, name); - //Add Nodereferences (Shapes) - List children = param.getChildren(); - if(children.size() > 0){ - List nodeRefList = new ArrayList<>(); - for(int i = 0; i < children.size(); i++){ - nodeRefList.add(getNodeReference(children.get(i))); - } - newdiagram.setNodeReferences(nodeRefList); - } - - return newdiagram; - } - - - /** - * This method process Electrical Stimulus, also called Clamps. - * Creation date: (6/6/2002 4:46:18 PM) - * - * @param param Element - * @return cbit.vcell.mapping.ElectricalStimulus - */ - private ElectricalStimulus getElectricalStimulus(Element param, SimulationContext currentSimulationContext) throws XmlParseException{ - ElectricalStimulus clampStimulus = null; - - //get name - // String name = unMangle( param.getAttributeValue(XMLTags.NameAttrTag) ); - - //get Electrode - Electrode electrode = getElectrode(param.getChild(XMLTags.ElectrodeTag, vcNamespace), currentSimulationContext); - - if(param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.VoltageClampTag)){ - //is a voltage clamp - clampStimulus = new VoltageClampStimulus(electrode, "voltClampElectrode", new Expression(0.0), currentSimulationContext); - } else if(param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.CurrentDensityClampTag) || - param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.CurrentDensityClampTag_oldName)){ - //is a current density clamp - clampStimulus = new CurrentDensityClampStimulus(electrode, "currDensityClampElectrode", new Expression(0.0), currentSimulationContext); - } else if(param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.TotalCurrentClampTag)){ - //is a "total" current clamp - clampStimulus = new TotalCurrentClampStimulus(electrode, "totalCurrClampElectrode", new Expression(0.0), currentSimulationContext); - } - - try { - clampStimulus.reading(true); // transaction begin flag ... yeah, this is a hack - - //Read all of the parameters - List list = param.getChildren(XMLTags.ParameterTag, vcNamespace); - - // add constants that may be used in the electrical stimulus. - VariableHash varHash = new VariableHash(); - Model model = currentSimulationContext.getModel(); - addResevedSymbols(varHash, model); - - // - // rename "special" parameters (those that are not "user defined") - // - for(Element xmlParam : list){ - String paramName = unMangle(xmlParam.getAttributeValue(XMLTags.NameAttrTag)); - String role = xmlParam.getAttributeValue(XMLTags.ParamRoleAttrTag); - String paramExpStr = xmlParam.getText(); - Expression paramExp = unMangleExpression(paramExpStr); - try { - if(varHash.getVariable(paramName) == null){ - Domain domain = null; - varHash.addVariable(new Function(paramName, paramExp, domain)); - } else { - if(model.getReservedSymbolByName(paramName) != null){ - varHash.removeVariable(paramName); - Domain domain = null; - varHash.addVariable(new Function(paramName, paramExp, domain)); - } - } - } catch(MathException e){ - throw new XmlParseException("error reordering parameters according to dependencies:", e); - } - LocalParameter tempParam = null; - if(!role.equals(XMLTags.ParamRoleUserDefinedTag)){ - if(role.equals(XMLTags.ParamRoleTotalCurrentTag)){ - if(clampStimulus instanceof TotalCurrentClampStimulus){ - tempParam = ((TotalCurrentClampStimulus) clampStimulus).getCurrentParameter(); - } else { - varHash.removeVariable(paramName); - continue; - } - } else if(role.equals(XMLTags.ParamRoleTotalCurrentDensityTag) || role.equals(XMLTags.ParamRoleTotalCurrentDensityOldNameTag)){ - if(clampStimulus instanceof CurrentDensityClampStimulus){ - tempParam = ((CurrentDensityClampStimulus) clampStimulus).getCurrentDensityParameter(); - } else { - varHash.removeVariable(paramName); - continue; - } - } else if(role.equals(XMLTags.ParamRolePotentialDifferenceTag)){ - if(clampStimulus instanceof VoltageClampStimulus){ - tempParam = ((VoltageClampStimulus) clampStimulus).getVoltageParameter(); - } else { - varHash.removeVariable(paramName); - continue; - } - } - } else { - continue; - } - if(tempParam == null){ - throw new XmlParseException("parameter with role '" + role + "' not found in electricalstimulus"); - } - // - // custom name for "special" parameter - // - if(!tempParam.getName().equals(paramName)){ - LocalParameter multNameParam = clampStimulus.getLocalParameter(paramName); - int n = 0; - while (multNameParam != null) { - String tempName = paramName + "_" + n++; - clampStimulus.renameParameter(paramName, tempName); - multNameParam = clampStimulus.getLocalParameter(tempName); - } - clampStimulus.renameParameter(tempParam.getName(), paramName); - } - } - // - // create unresolved parameters for all unresolved symbols - // - String unresolvedSymbol = varHash.getFirstUnresolvedSymbol(); - - while (unresolvedSymbol != null) { - try { - Domain domain = null; - varHash.addVariable(new Function(unresolvedSymbol, new Expression(0.0), domain)); // will turn into an UnresolvedParameter. - } catch(MathException e){ - throw new XmlParseException(e.getMessage()); - } - clampStimulus.addUnresolvedParameter(unresolvedSymbol); - unresolvedSymbol = varHash.getFirstUnresolvedSymbol(); - } - - Variable sortedVariables[] = varHash.getTopologicallyReorderedVariables(); - ModelUnitSystem modelUnitSystem = model.getUnitSystem(); - for(int i = sortedVariables.length - 1; i >= 0; i--){ - if(sortedVariables[i] instanceof Function){ - Function paramFunction = (Function) sortedVariables[i]; - Element xmlParam = null; - for(int j = 0; j < list.size(); j++){ - Element tempParam = (Element) list.get(j); - if(paramFunction.getName().equals(unMangle(tempParam.getAttributeValue(XMLTags.NameAttrTag)))){ - xmlParam = tempParam; - break; - } - } - if(xmlParam == null){ - continue; // must have been an unresolved parameter - } - String symbol = xmlParam.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); - VCUnitDefinition unit = null; - if(symbol != null){ - unit = modelUnitSystem.getInstance(symbol); - } - LocalParameter tempParam = clampStimulus.getLocalParameter(paramFunction.getName()); - if(tempParam == null){ - clampStimulus.addUserDefinedParameter(paramFunction.getName(), paramFunction.getExpression(), unit); - } else { - if(tempParam.getExpression() != null){ // if the expression is null, it should remain null. - clampStimulus.setParameterValue(tempParam, paramFunction.getExpression()); - } - tempParam.setUnitDefinition(unit); - } - } - } - - - } catch(PropertyVetoException | ExpressionException e){ - throw new XmlParseException("Exception while setting parameters for simContext : " + currentSimulationContext.getName(), e); - } finally { - clampStimulus.reading(false); - } - - return clampStimulus; - } - - - private void readParameters(List parameterElements, ParameterContext parameterContext, HashMap roleHash, ParameterRoleEnum userDefinedRole, HashSet xmlRolesTagsToIgnore, Model model) throws XmlParseException{ - - String contextName = parameterContext.getNameScope().getName(); - try { - // - // prepopulate varHash with reserved symbols - // - VariableHash varHash = new VariableHash(); - addResevedSymbols(varHash, model); - - // - // process each parameter: - // 1) put the parameter into the varHash - // 2) rename predefined parameters from the ParameterContext as necessary to avoid naming conflicts - // and use the stored names for pre-defined parameters. - // - for(Element xmlParam : parameterElements){ - String parsedParamName = unMangle(xmlParam.getAttributeValue(XMLTags.NameAttrTag)); - String parsedRoleString = xmlParam.getAttributeValue(XMLTags.ParamRoleAttrTag); - String parsedExpressionString = xmlParam.getText(); - - // - // should we skip this xml role tag? not used anymore. - // - if(xmlRolesTagsToIgnore.contains(parsedRoleString)){ - varHash.removeVariable(parsedParamName); - continue; - } - - Expression paramExp = null; - if(parsedExpressionString.trim().length() > 0){ - paramExp = unMangleExpression(parsedExpressionString); - } - - if(varHash.getVariable(parsedParamName) == null){ - Domain domain = null; - varHash.addVariable(new Function(parsedParamName, paramExp, domain)); - } else { - if(model.getReservedSymbolByName(parsedParamName) != null){ - varHash.removeVariable(parsedParamName); - Domain domain = null; - varHash.addVariable(new Function(parsedParamName, paramExp, domain)); - } - } - - // - // get the parameter for this xml role string - // - ParameterRoleEnum paramRole = roleHash.get(parsedRoleString); - if(paramRole == null){ - throw new XmlParseException("parameter '" + parsedParamName + "' has unexpected role '" + parsedRoleString + "' in '" + contextName + "'"); - } - - // - // if parameter is not user-defined, then force the parameter with the same role to have the same name. - // - if(paramRole != userDefinedRole){ - LocalParameter paramWithSameRole = parameterContext.getLocalParameterFromRole(paramRole); - if(paramWithSameRole == null){ - throw new XmlParseException("can't find parameter with role '" + parsedRoleString + "' in '" + contextName + "'"); - } - // - // "special" parameter with same role has a different name, rename - // - // - if(!paramWithSameRole.getName().equals(parsedParamName)){ - // - // first rename other parameters with same name - // - LocalParameter paramWithSameNameButDifferentRole = parameterContext.getLocalParameterFromName(parsedParamName); - if(paramWithSameNameButDifferentRole != null){ - // - // find available name - // - int n = 0; - String newName = parsedParamName + "_" + n++; - while (parameterContext.getEntry(newName) != null) { - newName = parsedParamName + "_" + n++; - } - parameterContext.renameLocalParameter(parsedParamName, newName); - } - // - // then rename parameter with correct role - // - parameterContext.renameLocalParameter(paramWithSameRole.getName(), parsedParamName); - } - } - } - - // - // create unresolved parameters for all unresolved symbols - // - String unresolvedSymbol = varHash.getFirstUnresolvedSymbol(); - while (unresolvedSymbol != null) { - try { - Domain domain = null; - varHash.addVariable(new Function(unresolvedSymbol, new Expression(0.0), domain)); // will turn into an UnresolvedParameter. - } catch(MathException e){ - throw new XmlParseException(e.getMessage(), e); - } - parameterContext.addUnresolvedParameter(unresolvedSymbol); - unresolvedSymbol = varHash.getFirstUnresolvedSymbol(); - } - - - // - // in topological order, add parameters to model (getting units also). - // note that all pre-defined parameters already have the correct names - // here we set expressions on pre-defined parameters and add user-defined parameters - // - Variable sortedVariables[] = varHash.getTopologicallyReorderedVariables(); - ModelUnitSystem modelUnitSystem = model.getUnitSystem(); - for(int i = sortedVariables.length - 1; i >= 0; i--){ - if(sortedVariables[i] instanceof Function){ - Function paramFunction = (Function) sortedVariables[i]; - Element xmlParam = null; - for(int j = 0; j < parameterElements.size(); j++){ - Element tempParam = (Element) parameterElements.get(j); - if(paramFunction.getName().equals(unMangle(tempParam.getAttributeValue(XMLTags.NameAttrTag)))){ - xmlParam = tempParam; - break; - } - } - if(xmlParam == null){ - continue; // must have been an unresolved parameter - } - String symbol = xmlParam.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); - VCUnitDefinition unit = null; - if(symbol != null){ - unit = modelUnitSystem.getInstance(symbol); - } - LocalParameter tempParam = parameterContext.getLocalParameterFromName(paramFunction.getName()); - if(tempParam == null){ - tempParam = parameterContext.addLocalParameter(paramFunction.getName(), new Expression(0.0), userDefinedRole, unit, userDefinedRole.getDescription()); - parameterContext.setParameterValue(tempParam, paramFunction.getExpression(), true); - } else { - if(tempParam.getExpression() != null){ // if the expression is null, it should remain null. - parameterContext.setParameterValue(tempParam, paramFunction.getExpression(), true); - } - tempParam.setUnitDefinition(unit); - } - } - } - - } catch(PropertyVetoException | ExpressionException | MathException e){ - throw new XmlParseException("Exception while setting parameters for '" + contextName + "': " + e.getMessage(), e); - } - } - - - /** - * This method returns an Electrode object from a XML representation. - * Creation date: (6/6/2002 4:22:55 PM) - * - * @return cbit.vcell.mapping.Electrode - */ - private Electrode getElectrode(Element elem, SimulationContext currentSimulationContext){ - //retrieve feature - String featureName = unMangle(elem.getAttributeValue(XMLTags.FeatureAttrTag)); - Feature feature = (Feature) currentSimulationContext.getModel().getStructure(featureName); - //retrieve position - Coordinate position = getCoordinate(elem.getChild(XMLTags.CoordinateTag, vcNamespace)); - - Electrode newElect = new Electrode(feature, position); - - return newElect; - } - - - /** - * This method returns a ErrorTolerance object from a XML Element. - * Creation date: (5/22/2001 11:50:07 AM) - * - * @param param Element - * @return cbit.vcell.solver.ErrorTolerance - */ - private ErrorTolerance getErrorTolerance(Element param){ - //getAttributes - double absolut = Double.parseDouble(param.getAttributeValue(XMLTags.AbsolutErrorToleranceTag)); - double relative = Double.parseDouble(param.getAttributeValue(XMLTags.RelativeErrorToleranceTag)); - - //*** create new ErrorTolerance object **** - ErrorTolerance errorTol = new ErrorTolerance(absolut, relative); - - return errorTol; - } - - - public Extent getExtent(Element parsed){ - double x = Double.parseDouble(parsed.getAttributeValue(XMLTags.XAttrTag)); - double y = Double.parseDouble(parsed.getAttributeValue(XMLTags.YAttrTag)); - double z = Double.parseDouble(parsed.getAttributeValue(XMLTags.ZAttrTag)); - Extent extent = new Extent(x, y, z); - - return extent; - } - - - /** - * This method returns a FastSystemImplicit from a XML Element. - * Creation date: (5/18/2001 2:38:56 PM) - * - * @param param Element - * @return cbit.vcell.math.FastSystemImplicit - * @throws cbit.vcell.xml.XmlParseException The exception description. - */ - private FastSystem getFastSystem( - Element param, - MathDescription mathDesc) - throws XmlParseException{ - //Create a new FastSystem - FastSystem fastSystem = new FastSystem(mathDesc); - - //Process the FastInvariants - Iterator iterator = param.getChildren(XMLTags.FastInvariantTag, vcNamespace).iterator(); - FastInvariant fastInvariant = null; - while (iterator.hasNext()) { - Element tempElement = (Element) iterator.next(); - String temp = tempElement.getText(); - - try { - Expression newExp = unMangleExpression(temp); - fastInvariant = new FastInvariant(newExp); - fastSystem.addFastInvariant(fastInvariant); - } catch(MathException e){ - throw new XmlParseException( - "A MathException was fired when adding the FastInvariant " + fastInvariant + ", to a FastSystem!" + " : ", e); - } - } - //Process the FastRate - iterator = param.getChildren(XMLTags.FastRateTag, vcNamespace).iterator(); - FastRate fastRate = null; - - while (iterator.hasNext()) { - Element tempElement = (Element) iterator.next(); - String temp = tempElement.getText(); - - try { - Expression newExp = unMangleExpression(temp); - fastRate = new FastRate(newExp); - fastSystem.addFastRate(fastRate); - } catch(MathException e){ - throw new XmlParseException( - "A MathException was fired when adding the FastRate " + fastRate + ", to a FastSystem!", e); - } - } - - return fastSystem; - } - - - /** - * This method returns a Feature object (Structure) from a XML representation. - * Creation date: (3/15/2001 6:12:36 PM) - * - * @param param Element - * @return cbit.vcell.model.Structure - */ - private Structure getFeature(Element param) throws XmlParseException{ - Feature newfeature = null; - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - - //retrieve the key if there is one - KeyValue key = null; - String keystring = param.getAttributeValue(XMLTags.KeyValueAttrTag); - - if(keystring != null && keystring.length() > 0 && this.readKeysFlag){ - key = new KeyValue(keystring); - } - - //---Create the new feature--- - try { - newfeature = new Feature(key, name); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException( - "An error occurred while creating the feature " - + param.getAttributeValue(XMLTags.NameAttrTag), e); - } - - return newfeature; - } - - - /** - * This method retuns a FeatureMapping object from a XML representation. - * Creation date: (5/7/2001 4:12:03 PM) - * - * @param param Element - * @return cbit.vcell.mapping.FeatureMapping - */ - private FeatureMapping getFeatureMapping(Element param, SimulationContext simulationContext) throws XmlParseException{ - //Retrieve attributes - String featurename = unMangle(param.getAttributeValue(XMLTags.FeatureAttrTag)); - String geometryClassName = param.getAttributeValue(XMLTags.SubVolumeAttrTag); - if(geometryClassName != null){ - geometryClassName = unMangle(geometryClassName); - } else { - geometryClassName = param.getAttributeValue(XMLTags.GeometryClassAttrTag); - if(geometryClassName != null){ - geometryClassName = unMangle(geometryClassName); - } - } - - Feature featureref = (Feature) simulationContext.getModel().getStructure(featurename); - if(featureref == null){ - throw new XmlParseException("The Feature " + featurename + " could not be resolved!"); - } - - //*** Create new Feature Mapping **** - FeatureMapping feamap = new FeatureMapping(featureref, simulationContext, simulationContext.getModel().getUnitSystem()); - - //Set Size - if(param.getAttributeValue(XMLTags.SizeTag) != null){ - String size = unMangle(param.getAttributeValue(XMLTags.SizeTag)); - try { - feamap.getSizeParameter().setExpression(unMangleExpression(size)); - } catch(ExpressionException e){ - throw new XmlParseException("An expressionException was fired when setting the size Expression " + size + " to a featureMapping!", e); - } - } else { - try { - feamap.getSizeParameter().setExpression(null); - } catch(Exception e){ - throw new RuntimeException("unexpected exception while setting structure size: " + e.getMessage(), e); - } - } - - //Set Volume/unit_area if it exists - if(param.getAttributeValue(XMLTags.VolumePerUnitAreaTag) != null){ - String volPerUnitArea = unMangle(param.getAttributeValue(XMLTags.VolumePerUnitAreaTag)); - try { - feamap.getVolumePerUnitAreaParameter().setExpression(unMangleExpression(volPerUnitArea)); - } catch(ExpressionException e){ - throw new XmlParseException("An expressionException was fired when setting the VolumePerUnitArea Expression " + volPerUnitArea + " to a featureMapping!", e); - } - } - - //Set Volume/unitVol if it exists - if(param.getAttributeValue(XMLTags.VolumePerUnitVolumeTag) != null){ - String volPerUnitVol = unMangle(param.getAttributeValue(XMLTags.VolumePerUnitVolumeTag)); - try { - feamap.getVolumePerUnitVolumeParameter().setExpression(unMangleExpression(volPerUnitVol)); - } catch(ExpressionException e){ - throw new XmlParseException("An expressionException was fired when setting the size Expression " + volPerUnitVol + " to a featureMapping!", e); - } - } - - if(geometryClassName != null){ - GeometryClass[] geometryClasses = simulationContext.getGeometry().getGeometryClasses(); - for(int i = 0; i < geometryClasses.length; i++){ - if(geometryClasses[i].getName().equals(geometryClassName)){ - try { - feamap.setGeometryClass(geometryClasses[i]); - } catch(PropertyVetoException e){ - throw new XmlParseException("A propertyVetoException was fired when trying to set the subvolume or surface " + geometryClassName + " to a MembraneMapping!", e); - } - } - } - } - - //Set Boundary conditions - Element tempElement = param.getChild(XMLTags.BoundariesTypesTag, vcNamespace); - - //Xm - String temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueXm); - BoundaryConditionType bct = new BoundaryConditionType(temp); - feamap.setBoundaryConditionTypeXm(bct); - //Xp - temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueXp); - bct = new BoundaryConditionType(temp); - feamap.setBoundaryConditionTypeXp(bct); - //Ym - temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueYm); - bct = new BoundaryConditionType(temp); - feamap.setBoundaryConditionTypeYm(bct); - //Yp - temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueYp); - bct = new BoundaryConditionType(temp); - feamap.setBoundaryConditionTypeYp(bct); - //Zm - temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueZm); - bct = new BoundaryConditionType(temp); - feamap.setBoundaryConditionTypeZm(bct); - //Zp - temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueZp); - bct = new BoundaryConditionType(temp); - feamap.setBoundaryConditionTypeZp(bct); - - return feamap; - } - - - /** - * This method returns a FilamentRegionVariable object from a XML Element. - * Creation date: (5/16/2001 2:56:34 PM) - * - * @param param Element - * @return cbit.vcell.math.FilamentRegionVariable - */ - private FilamentRegionVariable getFilamentRegionVariable(Element param){ - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); - Domain domain = null; - if(domainStr != null){ - domain = new Domain(domainStr); - } - - //-- create new FilamentRegionVariable object - FilamentRegionVariable filRegVariable = new FilamentRegionVariable(name, domain); - transcribeComments(param, filRegVariable); - - return filRegVariable; - } - - - /** - * This method returns a FilamentSubDomain object from a XMl element. - * Creation date: (5/18/2001 4:27:22 PM) - * - * @param param Element - * @return cbit.vcell.math.FilamentSubDomain - * @throws cbit.vcell.xml.XmlParseException The exception description. - */ - private FilamentSubDomain getFilamentSubDomain(Element param, MathDescription mathDesc) throws XmlParseException{ - //get name - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - - //get outside Compartment ref - String outsideName = unMangle(param.getAttributeValue(XMLTags.OutsideCompartmentTag)); - CompartmentSubDomain outsideRef = (CompartmentSubDomain) mathDesc.getCompartmentSubDomain(outsideName); - if(outsideRef == null){ - throw new XmlParseException("The reference to the CompartmentSubDomain " + outsideName + ", could not be resolved!"); - } - //*** create new filamentSubDomain object *** - FilamentSubDomain filDomain = new FilamentSubDomain(name, outsideRef); - - //add OdeEquations - Iterator iterator = param.getChildren(XMLTags.OdeEquationTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempElement = (Element) iterator.next(); - try { - filDomain.addEquation(getOdeEquation(tempElement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding an OdeEquation to the FilamentSubDomain " + name, e); - } - } - //Add the FastSytem - filDomain.setFastSystem(getFastSystem(param.getChild(XMLTags.FastSystemTag, vcNamespace), mathDesc)); - - return filDomain; - } - - private PointSubDomain getPointSubDomain(Element param, MathDescription mathDesc) throws XmlParseException{ - //get name - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - - //*** create new pointSubDomain object *** - PointSubDomain pointDomain = new PointSubDomain(name); - - //add OdeEquations - Iterator iterator = param.getChildren(XMLTags.OdeEquationTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempElement = (Element) iterator.next(); - try { - pointDomain.addEquation(getOdeEquation(tempElement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding an OdeEquation to the FilamentSubDomain " + name, e); - } - } - String temp = param.getChildText(XMLTags.PositionXTag, vcNamespace); - if(temp != null && temp.length() > 0){ - pointDomain.setPositionX(unMangleExpression(temp)); - } - temp = param.getChildText(XMLTags.PositionYTag, vcNamespace); - if(temp != null && temp.length() > 0){ - pointDomain.setPositionY(unMangleExpression(temp)); - } - temp = param.getChildText(XMLTags.PositionZTag, vcNamespace); - if(temp != null && temp.length() > 0){ - pointDomain.setPositionZ(unMangleExpression(temp)); - } - - -// //Add the FastSytem -// pointDomain.setFastSystem( getFastSystem(param.getChild(XMLTags.FastSystemTag, vcNamespace), mathDesc) ); - - return pointDomain; - } - - - /** - * This method returns a FilamentVariable object from a XML Element. - * Creation date: (5/16/2001 2:56:34 PM) - * - * @param param Element - * @return cbit.vcell.math.FilamentVariable - */ - private FilamentVariable getFilamentVariable(Element param){ - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); - Domain domain = null; - if(domainStr != null){ - domain = new Domain(domainStr); - } - //-- create new filVariable object - FilamentVariable filVariable = new FilamentVariable(name, domain); - transcribeComments(param, filVariable); - - return filVariable; - } - - - /** - * This method returns a FluxReaction object from a XML element. - * Creation date: (3/16/2001 11:52:02 AM) - * - * @param param Element - * @return cbit.vcell.model.FluxReaction - * @throws XmlParseException - * @throws PropertyVetoException - * @throws ModelException - * @throws Exception - */ - private FluxReaction getFluxReaction(Element param, Model model) throws XmlParseException, PropertyVetoException{ - //retrieve the key if there is one - KeyValue key = null; - String keystring = param.getAttributeValue(XMLTags.KeyValueAttrTag); - - if(keystring != null && keystring.length() > 0 && this.readKeysFlag){ - key = new KeyValue(keystring); - } - - //resolve reference to the Membrane - String structureName = unMangle(param.getAttributeValue(XMLTags.StructureAttrTag)); - Membrane structureref = (Membrane) model.getStructure(structureName); - - if(structureref == null){ - throw new XmlParseException( - "The membrane " + structureName + " could not be resolved in the dictionnary!"); - } - - - //-- Instantiate new FluxReaction -- - FluxReaction fluxreaction = null; - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - - String reversibleAttributeValue = param.getAttributeValue(XMLTags.ReversibleAttrTag); - boolean bReversible = true; - if(reversibleAttributeValue != null){ - if(Boolean.TRUE.toString().equals(reversibleAttributeValue)){ - bReversible = true; - } else if(Boolean.FALSE.toString().equals(reversibleAttributeValue)){ - bReversible = false; - } else { - throw new RuntimeException("unexpected value " + reversibleAttributeValue + " for reversible flag for reaction " + name); - } - } - - try { - fluxreaction = new FluxReaction(model, structureref, key, name, bReversible); - fluxreaction.setModel(model); - if(param.getAttributeValue(XMLTags.SbmlNameAttrTag) != null){ - fluxreaction.setSbmlName(unMangle(param.getAttributeValue(XMLTags.SbmlNameAttrTag))); - } - - } catch(Exception e){ - throw new XmlParseException("An exception occurred while trying to create the FluxReaction " + name, e); - } - //resolve reference to the fluxCarrier - if(param.getAttribute(XMLTags.FluxCarrierAttrTag) != null){ - String speciesname = unMangle(param.getAttributeValue(XMLTags.FluxCarrierAttrTag)); - Species specieref = model.getSpecies(speciesname); - if(specieref != null){ - Feature insideFeature = model.getStructureTopology().getInsideFeature(structureref); - try { - if(insideFeature != null){ - SpeciesContext insideSpeciesContext = model.getSpeciesContext(specieref, insideFeature); - fluxreaction.addProduct(insideSpeciesContext, 1); - } - Feature outsideFeature = model.getStructureTopology().getOutsideFeature(structureref); - if(outsideFeature != null){ - SpeciesContext outsideSpeciesContext = model.getSpeciesContext(specieref, outsideFeature); - fluxreaction.addReactant(outsideSpeciesContext, 1); - } - } catch(ModelException e){ - throw new XmlParseException(e.getMessage(), e); - } - } - } - //Annotation -// String rsAnnotation = null; -// String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace); -// if (annotationText!=null && annotationText.length()>0) { -// rsAnnotation = unMangle(annotationText); -// } -// fluxreaction.setAnnotation(rsAnnotation); - - //set the fluxOption - String fluxOptionString = null; - fluxOptionString = param.getAttributeValue(XMLTags.FluxOptionAttrTag); - if(fluxOptionString != null && fluxOptionString.length() > 0){ - try { - if(fluxOptionString.equals(XMLTags.FluxOptionElectricalOnly)){ - fluxreaction.setPhysicsOptions(FluxReaction.PHYSICS_ELECTRICAL_ONLY); - } else if(fluxOptionString.equals(XMLTags.FluxOptionMolecularAndElectrical)){ - fluxreaction.setPhysicsOptions(FluxReaction.PHYSICS_MOLECULAR_AND_ELECTRICAL); - } else if(fluxOptionString.equals(XMLTags.FluxOptionMolecularOnly)){ - fluxreaction.setPhysicsOptions(FluxReaction.PHYSICS_MOLECULAR_ONLY); - } - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A propertyVetoException was fired when setting the fluxOption to the flux reaction " + name, e); - } - } - - //Add Reactants, if any - try { - Iterator iterator = param.getChildren(XMLTags.ReactantTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element temp = iterator.next(); - //Add Reactant to this SimpleReaction - fluxreaction.addReactionParticipant(getReactant(temp, fluxreaction, model)); - } - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("Error adding a reactant to the reaction " + name + " : " + e.getMessage(), e); - } - - //Add Products, if any - try { - Iterator iterator = param.getChildren(XMLTags.ProductTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element temp = iterator.next(); - //Add Product to this simplereaction - fluxreaction.addReactionParticipant(getProduct(temp, fluxreaction, model)); - } - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("Error adding a product to the reaction " + name + " : " + e.getMessage(), e); - } - - //Add Catalyst(Modifiers) (if there are) - Iterator iterator = param.getChildren(XMLTags.CatalystTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element temp = iterator.next(); - fluxreaction.addReactionParticipant(getCatalyst(temp, fluxreaction, model)); - } - //Add Kinetics - fluxreaction.setKinetics(getKinetics(param.getChild(XMLTags.KineticsTag, vcNamespace), fluxreaction, model)); - - //set the valence (for legacy support for "chargeCarrierValence" stored with reaction). - String valenceString = null; - try { - valenceString = unMangle(param.getAttributeValue(XMLTags.FluxCarrierValenceAttrTag)); - if(valenceString != null && valenceString.length() > 0){ - KineticsParameter chargeValenceParameter = fluxreaction.getKinetics().getChargeValenceParameter(); - if(chargeValenceParameter != null){ - chargeValenceParameter.setExpression(new Expression(Integer.parseInt(unMangle(valenceString)))); - } - } - } catch(NumberFormatException e){ - throw new XmlParseException("A NumberFormatException was fired when setting the (integer) valence '" + valenceString + "' (integer) to the flux reaction " + name, e); - } - return fluxreaction; - } - - - /** - * This method creates a FormalSpeciesInfo from a XML representation. - * Creation date: (6/3/2003 9:11:26 PM) - * - * @param speciesInfoElement Element - * @return cbit.vcell.dictionary.FormalSpeciesInfo - */ - private FormalSpeciesInfo getFormalSpeciesInfo(Element speciesInfoElement) throws XmlParseException{ - //get formalID - String formalID = unMangle(speciesInfoElement.getAttributeValue(XMLTags.FormalIDTag)); - //get names - List namesList = speciesInfoElement.getChildren(XMLTags.NameTag, vcNamespace); - String[] namesArray = new String[namesList.size()]; - int nameCounter = 0; - for(Element nameElement : namesList){ - namesArray[nameCounter] = unMangle(nameElement.getText()); - nameCounter++; - } - String tempstring; - //get type - String type = speciesInfoElement.getAttributeValue(XMLTags.TypeAttrTag); - FormalSpeciesInfo formalSpeciesInfo = null; - - if(type.equalsIgnoreCase(XMLTags.CompoundTypeTag)){ - //get formula - String formula = null; - tempstring = speciesInfoElement.getAttributeValue(XMLTags.FormulaTag); - if(tempstring != null){ - formula = unMangle(tempstring); - } - - //get CASID - String casid = null; - tempstring = speciesInfoElement.getAttributeValue(XMLTags.CasIDTag); - if(tempstring != null){ - casid = unMangle(tempstring); - } - - //get Enzymes - List enzymelist = speciesInfoElement.getChildren(XMLTags.EnzymeTag, vcNamespace); - EnzymeRef[] enzymeArray = null; - - if(enzymelist != null && enzymelist.size() > 0){ - enzymeArray = new EnzymeRef[enzymelist.size()]; - int enzymeCounter = 0; - for(Element enzymeElement : enzymelist){ - //get ECNumber - String ecnumber = unMangle(enzymeElement.getAttributeValue(XMLTags.ECNumberTag)); - //get Enzymetype - String enztypestr = enzymeElement.getAttributeValue(XMLTags.TypeAttrTag); - char enzymetype = enztypestr.charAt(0); - enzymeArray[enzymeCounter] = new EnzymeRef(ecnumber, enzymetype); - enzymeCounter++; - } - } - - //create new CompoundInfo - formalSpeciesInfo = new CompoundInfo(formalID, namesArray, formula, casid, enzymeArray); - } else if(type.equalsIgnoreCase(XMLTags.EnzymeTypeTag)){ - //get reaction - String reaction = null; - tempstring = speciesInfoElement.getAttributeValue(XMLTags.ExpressionAttrTag); - if(tempstring != null){ - reaction = unMangle(tempstring); - } - //get sysname - String sysname = null; - tempstring = speciesInfoElement.getAttributeValue(XMLTags.SysNameTag); - if(tempstring != null){ - sysname = unMangle(tempstring); - } - //get argcasID - String casid = null; - tempstring = speciesInfoElement.getAttributeValue(XMLTags.CasIDTag); - if(tempstring != null){ - casid = unMangle(tempstring); - } - //create new EnzymeInfo - formalSpeciesInfo = new EnzymeInfo(formalID, namesArray, reaction, sysname, casid); - } else if(type.equalsIgnoreCase(XMLTags.ProteinTypeTag)){ - //get organism - String organism = null; - tempstring = speciesInfoElement.getAttributeValue(XMLTags.OrganismTag); - if(tempstring != null){ - organism = unMangle(tempstring); - } - //get accession - String accession = null; - tempstring = speciesInfoElement.getAttributeValue(XMLTags.AccessionTag); - if(tempstring != null){ - accession = unMangle(tempstring); - } - //get keywords - String keywords = null; - tempstring = speciesInfoElement.getAttributeValue(XMLTags.KeywordsTag); - if(tempstring != null){ - keywords = unMangle(tempstring); - } - //get description - String description = null; - tempstring = speciesInfoElement.getAttributeValue(XMLTags.DescriptionTag); - if(tempstring != null){ - description = unMangle(tempstring); - } - //create new ProteinInfo - formalSpeciesInfo = new ProteinInfo(formalID, namesArray, organism, accession, keywords, description); - } else { - throw new XmlParseException("FormalSpeciesInfo type " + type + ", not supported yet!"); - } - - return formalSpeciesInfo; - } - - - /** - * This method returns a Function variable object from a XML Element. - * Creation date: (5/16/2001 3:45:21 PM) - * - * @param param Element - * @return cbit.vcell.math.Function - * @throws cbit.vcell.xml.XmlParseException The exception description. - */ - private Function getFunction(Element param) throws XmlParseException{ - //get attributes - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - - -/** --------------------------------------------------------------- - * ATTENTATION: this is a quick fix for a specific user to load his model - * with a function name as "ATP/ADP". This syntax is not allowed. - -----------------------------------------------------------------------*/ - if(name.equals("ATP/ADP")){ - name = "ATP_ADP_renamed"; - System.err.print("Applying species function name change ATP/ADP to ATP_ADP for a specific user (key=2288008)"); - Thread.dumpStack(); - } - - - String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); - Domain domain = null; - if(domainStr != null){ - domain = new Domain(domainStr); - } - String temp = param.getText(); - - Expression exp = unMangleExpression(temp); - - //-- create new Function -- - Function function = new Function(name, exp, domain); - transcribeComments(param, function); - - return function; - } - - private AnnotatedFunction getOutputFunction(Element param) throws XmlParseException{ - //get attributes - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String temp = param.getText(); - Expression exp = unMangleExpression(temp); - String errStr = unMangle(param.getAttributeValue(XMLTags.ErrorStringTag)); - - VariableType funcType = VariableType.UNKNOWN; - String funcTypeAttr = param.getAttributeValue(XMLTags.FunctionTypeTag); - if(funcTypeAttr != null){ - String funcTypeStr = unMangle(funcTypeAttr); - funcType = VariableType.getVariableTypeFromVariableTypeName(funcTypeStr); - } - - //-- create new AnnotatedFunction -- - String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); - Domain domain = null; - if(domainStr != null){ - domain = new Domain(domainStr); - } - AnnotatedFunction function = new AnnotatedFunction(name, exp, domain, errStr, funcType, FunctionCategory.OUTPUTFUNCTION); - - return function; - } - - /** - * This method returns a Geometry object from a XML representation. - * Creation date: (4/26/2001 12:12:18 PM) - * - * @param param Element - * @return cbit.vcell.geometry.Geometry - * @throws cbit.vcell.xml.XmlParseException The exception description. - */ - public Geometry getGeometry(Element param) throws XmlParseException{ - //Get the Extent object - Extent newextent = getExtent(param.getChild(XMLTags.ExtentTag, vcNamespace)); - //Get VCimage information - VCImage newimage = null; - if(param.getChild(XMLTags.ImageTag, vcNamespace) != null){ - try { - newimage = getVCImage(param.getChild(XMLTags.ImageTag, vcNamespace), newextent); - } catch(Throwable e){ - throw new XmlParseException(e); - } - } - - //Get attributes - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - int newdimension = Integer.parseInt(param.getAttributeValue(XMLTags.DimensionAttrTag)); - //Get Version - Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace)); - - //Try to construct the geometry upon four different cases - Geometry newgeometry = null; - if(version != null && newimage != null){ - newgeometry = new Geometry(version, newimage); - } else if(version != null){ - newgeometry = new Geometry(version, newdimension); - } else if(newimage != null){ - newgeometry = new Geometry(name, newimage); - } else { - newgeometry = new Geometry(name, newdimension); - } - - //set attributes - try { - if(!newgeometry.getName().equalsIgnoreCase(name)){ - newgeometry.setName(name); - } - - //String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag); - - //if (annotation!=null) { - //newgeometry.setDescription( unMangle(annotation) ); - //} - //Add annotation - String annotation = param.getChildText(XMLTags.AnnotationTag, vcNamespace); - if(annotation != null && annotation.length() > 0){ - newgeometry.setDescription(unMangle(annotation)); - } - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A PropertyVetoException occurred when setting the name " + name + " to a Geometry object!", e); - } - //Add the Extent - try { - newgeometry.getGeometrySpec().setExtent(newextent); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A PropertyVetoException occurred while trying to set the Extent for the Geometry " + name, e); - } - //Add the Origin - newgeometry.getGeometrySpec().setOrigin(getOrigin(param.getChild(XMLTags.OriginTag, vcNamespace))); - - //Add the SubVolumes - List children = param.getChildren(XMLTags.SubVolumeTag, vcNamespace); - SubVolume[] newsubvolumes = new SubVolume[children.size()]; - int subvolumeCounter = 0; - for(Element child : children){ - newsubvolumes[subvolumeCounter] = getSubVolume(child); - subvolumeCounter++; - } - try { - newgeometry.getGeometrySpec().setSubVolumes(newsubvolumes); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A PropertyVetoException was generated when ading the subvolumes to the Geometry " + name, e); - } - if(newgeometry.getDimension() > 0){ - //Add SurfaceClasses - List surfaceClassChildren = param.getChildren(XMLTags.SurfaceClassTag, vcNamespace); - SurfaceClass[] newSurfaceClassArr = new SurfaceClass[surfaceClassChildren.size()]; - int surfClassCounter = 0; - for(Element surfClassChild : surfaceClassChildren){ - newSurfaceClassArr[surfClassCounter] = getSurfaceClass(surfClassChild, newgeometry); - surfClassCounter++; - } - try { - newgeometry.getGeometrySurfaceDescription().setSurfaceClasses(newSurfaceClassArr); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A PropertyVetoException was generated when ading the subvolumes to the Geometry " + name, e); - } - } - //read Filaments (if any) - Iterator iterator = param.getChildren(XMLTags.FilamentTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempElement = iterator.next(); - - String filname = unMangle(tempElement.getAttributeValue(XMLTags.NameAttrTag)); - Iterator curveiterator = tempElement.getChildren().iterator(); - while (curveiterator.hasNext()) { - ControlPointCurve curve = getControlPointCurve(curveiterator.next()); - newgeometry.getGeometrySpec().getFilamentGroup().addCurve(filname, curve); - } - } - //read Surface description (if any) - Element sd = param.getChild(XMLTags.SurfaceDescriptionTag, vcNamespace); - if(sd != null){ - GeometrySurfaceDescription dummy = getGeometrySurfaceDescription(sd, newgeometry); - } - - try { - newgeometry.precomputeAll(new GeometryThumbnailImageFactoryAWT(), false, false); - } catch(GeometryException | ImageException | ExpressionException e){ - lg.error(e); - } - return newgeometry; - } - - - private GeometrySurfaceDescription getGeometrySurfaceDescription(Element param, Geometry geom) throws XmlParseException{ - - GeometrySurfaceDescription gsd = geom.getGeometrySurfaceDescription(); - String cutoffStr = param.getAttributeValue(XMLTags.CutoffFrequencyAttrTag); - String xDim = param.getAttributeValue(XMLTags.NumSamplesXAttrTag); - String yDim = param.getAttributeValue(XMLTags.NumSamplesYAttrTag); - String zDim = param.getAttributeValue(XMLTags.NumSamplesZAttrTag); - if(cutoffStr == null || xDim == null || yDim == null || zDim == null){ - throw new XmlParseException("Attributes for element Surface Description not properly set, under geometry: " + - ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag)); - } - try { - ISize isize = new ISize(Integer.parseInt(xDim), Integer.parseInt(yDim), Integer.parseInt(zDim)); - gsd.setVolumeSampleSize(isize); - gsd.setFilterCutoffFrequency(Double.parseDouble(cutoffStr)); - - //these lists are allowed to be empty. - ArrayList memRegions = new ArrayList(param.getChildren(XMLTags.MembraneRegionTag, vcNamespace)); - ArrayList volRegions = new ArrayList(param.getChildren(XMLTags.VolumeRegionTag, vcNamespace)); - ArrayList regions = new ArrayList(); - GeometryUnitSystem geometryUnitSystem = geom.getUnitSystem(); - for(Element temp : volRegions){ - String regionID = temp.getAttributeValue(XMLTags.RegionIDAttrTag); - String name = temp.getAttributeValue(XMLTags.NameAttrTag); - String subvolumeRef = temp.getAttributeValue(XMLTags.SubVolumeAttrTag); - if(regionID == null || name == null || subvolumeRef == null){ - throw new XmlParseException("Attributes for element Volume Region not properly set, under geometry: " + - ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag)); - } - SubVolume subvolume = geom.getGeometrySpec().getSubVolume(subvolumeRef); - if(subvolume == null){ - throw new XmlParseException("The subvolume " + subvolumeRef + " could not be resolved."); - } - double size = -1; - VCUnitDefinition unit = null; - String sizeStr = temp.getAttributeValue(XMLTags.SizeAttrTag); - if(sizeStr != null){ - size = Double.parseDouble(sizeStr); - String unitSymbol = temp.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); - if(unitSymbol != null){ - unit = geometryUnitSystem.getInstance(unitSymbol); - } - } - VolumeGeometricRegion vgr = new VolumeGeometricRegion(name, size, unit, subvolume, Integer.parseInt(regionID)); - regions.add(vgr); - } - for(Element temp : memRegions){ - String volRegion_1 = temp.getAttributeValue(XMLTags.VolumeRegion_1AttrTag); - String volRegion_2 = temp.getAttributeValue(XMLTags.VolumeRegion_2AttrTag); - String name = temp.getAttributeValue(XMLTags.NameAttrTag); - if(volRegion_1 == null || volRegion_2 == null || name == null){ - throw new XmlParseException("Attributes for element Membrane Region not properly set, under geometry: " + - ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag)); - } - VolumeGeometricRegion region1 = getAdjacentVolumeRegion(regions, volRegion_1); - VolumeGeometricRegion region2 = getAdjacentVolumeRegion(regions, volRegion_2); - if(region1 == null || region2 == null){ - throw new XmlParseException("Element Membrane Region refernces invalid volume regions, under geometry: " + - ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag)); - } - double size = -1; - VCUnitDefinition unit = null; - String sizeStr = temp.getAttributeValue(XMLTags.SizeAttrTag); - if(sizeStr != null){ - size = Double.parseDouble(sizeStr); - String unitSymbol = temp.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); - if(unitSymbol != null){ - unit = geometryUnitSystem.getInstance(unitSymbol); - } - } - SurfaceGeometricRegion rsl = new SurfaceGeometricRegion(name, size, unit); - rsl.addAdjacentGeometricRegion(region1); - region1.addAdjacentGeometricRegion(rsl); - rsl.addAdjacentGeometricRegion(region2); - region2.addAdjacentGeometricRegion(rsl); - regions.add(rsl); - } - if(regions.size() > 0){ - gsd.setGeometricRegions((GeometricRegion[]) regions.toArray(new GeometricRegion[regions.size()])); - } - } catch(Exception e){ - lg.error("Unable to read geometry surface description from XML, for geometry: " + - ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag), e); - } - - return gsd; - } - - - /** - * This method returns a GroupAccess object from an XML format. - * Creation date: (5/23/2003 7:27:10 PM) - * - * @param xmlGroup Element - * @return cbit.vcell.server.GroupAccess - */ - private GroupAccess getGroupAccess(Element xmlGroup){ - //guess the type of group - String temp = xmlGroup.getAttributeValue(XMLTags.TypeAttrTag); - java.math.BigDecimal type = new java.math.BigDecimal(temp); - - if(type.equals(GroupAccess.GROUPACCESS_ALL)){ - //Type ALL - return new GroupAccessAll(); - } else if(type.equals(GroupAccess.GROUPACCESS_NONE)){ - //Type NONE - return new GroupAccessNone(); - } else { - //Type SOME - //Read attributes - //*groupid - temp = xmlGroup.getAttributeValue(XMLTags.TypeAttrTag); - java.math.BigDecimal groupid = new java.math.BigDecimal(temp); - //*hash - temp = xmlGroup.getAttributeValue(XMLTags.HashAttrTag); - java.math.BigDecimal hashcode = new java.math.BigDecimal(temp); - //*users - List userlist = xmlGroup.getChildren(XMLTags.UserTag, vcNamespace); - User[] userArray = new User[userlist.size()]; - boolean[] booleanArray = new boolean[userlist.size()]; - int counter = 0; - for(Element userElement : userlist){ - String userid = unMangle(userElement.getAttributeValue(XMLTags.NameAttrTag)); - KeyValue key = new KeyValue(userElement.getAttributeValue(XMLTags.KeyValueAttrTag)); - boolean hidden = Boolean.valueOf(userElement.getAttributeValue(XMLTags.HiddenTag)).booleanValue(); - userArray[counter] = new User(userid, key); - booleanArray[counter] = hidden; - counter++; - } - //create and return the GroupAccess - return new GroupAccessSome(groupid, hashcode, userArray, booleanArray); - } - } - - - /** - * This method returns an ImageSubVolume object from a XML representation. - * Creation date: (5/1/2001 5:26:17 PM) - * - * @param param Element - * @return cbit.vcell.geometry.ImageSubVolume - */ - private ImageSubVolume getImageSubVolume(Element param) throws XmlParseException{ - //retrieve the attributes - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - int handle = Integer.parseInt(param.getAttributeValue(XMLTags.HandleAttrTag)); - int imagePixelValue = Integer.parseInt(param.getAttributeValue(XMLTags.ImagePixelValueTag)); - - //Get the PixelClass from image (image should be a sibling of this subVolume element) - Element imageElement = ((Element) param.getParent()).getChild(XMLTags.ImageTag, vcNamespace); - if(imageElement == null){ - throw new XmlParseException("image not found in geometry corresponding to ImageSubVolume"); - } - - List pixelClassList = imageElement.getChildren(XMLTags.PixelClassTag, vcNamespace); - VCPixelClass pixelClass = null; - for(Element pixelClassElement : pixelClassList){ - VCPixelClass pc = getPixelClass(pixelClassElement); - if(pc.getPixel() == imagePixelValue){ - pixelClass = pc; - } - } - if(pixelClass == null){ - throw new XmlParseException("image pixelclass(pixel=" + imagePixelValue + ") not found while creating ImageSubVolume " + name); - } - - //retrieve the key if there is one - KeyValue key = null; - String stringkey = param.getAttributeValue(XMLTags.KeyValueAttrTag); - - if(stringkey != null && stringkey.length() > 0 && this.readKeysFlag){ - key = new KeyValue(stringkey); - } - - //Create the new Image SubVolume - ImageSubVolume newsubvolume = new ImageSubVolume(key, pixelClass, handle); - //set name - try { - newsubvolume.setName(name); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A propertyVetoException was generated when setting the name " + name + " to an ImageSubvolume object!", e); - } - - return newsubvolume; - } - - - /** - * This method returns an InsideVariable object from a XML Element - * Creation date: (5/18/2001 6:14:42 PM) - * - * @param param Element - * @return cbit.vcell.math.InsideVariable - */ - private InsideVariable getInsideVariable(Element param){ - //Get name - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - //get VolVariableRef - String volvarName = unMangle(param.getAttributeValue(XMLTags.VolumeVariableAttrTag)); - - //*** create new InsideVariable *** - InsideVariable variable = new InsideVariable(name, volvarName); - transcribeComments(param, variable); - - return variable; - } - - - /** - * This method returns a JumpCondition object from a XML Element. - * Creation date: (5/18/2001 5:10:10 PM) - * - * @param param Element - * @return cbit.vcell.math.JumpCondition - * @throws cbit.vcell.xml.XmlParseException The exception description. - */ - private JumpCondition getJumpCondition(Element param, MathDescription mathDesc) throws XmlParseException{ - //get VolVariable ref - String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - - Variable var = mathDesc.getVariable(varname); - if(var == null){ - throw new XmlParseException("The reference to the Variable " + varname + ", could not be resolved!"); - } - - JumpCondition jumpCondition = null; - if(var instanceof VolVariable){ - jumpCondition = new JumpCondition((VolVariable) var); - } else if(var instanceof VolumeRegionVariable){ - jumpCondition = new JumpCondition((VolumeRegionVariable) var); - } else { - throw new XmlParseException("unexpected variable type for jump condition"); - } - - //process InFlux - String temp = param.getChildText(XMLTags.InFluxTag, vcNamespace); - Expression exp = unMangleExpression(temp); - jumpCondition.setInFlux(exp); - - - //process OutFlux - temp = param.getChildText(XMLTags.OutFluxTag, vcNamespace); - exp = unMangleExpression(temp); - jumpCondition.setOutFlux(exp); - - return jumpCondition; - } - - - /** - * The method returns a JumpProcess object from a XML element. - * Creation date: (7/24/2006 6:28:42 PM) - * - * @param param Element - * @param md cbit.vcell.math.MathDescription - * @return cbit.vcell.math.JumpProcess - * @throws cbit.vcell.xml.XmlParseException The exception description. - */ - private JumpProcess getJumpProcess(Element param, MathDescription md) throws XmlParseException{ - //name - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - //probability rate - Element pb = param.getChild(XMLTags.ProbabilityRateTag, vcNamespace); - Expression exp = unMangleExpression(pb.getText()); - - JumpProcess jump = new JumpProcess(name, exp); - //add actions - Iterator iterator = param.getChildren(XMLTags.ActionTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - try { - jump.addAction(getAction(tempelement, md)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding a new Action to the JumpProcess " + name, e); - } catch(ExpressionException e){ - lg.error(e); - } - } - - return jump; - } - - private ParticleInitialConditionCount getParticleInitialConditionCount(Element param){ - String temp = param.getChildText(XMLTags.ParticleCountTag, vcNamespace); - Expression countExp = null; - if(temp != null && temp.length() > 0){ - countExp = unMangleExpression(temp); - } - temp = param.getChildText(XMLTags.ParticleLocationXTag, vcNamespace); - Expression locXExp = null; - if(temp != null && temp.length() > 0){ - locXExp = unMangleExpression(temp); - } - temp = param.getChildText(XMLTags.ParticleLocationYTag, vcNamespace); - Expression locYExp = null; - if(temp != null && temp.length() > 0){ - locYExp = unMangleExpression(temp); - } - temp = param.getChildText(XMLTags.ParticleLocationZTag, vcNamespace); - Expression locZExp = null; - if(temp != null && temp.length() > 0){ - locZExp = unMangleExpression(temp); - } - - return new ParticleInitialConditionCount(countExp, locXExp, locYExp, locZExp); - } - - private ParticleProperties getParticleProperties(Element param, MathDescription mathDesc) throws XmlParseException{ - //Retrieve the variable reference - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - Variable varref = mathDesc.getVariable(name); - if(varref == null){ - throw new XmlParseException("The variable " + name + " for a PdeEquation, could not be resolved!"); - } - - ArrayList initialConditions = new ArrayList(); - Iterator iterator = param.getChildren(XMLTags.ParticleInitialCountTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - initialConditions.add(getParticleInitialConditionCount(tempelement)); - } - iterator = param.getChildren(XMLTags.ParticleInitialCountTag_old, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - initialConditions.add(getParticleInitialConditionCount(tempelement)); - } - iterator = param.getChildren(XMLTags.ParticleInitialConcentrationTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - - String temp = tempelement.getChildText(XMLTags.ParticleDistributionTag, vcNamespace); - Expression distExp = null; - if(temp != null && temp.length() > 0){ - distExp = unMangleExpression(temp); - } - initialConditions.add(new ParticleInitialConditionConcentration(distExp)); - } - - String temp = param.getChildText(XMLTags.ParticleDiffusionTag, vcNamespace); - Expression diffExp = null; - if(temp != null && temp.length() > 0){ - diffExp = unMangleExpression(temp); - } - - String driftXString = param.getChildText(XMLTags.ParticleDriftXTag, vcNamespace); - Expression driftXExp = null; - if(driftXString != null && driftXString.length() > 0){ - driftXExp = unMangleExpression(driftXString); - } - - String driftYString = param.getChildText(XMLTags.ParticleDriftYTag, vcNamespace); - Expression driftYExp = null; - if(driftYString != null && driftYString.length() > 0){ - driftYExp = unMangleExpression(driftYString); - } - - String driftZString = param.getChildText(XMLTags.ParticleDriftZTag, vcNamespace); - Expression driftZExp = null; - if(driftZString != null && driftZString.length() > 0){ - driftZExp = unMangleExpression(driftZString); - } - - return new ParticleProperties(varref, diffExp, driftXExp, driftYExp, driftZExp, initialConditions); - } - - private ParticleJumpProcess getParticleJumpProcess(Element param, MathDescription md) throws XmlParseException{ - //name - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - - LangevinParticleJumpProcess.ParticleSubtype subtype = LangevinParticleJumpProcess.ParticleSubtype.INCOMPATIBLE; - boolean isLangevin = false; - if(param.getAttribute(XMLTags.LangevinParticleJumpProcessSubtypeTag) != null){ - isLangevin = true; - String stString = param.getAttributeValue(XMLTags.LangevinParticleJumpProcessSubtypeTag); - subtype = LangevinParticleJumpProcess.ParticleSubtype.fromName(stString); - } - LangevinParticleJumpProcess.ParticleTransitionCondition transitionCondition = null; - Expression bondLength = new Expression(1.0); // that's the default, even for non-binding rules (we hide it anyway for those) - if(isLangevin && param.getAttribute(XMLTags.LangevinParticleJumpProcessBondLengthTag) != null){ - try { - bondLength = new Expression(param.getAttributeValue(XMLTags.LangevinParticleJumpProcessBondLengthTag)); - } catch(ExpressionException e){ - throw new XmlParseException("unparseable " + XMLTags.LangevinParticleJumpProcessBondLengthTag - + " '" + param.getAttributeValue(XMLTags.LangevinParticleJumpProcessBondLengthTag) + "'", e); - } - } - if(isLangevin && param.getAttribute(XMLTags.LangevinParticleJumpProcessTransitionConditionTag) != null){ - String tcString = param.getAttributeValue(XMLTags.LangevinParticleJumpProcessTransitionConditionTag); - transitionCondition = LangevinParticleJumpProcess.ParticleTransitionCondition.fromVcellName(tcString); - } - - ProcessSymmetryFactor processSymmetryFactor = null; - Attribute symmetryFactorAttr = param.getAttribute(XMLTags.ProcessSymmetryFactorAttrTag); - if(symmetryFactorAttr != null){ - processSymmetryFactor = new ProcessSymmetryFactor(Double.parseDouble(symmetryFactorAttr.getValue())); - } - - // selected particle - List varList = new ArrayList(); - Iterator iterator = param.getChildren(XMLTags.SelectedParticleTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - String varname = unMangle(tempelement.getAttributeValue(XMLTags.NameAttrTag)); - Variable var = md.getVariable(varname); - if(!(var instanceof ParticleVariable)){ - throw new XmlParseException("Not a ParticleVariable in ParticleJumpProcess."); - } - varList.add((ParticleVariable) var); - } - - //probability rate - JumpProcessRateDefinition jprd = null; - //for old models - Element pb = param.getChild(XMLTags.ParticleProbabilityRateTag, vcNamespace); - if(pb != null){ - Expression exp = unMangleExpression(pb.getText()); - jprd = new MacroscopicRateConstant(exp); - } else //for new models - { - pb = param.getChild(XMLTags.MacroscopicRateConstantTag, vcNamespace); - if(pb != null) //jump process rate defined by macroscopic rate constant - { - Expression exp = unMangleExpression(pb.getText()); - jprd = new MacroscopicRateConstant(exp); - } else //jump process rate defined by binding radius - { - pb = param.getChild(XMLTags.InteractionRadiusTag, vcNamespace); - if(pb != null){ - Expression exp = unMangleExpression(pb.getText()); - jprd = new InteractionRadius(exp); - } - } - } - //add actions - List actionList = new ArrayList(); - iterator = param.getChildren(XMLTags.ActionTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - try { - actionList.add(getAction(tempelement, md)); - } catch(MathException | ExpressionException e){ - throw new XmlParseException(e); - } - } - - ParticleJumpProcess jump; - if(isLangevin){ - jump = new LangevinParticleJumpProcess(name, varList, jprd, actionList, processSymmetryFactor); - ((LangevinParticleJumpProcess) jump).setSubtype(subtype); - if(LangevinParticleJumpProcess.ParticleSubtype.TRANSITION == subtype){ - ((LangevinParticleJumpProcess) jump).setTransitionCondition(transitionCondition); - } else if(LangevinParticleJumpProcess.ParticleSubtype.BINDING == subtype){ - ((LangevinParticleJumpProcess) jump).setBondLength(bondLength); - } - } else { - jump = new ParticleJumpProcess(name, varList, jprd, actionList, processSymmetryFactor); - } - return jump; - } - - /** - * This method returns a Kinetics object from a XML Element based on the value of the kinetics type attribute. - * Creation date: (3/19/2001 4:42:04 PM) - * - * @param param Element - * @return cbit.vcell.model.Kinetics - */ - private Kinetics getKinetics(Element param, ReactionStep reaction, Model model) throws XmlParseException{ - VariableHash varHash = new VariableHash(); - addResevedSymbols(varHash, model); - - String type = param.getAttributeValue(XMLTags.KineticsTypeAttrTag); - Kinetics newKinetics = null; - try { - if(type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralKinetics)){ - //create a general kinetics - newKinetics = new GeneralKinetics(reaction); - } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralCurrentKinetics)){ - //Create GeneralCurrentKinetics - newKinetics = new GeneralCurrentKinetics(reaction); - } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeMassAction) && reaction instanceof SimpleReaction){ - //create a Mass Action kinetics - newKinetics = new MassActionKinetics((SimpleReaction) reaction); - } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeNernst) && reaction instanceof FluxReaction){ - // create NernstKinetics - newKinetics = new NernstKinetics((FluxReaction) reaction); - } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeGHK) && reaction instanceof FluxReaction){ - //create GHKKinetics - newKinetics = new GHKKinetics((FluxReaction) reaction); - } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeHMM_Irr) && reaction instanceof SimpleReaction){ - //create HMM_IrrKinetics - newKinetics = new HMM_IRRKinetics((SimpleReaction) reaction); - } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeHMM_Rev) && reaction instanceof SimpleReaction){ - //create HMM_RevKinetics - newKinetics = new HMM_REVKinetics((SimpleReaction) reaction); - } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralTotal_oldname)){ - //create GeneralTotalKinetics - newKinetics = new GeneralLumpedKinetics(reaction); - } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralLumped)){ - //create GeneralLumpedKinetics - newKinetics = new GeneralLumpedKinetics(reaction); - } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralCurrentLumped)){ - //create GeneralCurrentLumpedKinetics - newKinetics = new GeneralCurrentLumpedKinetics(reaction); - } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralPermeability) && reaction instanceof FluxReaction){ - // create GeneralPermeabilityKinetics - newKinetics = new GeneralPermeabilityKinetics((FluxReaction) reaction); - } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeMacroscopic_Irr) && reaction instanceof SimpleReaction){ - // create Macroscopic_IRRKinetics - newKinetics = new Macroscopic_IRRKinetics((SimpleReaction) reaction); - } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeMicroscopic_Irr) && reaction instanceof SimpleReaction){ - // create Microscopic_IRRKinetics - newKinetics = new Microscopic_IRRKinetics((SimpleReaction) reaction); - } else { - throw new XmlParseException("Unknown kinetics type: " + type); - } - } catch(ExpressionException e){ - throw new XmlParseException("Error creating the kinetics for reaction: " + reaction.getName(), e); - } - - try { - newKinetics.reading(true); // transaction begin flag ... yeah, this is a hack - - //Read all of the parameters - List list = param.getChildren(XMLTags.ParameterTag, vcNamespace); - - // add constants that may be used in kinetics. - // VariableHash varHash = getVariablesHash(); - ArrayList reserved = new ArrayList(); - - ReservedSymbol[] reservedSymbols = reaction.getModel().getReservedSymbols(); - for(ReservedSymbol rs : reservedSymbols){ - reserved.add(rs.getName()); - } - - try { - if(reaction.getStructure() instanceof Membrane){ - Membrane membrane = (Membrane) reaction.getStructure(); - varHash.addVariable(new Constant(membrane.getMembraneVoltage().getName(), new Expression(0.0))); - reserved.add(membrane.getMembraneVoltage().getName()); - } - // - // add Reactants, Products, and Catalysts (ReactionParticipants) - // - ReactionParticipant rp[] = reaction.getReactionParticipants(); - for(int i = 0; i < rp.length; i++){ - varHash.addVariable(new Constant(rp[i].getName(), new Expression(0.0))); - } - } catch(MathException e){ - throw new XmlParseException("error reordering parameters according to dependencies: ", e); - } - // - // rename "special" parameters (those that are not "user defined") - // - for(Element xmlParam : list){ - String paramName = unMangle(xmlParam.getAttributeValue(XMLTags.NameAttrTag)); - String role = xmlParam.getAttributeValue(XMLTags.ParamRoleAttrTag); - String paramExpStr = xmlParam.getText(); - Expression paramExp = unMangleExpression(paramExpStr); - try { - if(varHash.getVariable(paramName) == null){ - varHash.addVariable(new Function(paramName, paramExp, null)); - } else { - if(reserved.contains(paramName)){ - varHash.removeVariable(paramName); - varHash.addVariable(new Function(paramName, paramExp, null)); - } - } - } catch(MathException e){ - throw new XmlParseException("error reordering parameters according to dependencies: ", e); - } - Kinetics.KineticsParameter tempParam = null; - if(!role.equals(XMLTags.ParamRoleUserDefinedTag)){ - tempParam = newKinetics.getKineticsParameterFromRole(Kinetics.getParamRoleFromDefaultDesc(role)); - } else { - continue; - } - // hack for bringing in General Total kinetics without breaking. - if(tempParam == null && newKinetics instanceof GeneralLumpedKinetics){ - if(role.equals(Kinetics.GTK_AssumedCompartmentSize_oldname) || role.equals(Kinetics.GTK_ReactionRate_oldname) || role.equals(Kinetics.GTK_CurrentDensity_oldname)){ - continue; - } else if(role.equals(VCMODL.TotalRate_oldname)){ - tempParam = newKinetics.getKineticsParameterFromRole(Kinetics.ROLE_LumpedReactionRate); - } - } - // hack from bringing in chargeValence parameters without breaking - if(tempParam == null && Kinetics.getParamRoleFromDefaultDesc(role) == Kinetics.ROLE_ChargeValence){ - tempParam = newKinetics.getChargeValenceParameter(); - } - - if(tempParam == null){ - throw new XmlParseException("parameter with role '" + role + "' not found in kinetics type '" + type + "'"); - } - // - // custom name for "special" parameter - // - if(!tempParam.getName().equals(paramName)){ - Kinetics.KineticsParameter multNameParam = newKinetics.getKineticsParameter(paramName); - int n = 0; - while (multNameParam != null) { - String tempName = paramName + "_" + n++; - newKinetics.renameParameter(paramName, tempName); - multNameParam = newKinetics.getKineticsParameter(tempName); - } - newKinetics.renameParameter(tempParam.getName(), paramName); - } - } - // - // create unresolved parameters for all unresolved symbols - // - String unresolvedSymbol = varHash.getFirstUnresolvedSymbol(); - while (unresolvedSymbol != null) { - try { - varHash.addVariable(new Function(unresolvedSymbol, new Expression(0.0), null)); // will turn into an UnresolvedParameter. - } catch(MathException e){ - throw new XmlParseException(e); - } - newKinetics.addUnresolvedParameter(unresolvedSymbol); - unresolvedSymbol = varHash.getFirstUnresolvedSymbol(); - } - - Variable sortedVariables[] = varHash.getTopologicallyReorderedVariables(); - ModelUnitSystem modelUnitSystem = reaction.getModel().getUnitSystem(); - for(int i = sortedVariables.length - 1; i >= 0; i--){ - if(sortedVariables[i] instanceof Function){ - Function paramFunction = (Function) sortedVariables[i]; - Element xmlParam = null; - for(int j = 0; j < list.size(); j++){ - Element tempParam = (Element) list.get(j); - if(paramFunction.getName().equals(unMangle(tempParam.getAttributeValue(XMLTags.NameAttrTag)))){ - xmlParam = tempParam; - break; - } - } - if(xmlParam == null){ - - continue; // must have been an unresolved parameter - } - String symbol = xmlParam.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); - VCUnitDefinition unit = null; - if(symbol != null){ - unit = modelUnitSystem.getInstance(symbol); - } - Kinetics.KineticsParameter tempParam = newKinetics.getKineticsParameter(paramFunction.getName()); - if(tempParam == null){ - newKinetics.addUserDefinedKineticsParameter(paramFunction.getName(), paramFunction.getExpression(), unit); - } else { - newKinetics.setParameterValue(tempParam, paramFunction.getExpression()); - tempParam.setUnitDefinition(unit); - } - } - } - } catch(PropertyVetoException | ExpressionException e){ - throw new XmlParseException("Exception while setting parameters for Reaction : " + reaction.getName(), e); - } finally { - newKinetics.reading(false); - } - - return newKinetics; - } - - - /** - * This method returns a MathDescription from a XML element. - * Creation date: (4/26/2001 12:11:14 PM) - * - * @param param Element - * @return cbit.vcell.math.MathDescription - * @throws cbit.vcell.xml.XmlParseException The exception description. - */ - MathDescription getMathDescription(Element param, Geometry geometry) throws XmlParseException{ - MathDescription mathdes = null; - Element tempelement; - - //Retrieve Metadata(Version) - Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace)); - - //Retrieve attributes - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - - //Create new MathDescription - if(version != null){ - mathdes = new MathDescription(version); - } else { - mathdes = new MathDescription(name); - } - - try { - mathdes.setGeometry(geometry); //this step is needed! - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("a PropertyVetoException was fired when setting the Geometry to the Mathdescription in the simContext " + name, e); - } - //set attributes - try { - mathdes.setName(name); - //String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag); - - //if (annotation!=null) { - //mathdes.setDescription(unMangle(annotation)); - //} - //add Annotation - String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace); - if(annotationText != null && annotationText.length() > 0){ - mathdes.setDescription(unMangle(annotationText)); - } - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A PropertyVetoException was fired when setting the name " + name + ", to a new MathDescription!", e); - } - - VariableHash varHash = new VariableHash(); - - //Retrieve Constant - Iterator iterator = param.getChildren(XMLTags.ConstantTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - try { - varHash.addVariable(getConstant(tempelement)); - } catch(MathException e){ - throw new XmlParseException(e); - } - } - - //Retrieve FilamentRegionVariables - iterator = param.getChildren(XMLTags.FilamentRegionVariableTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - try { - varHash.addVariable(getFilamentRegionVariable(tempelement)); - } catch(MathException e){ - throw new XmlParseException(e); - } - } - - //Retrieve FilamentVariables - iterator = param.getChildren(XMLTags.FilamentVariableTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - try { - varHash.addVariable(getFilamentVariable(tempelement)); - } catch(MathException e){ - throw new XmlParseException(e); - } - } - - //retrieve InsideVariables - //**** This variables are for internal USE ****** - - //Retrieve MembraneRegionVariable - iterator = param.getChildren(XMLTags.MembraneRegionVariableTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - try { - varHash.addVariable(getMembraneRegionVariable(tempelement)); - } catch(MathException e){ - throw new XmlParseException(e); - } - - } - - //Retrieve MembraneVariable - iterator = param.getChildren(XMLTags.MembraneVariableTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - try { - varHash.addVariable(getMemVariable(tempelement)); - } catch(MathException e){ - throw new XmlParseException(e); - } - - } - - //Retrieve PointVariable - iterator = param.getChildren(XMLTags.PointVariableTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - try { - varHash.addVariable(getPointVariable(tempelement)); - } catch(MathException e){ - throw new XmlParseException(e); - } - - } - //retrieve OutsideVariables - //**** This variables are for internal USE ****** - - //Retrieve Volume Region variable - iterator = param.getChildren(XMLTags.VolumeRegionVariableTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - try { - varHash.addVariable(getVolumeRegionVariable(tempelement)); - } catch(MathException e){ - throw new XmlParseException(e); - } - - } - - //Retrieve VolumeVariable - iterator = param.getChildren(XMLTags.VolumeVariableTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - try { - varHash.addVariable(getVolVariable(tempelement)); - } catch(MathException e){ - throw new XmlParseException(e); - } - } - - //Retrieve StochVolVariable - iterator = param.getChildren(XMLTags.StochVolVariableTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - try { - varHash.addVariable(getStochVolVariable(tempelement)); - } catch(MathException e){ - throw new XmlParseException(e); - } - } - - //Retrieve all the Functions //This needs to be processed before all the variables are read! - iterator = param.getChildren(XMLTags.FunctionTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - try { - varHash.addVariable(getFunction(tempelement)); - } catch(MathException e){ - throw new XmlParseException(e); - } - } - - iterator = param.getChildren(XMLTags.VolumeRandomVariableTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - try { - varHash.addVariable(getRandomVariable(tempelement)); - } catch(MathException e){ - throw new XmlParseException(e); - } - } - iterator = param.getChildren(XMLTags.MembraneRandomVariableTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - try { - varHash.addVariable(getRandomVariable(tempelement)); - } catch(MathException e){ - throw new XmlParseException(e); - } - } - iterator = param.getChildren(XMLTags.VolumeParticleVariableTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - try { - varHash.addVariable(getVolumeParticalVariable(tempelement)); - } catch(MathException e){ - throw new XmlParseException(e); - } - } - iterator = param.getChildren(XMLTags.MembraneParticleVariableTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - try { - varHash.addVariable(getMembraneParticalVariable(tempelement)); - } catch(MathException e){ - throw new XmlParseException(e); - } - } - - // ParticleMolecularTypeTag getParticleMolecularTypes - // has to be done before VolumeParticleSpeciesPattern and VolumeParticleObservable - iterator = param.getChildren(XMLTags.ParticleMolecularTypeTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - mathdes.addParticleMolecularType(getParticleMolecularType(tempelement, false)); - } - iterator = param.getChildren(XMLTags.LangevinParticleMolecularTypeTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - mathdes.addParticleMolecularType(getParticleMolecularType(tempelement, true)); - } - // VolumeParticleSpeciesPatternTag - iterator = param.getChildren(XMLTags.VolumeParticleSpeciesPatternTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - try { - varHash.addVariable(getVolumeParticleSpeciesPattern(tempelement, mathdes)); - } catch(MathException e){ - throw new XmlParseException(e); - } - } - // VolumeParticleObservableTag getParticleObservables - iterator = param.getChildren(XMLTags.VolumeParticleObservableTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - try { - varHash.addVariable(getVolumeParticleObservable(tempelement, varHash)); - } catch(MathException e){ - throw new XmlParseException(e); - } - } - - // - // add all variables at once - // - try { - mathdes.setAllVariables(varHash.getAlphabeticallyOrderedVariables()); - } catch(MathException | ExpressionBindingException e){ - throw new XmlParseException("Error adding the Function variables to the MathDescription " + name, e); - } - - //Retrieve CompartmentsSubdomains - iterator = param.getChildren(XMLTags.CompartmentSubDomainTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - try { - mathdes.addSubDomain(getCompartmentSubDomain(tempelement, mathdes)); - } catch(MathException e){ - throw new XmlParseException("Error adding a new CompartmentSubDomain to the MathDescription " + name, e); - } - } - - //Retrieve MembraneSubdomains - iterator = param.getChildren(XMLTags.MembraneSubDomainTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - try { - mathdes.addSubDomain(getMembraneSubDomain(tempelement, mathdes)); - } catch(MathException e){ - throw new XmlParseException("Error adding a new MembraneSubDomain to the MathDescription " + name, e); - } - } - - //Retrieve the FilamentSubdomain (if any) - tempelement = param.getChild(XMLTags.FilamentSubDomainTag, vcNamespace); - if(tempelement != null){ - try { - mathdes.addSubDomain(getFilamentSubDomain(tempelement, mathdes)); - } catch(MathException e){ - throw new XmlParseException("Error adding a new FilamentSubDomain to the MathDescription " + name, e); - } - } - - //Retrieve the PointSubdomain (if any) - tempelement = param.getChild(XMLTags.PointSubDomainTag, vcNamespace); - if(tempelement != null){ - try { - mathdes.addSubDomain(getPointSubDomain(tempelement, mathdes)); - } catch(MathException e){ - throw new XmlParseException("Error adding a new PointSubDomain to the MathDescription " + name, e); - } - } - - iterator = param.getChildren(XMLTags.EventTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - Event event = getEvent(mathdes, tempelement); - try { - mathdes.addEvent(event); - } catch(MathException e){ - throw new XmlParseException(e); - } - } - iterator = param.getChildren(XMLTags.PostProcessingBlock, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - getPostProcessingBlock(mathdes, tempelement); - } - - mathdes.refreshDependencies(); - - return mathdes; - } - - private void getPostProcessingBlock(MathDescription mathDesc, Element element) throws XmlParseException{ - Iterator iterator = element.getChildren(XMLTags.ExplicitDataGenerator, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - - ExplicitDataGenerator explicitDataGenerator = getExplicitDataGenerator(tempelement); - try { - mathDesc.getPostProcessingBlock().addDataGenerator(explicitDataGenerator); - } catch(MathException e){ - throw new XmlParseException(e); - } - } - iterator = element.getChildren(XMLTags.ProjectionDataGenerator, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - - ProjectionDataGenerator projectionDataGenerator = getProjectionDataGenerator(tempelement); - try { - mathDesc.getPostProcessingBlock().addDataGenerator(projectionDataGenerator); - } catch(MathException e){ - throw new XmlParseException(e); - } - } - iterator = element.getChildren(XMLTags.ConvolutionDataGenerator, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - - ConvolutionDataGenerator convolutionDataGenerator = getConvolutionDataGenerator(tempelement); - try { - mathDesc.getPostProcessingBlock().addDataGenerator(convolutionDataGenerator); - } catch(MathException e){ - throw new XmlParseException(e); - } - } - } - - private ExplicitDataGenerator getExplicitDataGenerator(Element element){ - String name = unMangle(element.getAttributeValue(XMLTags.NameAttrTag)); - String domainStr = unMangle(element.getAttributeValue(XMLTags.DomainAttrTag)); - Domain domain = null; - if(domainStr != null){ - domain = new Domain(domainStr); - } - String temp = element.getText(); - - Expression exp = unMangleExpression(temp); - ExplicitDataGenerator explicitDataGenerator = new ExplicitDataGenerator(name, domain, exp); - return explicitDataGenerator; - } - - private ConvolutionDataGenerator getConvolutionDataGenerator(Element element){ - String name = unMangle(element.getAttributeValue(XMLTags.NameAttrTag)); - - Expression volumeFunction = null; - Element volumeFunctionElement = element.getChild(XMLTags.FunctionTag, vcNamespace); - if(volumeFunctionElement == null){ - volumeFunctionElement = element.getChild(XMLTags.VolumeFunctionTag, vcNamespace); - } - if(volumeFunctionElement != null){ - String s = volumeFunctionElement.getText(); - volumeFunction = unMangleExpression(s); - } - - Expression membraneFunction = null; - Element membraneFunctionElement = element.getChild(XMLTags.MembraneFunctionTag, vcNamespace); - if(membraneFunctionElement != null){ - String s = membraneFunctionElement.getText(); - membraneFunction = unMangleExpression(s); - } - - ConvolutionDataGeneratorKernel kernel = null; - Element kernelElement = element.getChild(XMLTags.Kernel, vcNamespace); - String kernelType = kernelElement.getAttributeValue(XMLTags.TypeAttrTag); - if(kernelType.equals(XMLTags.KernelType_Gaussian)){ - Element e0 = kernelElement.getChild(XMLTags.KernelGaussianSigmaXY, vcNamespace); - String s = e0.getText(); - Expression sigmaXY = unMangleExpression(s); - - e0 = kernelElement.getChild(XMLTags.KernelGaussianSigmaZ, vcNamespace); - s = e0.getText(); - Expression sigmaZ = unMangleExpression(s); - - kernel = new GaussianConvolutionDataGeneratorKernel(sigmaXY, sigmaZ); - } - - ConvolutionDataGenerator cdg = new ConvolutionDataGenerator(name, kernel, volumeFunction, membraneFunction); - return cdg; - } - - private ProjectionDataGenerator getProjectionDataGenerator(Element element){ - String name = unMangle(element.getAttributeValue(XMLTags.NameAttrTag)); - String domainStr = unMangle(element.getAttributeValue(XMLTags.DomainAttrTag)); - Domain domain = null; - if(domainStr != null){ - domain = new Domain(domainStr); - } - - Element e = element.getChild(XMLTags.ProjectionAxis, vcNamespace); - String axis = e.getText(); -// ProjectionDataGenerator.Axis axis = ProjectionDataGenerator.Axis.valueOf(s); - - e = element.getChild(XMLTags.ProjectionOperation, vcNamespace); - String operation = e.getText(); -// ProjectionDataGenerator.Operation operation = ProjectionDataGenerator.Operation.valueOf(s); - - e = element.getChild(XMLTags.FunctionTag, vcNamespace); - String s = e.getText(); - Expression exp = unMangleExpression(s); - ProjectionDataGenerator projectionDataGenerator = new ProjectionDataGenerator(name, domain, axis, operation, exp); - return projectionDataGenerator; - } - - private RandomVariable getRandomVariable(Element param) throws XmlParseException{ - //get attributes - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - Element element = param.getChild(XMLTags.RandomVariableSeedTag, vcNamespace); - Expression seed = null; - if(element != null){ - seed = unMangleExpression(element.getText()); - } - Distribution dist = null; - element = param.getChild(XMLTags.UniformDistributionTag, vcNamespace); - if(element != null){ - dist = getUniformDistribution(element); - } - element = param.getChild(XMLTags.GaussianDistributionTag, vcNamespace); - if(element != null){ - dist = getGaussianDistribution(element); - } - - String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); - Domain domain = null; - if(domainStr != null){ - domain = new Domain(domainStr); - } - - RandomVariable var = null; - if(param.getName().equals(XMLTags.VolumeRandomVariableTag)){ - var = new VolumeRandomVariable(name, seed, dist, domain); - } else if(param.getName().equals(XMLTags.MembraneRandomVariableTag)){ - var = new MembraneRandomVariable(name, seed, dist, domain); - } else { - throw new XmlParseException(param.getName() + " is not supported!"); - } - transcribeComments(param, var); - return var; - } - - private GaussianDistribution getGaussianDistribution(Element distElement){ - Element element = distElement.getChild(XMLTags.GaussianDistributionMeanTag, vcNamespace); - Expression mu = unMangleExpression(element.getText()); - - element = distElement.getChild(XMLTags.GaussianDistributionStandardDeviationTag, vcNamespace); - Expression sigma = unMangleExpression(element.getText()); - - return new GaussianDistribution(mu, sigma); - } - - private UniformDistribution getUniformDistribution(Element distElement){ - Element element = distElement.getChild(XMLTags.UniformDistributionMinimumTag, vcNamespace); - Expression low = unMangleExpression(element.getText()); - - element = distElement.getChild(XMLTags.UniformDistributionMaximumTag, vcNamespace); - Expression high = unMangleExpression(element.getText()); - - return new UniformDistribution(low, high); - } - - private Event getEvent(MathDescription mathdesc, Element eventElement) throws XmlParseException{ - - String name = unMangle(eventElement.getAttributeValue(XMLTags.NameAttrTag)); - Element element = eventElement.getChild(XMLTags.TriggerTag, vcNamespace); - Expression triggerExp = unMangleExpression(element.getText()); - - element = eventElement.getChild(XMLTags.DelayTag, vcNamespace); - Delay delay = null; - if(element != null){ - boolean useValuesFromTriggerTime = Boolean.valueOf(element.getAttributeValue(XMLTags.UseValuesFromTriggerTimeAttrTag)).booleanValue(); - Expression durationExp = unMangleExpression(element.getText()); - delay = new Delay(useValuesFromTriggerTime, durationExp); - } - - ArrayList eventAssignmentList = new ArrayList(); - Iterator iter = eventElement.getChildren(XMLTags.EventAssignmentTag, vcNamespace).iterator(); - while (iter.hasNext()) { - element = iter.next(); - String varname = element.getAttributeValue(XMLTags.EventAssignmentVariableAttrTag); - Expression assignExp = unMangleExpression(element.getText()); - Variable var = mathdesc.getVariable(varname); - EventAssignment eventAssignment = new EventAssignment(var, assignExp); - eventAssignmentList.add(eventAssignment); - } - - Event event = new Event(name, triggerExp, delay, eventAssignmentList); - transcribeComments(eventElement, event); - return event; - } - - public BioEvent[] getBioEvents(SimulationContext simContext, Element bioEventsElement) throws XmlParseException{ - Iterator bioEventsIterator = bioEventsElement.getChildren(XMLTags.BioEventTag, vcNamespace).iterator(); - Vector bioEventsVector = new Vector(); - while (bioEventsIterator.hasNext()) { - Element bEventElement = (Element) bioEventsIterator.next(); - - BioEvent newBioEvent = null; - String name = unMangle(bEventElement.getAttributeValue(XMLTags.NameAttrTag)); - Element triggerElement = bEventElement.getChild(XMLTags.TriggerTag, vcNamespace); - if(triggerElement != null && triggerElement.getText().length() > 0){ - // - // read legacy VCell 5.3 style trigger and delay elements - // - // (t>3.0) - // 3.0 [optional] - // - Expression triggerExpression = unMangleExpression(triggerElement.getText()); - - // read - Expression delayDurationExpression = null; - boolean useValuesFromTriggerTime = true; - Element delayElement = bEventElement.getChild(XMLTags.DelayTag, vcNamespace); - if(delayElement != null){ - useValuesFromTriggerTime = Boolean.valueOf(delayElement.getAttributeValue(XMLTags.UseValuesFromTriggerTimeAttrTag)).booleanValue(); - delayDurationExpression = unMangleExpression((delayElement.getText())); - } - - newBioEvent = new BioEvent(name, TriggerType.GeneralTrigger, useValuesFromTriggerTime, simContext); - try { - newBioEvent.setParameterValue(BioEventParameterType.GeneralTriggerFunction, triggerExpression); - if(delayDurationExpression != null){ - newBioEvent.setParameterValue(BioEventParameterType.TriggerDelay, delayDurationExpression); - } - } catch(ExpressionBindingException | PropertyVetoException e){ - throw new XmlParseException("failed to read trigger or delay expressions in bioEvent " + name + ": " + e.getMessage(), e); - } - - } else if(triggerElement != null && triggerElement.getText().length() == 0){ - // - // read legacy first-pass VCell 5.4 style trigger and delay elements - // - // - // - // (t > 500.0) - // - // - // 3.0 [optional] - // - final String TriggerParametersTag = "TriggerParameters"; - final String TriggerClassAttrTag = "triggerClass"; - final String TriggerClassAttrValue_TriggerGeneral = "TriggerGeneral"; - - Element triggerParametersElement = triggerElement.getChild(TriggerParametersTag, vcNamespace); - - Expression triggerExpression = null; - - String triggerClass = triggerParametersElement.getAttributeValue(TriggerClassAttrTag); - if(triggerClass.equals(TriggerClassAttrValue_TriggerGeneral)){ - triggerExpression = unMangleExpression(triggerParametersElement.getText()); - } else { - // not general trigger (just make it never happen, user will have to edit "t > -1") - triggerExpression = Expression.relational(">", new Expression(simContext.getModel().getTIME(), simContext.getModel().getNameScope()), new Expression(-1.0)); - } - - // read - Expression delayDurationExpression = null; - boolean useValuesFromTriggerTime = true; - Element delayElement = bEventElement.getChild(XMLTags.DelayTag, vcNamespace); - if(delayElement != null){ - useValuesFromTriggerTime = Boolean.valueOf(delayElement.getAttributeValue(XMLTags.UseValuesFromTriggerTimeAttrTag)).booleanValue(); - delayDurationExpression = unMangleExpression((delayElement.getText())); - } - - newBioEvent = new BioEvent(name, TriggerType.GeneralTrigger, useValuesFromTriggerTime, simContext); - try { - newBioEvent.setParameterValue(BioEventParameterType.GeneralTriggerFunction, triggerExpression); - if(delayDurationExpression != null){ - newBioEvent.setParameterValue(BioEventParameterType.TriggerDelay, delayDurationExpression); - } - } catch(ExpressionBindingException | PropertyVetoException e){ - throw new XmlParseException("failed to read trigger or delay expressions in bioEvent " + name + ": " + e.getMessage(), e); - } - - } else { - // - // VCell 5.4 style bioevent parameters - // - // - TriggerType triggerType = TriggerType.fromXmlName(bEventElement.getAttributeValue(XMLTags.BioEventTriggerTypeAttrTag)); - boolean bUseValuesFromTriggerTime = Boolean.parseBoolean(bEventElement.getAttributeValue(XMLTags.UseValuesFromTriggerTimeAttrTag)); - - newBioEvent = new BioEvent(name, triggerType, bUseValuesFromTriggerTime, simContext); - - Iterator paramElementIter = bEventElement.getChildren(XMLTags.ParameterTag, vcNamespace).iterator(); - ArrayList parameters = new ArrayList(); - - boolean bHasGeneralTriggerParam = false; - - while (paramElementIter.hasNext()) { - Element paramElement = paramElementIter.next(); - - //Get parameter attributes - String paramName = paramElement.getAttributeValue(XMLTags.NameAttrTag); - Expression exp = unMangleExpression(paramElement.getText()); - String roleStr = paramElement.getAttributeValue(XMLTags.ParamRoleAttrTag); - BioEventParameterType parameterType = BioEventParameterType.fromRoleXmlName(roleStr); - if(parameterType == BioEventParameterType.GeneralTriggerFunction){ - bHasGeneralTriggerParam = true; - } - VCUnitDefinition unit = simContext.getModel().getUnitSystem().getInstance_TBD(); - String unitSymbol = paramElement.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); - if(unitSymbol != null){ - unit = simContext.getModel().getUnitSystem().getInstance(unitSymbol); - } - - parameters.add(newBioEvent.createNewParameter(paramName, parameterType, exp, unit)); - } - if(!bHasGeneralTriggerParam){ - parameters.add(newBioEvent.createNewParameter( - BioEventParameterType.GeneralTriggerFunction.getDefaultName(), - BioEventParameterType.GeneralTriggerFunction, - null, // computed as needed - simContext.getModel().getUnitSystem().getInstance_DIMENSIONLESS())); - } - try { - newBioEvent.setParameters(parameters.toArray(new LocalParameter[0])); - } catch(PropertyVetoException | ExpressionBindingException e){ - throw new XmlParseException("failed to read parameters in bioEvent " + name + ": " + e.getMessage(), e); - } - } - - ArrayList eventAssignmentList = new ArrayList(); - Iterator iter = bEventElement.getChildren(XMLTags.EventAssignmentTag, vcNamespace).iterator(); - while (iter.hasNext()) { - Element eventAssignmentElement = iter.next(); - try { - String varname = eventAssignmentElement.getAttributeValue(XMLTags.EventAssignmentVariableAttrTag); - Expression assignExp = unMangleExpression(eventAssignmentElement.getText()); - SymbolTableEntry target = simContext.getEntry(varname); - if(!(target instanceof EditableSymbolTableEntry)){ - throw new XmlParseException("expecting an EditableSymbolTableEntry for event assignment target, found " + target); - } - BioEvent.EventAssignment eventAssignment = newBioEvent.new EventAssignment((EditableSymbolTableEntry) target, assignExp); - eventAssignmentList.add(eventAssignment); - } catch(ExpressionException e){ - throw new XmlParseException(e); - } - } - try { - newBioEvent.setEventAssignmentsList(eventAssignmentList); - } catch(PropertyVetoException e1){ - throw new XmlParseException(e1); - } - try { - newBioEvent.bind(); - } catch(ExpressionBindingException e){ - throw new XmlParseException(e); - } - bioEventsVector.add(newBioEvent); - } - - return bioEventsVector.toArray(BioEvent[]::new); - } - - public SpatialObject[] getSpatialObjects(SimulationContext simContext, Element spatialObjectsElement) throws XmlParseException{ - Iterator spatialObjectElementIterator = spatialObjectsElement.getChildren(XMLTags.SpatialObjectTag, vcNamespace).iterator(); - ArrayList spatialObjectList = new ArrayList(); - while (spatialObjectElementIterator.hasNext()) { - Element spatialObjectElement = (Element) spatialObjectElementIterator.next(); - - SpatialObject spatialObject = null; - String name = unMangle(spatialObjectElement.getAttributeValue(XMLTags.NameAttrTag)); - String type = unMangle(spatialObjectElement.getAttributeValue(XMLTags.SpatialObjectTypeAttrTag)); - switch(type){ - case XMLTags.SpatialObjectTypeAttrValue_Point -> { - spatialObject = new PointObject(name, simContext); - } - case XMLTags.SpatialObjectTypeAttrValue_Surface -> { - String insideSubvolumeName = unMangle(spatialObjectElement.getAttributeValue(XMLTags.SpatialObjectSubVolumeInsideAttrTag)); - String insideRegionIDString = spatialObjectElement.getAttributeValue(XMLTags.SpatialObjectRegionIdInsideAttrTag); - String outsideSubvolumeName = unMangle(spatialObjectElement.getAttributeValue(XMLTags.SpatialObjectSubVolumeOutsideAttrTag)); - String outsideRegionIDString = spatialObjectElement.getAttributeValue(XMLTags.SpatialObjectRegionIdOutsideAttrTag); - SubVolume insideSubvolume = null; - if(insideSubvolumeName != null){ - insideSubvolume = simContext.getGeometry().getGeometrySpec().getSubVolume(insideSubvolumeName); - } - Integer insideRegionID = null; - if(insideRegionIDString != null){ - insideRegionID = Integer.parseUnsignedInt(insideRegionIDString); - } - SubVolume outsideSubvolume = null; - if(outsideSubvolumeName != null){ - outsideSubvolume = simContext.getGeometry().getGeometrySpec().getSubVolume(outsideSubvolumeName); - } - Integer outsideRegionID = null; - if(outsideRegionIDString != null){ - outsideRegionID = Integer.parseUnsignedInt(outsideRegionIDString); - } - spatialObject = new SurfaceRegionObject(name, insideSubvolume, insideRegionID, outsideSubvolume, outsideRegionID, simContext); - } - case XMLTags.SpatialObjectTypeAttrValue_Volume -> { - String subvolumeName = unMangle(spatialObjectElement.getAttributeValue(XMLTags.SpatialObjectSubVolumeAttrTag)); - String regionIDString = spatialObjectElement.getAttributeValue(XMLTags.SpatialObjectRegionIdAttrTag); - SubVolume subvolume = null; - if(subvolumeName != null){ - subvolume = simContext.getGeometry().getGeometrySpec().getSubVolume(subvolumeName); - } - Integer regionID = null; - if(regionIDString != null){ - regionID = Integer.parseUnsignedInt(regionIDString); - } - spatialObject = new VolumeRegionObject(name, subvolume, regionID, simContext); - } - } - - // set Quantity enables - Element quantityCategoryListElement = spatialObjectElement.getChild(XMLTags.QuantityCategoryListTag, vcNamespace); - List quantityCategoryElements = quantityCategoryListElement.getChildren(XMLTags.QuantityCategoryTag, vcNamespace); - for(Element quantityCategoryElement : quantityCategoryElements){ - String quantityCategoryName = unMangle(quantityCategoryElement.getAttributeValue(XMLTags.QuantityCategoryNameAttrTag)); - boolean enabled = Boolean.parseBoolean(quantityCategoryElement.getAttributeValue(XMLTags.QuantityCategoryEnabledAttrTag)); - QuantityCategory category = QuantityCategory.fromXMLName(quantityCategoryName); - spatialObject.setQuantityCategoryEnabled(category, enabled); - } - - spatialObjectList.add(spatialObject); - } - return spatialObjectList.toArray(new SpatialObject[0]); - } - - public SpatialProcess[] getSpatialProcesses(SimulationContext simContext, Element spatialProcessesElement) throws XmlParseException{ - Iterator spatialProcessElementIterator = spatialProcessesElement.getChildren(XMLTags.SpatialProcessTag, vcNamespace).iterator(); - ArrayList spatialProcessList = new ArrayList(); - while (spatialProcessElementIterator.hasNext()) { - Element spatialProcessElement = (Element) spatialProcessElementIterator.next(); - - SpatialProcess spatialProcess = null; - String name = unMangle(spatialProcessElement.getAttributeValue(XMLTags.NameAttrTag)); - String type = unMangle(spatialProcessElement.getAttributeValue(XMLTags.SpatialProcessTypeAttrTag)); - if(type.equals(XMLTags.SpatialProcessTypeAttrValue_PointKinematics)){ - PointKinematics pointKinematics = new PointKinematics(name, simContext); - String pointObjectName = spatialProcessElement.getAttributeValue(XMLTags.SpatialProcessPointObjectAttrTag); - PointObject pointObject = (PointObject) simContext.getSpatialObject(pointObjectName); - pointKinematics.setPointObject(pointObject); - spatialProcess = pointKinematics; - } else if(type.equals(XMLTags.SpatialProcessTypeAttrValue_PointLocation)){ - PointLocation pointLocation = new PointLocation(name, simContext); - String pointObjectName = spatialProcessElement.getAttributeValue(XMLTags.SpatialProcessPointObjectAttrTag); - PointObject pointObject = (PointObject) simContext.getSpatialObject(pointObjectName); - pointLocation.setPointObject(pointObject); - spatialProcess = pointLocation; - } else if(type.equals(XMLTags.SpatialProcessTypeAttrValue_SurfaceKinematics)){ - SurfaceKinematics surfaceKinematics = new SurfaceKinematics(name, simContext); - String surfaceRegionObjectName = spatialProcessElement.getAttributeValue(XMLTags.SpatialProcessSurfaceObjectAttrTag); - SurfaceRegionObject surfaceRegionObject = (SurfaceRegionObject) simContext.getSpatialObject(surfaceRegionObjectName); - surfaceKinematics.setSurfaceRegionObject(surfaceRegionObject); - spatialProcess = surfaceKinematics; - } else if(type.equals(XMLTags.SpatialProcessTypeAttrValue_VolumeKinematics)){ - VolumeKinematics volumeKinematics = new VolumeKinematics(name, simContext); - String volumeRegionObjectName = spatialProcessElement.getAttributeValue(XMLTags.SpatialProcessVolumeObjectAttrTag); - VolumeRegionObject volumeRegionObject = (VolumeRegionObject) simContext.getSpatialObject(volumeRegionObjectName); - volumeKinematics.setVolumeRegionObject(volumeRegionObject); - spatialProcess = volumeKinematics; - } - - // set parameters - Iterator paramElementIter = spatialProcessElement.getChildren(XMLTags.ParameterTag, vcNamespace).iterator(); - ArrayList parameters = new ArrayList(); - - while (paramElementIter.hasNext()) { - Element paramElement = paramElementIter.next(); - - //Get parameter attributes - String paramName = paramElement.getAttributeValue(XMLTags.NameAttrTag); - Expression exp = unMangleExpression(paramElement.getText()); - String roleStr = paramElement.getAttributeValue(XMLTags.ParamRoleAttrTag); - SpatialProcessParameterType parameterType = SpatialProcessParameterType.fromRoleXmlName(roleStr); - VCUnitDefinition unit = simContext.getModel().getUnitSystem().getInstance_TBD(); - String unitSymbol = paramElement.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); - if(unitSymbol != null){ - unit = simContext.getModel().getUnitSystem().getInstance(unitSymbol); - } - parameters.add(spatialProcess.createNewParameter(paramName, parameterType, exp, unit)); - } - try { - spatialProcess.setParameters(parameters.toArray(new LocalParameter[0])); - } catch(PropertyVetoException | ExpressionBindingException e){ - throw new XmlParseException("failed to read parameters in bioEvent " + name + ": " + e.getMessage(), e); - } - - spatialProcessList.add(spatialProcess); - } - return spatialProcessList.toArray(new SpatialProcess[0]); - } - - public RateRule[] getRateRules(SimulationContext simContext, Element rateRulesElement) throws XmlParseException{ - Iterator rateRulesIterator = rateRulesElement.getChildren(XMLTags.RateRuleTag, vcNamespace).iterator(); - Vector rateRulesVector = new Vector(); - while (rateRulesIterator.hasNext()) { - Element rrElement = (Element) rateRulesIterator.next(); - - RateRule newRateRule = null; - try { - String rrName = unMangle(rrElement.getAttributeValue(XMLTags.NameAttrTag)); - String varname = rrElement.getAttributeValue(XMLTags.RateRuleVariableAttrTag); - SymbolTableEntry rrVar = simContext.getEntry(varname); - Expression rrExp = unMangleExpression(rrElement.getText()); - newRateRule = new RateRule(rrName, rrVar, rrExp, simContext); - newRateRule.bind(); - } catch(ExpressionBindingException e){ - throw new XmlParseException(e.getMessage()); - } - rateRulesVector.add(newRateRule); - } - return rateRulesVector.toArray(RateRule[]::new); - } - - public AssignmentRule[] getAssignmentRules(SimulationContext simContext, Element assignmentRulesElement) throws XmlParseException{ - Iterator assignmentRulesIterator = assignmentRulesElement.getChildren(XMLTags.AssignmentRuleTag, vcNamespace).iterator(); - Vector assignmentRulesVector = new Vector(); - while (assignmentRulesIterator.hasNext()) { - Element rrElement = (Element) assignmentRulesIterator.next(); - - AssignmentRule newAssignmentRule = null; - try { - String rrName = unMangle(rrElement.getAttributeValue(XMLTags.NameAttrTag)); - String varname = rrElement.getAttributeValue(XMLTags.AssignmentRuleVariableAttrTag); - SymbolTableEntry rrVar = simContext.getEntry(varname); - Expression rrExp = unMangleExpression(rrElement.getText()); - newAssignmentRule = new AssignmentRule(rrName, rrVar, rrExp, simContext); - newAssignmentRule.bind(); - } catch(ExpressionBindingException e){ - throw new XmlParseException(e.getMessage()); - } - if(newAssignmentRule != null){ - assignmentRulesVector.add(newAssignmentRule); - } - } - return assignmentRulesVector.toArray(AssignmentRule[]::new); - } - - - public ReactionRuleSpec[] getReactionRuleSpecs(SimulationContext simContext, Element reactionRuleSpecsElement) throws XmlParseException{ - List reactionRulesSpecIterator = reactionRuleSpecsElement.getChildren(XMLTags.ReactionRuleSpecTag, vcNamespace); - ArrayList reactionRuleSpecs = new ArrayList(); - for(Element rrElement : reactionRulesSpecIterator){ - String rrName = unMangle(rrElement.getAttributeValue(XMLTags.ReactionRuleRefAttrTag)); - String rrMappingString = rrElement.getAttributeValue(XMLTags.ReactionRuleMappingAttrTag); - ReactionRuleMappingType rrMapping = ReactionRuleMappingType.fromDatabaseName(rrMappingString); - ReactionRule reactionRule = simContext.getModel().getRbmModelContainer().getReactionRule(rrName); - ReactionRuleSpec reactionRuleSpec = new ReactionRuleSpec(reactionRule); - reactionRuleSpec.setReactionRuleMapping(rrMapping); - - if(SimulationContext.Application.SPRINGSALAD == simContext.getApplicationType()){ // Springsalad - // only the bondLength is needed, the subtype and transitionCondition may be used for sanity check against the math (LangevinParticleJumpProcess) - Subtype subtype = Subtype.INCOMPATIBLE; - if(rrElement.getAttribute(XMLTags.SubTypeAttrTag) != null){ - String stString = rrElement.getAttributeValue(XMLTags.SubTypeAttrTag); - subtype = Subtype.fromName(stString); - } - TransitionCondition transitionCondition = null; - double bondLength = 1; // that's the default, even for non-binding rules (we hide it anyway for those) - if(rrElement.getAttribute(XMLTags.BondLengthAttrTag) != null){ - bondLength = Double.valueOf(rrElement.getAttributeValue(XMLTags.BondLengthAttrTag)); - reactionRuleSpec.setFieldBondLength(bondLength); - - } - if(rrElement.getAttribute(XMLTags.TransitionConditionAttrTag) != null){ - String tcString = rrElement.getAttributeValue(XMLTags.TransitionConditionAttrTag); - transitionCondition = TransitionCondition.fromVcellName(tcString); - } - // TODO: (optional) verify consistency of subtype and transitionCondition against Math:CompartmentSubdomain:ParticleJumpProcess - } - reactionRuleSpecs.add(reactionRuleSpec); - } - return reactionRuleSpecs.toArray(new ReactionRuleSpec[0]); - } - - -/* -public RateRuleVariable[] getRateRuleVariables(Element rateRuleVarsElement, Model model) throws XmlParseException { - Iterator rateRuleVarsIterator = rateRuleVarsElement.getChildren(XMLTags.RateRuleVariableTag, vcNamespace).iterator(); - Vector rateRuleVarsVector = new Vector(); - while (rateRuleVarsIterator.hasNext()) { - Element rrvElement = (Element) rateRuleVarsIterator.next(); - - RateRuleVariable newRateRuleVar = null; - try { - String rrvName = unMangle(rrvElement.getAttributeValue(XMLTags.NameAttrTag)); - String rrvStructureName = unMangle(rrvElement.getAttributeValue(XMLTags.StructureAttrTag)); - // structure can be null - Structure rrvStructure = null; - if (rrvStructureName != null) { - rrvStructure = (Structure) model.getStructure(rrvStructureName); - } -// if (structureref == null) { -// throw new XmlParseException("The structure " + rrvStructureName + "could not be resolved!"); -// } - String rrvRoleStr = rrvElement.getAttributeValue(XMLTags.ParamRoleAttrTag); - int rrvRole = RateRuleVariable.getParamRoleFromDesc(rrvRoleStr); - Element rrvParamElement = rrvElement.getChild(XMLTags.ParameterTag, vcNamespace); - ModelParameter rrvParameter = getModelParameter(rrvParamElement, model); - newRateRuleVar = new RateRuleVariable(rrvName, rrvStructure, rrvParameter, rrvRole); - newRateRuleVar.bind(); - } catch (ExpressionBindingException e) { - lg.error(e); - throw new XmlParseException(e.getMessage()); - } - if (newRateRuleVar != null) { - rateRuleVarsVector.add(newRateRuleVar); - } - } - - return ((RateRuleVariable[])BeanUtils.getArray(rateRuleVarsVector, RateRuleVariable.class)); -} -*/ - - /** - * This method returns a MathModel object from a XML Element. - * Creation date: (3/13/2001 12:35:00 PM) - * - * @param param Element - * @return cbit.vcell.mathmodel.MathModel - */ - public MathModel getMathModel(Element param) throws XmlParseException{ - //Create it - //set Metadata (version), if any - Version versionObject = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace)); - MathModel mathmodel = new MathModel(versionObject); - - //Set attributes - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - try { - mathmodel.setName(name); - //String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag); - - //if (annotation!=null) { - //mathmodel.setDescription(unMangle(annotation)); - //} - //Add annotation - String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace); - if(annotationText != null && annotationText.length() > 0){ - mathmodel.setDescription(unMangle(annotationText)); - } - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("An error occurred while trying to set the name " + param.getAttributeValue(XMLTags.NameAttrTag) + "to a MathModel!", e); - } - - //set Geometry (if any) - Element tempElem = param.getChild(XMLTags.GeometryTag, vcNamespace); - Geometry tempGeometry = getGeometry(tempElem); - - - //set MathDescription - tempElem = param.getChild(XMLTags.MathDescriptionTag, vcNamespace); - MathDescription mathDesc = getMathDescription(tempElem, tempGeometry); - - if(tempElem != null){ - mathmodel.setMathDescription(mathDesc); - } else { - throw new XmlParseException("MathDescription missing in this MathModel!"); - } - - // set output functions (outputfunctionContext) - Element outputFunctionsElement = param.getChild(XMLTags.OutputFunctionsTag, vcNamespace); - if(outputFunctionsElement != null){ - ArrayList outputFunctions = getOutputFunctions(outputFunctionsElement); - try { - // construct OutputFnContext from mathmodel and add output functions that were read in from XML. - OutputFunctionContext outputFnContext = mathmodel.getOutputFunctionContext(); - for(AnnotatedFunction outputFunction : outputFunctions){ - outputFnContext.addOutputFunction(outputFunction); - } - } catch(PropertyVetoException e){ - throw new XmlParseException(e); - } - } - - //Set simulations contexts (if any) - List childList = param.getChildren(XMLTags.SimulationTag, vcNamespace); - Simulation[] simList = new Simulation[childList.size()]; - int simCounter = 0; - for(Element simElement : childList){ - simList[simCounter] = getSimulation(simElement, mathDesc, mathmodel); - simCounter++; - } - try { - mathmodel.setSimulations(simList); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A PropertyVetoException occurred when adding the Simulations to the MathModel " + name, e); - } - - return mathmodel; - } - - - /** - * This method returns a MathOverrides object from a XML Element. - * Creation date: (5/21/2001 3:05:17 PM) - * - * @param param Element - * @return cbit.vcell.solver.MathOverrides - */ - private MathOverrides getMathOverrides(Element param, Simulation simulation) throws XmlParseException{ - - MathOverrides mathOverrides; - try { - //Get the constants - Object[] elements = param.getChildren().toArray(); - Vector v1 = new Vector<>(); - Vector v2 = new Vector<>(); - for(Object element : elements){ - Element e = (Element) element; - Attribute array = e.getAttribute(XMLTags.ConstantArraySpec); - if(array != null){ - // collect scan overrides - String name = e.getAttributeValue(XMLTags.NameAttrTag); - int type = array.getIntValue(); - v1.add(ConstantArraySpec.createFromString(name, e.getText(), type)); - } else { - // collect regular overrides - v2.add(getConstant(e)); - } - } - Constant[] constants = v2.toArray(Constant[]::new); - ConstantArraySpec[] specs = v1.toArray(ConstantArraySpec[]::new); - //create new MathOverrides object - mathOverrides = new MathOverrides(simulation, constants, specs); - } catch(ExpressionException | DataConversionException e){ - throw new XmlParseException("failed to add a Constant to the MathOverrides", e); - } - return mathOverrides; - } - - - /** - * This method returns a Membrane object from a XML element. - * Creation date: (4/4/2001 4:17:32 PM) - * - * @param param Element - * @return cbit.vcell.model.Membrane - */ - private Membrane getMembrane(Model model, Element param, List featureList) throws XmlParseException{ - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - Membrane newmembrane = null; - - //retrieve the key if there is one - KeyValue key = null; - String stringkey = param.getAttributeValue(XMLTags.KeyValueAttrTag); - - if(stringkey != null && stringkey.length() > 0 && this.readKeysFlag){ - key = new KeyValue(stringkey); - } - - //try to create new Membrane named "name" - try { - newmembrane = new Membrane(key, name); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException( - "An error occurred while trying to create the Membrane object " + name, e); - } - //set inside feature - String infeaturename = unMangle(param.getAttributeValue(XMLTags.InsideFeatureTag)); - String outfeaturename = unMangle(param.getAttributeValue(XMLTags.OutsideFeatureTag)); - - String posFeatureName = unMangle(param.getAttributeValue(XMLTags.PositiveFeatureTag)); - String negFeatureName = unMangle(param.getAttributeValue(XMLTags.NegativeFeatureTag)); - - Feature infeatureref = null; - Feature outfeatureref = null; - Feature posFeature = null; - Feature negFeature = null; - - for(Structure s : featureList){ - String sname = s.getName(); - if(sname.equals(infeaturename)){ - infeatureref = (Feature) s; - } - if(sname.equals(outfeaturename)){ - outfeatureref = (Feature) s; - } - if(sname.equals(posFeatureName)){ - posFeature = (Feature) s; - } - if(sname.equals(negFeatureName)){ - negFeature = (Feature) s; - } - } - - //set inside and outside features - if(infeatureref != null){ - model.getStructureTopology().setInsideFeature(newmembrane, infeatureref); - } - if(outfeatureref != null){ - model.getStructureTopology().setOutsideFeature(newmembrane, outfeatureref); - } - //set positive & negative features - if(posFeature != null){ - model.getElectricalTopology().setPositiveFeature(newmembrane, posFeature); - } - if(negFeature != null){ - model.getElectricalTopology().setNegativeFeature(newmembrane, negFeature); - } - //set MemVoltName - if(param.getAttribute(XMLTags.MemVoltNameTag) == null){ - throw new XmlParseException("Error reading membrane Voltage Name!"); - } - String memvoltName = unMangle(param.getAttributeValue(XMLTags.MemVoltNameTag)); - try { - newmembrane.getMembraneVoltage().setName(memvoltName); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("Error setting the membrane Voltage Name", e); - } - - return newmembrane; - } - - - /** - * This method retuns a MembraneMapping object from a XML representation. - * Creation date: (5/7/2001 4:12:03 PM) - * - * @param param Element - * @return cbit.vcell.mapping.MembraneMapping - */ - private MembraneMapping getMembraneMapping(Element param, SimulationContext simulationContext) throws XmlParseException{ - //Retrieve attributes - String membranename = unMangle(param.getAttributeValue(XMLTags.MembraneAttrTag)); - - Membrane membraneref = (Membrane) simulationContext.getModel().getStructure(membranename); - if(membraneref == null){ - throw new XmlParseException("The Membrane " + membranename + " could not be resolved!"); - } - - //*** Create new Membrane Mapping **** - MembraneMapping memmap = new MembraneMapping(membraneref, simulationContext, simulationContext.getModel().getUnitSystem()); - - //Set SurfacetoVolumeRatio when it exists, amended Sept. 27th, 2007 - if(param.getAttributeValue(XMLTags.SurfaceToVolumeRatioTag) != null){ - String ratio = unMangle(param.getAttributeValue(XMLTags.SurfaceToVolumeRatioTag)); - try { - memmap.getSurfaceToVolumeParameter().setExpression(unMangleExpression(ratio)); - } catch(ExpressionException e){ - throw new XmlParseException("An expressionException was fired when setting the SurfacetoVolumeRatio Expression " + ratio + " to a membraneMapping!", e); - } - } - - //Set VolumeFraction when it exists, amended Sept. 27th, 2007 - if(param.getAttributeValue(XMLTags.VolumeFractionTag) != null){ - String fraction = unMangle(param.getAttributeValue(XMLTags.VolumeFractionTag)); - try { - memmap.getVolumeFractionParameter().setExpression(unMangleExpression(fraction)); - } catch(ExpressionException e){ - throw new XmlParseException("An expressionException was fired when setting the VolumeFraction Expression " + fraction + " to a membraneMapping!", e); - } - } - - //Set Area/unit_area if it exists, amended Sept. 27th, 2007 - if(param.getAttributeValue(XMLTags.AreaPerUnitAreaTag) != null){ - String ratio = unMangle(param.getAttributeValue(XMLTags.AreaPerUnitAreaTag)); - try { - memmap.getAreaPerUnitAreaParameter().setExpression(unMangleExpression(ratio)); - } catch(ExpressionException e){ - throw new XmlParseException("An expressionException was fired when setting the AreaPerUnitArea Expression " + ratio + " to a membraneMapping!", e); - } - } - - //Set SurfacetoVolumeRatio when it exists, amended Sept. 27th, 2007 - if(param.getAttributeValue(XMLTags.AreaPerUnitVolumeTag) != null){ - String ratio = unMangle(param.getAttributeValue(XMLTags.AreaPerUnitVolumeTag)); - try { - memmap.getAreaPerUnitVolumeParameter().setExpression(unMangleExpression(ratio)); - } catch(ExpressionException e){ - throw new XmlParseException("An expressionException was fired when setting the AreaPerUnitVolume Expression " + ratio + " to a membraneMapping!", e); - } - } - - //Set Size - if(param.getAttributeValue(XMLTags.SizeTag) != null){ - String size = unMangle(param.getAttributeValue(XMLTags.SizeTag)); - try { - memmap.getSizeParameter().setExpression(unMangleExpression(size)); - } catch(ExpressionException e){ - throw new XmlParseException("An expressionException was fired when setting the size Expression " + size + " to a membraneMapping!", e); - } - } else { - try { - memmap.getSizeParameter().setExpression(null); - } catch(Exception e){ - throw new RuntimeException("unexpected exception while setting structure size", e); - } - } - //** Set electrical properties ** - //set specific capacitance - double specificCap = Double.parseDouble(param.getAttributeValue(XMLTags.SpecificCapacitanceTag)); - try { - memmap.getSpecificCapacitanceParameter().setExpression(new Expression(specificCap)); - } catch(ExpressionException e){ - throw new XmlParseException(e); - } - - //set flag calculate voltage - boolean calculateVolt = (Boolean.valueOf(param.getAttributeValue(XMLTags.CalculateVoltageTag))).booleanValue(); - memmap.setCalculateVoltage(calculateVolt); - - //set initial Voltage - String initialVoltString = param.getAttributeValue(XMLTags.InitialVoltageTag); - try { - Expression initialExpr = unMangleExpression(initialVoltString); - memmap.getInitialVoltageParameter().setExpression(initialExpr); - } catch(ExpressionException e){ - throw new XmlParseException(e); - } - - String geometryClassName = param.getAttributeValue(XMLTags.GeometryClassAttrTag); - if(geometryClassName != null){ - geometryClassName = unMangle(geometryClassName); - } - //Retrieve subvolumeref, allow subvolumes to be 'null' - if(geometryClassName != null){ - GeometryClass[] geometryClasses = simulationContext.getGeometry().getGeometryClasses(); - for(int i = 0; i < geometryClasses.length; i++){ - if(geometryClasses[i].getName().equals(geometryClassName)){ - try { - memmap.setGeometryClass(geometryClasses[i]); - } catch(PropertyVetoException e){ - throw new XmlParseException("A propertyVetoException was fired when trying to set the subvolume or surface " + geometryClassName + " to a MembraneMapping!", e); - } - } - } - } - - //Set Boundary conditions - Element tempElement = param.getChild(XMLTags.BoundariesTypesTag, vcNamespace); - if(tempElement != null){ - //Xm - String temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueXm); - BoundaryConditionType bct = new BoundaryConditionType(temp); - memmap.setBoundaryConditionTypeXm(bct); - //Xp - temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueXp); - bct = new BoundaryConditionType(temp); - memmap.setBoundaryConditionTypeXp(bct); - //Ym - temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueYm); - bct = new BoundaryConditionType(temp); - memmap.setBoundaryConditionTypeYm(bct); - //Yp - temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueYp); - bct = new BoundaryConditionType(temp); - memmap.setBoundaryConditionTypeYp(bct); - //Zm - temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueZm); - bct = new BoundaryConditionType(temp); - memmap.setBoundaryConditionTypeZm(bct); - //Zp - temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueZp); - bct = new BoundaryConditionType(temp); - memmap.setBoundaryConditionTypeZp(bct); - } - - return memmap; - } - - - /** - * This method returns a MembraneRegionEquation from a XML Element. - * Creation date: (5/17/2001 3:52:40 PM) - * - * @param param Element - * @return cbit.vcell.math.MembraneRegionEquation - * @throws cbit.vcell.xml.XmlParseException The exception description. - */ - private MembraneRegionEquation getMembraneRegionEquation(Element param, MathDescription mathDesc) throws XmlParseException{ - //get attributes - String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - - //find reference in the dictionnary - //try a MembraneRegionVariable - MembraneRegionVariable varref = (MembraneRegionVariable) mathDesc.getVariable(varname); - if(varref == null){ - throw new XmlParseException("The reference to the MembraneRegion variable " + varname + " could not be resolved!"); - } - - //get Initial condition - String temp = param.getChildText(XMLTags.InitialTag, vcNamespace); - Expression exp; - exp = unMangleExpression(temp); - // ** Create the Equation ** - MembraneRegionEquation memRegEq = new MembraneRegionEquation(varref, exp); - - //set the Uniform Rate - temp = param.getChildText(XMLTags.UniformRateTag, vcNamespace); - exp = unMangleExpression(temp); - memRegEq.setUniformRateExpression(exp); - - //set the Membrane Rate - temp = param.getChildText(XMLTags.MembraneRateTag, vcNamespace); - exp = unMangleExpression(temp); - memRegEq.setMembraneRateExpression(exp); - - //get ExactSolution (if any) -/* temp = param.getChildText(XMLTags.ExactTag); - if (temp !=null) { - try { - Expression expression = new Expression( unMangle( temp) ); - odeEquation.setExactSolution( expression); - } catch (ExpressionException e) { - lg.error(e); - throw new XmlParseException("An ExpressionException was fired when creating the expression: "+ unMangle(temp)+" : "+e.getMessage()); - } - } - //get ConstructedSolution (if any) - temp = param.getChildText(XMLTags.ConstructedTag); - if (temp != null) { - try { - Expression expression = new Expression(unMangle(temp)); - odeEquation.setConstructedSolution( expression ); - } catch (ExpressionException e) { - lg.error(e); - throw new XmlParseException("An ExpressionException was fired when creating the expression: "+ unMangle(temp)+" : "+e.getMessage()); - } - }*/ - - return memRegEq; - } - - private ComputeNormalComponentEquation getComputeNormal(Element param, MathDescription mathDesc) throws XmlParseException{ - //get attributes - String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - - //find reference in the dictionnary - //try a MembraneRegionVariable - MemVariable varref = (MemVariable) mathDesc.getVariable(varname); - if(varref == null){ - throw new XmlParseException("The reference to the Membrane variable " + varname + " could not be resolved!"); - } - - NormalComponent normalComponent = null; - String normalComponentString = param.getAttributeValue(XMLTags.ComputeNormalComponentAttrTag); - if(normalComponentString.equals(XMLTags.ComputeNormalComponentAttrTagValue_X)){ - normalComponent = NormalComponent.X; - } else if(normalComponentString.equals(XMLTags.ComputeNormalComponentAttrTagValue_Y)){ - normalComponent = NormalComponent.Y; - } else if(normalComponentString.equals(XMLTags.ComputeNormalComponentAttrTagValue_Z)){ - normalComponent = NormalComponent.Z; - } - - ComputeNormalComponentEquation computeNormal = new ComputeNormalComponentEquation(varref, normalComponent); - return computeNormal; - } - - private ComputeMembraneMetricEquation getComputeMembraneMetric(Element param, MathDescription mathDesc) throws XmlParseException{ - //get attributes - String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - - //find reference in the dictionnary - //try a MembraneRegionVariable - VolVariable varref = (VolVariable) mathDesc.getVariable(varname); - if(varref == null){ - throw new XmlParseException("The reference to the Volume variable " + varname + " could not be resolved!"); - } - - MembraneMetricComponent normalComponent = null; - String normalComponentString = param.getAttributeValue(XMLTags.ComputeMembraneMetricComponentAttrTag); - if(normalComponentString.equals(XMLTags.ComputeMembraneMetricComponentAttrTagValue_directionX)){ - normalComponent = MembraneMetricComponent.directionToMembraneX; - } else if(normalComponentString.equals(XMLTags.ComputeMembraneMetricComponentAttrTagValue_directionY)){ - normalComponent = MembraneMetricComponent.directionToMembraneY; - } else if(normalComponentString.equals(XMLTags.ComputeMembraneMetricComponentAttrTagValue_directionZ)){ - normalComponent = MembraneMetricComponent.directionToMembraneZ; - } else if(normalComponentString.equals(XMLTags.ComputeMembraneMetricComponentAttrTagValue_distance)){ - normalComponent = MembraneMetricComponent.distanceToMembrane; - } - - ComputeMembraneMetricEquation computeMembraneMetric = new ComputeMembraneMetricEquation(varref, normalComponent); - String membraneName = param.getAttributeValue(XMLTags.ComputeMembraneMetricTargetMembraneAttrTag); - computeMembraneMetric.setTargetMembraneName(membraneName); - return computeMembraneMetric; - } - - private ComputeCentroidComponentEquation getComputeCentroid(Element param, MathDescription mathDesc) throws XmlParseException{ - //get attributes - String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - - //find reference in the dictionnary - //try a MembraneRegionVariable - VolumeRegionVariable varref = (VolumeRegionVariable) mathDesc.getVariable(varname); - if(varref == null){ - throw new XmlParseException("The reference to the Volume Region variable " + varname + " could not be resolved!"); - } - - CentroidComponent normalComponent = null; - String normalComponentString = param.getAttributeValue(XMLTags.ComputeCentroidComponentAttrTag); - if(normalComponentString.equals(XMLTags.ComputeCentroidComponentAttrTagValue_X)){ - normalComponent = CentroidComponent.X; - } else if(normalComponentString.equals(XMLTags.ComputeCentroidComponentAttrTagValue_Y)){ - normalComponent = CentroidComponent.Y; - } else if(normalComponentString.equals(XMLTags.ComputeCentroidComponentAttrTagValue_Z)){ - normalComponent = CentroidComponent.Z; - } - - ComputeCentroidComponentEquation centroid = new ComputeCentroidComponentEquation(varref, normalComponent); - return centroid; - } - - /** - * This method returns a MembraneRegionVariable object from a XML Element. - * Creation date: (5/16/2001 2:56:34 PM) - * - * @param param Element - * @return cbit.vcell.math.MembraneRegionVariable - */ - private MembraneRegionVariable getMembraneRegionVariable(Element param){ - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); - Domain domain = null; - if(domainStr != null){ - domain = new Domain(domainStr); - } - - //-- create new MembraneRegionVariable object - MembraneRegionVariable memRegVariable = new MembraneRegionVariable(name, domain); - transcribeComments(param, memRegVariable); - - return memRegVariable; - } - - - /** - * This method returns a MembraneSubDomain object from a XML Element. - * Creation date: (5/18/2001 4:23:30 PM) - * - * @param param Element - * @return cbit.vcell.math.MembraneSubDomain - * @throws cbit.vcell.xml.XmlParseException The exception description. - */ - @SuppressWarnings("unchecked") - private MembraneSubDomain getMembraneSubDomain(Element param, MathDescription mathDesc) throws XmlParseException{ - - // no need to do anything with the 'Name' attribute : constructor of MembraneSubDomain creates name from inside/outside compartmentSubDomains. -// String msdName = unMangle( param.getAttributeValue(XMLTags.NameAttrTag) ); -// if ( msdName != null) { -// } - - //get compartmentSubDomain references - //inside - String name = unMangle(param.getAttributeValue(XMLTags.InsideCompartmentTag)); - CompartmentSubDomain insideRef = (CompartmentSubDomain) mathDesc.getCompartmentSubDomain(name); - if(insideRef == null){ - throw new XmlParseException("The reference to the inside CompartmentSubDomain " + name + ", could not be resolved!"); - } - //outside - name = unMangle(param.getAttributeValue(XMLTags.OutsideCompartmentTag)); - CompartmentSubDomain outsideRef = (CompartmentSubDomain) mathDesc.getCompartmentSubDomain(name); - if(outsideRef == null){ - throw new XmlParseException("The reference to the outside CompartmentSubDomain " + name + ", could not be resolved!"); - } - //*** create new Membrane SubDomain *** - SubVolume insideSubVolume = mathDesc.getGeometry().getGeometrySpec().getSubVolume(insideRef.getName()); - SubVolume outsideSubVolume = mathDesc.getGeometry().getGeometrySpec().getSubVolume(outsideRef.getName()); - SurfaceClass surfaceClass = mathDesc.getGeometry().getGeometrySurfaceDescription().getSurfaceClass(insideSubVolume, outsideSubVolume); - - MembraneSubDomain subDomain = new MembraneSubDomain(insideRef, outsideRef, surfaceClass.getName()); - transcribeComments(param, subDomain); - - //Process BoundaryConditions - Iterator iterator = param.getChildren(XMLTags.BoundaryTypeTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - - //create BoundaryConditionType - String temp = tempelement.getAttributeValue(XMLTags.BoundaryTypeAttrTag); - BoundaryConditionType bType = new BoundaryConditionType(temp); - - //check where it goes - //Process Xm - if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueXm)){ - subDomain.setBoundaryConditionXm(bType); - } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueXp)){ - //Process Xp - subDomain.setBoundaryConditionXp(bType); - } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueYm)){ - //Process Ym - subDomain.setBoundaryConditionYm(bType); - } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueYp)){ - //Process Yp - subDomain.setBoundaryConditionYp(bType); - } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueZm)){ - //Process Zm - subDomain.setBoundaryConditionZm(bType); - } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueZp)){ - //Process Zp - subDomain.setBoundaryConditionZp(bType); - } else { - // If not indentified throw an exception!! - throw new XmlParseException("Unknown BoundaryConditionType: " + tempelement.getAttributeValue(XMLTags.BoundaryAttrTag)); - } - } - - //Add OdeEquations - iterator = param.getChildren(XMLTags.OdeEquationTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempElement = (Element) iterator.next(); - OdeEquation odeEquation = getOdeEquation(tempElement, mathDesc); - - try { - subDomain.addEquation(odeEquation); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding an OdeEquation to a MembraneSubDomain!", e); - } - } - - //process PdeEquations - iterator = param.getChildren(XMLTags.PdeEquationTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempElement = (Element) iterator.next(); - - try { - subDomain.addEquation(getPdeEquation(tempElement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding an PdeEquation to the MembraneSubDomain " + name, e); - } - } - - //Add JumpConditions - iterator = param.getChildren(XMLTags.JumpConditionTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempElement = (Element) iterator.next(); - try { - subDomain.addJumpCondition(getJumpCondition(tempElement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding a JumpCondition to a MembraneSubDomain!", e); - } - } - - //Add the FastSystem (if any) - Element tempElement = param.getChild(XMLTags.FastSystemTag, vcNamespace); - if(tempElement != null){ - subDomain.setFastSystem(getFastSystem(tempElement, mathDesc)); - } - - //add MembraneRegionEquation - iterator = param.getChildren(XMLTags.MembraneRegionEquationTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - tempElement = (Element) iterator.next(); - try { - subDomain.addEquation(getMembraneRegionEquation(tempElement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding a MembraneRegionEquation to a MEmbraneSubDomain!", e); - } - } - - iterator = param.getChildren(XMLTags.ParticleJumpProcessTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - try { - subDomain.addParticleJumpProcess(getParticleJumpProcess(tempelement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding a jump process to the MembraneSubDomain " + name, e); - } - } - - iterator = param.getChildren(XMLTags.LangevinParticleJumpProcessTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - try { - subDomain.addParticleJumpProcess(getParticleJumpProcess(tempelement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding a jump process to the MembraneSubDomain " + name, e); - } - } - - iterator = param.getChildren(XMLTags.ParticlePropertiesTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - try { - subDomain.addParticleProperties(getParticleProperties(tempelement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding a jump process to the MembraneSubDomain " + name, e); - } - } - - //process ComputeNormal "equations" - iterator = param.getChildren(XMLTags.ComputeNormalTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element tempelement = (Element) iterator.next(); - - try { - subDomain.addEquation(getComputeNormal(tempelement, mathDesc)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding an ComputeNormal 'equation' to the MembraneSubDomain " + name, e); - } - } - - - Element velElem = param.getChild(XMLTags.VelocityTag, vcNamespace); - setMembraneSubdomainVelocity(velElem, XMLTags.XAttrTag, subDomain::setVelocityX); - setMembraneSubdomainVelocity(velElem, XMLTags.YAttrTag, subDomain::setVelocityY); - - return subDomain; - } - - /** - * MembraneSubDomain velocity - * - * @param vel could be null - * @param tag - * @param dest - * @throws XmlParseException - */ - private void setMembraneSubdomainVelocity(Element vel, String tag, Consumer dest) throws XmlParseException{ - Expression exp = null; - if(vel != null){ - Element e = vel.getChild(tag, vcNamespace); - if(e != null){ - String expStr = e.getValue(); - try { - exp = new Expression(expStr); - } catch(ExpressionException ee){ - throw new XmlParseException("Error parsing " + expStr, ee); - } - } - } - dest.accept(exp); - } - - - /** - * This method returns a MemVariable object from a XML element. - * Creation date: (5/16/2001 3:17:18 PM) - * - * @param param Element - * @return cbit.vcell.math.MemVariable - */ - private MemVariable getMemVariable(Element param){ - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); - Domain domain = null; - if(domainStr != null){ - domain = new Domain(domainStr); - } - - //Create new memVariable - MemVariable memVariable = new MemVariable(name, domain); - transcribeComments(param, memVariable); - - return memVariable; - } - - - private PointVariable getPointVariable(Element param){ - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); - Domain domain = null; - if(domainStr != null){ - domain = new Domain(domainStr); - } - - //Create new memVariable - PointVariable pointVariable = new PointVariable(name, domain); - transcribeComments(param, pointVariable); - - return pointVariable; - } - - - /** - * This method returns a MeshSpecification object from a XML Element. - * Creation date: (5/22/2001 12:05:21 PM) - * - * @param param Element - * @return cbit.vcell.mesh.MeshSpecification - */ - private MeshSpecification getMeshSpecification(Element param, Geometry geometry) throws XmlParseException{ - //*** create new MeshSpecification *** - MeshSpecification meshSpec = new MeshSpecification(geometry); - - //get ISize - Element size = param.getChild(XMLTags.SizeTag, vcNamespace); - int x = Integer.parseInt(size.getAttributeValue(XMLTags.XAttrTag)); - int y = Integer.parseInt(size.getAttributeValue(XMLTags.YAttrTag)); - int z = Integer.parseInt(size.getAttributeValue(XMLTags.ZAttrTag)); - - ISize newsize = new ISize(x, y, z); - - //set ISize - try { - meshSpec.setSamplingSize(newsize); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A PropertyVetoException was fired when setting the ISize object to a new MeshSpecification", e); - } - - return meshSpec; - } - - - /** - * This method creates a Model object from a XML element. - * Creation date: (3/14/2001 6:14:37 PM) - * - * @param param Element - * @return cbit.vcell.model.Model - */ - public Model getModel(Element param) throws XmlParseException{ - if(param == null){ - throw new XmlParseException("Invalid 'NULL' XML 'model' element arrived!"); - } - //Get version, if any - Model newmodel = null; - Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace)); - - // read in unit system - // if forcedModelUnitSystem has been set, ues that (could be overriding unit system for SBML export) - if(forcedModelUnitSystem != null){ - newmodel = new Model(version, forcedModelUnitSystem); - } else { - Element unitSystemNode = param.getChild(XMLTags.ModelUnitSystemTag, vcNamespace); - if(unitSystemNode != null){ - ModelUnitSystem modelUnitSystem = getUnitSystem(unitSystemNode); - newmodel = new Model(version, modelUnitSystem); - } else { - newmodel = new Model(version); - } - } - - try { - //Set attributes - newmodel.setName(unMangle(param.getAttributeValue(XMLTags.NameAttrTag))); - //Add annotation - String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace); - if(annotationText != null && annotationText.length() > 0){ - newmodel.setDescription(unMangle(annotationText)); - } - - // Add global parameters - Element globalParamsElement = param.getChild(XMLTags.ModelParametersTag, vcNamespace); - if(globalParamsElement != null){ - ModelParameter[] modelParams = getModelParams(globalParamsElement, newmodel); - // add global/model param to model - done inside getModelParam by passing newModel - newmodel.setModelParameters(modelParams); - } - - //Add Species (Compounds) - Iterator iterator = param.getChildren(XMLTags.SpeciesTag, vcNamespace).iterator(); - ArrayList speciesList = new ArrayList(); - while (iterator.hasNext()) { - Element temp = (Element) iterator.next(); - speciesList.add(getSpecies(temp)); - } - newmodel.setSpecies(speciesList.toArray(new Species[speciesList.size()])); - //Add Structures - LinkedList newstructures = new LinkedList(); - //(features) - List children = param.getChildren(XMLTags.FeatureTag, vcNamespace); - for(Element featureElement : children){ - newstructures.add(getFeature(featureElement)); - } - //(Membrane) - children = param.getChildren(XMLTags.MembraneTag, vcNamespace); - for(Element memElement : children){ - newstructures.add(getMembrane(newmodel, memElement, newstructures)); - } - if(newstructures.size() > 0){ - Structure[] structarray = new Structure[newstructures.size()]; - newstructures.toArray(structarray); - // Add all the retrieved structures - newmodel.setStructures(structarray); - } - - // retrieve the RbmModelContainer, if present - must be done before we retrieve species context! - Element element = param.getChild(XMLTags.RbmModelContainerTag, vcNamespace); - if(element != null){ - getRbmModelContainer(element, newmodel); - } else { - lg.debug("RbmModelContainer is missing."); - } - - //Add SpeciesContexts - children = param.getChildren(XMLTags.SpeciesContextTag, vcNamespace); - SpeciesContext[] newspeccon = new SpeciesContext[children.size()]; - int scCounter = 0; - for(Element scElement : children){ - newspeccon[scCounter] = getSpeciesContext(scElement, newmodel); - scCounter++; - } - newmodel.setSpeciesContexts(newspeccon); - - // Retrieve rateRules and add to model -// Element rateRuleVarsElement = param.getChild(XMLTags.RateRuleVariablesTag, vcNamespace); -// if(rateRuleVarsElement != null){ -// RateRuleVariable[] rateRuleVars = getRateRuleVariables(rateRuleVarsElement, newmodel); -// newmodel.setRateRuleVariables(rateRuleVars); -// } - - //Add Reaction steps (if available) - - //(Simplereaction) - // Create a varHash with reserved symbols and global parameters, if any, to pass on to Kinetics - // must create new hash for each reaction and flux, since each kinetics uses new variables hash - iterator = param.getChildren(XMLTags.SimpleReactionTag, vcNamespace).iterator(); - ArrayList reactionStepList = new ArrayList(); - while (iterator.hasNext()) { - Element temp = iterator.next(); - reactionStepList.add(getSimpleReaction(temp, newmodel)); - } - //(fluxStep) - iterator = param.getChildren(XMLTags.FluxStepTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - Element temp = iterator.next(); - reactionStepList.add(getFluxReaction(temp, newmodel)); - } - newmodel.setReactionSteps(reactionStepList.toArray(new ReactionStep[reactionStepList.size()])); - //Add Diagrams - children = param.getChildren(XMLTags.DiagramTag, vcNamespace); - if(children.size() > 0){ - Diagram[] newdiagrams = new Diagram[children.size()]; - int diagramCounter = 0; - for(Element diagramElement : children){ - newdiagrams[diagramCounter] = getDiagram(diagramElement, newmodel); - diagramCounter++; - } - reorderDiagramsInPlace_UponRead(docVCellSoftwareVersion, newdiagrams, newmodel.getStructureTopology()); -// if(docVCellSoftwareVersion != null && !docVCellSoftwareVersion.isValid() && docVCellSoftwareVersion.getMajorVersion()<=5 && docVCellSoftwareVersion.getMinorVersion() <=2){ -// //In Vcell 5.2 and previous we need to order diagrams topologically, in 5.3 and later the diagrams are displayed as they are ordered when read from document -// final StructureTopology structureTopology = newmodel.getStructureTopology(); -// Arrays.sort(newdiagrams, new Comparator() { -// @Override -// public int compare(Diagram o1, Diagram o2) { -// return getStructureLevel(o1.getStructure(), structureTopology) - getStructureLevel(o2.getStructure(), structureTopology); -// } -// }); -// } - newmodel.setDiagrams(newdiagrams); - } - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException(e); - } catch(ModelException e){ - lg.error(e); - } - - // model param expresions are not bound when they are read in, since they could be functions of each other or structures/speciesContexts. - // Hence bind the model param exprs at the end, after reading all model level quantities. - ModelParameter[] modelParameters = newmodel.getModelParameters(); - for(int i = 0; modelParameters != null && i < modelParameters.length; i++){ - try { - modelParameters[i].getExpression().bindExpression(newmodel); - } catch(ExpressionBindingException e){ - throw new RuntimeException("Error binding global parameter '" + modelParameters[i].getName() + "' to model." + e.getMessage(), e); - } - } - return newmodel; - } - - @SuppressWarnings("unchecked") - public void getRbmModelContainer(Element param, Model newModel) throws ModelException, PropertyVetoException, XmlParseException{ - Element element = param.getChild(XMLTags.RbmMolecularTypeListTag, vcNamespace); - if(element != null){ - getRbmMolecularTypeList(element, newModel); - } - element = param.getChild(XMLTags.RbmObservableListTag, vcNamespace); - if(element != null){ - getRbmObservableList(element, newModel); - } - element = param.getChild(XMLTags.RbmReactionRuleListTag, vcNamespace); - if(element != null){ - getRbmReactionRuleList(element, newModel); - } - element = param.getChild(XMLTags.RbmNetworkConstraintsTag, vcNamespace); - if(element != null){ - getRbmNetworkConstraints(element, newModel); // one network constraint element - } - } - - private void getRbmMolecularTypeList(Element param, Model newModel){ - RbmModelContainer mc = newModel.getRbmModelContainer(); - List mtl = mc.getMolecularTypeList(); - List children = param.getChildren(XMLTags.RbmMolecularTypeTag, vcNamespace); - for(Element element : children){ - MolecularType t = getRbmMolecularType(element, newModel); - if(t != null){ - mtl.add(t); - } - } - } - - //private void getRbmSeedSpeciesList(Element param, Model newModel) { -// RbmModelContainer mc = newModel.getRbmModelContainer(); -// List ssl = mc.getSeedSpeciesList(); -// List children = param.getChildren(XMLTags.RbmSeedSpeciesTag, vcNamespace); -// for (Element element : children) { -// SeedSpecies s = getRbmSeedSpecies(element, newModel); -// if(s != null) { ssl.add(s); } -// } -//} - private void getRbmObservableList(Element param, Model newModel) throws ModelException, PropertyVetoException{ - RbmModelContainer mc = newModel.getRbmModelContainer(); - List children = new ArrayList(); - children = param.getChildren(XMLTags.RbmObservableTag, vcNamespace); - for(Element element : children){ - RbmObservable o = getRbmObservables(element, newModel); - if(o != null){ - mc.addObservable(o); - } - } - } - - private void getRbmReactionRuleList(Element param, Model newModel) throws XmlParseException{ - RbmModelContainer mc = newModel.getRbmModelContainer(); - List rrl = mc.getReactionRuleList(); - List children = new ArrayList(); - children = param.getChildren(XMLTags.RbmReactionRuleTag, vcNamespace); - for(Element element : children){ - ReactionRule r = getRbmReactionRule(element, newModel); - if(r != null){ - rrl.add(r); - } - } - } - - private MolecularType getRbmMolecularType(Element e, Model newModel){ - String s = e.getAttributeValue(XMLTags.NameAttrTag); - if(s == null || s.isEmpty()){ - System.out.println("XMLReader: getRBMMolecularType: name is missing."); - return null; - } - MolecularType mt = new MolecularType(s, newModel); - - final String attributeValue = e.getAttributeValue(XMLTags.RbmMolecularTypeAnchorAllAttrTag); - if(attributeValue != null){ - boolean anchorAll = Boolean.parseBoolean(attributeValue); - mt.setAnchorAll(anchorAll); - } - List anchors = e.getChildren(XMLTags.RbmMolecularTypeAnchorTag, vcNamespace); - for(Element element : anchors){ - String anchor = element.getAttributeValue(XMLTags.StructureAttrTag); - Structure structure = newModel.getStructure(anchor); - if(structure == null){ - System.out.println("XMLReader: getRbmMolecularType: anchor is missing from the structures list."); - } - if(structure != null){ - mt.addAnchor(structure); - } - } - List children = e.getChildren(XMLTags.RbmMolecularComponentTag, vcNamespace); - for(Element element : children){ - MolecularComponent mc = getRbmMolecularComponent(element, newModel); - if(mc != null){ - mt.addMolecularComponent(mc); - } - } - return mt; - } - - private MolecularComponent getRbmMolecularComponent(Element e, Model newModel){ - String s = e.getAttributeValue(XMLTags.NameAttrTag); - if(s == null || s.isEmpty()){ - System.out.println("XMLReader: getRbmMolecularComponent: name is missing."); - return null; - } - MolecularComponent mc = new MolecularComponent(s); - s = e.getAttributeValue(XMLTags.RbmIndexAttrTag); - if(s == null || s.isEmpty()){ - System.out.println("XMLReader: getRbmMolecularComponent: index is missing."); - return null; - } - int index = Integer.parseInt(s); - mc.setIndex(index); - List children = e.getChildren(XMLTags.RbmMolecularTypeAllowableStateTag, vcNamespace); - for(Element element : children){ - ComponentStateDefinition cs = getRbmComponentStateDefinition(element, newModel); - if(cs != null){ - mc.addComponentStateDefinition(cs); - } - } - return mc; - } - - private ComponentStateDefinition getRbmComponentStateDefinition(Element e, Model newModel){ - String s = e.getAttributeValue(XMLTags.NameAttrTag); - if(s == null || s.isEmpty()){ - System.out.println("XMLReader: getRbmComponentState: name is missing."); - return null; - } - ComponentStateDefinition cs = new ComponentStateDefinition(s); -// s = e.getAttributeValue(XMLTags.RbmMolecularTypeAnyTag); -// if(s!=null && !s.isEmpty()) { -// boolean any = Boolean.parseBoolean(s); -// cs.setAny(any); -// } - return cs; - } - - //private SeedSpecies getRbmSeedSpecies(Element e, Model newModel) { -// String s = e.getAttributeValue(XMLTags.RbmInitialConditionTag); -// if(s == null || s.isEmpty()) { -// System.out.println("XMLReader: getRbmSeedSpecies: initial condition is missing."); -// return null; -// } -// Expression exp = unMangleExpression(s); -// Element element = e.getChild(XMLTags.RbmSpeciesPatternTag, vcNamespace); -// SpeciesPattern sp = getSpeciesPattern(element, newModel); -// if(sp == null) { -// System.out.println("XMLReader: getRbmSeedSpecies: SpeciesPattern is missing."); -// return null; -// } -// SeedSpecies ss = new SeedSpecies(sp, exp); -// return ss; -//} - private SpeciesPattern getSpeciesPattern(Element e, Model newModel){ - - SpeciesPattern sp = new SpeciesPattern(); - List children = e.getChildren(XMLTags.RbmMolecularTypePatternTag, vcNamespace); - for(Element element : children){ - MolecularTypePattern tp = getRbmMolecularTypePattern(element, newModel); - if(tp != null){ - sp.addMolecularTypePattern(tp); - } - } - return sp; - } - - private MolecularTypePattern getRbmMolecularTypePattern(Element e, Model newModel){ - RbmModelContainer mc = newModel.getRbmModelContainer(); - Element e1 = e.getChild(XMLTags.RbmMolecularTypeTag, vcNamespace); - String molecularTypeName = e1.getAttributeValue(XMLTags.NameAttrTag); - MolecularType mt = mc.getMolecularType(molecularTypeName); - if(mt == null){ - System.out.println("XMLReader: getRbmMolecularTypePattern: encountered reference to non-existing MolecularType."); - return null; - } - MolecularTypePattern tp = new MolecularTypePattern(mt, false); // we insert the component patterns below - String index = e.getAttributeValue(XMLTags.RbmIndexAttrTag); - if(index != null && !index.isEmpty()){ - tp.setIndex(Integer.parseInt(index)); - } - String match = e.getAttributeValue(XMLTags.RbmParticipantPatternMatchTag); - if(match != null && !match.isEmpty()){ - tp.setParticipantMatchLabel(match); - } - List cpl = new ArrayList(); - List children = e.getChildren(XMLTags.RbmMolecularComponentPatternTag, vcNamespace); - for(Element e2 : children){ - MolecularComponentPattern cp = getRbmMolecularComponentPattern(e2, tp, mt, newModel); - if(cp != null){ - cpl.add(cp); - } - } - tp.setComponentPatterns(cpl); - return tp; - } - - public static void reorderDiagramsInPlace_UponRead(VCellSoftwareVersion docVCellSoftwareVersion, final Diagram[] diagramArr, final StructureTopology structureTopology){ - if(docVCellSoftwareVersion != null && (docVCellSoftwareVersion.getMajorVersion() < 5 || (docVCellSoftwareVersion.getMajorVersion() == 5 && docVCellSoftwareVersion.getMinorVersion() <= 2))){ - //In Vcell 5.2 and previous we need to order diagrams topologically, in 5.3 and later the diagrams are displayed as they are ordered when read from document - Arrays.sort(diagramArr, new Comparator() { - @Override - public int compare(Diagram o1, Diagram o2){ - return getStructureLevel(o1.getStructure(), structureTopology) - getStructureLevel(o2.getStructure(), structureTopology); - } - }); - } - } - - private static Integer getStructureLevel(Structure s, StructureTopology structureTopology){ - Structure s0 = s; - int level = 0; - while (s0 != null) { - level += 1; - s0 = structureTopology.getParentStructure(s0); - } - return level; - } - - private MolecularComponentPattern getRbmMolecularComponentPattern(Element e, MolecularTypePattern mtp, MolecularType mt, Model newModel){ - RbmModelContainer mc = newModel.getRbmModelContainer(); - String s = e.getAttributeValue(XMLTags.RbmMolecularComponentTag); - if(s == null || s.isEmpty()){ - System.out.println("XMLReader: getRbmMolecularComponentPattern: MolecularComponent name is missing."); - return null; - } - MolecularComponent c = mt.getMolecularComponent(s); - if(c == null){ - System.out.println("XMLReader: getRbmMolecularComponentPattern: encountered reference " + s + " to non-existing MolecularComponent."); - return null; - } - ComponentStatePattern csp = new ComponentStatePattern(); - MolecularComponentPattern mcp = new MolecularComponentPattern(c); - s = e.getAttributeValue(XMLTags.RbmMolecularComponentStatePatternTag); - if(s != null && !s.isEmpty()){ // state may be missing, we set it only if is present - ComponentStateDefinition cs = c.getComponentStateDefinition(s); - if(cs == null){ - System.out.println("XMLReader: getRbmMolecularComponentPattern: encountered reference " + s + " to non-existing MolecularComponentState."); - return null; - } - csp = new ComponentStatePattern(cs); - mcp.setComponentStatePattern(csp); - } -// s = e.getAttributeValue(XMLTags.RbmMolecularTypeAnyTag); -// if(s!=null && !s.isEmpty()) { -// boolean any = Boolean.parseBoolean(s); -// csp.setAny(any); -// } - - s = e.getAttributeValue(XMLTags.RbmBondTypeAttrTag); - BondType bondType = BondType.fromSymbol(s); - if(bondType == BondType.Specified){ - int bondId = Integer.parseInt(s); - mcp.setBondId(bondId); - } - mcp.setBondType(bondType); - // sanity check, we only read the names here and make sure they make sense - Element bondElement = e.getChild(XMLTags.RbmBondTag, vcNamespace); - if(bondElement != null){ - String molecularTypeName = bondElement.getAttributeValue(XMLTags.RbmMolecularTypePatternTag); // it's actually the name of the MolecularType inside this pattern - String molecularComponentName = bondElement.getAttributeValue(XMLTags.RbmMolecularComponentPatternTag); - if(molecularTypeName == null || molecularTypeName.isEmpty()){ - System.out.println("XMLReader: getRbmMolecularComponentPattern: Bond Attribute molecularTypeName missing."); - return mcp; - } - if(molecularComponentName == null || molecularComponentName.isEmpty()){ - System.out.println("XMLReader: getRbmMolecularComponentPattern: Bond Attribute molecularComponentName missing."); - return mcp; - } - Bond bond = new Bond(); // we'll have a bond here, it will be properly initialized during RbmObservable.resolveBonds() call !!! - mcp.setBond(bond); - } - return mcp; - } - - private RbmObservable getRbmObservables(Element e, Model newModel){ - String n = e.getAttributeValue(XMLTags.NameAttrTag); - if(n == null || n.isEmpty()){ - System.out.println("XMLReader: getRbmObservables: name is missing."); - return null; - } - String t = e.getAttributeValue(XMLTags.RbmObservableTypeTag); - if(t == null || t.isEmpty()){ - System.out.println("XMLReader: getRbmObservables: type is missing."); - return null; - } - RbmObservable.ObservableType ot = RbmObservable.ObservableType.Molecules; - if(!t.equals(ot.name())){ - ot = RbmObservable.ObservableType.Species; - } - Structure structure = null; - String structureName = e.getAttributeValue(XMLTags.StructureAttrTag); - if(structureName == null || structureName.isEmpty()){ // the tag is missing - if(newModel.getStructures().length == 1){ - structure = newModel.getStructure(0); // possible old single compartment model where we were not saving the structure for observable - } else { - throw new RuntimeException("XMLReader: structure missing for observable " + n); - } - } else { - structure = newModel.getStructure(structureName); - } - RbmObservable o = new RbmObservable(newModel, n, structure, ot); - - RbmObservable.Sequence se = RbmObservable.Sequence.Multimolecular; // Sequence - String ses = e.getAttributeValue(XMLTags.RbmObservableSequenceAttrTag); - if(ses != null && ses.equals(RbmObservable.Sequence.PolymerLengthEqual.name())){ - se = RbmObservable.Sequence.PolymerLengthEqual; - } else if(ses != null && ses.equals(RbmObservable.Sequence.PolymerLengthGreater.name())){ - se = RbmObservable.Sequence.PolymerLengthGreater; - } - o.setSequence(se); - - String lens = e.getAttributeValue(XMLTags.RbmObservableLenEqualAttrTag); - if(lens != null){ // may be null for older models in which case the observable has default initial values - int len = Integer.parseInt(lens); - o.setSequenceLength(RbmObservable.Sequence.PolymerLengthEqual, len); - } - lens = e.getAttributeValue(XMLTags.RbmObservableLenGreaterAttrTag); - if(lens != null){ - int len = Integer.parseInt(lens); - o.setSequenceLength(RbmObservable.Sequence.PolymerLengthGreater, len); - } - -// Element element = e.getChild(XMLTags.RbmSpeciesPatternTag, vcNamespace); -// SpeciesPattern sp = getSpeciesPattern(element, newModel); - List children = e.getChildren(XMLTags.RbmSpeciesPatternTag, vcNamespace); - for(Element e2 : children){ - SpeciesPattern sp = getSpeciesPattern(e2, newModel); - if(sp != null){ - o.addSpeciesPattern(sp); - } // setSpeciesPattern() will call resolveBonds() - } - return o; - } - - private ReactionRule getRbmReactionRule(Element reactionRuleElement, Model newModel) throws XmlParseException{ - String n = reactionRuleElement.getAttributeValue(XMLTags.NameAttrTag); - if(n == null || n.isEmpty()){ - System.out.println("XMLReader: getRbmReactionRule: name is missing."); - return null; - } - try { - boolean reversible = Boolean.valueOf(reactionRuleElement.getAttributeValue(XMLTags.RbmReactionRuleReversibleTag)); - String structureName = reactionRuleElement.getAttributeValue(XMLTags.StructureAttrTag, newModel.getStructures()[0].getName()); // get 1st structure if attribute missing - Structure structure = newModel.getStructure(structureName); - ReactionRule reactionRule = new ReactionRule(newModel, n, structure, reversible); - String reactionRuleLabel = reactionRuleElement.getAttributeValue(XMLTags.RbmReactionRuleLabelTag); // we ignore this, name and label are the same thing for now - - // - // old style kinetics placed parameter values as attributes - // look for attributes named ("MassActionKf","MassActionKr","MichaelisMentenKcat","MichaelisMentenKm","SaturableKs","SaturableVmax") - String[] oldKineticsAttributes = new String[]{ - XMLTags.RbmMassActionKfAttrTag_DEPRECATED, - XMLTags.RbmMassActionKrAttrTag_DEPRECATED, - XMLTags.RbmMichaelisMentenKcatAttrTag_DEPRECATED, - XMLTags.RbmMichaelisMentenKmAttrTag_DEPRECATED, - XMLTags.RbmSaturableKsAttrTag_DEPRECATED, - XMLTags.RbmSaturableVmaxAttrTag_DEPRECATED - }; - boolean bOldKineticsFound = false; - for(String oldKineticsAttribute : oldKineticsAttributes){ - if(reactionRuleElement.getAttribute(oldKineticsAttribute) != null){ - bOldKineticsFound = true; - } - } - - if(bOldKineticsFound){ - readOldRbmKineticsAttributes(reactionRuleElement, reactionRule); - } else { - Element kineticsElement = reactionRuleElement.getChild(XMLTags.KineticsTag, vcNamespace); - if(kineticsElement != null){ - String kineticLawTypeString = kineticsElement.getAttributeValue(XMLTags.KineticsTypeAttrTag); - RbmKineticLaw.RateLawType rateLawType = null; - if(XMLTags.RbmKineticTypeMassAction.equals(kineticLawTypeString)){ - rateLawType = RateLawType.MassAction; - } else if(XMLTags.RbmKineticTypeMichaelisMenten.equals(kineticLawTypeString)){ - rateLawType = RateLawType.MichaelisMenten; - } else if(XMLTags.RbmKineticTypeSaturable.equals(kineticLawTypeString)){ - rateLawType = RateLawType.Saturable; - } else { - throw new RuntimeException("unexpected rate law type " + kineticLawTypeString); - } - reactionRule.setKineticLaw(new RbmKineticLaw(reactionRule, rateLawType)); - List parameterElements = kineticsElement.getChildren(XMLTags.ParameterTag, vcNamespace); - HashMap roleHash = new HashMap(); - roleHash.put(XMLTags.RbmMassActionKfRole, RbmKineticLawParameterType.MassActionForwardRate); - roleHash.put(XMLTags.RbmMassActionKrRole, RbmKineticLawParameterType.MassActionReverseRate); - roleHash.put(XMLTags.RbmMichaelisMentenVmaxRole, RbmKineticLawParameterType.MichaelisMentenVmax); - roleHash.put(XMLTags.RbmMichaelisMentenKmRole, RbmKineticLawParameterType.MichaelisMentenKm); - roleHash.put(XMLTags.RbmSaturableVmaxRole, RbmKineticLawParameterType.SaturableVmax); - roleHash.put(XMLTags.RbmSaturableKsRole, RbmKineticLawParameterType.SaturableKs); - roleHash.put(XMLTags.RbmUserDefinedRole, RbmKineticLawParameterType.UserDefined); - HashSet xmlRolesToIgnore = new HashSet(); - xmlRolesToIgnore.add(XMLTags.RbmRuleRateRole); - ParameterContext parameterContext = reactionRule.getKineticLaw().getParameterContext(); - readParameters(parameterElements, parameterContext, roleHash, RbmKineticLawParameterType.UserDefined, xmlRolesToIgnore, newModel); - } - } - Element e1 = reactionRuleElement.getChild(XMLTags.RbmReactantPatternsListTag, vcNamespace); - getRbmReactantPatternsList(e1, reactionRule, newModel); - Element e2 = reactionRuleElement.getChild(XMLTags.RbmProductPatternsListTag, vcNamespace); - getRbmProductPatternsList(e2, reactionRule, newModel); - reactionRule.checkMatchConsistency(); - return reactionRule; - } catch(PropertyVetoException | ExpressionException ex){ - throw new RuntimeException("failed to parse kinetics for reaction rule '" + n + "': " + ex.getMessage(), ex); - } - } - - private void readOldRbmKineticsAttributes(Element reactionRuleElement, ReactionRule reactionRule) throws PropertyVetoException, ExpressionException{ - boolean reversible = reactionRule.isReversible(); - - // - // try Mass Action Kinetics attributes - // - { - String massActionForwardRate = reactionRuleElement.getAttributeValue(XMLTags.RbmMassActionKfAttrTag_DEPRECATED); - if(massActionForwardRate != null && !massActionForwardRate.isEmpty()){ - reactionRule.setKineticLaw(new RbmKineticLaw(reactionRule, RateLawType.MassAction)); - Expression massActionKfExp = unMangleExpression(massActionForwardRate); - LocalParameter forwardRateParameter = reactionRule.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate); - reactionRule.getKineticLaw().setParameterValue(forwardRateParameter, massActionKfExp, true); - if(reversible == true){ - String massActionReverseRate = reactionRuleElement.getAttributeValue(XMLTags.RbmMassActionKrAttrTag_DEPRECATED); - if(massActionReverseRate == null || massActionReverseRate.isEmpty()){ - throw new RuntimeException("XMLReader: getRbmReactionRule: Mass Action: Reverse Rate is missing."); - } else { - Expression massActionKrExp = unMangleExpression(massActionReverseRate); - LocalParameter reverseRateParameter = reactionRule.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate); - reactionRule.getKineticLaw().setParameterValue(reverseRateParameter, massActionKrExp, true); - } - } - return; - } - } - - // - // try Michaelis Menten Kinetics attributes - // - { - String MM_Kcat = reactionRuleElement.getAttributeValue(XMLTags.RbmMichaelisMentenKcatAttrTag_DEPRECATED); - if(MM_Kcat != null && !MM_Kcat.isEmpty()){ - reactionRule.setKineticLaw(new RbmKineticLaw(reactionRule, RateLawType.MichaelisMenten)); - Expression MM_Kcat_exp = unMangleExpression(MM_Kcat); - LocalParameter kcatParameter = reactionRule.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MichaelisMentenVmax); - reactionRule.getKineticLaw().setParameterValue(kcatParameter, MM_Kcat_exp, true); - String MM_Km = reactionRuleElement.getAttributeValue(XMLTags.RbmMichaelisMentenKmAttrTag_DEPRECATED); - if(MM_Km == null || MM_Km.isEmpty()){ - System.out.println("XMLReader: getRbmReactionRule: MM_Km is missing."); - } else { - Expression MM_Km_exp = unMangleExpression(MM_Km); - LocalParameter kmParameter = reactionRule.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MichaelisMentenKm); - reactionRule.getKineticLaw().setParameterValue(kmParameter, MM_Km_exp, true); - } - return; - } - } - - // - // try Saturable Kinetics attributes - // - { - String Sat_Ks = reactionRuleElement.getAttributeValue(XMLTags.RbmSaturableKsAttrTag_DEPRECATED); - if(Sat_Ks != null && !Sat_Ks.isEmpty()){ - reactionRule.setKineticLaw(new RbmKineticLaw(reactionRule, RateLawType.Saturable)); - Expression Sat_Ks_exp = unMangleExpression(Sat_Ks); - LocalParameter ksParameter = reactionRule.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.SaturableKs); - reactionRule.getKineticLaw().setParameterValue(ksParameter, Sat_Ks_exp, true); - String Sat_Vmax = reactionRuleElement.getAttributeValue(XMLTags.RbmSaturableVmaxAttrTag_DEPRECATED); - if(Sat_Vmax == null || Sat_Vmax.isEmpty()){ - System.out.println("XMLReader: getRbmReactionRule: Sat_Vmax is missing."); - } else { - Expression Sat_Vmax_exp = unMangleExpression(Sat_Vmax); - LocalParameter vmaxParameter = reactionRule.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.SaturableVmax); - reactionRule.getKineticLaw().setParameterValue(vmaxParameter, Sat_Vmax_exp, true); - } - return; - } - } - - throw new RuntimeException("Kinetic law unsupported or missing. Must be Mass Action, Michaelis Menten or Saturable."); - } - - private void getRbmReactantPatternsList(Element e, ReactionRule r, Model newModel){ - if(e != null){ - List rpChildren = e.getChildren(XMLTags.RbmReactantPatternTag, vcNamespace); - for(Element rpElement : rpChildren){ - Structure structure = null; - String structureName = rpElement.getAttributeValue(XMLTags.StructureAttrTag); - if(structureName == null || structureName.isEmpty()){ // the tag is missing - throw new RuntimeException("XMLReader: structure missing for reaction rule pattern."); - } else { - structure = newModel.getStructure(structureName); - } - Element spe = rpElement.getChild(XMLTags.RbmSpeciesPatternTag, vcNamespace); - SpeciesPattern s = getSpeciesPattern(spe, newModel); - if(s != null){ - r.addReactant(new ReactantPattern(s, structure), false); - } - } - // older models have the species pattern saved directly and using the structure or the rule - List spChildren = e.getChildren(XMLTags.RbmSpeciesPatternTag, vcNamespace); - for(Element element : spChildren){ - SpeciesPattern s = getSpeciesPattern(element, newModel); - if(s != null){ - r.addReactant(new ReactantPattern(s, r.getStructure()), false); - } - } - } - } - - private void getRbmProductPatternsList(Element e, ReactionRule r, Model newModel){ - if(e != null){ - List ppChildren = e.getChildren(XMLTags.RbmProductPatternTag, vcNamespace); - for(Element ppElement : ppChildren){ - Structure structure = null; - String structureName = ppElement.getAttributeValue(XMLTags.StructureAttrTag); - if(structureName == null || structureName.isEmpty()){ // the tag is missing - throw new RuntimeException("XMLReader: structure missing for reaction rule pattern."); - } else { - structure = newModel.getStructure(structureName); - } - Element spe = ppElement.getChild(XMLTags.RbmSpeciesPatternTag, vcNamespace); - SpeciesPattern s = getSpeciesPattern(spe, newModel); - if(s != null){ - r.addProduct(new ProductPattern(s, structure), false); - } - } - // older models have the species pattern saved directly and using the structure or the rule - List spChildren = GenericUtils.convert(e.getChildren(XMLTags.RbmSpeciesPatternTag, vcNamespace), Element.class); - for(Element element : spChildren){ - SpeciesPattern s = getSpeciesPattern(element, newModel); - if(s != null){ - r.addProduct(new ProductPattern(s, r.getStructure()), false); - } - } - } - } - - // -// Legacy NetworkConstraints was the single NetworkConstraints object formerly stored -// in the Model's RbmModelContainer. The NetworkConstraints are now stored in each -// SimulationContext instead (inheriting the "global" NetworkConstraint) upon first -// load. -// -// We read the single BioModel network constraints from legacy Rule-based models -// (pre-release VCell 6.0 models only). -// -// Warning: We will NOT preserve this default NetworkConstraints object for saved BioModels -// where the database cached XML document is lost and must be regenerated. -// This rare condition for few models would have added complexity and been of limited value. -// -// - private NetworkConstraints legacyNetworkConstraints = null; - - private void getRbmNetworkConstraints(Element e, Model newModel){ - RbmModelContainer mc = newModel.getRbmModelContainer(); - NetworkConstraints nc = new NetworkConstraints(); - this.legacyNetworkConstraints = nc; - - String s = e.getAttributeValue(XMLTags.RbmMaxIterationTag); - if(s != null && !s.isEmpty()){ - int maxIteration = Integer.parseInt(s); - nc.setMaxIteration(maxIteration); - } - s = e.getAttributeValue(XMLTags.RbmMaxMoleculesPerSpeciesTag); - if(s != null && !s.isEmpty()){ - int maxMoleculesPerSpecies = Integer.parseInt(s); - nc.setMaxMoleculesPerSpecies(maxMoleculesPerSpecies); - } - /* - * there has never been a species limit or a reaction limit here, so we don't even try to read them - */ - List children = e.getChildren(XMLTags.RbmMaxStoichiometryTag, vcNamespace); - for(Element element : children){ - Integer i = 1; - MolecularType mt = null; - s = element.getAttributeValue(XMLTags.RbmIntegerAttrTag); - if(s != null && !s.isEmpty()){ - i = Integer.valueOf(s); - } - s = element.getAttributeValue(XMLTags.RbmMolecularTypeTag); - if(s != null && !s.isEmpty()){ - mt = mc.getMolecularType(s); - } - if(mt != null){ - nc.setMaxStoichiometry(mt, i); - } - } - } - -// -------------------------------------------------------------------- - - public ModelUnitSystem getUnitSystem(Element unitSystemNode){ - - //Read all the attributes - String volSubsUnit = unMangle(unitSystemNode.getAttributeValue(XMLTags.VolumeSubstanceUnitTag)); - String memSubsUnit = unMangle(unitSystemNode.getAttributeValue(XMLTags.MembraneSubstanceUnitTag)); - String lumpedSubsUnit = unMangle(unitSystemNode.getAttributeValue(XMLTags.LumpedReactionSubstanceUnitTag)); - String volUnit = unMangle(unitSystemNode.getAttributeValue(XMLTags.VolumeUnitTag)); - String areaUnit = unMangle(unitSystemNode.getAttributeValue(XMLTags.AreaUnitTag)); - String lengthUnit = unMangle(unitSystemNode.getAttributeValue(XMLTags.LengthUnitTag)); - String timeUnit = unMangle(unitSystemNode.getAttributeValue(XMLTags.TimeUnitTag)); - - return ModelUnitSystem.createVCModelUnitSystem(volSubsUnit, memSubsUnit, lumpedSubsUnit, volUnit, areaUnit, lengthUnit, timeUnit); - } - - /** - * This method returns a nodeReference onject from a XML representation. - * Creation date: (4/24/2001 5:35:56 PM) - * - * @param param Element - * @return cbit.vcell.model.NodeReference - */ - private NodeReference getNodeReference(Element param) throws XmlParseException{ - String tempname = param.getName(); - NodeReference newNodeRef = null; - - int type = NodeReference.UNKNOWN_NODE; - String name = null; - //determine the type of nodereference to create - if(tempname.equalsIgnoreCase(XMLTags.SpeciesContextShapeTag)){ - type = NodeReference.SPECIES_CONTEXT_NODE; - name = unMangle(param.getAttributeValue(XMLTags.SpeciesContextRefAttrTag)); - } else if(tempname.equalsIgnoreCase(XMLTags.SimpleReactionShapeTag)){ - type = NodeReference.SIMPLE_REACTION_NODE; - name = unMangle(param.getAttributeValue(XMLTags.SimpleReactionRefAttrTag)); - } else if(tempname.equalsIgnoreCase(XMLTags.FluxReactionShapeTag)){ - type = NodeReference.FLUX_REACTION_NODE; - name = unMangle(param.getAttributeValue(XMLTags.FluxReactionRefAttrTag)); - } else if(tempname.equalsIgnoreCase(XMLTags.ReactionRuleShapeTag)){ - type = NodeReference.REACTION_RULE_NODE; - name = unMangle(param.getAttributeValue(XMLTags.ReactionRuleRef2AttrTag)); - } else if(tempname.equalsIgnoreCase(XMLTags.RuleParticipantFullShapeTag) || tempname.equalsIgnoreCase(XMLTags.RuleParticipantShapeTag)){ - type = NodeReference.RULE_PARTICIPANT_SIGNATURE_FULL_NODE; - name = unMangle(param.getAttributeValue(XMLTags.RuleParticipantRefAttrTag)); - } else if(tempname.equalsIgnoreCase(XMLTags.RuleParticipantShortShapeTag)){ - type = NodeReference.RULE_PARTICIPANT_SIGNATURE_SHORT_NODE; - name = unMangle(param.getAttributeValue(XMLTags.RuleParticipantRefAttrTag)); - } else { - throw new XmlParseException("An unknown type was found " + tempname + ",when processing noderefence!"); - } - String modeString = unMangle(param.getAttributeValue(XMLTags.NodeReferenceModeAttrTag)); - NodeReference.Mode mode = NodeReference.Mode.none; - if(modeString != null){ - mode = Mode.fromValue(modeString); - } - java.awt.Point location = new java.awt.Point(Integer.parseInt(param.getAttributeValue(XMLTags.LocationXAttrTag)), Integer.parseInt(param.getAttributeValue(XMLTags.LocationYAttrTag))); - newNodeRef = new NodeReference(mode, type, name, location); - return newNodeRef; - } - - - /** - * This method returns an OdeEquation from a XML Element. - * Creation date: (5/17/2001 3:52:40 PM) - * - * @param param Element - * @return cbit.vcell.math.OdeEquation - * @throws cbit.vcell.xml.XmlParseException The exception description. - */ - private OdeEquation getOdeEquation(Element param, MathDescription mathDesc) throws XmlParseException{ - //get attributes - String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - //find reference in the dictionnary - //try as a VolVariable - Variable varref = mathDesc.getVariable(varname); - - //Make sure that the reference is not empty!!! - if(varref == null){ - throw new XmlParseException("The reference to the variable " + varname + " in a OdeEquation could not be resolved!"); - } - - //get Initial condition - String temp = param.getChildText(XMLTags.InitialTag, vcNamespace); - Expression initialexp = null; - - if(temp != null && temp.length() > 0){ - initialexp = unMangleExpression(temp); - } - - //Get Rate condition - temp = param.getChildText(XMLTags.RateTag, vcNamespace); - Expression rateexp = null; - if(temp != null && temp.length() > 0){ - rateexp = unMangleExpression((temp)); - } - - //--- Create the OdeEquation object --- - OdeEquation odeEquation = new OdeEquation(varref, initialexp, rateexp); - - //add specific solutions expressions - String solType = param.getAttributeValue(XMLTags.SolutionTypeTag); - - if(solType.equalsIgnoreCase(XMLTags.ExactTypeTag)){ - String solutionExp = param.getChildText(XMLTags.SolutionExpressionTag, vcNamespace); - - if(solutionExp != null && solutionExp.length() > 0){ - Expression expression = unMangleExpression(solutionExp); - odeEquation.setExactSolution(expression); - } - } - - return odeEquation; - } - - - public Origin getOrigin(Element parsed){ - double x = Double.parseDouble(parsed.getAttributeValue(XMLTags.XAttrTag)); - double y = Double.parseDouble(parsed.getAttributeValue(XMLTags.YAttrTag)); - double z = Double.parseDouble(parsed.getAttributeValue(XMLTags.ZAttrTag)); - Origin origin = new Origin(x, y, z); - - return origin; - } - - - /** - * This method returns a TimeStep object from a XML Element. - * Creation date: (5/22/2001 11:45:33 AM) - * - * @param param Element - * @return cbit.vcell.solver.TimeStep - */ - private OutputTimeSpec getOutputTimeSpec(Element param){ - if(param != null){ - //get attributes - if(param.getAttributeValue(XMLTags.KeepEveryAttrTag) != null){ - int keepEvery = Integer.parseInt(param.getAttributeValue(XMLTags.KeepEveryAttrTag)); - int keepAtMost = Integer.parseInt(param.getAttributeValue(XMLTags.KeepAtMostAttrTag)); - return new DefaultOutputTimeSpec(keepEvery, keepAtMost); - } else if(param.getAttributeValue(XMLTags.OutputTimeStepAttrTag) != null){ - double outputStep = Double.parseDouble(param.getAttributeValue(XMLTags.OutputTimeStepAttrTag)); - return new UniformOutputTimeSpec(outputStep); - } else if(param.getAttributeValue(XMLTags.OutputTimesAttrTag) != null){ - String line = param.getAttributeValue(XMLTags.OutputTimesAttrTag); - return ExplicitOutputTimeSpec.fromString(line); - } - } - return null; - } - - - /** - * This method returns an OutsideVariable object from a XML Element - * Creation date: (5/18/2001 6:14:42 PM) - * - * @param param Element - * @return cbit.vcell.math.InsideVariable - */ - private OutsideVariable getOutsideVariable(Element param){ - //Get name - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - //get VolVariableRef - String volvarName = unMangle(param.getAttributeValue(XMLTags.VolumeVariableAttrTag)); - - //*** create new OutsideVariable *** - OutsideVariable variable = new OutsideVariable(name, volvarName); - transcribeComments(param, variable); - - return variable; - } - - - /** - * This method returns a PdeEquation from a XML element. - * Creation date: (4/26/2001 12:11:14 PM) - * - * @param param Element - * @return cbit.vcell.math.PdeEquation - * @throws cbit.vcell.xml.XmlParseException The exception description. - */ - - private PdeEquation getPdeEquation(Element param, MathDescription mathDesc) throws XmlParseException{ - //Retrieve the variable reference - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - boolean bSteady = false; - String bSteadyAttr = param.getAttributeValue(XMLTags.SteadyTag); - if(bSteadyAttr != null && bSteadyAttr.equals("1")){ - bSteady = true; - } - Variable varref = mathDesc.getVariable(name); - if(varref == null){ - throw new XmlParseException("The variable " + name + " for a PdeEquation, could not be resolved!"); - } - PdeEquation pdeEquation = null; - - try { - //Retrieve the initial expression - String temp = param.getChildText(XMLTags.InitialTag, vcNamespace); - Expression initialExp = null; - if(temp != null && temp.length() > 0){ - initialExp = unMangleExpression(temp); - } - - //Retrieve the Rate Expression - temp = param.getChildText(XMLTags.RateTag, vcNamespace); - Expression rateExp = null; - if(temp != null && temp.length() > 0){ - rateExp = unMangleExpression(temp); - } - - //Retrieve the diffusion rate expression - temp = param.getChildText(XMLTags.DiffusionTag, vcNamespace); - Expression difExp = null; - if(temp != null && temp.length() > 0){ - difExp = unMangleExpression(temp); - } - - //*** Create new PdeEquation object **** - pdeEquation = new PdeEquation(varref, bSteady, initialExp, rateExp, difExp); - //***** ***** - - //add specific solutions expressions - String solType = param.getAttributeValue(XMLTags.SolutionTypeTag); - - if(solType.equalsIgnoreCase(XMLTags.ExactTypeTag)){ - String solutionExp = param.getChildText(XMLTags.SolutionExpressionTag, vcNamespace); - - if(solutionExp != null && solutionExp.length() > 0){ - Expression expression = unMangleExpression(solutionExp); - pdeEquation.setExactSolution(expression); - } - } - - //Retrieve Boudaries (if any) - Element tempelement = param.getChild(XMLTags.BoundariesTag, vcNamespace); - if(tempelement != null){ - Expression newexp = null; - //Xm - temp = tempelement.getAttributeValue(XMLTags.BoundaryAttrValueXm); - if(temp != null){ - newexp = unMangleExpression(temp); - pdeEquation.setBoundaryXm(newexp); - } - //Xp - temp = tempelement.getAttributeValue(XMLTags.BoundaryAttrValueXp); - if(temp != null){ - newexp = unMangleExpression(temp); - pdeEquation.setBoundaryXp(newexp); - } - //Ym - temp = tempelement.getAttributeValue(XMLTags.BoundaryAttrValueYm); - if(temp != null){ - newexp = unMangleExpression(temp); - pdeEquation.setBoundaryYm(newexp); - } - //Yp - temp = tempelement.getAttributeValue(XMLTags.BoundaryAttrValueYp); - if(temp != null){ - newexp = unMangleExpression(temp); - pdeEquation.setBoundaryYp(newexp); - } - //Zm - temp = tempelement.getAttributeValue(XMLTags.BoundaryAttrValueZm); - if(temp != null){ - newexp = unMangleExpression(temp); - pdeEquation.setBoundaryZm(newexp); - } - //Zp - temp = tempelement.getAttributeValue(XMLTags.BoundaryAttrValueZp); - if(temp != null){ - newexp = unMangleExpression(temp); - pdeEquation.setBoundaryZp(newexp); - } - } - - //process BoundaryConditionValues - { - Iterator iterator = param.getChildren(XMLTags.BoundaryConditionValueTag, vcNamespace).iterator(); - if(iterator != null){ - while (iterator.hasNext()) { - tempelement = (Element) iterator.next(); - try { - pdeEquation.addBoundaryConditionValue(getBoundaryConditionValue(tempelement, pdeEquation)); - } catch(MathException e){ - throw new XmlParseException("A MathException was fired when adding a BoundaryConditionValue to the compartmentSubDomain " + name, e); - } - } - } - } - - { - //add Velocity - Element velocityE = param.getChild(XMLTags.VelocityTag, vcNamespace); - if(velocityE != null){ - String tempStr = null; - boolean dummyVel = true; - tempStr = velocityE.getAttributeValue(XMLTags.XAttrTag); - if(tempStr != null){ - pdeEquation.setVelocityX(unMangleExpression(tempStr)); //all velocity dimensions are optional. - if(dummyVel){ - dummyVel = false; - } - } - tempStr = velocityE.getAttributeValue(XMLTags.YAttrTag); - if(tempStr != null){ - pdeEquation.setVelocityY(unMangleExpression(tempStr)); - if(dummyVel){ - dummyVel = false; - } - } - tempStr = velocityE.getAttributeValue(XMLTags.ZAttrTag); - if(tempStr != null){ - pdeEquation.setVelocityZ(unMangleExpression(tempStr)); - if(dummyVel){ - dummyVel = false; - } - } - if(dummyVel){ - throw new XmlParseException("Void Velocity element found under PDE for: " + name); - } - } - } - { - //add Grad - Element gradElement = param.getChild(XMLTags.GradientTag, vcNamespace); - if(gradElement != null){ - String tempStr = null; - tempStr = gradElement.getAttributeValue(XMLTags.XAttrTag); - if(tempStr != null){ - pdeEquation.setGradientX(unMangleExpression(tempStr)); //all grad dimensions are optional. - } - tempStr = gradElement.getAttributeValue(XMLTags.YAttrTag); - if(tempStr != null){ - pdeEquation.setGradientY(unMangleExpression(tempStr)); - } - tempStr = gradElement.getAttributeValue(XMLTags.ZAttrTag); - if(tempStr != null){ - pdeEquation.setGradientZ(unMangleExpression(tempStr)); - } - } - } - } catch(Exception e){ - throw new XmlParseException(e); - } - - return pdeEquation; - } - - - /** - * This method returns a VCImageRegion from a XML Representation. - * Creation date: (5/2/2001 12:17:05 PM) - * - * @param param Element - * @return cbit.image.VCImageRegion - */ - private VCPixelClass getPixelClass(Element param){ - //Read attributes - String pixelClassName = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - int pixelvalue = Integer.parseInt(param.getAttributeValue(XMLTags.ImagePixelValueTag)); - - //retrieve the key if there is one - KeyValue key = null; - String stringkey = param.getAttributeValue(XMLTags.KeyValueAttrTag); - - if(stringkey != null && stringkey.length() > 0 && this.readKeysFlag){ - key = new KeyValue(stringkey); - } - - return new VCPixelClass(key, pixelClassName, pixelvalue); - } - - - /** - * This method returns a Product object from a XML representation. - * Creation date: (5/4/2001 2:22:56 PM) - * - * @param param Element - * @return cbit.vcell.model.Product - * @throws cbit.vcell.xml.XmlParseException The exception description. - */ - private Product getProduct(Element param, ReactionStep reaction, Model model) throws XmlParseException{ - //retrieve the key if there is one - KeyValue key = null; - String keystring = param.getAttributeValue(XMLTags.KeyValueAttrTag); - - if(keystring != null && keystring.length() > 0 && this.readKeysFlag){ - key = new KeyValue(keystring); - } - - String speccontref = unMangle(param.getAttributeValue(XMLTags.SpeciesContextRefAttrTag)); - SpeciesContext speccont = model.getSpeciesContext(speccontref); - if(speccont == null){ - throw new XmlParseException( - "The reference to the SpecieContext " - + speccontref - + " for a Product could not be resolved!"); - } - //Retrieve Stoichiometry - int stoch = 1; - Attribute tempAttrib = param.getAttribute(XMLTags.StoichiometryAttrTag); - if(tempAttrib != null){ - String temp = tempAttrib.getValue(); - if(temp.length() > 0){ - stoch = Integer.parseInt(temp); - } - } - //int stoch = Integer.parseInt(param.getAttributeValue(XMLTags.StoichiometryAttrTag)); - - return new Product(key, reaction, speccont, stoch); - } - - - /** - * This method returns a Reactant object from a XML representation. - * Creation date: (5/4/2001 2:22:56 PM) - * - * @param param Element - * @return cbit.vcell.model.Reactant - * @throws cbit.vcell.xml.XmlParseException The exception description. - */ - private Reactant getReactant(Element param, ReactionStep reaction, Model model) throws XmlParseException{ - //retrieve the key if there is one - String keystring = param.getAttributeValue(XMLTags.KeyValueAttrTag); - KeyValue key = null; - - if(keystring != null && keystring.length() > 0 && this.readKeysFlag){ - key = new KeyValue(keystring); - } - - String speccontref = unMangle(param.getAttributeValue(XMLTags.SpeciesContextRefAttrTag)); - SpeciesContext speccont = model.getSpeciesContext(speccontref); - if(speccont == null){ - throw new XmlParseException( - "The reference to the SpecieContext " - + speccontref - + " for a SimpleReaction could not be resolved!"); - } - //Retrieve Stoichiometry - int stoch = 1; - Attribute tempArg = param.getAttribute(XMLTags.StoichiometryAttrTag); - if(tempArg != null){ - String tempValue = tempArg.getValue(); - if(tempValue.length() > 0) - stoch = Integer.parseInt(tempValue); - //param.getAttributeValue(XMLTags.StoichiometryAttrTag)); - } - - //return new Reactant(newkey, reaction, speccont, stoch); - return new Reactant(key, reaction, speccont, stoch); - } - - - /** - * Insert the method's description here. - * Creation date: (4/26/2001 4:13:26 PM) - * - * @param param Element - * @return cbit.vcell.mapping.ReactionSpec - */ - private ReactionSpec getReactionSpec(Element param, SimulationContext simulationContext) throws XmlParseException{ - ReactionSpec reactionspec = null; - - //retrieve the reactionstep reference - String reactionstepname = unMangle(param.getAttributeValue(XMLTags.ReactionStepRefAttrTag)); - ReactionStep reactionstepref = (ReactionStep) simulationContext.getModel().getReactionStep(reactionstepname); - - if(reactionstepref == null){ - throw new XmlParseException("The reference to the ReactionStep " + reactionstepname + ", could not be resolved!"); - } - //Create the new SpeciesContextSpec - reactionspec = new ReactionSpec(reactionstepref, simulationContext); - - //set the reactionMapping value - String temp = param.getAttributeValue(XMLTags.ReactionMappingAttrTag); - try { - reactionspec.setReactionMapping(temp); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A PropertyVetoException was fired when setting the reactionMapping value " + temp + ", in a reactionSpec object!", e); - } - - return reactionspec; - } - - - /** - * This method returns a SimpleReaction object from a XML element. - * Creation date: (3/16/2001 11:52:02 AM) - * - * @param param Element - * @return cbit.vcell.model.SimpleReaction - */ - private SimpleReaction getSimpleReaction(Element param, Model model) throws XmlParseException{ - //resolve reference to the structure that it belongs to. - String structureName = unMangle(param.getAttributeValue(XMLTags.StructureAttrTag)); - Structure structureref = (Structure) model.getStructure(structureName); - - if(structureref == null){ - throw new XmlParseException("The structure " + structureName + "could not be resolved!"); - } - - //try to get keValue information - String keystring = param.getAttributeValue(XMLTags.KeyValueAttrTag); - KeyValue key = null; - - if(keystring != null && keystring.length() > 0 && this.readKeysFlag){ - key = new KeyValue(keystring); - } - - //---Instantiate a new Simplereaction--- - SimpleReaction simplereaction = null; - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - - String reversibleAttributeValue = param.getAttributeValue(XMLTags.ReversibleAttrTag); - boolean bReversible = true; - if(reversibleAttributeValue != null){ - if(Boolean.TRUE.toString().equals(reversibleAttributeValue)){ - bReversible = true; - } else if(Boolean.FALSE.toString().equals(reversibleAttributeValue)){ - bReversible = false; - } else { - throw new RuntimeException("unexpected value " + reversibleAttributeValue + " for reversible flag for reaction " + name); - } - } - - try { - simplereaction = new SimpleReaction(model, structureref, key, name, bReversible); - if(param.getAttributeValue(XMLTags.SbmlNameAttrTag) != null){ - simplereaction.setSbmlName(unMangle(param.getAttributeValue(XMLTags.SbmlNameAttrTag))); - } - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("An error occurred while trying to create the simpleReaction " + name, e); - } - //Annotation -// String rsAnnotation = null; -// String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace); -// if (annotationText!=null && annotationText.length()>0) { -// rsAnnotation = unMangle(annotationText); -// } -// simplereaction.setAnnotation(rsAnnotation); - - //set the fluxOption - String fluxOptionString = null; - fluxOptionString = param.getAttributeValue(XMLTags.FluxOptionAttrTag); - - if(fluxOptionString != null && fluxOptionString.length() > 0){ - try { - if(fluxOptionString.equals(XMLTags.FluxOptionElectricalOnly)){ - simplereaction.setPhysicsOptions(SimpleReaction.PHYSICS_ELECTRICAL_ONLY); - } else if(fluxOptionString.equals(XMLTags.FluxOptionMolecularAndElectrical)){ - simplereaction.setPhysicsOptions(SimpleReaction.PHYSICS_MOLECULAR_AND_ELECTRICAL); - } else if(fluxOptionString.equals(XMLTags.FluxOptionMolecularOnly)){ - simplereaction.setPhysicsOptions(SimpleReaction.PHYSICS_MOLECULAR_ONLY); - } - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A propertyVetoException was fired when setting the fluxOption to the flux reaction " + name, e); - } - } - //Add Reactants - try { - Iterator iterator = param.getChildren(XMLTags.ReactantTag, vcNamespace).iterator(); - - while (iterator.hasNext()) { - Element temp = iterator.next(); - - //Add Reactant to this SimpleReaction - simplereaction.addReactionParticipant(getReactant(temp, simplereaction, model)); - } - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("Error adding a reactant to the reaction " + name, e); - } - - //Add Products - try { - Iterator iterator = param.getChildren(XMLTags.ProductTag, vcNamespace).iterator(); - - while (iterator.hasNext()) { - Element temp = iterator.next(); - - //Add Product to this simplereaction - simplereaction.addReactionParticipant(getProduct(temp, simplereaction, model)); - } - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("Error adding a product to the reaction " + name + " : ", e); - } - - //Add Catalyst(Modifiers) - try { - Iterator iterator = param.getChildren(XMLTags.CatalystTag, vcNamespace).iterator(); - - while (iterator.hasNext()) { - Element temp = iterator.next(); - simplereaction.addReactionParticipant(getCatalyst(temp, simplereaction, model)); - } - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("Error adding a catalyst to the reaction " + name, e); - } - - //Add Kinetics - Element tempKinet = param.getChild(XMLTags.KineticsTag, vcNamespace); - - if(tempKinet != null){ - simplereaction.setKinetics(getKinetics(tempKinet, simplereaction, model)); - } - - //set the valence (for legacy support for "chargeCarrierValence" stored with reaction). - String valenceString = null; - try { - valenceString = unMangle(param.getAttributeValue(XMLTags.FluxCarrierValenceAttrTag)); - if(valenceString != null && valenceString.length() > 0){ - KineticsParameter chargeValenceParameter = simplereaction.getKinetics().getChargeValenceParameter(); - if(chargeValenceParameter != null){ - chargeValenceParameter.setExpression(new Expression(Integer.parseInt(unMangle(valenceString)))); - } - } - } catch(NumberFormatException e){ - throw new XmlParseException("A NumberFormatException was fired when setting the (integer) valence '" + valenceString + "' (integer) to the reaction " + name, e); - } - - - return simplereaction; - } - - Simulation getSimulation(Element param, MathDescription mathDesc) throws XmlParseException{ - return getSimulation(param, mathDesc, null); - } - - - Simulation getSimulation(Element param, MathDescription mathDesc, SimulationOwner simulationOwner) throws XmlParseException{ - //retrive metadata (if any) - SimulationVersion simulationVersion = getSimulationVersion(param.getChild(XMLTags.VersionTag, vcNamespace)); - - //create new simulation - Simulation simulation = null; - - if(simulationVersion != null){ - simulation = new Simulation(simulationVersion, mathDesc, simulationOwner); - } else { - simulation = new Simulation(mathDesc, simulationOwner); - } - - //set attributes - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - - try { - simulation.setName(name); - String importedTaskId = param.getAttributeValue(XMLTags.ImportedTaskIdTag); - if(importedTaskId != null){ - simulation.setImportedTaskID(importedTaskId); - } - - //String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag); - //if (annotation!=null) { - //simulation.setDescription(unMangle(annotation)); - //} - //Add Annotation - String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace); - if(annotationText != null && annotationText.length() > 0){ - simulation.setDescription(unMangle(annotationText)); - } - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException(e); - } - - //Retrieve MathOverrides - simulation.setMathOverrides(getMathOverrides(param.getChild(XMLTags.MathOverridesTag, vcNamespace), simulation)); - - //Retrieve SolverTaskDescription - try { - simulation.setSolverTaskDescription(getSolverTaskDescription(param.getChild(XMLTags.SolverTaskDescriptionTag, vcNamespace), simulation)); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A PropertyVetoException was fired when setting the SolverTaskDescroiption object to the Simulation object " + name, e); - } - - Element dataProcessingInstructionsElement = param.getChild(XMLTags.DataProcessingInstructionsTag, vcNamespace); - if(dataProcessingInstructionsElement != null){ - String scriptName = dataProcessingInstructionsElement.getAttributeValue(XMLTags.DataProcessingScriptNameAttrTag); - String scriptInput = dataProcessingInstructionsElement.getText(); - simulation.setDataProcessingInstructions(new DataProcessingInstructions(scriptName, scriptInput)); - } - - //Retrieve MeshEspecification (if any) - Element tempElement = param.getChild(XMLTags.MeshSpecTag, vcNamespace); - - if(tempElement != null){ - try { - simulation.setMeshSpecification(getMeshSpecification(tempElement, mathDesc.getGeometry())); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A ProperyVetoException was fired when setting the MeshSpecification to a new Simulation!", e); - } - } - - return simulation; - } - - //public because it's being called in simcontexttable to read from the app components element - public NetworkConstraints getAppNetworkConstraints(Element e, Model newModel){ - RbmModelContainer mc = newModel.getRbmModelContainer(); - NetworkConstraints nc = new NetworkConstraints(); - String s = e.getAttributeValue(XMLTags.RbmMaxIterationTag); - if(s != null && !s.isEmpty()){ - int maxIteration = Integer.parseInt(s); - nc.setMaxIteration(maxIteration); - } - s = e.getAttributeValue(XMLTags.RbmMaxMoleculesPerSpeciesTag); - if(s != null && !s.isEmpty()){ - int maxMoleculesPerSpecies = Integer.parseInt(s); - nc.setMaxMoleculesPerSpecies(maxMoleculesPerSpecies); - } - s = e.getAttributeValue(XMLTags.RbmSpeciesLimitTag); - if(s != null && !s.isEmpty()){ - int speciesLimit = Integer.parseInt(s); - nc.setSpeciesLimit(speciesLimit); - } - s = e.getAttributeValue(XMLTags.RbmReactionsLimitTag); - if(s != null && !s.isEmpty()){ - int reactionsLimit = Integer.parseInt(s); - nc.setReactionsLimit(reactionsLimit); - } - List children = e.getChildren(XMLTags.RbmMaxStoichiometryTag, vcNamespace); - for(Element element : children){ - Integer i = 1; - MolecularType mt = null; - s = element.getAttributeValue(XMLTags.RbmIntegerAttrTag); - if(s != null && !s.isEmpty()){ - i = Integer.valueOf(s); - } - s = element.getAttributeValue(XMLTags.RbmMolecularTypeTag); - if(s != null && !s.isEmpty()){ - mt = mc.getMolecularType(s); - } - if(mt != null){ - nc.setMaxStoichiometry(mt, i); - } - } - return nc; - } - - /** - * This method returns a SimulationContext from a XML representation. - * Creation date: (4/2/2001 3:19:01 PM) - * - * @param param Element - * @return cbit.vcell.mapping.SimulationContext - */ - private SimulationContext getSimulationContext(Element param, BioModel biomodel) throws XmlParseException{ - //get the attributes - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); //name - boolean bStoch = false; - boolean bRuleBased = false; - boolean bSpringSaLaD = false; - boolean bUseConcentration = true; - boolean bRandomizeInitCondition = false; - boolean bInsufficientIterations = false; - boolean bInsufficientMaxMolecules = false; - boolean bMassConservationModelReduction = true; // default is true for now - - NetworkConstraints nc = null; - Element ncElement = param.getChild(XMLTags.RbmNetworkConstraintsTag, vcNamespace); - if(ncElement != null){ - nc = getAppNetworkConstraints(ncElement, biomodel.getModel()); // one network constraint element - } else { - if(legacyNetworkConstraints != null){ - nc = legacyNetworkConstraints; - } - } - - if((param.getAttributeValue(XMLTags.StochAttrTag) != null) && (param.getAttributeValue(XMLTags.StochAttrTag).equals("true"))){ - bStoch = true; - } - if(bStoch){ - // stochastic and using concentration vs amount - if((param.getAttributeValue(XMLTags.ConcentrationAttrTag) != null) && (param.getAttributeValue(XMLTags.ConcentrationAttrTag).equals("false"))){ - bUseConcentration = false; - } - - // stochastic and randomizing initial conditions or not (for non-spatial) - if((param.getAttributeValue(XMLTags.RandomizeInitConditionTag) != null) && (param.getAttributeValue(XMLTags.RandomizeInitConditionTag).equals("true"))){ - bRandomizeInitCondition = true; - } - } - if((param.getAttributeValue(XMLTags.MassConservationModelReductionTag) != null) && (param.getAttributeValue(XMLTags.MassConservationModelReductionTag).equals("false"))){ - bMassConservationModelReduction = false; - } - if((param.getAttributeValue(XMLTags.InsufficientIterationsTag) != null) && (param.getAttributeValue(XMLTags.InsufficientIterationsTag).equals("true"))){ - bInsufficientIterations = true; - } - if((param.getAttributeValue(XMLTags.InsufficientMaxMoleculesTag) != null) && (param.getAttributeValue(XMLTags.InsufficientMaxMoleculesTag).equals("true"))){ - bInsufficientMaxMolecules = true; - } - if((param.getAttributeValue(XMLTags.RuleBasedAttrTag) != null) && (param.getAttributeValue(XMLTags.RuleBasedAttrTag).equals("true"))){ - bRuleBased = true; - if((param.getAttributeValue(XMLTags.ConcentrationAttrTag) != null) && (param.getAttributeValue(XMLTags.ConcentrationAttrTag).equals("false"))){ - bUseConcentration = false; - } - if((param.getAttributeValue(XMLTags.RandomizeInitConditionTag) != null) && (param.getAttributeValue(XMLTags.RandomizeInitConditionTag).equals("true"))){ - // we propagate the flag but we don't use it for now - bRandomizeInitCondition = true; - } - } else if((param.getAttributeValue(XMLTags.SpringSaLaDAttrTag) != null) && (param.getAttributeValue(XMLTags.SpringSaLaDAttrTag).equals("true"))){ - bSpringSaLaD = true; - if((param.getAttributeValue(XMLTags.ConcentrationAttrTag) != null) && (param.getAttributeValue(XMLTags.ConcentrationAttrTag).equals("false"))){ - bUseConcentration = false; - } - } - - //Retrieve Geometry - Geometry newgeometry = null; - try { - newgeometry = getGeometry(param.getChild(XMLTags.GeometryTag, vcNamespace)); - } catch(Exception e){ - lg.error(e.getMessage(), e); - String stackTrace = null; - try { - java.io.ByteArrayOutputStream bos = new java.io.ByteArrayOutputStream(); - java.io.PrintStream ps = new java.io.PrintStream(bos); - e.printStackTrace(ps); - ps.flush(); - bos.flush(); - stackTrace = new String(bos.toByteArray()); - ps.close(); - bos.close(); - } catch(Exception e2){ - //do Nothing - } - throw new XmlParseException( - "A Problem occurred while retrieving the geometry for the simulationContext " + name, e); - } - - //Retrieve MathDescription(if there is no MathDescription skip it) - MathDescription newmathdesc = null; - Element xmlMathDescription = param.getChild(XMLTags.MathDescriptionTag, vcNamespace); - if(xmlMathDescription != null){ - newmathdesc = getMathDescription(xmlMathDescription, newgeometry); - if(biomodel.getVersion() != null && biomodel.getVersion().getVersionKey() != null){ - Long lpcBMKey = Long.valueOf(biomodel.getVersion().getVersionKey().toString()); - - // MathDescription.originalHasLowPrecisionConstants.remove(lpcBMKey); - try { - Enumeration myenum = newmathdesc.getConstants(); - while (myenum.hasMoreElements()) { - Constant nextElement = myenum.nextElement(); - String name2 = nextElement.getName(); - ReservedSymbol reservedSymbolByName = biomodel.getModel().getReservedSymbolByName(name2); - if(reservedSymbolByName != null && nextElement.getExpression() != null && reservedSymbolByName.getExpression() != null){ - // System.out.println(name2); - boolean equals = nextElement.getExpression().infix().equals(reservedSymbolByName.getExpression().infix()); - // System.out.println("--"+" "+nextElement.getExpression().infix() +" "+reservedSymbolByName.getExpression().infix()+" "+equals); - if(!equals){ - TreeSet treeSet = MathDescription.originalHasLowPrecisionConstants.get(lpcBMKey); - if(treeSet == null){ - treeSet = new TreeSet<>(); - MathDescription.originalHasLowPrecisionConstants.put(lpcBMKey, treeSet); - } - treeSet.add(newmathdesc.getVersion().getVersionKey().toString()); - break; - } - } - } - } catch(Exception e){ - lg.error(e.getMessage(), e); - } - } - } - - //Retrieve Version (Metada) - Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace)); - - //------ Create SimContext ------ - SimulationContext newsimcontext = null; - Application type = Application.NETWORK_DETERMINISTIC; - if(bSpringSaLaD){ - type = Application.SPRINGSALAD; - } else if(bRuleBased){ - type = Application.RULE_BASED_STOCHASTIC; - } else if(bStoch){ - type = Application.NETWORK_STOCHASTIC; - } - try { - newsimcontext = new SimulationContext(biomodel.getModel(), newgeometry, newmathdesc, version, type); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A propertyveto exception was generated when creating the new SimulationContext " + name, e); - } - - //set attributes - try { - newsimcontext.setName(name); - //Add annotation - String annotation = param.getChildText(XMLTags.AnnotationTag, vcNamespace); - if(annotation != null/* && annotation.length()>0*/){ - newsimcontext.setDescription(unMangle(annotation)); - } - //set if using concentration - newsimcontext.setUsingConcentration(bUseConcentration, false); - // set mass conservation model reduction flag - newsimcontext.setUsingMassConservationModelReduction(bMassConservationModelReduction); - // set if randomizing init condition or not (for stochastic applications - if(bStoch){ - newsimcontext.setRandomizeInitConditions(bRandomizeInitCondition); - } - if(bInsufficientIterations){ - newsimcontext.setInsufficientIterations(bInsufficientIterations); - } - if(bInsufficientMaxMolecules){ - newsimcontext.setInsufficientMaxMolecules(bInsufficientMaxMolecules); - } - if(nc != null){ - newsimcontext.setNetworkConstraints(nc); - } - - } catch(Exception e){ - throw new XmlParseException("Exception", e); - } - - String tempchar = param.getAttributeValue(XMLTags.CharacteristicSizeTag); - if(tempchar != null){ - try { - newsimcontext.setCharacteristicSize(Double.valueOf(tempchar)); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A PropertyVetoException was fired when setting the CharacteristicSize " + tempchar, e); - } - } - - // Retrieve DataContext - Element dataContextElement = param.getChild(XMLTags.DataContextTag, vcNamespace); - if(dataContextElement != null){ - DataContext dataContext = newsimcontext.getDataContext(); - ArrayList dataSymbols = getDataSymbols(dataContextElement, dataContext, newsimcontext.getModel().getUnitSystem()); - for(int i = 0; i < dataSymbols.size(); i++){ - dataContext.addDataSymbol(dataSymbols.get(i)); - } - } - - // Retrieve spatialObjects and add to simContext - Element spatialObjectsElement = param.getChild(XMLTags.SpatialObjectsTag, vcNamespace); - if(spatialObjectsElement != null){ - SpatialObject[] spatialObjects = getSpatialObjects(newsimcontext, spatialObjectsElement); - try { - newsimcontext.setSpatialObjects(spatialObjects); - } catch(PropertyVetoException e){ - throw new RuntimeException("Error adding spatialObjects to simulationContext", e); - } - } - - // Retrieve application parameters and add to simContext - Element appParamsElement = param.getChild(XMLTags.ApplicationParametersTag, vcNamespace); - if(appParamsElement != null){ - SimulationContextParameter[] appParameters = getSimulationContextParams(appParamsElement, newsimcontext); - try { - newsimcontext.setSimulationContextParameters(appParameters); - } catch(PropertyVetoException e){ - throw new RuntimeException("Error adding application parameters to simulationContext", e); - } - } - - // - //-Process the GeometryContext- - // - Element tempelement = param.getChild(XMLTags.GeometryContextTag, vcNamespace); - LinkedList maplist = new LinkedList(); - //Retrieve FeatureMappings - Iterator iterator = tempelement.getChildren(XMLTags.FeatureMappingTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - maplist.add(getFeatureMapping((Element) (iterator.next()), newsimcontext)); - } - //Retrieve MembraneMappings - iterator = tempelement.getChildren(XMLTags.MembraneMappingTag, vcNamespace).iterator(); - while (iterator.hasNext()) { - maplist.add(getMembraneMapping((Element) (iterator.next()), newsimcontext)); - } - // Add these mappings to the internal geometryContext of this simcontext - StructureMapping[] structarray = new StructureMapping[maplist.size()]; - maplist.toArray(structarray); - try { - newsimcontext.getGeometryContext().setStructureMappings(structarray); - newsimcontext.getGeometryContext().refreshStructureMappings(); - newsimcontext.refreshSpatialObjects(); - } catch(MappingException | PropertyVetoException e){ - throw new XmlParseException("failed to set the StructureMappings array to the Geometrycontext of the SimContext " + name, e); - } - // - //-Process the ReactionContext- - // - tempelement = param.getChild(XMLTags.ReactionContextTag, vcNamespace); - // Retrieve ReactionSpecs - List children = tempelement.getChildren(XMLTags.ReactionSpecTag, vcNamespace); - if(children.size() != 0){ - if(children.size() != biomodel.getModel().getReactionSteps().length){ - throw new XmlParseException("The number of reactions is not consistent.\n" + "Model reactions=" + biomodel.getModel().getReactionSteps().length + ", Reaction specs=" + children.size()); - } - //*NOTE: Importing a model from other languages does not generates reaction specs. - // A more robust code will read the reactions in the source file and replace the ones created by the default by the VirtualCell framework. - ReactionSpec reactionSpecs[] = new ReactionSpec[children.size()]; - int rSpecCounter = 0; - for(Element rsElement : children){ - reactionSpecs[rSpecCounter] = getReactionSpec(rsElement, newsimcontext); - rSpecCounter++; - } - try { - newsimcontext.getReactionContext().setReactionSpecs(reactionSpecs); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A PropertyVetoException occurred while setting the ReactionSpecs to the SimContext " + name, e); - } - } - - // Retrieve ReactionRuleSpecs - Element reactionRuleSpecsElement = tempelement.getChild(XMLTags.ReactionRuleSpecsTag, vcNamespace); - if(reactionRuleSpecsElement != null){ - ReactionRuleSpec[] reactionRuleSpecs = getReactionRuleSpecs(newsimcontext, reactionRuleSpecsElement); - try { - newsimcontext.getReactionContext().setReactionRuleSpecs(reactionRuleSpecs); - } catch(PropertyVetoException e){ - throw new XmlParseException("A PropertyVetoException occurred while setting the ReactionRuleSpecs to the SimContext " + name, e); - } - } - - children = tempelement.getChildren(XMLTags.SpeciesContextSpecTag, vcNamespace); - getSpeciesContextSpecs(children, newsimcontext.getReactionContext(), biomodel.getModel()); - - // Retrieve output functions - Element outputFunctionsElement = param.getChild(XMLTags.OutputFunctionsTag, vcNamespace); - if(outputFunctionsElement != null){ - ArrayList outputFunctions = getOutputFunctions(outputFunctionsElement); - try { - // construct OutputFnContext from mathDesc in newSimContext and add output functions that were read in from XML. - OutputFunctionContext outputFnContext = newsimcontext.getOutputFunctionContext(); - for(AnnotatedFunction outputFunction : outputFunctions){ - outputFnContext.addOutputFunction(outputFunction); - } - } catch(PropertyVetoException e){ - throw new XmlParseException(e); - } - } - - - //Retrieve Electrical context - Element electElem = param.getChild(XMLTags.ElectricalContextTag, vcNamespace); - //this information is optional! - if(electElem != null){ - if(electElem.getChild(XMLTags.ClampTag, vcNamespace) != null){ - //read clamp - ElectricalStimulus[] electArray = new ElectricalStimulus[1]; - electArray[0] = getElectricalStimulus(electElem.getChild(XMLTags.ClampTag, vcNamespace), newsimcontext); - - try { - newsimcontext.setElectricalStimuli(electArray); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException(e); - } - } - - //read ground electrode - if(electElem.getChild(XMLTags.ElectrodeTag, vcNamespace) != null){ - Electrode groundElectrode = getElectrode(electElem.getChild(XMLTags.ElectrodeTag, vcNamespace), newsimcontext); - - try { - newsimcontext.setGroundElectrode(groundElectrode); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException(e); - } - } - } - - // Retrieve (bio)events and add to simContext - tempelement = param.getChild(XMLTags.BioEventsTag, vcNamespace); - if(tempelement != null){ - BioEvent[] bioEvents = getBioEvents(newsimcontext, tempelement); - try { - newsimcontext.setBioEvents(bioEvents); - } catch(PropertyVetoException e){ - throw new RuntimeException("Error adding events to simulationContext", e); - } - } - - // Retrieve spatialProcesses and add to simContext - tempelement = param.getChild(XMLTags.SpatialProcessesTag, vcNamespace); - if(tempelement != null){ - SpatialProcess[] spatialProcesses = getSpatialProcesses(newsimcontext, tempelement); - try { - newsimcontext.setSpatialProcesses(spatialProcesses); - } catch(PropertyVetoException e){ - throw new RuntimeException("Error adding spatialProcesses to simulationContext", e); - } - } - - // Retrieve rate rules and add to simContext - tempelement = param.getChild(XMLTags.RateRulesTag, vcNamespace); - if(tempelement != null){ - RateRule[] rateRules = getRateRules(newsimcontext, tempelement); - try { - newsimcontext.setRateRules(rateRules); - } catch(PropertyVetoException e){ - throw new RuntimeException("Error adding rate rules to simulationContext", e); - } - } - tempelement = param.getChild(XMLTags.AssignmentRulesTag, vcNamespace); - if(tempelement != null){ - AssignmentRule[] assignmentRules = getAssignmentRules(newsimcontext, tempelement); - try { - newsimcontext.setAssignmentRules(assignmentRules); - } catch(PropertyVetoException e){ - throw new RuntimeException("Error adding assignment rules to simulationContext", e); - } - } - - Element analysisTaskListElement = param.getChild(XMLTags.AnalysisTaskListTag, vcNamespace); - if(analysisTaskListElement != null){ - children = analysisTaskListElement.getChildren(XMLTags.ParameterEstimationTaskTag, vcNamespace); - if(children.size() != 0){ - Vector analysisTaskList = new Vector(); - for(Element parameterEstimationTaskElement : children){ - try { - ParameterEstimationTask parameterEstimationTask = ParameterEstimationTaskXMLPersistence.getParameterEstimationTask(parameterEstimationTaskElement, newsimcontext); - analysisTaskList.add(parameterEstimationTask); - } catch(Exception e){ - throw new XmlParseException("An Exception occurred when parsing AnalysisTasks of SimContext " + name, e); - } - } - try { - newsimcontext.setAnalysisTasks(analysisTaskList.toArray(AnalysisTask[]::new)); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A PropertyVetoException occurred when setting the AnalysisTasks of the SimContext " + name, e); - } - } - } - - // Microscope Measurement - Element element = param.getChild(XMLTags.MicroscopeMeasurement, vcNamespace); - if(element != null){ - getMicroscopeMeasurement(element, newsimcontext); - } - - -// for (GeometryClass gc : newsimcontext.getGeometry().getGeometryClasses()) { -// try { -// StructureSizeSolver.updateUnitStructureSizes(newsimcontext, gc); -// } catch (Exception e) { -// lg.error(e); -// } -// } - - newsimcontext.getGeometryContext().enforceHierarchicalBoundaryConditions(newsimcontext.getModel().getStructureTopology()); - - return newsimcontext; - } - - public void getMicroscopeMeasurement(Element element, SimulationContext simContext){ - MicroscopeMeasurement microscopeMeasurement = simContext.getMicroscopeMeasurement(); - - String name = element.getAttributeValue(XMLTags.NameAttrTag); - microscopeMeasurement.setName(name); - - Element kernelElement = element.getChild(XMLTags.ConvolutionKernel, vcNamespace); - String type = kernelElement.getAttributeValue(XMLTags.TypeAttrTag); - ConvolutionKernel ck = null; - if(type.equals(XMLTags.ConvolutionKernel_Type_ProjectionZKernel)){ - ck = new ProjectionZKernel(); - } else if(type.equals(XMLTags.ConvolutionKernel_Type_GaussianConvolutionKernel)){ - Element e = kernelElement.getChild(XMLTags.KernelGaussianSigmaXY, vcNamespace); - String s = e.getText(); - Expression sigmaXY = unMangleExpression(s); - - e = kernelElement.getChild(XMLTags.KernelGaussianSigmaZ, vcNamespace); - s = e.getText(); - Expression sigmaZ = unMangleExpression(s); - - ck = new GaussianConvolutionKernel(sigmaXY, sigmaZ); - } - microscopeMeasurement.setConvolutionKernel(ck); - List children = element.getChildren(XMLTags.FluorescenceSpecies, vcNamespace); - for(Element c : children){ - String speciesName = c.getAttributeValue(XMLTags.NameAttrTag); - SpeciesContext sc = simContext.getModel().getSpeciesContext(speciesName); - microscopeMeasurement.addFluorescentSpecies(sc); - } - } - - private ArrayList getDataSymbols(Element dataContextElement, DataContext dataContext, ModelUnitSystem modelUnitSystem){ - ArrayList dataSymbolsList = new ArrayList(); - // iterate over fieldDatasymbols. When other dataSymbol types are implemented, repeat this loop. - Iterator dataSymbolsElementIter = dataContextElement.getChildren(XMLTags.FieldDataSymbolTag, vcNamespace).iterator(); - while (dataSymbolsElementIter.hasNext()) { - Element dataSymbolElement = (Element) dataSymbolsElementIter.next(); - String dataSymbolName = unMangle(dataSymbolElement.getAttributeValue(XMLTags.DataSymbolNameTag)); - DataSymbolType dataSymbolType = DataSymbolType.fromDatabaseName(unMangle(dataSymbolElement.getAttributeValue(XMLTags.DataSymbolTypeTag))); - String symbol = dataSymbolElement.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); - VCUnitDefinition vcUnitDefinition = null; - if(symbol != null){ - vcUnitDefinition = modelUnitSystem.getInstance(symbol); - } - // ExternalDataIdentifier dataSetID in FieldDataSymbol - Element dataSetIDElement = dataSymbolElement.getChild(XMLTags.ExternalDataIdentifierTag, vcNamespace); - String name = unMangle(dataSetIDElement.getAttributeValue(XMLTags.NameAttrTag)); - String key = unMangle(dataSetIDElement.getAttributeValue(XMLTags.KeyValueAttrTag)); - String userID = unMangle(dataSetIDElement.getAttributeValue(XMLTags.OwnerNameAttrTag)); - String userKey = unMangle(dataSetIDElement.getAttributeValue(XMLTags.OwnerKeyAttrTag)); - User owner = new User(userID, new KeyValue(userKey)); - ExternalDataIdentifier edi = new ExternalDataIdentifier(new KeyValue(key), owner, name); - // --- - String fieldItemName = unMangle(dataSymbolElement.getAttributeValue(XMLTags.FieldItemNameTag)); - String fieldItemType = unMangle(dataSymbolElement.getAttributeValue(XMLTags.FieldItemTypeTag)); - double fieldItemTime = Double.parseDouble(unMangle(dataSymbolElement.getAttributeValue(XMLTags.FieldItemTimeTag))); - - FieldDataSymbol fds = new FieldDataSymbol(dataSymbolName, dataSymbolType, dataContext, vcUnitDefinition, - edi, fieldItemName, fieldItemType, fieldItemTime); - dataSymbolsList.add(fds); - } - // other while loops for other dataSymbol types; then return cumulative list - // ... - - return dataSymbolsList; - } - - private SimulationVersion getSimulationVersion(Element xmlVersion) throws XmlParseException{ - if(xmlVersion == null){ - return null; - } - - //determine if it should be processed using the 'fromVersionable' - if(xmlVersion.getAttributeValue(XMLTags.FromVersionableTag) == null || Boolean.valueOf(xmlVersion.getAttributeValue(XMLTags.FromVersionableTag)).booleanValue() || this.readKeysFlag == false){ - //this came from a versionable object, so skip! Or it should not explicitly import the information inside the Version - return null; - } - - //Read all the attributes - //*name - String name = unMangle(xmlVersion.getAttributeValue(XMLTags.NameAttrTag)); - //*key - String temp = xmlVersion.getAttributeValue(XMLTags.KeyValueAttrTag); - KeyValue key = new KeyValue(temp); - //*owner - Element tempElement = xmlVersion.getChild(XMLTags.OwnerTag, vcNamespace); - User owner = new User(unMangle(tempElement.getAttributeValue(XMLTags.NameAttrTag)), new KeyValue(tempElement.getAttributeValue(XMLTags.IdentifierAttrTag))); - //*access - GroupAccess groupAccess = getGroupAccess(xmlVersion.getChild(XMLTags.GroupAccessTag, vcNamespace)); - //*Branchpointref - temp = xmlVersion.getAttributeValue(XMLTags.BranchPointRefTag); - KeyValue branchpointref = null; - - if(temp != null){ - branchpointref = new KeyValue(temp); - } - - //*BranchID - java.math.BigDecimal branchId = new java.math.BigDecimal(xmlVersion.getAttributeValue(XMLTags.BranchIdAttrTag)); - //*Flag - temp = xmlVersion.getAttributeValue(XMLTags.FlagAttrTag); - VersionFlag flag = VersionFlag.fromInt(Integer.parseInt(temp)); - //*Date - java.util.Date date = null; - temp = xmlVersion.getAttributeValue(XMLTags.DateAttrTag); - - if(temp != null){ - try { - SimpleDateFormat simpleDateFormat = new SimpleDateFormat(BeanUtils.vcDateFormat, Locale.US); - date = simpleDateFormat.parse(temp); - } catch(java.text.ParseException e){ - throw new XmlParseException("Invalid date:" + temp, e); - } - } - - //*DataSimulationRef - KeyValue parentSimRefKey = null; - tempElement = xmlVersion.getChild(XMLTags.ParentSimRefTag, vcNamespace); - if(tempElement != null){ - parentSimRefKey = new KeyValue(tempElement.getAttributeValue(XMLTags.KeyValueAttrTag)); - } - - //*Annotation - String annotation = null; - String annotationText = xmlVersion.getChildText(XMLTags.AnnotationTag, vcNamespace); - if(annotationText != null && annotationText.length() > 0){ - annotation = unMangle(annotationText); - } - - //Create and return the version object - return new SimulationVersion(key, name, owner, groupAccess, branchpointref, branchId, date, flag, annotation, parentSimRefKey); - } - - - /** - * This method returns a SolverTaskDescription Object from a XML Element. - * Creation date: (5/22/2001 10:51:23 AM) - * - * @param param Element - * @param simulation cbit.vcell.solver.Simulation - * @return cbit.vcell.solver.SolverTaskDescription - */ - private SolverTaskDescription getSolverTaskDescription(Element param, Simulation simulation) throws XmlParseException{ - //*** create new SolverTaskDescription *** - SolverTaskDescription solverTaskDesc = new SolverTaskDescription(simulation); - //Added July 22nd, 2007, used as condition for stochSimOptions or stochHybridOprtions - SolverDescription sd = null; - //Retrieve attributes - String taskType = param.getAttributeValue(XMLTags.TaskTypeTag); - int keepEvery = -1; - int keepAtMost = -1; - if(param.getAttributeValue(XMLTags.KeepEveryTag) != null){ - keepEvery = Integer.parseInt(param.getAttributeValue(XMLTags.KeepEveryTag)); - keepAtMost = Integer.parseInt(param.getAttributeValue(XMLTags.KeepAtMostTag)); - } - boolean useSymJacob = Boolean.parseBoolean(param.getAttributeValue(XMLTags.UseSymbolicJacobianAttrTag)); - String solverName = param.getAttributeValue(XMLTags.SolverNameTag); - //get sentivity parameter - Element sensparamElement = param.getChild(XMLTags.ConstantTag, vcNamespace); - Constant sensitivityparam = null; - - if(sensparamElement != null){ - sensitivityparam = getConstant(sensparamElement); - } - - //set Attributes - try { - //set solver - sd = SolverDescription.fromDatabaseName(solverName); - if(sd == null){ - System.err.println("====================================== couldn't find solver description name =========================================="); - } - solverTaskDesc.setSolverDescription(sd); - - if(taskType.equalsIgnoreCase(XMLTags.UnsteadyTag)){ - solverTaskDesc.setTaskType(SolverTaskDescription.TASK_UNSTEADY); - } else if(taskType.equalsIgnoreCase(XMLTags.SteadyTag)){ - solverTaskDesc.setTaskType(SolverTaskDescription.TASK_STEADY); - } else { - throw new XmlParseException("Unexpected task type: " + taskType); - } - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException("A PropertyVetoException was fired when setting the taskType: " + taskType, e); - } - int numProcessors = parseIntWithDefault(param, XMLTags.NUM_PROCESSORS, 1); - int numTrials = parseIntWithDefault(param, XMLTags.SolverTaskDescriptionNumTrials, 1); - - try { - solverTaskDesc.setNumProcessors(numProcessors); - solverTaskDesc.setNumTrials(numTrials); - solverTaskDesc.setUseSymbolicJacobian(useSymJacob); - //get TimeBound - solverTaskDesc.setTimeBounds(getTimeBounds(param.getChild(XMLTags.TimeBoundTag, vcNamespace))); - //get TimeStep - solverTaskDesc.setTimeStep(getTimeStep(param.getChild(XMLTags.TimeStepTag, vcNamespace))); - //get ErrorTolerance - solverTaskDesc.setErrorTolerance(getErrorTolerance(param.getChild(XMLTags.ErrorToleranceTag, vcNamespace))); - //get StochSimOptions - if(simulation != null && simulation.getMathDescription() != null){ - if(simulation.getMathDescription().isNonSpatialStoch() && param.getChild(XMLTags.StochSimOptionsTag, vcNamespace) != null){ //Amended July 22nd, 2007 to read either stochSimOptions or stochHybridOptions - solverTaskDesc.setStochOpt(getStochSimOptions(param.getChild(XMLTags.StochSimOptionsTag, vcNamespace))); - if(sd != null && !sd.equals(SolverDescription.StochGibson)){ - solverTaskDesc.setStochHybridOpt(getStochHybridOptions(param.getChild(XMLTags.StochSimOptionsTag, vcNamespace))); - } - } - } - //get OutputOptions - if(keepEvery != -1){ - solverTaskDesc.setOutputTimeSpec(new DefaultOutputTimeSpec(keepEvery, keepAtMost)); - } - OutputTimeSpec ots = getOutputTimeSpec(param.getChild(XMLTags.OutputOptionsTag, vcNamespace)); - if(ots != null){ - solverTaskDesc.setOutputTimeSpec(getOutputTimeSpec(param.getChild(XMLTags.OutputOptionsTag, vcNamespace))); - } - //set SensitivityParameter - solverTaskDesc.setSensitivityParameter(sensitivityparam); - - // set StopAtSpatiallyUniform - Element stopSpatiallyElement = param.getChild(XMLTags.StopAtSpatiallyUniform, vcNamespace); - if(stopSpatiallyElement != null){ - Element errTolElement = stopSpatiallyElement.getChild(XMLTags.ErrorToleranceTag, vcNamespace); - if(errTolElement != null){ - solverTaskDesc.setStopAtSpatiallyUniformErrorTolerance(getErrorTolerance(errTolElement)); - } - } - - String runParameterScanSeriallyAttributeValue = param.getAttributeValue(XMLTags.RunParameterScanSerially); - if(runParameterScanSeriallyAttributeValue != null){ - solverTaskDesc.setSerialParameterScan(Boolean.parseBoolean(runParameterScanSeriallyAttributeValue)); - } - String timeoutDisabledAttributeValue = param.getAttributeValue(XMLTags.TimeoutSimulationDisabled); - if(timeoutDisabledAttributeValue != null){ - solverTaskDesc.setTimeoutDisabled(Boolean.parseBoolean(timeoutDisabledAttributeValue)); - } - String borderExtrapolationDisabled = param.getAttributeValue(XMLTags.BorderExtrapolationDisabled); - if(borderExtrapolationDisabled != null){ - solverTaskDesc.setBorderExtrapolationDisabled(Boolean.parseBoolean(borderExtrapolationDisabled)); - } - - Element nfsimSimulationOptionsElement = param.getChild(XMLTags.NFSimSimulationOptions, vcNamespace); - if(nfsimSimulationOptionsElement != null){ - NFsimSimulationOptions nfsimSimulationOptions = getNFSimSimulationOptions(nfsimSimulationOptionsElement); - solverTaskDesc.setNFSimSimulationOptions(nfsimSimulationOptions); - } - Element langevinSimulationOptionsElement = param.getChild(XMLTags.LangevinSimulationOptions, vcNamespace); - if(langevinSimulationOptionsElement != null){ - LangevinSimulationOptions langevinSimulationOptions = getLangevinSimulationOptions(langevinSimulationOptionsElement); - solverTaskDesc.setLangevinSimulationOptions(langevinSimulationOptions); - } - Element smoldySimulationOptionsElement = param.getChild(XMLTags.SmoldynSimulationOptions, vcNamespace); - if(smoldySimulationOptionsElement != null){ - SmoldynSimulationOptions smoldynSimulationOptions = getSmoldySimulationOptions(smoldySimulationOptionsElement); - solverTaskDesc.setSmoldynSimulationOptions(smoldynSimulationOptions); - } - Element sundialsPdeSolverOptionsElement = param.getChild(XMLTags.SundialsSolverOptions, vcNamespace); - if(sundialsPdeSolverOptionsElement != null){ - SundialsPdeSolverOptions sundialsPdeSolverOptions = getSundialsPdeSolverOptions(sundialsPdeSolverOptionsElement); - solverTaskDesc.setSundialsPdeSolverOptions(sundialsPdeSolverOptions); - } - Element chomboElement = param.getChild(XMLTags.ChomboSolverSpec, vcNamespace); - if(chomboElement != null){ - ChomboSolverSpec chombo = getChomboSolverSpec(solverTaskDesc, chomboElement, simulation.getMathDescription().getGeometry().getDimension()); - solverTaskDesc.setChomboSolverSpec(chombo); - } - Element mbElement = param.getChild(XMLTags.MovingBoundarySolverOptionsTag, vcNamespace); - if(mbElement != null){ - MovingBoundarySolverOptions mb = getMovingBoundarySolverOptions(solverTaskDesc, mbElement); - solverTaskDesc.setMovingBoundarySolverOptions(mb); - } - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException(e); - } - - return solverTaskDesc; - } - - private NFsimSimulationOptions getNFSimSimulationOptions(Element nfsimSimulationOptionsElement) throws XmlParseException{ - NFsimSimulationOptions so = new NFsimSimulationOptions(); - String temp = null; - - temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_observableComputationOff, vcNamespace); - if(temp != null){ - so.setObservableComputationOff(Boolean.parseBoolean(temp)); - } - temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_moleculeDistance, vcNamespace); - if(temp != null){ - so.setMoleculeDistance(Integer.parseInt(temp)); - } - temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_aggregateBookkeeping, vcNamespace); - if(temp != null){ - so.setAggregateBookkeeping(Boolean.parseBoolean(temp)); - } - temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_maxMoleculesPerType, vcNamespace); - if(temp != null){ - so.setMaxMoleculesPerType(Integer.parseInt(temp)); - } - temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_equilibrateTime, vcNamespace); - if(temp != null){ - so.setEquilibrateTime(Integer.parseInt(temp)); - } - temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_randomSeed, vcNamespace); - if(temp != null){ - so.setRandomSeed(Integer.parseInt(temp)); - } - temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_preventIntraBonds, vcNamespace); - if(temp != null){ - so.setPreventIntraBonds(Boolean.parseBoolean(temp)); - } - temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_matchComplexes, vcNamespace); - if(temp != null){ - so.setMatchComplexes(Boolean.parseBoolean(temp)); - } - temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_numOfTrials, vcNamespace); - if(temp != null){ - so.setNumOfTrials(Integer.parseInt(temp)); - } - return so; - } - - private LangevinSimulationOptions getLangevinSimulationOptions(Element langevinSimulationOptionsElement) throws XmlParseException{ - LangevinSimulationOptions lo = new LangevinSimulationOptions(); - String temp = null; - temp = langevinSimulationOptionsElement.getChildText(XMLTags.LangevinSO_intervalSpring, vcNamespace); - if(temp != null){ - lo.setIntervalSpring(Double.parseDouble(temp)); - } - temp = langevinSimulationOptionsElement.getChildText(XMLTags.LangevinSO_intervalImage, vcNamespace); - if(temp != null){ - lo.setIntervalImage(Double.parseDouble(temp)); - } - temp = langevinSimulationOptionsElement.getChildText(XMLTags.LangevinSO_Partition_Nx, vcNamespace); - if(temp != null) { - lo.setNPart(0, Integer.parseInt(temp)); - } - temp = langevinSimulationOptionsElement.getChildText(XMLTags.LangevinSO_Partition_Ny, vcNamespace); - if(temp != null) { - lo.setNPart(1, Integer.parseInt(temp)); - } - temp = langevinSimulationOptionsElement.getChildText(XMLTags.LangevinSO_Partition_Nz, vcNamespace); - if(temp != null) { - lo.setNPart(2, Integer.parseInt(temp)); - } - temp = langevinSimulationOptionsElement.getChildText(XMLTags.LangevinSO_totalNumberOfJobs, vcNamespace); - if(temp != null) { - lo.setTotalNumberOfJobs(Integer.parseInt(temp)); - } - temp = langevinSimulationOptionsElement.getChildText(XMLTags.LangevinSO_numberOfConcurrentJobs, vcNamespace); - if(temp != null) { - lo.setNumberOfConcurrentJobs(Integer.parseInt(temp)); - } - temp = langevinSimulationOptionsElement.getChildText(XMLTags.LangevinSO_randomSeed, vcNamespace); - if(temp != null) { - lo.setRandomSeed(new BigInteger(temp)); - } else { - lo.setRandomSeed(null); - } - return lo; - } - - private SmoldynSimulationOptions getSmoldySimulationOptions(Element smoldySimulationOptionsElement) throws XmlParseException{ - - SmoldynSimulationOptions sso = null; - if(smoldySimulationOptionsElement != null){ - sso = new SmoldynSimulationOptions(); - String temp = smoldySimulationOptionsElement.getChildText(XMLTags.SmoldynSimulationOptions_accuracy, vcNamespace); - if(temp != null){ - sso.setAccuracy(Double.parseDouble(temp)); - } - temp = smoldySimulationOptionsElement.getChildText(XMLTags.SmoldynSimulationOptions_randomSeed, vcNamespace); - if(temp != null){ - sso.setRandomSeed(Integer.parseInt(temp)); - } - temp = smoldySimulationOptionsElement.getChildText(XMLTags.SmoldynSimulationOptions_gaussianTableSize, vcNamespace); - if(temp != null){ - try { - sso.setGaussianTableSize(Integer.parseInt(temp)); - } catch(NumberFormatException | PropertyVetoException e){ - throw new XmlParseException(e); - } - } - temp = smoldySimulationOptionsElement.getChildText(XMLTags.SmoldynSimulationOptions_high_res, vcNamespace); - if(temp != null){ - sso.setUseHighResolutionSample(Boolean.parseBoolean(temp)); - } - temp = smoldySimulationOptionsElement.getChildText(XMLTags.SmoldynSimulationOptions_saveParticleFiles, vcNamespace); - if(temp != null){ - sso.setSaveParticleLocations(Boolean.parseBoolean(temp)); - } - temp = smoldySimulationOptionsElement.getChildText(XMLTags.SmoldynSimulationOptions_stepMultiplier, vcNamespace); - if(temp != null){ - sso.setSmoldynStepMultiplier(Integer.parseInt(temp)); - } - } - return sso; - } - - private SundialsPdeSolverOptions getSundialsPdeSolverOptions(Element sundialsPdeSolverOptionsElement) throws XmlParseException{ - - SundialsPdeSolverOptions sundialsPdeSolverOptions = null; - if(sundialsPdeSolverOptionsElement != null){ - String temp = sundialsPdeSolverOptionsElement.getChildText(XMLTags.SundialsSolverOptions_maxOrderAdvection, vcNamespace); - if(temp != null){ - sundialsPdeSolverOptions = new SundialsPdeSolverOptions(Integer.parseInt(temp)); - } - } - return sundialsPdeSolverOptions; - } - - public ModelParameter[] getModelParams(Element globalParams, Model model) throws XmlParseException{ - List parameterElements = globalParams.getChildren(XMLTags.ParameterTag, vcNamespace); - Vector modelParamsVector = new Vector<>(); - for(Element paramElement : parameterElements){ - modelParamsVector.add(getModelParameter(paramElement, model)); - } - return modelParamsVector.toArray(ModelParameter[]::new); - } - - - public ModelParameter getModelParameter(Element paramElement, Model model) throws XmlParseException{ - //get its attributes : name, role and unit definition - String glParamName = unMangle(paramElement.getAttributeValue(XMLTags.NameAttrTag)); - String role = paramElement.getAttributeValue(XMLTags.ParamRoleAttrTag); - ModelUnitSystem modelUnitSystem = model.getUnitSystem(); - int glParamRole = -1; - if(role.equals(XMLTags.ParamRoleUserDefinedTag)){ - glParamRole = Model.ROLE_UserDefined; - } else { - throw new RuntimeException("unknown type of model parameter (not user-defined)"); - } -// -// int glParamRole = -1; -// if (role.equals(XMLTags.ParamRoleUserDefinedTag)) { -// glParamRole = Model.ROLE_UserDefined; -// } else if (role.equals(XMLTags.RoleVariableRateTag)) { -// glParamRole = Model.ROLE_VariableRate; -// } else { -// throw new RuntimeException("unknown type of model parameter (not user-defined or variable rate)"); -// } - String unitSymbol = paramElement.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); - VCUnitDefinition glParamUnit = null; - if(unitSymbol != null){ - glParamUnit = modelUnitSystem.getInstance(unitSymbol); - } - //get parameter contents : expression; annotation, if any. - String glParamExpStr = paramElement.getText(); - Expression glParamExp = unMangleExpression(glParamExpStr); - String glParamAnnotation = null; - String annotationText = paramElement.getChildText(XMLTags.AnnotationTag, vcNamespace); - if(annotationText != null && annotationText.length() > 0){ - glParamAnnotation = unMangle(annotationText); - } - - //create new global parameter - try { - ModelParameter newGlParam = model.new ModelParameter(glParamName, glParamExp, glParamRole, glParamUnit); - if(paramElement.getAttributeValue(XMLTags.SbmlNameAttrTag) != null){ - String sbmlName = unMangle(paramElement.getAttributeValue(XMLTags.SbmlNameAttrTag)); - if(sbmlName != null && !sbmlName.isEmpty()){ - newGlParam.setSbmlName(sbmlName); - } - } - newGlParam.setModelParameterAnnotation(glParamAnnotation); - return newGlParam; - } catch(PropertyVetoException e){ - throw new XmlParseException("An error occurred while trying to create the ModelParameter " + glParamName, e); - } - } - - public SimulationContextParameter[] getSimulationContextParams(Element appParams, SimulationContext simContext) throws XmlParseException{ - Iterator appParamIterator = appParams.getChildren(XMLTags.ParameterTag, vcNamespace).iterator(); - ArrayList appParamsList = new ArrayList(); - while (appParamIterator.hasNext()) { - Element paramElement = (Element) appParamIterator.next(); - appParamsList.add(getSimulationContextParameter(paramElement, simContext)); - } - return appParamsList.toArray(new SimulationContextParameter[0]); - } - - - public SimulationContextParameter getSimulationContextParameter(Element paramElement, SimulationContext simContext){ - //get its attributes : name, role and unit definition - String appParamName = unMangle(paramElement.getAttributeValue(XMLTags.NameAttrTag)); - String role = paramElement.getAttributeValue(XMLTags.ParamRoleAttrTag); - ModelUnitSystem modelUnitSystem = simContext.getModel().getUnitSystem(); - int appParamRole = -1; - if(role.equals(XMLTags.ParamRoleUserDefinedTag)){ - appParamRole = SimulationContext.ROLE_UserDefined; - } else { - throw new RuntimeException("unknown type of application parameter (not user-defined)"); - } - String unitSymbol = paramElement.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); - VCUnitDefinition appParamUnit = null; - if(unitSymbol != null){ - appParamUnit = modelUnitSystem.getInstance(unitSymbol); - } - //get parameter contents : expression; annotation, if any. - String appParamExpStr = paramElement.getText(); - Expression appParamExp = unMangleExpression(appParamExpStr); -// String appParamAnnotation = null; -// String annotationText = paramElement.getChildText(XMLTags.AnnotationTag, vcNamespace); -// if (annotationText != null && annotationText.length() > 0) { -// appParamAnnotation = unMangle(annotationText); -// } - - //create new global parameter - SimulationContextParameter newAppParam = simContext.new SimulationContextParameter(appParamName, appParamExp, appParamRole, appParamUnit); -// newGlParam.setModelParameterAnnotation(appParamAnnotation); - - return newAppParam; - } - - public ArrayList getOutputFunctions(Element outputFunctionsElement) throws XmlParseException{ - Iterator outputFnsIterator = outputFunctionsElement.getChildren(XMLTags.AnnotatedFunctionTag, vcNamespace).iterator(); - ArrayList outputFunctions = new ArrayList(); - while (outputFnsIterator.hasNext()) { - Element observableElement = (Element) outputFnsIterator.next(); - AnnotatedFunction func = getOutputFunction(observableElement); - outputFunctions.add(func); - } - return (outputFunctions); - } - - /** - * This method creates a Specie (Compound) object from an XML Element. - * Creation date: (3/15/2001 12:57:43 PM) - * - * @param param Element - * @return cbit.vcell.model.Species - */ - private Species getSpecies(Element param) throws XmlParseException{ - //get its data - String specieName = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String specieAnnotation = null; - - //the Annotation paramater can be optional - //String temp = param.getAttributeValue(XMLTags.AnnotationAttrTag); - //if (temp!=null && temp.length()!=0) { - //specieAnnotation = unMangle(temp); - //} - String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace); - if(annotationText != null && annotationText.length() > 0){ - specieAnnotation = unMangle(annotationText); - } - //create new Specie - Species newspecie = new Species(specieName, specieAnnotation); - - //Try to read the DBSpecie data - Element dbspecieElement = param.getChild(XMLTags.DBSpeciesTag, vcNamespace); - - if(dbspecieElement != null && this.readKeysFlag){ - //read the data - try { - newspecie.setDBSpecies(getDBSpecies(dbspecieElement)); - } catch(PropertyVetoException e){ - throw new XmlParseException(e); - } - } - - return newspecie; - } - - /** - * This method returns a Speciecontext object from a XML Element. - * Creation date: (4/16/2001 6:32:23 PM) - * - * @param param Element - * @return cbit.vcell.model.SpeciesContext - */ - private SpeciesContext getSpeciesContext(Element param, Model model) throws XmlParseException{ - //retrieve its information - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String sbmlName = unMangle(param.getAttributeValue(XMLTags.SbmlNameAttrTag)); - String hasOverrideString = param.getAttributeValue(XMLTags.HasOverrideAttrTag); - String speciesName = unMangle(param.getAttributeValue(XMLTags.SpeciesRefAttrTag)); - Species specieref = (Species) model.getSpecies(speciesName); - if(specieref == null){ - throw new XmlParseException("The Species " + speciesName + "could not be resolved!"); - } - - String structureName = unMangle(param.getAttributeValue(XMLTags.StructureAttrTag)); - Structure structureref = (Structure) model.getStructure(structureName); - if(structureref == null){ - //the structure coul not be retrieved, so throw an exception! - throw new XmlParseException("The Structure " + structureName + "could not be resolved!"); - } - - //Try to read KeyValue data - String keystring = param.getAttributeValue(XMLTags.KeyValueAttrTag); - KeyValue key = null; - - if(keystring != null && keystring.length() > 0 && this.readKeysFlag){ - key = new KeyValue(keystring); - } - - SpeciesPattern sp = null; - Element element = param.getChild(XMLTags.RbmSpeciesPatternTag, vcNamespace); - if(element != null){ - sp = getSpeciesPattern(element, model); - sp.resolveBonds(); - if(sp == null){ - throw new XmlParseException("XMLReader: getSpeciesContext: SpeciesPattern is missing."); - } - } - //---try to create the speciesContext--- - SpeciesContext speciecontext = null; - speciecontext = new SpeciesContext(key, name, specieref, structureref, sp); - try { - speciecontext.setSbmlName(sbmlName); - } catch(PropertyVetoException e){ // can't happen here, whatever we saved must have been correct - // throw new XmlParseException("The SbmlName is invalid"); - lg.error(e); - } - return speciecontext; - } - - - private void getSpeciesContextSpecs(List scsChildren, ReactionContext rxnContext, Model model) throws XmlParseException{ - for(int i = 0; i < scsChildren.size(); i++){ - Element scsElement = scsChildren.get(i); - SpeciesContextSpec specspec = null; - //Get Atributes - String speccontname = unMangle(scsElement.getAttributeValue(XMLTags.SpeciesContextRefAttrTag)); - boolean constant = Boolean.valueOf(scsElement.getAttributeValue(XMLTags.ForceConstantAttrTag)).booleanValue(); - //boolean enabledif = Boolean.valueOf(scsElement.getAttributeValue(XMLTags.EnableDiffusionAttrTag)).booleanValue(); - String spatialStr = scsElement.getAttributeValue(XMLTags.SpatialAttrTag); - Boolean spatial = null; - if(spatialStr != null){ - spatial = Boolean.valueOf(spatialStr); - } - - String bWellMixedStr = scsElement.getAttributeValue(XMLTags.WellMixedAttrTag); - Boolean bWellMixed = null; - if(bWellMixedStr != null){ - bWellMixed = Boolean.valueOf(bWellMixedStr); - } - - String bForceContinuousStr = scsElement.getAttributeValue(XMLTags.ForceContinuousAttrTag); - Boolean bForceContinuous = null; - if(bForceContinuousStr != null){ - bForceContinuous = Boolean.valueOf(bForceContinuousStr); - } - - //Retrieve reference - SpeciesContext specref = model.getSpeciesContext(speccontname); - if(specref == null){ - throw new XmlParseException("The SpeciesContext " + speccontname + " refrence could not be resolved!"); - } - - // get SpeciesContextSpec from reactionContext & specRef - specspec = rxnContext.getSpeciesContextSpec(specref); - //set attributes - specspec.setConstant(constant); -// try { -// specspec.setEnableDiffusing( enabledif ); -// } catch (MappingException e) { -// lg.error(e); -// throw new XmlParseException("error setting the 'enableDiffusing' property of a SpeciesContext: "+e.getMessage()); -// } - if(spatial != null){ - specspec.setWellMixed(!spatial); - } - if(bWellMixed != null){ - specspec.setWellMixed(bWellMixed); - } - if(bForceContinuous != null){ - specspec.setForceContinuous(bForceContinuous); - } - //set expressions - //Initial - String tempCon = scsElement.getChildText(XMLTags.InitialConcentrationTag, vcNamespace); - String tempAmt = scsElement.getChildText(XMLTags.InitialAmountTag, vcNamespace); - String temp = scsElement.getChildText(XMLTags.InitialTag, vcNamespace); - try { - if(temp != null)//old model - { - Expression expression = unMangleExpression(temp); - specspec.getInitialConcentrationParameter().setExpression(expression); - specspec.getInitialCountParameter().setExpression(null); - } else //new model - { - if(tempCon != null)//use concentration as initial condition - { - Expression expression = unMangleExpression(tempCon); - specspec.getInitialConcentrationParameter().setExpression(expression); - specspec.getInitialCountParameter().setExpression(null); - } else if(tempAmt != null)//use number of particles as initial condition - { - Expression expression = unMangleExpression(tempAmt); - specspec.getInitialCountParameter().setExpression(expression); - specspec.getInitialConcentrationParameter().setExpression(null); - } else { - throw new XmlParseException("Unrecognizable initial condition when parsing VCML file."); - } - } - - // Expression expression = unMangleExpression(temp); - // specspec.getInitialConditionParameter().setExpression(expression); - } catch(ExpressionException e){ - throw new XmlParseException("An expressionException was fired when setting the InitilaconditionExpression " + temp + ", for a SpeciesContextSpec!", e); - } - //diffusion (if there is no diffusion information skip it) - Element xmlDiffusionElement = scsElement.getChild(XMLTags.DiffusionTag, vcNamespace); - if(xmlDiffusionElement != null){ - temp = xmlDiffusionElement.getText(); - try { - Expression expression = unMangleExpression(temp); - specspec.getDiffusionParameter().setExpression(expression); - } catch(ExpressionException e){ - throw new XmlParseException("An ExpressionException was fired when setting the diffusionExpression " + temp + " to a SpeciesContextSpec!", e); - } - } - - //Get Boundaries if any - Element tempElement = scsElement.getChild(XMLTags.BoundariesTag, vcNamespace); - if(tempElement != null){ - try { - //Xm - temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueXm); - if(temp != null){ - specspec.getBoundaryXmParameter().setExpression(unMangleExpression(temp)); - } - //Xp - temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueXp); - if(temp != null){ - specspec.getBoundaryXpParameter().setExpression(unMangleExpression(temp)); - } - //Ym - temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueYm); - if(temp != null){ - specspec.getBoundaryYmParameter().setExpression(unMangleExpression(temp)); - } - //Yp - temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueYp); - if(temp != null){ - specspec.getBoundaryYpParameter().setExpression(unMangleExpression(temp)); - } - //Zm - temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueZm); - if(temp != null){ - specspec.getBoundaryZmParameter().setExpression(unMangleExpression(temp)); - } - //Zp - temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueZp); - if(temp != null){ - specspec.getBoundaryZpParameter().setExpression(unMangleExpression(temp)); - } - } catch(ExpressionException e){ - throw new XmlParseException("An ExpressionException was fired when Setting the boundary Expression: " + unMangle(temp), e); - } - } - - // Get Velocities if any - Element velocityE = scsElement.getChild(XMLTags.VelocityTag, vcNamespace); - if(velocityE != null){ - String tempStr = null; - boolean dummyVel = true; - try { - tempStr = velocityE.getAttributeValue(XMLTags.XAttrTag); - if(tempStr != null){ - specspec.getVelocityXParameter().setExpression(unMangleExpression(tempStr)); //all velocity dimensions are optional. - if(dummyVel){ - dummyVel = false; - } - } - tempStr = velocityE.getAttributeValue(XMLTags.YAttrTag); - if(tempStr != null){ - specspec.getVelocityYParameter().setExpression(unMangleExpression(tempStr)); - if(dummyVel){ - dummyVel = false; - } - } - tempStr = velocityE.getAttributeValue(XMLTags.ZAttrTag); - if(tempStr != null){ - specspec.getVelocityZParameter().setExpression(unMangleExpression(tempStr)); - if(dummyVel){ - dummyVel = false; - } - } - } catch(ExpressionException e){ - throw new XmlParseException("Error setting Velocity parameter for '" + specspec.getSpeciesContext().getName(), e); - } - if(dummyVel){ - throw new XmlParseException("Void Velocity element found under PDE for: " + specspec.getSpeciesContext().getName()); - } - } - - if(!(SimulationContext.Application.SPRINGSALAD == rxnContext.getSimulationContext().getApplicationType())){ - continue; - } - // we could do extra validation to make sure that sc has a sp, which has exactly one mtp, aso - // but probably it would be superfluous - SpeciesContext sc = specspec.getSpeciesContext(); - SpeciesPattern sp = sc.getSpeciesPattern(); - if(sp == null){ - throw new XmlParseException("Expected non-null SpeciesPattern for " + specspec.getDisplayName()); - } - MolecularTypePattern mtp = sp.getMolecularTypePatterns().get(0); - - // we maintain a map between the names of the LinkNodes (siteRef) which may be MolecularComponentPatterns or - // StructuralSites, so that we could get the right instances once we'll start parsing the InternalLinkSpecs. - Map refToLinkNodeMap = new LinkedHashMap<>(); - // all SpeciesContextSpec objects now have a siteAttributesMap, if the app is not Springsalad it will be empty - Map siteAttributesMap = new LinkedHashMap<>(); - List saSpecs = scsElement.getChildren(XMLTags.SiteAttributesSpecTag, vcNamespace); - for(Element attributeSpec : saSpecs){ // should map to Math's ParticleJumpProcess (1 -> 1) - String moleculeRef = attributeSpec.getAttributeValue(XMLTags.MoleculeRefAttrTag); - if(!mtp.getMolecularType().getName().equals(moleculeRef)) { // sanity check, we need the right mtp for the mcp instance - throw new XmlParseException("Bad SiteAttributeSpec molecular type for " + specspec.getDisplayName()); - } - String siteRef = attributeSpec.getAttributeValue(XMLTags.SiteRefAttrTag); - double radius = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteRadiusAttrTag)); - double diff = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteDiffusionAttrTag)); - String locationName = attributeSpec.getAttributeValue(XMLTags.SiteLocationRefAttrTag); - NamedColor color = Colors.getColorByName(attributeSpec.getAttributeValue(XMLTags.SiteColorAttrTag)); - double x = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteCoordXAttrTag)); - double y = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteCoordYAttrTag)); - double z = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteCoordZAttrTag)); - Coordinate coordinate = new Coordinate(x, y, z); - MolecularComponentPattern mcp = mtp.getMolecularComponentPattern(siteRef); - refToLinkNodeMap.put(siteRef, mcp); - Structure structure = model.getStructure(locationName); - SiteAttributesSpec sas = new SiteAttributesSpec(specspec, mcp, radius, diff, structure, coordinate, color); - siteAttributesMap.put(mcp, sas); - } - specspec.setSiteAttributesMap(siteAttributesMap); - - // all SpeciesContextSpec objects now have a structuralSiteAttributesMap, if the app is not Springsalad it will be empty - Map structuralSiteAttributesMap = new LinkedHashMap<>(); - List ssaSpecs = scsElement.getChildren(XMLTags.StructuralSiteAttributesSpecTag, vcNamespace); - for(Element attributeSpec : ssaSpecs){ // should map to Math's ParticleJumpProcess (1 -> 1) - String moleculeRef = attributeSpec.getAttributeValue(XMLTags.MoleculeRefAttrTag); - if(!mtp.getMolecularType().getName().equals(moleculeRef)) { // sanity check, we don't need it for StructuralSites - throw new XmlParseException("Bad SiteAttributeSpec molecular type for " + specspec.getDisplayName()); - } - String siteRef = attributeSpec.getAttributeValue(XMLTags.SiteRefAttrTag); - double radius = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteRadiusAttrTag)); - double diff = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteDiffusionAttrTag)); - String locationName = attributeSpec.getAttributeValue(XMLTags.SiteLocationRefAttrTag); - NamedColor color = Colors.getColorByName(attributeSpec.getAttributeValue(XMLTags.SiteColorAttrTag)); - double x = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteCoordXAttrTag)); - double y = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteCoordYAttrTag)); - double z = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteCoordZAttrTag)); - Coordinate coordinate = new Coordinate(x, y, z); - StructuralSite mcp = new StructuralSite(siteRef); - refToLinkNodeMap.put(siteRef, mcp); - Structure structure = model.getStructure(locationName); - SiteAttributesSpec sas = new SiteAttributesSpec(specspec, mcp, radius, diff, structure, coordinate, color); - structuralSiteAttributesMap.put(mcp, sas); - } - specspec.setStructuralSiteAttributesMap(structuralSiteAttributesMap); - - // all SpeciesContextSpec objects now have an internalLinkSet, if the app is not Springsalad it will be empty - Set internalLinkSet = new LinkedHashSet<>(); - List linkSpecs = scsElement.getChildren(XMLTags.InternalLinkSpecTag, vcNamespace); - for(Element linkSpec : linkSpecs){ // should map to Math's ParticleMolecularType (n -> 1) - String oneName = unMangle(linkSpec.getAttributeValue(XMLTags.SiteOneRefAttrTag)); - String twoName = unMangle(linkSpec.getAttributeValue(XMLTags.SiteTwoRefAttrTag)); - LinkNode one = refToLinkNodeMap.get(oneName); - LinkNode two = refToLinkNodeMap.get(twoName); - MolecularInternalLinkSpec internalLink = new MolecularInternalLinkSpec(specspec, one, two); - internalLinkSet.add(internalLink); - } - specspec.setInternalLinkSet(internalLinkSet); - } - } - - /** - * This method returns a TimeStep object from a XML Element. - * Creation date: (5/22/2001 11:45:33 AM) - * - * @param param Element - * @return cbit.vcell.solver.TimeStep - */ - private NonspatialStochSimOptions getStochSimOptions(Element param){ - //get attributes - boolean isUseCustomSeed = Boolean.parseBoolean(param.getAttributeValue(XMLTags.UseCustomSeedAttrTag)); - int customSeed = 0; - if(isUseCustomSeed) - customSeed = Integer.parseInt(param.getAttributeValue(XMLTags.CustomSeedAttrTag)); - int numOfTrials = Integer.parseInt(param.getAttributeValue(XMLTags.NumberOfTrialAttrTag)); - boolean bHistogram = true; // initialize for old style cases when XMLTags.IsHistogram may be missing - if(numOfTrials == 1){ - bHistogram = false; - } - String histAttr = param.getAttributeValue(XMLTags.IsHistogram); - if(histAttr != null && !histAttr.isEmpty()){ - bHistogram = Boolean.parseBoolean(histAttr); - } - - return new NonspatialStochSimOptions(isUseCustomSeed, customSeed, numOfTrials, bHistogram); - } - - - /** - * This method returns a TimeStep object from a XML Element. - * Creation date: (5/22/2001 11:45:33 AM) - * - * @param param Element - * @return cbit.vcell.solver.TimeStep - */ - private NonspatialStochHybridOptions getStochHybridOptions(Element param){ - // StochHybridOptions are immutable, so we grab the default values from the default constructor - and read the options which are stored in XML - NonspatialStochHybridOptions defaultStochHybridOptions = new NonspatialStochHybridOptions(); - double epsilon = defaultStochHybridOptions.getEpsilon(); - double lambda = defaultStochHybridOptions.getLambda(); - double MSRTolerance = defaultStochHybridOptions.getMSRTolerance(); - double SDETDolerance = defaultStochHybridOptions.getSDETolerance(); - if(param.getAttributeValue(XMLTags.HybridEpsilonAttrTag) != null){ - epsilon = Double.parseDouble(param.getAttributeValue(XMLTags.HybridEpsilonAttrTag)); - } - if(param.getAttributeValue(XMLTags.HybridLambdaAttrTag) != null){ - lambda = Double.parseDouble(param.getAttributeValue(XMLTags.HybridLambdaAttrTag)); - } - if(param.getAttributeValue(XMLTags.HybridMSRToleranceAttrTag) != null){ - MSRTolerance = Double.parseDouble(param.getAttributeValue(XMLTags.HybridMSRToleranceAttrTag)); - } - if(param.getAttributeValue(XMLTags.HybridSDEToleranceAttrTag) != null){ - SDETDolerance = Double.parseDouble(param.getAttributeValue(XMLTags.HybridSDEToleranceAttrTag)); - } - //**** create a new StochHybridOptions object and return **** - return new NonspatialStochHybridOptions(epsilon, lambda, MSRTolerance, SDETDolerance); - } - - - /** - * This method returns a Stochasitc volumn variable from a XML element. - * Creation date: (7/24/2006 5:05:51 PM) - * - * @param param Element - * @return cbit.vcell.math.StochVolVariable - */ - private StochVolVariable getStochVolVariable(Element param){ - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - //-- create new StochVolVariable object - StochVolVariable stochVar = new StochVolVariable(name); - transcribeComments(param, stochVar); - - return stochVar; - } - - /** - * This method returns a SubVolume element type from a XML representation. - * Creation date: (4/26/2001 4:14:01 PM) - * - * @param param Element - * @return SubVolume - */ - private SubVolume getSubVolume(Element param) throws XmlParseException{ - String typeString = param.getAttributeValue(XMLTags.TypeAttrTag); - SubVolume newsubvolume = null; - - if(typeString != null){ - //process the subvolume upon the 'type' - if(typeString.equalsIgnoreCase(XMLTags.CompartmentBasedTypeTag)){ - //Process compartmental based - newsubvolume = getCompartmentSubVolume(param); - } else if(typeString.equalsIgnoreCase(XMLTags.AnalyticBasedTypeTag)){ - //Process Analytic based - newsubvolume = getAnalyticSubVolume(param); - } else if(typeString.equalsIgnoreCase(XMLTags.ImageBasedTypeTag)){ - //Process Image based - newsubvolume = getImageSubVolume(param); - } else if(typeString.equalsIgnoreCase(XMLTags.CSGBasedTypeTag)){ - //Process Constructed Solid Geometry based - newsubvolume = getCSGObject(param, null); - } else { - //Throw an exception - throw new XmlParseException("Parse Error! Unknown Subvolume type:" + typeString); - } - - } else { - System.out.println("Invalid VCML format! Error in "); - System.out.println("Valid format is:"); - System.out.println(""); - throw new XmlParseException("Invalid VCML syntax in "); - } - - return newsubvolume; - } - - public CSGObject getCSGObject(Element param, KeyValue keyFromDB) throws XmlParseException{ - //retrieve the attributes - String name = param.getAttributeValue(XMLTags.NameAttrTag); - int handle = Integer.parseInt(param.getAttributeValue(XMLTags.HandleAttrTag)); - - //process the key - KeyValue key = null; - String temp = param.getAttributeValue(XMLTags.KeyValueAttrTag); - - if(temp != null && temp.length() > 0 && this.readKeysFlag){ - key = new KeyValue(temp); - } - if(keyFromDB != null){ - key = keyFromDB; - } - - //Retrieve CSGObject CSGNode - CSGObject element should have one child (the root node of the CSGObject) - Object[] elements = param.getChildren().toArray(); - if(elements.length > 1){ - throw new XmlParseException("CSGObject subvolume element cannot have more than one child element"); - } - CSGNode csgRootNode = getCSGNode((Element) elements[0]); - - //Create the CSGObject - CSGObject newCSGObjectSubvol = new CSGObject(key, name, handle); - newCSGObjectSubvol.setRoot(csgRootNode); - - return newCSGObjectSubvol; - } - - private CSGNode getCSGNode(Element param) throws XmlParseException{ - String nodeNameString = param.getName(); - CSGNode csgNode = null; - - if(nodeNameString != null){ - if(nodeNameString.equalsIgnoreCase(XMLTags.CSGPrimitiveTag)){ - //Process CSGPrimitive - csgNode = getCSGPrimitive(param); - } else if(nodeNameString.equalsIgnoreCase(XMLTags.CSGPseudoPrimitiveTag)){ - //Process CSGPseudoPrimitive - csgNode = getCSGPseudoPrimitive(param); - } else if(nodeNameString.equalsIgnoreCase(XMLTags.CSGSetOperatorTag)){ - //Process CSGSetOperator - csgNode = getCSGSetOperator(param); - } else if(nodeNameString.equalsIgnoreCase(XMLTags.CSGHomogeneousTransformationTag)){ - //Process CSGHomogeneousTransformation - csgNode = getCSGHomogeneousTransformation(param); - } else if(nodeNameString.equalsIgnoreCase(XMLTags.CSGRotationTag)){ - //Process CSGRotation - csgNode = getCSGRotation(param); - } else if(nodeNameString.equalsIgnoreCase(XMLTags.CSGScaleTag)){ - //Process CSGScale - csgNode = getCSGScale(param); - } else if(nodeNameString.equalsIgnoreCase(XMLTags.CSGTranslationTag)){ - //Process CSGTranslation - csgNode = getCSGTranslation(param); - } else { - //Throw an exception - throw new XmlParseException("Parse Error! Unknown CSGNode type : " + nodeNameString); - } - - } else { - throw new XmlParseException("CSGNode : cannot be null"); - } - - return csgNode; - } - - - private CSGPrimitive getCSGPrimitive(Element param){ - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String primitiveTypeStr = unMangle(param.getAttributeValue(XMLTags.CSGPrimitiveTypeTag)); - - //---Create the new CSGPrimitive object --- - PrimitiveType type = CSGPrimitive.PrimitiveType.valueOf(primitiveTypeStr); - CSGPrimitive csgPrimitive = new CSGPrimitive(name, type); - - return csgPrimitive; - } - - private CSGPseudoPrimitive getCSGPseudoPrimitive(Element param) throws XmlParseException{ - throw new XmlParseException("CSGPseudoPrimitive not implemented yet."); - } - - - private CSGSetOperator getCSGSetOperator(Element param) throws XmlParseException{ - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String operatorTypeStr = unMangle(param.getAttributeValue(XMLTags.CSGSetOperatorTypeTag)); - - //---Create the new CSGSetOperator object --- - OperatorType type = CSGSetOperator.OperatorType.valueOf(operatorTypeStr); - CSGSetOperator csgSetOperator = new CSGSetOperator(name, type); - - List children = param.getChildren(); - Iterator iterator = children.iterator(); - int count = 0; - while (iterator.hasNext()) { - Element tempElement = iterator.next(); - CSGNode csgNode = getCSGNode(tempElement); - csgSetOperator.addChild(csgNode); - } - - return csgSetOperator; - } - - private CSGHomogeneousTransformation getCSGHomogeneousTransformation(Element param) throws XmlParseException{ - throw new XmlParseException("CSGHomogeneousTransformation not implemented yet."); - } - - - private CSGRotation getCSGRotation(Element param) throws XmlParseException{ - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String rotateXStr = unMangle(param.getAttributeValue(XMLTags.CSGRotationXTag)); - String rotateYStr = unMangle(param.getAttributeValue(XMLTags.CSGRotationYTag)); - String rotateZStr = unMangle(param.getAttributeValue(XMLTags.CSGRotationZTag)); - String rotationAngleStr = unMangle(param.getAttributeValue(XMLTags.CSGRotationAngleInRadiansTag)); - Vect3d rotationAxis = new Vect3d(Double.parseDouble(rotateXStr), Double.parseDouble(rotateYStr), Double.parseDouble(rotateZStr)); - CSGRotation csgRotation = new CSGRotation(name, rotationAxis, Double.parseDouble(rotationAngleStr)); - - //Retrieve CSGNode - CSGRotation element should have one child - Object[] elements = param.getChildren().toArray(); - if(elements.length > 1){ - throw new XmlParseException("CSGRotation element cannot have more than one child element"); - } - CSGNode csgChildNode = getCSGNode((Element) elements[0]); - - csgRotation.setChild(csgChildNode); - return csgRotation; - } - - - private CSGScale getCSGScale(Element param) throws XmlParseException{ - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String scaleXStr = unMangle(param.getAttributeValue(XMLTags.CSGScaleXTag)); - String scaleYStr = unMangle(param.getAttributeValue(XMLTags.CSGScaleYTag)); - String scaleZStr = unMangle(param.getAttributeValue(XMLTags.CSGScaleZTag)); - Vect3d scaleAxis = new Vect3d(Double.parseDouble(scaleXStr), Double.parseDouble(scaleYStr), Double.parseDouble(scaleZStr)); - CSGScale csgScale = new CSGScale(name, scaleAxis); - - //Retrieve CSGNode - CSGScale element should have one child - Object[] elements = param.getChildren().toArray(); - if(elements.length > 1){ - throw new XmlParseException("CSGScale element cannot have more than one child element"); - } - CSGNode csgChildNode = getCSGNode((Element) elements[0]); - - csgScale.setChild(csgChildNode); - return csgScale; - } - - private CSGTranslation getCSGTranslation(Element param) throws XmlParseException{ - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String translateXStr = unMangle(param.getAttributeValue(XMLTags.CSGTranslationXTag)); - String translateYStr = unMangle(param.getAttributeValue(XMLTags.CSGTranslationYTag)); - String translateZStr = unMangle(param.getAttributeValue(XMLTags.CSGTranslationZTag)); - Vect3d translateAxis = new Vect3d(Double.parseDouble(translateXStr), Double.parseDouble(translateYStr), Double.parseDouble(translateZStr)); - CSGTranslation csgTranslation = new CSGTranslation(name, translateAxis); - - //Retrieve CSGNode - CSGScale element should have one child - Object[] elements = param.getChildren().toArray(); - if(elements.length > 1){ - throw new XmlParseException("CSGScale element cannot have more than one child element"); - } - CSGNode csgChildNode = getCSGNode((Element) elements[0]); - - csgTranslation.setChild(csgChildNode); - return csgTranslation; - } - - - private SurfaceClass getSurfaceClass(Element param, Geometry geom) throws XmlParseException{ - - Set surfaceClassSubVolumeSet = new HashSet(); - KeyValue surfaceClassKey = null; - String surfaceClassName = null; - - surfaceClassName = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String surfaceClassKeyStr = param.getAttributeValue(XMLTags.KeyValueAttrTag); - surfaceClassKey = (surfaceClassKeyStr == null ? null : new KeyValue(surfaceClassKeyStr)); - String subVol1Ref = param.getAttributeValue(XMLTags.SubVolume1RefAttrTag); - String subVol2Ref = param.getAttributeValue(XMLTags.SubVolume2RefAttrTag); - if(subVol1Ref != null){ - SubVolume subVolume = geom.getGeometrySpec().getSubVolume(subVol1Ref); - if(subVolume == null){ - throw new XmlParseException("SurfaceClass missing subvolume '" + subVol1Ref + "'"); - } - surfaceClassSubVolumeSet.add(subVolume); - } - if(subVol2Ref != null){ - SubVolume subVolume = geom.getGeometrySpec().getSubVolume(subVol2Ref); - if(subVolume == null){ - throw new XmlParseException("SurfaceClass missing subvolume '" + subVol2Ref + "'"); - } - surfaceClassSubVolumeSet.add(subVolume); - } - - return new SurfaceClass(surfaceClassSubVolumeSet, surfaceClassKey, surfaceClassName); - } - - /** - * This method returns a TimeBounds object from a XML Element. - * Creation date: (5/22/2001 11:41:04 AM) - * - * @param param Element - * @return cbit.vcell.solver.TimeBounds - */ - private TimeBounds getTimeBounds(Element param){ - //get Attributes - double start = Double.parseDouble(param.getAttributeValue(XMLTags.StartTimeAttrTag)); - double end = Double.parseDouble(param.getAttributeValue(XMLTags.EndTimeAttrTag)); - - //*** create new TimeBounds object **** - TimeBounds timeBounds = new TimeBounds(start, end); - - return timeBounds; - } - - - /** - * This method returns a TimeStep object from a XML Element. - * Creation date: (5/22/2001 11:45:33 AM) - * - * @param param Element - * @return cbit.vcell.solver.TimeStep - */ - private TimeStep getTimeStep(Element param){ - //get attributes - double min = Double.parseDouble(param.getAttributeValue(XMLTags.MinTimeAttrTag)); - double def = Double.parseDouble(param.getAttributeValue(XMLTags.DefaultTimeAttrTag)); - double max = Double.parseDouble(param.getAttributeValue(XMLTags.MaxTimeAttrTag)); - - //**** create new TimeStep object **** - TimeStep timeStep = new TimeStep(min, def, max); - - return timeStep; - } - - - /** - * This methos returns a User object from a XML Element. - * Creation date: (3/16/2001 3:52:30 PM) - * - * @param param Element - * @return cbit.vcell.server.User - */ - private User getUser(Element param){ - User newuser = - new User( - param.getAttributeValue(XMLTags.NameAttrTag), - new KeyValue(param.getAttributeValue(XMLTags.IdentifierAttrTag))); - - return newuser; - } - - private void addResevedSymbols(VariableHash varHash, Model model) throws XmlParseException{ - - // - // add constants that may be used in kinetics. - // - try { - // add reserved symbols - varHash.addVariable(new Constant(model.getPI_CONSTANT().getName(), new Expression(0.0))); - varHash.addVariable(new Constant(model.getFARADAY_CONSTANT().getName(), new Expression(0.0))); - varHash.addVariable(new Constant(model.getFARADAY_CONSTANT_NMOLE().getName(), new Expression(0.0))); - varHash.addVariable(new Constant(model.getGAS_CONSTANT().getName(), new Expression(0.0))); - varHash.addVariable(new Constant(model.getKMILLIVOLTS().getName(), new Expression(0.0))); - varHash.addVariable(new Constant(model.getN_PMOLE().getName(), new Expression(0.0))); - varHash.addVariable(new Constant(model.getKMOLE().getName(), new Expression(0.0))); - varHash.addVariable(new Constant(model.getTEMPERATURE().getName(), new Expression(0.0))); - varHash.addVariable(new Constant(model.getK_GHK().getName(), new Expression(0.0))); - varHash.addVariable(new Constant(model.getTIME().getName(), new Expression(0.0))); - } catch(MathException e){ - throw new XmlParseException("error reordering parameters according to dependencies", e); - } - } - - /** - * This method return a VarIniCondition object from a XML element. - * Creation date: (7/24/2006 5:26:05 PM) - * - * @param param Element - * @return cbit.vcell.math.VarIniCondition - * @throws cbit.vcell.xml.XmlParseException The exception description. - */ - private VarIniCondition getVarIniCount(Element param, MathDescription md) throws XmlParseException, MathException, ExpressionException{ - //retrieve values - Expression exp = unMangleExpression(param.getText()); - - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - Variable var = md.getVariable(name); - if(var == null){ - throw new MathFormatException("variable " + name + " not defined"); - } - if(!(var instanceof StochVolVariable)){ - throw new MathFormatException("variable " + name + " not a Stochastic Volume Variable"); - } - try { - VarIniCondition varIni = new VarIniCount(var, exp); - return varIni; - } catch(Exception e){ - lg.error(e.getMessage(), e); - } - - return null; - } - - - private BoundaryConditionSpec getBoundaryConditionSpec(Element param) throws XmlParseException, MathException{ - //retrieve values - String boundarySubdomainName = unMangle(param.getAttributeValue(XMLTags.BoundarySubdomainNameTag)); - String boundarySubdomainType = unMangle(param.getAttributeValue(XMLTags.BoundaryTypeTag)); - - if(boundarySubdomainName != null && boundarySubdomainType != null){ - BoundaryConditionSpec bcs = new BoundaryConditionSpec(boundarySubdomainName, new BoundaryConditionType(boundarySubdomainType)); - return bcs; - } - return null; - } - - - private BoundaryConditionValue getBoundaryConditionValue(Element param, PdeEquation pde) throws XmlParseException, MathException{ - //retrieve values - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - Expression valueExpr = unMangleExpression(param.getAttributeValue(XMLTags.BoundaryValueExpressionTag)); - - if(name != null && valueExpr != null){ - BoundaryConditionValue bcv = pde.new BoundaryConditionValue(name, valueExpr); - return bcv; - } - return null; - } - - private VarIniCondition getVarIniPoissonExpectedCount(Element param, MathDescription md) throws XmlParseException, MathException, ExpressionException{ - //retrieve values - Expression exp = unMangleExpression(param.getText()); - - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - Variable var = md.getVariable(name); - if(var == null){ - throw new MathFormatException("variable " + name + " not defined"); - } - if(!(var instanceof StochVolVariable)){ - throw new MathFormatException("variable " + name + " not a Stochastic Volume Variable"); - } - try { - VarIniCondition varIni = new VarIniPoissonExpectedCount(var, exp); - return varIni; - } catch(Exception e){ - lg.error(e.getMessage(), e); - } - - return null; - } - - - /** - * This method returns a VCIMage object from a XML representation. - * Creation date: (3/16/2001 3:41:24 PM) - * - * @param param Element - * @return VCImage - */ - VCImage getVCImage(Element param, Extent extent) throws XmlParseException{ - //try to get metadata(version) - Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace)); - - //get the attributes - Element tempelement = param.getChild(XMLTags.ImageDataTag, vcNamespace); - int aNumX = Integer.parseInt(tempelement.getAttributeValue(XMLTags.XAttrTag)); - int aNumY = Integer.parseInt(tempelement.getAttributeValue(XMLTags.YAttrTag)); - int aNumZ = Integer.parseInt(tempelement.getAttributeValue(XMLTags.ZAttrTag)); - - //getpixels - String temp = tempelement.getText(); - byte[] data = Hex.toBytes(temp); //decode - - //create the VCImage object - VCImageCompressed newimage = null; - try { - newimage = new VCImageCompressed(version, data, extent, aNumX, aNumY, aNumZ); - } catch(ImageException e){ - throw new XmlParseException("An imageException occurred while trying to create a VCImage!", e); - } - //set attributes - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - - try { - newimage.setName(name); - //String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag); - //if (annotation!=null) { - //newimage.setDescription(unMangle(annotation)); - //} - - //read the annotation - String annotation = param.getChildText(XMLTags.AnnotationTag, vcNamespace); - if(annotation != null && annotation.length() > 0){ - newimage.setDescription(unMangle(annotation)); - } - - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException(e); - } - - //get PixelClasses - List pixelClassList = param.getChildren(XMLTags.PixelClassTag, vcNamespace); - - if(pixelClassList.size() != 0){ - VCPixelClass[] pixelClassArray = new VCPixelClass[pixelClassList.size()]; - int pixelClassCounter = 0; - for(Element pcElement : pixelClassList){ - pixelClassArray[pixelClassCounter] = getPixelClass(pcElement); - pixelClassCounter++; - } - try { - newimage.setPixelClasses(pixelClassArray); - } catch(java.beans.PropertyVetoException e){ - throw new XmlParseException(e); - } - } else {//Invalid format - System.out.println("Format Error! No references found inside !"); - System.out.println("Valid format for images is:"); - System.out.println(""); - System.out.println(" "); - System.out.println(" ......Image content..."); - System.out.println(" "); - System.out.println(" "); - System.out.println(" ..."); - System.out.println(" "); - System.out.println(" "); - System.out.println(""); - throw new XmlParseException("Invalid VCML format error!\nNo references found inside !"); - } - - return newimage; - } - - - private Version getVersion(Element xmlVersion) throws XmlParseException{ - if(xmlVersion == null){ - return null; - } - - //determine if it should be processed using the 'fromVersionable' - if(xmlVersion.getAttributeValue(XMLTags.FromVersionableTag) == null || Boolean.valueOf(xmlVersion.getAttributeValue(XMLTags.FromVersionableTag)).booleanValue() || this.readKeysFlag == false){ - //this came from a versionable object, so skip! Or it should not explicitly import the information inside the Version - return null; - } - - //Read all the attributes - //*name - String name = unMangle(xmlVersion.getAttributeValue(XMLTags.NameAttrTag)); - //*key - String temp = xmlVersion.getAttributeValue(XMLTags.KeyValueAttrTag); - KeyValue key = new KeyValue(temp); - //*owner - Element tempElement = xmlVersion.getChild(XMLTags.OwnerTag, vcNamespace); - User owner = new User(unMangle(tempElement.getAttributeValue(XMLTags.NameAttrTag)), new KeyValue(tempElement.getAttributeValue(XMLTags.IdentifierAttrTag))); - //*access - GroupAccess groupAccess = getGroupAccess(xmlVersion.getChild(XMLTags.GroupAccessTag, vcNamespace)); - //*Branchpointref - temp = xmlVersion.getAttributeValue(XMLTags.BranchPointRefTag); - KeyValue branchpointref = null; - - if(temp != null){ - branchpointref = new KeyValue(temp); - } - - //*BranchID - java.math.BigDecimal branchId = new java.math.BigDecimal(xmlVersion.getAttributeValue(XMLTags.BranchIdAttrTag)); - //*Flag - temp = xmlVersion.getAttributeValue(XMLTags.FlagAttrTag); - VersionFlag flag = VersionFlag.fromInt(Integer.parseInt(temp)); - //*Date - java.util.Date date = null; - temp = xmlVersion.getAttributeValue(XMLTags.DateAttrTag); - - if(temp != null){ - try { - SimpleDateFormat simpleDateFormat = new SimpleDateFormat(BeanUtils.vcDateFormat, Locale.US); - date = simpleDateFormat.parse(temp); - } catch(java.text.ParseException e){ - throw new XmlParseException("Invalid date:" + temp, e); - } - } - - //*Annotation - String annotation = null; - String annotationText = xmlVersion.getChildText(XMLTags.AnnotationTag, vcNamespace); - if(annotationText != null && annotationText.length() > 0){ - annotation = unMangle(annotationText); - } - - //Create and return the version object - return new Version(key, name, owner, groupAccess, branchpointref, branchId, date, flag, annotation); - } - - - /** - * This method returns a VolumeRegionEquation from a XML Element. - * Creation date: (5/17/2001 3:52:40 PM) - * - * @param param Element - * @return cbit.vcell.math.VolumeRegionEquation - * @throws cbit.vcell.xml.XmlParseException The exception description. - */ - private VolumeRegionEquation getVolumeRegionEquation(Element param, MathDescription mathDesc) throws XmlParseException{ - //get attributes - String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - - //try a VolumeRegionVariable - VolumeRegionVariable varref = (VolumeRegionVariable) mathDesc.getVariable(varname); - if(varref == null){ - throw new XmlParseException("The reference to the VolumeRegion variable " + varname + " could not be resolved!"); - } - - //get Initial condition - String temp = param.getChildText(XMLTags.InitialTag, vcNamespace); - Expression exp = unMangleExpression(temp); - // ** Create the Equation ** - VolumeRegionEquation volRegEq = new VolumeRegionEquation(varref, exp); - - //set the Uniform Rate - temp = param.getChildText(XMLTags.UniformRateTag, vcNamespace); - exp = unMangleExpression(temp); - volRegEq.setUniformRateExpression(exp); - - //Set the Volume Rate - temp = param.getChildText(XMLTags.VolumeRateTag, vcNamespace); - exp = unMangleExpression(temp); - volRegEq.setVolumeRateExpression(exp); - - //get ExactSolution (if any) -/* temp = param.getChildText(XMLTags.ExactTag); - if (temp !=null) { - try { - Expression expression = new Expression( unMangle( temp) ); - odeEquation.setExactSolution( expression); - } catch (ExpressionException e) { - lg.error(e); - throw new XmlParseException("An ExpressionException was fired when creating the expression: "+ unMangle(temp)+" : "+e.getMessage()); - } - } - //get ConstructedSolution (if any) - temp = param.getChildText(XMLTags.ConstructedTag); - if (temp != null) { - try { - Expression expression = new Expression(unMangle(temp)); - odeEquation.setConstructedSolution( expression ); - } catch (ExpressionException e) { - lg.error(e); - throw new XmlParseException("An ExpressionException was fired when creating the expression: "+ unMangle(temp) +" : "+e.getMessage()); - } - }*/ - - return volRegEq; - } - - - /** - * This method returns a VolumeRegionVariable object from a XML Element. - * Creation date: (5/16/2001 2:56:34 PM) - * - * @param param Element - * @return cbit.vcell.math.VolumeRegionVariable - */ - private VolumeRegionVariable getVolumeRegionVariable(Element param){ - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); - Domain domain = null; - if(domainStr != null){ - domain = new Domain(domainStr); - } - //-- create new VolumeRegionVariable object - VolumeRegionVariable volRegVariable = new VolumeRegionVariable(name, domain); - transcribeComments(param, volRegVariable); - - return volRegVariable; - } - - - /** - * This method returns a VolVariable object from a XML Element. - * Creation date: (5/16/2001 2:56:34 PM) - * - * @param param Element - * @return cbit.vcell.math.VolVariable - */ - private VolVariable getVolVariable(Element param){ - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); - Domain domain = null; - if(domainStr != null){ - domain = new Domain(domainStr); - } - - //-- create new VolVariable object - VolVariable volVariable = new VolVariable(name, domain); - transcribeComments(param, volVariable); - - return volVariable; - } - - private VolumeParticleObservable getVolumeParticleObservable(Element param, VariableHash varHash) throws XmlParseException{ - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); - Domain domain = null; - if(domainStr != null){ - domain = new Domain(domainStr); - } - String molecularTypeString = unMangle(param.getAttributeValue(XMLTags.ParticleMolecularTypePatternTag)); - ObservableType observableType = ObservableType.fromString(molecularTypeString); - VolumeParticleObservable var = new VolumeParticleObservable(name, domain, observableType); - String sequenceAttr = param.getAttributeValue(XMLTags.ParticleObservableSequenceTypeAttrTag); - - if(sequenceAttr != null){ - Sequence sequence = Sequence.fromString(sequenceAttr); - String sequenceLength = param.getAttributeValue(XMLTags.ParticleObservableSequenceLengthAttrTag); - var.setSequence(sequence); - if(sequence != Sequence.Multimolecular){ - var.setQuantity(Integer.parseInt(sequenceLength)); - } - } else { - var.setSequence(Sequence.Multimolecular); - } - - Element volumeParticleSpeciesPatternsElement = param.getChild(XMLTags.VolumeParticleSpeciesPatternsTag, vcNamespace); - if(volumeParticleSpeciesPatternsElement != null){ - List volumeParticleSpeciesPatternList = volumeParticleSpeciesPatternsElement.getChildren(XMLTags.VolumeParticleSpeciesPatternTag, vcNamespace); - for(Element volumeParticleSpeciesPattern : volumeParticleSpeciesPatternList){ - String volumeParticleSpeciesPatternName = unMangle(volumeParticleSpeciesPattern.getAttributeValue(XMLTags.NameAttrTag)); - - Variable v = varHash.getVariable(volumeParticleSpeciesPatternName); - if(v == null){ - throw new XmlParseException("failed to find VolumeParticleSpeciesPattern named " + volumeParticleSpeciesPatternName); - } - if(v instanceof ParticleSpeciesPattern){ - var.addParticleSpeciesPattern((ParticleSpeciesPattern) v); - } else { - throw new XmlParseException("Variable " + volumeParticleSpeciesPatternName + " is not a ParticleSpeciesPattern"); - } - } - } - return var; - } - - private ParticleMolecularComponent getParticleMolecularComponent(String pmtName, Element param, boolean isLangevin) throws XmlParseException { - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - ParticleMolecularComponent var; - if(isLangevin){ - var = new LangevinParticleMolecularComponent(pmtName + "_" + name, name); - if(param.getAttributeValue(XMLTags.ParticleMolecularComponentRadiusTag) != null){ - Expression radius; - try { - radius = new Expression(param.getAttributeValue(XMLTags.ParticleMolecularComponentRadiusTag)); - } catch(ExpressionException e){ - throw new XmlParseException("unparseable " + XMLTags.ParticleMolecularComponentRadiusTag, e); - } - ((LangevinParticleMolecularComponent) var).setRadius(radius); - } - if(param.getAttributeValue(XMLTags.ParticleMolecularComponentDiffusionRateTag) != null){ - Expression diff; - try { - diff = new Expression(param.getAttributeValue(XMLTags.ParticleMolecularComponentDiffusionRateTag)); - } catch(ExpressionException e){ - throw new XmlParseException("unparseable " + XMLTags.ParticleMolecularComponentDiffusionRateTag, e); - } - ((LangevinParticleMolecularComponent) var).setDiffusionRate(diff); - } - if(param.getAttributeValue(XMLTags.ParticleMolecularComponentLocationTag) != null){ - String location = param.getAttributeValue(XMLTags.ParticleMolecularComponentLocationTag); - ((LangevinParticleMolecularComponent) var).setLocation(location); - } - double x = 0; - double y = 0; - double z = 0; - if(param.getAttributeValue(XMLTags.ParticleMolecularComponentCoordXAttrTag) != null){ - x = Double.parseDouble(param.getAttributeValue(XMLTags.ParticleMolecularComponentCoordXAttrTag)); - } - if(param.getAttributeValue(XMLTags.ParticleMolecularComponentCoordYAttrTag) != null){ - y = Double.parseDouble(param.getAttributeValue(XMLTags.ParticleMolecularComponentCoordYAttrTag)); - } - if(param.getAttributeValue(XMLTags.ParticleMolecularComponentCoordZAttrTag) != null){ - z = Double.parseDouble(param.getAttributeValue(XMLTags.ParticleMolecularComponentCoordZAttrTag)); - } - ((LangevinParticleMolecularComponent) var).setCoordinate(new Coordinate(x, y, z)); - if(param.getAttributeValue(XMLTags.ParticleMolecularComponentColorTag) != null){ - NamedColor color = Colors.getColorByName(param.getAttributeValue(XMLTags.ParticleMolecularComponentColorTag)); - ((LangevinParticleMolecularComponent) var).setColor(color); - } - } else { - var = new ParticleMolecularComponent(pmtName + "_" + name, name); - } - List componentStateList = param.getChildren(XMLTags.ParticleMolecularTypeAllowableStateTag, vcNamespace); - for(Element componentState : componentStateList){ - String componentStateName = unMangle(componentState.getAttributeValue(XMLTags.NameAttrTag)); - if(!componentStateName.equals("*")){ - ParticleComponentStateDefinition p = var.getComponentStateDefinition(componentStateName); - if(p == null){ - p = new ParticleComponentStateDefinition(componentStateName); - var.addComponentStateDefinition(p); - } - } - } - return var; - } - - private ParticleMolecularType getParticleMolecularType(Element param, boolean isLangevin) throws XmlParseException { - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - ParticleMolecularType var; - if(isLangevin){ - LangevinParticleMolecularType langevinVar = new LangevinParticleMolecularType(name); - if(param.getAttribute(XMLTags.ParticleMolecularTypeIs2DTag) != null){ - langevinVar.setIs2D(Boolean.parseBoolean(param.getAttributeValue(XMLTags.ParticleMolecularTypeIs2DTag))); - } - var = langevinVar; - } else { - var = new ParticleMolecularType(name); - } - List molecularComponentList = param.getChildren(XMLTags.ParticleMolecularComponentPatternTag, vcNamespace); - for(Element molecularComponent : molecularComponentList){ - ParticleMolecularComponent p = getParticleMolecularComponent(name, molecularComponent, isLangevin); - var.addMolecularComponent(p); - } - - if(var instanceof LangevinParticleMolecularType){ - List molecularTypeLinkList = param.getChildren(XMLTags.ParticleMolecularTypeLinksTag, vcNamespace); - Set> internalLinkSet = new LinkedHashSet<>(); - for(Element molecularTypeLink : molecularTypeLinkList){ - Pair internalLink = getInternalLink((LangevinParticleMolecularType) var, molecularTypeLink); - internalLinkSet.add(internalLink); - } - ((LangevinParticleMolecularType) var).setInternalLinkSpec(internalLinkSet); - } - - List anchorList = param.getChildren(XMLTags.ParticleMolecularTypeAnchorTag, vcNamespace); - for(Element anchorElement : anchorList){ - String anchor = unMangle(anchorElement.getAttributeValue(XMLTags.NameAttrTag)); - var.addAnchor(anchor); - } - return var; - } - - private Pair getInternalLink(LangevinParticleMolecularType var, Element param){ - String oneName = unMangle(param.getAttributeValue(XMLTags.LangevinParticleMolecularComponentOneTag)); - String twoName = unMangle(param.getAttributeValue(XMLTags.LangevinParticleMolecularComponentTwoTag)); - // by this time the molecullar components are the correct class LangevinParticleMolecularComponent and won't throw cast exception - LangevinParticleMolecularComponent one = (LangevinParticleMolecularComponent) var.getMolecularComponent(oneName); - LangevinParticleMolecularComponent two = (LangevinParticleMolecularComponent) var.getMolecularComponent(twoName); - Pair pair = new Pair<>(one, two); - return pair; - } - - - private ParticleMolecularComponentPattern getParticleMolecularComponentPattern(Element param, ParticleMolecularType particleMolecularType) throws XmlParseException{ - String molecularComponentName = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - ParticleMolecularComponent particleMolecularComponent = particleMolecularType.getMolecularComponent(molecularComponentName); - if(particleMolecularComponent != null){ - ParticleMolecularComponentPattern var = new ParticleMolecularComponentPattern(particleMolecularComponent); - ParticleComponentStatePattern pcsp = null; - String componentStateName = unMangle(param.getAttributeValue(XMLTags.StateAttrTag)); - if(componentStateName.equals("*")){ - pcsp = new ParticleComponentStatePattern(); - } else { - //ParticleComponentStateDefinition pcsd = new ParticleComponentStateDefinition(componentStateName); // bad?? - ParticleComponentStateDefinition pcsd = particleMolecularComponent.getComponentStateDefinition(componentStateName); - if(pcsd == null){ - throw new XmlParseException("failed to find ParticleComponentStateDefinition named " + molecularComponentName); - } - pcsp = new ParticleComponentStatePattern(pcsd); - } - var.setComponentStatePattern(pcsp); - String bondString = unMangle(param.getAttributeValue(XMLTags.BondAttrTag)); - - ParticleBondType bondType = ParticleBondType.fromSymbol(bondString); - if(bondType == ParticleBondType.Specified){ - int bondId = Integer.parseInt(bondString); - var.setBondId(bondId); - } - var.setBondType(bondType); - return var; - } else { - throw new XmlParseException("failed to find ParticleMolecularComponent named " + molecularComponentName); - } - } - - private ParticleMolecularTypePattern getParticleMolecularTypePattern(Element param, MathDescription mathDescription) throws XmlParseException{ - String molecularTypeName = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String matchLabel = unMangle(param.getAttributeValue(XMLTags.ParticleMolecularTypePatternMatchLabelAttrTag)); - ParticleMolecularType particleMolecularType = mathDescription.getParticleMolecularType(molecularTypeName); - if(particleMolecularType != null){ - ParticleMolecularTypePattern var = new ParticleMolecularTypePattern(particleMolecularType); - if(matchLabel != null){ - var.setMatchLabel(matchLabel); - } - List componentPatternList = param.getChildren(XMLTags.ParticleMolecularComponentPatternTag, vcNamespace); - for(Element componentPattern : componentPatternList){ - ParticleMolecularComponentPattern p = getParticleMolecularComponentPattern(componentPattern, particleMolecularType); - var.addMolecularComponentPattern(p); - } - return var; - } else { - throw new XmlParseException("failed to find ParticleMolecularType named " + molecularTypeName); - } - } - - private VolumeParticleSpeciesPattern getVolumeParticleSpeciesPattern(Element param, MathDescription mathdes) throws XmlParseException{ - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); - Domain domain = null; - if(domainStr != null){ - domain = new Domain(domainStr); - } - String location = unMangle(param.getAttributeValue(XMLTags.LocationAttrTag)); - VolumeParticleSpeciesPattern var = new VolumeParticleSpeciesPattern(name, domain, location); - - List molecularTypeList = param.getChildren(XMLTags.ParticleMolecularTypePatternTag, vcNamespace); - for(Element molecularType : molecularTypeList){ - ParticleMolecularTypePattern p = getParticleMolecularTypePattern(molecularType, mathdes); - var.addMolecularTypePattern(p); - } - -// Element meshRefineElement = param.getChild(XMLTags.ParticleMolecularTypePatternTag, vcNamespace); -// if (meshRefineElement != null) { -// List levelElementList = meshRefineElement.getChildren(XMLTags.RefinementLevelTag, vcNamespace); -// for (Element levelElement : levelElementList) { - return var; - } - - private VolumeParticleVariable getVolumeParticalVariable(Element param){ - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); - Domain domain = null; - if(domainStr != null){ - domain = new Domain(domainStr); - } - - //-- create new VolVariable object - VolumeParticleVariable var = new VolumeParticleVariable(name, domain); - transcribeComments(param, var); - - return var; - } - - private MembraneParticleVariable getMembraneParticalVariable(Element param){ - String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); - String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); - Domain domain = null; - if(domainStr != null){ - domain = new Domain(domainStr); - } - - //-- create new VolVariable object - MembraneParticleVariable var = new MembraneParticleVariable(name, domain); - transcribeComments(param, var); - return var; - } - - private interface Convert { - T parse(String in); - } - - private Convert convertInt = new Convert() { - public Integer parse(String in){ - return Integer.parseInt(in); - } - }; - - private Convert convertDouble = new Convert() { - public Double parse(String in){ - return Double.parseDouble(in); - } - }; - - private Convert convertBoolean = new Convert() { - public Boolean parse(String in){ - return Boolean.parseBoolean(in); - } - }; - - /** - * parse parent for specified element. Return defaultValue if it's not present - * - * @param parent - * @param tagName - * @param defaultValue - * @param c converter to change string into T - * @return parsed value, if present, default otherwise - */ - private T parseWithDefault(Element parent, String tagName, T defaultValue, Convert c){ - Element child = parent.getChild(tagName, vcNamespace); - if(child != null){ - return c.parse(child.getText()); - } - return defaultValue; - } - - /** - * read integer XML - * - * @see #parseWithDefault(Element, String, Object, Convert) - */ - private int parseIntWithDefault(Element parent, String tagName, int defaultValue){ - return parseWithDefault(parent, tagName, defaultValue, convertInt); - } - - /** - * read double XML - * - * @see #parseWithDefault(Element, String, Object, Convert) - */ - private double parseDoubleWithDefault(Element parent, String tagName, double defaultValue){ - return parseWithDefault(parent, tagName, defaultValue, convertDouble); - } - - /** - * read boolean XML - * - * @see #parseWithDefault(Element, String, Object, Convert) - */ - private boolean parseBooleanWithDefault(Element parent, String tagName, boolean defaultValue){ - return parseWithDefault(parent, tagName, defaultValue, convertBoolean); - } - - private ChomboSolverSpec getChomboSolverSpec(SolverTaskDescription solverTaskDesc, Element element, int dimension) throws XmlParseException{ - int maxBoxSize = parseIntWithDefault(element, XMLTags.MaxBoxSizeTag, ChomboSolverSpec.getDefaultMaxBoxSize(dimension)); - double fillRatio = parseDoubleWithDefault(element, XMLTags.FillRatioTag, ChomboSolverSpec.getDefaultFillRatio()); - boolean bSaveVCellOutput = parseBooleanWithDefault(element, XMLTags.SaveVCellOutput, true); - boolean bSaveChomboOutput = parseBooleanWithDefault(element, XMLTags.SaveChomboOutput, false); - Element childElement = element.getChild(XMLTags.RefineRatios, vcNamespace); - List refineRatioList = null; - if(childElement != null){ - String text = childElement.getText(); - if(text != null && !text.isEmpty()){ - StringTokenizer st = new StringTokenizer(text, ","); - if(st.hasMoreTokens()){ - refineRatioList = new ArrayList(); - while (st.hasMoreElements()) { - String token = st.nextToken(); - if(token != null){ - int n = Integer.parseInt(token); - refineRatioList.add(n); - } - } - } - } - } - Integer viewLevel = null; - try { - ChomboSolverSpec css = new ChomboSolverSpec(maxBoxSize, fillRatio, viewLevel, bSaveVCellOutput, bSaveChomboOutput, refineRatioList); - double smallVolfracThreshold = parseDoubleWithDefault(element, XMLTags.SmallVolfracThreshold, 0); - int blockFactor = parseIntWithDefault(element, XMLTags.BlockFactorTag, ChomboSolverSpec.DEFAULT_BLOCK_FACTOR); - boolean bActivateFeatureUnderDevelopment = parseBooleanWithDefault(element, XMLTags.ActivateFeatureUnderDevelopment, false); - css.setSmallVolfracThreshold(smallVolfracThreshold); - css.setActivateFeatureUnderDevelopment(bActivateFeatureUnderDevelopment); - css.setBlockFactor(blockFactor); - - int tagsGrow = parseIntWithDefault(element, XMLTags.TagsGrowTag, ChomboSolverSpec.defaultTagsGrow); - css.setTagsGrow(tagsGrow); - - Element timeBoundsElement = element.getChild(XMLTags.TimeBoundTag, vcNamespace); - List timeIntervalElementList = null; - boolean noTimeBounds = false; - if(timeBoundsElement == null){ - noTimeBounds = true; - } else { - timeIntervalElementList = timeBoundsElement.getChildren(XMLTags.TimeIntervalTag, vcNamespace); - if(timeIntervalElementList.size() == 0){ - noTimeBounds = true; - } - } - - if(noTimeBounds){ - // old format - double startTime = 0; - double endTime = solverTaskDesc.getTimeBounds().getEndingTime(); - double timeStep = solverTaskDesc.getTimeStep().getDefaultTimeStep(); - double outputTimeStep = ((UniformOutputTimeSpec) solverTaskDesc.getOutputTimeSpec()).getOutputTimeStep(); - try { - TimeInterval ti = new TimeInterval(startTime, endTime, timeStep, outputTimeStep); - css.addTimeInterval(ti); - } catch(IllegalArgumentException ex){ - css.addTimeInterval(TimeInterval.getDefaultTimeInterval()); - } - } else { - for(Element e : timeIntervalElementList){ - String s = e.getAttributeValue(XMLTags.StartTimeAttrTag); - double startTime = Double.valueOf(s); - - s = e.getAttributeValue(XMLTags.EndTimeAttrTag); - double endTime = Double.valueOf(s); - - s = e.getAttributeValue(XMLTags.TimeStepAttrTag); - double timeStep = Double.valueOf(s); - - s = e.getAttributeValue(XMLTags.OutputTimeStepAttrTag); - double outputTimeStep = Double.valueOf(s); - TimeInterval ti = new TimeInterval(startTime, endTime, timeStep, outputTimeStep); - css.addTimeInterval(ti); - } - } - - Element meshRefineElement = element.getChild(XMLTags.MeshRefinementTag, vcNamespace); - if(meshRefineElement != null){ - if(meshRefineElement.getChildren().size() != 0){ - // in old model, if there is no refinement, set view level to finest - // only set viewLevel when meshRefinement has children - Element viewLevelChild = element.getChild(XMLTags.ViewLevelTag, vcNamespace); - if(viewLevelChild != null){ - viewLevel = parseIntWithDefault(element, XMLTags.ViewLevelTag, 0); - css.setViewLevel(viewLevel); - } - } - List levelElementList = meshRefineElement.getChildren(XMLTags.RefinementRoiTag, vcNamespace); - for(Element levelElement : levelElementList){ - String levelStr = levelElement.getAttributeValue(XMLTags.RefineRoiLevelAttrTag); - int level = 1; - if(levelStr != null){ - level = Integer.parseInt(levelStr); - } - String type = levelElement.getAttributeValue(XMLTags.RefinementRoiTypeAttrTag); - RoiType roiType = RoiType.Membrane; - if(type != null){ - try { - roiType = RoiType.valueOf(type); - } catch(Exception ex){ - // ignore - } - } - - Element expElement = levelElement.getChild(XMLTags.ROIExpressionTag, vcNamespace); - String roiExp = null; - if(expElement != null){ - roiExp = expElement.getText(); - RefinementRoi roi = new RefinementRoi(roiType, level, roiExp); - css.addRefinementRoi(roi); - } - } - } - return css; - } catch(ExpressionException e){ - throw new XmlParseException(e); - } - } - - private MovingBoundarySolverOptions getMovingBoundarySolverOptions(SolverTaskDescription solverTaskDesc, - Element mbElement){ - double frontToNodeRatio = parseDoubleWithDefault(mbElement, XMLTags.FrontToNodeRatioTag, - MovingBoundarySolverOptions.DEFAULT_FRONT_TO_NODE_RATIO); - int redistributionFrequency = parseIntWithDefault(mbElement, XMLTags.RedistributionFrequencyTag, - MovingBoundarySolverOptions.DEFAULT_REDISTRIBUTION_FREQUENCY); - - RedistributionMode redistributionMode = RedistributionMode.FULL_REDIST; - Element child = mbElement.getChild(XMLTags.RedistributionModeTag, vcNamespace); - if(child != null){ - String text = child.getText(); - redistributionMode = RedistributionMode.valueOf(text); - } - RedistributionVersion redistributionVersion = RedistributionVersion.EQUI_BOND_REDISTRIBUTE; - child = mbElement.getChild(XMLTags.RedistributionVersionTag, vcNamespace); - if(child != null){ - String text = child.getText(); - redistributionVersion = RedistributionVersion.valueOf(text); - } - ExtrapolationMethod extrapolationMethod = ExtrapolationMethod.NEAREST_NEIGHBOR; - child = mbElement.getChild(XMLTags.ExtrapolationMethodTag, vcNamespace); - if(child != null){ - String text = child.getText(); - extrapolationMethod = ExtrapolationMethod.valueOf(text); - } - MovingBoundarySolverOptions mb = new MovingBoundarySolverOptions(frontToNodeRatio, redistributionMode, redistributionVersion, redistributionFrequency, extrapolationMethod); - return mb; - } -} +/* + * Copyright (C) 1999-2011 University of Connecticut Health Center + * + * Licensed under the MIT License (the "License"). + * You may not use this file except in compliance with the License. + * You may obtain a copy of the License at: + * + * http://www.opensource.org/licenses/mit-license.php + */ + +package cbit.vcell.xml; + +import java.beans.PropertyVetoException; +import java.math.BigInteger; +import java.text.SimpleDateFormat; +import java.util.*; +import java.util.function.Consumer; + +import cbit.vcell.mapping.*; +import cbit.vcell.model.*; +import cbit.vcell.solver.*; +import org.jdom2.Attribute; +import org.jdom2.DataConversionException; +import org.jdom2.Element; +import org.jdom2.Namespace; +import org.vcell.chombo.ChomboSolverSpec; +import org.vcell.chombo.RefinementRoi; +import org.vcell.chombo.RefinementRoi.RoiType; +import org.vcell.chombo.TimeInterval; +import org.vcell.model.rbm.*; +import org.vcell.model.rbm.MolecularComponentPattern.BondType; +import org.vcell.model.rbm.SpeciesPattern.Bond; +import org.vcell.pathway.PathwayModel; +import org.vcell.pathway.persistence.PathwayReaderBiopax3; +import org.vcell.pathway.persistence.RDFXMLContext; +import org.vcell.relationship.RelationshipModel; +import org.vcell.relationship.persistence.RelationshipReader; +import org.vcell.util.BeanUtils; +import org.vcell.util.Commented; +import org.vcell.util.Coordinate; +import org.vcell.util.Extent; +import org.vcell.util.GenericUtils; +import org.vcell.util.Hex; +import java.security.MessageDigest; +import cbit.vcell.resource.PropertyLoader; +import org.vcell.util.ISize; +import org.vcell.util.Origin; +import org.vcell.util.Pair; +import org.vcell.util.document.ExternalDataIdentifier; +import org.vcell.util.document.GroupAccess; +import org.vcell.util.document.GroupAccessAll; +import org.vcell.util.document.GroupAccessNone; +import org.vcell.util.document.GroupAccessSome; +import org.vcell.util.document.KeyValue; +import org.vcell.util.document.SimulationVersion; +import org.vcell.util.document.User; +import org.vcell.util.document.VCellSoftwareVersion; +import org.vcell.util.document.Version; +import org.vcell.util.document.VersionFlag; +import org.vcell.util.springsalad.Colors; +import org.vcell.util.springsalad.NamedColor; + +import cbit.image.ImageException; +import cbit.image.VCImage; +import cbit.image.VCImageCompressed; +import cbit.image.VCPixelClass; +import cbit.vcell.biomodel.BioModel; +import cbit.vcell.biomodel.meta.VCMetaData; +import cbit.vcell.biomodel.meta.xml.XMLMetaData; +import cbit.vcell.biomodel.meta.xml.XMLMetaDataReader; +import cbit.vcell.biomodel.meta.xml.rdf.XMLRDF; +import cbit.vcell.data.DataContext; +import cbit.vcell.data.DataSymbol; +import cbit.vcell.data.DataSymbol.DataSymbolType; +import cbit.vcell.data.FieldDataSymbol; +import cbit.vcell.dictionary.BoundCompound; +import cbit.vcell.dictionary.BoundEnzyme; +import cbit.vcell.dictionary.BoundProtein; +import cbit.vcell.dictionary.CompoundInfo; +import cbit.vcell.dictionary.EnzymeInfo; +import cbit.vcell.dictionary.EnzymeRef; +import cbit.vcell.dictionary.FormalCompound; +import cbit.vcell.dictionary.FormalEnzyme; +import cbit.vcell.dictionary.FormalProtein; +import cbit.vcell.dictionary.ProteinInfo; +import cbit.vcell.geometry.AnalyticSubVolume; +import cbit.vcell.geometry.CSGHomogeneousTransformation; +import cbit.vcell.geometry.CSGNode; +import cbit.vcell.geometry.CSGObject; +import cbit.vcell.geometry.CSGPrimitive; +import cbit.vcell.geometry.CSGPrimitive.PrimitiveType; +import cbit.vcell.geometry.CSGPseudoPrimitive; +import cbit.vcell.geometry.CSGRotation; +import cbit.vcell.geometry.CSGScale; +import cbit.vcell.geometry.CSGSetOperator; +import cbit.vcell.geometry.CSGSetOperator.OperatorType; +import cbit.vcell.geometry.CSGTranslation; +import cbit.vcell.geometry.CompartmentSubVolume; +import cbit.vcell.geometry.ControlPointCurve; +import cbit.vcell.geometry.Geometry; +import cbit.vcell.geometry.GeometryClass; +import cbit.vcell.geometry.GeometryException; +import cbit.vcell.geometry.GeometryThumbnailImageFactoryAWT; +import cbit.vcell.geometry.GeometryUnitSystem; +import cbit.vcell.geometry.ImageSubVolume; +import cbit.vcell.geometry.Line; +import cbit.vcell.geometry.SampledCurve; +import cbit.vcell.geometry.Spline; +import cbit.vcell.geometry.SubVolume; +import cbit.vcell.geometry.SurfaceClass; +import cbit.vcell.geometry.surface.GeometricRegion; +import cbit.vcell.geometry.surface.GeometrySurfaceDescription; +import cbit.vcell.geometry.surface.SurfaceGeometricRegion; +import cbit.vcell.geometry.surface.VolumeGeometricRegion; +import cbit.vcell.mapping.BioEvent.BioEventParameterType; +import cbit.vcell.mapping.BioEvent.TriggerType; +import cbit.vcell.mapping.MicroscopeMeasurement.ConvolutionKernel; +import cbit.vcell.mapping.MicroscopeMeasurement.GaussianConvolutionKernel; +import cbit.vcell.mapping.MicroscopeMeasurement.ProjectionZKernel; +import cbit.vcell.mapping.ParameterContext.LocalParameter; +import cbit.vcell.mapping.ParameterContext.ParameterRoleEnum; +import cbit.vcell.mapping.ReactionRuleSpec.ReactionRuleMappingType; +import cbit.vcell.mapping.ReactionRuleSpec.Subtype; +import cbit.vcell.mapping.ReactionRuleSpec.TransitionCondition; +import cbit.vcell.mapping.SimulationContext.Application; +import cbit.vcell.mapping.SimulationContext.SimulationContextParameter; +import cbit.vcell.mapping.spatial.PointObject; +import cbit.vcell.mapping.spatial.SpatialObject; +import cbit.vcell.mapping.spatial.SpatialObject.QuantityCategory; +import cbit.vcell.mapping.spatial.SurfaceRegionObject; +import cbit.vcell.mapping.spatial.VolumeRegionObject; +import cbit.vcell.mapping.spatial.processes.PointKinematics; +import cbit.vcell.mapping.spatial.processes.PointLocation; +import cbit.vcell.mapping.spatial.processes.SpatialProcess; +import cbit.vcell.mapping.spatial.processes.SpatialProcess.SpatialProcessParameterType; +import cbit.vcell.mapping.spatial.processes.SurfaceKinematics; +import cbit.vcell.mapping.spatial.processes.VolumeKinematics; +import cbit.vcell.math.Action; +import cbit.vcell.math.BoundaryConditionType; +import cbit.vcell.math.CompartmentSubDomain; +import cbit.vcell.math.ComputeCentroidComponentEquation; +import cbit.vcell.math.ComputeCentroidComponentEquation.CentroidComponent; +import cbit.vcell.math.ComputeMembraneMetricEquation; +import cbit.vcell.math.ComputeMembraneMetricEquation.MembraneMetricComponent; +import cbit.vcell.math.ComputeNormalComponentEquation; +import cbit.vcell.math.ComputeNormalComponentEquation.NormalComponent; +import cbit.vcell.math.Constant; +import cbit.vcell.math.ConvolutionDataGenerator; +import cbit.vcell.math.ConvolutionDataGenerator.ConvolutionDataGeneratorKernel; +import cbit.vcell.math.ConvolutionDataGenerator.GaussianConvolutionDataGeneratorKernel; +import cbit.vcell.math.Distribution; +import cbit.vcell.math.Event; +import cbit.vcell.math.Event.Delay; +import cbit.vcell.math.Event.EventAssignment; +import cbit.vcell.math.ExplicitDataGenerator; +import cbit.vcell.math.FastInvariant; +import cbit.vcell.math.FastRate; +import cbit.vcell.math.FastSystem; +import cbit.vcell.math.FilamentRegionVariable; +import cbit.vcell.math.FilamentSubDomain; +import cbit.vcell.math.FilamentVariable; +import cbit.vcell.math.Function; +import cbit.vcell.math.GaussianDistribution; +import cbit.vcell.math.InsideVariable; +import cbit.vcell.math.InteractionRadius; +import cbit.vcell.math.JumpCondition; +import cbit.vcell.math.JumpProcess; +import cbit.vcell.math.JumpProcessRateDefinition; +import cbit.vcell.math.LangevinParticleJumpProcess; +import cbit.vcell.math.LangevinParticleMolecularComponent; +import cbit.vcell.math.LangevinParticleMolecularType; +import cbit.vcell.math.MacroscopicRateConstant; +import cbit.vcell.math.MathDescription; +import cbit.vcell.math.MathException; +import cbit.vcell.math.MathFormatException; +import cbit.vcell.math.MemVariable; +import cbit.vcell.math.MembraneParticleVariable; +import cbit.vcell.math.MembraneRandomVariable; +import cbit.vcell.math.MembraneRegionEquation; +import cbit.vcell.math.MembraneRegionVariable; +import cbit.vcell.math.MembraneSubDomain; +import cbit.vcell.math.OdeEquation; +import cbit.vcell.math.OutsideVariable; +import cbit.vcell.math.ParticleComponentStateDefinition; +import cbit.vcell.math.ParticleComponentStatePattern; +import cbit.vcell.math.ParticleJumpProcess; +import cbit.vcell.math.ParticleJumpProcess.ProcessSymmetryFactor; +import cbit.vcell.math.ParticleMolecularComponent; +import cbit.vcell.math.ParticleMolecularComponentPattern; +import cbit.vcell.math.ParticleMolecularComponentPattern.ParticleBondType; +import cbit.vcell.math.ParticleMolecularType; +import cbit.vcell.math.ParticleMolecularTypePattern; +import cbit.vcell.math.ParticleObservable.ObservableType; +import cbit.vcell.math.ParticleObservable.Sequence; +import cbit.vcell.math.ParticleProperties; +import cbit.vcell.math.ParticleProperties.ParticleInitialCondition; +import cbit.vcell.math.ParticleProperties.ParticleInitialConditionConcentration; +import cbit.vcell.math.ParticleProperties.ParticleInitialConditionCount; +import cbit.vcell.math.ParticleSpeciesPattern; +import cbit.vcell.math.ParticleVariable; +import cbit.vcell.math.PdeEquation; +import cbit.vcell.math.PdeEquation.BoundaryConditionValue; +import cbit.vcell.math.PointSubDomain; +import cbit.vcell.math.PointVariable; +import cbit.vcell.math.ProjectionDataGenerator; +import cbit.vcell.math.RandomVariable; +import cbit.vcell.math.StochVolVariable; +import cbit.vcell.math.SubDomain.BoundaryConditionSpec; +import cbit.vcell.math.UniformDistribution; +import cbit.vcell.math.VarIniCondition; +import cbit.vcell.math.VarIniCount; +import cbit.vcell.math.VarIniPoissonExpectedCount; +import cbit.vcell.math.Variable; +import cbit.vcell.math.Variable.Domain; +import cbit.vcell.math.VariableHash; +import cbit.vcell.math.VariableType; +import cbit.vcell.math.VolVariable; +import cbit.vcell.math.VolumeParticleObservable; +import cbit.vcell.math.VolumeParticleSpeciesPattern; +import cbit.vcell.math.VolumeParticleVariable; +import cbit.vcell.math.VolumeRandomVariable; +import cbit.vcell.math.VolumeRegionEquation; +import cbit.vcell.math.VolumeRegionVariable; +import cbit.vcell.mathmodel.MathModel; +import cbit.vcell.model.Kinetics.KineticsParameter; +import cbit.vcell.model.Model.ModelParameter; +import cbit.vcell.model.Model.RbmModelContainer; +import cbit.vcell.model.Model.ReservedSymbol; +import cbit.vcell.model.Model.StructureTopology; +import cbit.vcell.model.NodeReference.Mode; +import cbit.vcell.model.RbmKineticLaw.RateLawType; +import cbit.vcell.model.RbmKineticLaw.RbmKineticLawParameterType; +import cbit.vcell.modelopt.AnalysisTask; +import cbit.vcell.modelopt.ParameterEstimationTask; +import cbit.vcell.modelopt.ParameterEstimationTaskXMLPersistence; +import cbit.vcell.parser.Expression; +import cbit.vcell.parser.ExpressionBindingException; +import cbit.vcell.parser.ExpressionException; +import cbit.vcell.parser.SymbolTableEntry; +import cbit.vcell.render.Vect3d; +import cbit.vcell.solver.AnnotatedFunction.FunctionCategory; +import cbit.vcell.solvers.mb.MovingBoundarySolverOptions; +import cbit.vcell.solvers.mb.MovingBoundarySolverOptions.ExtrapolationMethod; +import cbit.vcell.solvers.mb.MovingBoundarySolverOptions.RedistributionMode; +import cbit.vcell.solvers.mb.MovingBoundarySolverOptions.RedistributionVersion; +import cbit.vcell.units.VCUnitDefinition; + + +/** + * This class implements the translation of XML data into Java Vcell objects.. + * Creation date: (7/17/2000 12:22:50 PM) + * + * @author: + */ + +public class XmlReader extends XmlBase { + + //The following parameter specifies if the keys should be read. + //By default the value is FALSE to not affect of the current software. + private boolean readKeysFlag = false; + private Namespace vcNamespace = Namespace.getNamespace(XMLTags.VCML_NS_BLANK); // default - blank namespace + private ModelUnitSystem forcedModelUnitSystem = null; + + /** + * Share one decoded {@link VCImage} between identical elements in a document. ON by + * default: a VCImage is immutable payload, so sharing it leaves every editable thing -- + * subvolumes, names, extent, surfaces -- private to each application. + */ + public final static String PROPERTY_SHARE_IDENTICAL_IMAGES = "vcell.xml.shareIdenticalImages"; + + /** + * Share one whole {@link Geometry} between identical elements in a document. + * OFF by default, deliberately: a Geometry is MUTABLE, and two applications that shared one + * would see each other's subvolume renames and geometry edits. Enable it only where + * documents are read and never edited -- a server that parses to serialise or to generate + * math. See {@link #getGeometry(Element)}. + */ + public final static String PROPERTY_SHARE_IDENTICAL_GEOMETRIES = "vcell.xml.shareIdenticalGeometries"; + + /** + * Geometries already parsed during THIS document, by digest of their element. + * One XmlReader is constructed per document (XmlHelper.XMLToBioModel), so the cache lives + * exactly as long as one parse and is never shared between documents or threads. + */ + private final Map parsedGeometriesByDigest = new HashMap<>(); + + /** Decoded images already parsed during THIS document, by digest of their element. */ + private final Map parsedImagesByDigest = new HashMap<>(); + + /** + * This constructor takes a parameter to specify if the KeyValue should be ignored + * Creation date: (3/13/2001 12:16:30 PM) + */ + public XmlReader(boolean readKeys){ + super(); + this.readKeysFlag = readKeys; + } + + public XmlReader(boolean readKeys, Namespace argNS){ + super(); + this.readKeysFlag = readKeys; + this.vcNamespace = argNS; + } + + public void setForcedModelUnitSystem(ModelUnitSystem newModelUnitSystem){ + forcedModelUnitSystem = newModelUnitSystem; + } + + /** + * This method returns a Action object from a XML element. + * Creation date: (7/24/2006 5:56:36 PM) + * + * @param param Element + * @return cbit.vcell.math.Action + * @throws cbit.vcell.xml.XmlParseException The exception description. + */ + private Action getAction(Element param, MathDescription md) throws XmlParseException, MathException, ExpressionException{ + //retrieve values + String operation = unMangle(param.getAttributeValue(XMLTags.OperationAttrTag)); + String operand = param.getText(); + Expression exp = null; + if(operand != null && operand.length() != 0){ + exp = unMangleExpression(operand); + } + String name = unMangle(param.getAttributeValue(XMLTags.VarNameAttrTag)); + + Variable var = md.getVariable(name); + if(var == null){ + throw new MathFormatException("variable " + name + " not defined"); + } + if(!(var instanceof StochVolVariable) && !(var instanceof ParticleVariable)){ + throw new MathFormatException("variable " + name + " not a Stochastic Volume Variable"); + } + try { + Action action = new Action(var, operation, exp); + return action; + } catch(Exception e){ + lg.error(e.getMessage(), e); + } + + return null; + } + + private VolumeGeometricRegion getAdjacentVolumeRegion(ArrayList regions, String regionName){ + for(int i = 0; i < regions.size(); i++){ + GeometricRegion rvl = regions.get(i); + if(rvl instanceof VolumeGeometricRegion && rvl.getName().equals(regionName)){ + return (VolumeGeometricRegion) rvl; + } + } + + return null; + } + + + /** + * This method returns an AnalyticSubVolume object from a XML representation. + * Creation date: (5/1/2001 5:26:17 PM) + * + * @param param Element + * @return cbit.vcell.geometry.AnalyticSubVolume + */ + private AnalyticSubVolume getAnalyticSubVolume(Element param) throws XmlParseException{ + //retrieve the attributes + String name = param.getAttributeValue(XMLTags.NameAttrTag); + int handle = Integer.parseInt(param.getAttributeValue(XMLTags.HandleAttrTag)); + + //process the key + KeyValue key = null; + String temp = param.getAttributeValue(XMLTags.KeyValueAttrTag); + + if(temp != null && temp.length() > 0 && this.readKeysFlag){ + key = new KeyValue(temp); + } + + //Retrieve the expression + temp = param.getChildText(XMLTags.AnalyticExpressionTag, vcNamespace); + if(temp == null){ + throw new XmlParseException("A Problem occured while retrieving the analytic expression of the AnalyticSubvolume " + name); + } + Expression newexpression = unMangleExpression(temp); + + //Create the AnalyticCompartment + AnalyticSubVolume newsubvolume = null; + try { + newsubvolume = new AnalyticSubVolume(key, name, newexpression, handle); + } catch(ExpressionException e){ + throw new XmlParseException("An ExpressionException occured when creating the new AnalyticSubvolume " + name, e); + } + + return newsubvolume; + } + + private VCellSoftwareVersion docVCellSoftwareVersion = null; + + /** + * This method returns a Biomodel object from a XML Element. + * Creation date: (3/13/2001 12:35:00 PM) + * + * @param param Element + * @return cbit.vcell.biomodel.BioModel + */ + public BioModel getBioModel(Element param, VCellSoftwareVersion docVcellSoftwareVersion) throws XmlParseException{ + this.docVCellSoftwareVersion = docVcellSoftwareVersion; +//long l1 = System.currentTimeMillis(); + //Get metadata information Version (if available) + Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace)); + + //Create new biomodel + BioModel biomodel = new BioModel(version); + + //Set name + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + try { + biomodel.setName(name); +// String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag); + +// if (annotation!=null) { +// biomodel.setDescription(unMangle(annotation)); +// } + //get annotation + String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace); + if(annotationText != null && annotationText.length() > 0){ + biomodel.setDescription(unMangle(annotationText)); + } + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException(e); + } +//long l2 = System.currentTimeMillis(); +//System.out.println("biomodel-------- "+((double)(l2-l1))/1000); + + //***Add biomodel to the dictionnary*** + //dictionnary.put(simcontext.getClass().getName()+":"+simcontext.getName(), simcontext); + //Set model + Model newmodel = getModel(param.getChild(XMLTags.ModelTag, vcNamespace)); + biomodel.setModel(newmodel); + //Set simulation contexts + java.util.List children = param.getChildren(XMLTags.SimulationSpecTag, vcNamespace); + java.util.Iterator iterator = children.iterator(); +//long l3 = System.currentTimeMillis(); +//System.out.println("model-------- "+((double)(l3-l2))/1000); + if(biomodel.getVersion() != null && biomodel.getVersion().getVersionKey() != null){ + Long lpcBMKey = Long.valueOf(biomodel.getVersion().getVersionKey().toString()); + MathDescription.originalHasLowPrecisionConstants.remove(lpcBMKey); + } + while (iterator.hasNext()) { +//long l4 = System.currentTimeMillis(); + Element tempElement = iterator.next(); + SimulationContext simContext = getSimulationContext(tempElement, biomodel); + try { + biomodel.addSimulationContext(simContext); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("An error occurred while trying to add the SimContext " + simContext.getName() + " to the BioModel Object!", e); + } + //process the simulations within this Simspec + Iterator simIterator = tempElement.getChildren(XMLTags.SimulationTag, vcNamespace).iterator(); +//long l5 = System.currentTimeMillis(); +//System.out.println("simcontext-------- "+((double)(l5-l4))/1000); + while (simIterator.hasNext()) { + try { + biomodel.addSimulation(getSimulation((Element) simIterator.next(), simContext.getMathDescription(), simContext)); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A PropertyVetoException occurred when adding a Simulation entity to the BioModel " + name, e); + } + } +//long l6 = System.currentTimeMillis(); +//System.out.println("sims-------- "+((double)(l6-l5))/1000); + } + + // biomodel.getVCMetaData().setAnnotation(biomodel, param); + // biomodel.getVCMetaData().setNotes(biomodel, param); + boolean bMetaDataPopulated = false; + List elementsMetaData = param.getChildren(XMLMetaData.VCMETADATA_TAG, VCMetaData.nsVCML); + if(elementsMetaData != null && elementsMetaData.size() > 0){ + for(Element elementMetaData : elementsMetaData){ + XMLMetaDataReader.readFromElement(biomodel.getVCMetaData(), biomodel, elementMetaData); + } + bMetaDataPopulated = true; + } else { + // no metadata was found, populate vcMetaData from biomodel (mainly free text annotation for identifiables) + if(!bMetaDataPopulated){ + biomodel.populateVCMetadata(bMetaDataPopulated); + } + } + Element pathwayElement = param.getChild(XMLTags.PathwayModelTag, vcNamespace); + if(pathwayElement != null){ + Element rdfElement = pathwayElement.getChild(XMLRDF.tagRDF, XMLRDF.nsRDF); + if(rdfElement != null){ + PathwayReaderBiopax3 pathwayReader = new PathwayReaderBiopax3(new RDFXMLContext()); + PathwayModel pathwayModel = pathwayReader.parse(rdfElement, false); + pathwayModel.reconcileReferences(null); // ??? is this needed ??? + // we keep as lvl 1 only the objects which we want to show in the diagram + pathwayModel.filterDiagramObjects(); + biomodel.getPathwayModel().merge(pathwayModel); + } else { + throw new XmlParseException("expecting RDF element as child of pathwayModel within VCML document"); + } + } + + Element relationshipElement = param.getChild(XMLTags.RelationshipModelTag, vcNamespace); + if(relationshipElement != null){ + Element rmnsElement = relationshipElement.getChild("RMNS", vcNamespace); + if(rmnsElement != null){ + RelationshipReader relationshipReader = new RelationshipReader(); + RelationshipModel relationshipModel = relationshipReader.parse(rmnsElement, biomodel); + biomodel.getRelationshipModel().merge(relationshipModel); + } else { +// throw new XmlParseException("expecting RMNS element as child of pathwayModel within VCML document"); + } + } + + return biomodel; + } + + + /** + * This method returns a Catalyst object from a XML representation. + * Creation date: (5/4/2001 2:22:56 PM) + * + * @param param Element + * @return cbit.vcell.model.Product + * @throws cbit.vcell.xml.XmlParseException The exception description. + */ + private Catalyst getCatalyst(Element param, ReactionStep reaction, Model model) throws XmlParseException{ + //retrieve the key if there is one + KeyValue key = null; + String keystring = param.getAttributeValue(XMLTags.KeyValueAttrTag); + if(keystring != null && keystring.length() > 0 && this.readKeysFlag){ + key = new KeyValue(keystring); + } + + String speccontref = unMangle(param.getAttributeValue(XMLTags.SpeciesContextRefAttrTag)); + SpeciesContext speccont = model.getSpeciesContext(speccontref); + if(speccont == null){ + throw new XmlParseException( + "The reference to the SpecieContext " + speccontref + + " for a Catalyst could not be resolved!"); + } + + return new Catalyst(key, reaction, speccont); + } + + + /** + * This method returns a CompartmentSubDomain objecy from a XML element. + * Creation date: (5/17/2001 11:59:45 AM) + * + * @param param Element + * @return cbit.vcell.math.CompartmentSubDomain + * @throws cbit.vcell.xml.XmlParseException The exception description. + */ + private CompartmentSubDomain getCompartmentSubDomain(Element param, MathDescription mathDesc) throws XmlParseException{ + //get attributes + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + int priority = -1; + String temp = param.getAttributeValue(XMLTags.PriorityAttrTag); + if(temp != null){ + priority = Integer.parseInt(temp); + } + //--- create new CompartmentSubDomain --- + CompartmentSubDomain subDomain = new CompartmentSubDomain(name, priority); + transcribeComments(param, subDomain); + + //Process BoundaryConditions + Iterator iterator = param.getChildren(XMLTags.BoundaryTypeTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + + //create BoundaryConditionType + temp = tempelement.getAttributeValue(XMLTags.BoundaryTypeAttrTag); + BoundaryConditionType bType = new BoundaryConditionType(temp); + + //check where it goes + //Process Xm + if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueXm)){ + subDomain.setBoundaryConditionXm(bType); + } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueXp)){ + //Process Xp + subDomain.setBoundaryConditionXp(bType); + } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueYm)){ + //Process Ym + subDomain.setBoundaryConditionYm(bType); + } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueYp)){ + //Process Yp + subDomain.setBoundaryConditionYp(bType); + } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueZm)){ + //Process Zm + subDomain.setBoundaryConditionZm(bType); + } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueZp)){ + //Process Zp + subDomain.setBoundaryConditionZp(bType); + } else { + // If not indentified throw an exception!! + throw new XmlParseException("Unknown BoundaryConditionType: " + tempelement.getAttributeValue(XMLTags.BoundaryAttrTag)); + } + } + + //process BoundaryConditionSpecs + iterator = param.getChildren(XMLTags.BoundaryConditionSpecTag, vcNamespace).iterator(); + if(iterator != null){ + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + try { + subDomain.addBoundaryConditionSpec(getBoundaryConditionSpec(tempelement)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding a BoundaryConditionSpec to the compartmentSubDomain " + name, e); + } + } + } + + + //process OdeEquations + iterator = param.getChildren(XMLTags.OdeEquationTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + + try { + subDomain.addEquation(getOdeEquation(tempelement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding an OdeEquation to the compartmentSubDomain " + name, e); + } + } + + //process PdeEquations + iterator = param.getChildren(XMLTags.PdeEquationTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + + try { + subDomain.addEquation(getPdeEquation(tempelement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding an PdeEquation to the compartmentSubDomain " + name, e); + } + } + + //Process VolumeRegionEquation + iterator = param.getChildren(XMLTags.VolumeRegionEquationTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + + try { + subDomain.addEquation(getVolumeRegionEquation(tempelement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding a VolumeRegionEquation to the compartmentSubDomain " + name, e); + } + } + + //Process Variable initial conditions (added for stochastic algos) + iterator = param.getChildren(XMLTags.VarIniCount_OldTag, vcNamespace).iterator(); + if(iterator != null){ + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + try { + subDomain.addVarIniCondition(getVarIniCount(tempelement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding a variable initial condition to the compartmentSubDomain " + name, e); + } catch(ExpressionException e){ + lg.error(e); + } + } + } + + iterator = param.getChildren(XMLTags.VarIniCountTag, vcNamespace).iterator(); + if(iterator != null){ + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + try { + subDomain.addVarIniCondition(getVarIniCount(tempelement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding a variable initial condition to the compartmentSubDomain " + name, e); + } catch(ExpressionException e){ + lg.error(e); + } + } + } + + iterator = param.getChildren(XMLTags.VarIniPoissonExpectedCountTag, vcNamespace).iterator(); + if(iterator != null){ + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + try { + subDomain.addVarIniCondition(getVarIniPoissonExpectedCount(tempelement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding a variable initial condition to the compartmentSubDomain " + name, e); + } catch(ExpressionException e){ + lg.error(e); + } + } + } + // + //Process JumpProcesses (added for stochastic algos) + iterator = param.getChildren(XMLTags.JumpProcessTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + try { + subDomain.addJumpProcess(getJumpProcess(tempelement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding a jump process to the compartmentSubDomain " + name, e); + } + } + + iterator = param.getChildren(XMLTags.ParticleJumpProcessTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + try { + subDomain.addParticleJumpProcess(getParticleJumpProcess(tempelement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding a jump process to the compartmentSubDomain " + name, e); + } + } + iterator = param.getChildren(XMLTags.LangevinParticleJumpProcessTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + try { + subDomain.addParticleJumpProcess(getParticleJumpProcess(tempelement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding a jump process to the compartmentSubDomain " + name, e); + } + } + + iterator = param.getChildren(XMLTags.ParticlePropertiesTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + try { + subDomain.addParticleProperties(getParticleProperties(tempelement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding a jump process to the compartmentSubDomain " + name, e); + } + } + + //process ComputeCentroid "equations" + iterator = param.getChildren(XMLTags.ComputeCentroidTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + + try { + subDomain.addEquation(getComputeCentroid(tempelement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding an ComputeCentroid 'equation' to the compartmentSubDomain " + name, e); + } + } + + //process ComputeMembraneMetric "equations" + iterator = param.getChildren(XMLTags.ComputeMembraneMetricTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + + try { + subDomain.addEquation(getComputeMembraneMetric(tempelement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding an ComputeMembraneMetric 'equation' to the compartmentSubDomain " + name, e); + } + } + + //Process the FastSystem (if thre is) + Element tempelement = param.getChild(XMLTags.FastSystemTag, vcNamespace); + if(tempelement != null){ + subDomain.setFastSystem(getFastSystem(tempelement, mathDesc)); + } + return subDomain; + } + + + /** + * This method returns a CompartmentSubVolume object from a XML representation. + * Creation date: (5/1/2001 5:26:17 PM) + * + * @param param Element + * @return cbit.vcell.geometry.CompartmentSubVolume + */ + private CompartmentSubVolume getCompartmentSubVolume(Element param) throws XmlParseException{ + //retrieve the attributes + String name = param.getAttributeValue(XMLTags.NameAttrTag); + int handle = Integer.parseInt(param.getAttributeValue(XMLTags.HandleAttrTag)); + + //process the key + KeyValue key = null; + String temp = param.getAttributeValue(XMLTags.KeyValueAttrTag); + if(temp != null && temp.length() > 0 && this.readKeysFlag){ + key = new KeyValue(temp); + } + + //Create the CompartmentVolume + CompartmentSubVolume newcompartment = new CompartmentSubVolume(key, handle); + + //set the name + try { + newcompartment.setName(name); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A propertyVetoException was fired when setting the name to the compartmentSubVolume " + name, e); + } + + return newcompartment; + } + + private void transcribeComments(Element source, Object destination){ + String before = source.getAttributeValue(XMLTags.BEFORE_COMMENT_ATTR_TAG); + String after = source.getAttributeValue(XMLTags.AFTER_COMMENT_ATTR_TAG); + if(before != null || after != null){ + if(!(destination instanceof Commented)){ + throw new UnsupportedOperationException("Can't add comments, " + destination.getClass().toString() + " does not implement " + Commented.class.toString()); + + } + Commented c = (Commented) destination; + c.setBeforeComment(before); + c.setAfterComment(after); + } + } + + /** + * This method returns a Constant object from a XML element. + * Creation date: (5/16/2001 1:50:07 PM) + * + * @param param Element + * @return cbit.vcell.math.Constant + * @throws cbit.vcell.xml.XmlParseException The exception description. + */ + private Constant getConstant(Element param) throws XmlParseException{ + //retrieve values + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + Expression exp = unMangleExpression(param.getText()); + + //-- create new constant object --- + Constant newconstant = new Constant(name, exp); + transcribeComments(param, newconstant); + + return newconstant; + } + + + /** + * This method returns a ControlPointcurve object from a XML element. + * Creation date: (5/22/2001 5:20:39 PM) + * + * @param param Element + * @return cbit.vcell.geometry.ControlPointCurve + */ + private ControlPointCurve getControlPointCurve(Element param){ + ControlPointCurve curve = null; + //get Attributes + String type = param.getAttributeValue(XMLTags.TypeAttrTag); + boolean closed = Boolean.valueOf(param.getAttributeValue(XMLTags.ClosedAttrTag)).booleanValue(); + List coordList = param.getChildren(); + + //Upon de type, decide which Curve type to create + if(type.equalsIgnoreCase(XMLTags.PolyLineTypeTag)){ + if(coordList.size() == 2){ //I have a Line + Coordinate begin = getCoordinate(coordList.get(0)); + Coordinate end = getCoordinate(coordList.get(1)); + // ****create new Line **** + curve = new Line(begin, end); + } else { + //If it it is not a Line, then it is a SampledCurve + Coordinate[] coords = new Coordinate[coordList.size()]; + for(int i = 0; i < coordList.size(); i++){ + coords[i] = getCoordinate(coordList.get(i)); + } + //****create new SampledCurve **** + curve = new SampledCurve(coords); + } + } else if(type.equalsIgnoreCase(XMLTags.SplineTypeTag)){ + Coordinate[] coords = new Coordinate[coordList.size()]; + for(int i = 0; i < coordList.size(); i++){ + coords[i] = getCoordinate(coordList.get(i)); + } + //****create new Spline **** + curve = new Spline(coords); + } + + //set Atributes + curve.setClosed(closed); + + return curve; + } + + + /** + * This method returns a Coordinate object from a XML Element. + * Creation date: (5/22/2001 5:53:05 PM) + * + * @param param Element + * @return cbit.vcell.geometry.Coordinate + */ + public Coordinate getCoordinate(Element param){ + //get attributes + double x = Double.parseDouble(param.getAttributeValue(XMLTags.XAttrTag)); + double y = Double.parseDouble(param.getAttributeValue(XMLTags.YAttrTag)); + double z = Double.parseDouble(param.getAttributeValue(XMLTags.ZAttrTag)); + + //**** create coordinate *** + Coordinate coord = new Coordinate(x, y, z); + + return coord; + } + + + /** + * This method returns a DBFormalSpecies from a XML representation. + * Creation date: (6/3/2003 8:46:44 PM) + * + * @param formalSpeciesElement Element + * @return cbit.vcell.dictionary.DBFormalSpecies + */ + private DBFormalSpecies getDBFormalSpecies(Element formalSpeciesElement) throws XmlParseException{ + //read key + String keystring = formalSpeciesElement.getAttributeValue(XMLTags.KeyValueAttrTag); + KeyValue key = new KeyValue(keystring); + //read type + String typestring = formalSpeciesElement.getAttributeValue(XMLTags.TypeAttrTag); + //read the FormalSpeciesInfo + Element speciesInfoElement = formalSpeciesElement.getChild(XMLTags.FormalSpeciesInfoTag, vcNamespace); + + //create the DBFormalSpecies upon the type + DBFormalSpecies formalSpecies = null; + + if(typestring.equalsIgnoreCase(XMLTags.CompoundTypeTag)){ + formalSpecies = new FormalCompound(key, (CompoundInfo) getFormalSpeciesInfo(speciesInfoElement)); + } else if(typestring.equalsIgnoreCase(XMLTags.EnzymeTypeTag)){ + formalSpecies = new FormalEnzyme(key, (EnzymeInfo) getFormalSpeciesInfo(speciesInfoElement)); + } else if(typestring.equalsIgnoreCase(XMLTags.ProteinTypeTag)){ + formalSpecies = new FormalProtein(key, (ProteinInfo) getFormalSpeciesInfo(speciesInfoElement)); + } else { + throw new XmlParseException("DBFormalSpecies type:" + typestring + ", not supported yet!"); + } + + return formalSpecies; + } + + + /** + * This method reads a DBSpecies from a XML representation. + * Creation date: (6/3/2003 8:20:54 PM) + * + * @param dbSpeciesElement Element + * @return cbit.vcell.dictionary.DBSpecies + */ + private DBSpecies getDBSpecies(Element dbSpeciesElement) throws XmlParseException{ + //Read the key + String keystring = dbSpeciesElement.getAttributeValue(XMLTags.KeyValueAttrTag); + KeyValue key = new KeyValue(keystring); + DBSpecies dbSpecies = null; + + //read the type + String type = dbSpeciesElement.getAttributeValue(XMLTags.TypeAttrTag); + //Read the DBFormalSpecies + Element formalSpeciesElement = dbSpeciesElement.getChild(XMLTags.DBFormalSpeciesTag, vcNamespace); + + if(type.equalsIgnoreCase(XMLTags.CompoundTypeTag)){ + //Create a BoundCompound + dbSpecies = new BoundCompound(key, (FormalCompound) getDBFormalSpecies(formalSpeciesElement)); + } else if(type.equalsIgnoreCase(XMLTags.EnzymeTypeTag)){ + //Create a BoundEnzyme + dbSpecies = new BoundEnzyme(key, (FormalEnzyme) getDBFormalSpecies(formalSpeciesElement)); + } else if(type.equalsIgnoreCase(XMLTags.ProteinTypeTag)){ + //Create a BoundProtein + dbSpecies = new BoundProtein(key, (FormalProtein) getDBFormalSpecies(formalSpeciesElement)); + } else { + throw new XmlParseException("DBSpecies type: " + type + ", not supported yet!"); + } + + return dbSpecies; + } + + + /** + * This method returns a Diagram object from a XML element. + * Creation date: (4/4/2001 4:20:52 PM) + * + * @param param Element + * @return cbit.vcell.model.Diagram + */ + private Diagram getDiagram(Element param, Model model) throws XmlParseException{ + //get Attibutes + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String structureName = unMangle(param.getAttributeValue(XMLTags.StructureAttrTag)); + Structure structureref = model.getStructure(structureName); + if(structureref == null){ + throw new XmlParseException("The structure " + structureName + "could not be resolved!"); + } + //try to create the new Diagram + Diagram newdiagram = new Diagram(structureref, name); + //Add Nodereferences (Shapes) + List children = param.getChildren(); + if(children.size() > 0){ + List nodeRefList = new ArrayList<>(); + for(int i = 0; i < children.size(); i++){ + nodeRefList.add(getNodeReference(children.get(i))); + } + newdiagram.setNodeReferences(nodeRefList); + } + + return newdiagram; + } + + + /** + * This method process Electrical Stimulus, also called Clamps. + * Creation date: (6/6/2002 4:46:18 PM) + * + * @param param Element + * @return cbit.vcell.mapping.ElectricalStimulus + */ + private ElectricalStimulus getElectricalStimulus(Element param, SimulationContext currentSimulationContext) throws XmlParseException{ + ElectricalStimulus clampStimulus = null; + + //get name + // String name = unMangle( param.getAttributeValue(XMLTags.NameAttrTag) ); + + //get Electrode + Electrode electrode = getElectrode(param.getChild(XMLTags.ElectrodeTag, vcNamespace), currentSimulationContext); + + if(param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.VoltageClampTag)){ + //is a voltage clamp + clampStimulus = new VoltageClampStimulus(electrode, "voltClampElectrode", new Expression(0.0), currentSimulationContext); + } else if(param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.CurrentDensityClampTag) || + param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.CurrentDensityClampTag_oldName)){ + //is a current density clamp + clampStimulus = new CurrentDensityClampStimulus(electrode, "currDensityClampElectrode", new Expression(0.0), currentSimulationContext); + } else if(param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.TotalCurrentClampTag)){ + //is a "total" current clamp + clampStimulus = new TotalCurrentClampStimulus(electrode, "totalCurrClampElectrode", new Expression(0.0), currentSimulationContext); + } + + try { + clampStimulus.reading(true); // transaction begin flag ... yeah, this is a hack + + //Read all of the parameters + List list = param.getChildren(XMLTags.ParameterTag, vcNamespace); + + // add constants that may be used in the electrical stimulus. + VariableHash varHash = new VariableHash(); + Model model = currentSimulationContext.getModel(); + addResevedSymbols(varHash, model); + + // + // rename "special" parameters (those that are not "user defined") + // + for(Element xmlParam : list){ + String paramName = unMangle(xmlParam.getAttributeValue(XMLTags.NameAttrTag)); + String role = xmlParam.getAttributeValue(XMLTags.ParamRoleAttrTag); + String paramExpStr = xmlParam.getText(); + Expression paramExp = unMangleExpression(paramExpStr); + try { + if(varHash.getVariable(paramName) == null){ + Domain domain = null; + varHash.addVariable(new Function(paramName, paramExp, domain)); + } else { + if(model.getReservedSymbolByName(paramName) != null){ + varHash.removeVariable(paramName); + Domain domain = null; + varHash.addVariable(new Function(paramName, paramExp, domain)); + } + } + } catch(MathException e){ + throw new XmlParseException("error reordering parameters according to dependencies:", e); + } + LocalParameter tempParam = null; + if(!role.equals(XMLTags.ParamRoleUserDefinedTag)){ + if(role.equals(XMLTags.ParamRoleTotalCurrentTag)){ + if(clampStimulus instanceof TotalCurrentClampStimulus){ + tempParam = ((TotalCurrentClampStimulus) clampStimulus).getCurrentParameter(); + } else { + varHash.removeVariable(paramName); + continue; + } + } else if(role.equals(XMLTags.ParamRoleTotalCurrentDensityTag) || role.equals(XMLTags.ParamRoleTotalCurrentDensityOldNameTag)){ + if(clampStimulus instanceof CurrentDensityClampStimulus){ + tempParam = ((CurrentDensityClampStimulus) clampStimulus).getCurrentDensityParameter(); + } else { + varHash.removeVariable(paramName); + continue; + } + } else if(role.equals(XMLTags.ParamRolePotentialDifferenceTag)){ + if(clampStimulus instanceof VoltageClampStimulus){ + tempParam = ((VoltageClampStimulus) clampStimulus).getVoltageParameter(); + } else { + varHash.removeVariable(paramName); + continue; + } + } + } else { + continue; + } + if(tempParam == null){ + throw new XmlParseException("parameter with role '" + role + "' not found in electricalstimulus"); + } + // + // custom name for "special" parameter + // + if(!tempParam.getName().equals(paramName)){ + LocalParameter multNameParam = clampStimulus.getLocalParameter(paramName); + int n = 0; + while (multNameParam != null) { + String tempName = paramName + "_" + n++; + clampStimulus.renameParameter(paramName, tempName); + multNameParam = clampStimulus.getLocalParameter(tempName); + } + clampStimulus.renameParameter(tempParam.getName(), paramName); + } + } + // + // create unresolved parameters for all unresolved symbols + // + String unresolvedSymbol = varHash.getFirstUnresolvedSymbol(); + + while (unresolvedSymbol != null) { + try { + Domain domain = null; + varHash.addVariable(new Function(unresolvedSymbol, new Expression(0.0), domain)); // will turn into an UnresolvedParameter. + } catch(MathException e){ + throw new XmlParseException(e.getMessage()); + } + clampStimulus.addUnresolvedParameter(unresolvedSymbol); + unresolvedSymbol = varHash.getFirstUnresolvedSymbol(); + } + + Variable sortedVariables[] = varHash.getTopologicallyReorderedVariables(); + ModelUnitSystem modelUnitSystem = model.getUnitSystem(); + for(int i = sortedVariables.length - 1; i >= 0; i--){ + if(sortedVariables[i] instanceof Function){ + Function paramFunction = (Function) sortedVariables[i]; + Element xmlParam = null; + for(int j = 0; j < list.size(); j++){ + Element tempParam = (Element) list.get(j); + if(paramFunction.getName().equals(unMangle(tempParam.getAttributeValue(XMLTags.NameAttrTag)))){ + xmlParam = tempParam; + break; + } + } + if(xmlParam == null){ + continue; // must have been an unresolved parameter + } + String symbol = xmlParam.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); + VCUnitDefinition unit = null; + if(symbol != null){ + unit = modelUnitSystem.getInstance(symbol); + } + LocalParameter tempParam = clampStimulus.getLocalParameter(paramFunction.getName()); + if(tempParam == null){ + clampStimulus.addUserDefinedParameter(paramFunction.getName(), paramFunction.getExpression(), unit); + } else { + if(tempParam.getExpression() != null){ // if the expression is null, it should remain null. + clampStimulus.setParameterValue(tempParam, paramFunction.getExpression()); + } + tempParam.setUnitDefinition(unit); + } + } + } + + + } catch(PropertyVetoException | ExpressionException e){ + throw new XmlParseException("Exception while setting parameters for simContext : " + currentSimulationContext.getName(), e); + } finally { + clampStimulus.reading(false); + } + + return clampStimulus; + } + + + private void readParameters(List parameterElements, ParameterContext parameterContext, HashMap roleHash, ParameterRoleEnum userDefinedRole, HashSet xmlRolesTagsToIgnore, Model model) throws XmlParseException{ + + String contextName = parameterContext.getNameScope().getName(); + try { + // + // prepopulate varHash with reserved symbols + // + VariableHash varHash = new VariableHash(); + addResevedSymbols(varHash, model); + + // + // process each parameter: + // 1) put the parameter into the varHash + // 2) rename predefined parameters from the ParameterContext as necessary to avoid naming conflicts + // and use the stored names for pre-defined parameters. + // + for(Element xmlParam : parameterElements){ + String parsedParamName = unMangle(xmlParam.getAttributeValue(XMLTags.NameAttrTag)); + String parsedRoleString = xmlParam.getAttributeValue(XMLTags.ParamRoleAttrTag); + String parsedExpressionString = xmlParam.getText(); + + // + // should we skip this xml role tag? not used anymore. + // + if(xmlRolesTagsToIgnore.contains(parsedRoleString)){ + varHash.removeVariable(parsedParamName); + continue; + } + + Expression paramExp = null; + if(parsedExpressionString.trim().length() > 0){ + paramExp = unMangleExpression(parsedExpressionString); + } + + if(varHash.getVariable(parsedParamName) == null){ + Domain domain = null; + varHash.addVariable(new Function(parsedParamName, paramExp, domain)); + } else { + if(model.getReservedSymbolByName(parsedParamName) != null){ + varHash.removeVariable(parsedParamName); + Domain domain = null; + varHash.addVariable(new Function(parsedParamName, paramExp, domain)); + } + } + + // + // get the parameter for this xml role string + // + ParameterRoleEnum paramRole = roleHash.get(parsedRoleString); + if(paramRole == null){ + throw new XmlParseException("parameter '" + parsedParamName + "' has unexpected role '" + parsedRoleString + "' in '" + contextName + "'"); + } + + // + // if parameter is not user-defined, then force the parameter with the same role to have the same name. + // + if(paramRole != userDefinedRole){ + LocalParameter paramWithSameRole = parameterContext.getLocalParameterFromRole(paramRole); + if(paramWithSameRole == null){ + throw new XmlParseException("can't find parameter with role '" + parsedRoleString + "' in '" + contextName + "'"); + } + // + // "special" parameter with same role has a different name, rename + // + // + if(!paramWithSameRole.getName().equals(parsedParamName)){ + // + // first rename other parameters with same name + // + LocalParameter paramWithSameNameButDifferentRole = parameterContext.getLocalParameterFromName(parsedParamName); + if(paramWithSameNameButDifferentRole != null){ + // + // find available name + // + int n = 0; + String newName = parsedParamName + "_" + n++; + while (parameterContext.getEntry(newName) != null) { + newName = parsedParamName + "_" + n++; + } + parameterContext.renameLocalParameter(parsedParamName, newName); + } + // + // then rename parameter with correct role + // + parameterContext.renameLocalParameter(paramWithSameRole.getName(), parsedParamName); + } + } + } + + // + // create unresolved parameters for all unresolved symbols + // + String unresolvedSymbol = varHash.getFirstUnresolvedSymbol(); + while (unresolvedSymbol != null) { + try { + Domain domain = null; + varHash.addVariable(new Function(unresolvedSymbol, new Expression(0.0), domain)); // will turn into an UnresolvedParameter. + } catch(MathException e){ + throw new XmlParseException(e.getMessage(), e); + } + parameterContext.addUnresolvedParameter(unresolvedSymbol); + unresolvedSymbol = varHash.getFirstUnresolvedSymbol(); + } + + + // + // in topological order, add parameters to model (getting units also). + // note that all pre-defined parameters already have the correct names + // here we set expressions on pre-defined parameters and add user-defined parameters + // + Variable sortedVariables[] = varHash.getTopologicallyReorderedVariables(); + ModelUnitSystem modelUnitSystem = model.getUnitSystem(); + for(int i = sortedVariables.length - 1; i >= 0; i--){ + if(sortedVariables[i] instanceof Function){ + Function paramFunction = (Function) sortedVariables[i]; + Element xmlParam = null; + for(int j = 0; j < parameterElements.size(); j++){ + Element tempParam = (Element) parameterElements.get(j); + if(paramFunction.getName().equals(unMangle(tempParam.getAttributeValue(XMLTags.NameAttrTag)))){ + xmlParam = tempParam; + break; + } + } + if(xmlParam == null){ + continue; // must have been an unresolved parameter + } + String symbol = xmlParam.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); + VCUnitDefinition unit = null; + if(symbol != null){ + unit = modelUnitSystem.getInstance(symbol); + } + LocalParameter tempParam = parameterContext.getLocalParameterFromName(paramFunction.getName()); + if(tempParam == null){ + tempParam = parameterContext.addLocalParameter(paramFunction.getName(), new Expression(0.0), userDefinedRole, unit, userDefinedRole.getDescription()); + parameterContext.setParameterValue(tempParam, paramFunction.getExpression(), true); + } else { + if(tempParam.getExpression() != null){ // if the expression is null, it should remain null. + parameterContext.setParameterValue(tempParam, paramFunction.getExpression(), true); + } + tempParam.setUnitDefinition(unit); + } + } + } + + } catch(PropertyVetoException | ExpressionException | MathException e){ + throw new XmlParseException("Exception while setting parameters for '" + contextName + "': " + e.getMessage(), e); + } + } + + + /** + * This method returns an Electrode object from a XML representation. + * Creation date: (6/6/2002 4:22:55 PM) + * + * @return cbit.vcell.mapping.Electrode + */ + private Electrode getElectrode(Element elem, SimulationContext currentSimulationContext){ + //retrieve feature + String featureName = unMangle(elem.getAttributeValue(XMLTags.FeatureAttrTag)); + Feature feature = (Feature) currentSimulationContext.getModel().getStructure(featureName); + //retrieve position + Coordinate position = getCoordinate(elem.getChild(XMLTags.CoordinateTag, vcNamespace)); + + Electrode newElect = new Electrode(feature, position); + + return newElect; + } + + + /** + * This method returns a ErrorTolerance object from a XML Element. + * Creation date: (5/22/2001 11:50:07 AM) + * + * @param param Element + * @return cbit.vcell.solver.ErrorTolerance + */ + private ErrorTolerance getErrorTolerance(Element param){ + //getAttributes + double absolut = Double.parseDouble(param.getAttributeValue(XMLTags.AbsolutErrorToleranceTag)); + double relative = Double.parseDouble(param.getAttributeValue(XMLTags.RelativeErrorToleranceTag)); + + //*** create new ErrorTolerance object **** + ErrorTolerance errorTol = new ErrorTolerance(absolut, relative); + + return errorTol; + } + + + public Extent getExtent(Element parsed){ + double x = Double.parseDouble(parsed.getAttributeValue(XMLTags.XAttrTag)); + double y = Double.parseDouble(parsed.getAttributeValue(XMLTags.YAttrTag)); + double z = Double.parseDouble(parsed.getAttributeValue(XMLTags.ZAttrTag)); + Extent extent = new Extent(x, y, z); + + return extent; + } + + + /** + * This method returns a FastSystemImplicit from a XML Element. + * Creation date: (5/18/2001 2:38:56 PM) + * + * @param param Element + * @return cbit.vcell.math.FastSystemImplicit + * @throws cbit.vcell.xml.XmlParseException The exception description. + */ + private FastSystem getFastSystem( + Element param, + MathDescription mathDesc) + throws XmlParseException{ + //Create a new FastSystem + FastSystem fastSystem = new FastSystem(mathDesc); + + //Process the FastInvariants + Iterator iterator = param.getChildren(XMLTags.FastInvariantTag, vcNamespace).iterator(); + FastInvariant fastInvariant = null; + while (iterator.hasNext()) { + Element tempElement = (Element) iterator.next(); + String temp = tempElement.getText(); + + try { + Expression newExp = unMangleExpression(temp); + fastInvariant = new FastInvariant(newExp); + fastSystem.addFastInvariant(fastInvariant); + } catch(MathException e){ + throw new XmlParseException( + "A MathException was fired when adding the FastInvariant " + fastInvariant + ", to a FastSystem!" + " : ", e); + } + } + //Process the FastRate + iterator = param.getChildren(XMLTags.FastRateTag, vcNamespace).iterator(); + FastRate fastRate = null; + + while (iterator.hasNext()) { + Element tempElement = (Element) iterator.next(); + String temp = tempElement.getText(); + + try { + Expression newExp = unMangleExpression(temp); + fastRate = new FastRate(newExp); + fastSystem.addFastRate(fastRate); + } catch(MathException e){ + throw new XmlParseException( + "A MathException was fired when adding the FastRate " + fastRate + ", to a FastSystem!", e); + } + } + + return fastSystem; + } + + + /** + * This method returns a Feature object (Structure) from a XML representation. + * Creation date: (3/15/2001 6:12:36 PM) + * + * @param param Element + * @return cbit.vcell.model.Structure + */ + private Structure getFeature(Element param) throws XmlParseException{ + Feature newfeature = null; + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + + //retrieve the key if there is one + KeyValue key = null; + String keystring = param.getAttributeValue(XMLTags.KeyValueAttrTag); + + if(keystring != null && keystring.length() > 0 && this.readKeysFlag){ + key = new KeyValue(keystring); + } + + //---Create the new feature--- + try { + newfeature = new Feature(key, name); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException( + "An error occurred while creating the feature " + + param.getAttributeValue(XMLTags.NameAttrTag), e); + } + + return newfeature; + } + + + /** + * This method retuns a FeatureMapping object from a XML representation. + * Creation date: (5/7/2001 4:12:03 PM) + * + * @param param Element + * @return cbit.vcell.mapping.FeatureMapping + */ + private FeatureMapping getFeatureMapping(Element param, SimulationContext simulationContext) throws XmlParseException{ + //Retrieve attributes + String featurename = unMangle(param.getAttributeValue(XMLTags.FeatureAttrTag)); + String geometryClassName = param.getAttributeValue(XMLTags.SubVolumeAttrTag); + if(geometryClassName != null){ + geometryClassName = unMangle(geometryClassName); + } else { + geometryClassName = param.getAttributeValue(XMLTags.GeometryClassAttrTag); + if(geometryClassName != null){ + geometryClassName = unMangle(geometryClassName); + } + } + + Feature featureref = (Feature) simulationContext.getModel().getStructure(featurename); + if(featureref == null){ + throw new XmlParseException("The Feature " + featurename + " could not be resolved!"); + } + + //*** Create new Feature Mapping **** + FeatureMapping feamap = new FeatureMapping(featureref, simulationContext, simulationContext.getModel().getUnitSystem()); + + //Set Size + if(param.getAttributeValue(XMLTags.SizeTag) != null){ + String size = unMangle(param.getAttributeValue(XMLTags.SizeTag)); + try { + feamap.getSizeParameter().setExpression(unMangleExpression(size)); + } catch(ExpressionException e){ + throw new XmlParseException("An expressionException was fired when setting the size Expression " + size + " to a featureMapping!", e); + } + } else { + try { + feamap.getSizeParameter().setExpression(null); + } catch(Exception e){ + throw new RuntimeException("unexpected exception while setting structure size: " + e.getMessage(), e); + } + } + + //Set Volume/unit_area if it exists + if(param.getAttributeValue(XMLTags.VolumePerUnitAreaTag) != null){ + String volPerUnitArea = unMangle(param.getAttributeValue(XMLTags.VolumePerUnitAreaTag)); + try { + feamap.getVolumePerUnitAreaParameter().setExpression(unMangleExpression(volPerUnitArea)); + } catch(ExpressionException e){ + throw new XmlParseException("An expressionException was fired when setting the VolumePerUnitArea Expression " + volPerUnitArea + " to a featureMapping!", e); + } + } + + //Set Volume/unitVol if it exists + if(param.getAttributeValue(XMLTags.VolumePerUnitVolumeTag) != null){ + String volPerUnitVol = unMangle(param.getAttributeValue(XMLTags.VolumePerUnitVolumeTag)); + try { + feamap.getVolumePerUnitVolumeParameter().setExpression(unMangleExpression(volPerUnitVol)); + } catch(ExpressionException e){ + throw new XmlParseException("An expressionException was fired when setting the size Expression " + volPerUnitVol + " to a featureMapping!", e); + } + } + + if(geometryClassName != null){ + GeometryClass[] geometryClasses = simulationContext.getGeometry().getGeometryClasses(); + for(int i = 0; i < geometryClasses.length; i++){ + if(geometryClasses[i].getName().equals(geometryClassName)){ + try { + feamap.setGeometryClass(geometryClasses[i]); + } catch(PropertyVetoException e){ + throw new XmlParseException("A propertyVetoException was fired when trying to set the subvolume or surface " + geometryClassName + " to a MembraneMapping!", e); + } + } + } + } + + //Set Boundary conditions + Element tempElement = param.getChild(XMLTags.BoundariesTypesTag, vcNamespace); + + //Xm + String temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueXm); + BoundaryConditionType bct = new BoundaryConditionType(temp); + feamap.setBoundaryConditionTypeXm(bct); + //Xp + temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueXp); + bct = new BoundaryConditionType(temp); + feamap.setBoundaryConditionTypeXp(bct); + //Ym + temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueYm); + bct = new BoundaryConditionType(temp); + feamap.setBoundaryConditionTypeYm(bct); + //Yp + temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueYp); + bct = new BoundaryConditionType(temp); + feamap.setBoundaryConditionTypeYp(bct); + //Zm + temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueZm); + bct = new BoundaryConditionType(temp); + feamap.setBoundaryConditionTypeZm(bct); + //Zp + temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueZp); + bct = new BoundaryConditionType(temp); + feamap.setBoundaryConditionTypeZp(bct); + + return feamap; + } + + + /** + * This method returns a FilamentRegionVariable object from a XML Element. + * Creation date: (5/16/2001 2:56:34 PM) + * + * @param param Element + * @return cbit.vcell.math.FilamentRegionVariable + */ + private FilamentRegionVariable getFilamentRegionVariable(Element param){ + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); + Domain domain = null; + if(domainStr != null){ + domain = new Domain(domainStr); + } + + //-- create new FilamentRegionVariable object + FilamentRegionVariable filRegVariable = new FilamentRegionVariable(name, domain); + transcribeComments(param, filRegVariable); + + return filRegVariable; + } + + + /** + * This method returns a FilamentSubDomain object from a XMl element. + * Creation date: (5/18/2001 4:27:22 PM) + * + * @param param Element + * @return cbit.vcell.math.FilamentSubDomain + * @throws cbit.vcell.xml.XmlParseException The exception description. + */ + private FilamentSubDomain getFilamentSubDomain(Element param, MathDescription mathDesc) throws XmlParseException{ + //get name + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + + //get outside Compartment ref + String outsideName = unMangle(param.getAttributeValue(XMLTags.OutsideCompartmentTag)); + CompartmentSubDomain outsideRef = (CompartmentSubDomain) mathDesc.getCompartmentSubDomain(outsideName); + if(outsideRef == null){ + throw new XmlParseException("The reference to the CompartmentSubDomain " + outsideName + ", could not be resolved!"); + } + //*** create new filamentSubDomain object *** + FilamentSubDomain filDomain = new FilamentSubDomain(name, outsideRef); + + //add OdeEquations + Iterator iterator = param.getChildren(XMLTags.OdeEquationTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempElement = (Element) iterator.next(); + try { + filDomain.addEquation(getOdeEquation(tempElement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding an OdeEquation to the FilamentSubDomain " + name, e); + } + } + //Add the FastSytem + filDomain.setFastSystem(getFastSystem(param.getChild(XMLTags.FastSystemTag, vcNamespace), mathDesc)); + + return filDomain; + } + + private PointSubDomain getPointSubDomain(Element param, MathDescription mathDesc) throws XmlParseException{ + //get name + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + + //*** create new pointSubDomain object *** + PointSubDomain pointDomain = new PointSubDomain(name); + + //add OdeEquations + Iterator iterator = param.getChildren(XMLTags.OdeEquationTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempElement = (Element) iterator.next(); + try { + pointDomain.addEquation(getOdeEquation(tempElement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding an OdeEquation to the FilamentSubDomain " + name, e); + } + } + String temp = param.getChildText(XMLTags.PositionXTag, vcNamespace); + if(temp != null && temp.length() > 0){ + pointDomain.setPositionX(unMangleExpression(temp)); + } + temp = param.getChildText(XMLTags.PositionYTag, vcNamespace); + if(temp != null && temp.length() > 0){ + pointDomain.setPositionY(unMangleExpression(temp)); + } + temp = param.getChildText(XMLTags.PositionZTag, vcNamespace); + if(temp != null && temp.length() > 0){ + pointDomain.setPositionZ(unMangleExpression(temp)); + } + + +// //Add the FastSytem +// pointDomain.setFastSystem( getFastSystem(param.getChild(XMLTags.FastSystemTag, vcNamespace), mathDesc) ); + + return pointDomain; + } + + + /** + * This method returns a FilamentVariable object from a XML Element. + * Creation date: (5/16/2001 2:56:34 PM) + * + * @param param Element + * @return cbit.vcell.math.FilamentVariable + */ + private FilamentVariable getFilamentVariable(Element param){ + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); + Domain domain = null; + if(domainStr != null){ + domain = new Domain(domainStr); + } + //-- create new filVariable object + FilamentVariable filVariable = new FilamentVariable(name, domain); + transcribeComments(param, filVariable); + + return filVariable; + } + + + /** + * This method returns a FluxReaction object from a XML element. + * Creation date: (3/16/2001 11:52:02 AM) + * + * @param param Element + * @return cbit.vcell.model.FluxReaction + * @throws XmlParseException + * @throws PropertyVetoException + * @throws ModelException + * @throws Exception + */ + private FluxReaction getFluxReaction(Element param, Model model) throws XmlParseException, PropertyVetoException{ + //retrieve the key if there is one + KeyValue key = null; + String keystring = param.getAttributeValue(XMLTags.KeyValueAttrTag); + + if(keystring != null && keystring.length() > 0 && this.readKeysFlag){ + key = new KeyValue(keystring); + } + + //resolve reference to the Membrane + String structureName = unMangle(param.getAttributeValue(XMLTags.StructureAttrTag)); + Membrane structureref = (Membrane) model.getStructure(structureName); + + if(structureref == null){ + throw new XmlParseException( + "The membrane " + structureName + " could not be resolved in the dictionnary!"); + } + + + //-- Instantiate new FluxReaction -- + FluxReaction fluxreaction = null; + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + + String reversibleAttributeValue = param.getAttributeValue(XMLTags.ReversibleAttrTag); + boolean bReversible = true; + if(reversibleAttributeValue != null){ + if(Boolean.TRUE.toString().equals(reversibleAttributeValue)){ + bReversible = true; + } else if(Boolean.FALSE.toString().equals(reversibleAttributeValue)){ + bReversible = false; + } else { + throw new RuntimeException("unexpected value " + reversibleAttributeValue + " for reversible flag for reaction " + name); + } + } + + try { + fluxreaction = new FluxReaction(model, structureref, key, name, bReversible); + fluxreaction.setModel(model); + if(param.getAttributeValue(XMLTags.SbmlNameAttrTag) != null){ + fluxreaction.setSbmlName(unMangle(param.getAttributeValue(XMLTags.SbmlNameAttrTag))); + } + + } catch(Exception e){ + throw new XmlParseException("An exception occurred while trying to create the FluxReaction " + name, e); + } + //resolve reference to the fluxCarrier + if(param.getAttribute(XMLTags.FluxCarrierAttrTag) != null){ + String speciesname = unMangle(param.getAttributeValue(XMLTags.FluxCarrierAttrTag)); + Species specieref = model.getSpecies(speciesname); + if(specieref != null){ + Feature insideFeature = model.getStructureTopology().getInsideFeature(structureref); + try { + if(insideFeature != null){ + SpeciesContext insideSpeciesContext = model.getSpeciesContext(specieref, insideFeature); + fluxreaction.addProduct(insideSpeciesContext, 1); + } + Feature outsideFeature = model.getStructureTopology().getOutsideFeature(structureref); + if(outsideFeature != null){ + SpeciesContext outsideSpeciesContext = model.getSpeciesContext(specieref, outsideFeature); + fluxreaction.addReactant(outsideSpeciesContext, 1); + } + } catch(ModelException e){ + throw new XmlParseException(e.getMessage(), e); + } + } + } + //Annotation +// String rsAnnotation = null; +// String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace); +// if (annotationText!=null && annotationText.length()>0) { +// rsAnnotation = unMangle(annotationText); +// } +// fluxreaction.setAnnotation(rsAnnotation); + + //set the fluxOption + String fluxOptionString = null; + fluxOptionString = param.getAttributeValue(XMLTags.FluxOptionAttrTag); + if(fluxOptionString != null && fluxOptionString.length() > 0){ + try { + if(fluxOptionString.equals(XMLTags.FluxOptionElectricalOnly)){ + fluxreaction.setPhysicsOptions(FluxReaction.PHYSICS_ELECTRICAL_ONLY); + } else if(fluxOptionString.equals(XMLTags.FluxOptionMolecularAndElectrical)){ + fluxreaction.setPhysicsOptions(FluxReaction.PHYSICS_MOLECULAR_AND_ELECTRICAL); + } else if(fluxOptionString.equals(XMLTags.FluxOptionMolecularOnly)){ + fluxreaction.setPhysicsOptions(FluxReaction.PHYSICS_MOLECULAR_ONLY); + } + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A propertyVetoException was fired when setting the fluxOption to the flux reaction " + name, e); + } + } + + //Add Reactants, if any + try { + Iterator iterator = param.getChildren(XMLTags.ReactantTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element temp = iterator.next(); + //Add Reactant to this SimpleReaction + fluxreaction.addReactionParticipant(getReactant(temp, fluxreaction, model)); + } + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("Error adding a reactant to the reaction " + name + " : " + e.getMessage(), e); + } + + //Add Products, if any + try { + Iterator iterator = param.getChildren(XMLTags.ProductTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element temp = iterator.next(); + //Add Product to this simplereaction + fluxreaction.addReactionParticipant(getProduct(temp, fluxreaction, model)); + } + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("Error adding a product to the reaction " + name + " : " + e.getMessage(), e); + } + + //Add Catalyst(Modifiers) (if there are) + Iterator iterator = param.getChildren(XMLTags.CatalystTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element temp = iterator.next(); + fluxreaction.addReactionParticipant(getCatalyst(temp, fluxreaction, model)); + } + //Add Kinetics + fluxreaction.setKinetics(getKinetics(param.getChild(XMLTags.KineticsTag, vcNamespace), fluxreaction, model)); + + //set the valence (for legacy support for "chargeCarrierValence" stored with reaction). + String valenceString = null; + try { + valenceString = unMangle(param.getAttributeValue(XMLTags.FluxCarrierValenceAttrTag)); + if(valenceString != null && valenceString.length() > 0){ + KineticsParameter chargeValenceParameter = fluxreaction.getKinetics().getChargeValenceParameter(); + if(chargeValenceParameter != null){ + chargeValenceParameter.setExpression(new Expression(Integer.parseInt(unMangle(valenceString)))); + } + } + } catch(NumberFormatException e){ + throw new XmlParseException("A NumberFormatException was fired when setting the (integer) valence '" + valenceString + "' (integer) to the flux reaction " + name, e); + } + return fluxreaction; + } + + + /** + * This method creates a FormalSpeciesInfo from a XML representation. + * Creation date: (6/3/2003 9:11:26 PM) + * + * @param speciesInfoElement Element + * @return cbit.vcell.dictionary.FormalSpeciesInfo + */ + private FormalSpeciesInfo getFormalSpeciesInfo(Element speciesInfoElement) throws XmlParseException{ + //get formalID + String formalID = unMangle(speciesInfoElement.getAttributeValue(XMLTags.FormalIDTag)); + //get names + List namesList = speciesInfoElement.getChildren(XMLTags.NameTag, vcNamespace); + String[] namesArray = new String[namesList.size()]; + int nameCounter = 0; + for(Element nameElement : namesList){ + namesArray[nameCounter] = unMangle(nameElement.getText()); + nameCounter++; + } + String tempstring; + //get type + String type = speciesInfoElement.getAttributeValue(XMLTags.TypeAttrTag); + FormalSpeciesInfo formalSpeciesInfo = null; + + if(type.equalsIgnoreCase(XMLTags.CompoundTypeTag)){ + //get formula + String formula = null; + tempstring = speciesInfoElement.getAttributeValue(XMLTags.FormulaTag); + if(tempstring != null){ + formula = unMangle(tempstring); + } + + //get CASID + String casid = null; + tempstring = speciesInfoElement.getAttributeValue(XMLTags.CasIDTag); + if(tempstring != null){ + casid = unMangle(tempstring); + } + + //get Enzymes + List enzymelist = speciesInfoElement.getChildren(XMLTags.EnzymeTag, vcNamespace); + EnzymeRef[] enzymeArray = null; + + if(enzymelist != null && enzymelist.size() > 0){ + enzymeArray = new EnzymeRef[enzymelist.size()]; + int enzymeCounter = 0; + for(Element enzymeElement : enzymelist){ + //get ECNumber + String ecnumber = unMangle(enzymeElement.getAttributeValue(XMLTags.ECNumberTag)); + //get Enzymetype + String enztypestr = enzymeElement.getAttributeValue(XMLTags.TypeAttrTag); + char enzymetype = enztypestr.charAt(0); + enzymeArray[enzymeCounter] = new EnzymeRef(ecnumber, enzymetype); + enzymeCounter++; + } + } + + //create new CompoundInfo + formalSpeciesInfo = new CompoundInfo(formalID, namesArray, formula, casid, enzymeArray); + } else if(type.equalsIgnoreCase(XMLTags.EnzymeTypeTag)){ + //get reaction + String reaction = null; + tempstring = speciesInfoElement.getAttributeValue(XMLTags.ExpressionAttrTag); + if(tempstring != null){ + reaction = unMangle(tempstring); + } + //get sysname + String sysname = null; + tempstring = speciesInfoElement.getAttributeValue(XMLTags.SysNameTag); + if(tempstring != null){ + sysname = unMangle(tempstring); + } + //get argcasID + String casid = null; + tempstring = speciesInfoElement.getAttributeValue(XMLTags.CasIDTag); + if(tempstring != null){ + casid = unMangle(tempstring); + } + //create new EnzymeInfo + formalSpeciesInfo = new EnzymeInfo(formalID, namesArray, reaction, sysname, casid); + } else if(type.equalsIgnoreCase(XMLTags.ProteinTypeTag)){ + //get organism + String organism = null; + tempstring = speciesInfoElement.getAttributeValue(XMLTags.OrganismTag); + if(tempstring != null){ + organism = unMangle(tempstring); + } + //get accession + String accession = null; + tempstring = speciesInfoElement.getAttributeValue(XMLTags.AccessionTag); + if(tempstring != null){ + accession = unMangle(tempstring); + } + //get keywords + String keywords = null; + tempstring = speciesInfoElement.getAttributeValue(XMLTags.KeywordsTag); + if(tempstring != null){ + keywords = unMangle(tempstring); + } + //get description + String description = null; + tempstring = speciesInfoElement.getAttributeValue(XMLTags.DescriptionTag); + if(tempstring != null){ + description = unMangle(tempstring); + } + //create new ProteinInfo + formalSpeciesInfo = new ProteinInfo(formalID, namesArray, organism, accession, keywords, description); + } else { + throw new XmlParseException("FormalSpeciesInfo type " + type + ", not supported yet!"); + } + + return formalSpeciesInfo; + } + + + /** + * This method returns a Function variable object from a XML Element. + * Creation date: (5/16/2001 3:45:21 PM) + * + * @param param Element + * @return cbit.vcell.math.Function + * @throws cbit.vcell.xml.XmlParseException The exception description. + */ + private Function getFunction(Element param) throws XmlParseException{ + //get attributes + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + + +/** --------------------------------------------------------------- + * ATTENTATION: this is a quick fix for a specific user to load his model + * with a function name as "ATP/ADP". This syntax is not allowed. + -----------------------------------------------------------------------*/ + if(name.equals("ATP/ADP")){ + name = "ATP_ADP_renamed"; + System.err.print("Applying species function name change ATP/ADP to ATP_ADP for a specific user (key=2288008)"); + Thread.dumpStack(); + } + + + String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); + Domain domain = null; + if(domainStr != null){ + domain = new Domain(domainStr); + } + String temp = param.getText(); + + Expression exp = unMangleExpression(temp); + + //-- create new Function -- + Function function = new Function(name, exp, domain); + transcribeComments(param, function); + + return function; + } + + private AnnotatedFunction getOutputFunction(Element param) throws XmlParseException{ + //get attributes + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String temp = param.getText(); + Expression exp = unMangleExpression(temp); + String errStr = unMangle(param.getAttributeValue(XMLTags.ErrorStringTag)); + + VariableType funcType = VariableType.UNKNOWN; + String funcTypeAttr = param.getAttributeValue(XMLTags.FunctionTypeTag); + if(funcTypeAttr != null){ + String funcTypeStr = unMangle(funcTypeAttr); + funcType = VariableType.getVariableTypeFromVariableTypeName(funcTypeStr); + } + + //-- create new AnnotatedFunction -- + String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); + Domain domain = null; + if(domainStr != null){ + domain = new Domain(domainStr); + } + AnnotatedFunction function = new AnnotatedFunction(name, exp, domain, errStr, funcType, FunctionCategory.OUTPUTFUNCTION); + + return function; + } + + /** + * This method returns a Geometry object from a XML representation. + * Creation date: (4/26/2001 12:12:18 PM) + * + * @param param Element + * @return cbit.vcell.geometry.Geometry + * @throws cbit.vcell.xml.XmlParseException The exception description. + */ + public Geometry getGeometry(Element param) throws XmlParseException{ + // + // A BioModel stores a full copy of its geometry -- image included -- inside EVERY + // (Xmlproducer writes it there), so a model with N spatial + // applications on one geometry arrives here N times with byte-identical elements. + // Parsing each one separately cost a 62 MP model ~1.4 GB of peak heap PER COPY and + // killed two prod api pods (#2021); the same element is parsed once and shared. + // + // Only exactly identical elements share. Nothing here tries to decide that two + // *different* geometries are equivalent -- that is a much harder question and not + // one a parser should be answering. + // + String digest = geometryElementDigest(param); + if(digest != null){ + Geometry alreadyParsed = parsedGeometriesByDigest.get(digest); + if(alreadyParsed != null){ + if(lg.isDebugEnabled()){ + lg.debug("reusing already-parsed geometry '" + alreadyParsed.getName() + + "' for an identical element in this document"); + } + return alreadyParsed; + } + } + Geometry geometry = parseGeometry(param); + if(digest != null){ + parsedGeometriesByDigest.put(digest, geometry); + } + return geometry; + } + + /** + * A stable key for a element, or null to disable sharing for this element. + * + * The element is streamed through the digest rather than turned into a String first: the + * element holds the image as hex text, so for the model in #2021 that String would be tens + * of MB -- allocating it to avoid allocations would be self-defeating. + * + * Returns null (meaning "parse it, do not share it") if sharing is switched off or if the + * digest cannot be computed, so a failure here costs performance and never correctness. + */ + private String geometryElementDigest(Element param){ + if(param == null || !PropertyLoader.getBooleanProperty(PROPERTY_SHARE_IDENTICAL_GEOMETRIES, false)){ + return null; + } + return elementDigest(param); + } + + private String imageElementDigest(Element param){ + if(param == null || !PropertyLoader.getBooleanProperty(PROPERTY_SHARE_IDENTICAL_IMAGES, true)){ + return null; + } + return elementDigest(param); + } + + private String elementDigest(Element param){ + try { + MessageDigest md = MessageDigest.getInstance("SHA-256"); + try (java.io.OutputStream sink = new java.security.DigestOutputStream( + java.io.OutputStream.nullOutputStream(), md)) { + new org.jdom2.output.XMLOutputter().output(param, sink); + } + return Hex.toString(md.digest()); + } catch(Exception e){ + lg.warn("could not digest <" + param.getName() + "> element, parsing it without sharing: " + + e.getMessage()); + return null; + } + } + + private Geometry parseGeometry(Element param) throws XmlParseException{ + //Get the Extent object + Extent newextent = getExtent(param.getChild(XMLTags.ExtentTag, vcNamespace)); + //Get VCimage information + VCImage newimage = null; + if(param.getChild(XMLTags.ImageTag, vcNamespace) != null){ + try { + newimage = getVCImage(param.getChild(XMLTags.ImageTag, vcNamespace), newextent); + } catch(Throwable e){ + throw new XmlParseException(e); + } + } + + //Get attributes + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + int newdimension = Integer.parseInt(param.getAttributeValue(XMLTags.DimensionAttrTag)); + //Get Version + Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace)); + + //Try to construct the geometry upon four different cases + Geometry newgeometry = null; + if(version != null && newimage != null){ + newgeometry = new Geometry(version, newimage); + } else if(version != null){ + newgeometry = new Geometry(version, newdimension); + } else if(newimage != null){ + newgeometry = new Geometry(name, newimage); + } else { + newgeometry = new Geometry(name, newdimension); + } + + //set attributes + try { + if(!newgeometry.getName().equalsIgnoreCase(name)){ + newgeometry.setName(name); + } + + //String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag); + + //if (annotation!=null) { + //newgeometry.setDescription( unMangle(annotation) ); + //} + //Add annotation + String annotation = param.getChildText(XMLTags.AnnotationTag, vcNamespace); + if(annotation != null && annotation.length() > 0){ + newgeometry.setDescription(unMangle(annotation)); + } + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A PropertyVetoException occurred when setting the name " + name + " to a Geometry object!", e); + } + //Add the Extent + try { + newgeometry.getGeometrySpec().setExtent(newextent); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A PropertyVetoException occurred while trying to set the Extent for the Geometry " + name, e); + } + //Add the Origin + newgeometry.getGeometrySpec().setOrigin(getOrigin(param.getChild(XMLTags.OriginTag, vcNamespace))); + + //Add the SubVolumes + List children = param.getChildren(XMLTags.SubVolumeTag, vcNamespace); + SubVolume[] newsubvolumes = new SubVolume[children.size()]; + int subvolumeCounter = 0; + for(Element child : children){ + newsubvolumes[subvolumeCounter] = getSubVolume(child); + subvolumeCounter++; + } + try { + newgeometry.getGeometrySpec().setSubVolumes(newsubvolumes); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A PropertyVetoException was generated when ading the subvolumes to the Geometry " + name, e); + } + if(newgeometry.getDimension() > 0){ + //Add SurfaceClasses + List surfaceClassChildren = param.getChildren(XMLTags.SurfaceClassTag, vcNamespace); + SurfaceClass[] newSurfaceClassArr = new SurfaceClass[surfaceClassChildren.size()]; + int surfClassCounter = 0; + for(Element surfClassChild : surfaceClassChildren){ + newSurfaceClassArr[surfClassCounter] = getSurfaceClass(surfClassChild, newgeometry); + surfClassCounter++; + } + try { + newgeometry.getGeometrySurfaceDescription().setSurfaceClasses(newSurfaceClassArr); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A PropertyVetoException was generated when ading the subvolumes to the Geometry " + name, e); + } + } + //read Filaments (if any) + Iterator iterator = param.getChildren(XMLTags.FilamentTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempElement = iterator.next(); + + String filname = unMangle(tempElement.getAttributeValue(XMLTags.NameAttrTag)); + Iterator curveiterator = tempElement.getChildren().iterator(); + while (curveiterator.hasNext()) { + ControlPointCurve curve = getControlPointCurve(curveiterator.next()); + newgeometry.getGeometrySpec().getFilamentGroup().addCurve(filname, curve); + } + } + //read Surface description (if any) + Element sd = param.getChild(XMLTags.SurfaceDescriptionTag, vcNamespace); + if(sd != null){ + GeometrySurfaceDescription dummy = getGeometrySurfaceDescription(sd, newgeometry); + } + + try { + newgeometry.precomputeAll(new GeometryThumbnailImageFactoryAWT(), false, false); + } catch(GeometryException | ImageException | ExpressionException e){ + lg.error(e); + } + return newgeometry; + } + + + private GeometrySurfaceDescription getGeometrySurfaceDescription(Element param, Geometry geom) throws XmlParseException{ + + GeometrySurfaceDescription gsd = geom.getGeometrySurfaceDescription(); + String cutoffStr = param.getAttributeValue(XMLTags.CutoffFrequencyAttrTag); + String xDim = param.getAttributeValue(XMLTags.NumSamplesXAttrTag); + String yDim = param.getAttributeValue(XMLTags.NumSamplesYAttrTag); + String zDim = param.getAttributeValue(XMLTags.NumSamplesZAttrTag); + if(cutoffStr == null || xDim == null || yDim == null || zDim == null){ + throw new XmlParseException("Attributes for element Surface Description not properly set, under geometry: " + + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag)); + } + try { + ISize isize = new ISize(Integer.parseInt(xDim), Integer.parseInt(yDim), Integer.parseInt(zDim)); + gsd.setVolumeSampleSize(isize); + gsd.setFilterCutoffFrequency(Double.parseDouble(cutoffStr)); + + //these lists are allowed to be empty. + ArrayList memRegions = new ArrayList(param.getChildren(XMLTags.MembraneRegionTag, vcNamespace)); + ArrayList volRegions = new ArrayList(param.getChildren(XMLTags.VolumeRegionTag, vcNamespace)); + ArrayList regions = new ArrayList(); + GeometryUnitSystem geometryUnitSystem = geom.getUnitSystem(); + for(Element temp : volRegions){ + String regionID = temp.getAttributeValue(XMLTags.RegionIDAttrTag); + String name = temp.getAttributeValue(XMLTags.NameAttrTag); + String subvolumeRef = temp.getAttributeValue(XMLTags.SubVolumeAttrTag); + if(regionID == null || name == null || subvolumeRef == null){ + throw new XmlParseException("Attributes for element Volume Region not properly set, under geometry: " + + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag)); + } + SubVolume subvolume = geom.getGeometrySpec().getSubVolume(subvolumeRef); + if(subvolume == null){ + throw new XmlParseException("The subvolume " + subvolumeRef + " could not be resolved."); + } + double size = -1; + VCUnitDefinition unit = null; + String sizeStr = temp.getAttributeValue(XMLTags.SizeAttrTag); + if(sizeStr != null){ + size = Double.parseDouble(sizeStr); + String unitSymbol = temp.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); + if(unitSymbol != null){ + unit = geometryUnitSystem.getInstance(unitSymbol); + } + } + VolumeGeometricRegion vgr = new VolumeGeometricRegion(name, size, unit, subvolume, Integer.parseInt(regionID)); + regions.add(vgr); + } + for(Element temp : memRegions){ + String volRegion_1 = temp.getAttributeValue(XMLTags.VolumeRegion_1AttrTag); + String volRegion_2 = temp.getAttributeValue(XMLTags.VolumeRegion_2AttrTag); + String name = temp.getAttributeValue(XMLTags.NameAttrTag); + if(volRegion_1 == null || volRegion_2 == null || name == null){ + throw new XmlParseException("Attributes for element Membrane Region not properly set, under geometry: " + + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag)); + } + VolumeGeometricRegion region1 = getAdjacentVolumeRegion(regions, volRegion_1); + VolumeGeometricRegion region2 = getAdjacentVolumeRegion(regions, volRegion_2); + if(region1 == null || region2 == null){ + throw new XmlParseException("Element Membrane Region refernces invalid volume regions, under geometry: " + + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag)); + } + double size = -1; + VCUnitDefinition unit = null; + String sizeStr = temp.getAttributeValue(XMLTags.SizeAttrTag); + if(sizeStr != null){ + size = Double.parseDouble(sizeStr); + String unitSymbol = temp.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); + if(unitSymbol != null){ + unit = geometryUnitSystem.getInstance(unitSymbol); + } + } + SurfaceGeometricRegion rsl = new SurfaceGeometricRegion(name, size, unit); + rsl.addAdjacentGeometricRegion(region1); + region1.addAdjacentGeometricRegion(rsl); + rsl.addAdjacentGeometricRegion(region2); + region2.addAdjacentGeometricRegion(rsl); + regions.add(rsl); + } + if(regions.size() > 0){ + gsd.setGeometricRegions((GeometricRegion[]) regions.toArray(new GeometricRegion[regions.size()])); + } + } catch(Exception e){ + lg.error("Unable to read geometry surface description from XML, for geometry: " + + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag), e); + } + + return gsd; + } + + + /** + * This method returns a GroupAccess object from an XML format. + * Creation date: (5/23/2003 7:27:10 PM) + * + * @param xmlGroup Element + * @return cbit.vcell.server.GroupAccess + */ + private GroupAccess getGroupAccess(Element xmlGroup){ + //guess the type of group + String temp = xmlGroup.getAttributeValue(XMLTags.TypeAttrTag); + java.math.BigDecimal type = new java.math.BigDecimal(temp); + + if(type.equals(GroupAccess.GROUPACCESS_ALL)){ + //Type ALL + return new GroupAccessAll(); + } else if(type.equals(GroupAccess.GROUPACCESS_NONE)){ + //Type NONE + return new GroupAccessNone(); + } else { + //Type SOME + //Read attributes + //*groupid + temp = xmlGroup.getAttributeValue(XMLTags.TypeAttrTag); + java.math.BigDecimal groupid = new java.math.BigDecimal(temp); + //*hash + temp = xmlGroup.getAttributeValue(XMLTags.HashAttrTag); + java.math.BigDecimal hashcode = new java.math.BigDecimal(temp); + //*users + List userlist = xmlGroup.getChildren(XMLTags.UserTag, vcNamespace); + User[] userArray = new User[userlist.size()]; + boolean[] booleanArray = new boolean[userlist.size()]; + int counter = 0; + for(Element userElement : userlist){ + String userid = unMangle(userElement.getAttributeValue(XMLTags.NameAttrTag)); + KeyValue key = new KeyValue(userElement.getAttributeValue(XMLTags.KeyValueAttrTag)); + boolean hidden = Boolean.valueOf(userElement.getAttributeValue(XMLTags.HiddenTag)).booleanValue(); + userArray[counter] = new User(userid, key); + booleanArray[counter] = hidden; + counter++; + } + //create and return the GroupAccess + return new GroupAccessSome(groupid, hashcode, userArray, booleanArray); + } + } + + + /** + * This method returns an ImageSubVolume object from a XML representation. + * Creation date: (5/1/2001 5:26:17 PM) + * + * @param param Element + * @return cbit.vcell.geometry.ImageSubVolume + */ + private ImageSubVolume getImageSubVolume(Element param) throws XmlParseException{ + //retrieve the attributes + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + int handle = Integer.parseInt(param.getAttributeValue(XMLTags.HandleAttrTag)); + int imagePixelValue = Integer.parseInt(param.getAttributeValue(XMLTags.ImagePixelValueTag)); + + //Get the PixelClass from image (image should be a sibling of this subVolume element) + Element imageElement = ((Element) param.getParent()).getChild(XMLTags.ImageTag, vcNamespace); + if(imageElement == null){ + throw new XmlParseException("image not found in geometry corresponding to ImageSubVolume"); + } + + List pixelClassList = imageElement.getChildren(XMLTags.PixelClassTag, vcNamespace); + VCPixelClass pixelClass = null; + for(Element pixelClassElement : pixelClassList){ + VCPixelClass pc = getPixelClass(pixelClassElement); + if(pc.getPixel() == imagePixelValue){ + pixelClass = pc; + } + } + if(pixelClass == null){ + throw new XmlParseException("image pixelclass(pixel=" + imagePixelValue + ") not found while creating ImageSubVolume " + name); + } + + //retrieve the key if there is one + KeyValue key = null; + String stringkey = param.getAttributeValue(XMLTags.KeyValueAttrTag); + + if(stringkey != null && stringkey.length() > 0 && this.readKeysFlag){ + key = new KeyValue(stringkey); + } + + //Create the new Image SubVolume + ImageSubVolume newsubvolume = new ImageSubVolume(key, pixelClass, handle); + //set name + try { + newsubvolume.setName(name); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A propertyVetoException was generated when setting the name " + name + " to an ImageSubvolume object!", e); + } + + return newsubvolume; + } + + + /** + * This method returns an InsideVariable object from a XML Element + * Creation date: (5/18/2001 6:14:42 PM) + * + * @param param Element + * @return cbit.vcell.math.InsideVariable + */ + private InsideVariable getInsideVariable(Element param){ + //Get name + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + //get VolVariableRef + String volvarName = unMangle(param.getAttributeValue(XMLTags.VolumeVariableAttrTag)); + + //*** create new InsideVariable *** + InsideVariable variable = new InsideVariable(name, volvarName); + transcribeComments(param, variable); + + return variable; + } + + + /** + * This method returns a JumpCondition object from a XML Element. + * Creation date: (5/18/2001 5:10:10 PM) + * + * @param param Element + * @return cbit.vcell.math.JumpCondition + * @throws cbit.vcell.xml.XmlParseException The exception description. + */ + private JumpCondition getJumpCondition(Element param, MathDescription mathDesc) throws XmlParseException{ + //get VolVariable ref + String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + + Variable var = mathDesc.getVariable(varname); + if(var == null){ + throw new XmlParseException("The reference to the Variable " + varname + ", could not be resolved!"); + } + + JumpCondition jumpCondition = null; + if(var instanceof VolVariable){ + jumpCondition = new JumpCondition((VolVariable) var); + } else if(var instanceof VolumeRegionVariable){ + jumpCondition = new JumpCondition((VolumeRegionVariable) var); + } else { + throw new XmlParseException("unexpected variable type for jump condition"); + } + + //process InFlux + String temp = param.getChildText(XMLTags.InFluxTag, vcNamespace); + Expression exp = unMangleExpression(temp); + jumpCondition.setInFlux(exp); + + + //process OutFlux + temp = param.getChildText(XMLTags.OutFluxTag, vcNamespace); + exp = unMangleExpression(temp); + jumpCondition.setOutFlux(exp); + + return jumpCondition; + } + + + /** + * The method returns a JumpProcess object from a XML element. + * Creation date: (7/24/2006 6:28:42 PM) + * + * @param param Element + * @param md cbit.vcell.math.MathDescription + * @return cbit.vcell.math.JumpProcess + * @throws cbit.vcell.xml.XmlParseException The exception description. + */ + private JumpProcess getJumpProcess(Element param, MathDescription md) throws XmlParseException{ + //name + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + //probability rate + Element pb = param.getChild(XMLTags.ProbabilityRateTag, vcNamespace); + Expression exp = unMangleExpression(pb.getText()); + + JumpProcess jump = new JumpProcess(name, exp); + //add actions + Iterator iterator = param.getChildren(XMLTags.ActionTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + try { + jump.addAction(getAction(tempelement, md)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding a new Action to the JumpProcess " + name, e); + } catch(ExpressionException e){ + lg.error(e); + } + } + + return jump; + } + + private ParticleInitialConditionCount getParticleInitialConditionCount(Element param){ + String temp = param.getChildText(XMLTags.ParticleCountTag, vcNamespace); + Expression countExp = null; + if(temp != null && temp.length() > 0){ + countExp = unMangleExpression(temp); + } + temp = param.getChildText(XMLTags.ParticleLocationXTag, vcNamespace); + Expression locXExp = null; + if(temp != null && temp.length() > 0){ + locXExp = unMangleExpression(temp); + } + temp = param.getChildText(XMLTags.ParticleLocationYTag, vcNamespace); + Expression locYExp = null; + if(temp != null && temp.length() > 0){ + locYExp = unMangleExpression(temp); + } + temp = param.getChildText(XMLTags.ParticleLocationZTag, vcNamespace); + Expression locZExp = null; + if(temp != null && temp.length() > 0){ + locZExp = unMangleExpression(temp); + } + + return new ParticleInitialConditionCount(countExp, locXExp, locYExp, locZExp); + } + + private ParticleProperties getParticleProperties(Element param, MathDescription mathDesc) throws XmlParseException{ + //Retrieve the variable reference + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + Variable varref = mathDesc.getVariable(name); + if(varref == null){ + throw new XmlParseException("The variable " + name + " for a PdeEquation, could not be resolved!"); + } + + ArrayList initialConditions = new ArrayList(); + Iterator iterator = param.getChildren(XMLTags.ParticleInitialCountTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + initialConditions.add(getParticleInitialConditionCount(tempelement)); + } + iterator = param.getChildren(XMLTags.ParticleInitialCountTag_old, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + initialConditions.add(getParticleInitialConditionCount(tempelement)); + } + iterator = param.getChildren(XMLTags.ParticleInitialConcentrationTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + + String temp = tempelement.getChildText(XMLTags.ParticleDistributionTag, vcNamespace); + Expression distExp = null; + if(temp != null && temp.length() > 0){ + distExp = unMangleExpression(temp); + } + initialConditions.add(new ParticleInitialConditionConcentration(distExp)); + } + + String temp = param.getChildText(XMLTags.ParticleDiffusionTag, vcNamespace); + Expression diffExp = null; + if(temp != null && temp.length() > 0){ + diffExp = unMangleExpression(temp); + } + + String driftXString = param.getChildText(XMLTags.ParticleDriftXTag, vcNamespace); + Expression driftXExp = null; + if(driftXString != null && driftXString.length() > 0){ + driftXExp = unMangleExpression(driftXString); + } + + String driftYString = param.getChildText(XMLTags.ParticleDriftYTag, vcNamespace); + Expression driftYExp = null; + if(driftYString != null && driftYString.length() > 0){ + driftYExp = unMangleExpression(driftYString); + } + + String driftZString = param.getChildText(XMLTags.ParticleDriftZTag, vcNamespace); + Expression driftZExp = null; + if(driftZString != null && driftZString.length() > 0){ + driftZExp = unMangleExpression(driftZString); + } + + return new ParticleProperties(varref, diffExp, driftXExp, driftYExp, driftZExp, initialConditions); + } + + private ParticleJumpProcess getParticleJumpProcess(Element param, MathDescription md) throws XmlParseException{ + //name + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + + LangevinParticleJumpProcess.ParticleSubtype subtype = LangevinParticleJumpProcess.ParticleSubtype.INCOMPATIBLE; + boolean isLangevin = false; + if(param.getAttribute(XMLTags.LangevinParticleJumpProcessSubtypeTag) != null){ + isLangevin = true; + String stString = param.getAttributeValue(XMLTags.LangevinParticleJumpProcessSubtypeTag); + subtype = LangevinParticleJumpProcess.ParticleSubtype.fromName(stString); + } + LangevinParticleJumpProcess.ParticleTransitionCondition transitionCondition = null; + Expression bondLength = new Expression(1.0); // that's the default, even for non-binding rules (we hide it anyway for those) + if(isLangevin && param.getAttribute(XMLTags.LangevinParticleJumpProcessBondLengthTag) != null){ + try { + bondLength = new Expression(param.getAttributeValue(XMLTags.LangevinParticleJumpProcessBondLengthTag)); + } catch(ExpressionException e){ + throw new XmlParseException("unparseable " + XMLTags.LangevinParticleJumpProcessBondLengthTag + + " '" + param.getAttributeValue(XMLTags.LangevinParticleJumpProcessBondLengthTag) + "'", e); + } + } + if(isLangevin && param.getAttribute(XMLTags.LangevinParticleJumpProcessTransitionConditionTag) != null){ + String tcString = param.getAttributeValue(XMLTags.LangevinParticleJumpProcessTransitionConditionTag); + transitionCondition = LangevinParticleJumpProcess.ParticleTransitionCondition.fromVcellName(tcString); + } + + ProcessSymmetryFactor processSymmetryFactor = null; + Attribute symmetryFactorAttr = param.getAttribute(XMLTags.ProcessSymmetryFactorAttrTag); + if(symmetryFactorAttr != null){ + processSymmetryFactor = new ProcessSymmetryFactor(Double.parseDouble(symmetryFactorAttr.getValue())); + } + + // selected particle + List varList = new ArrayList(); + Iterator iterator = param.getChildren(XMLTags.SelectedParticleTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + String varname = unMangle(tempelement.getAttributeValue(XMLTags.NameAttrTag)); + Variable var = md.getVariable(varname); + if(!(var instanceof ParticleVariable)){ + throw new XmlParseException("Not a ParticleVariable in ParticleJumpProcess."); + } + varList.add((ParticleVariable) var); + } + + //probability rate + JumpProcessRateDefinition jprd = null; + //for old models + Element pb = param.getChild(XMLTags.ParticleProbabilityRateTag, vcNamespace); + if(pb != null){ + Expression exp = unMangleExpression(pb.getText()); + jprd = new MacroscopicRateConstant(exp); + } else //for new models + { + pb = param.getChild(XMLTags.MacroscopicRateConstantTag, vcNamespace); + if(pb != null) //jump process rate defined by macroscopic rate constant + { + Expression exp = unMangleExpression(pb.getText()); + jprd = new MacroscopicRateConstant(exp); + } else //jump process rate defined by binding radius + { + pb = param.getChild(XMLTags.InteractionRadiusTag, vcNamespace); + if(pb != null){ + Expression exp = unMangleExpression(pb.getText()); + jprd = new InteractionRadius(exp); + } + } + } + //add actions + List actionList = new ArrayList(); + iterator = param.getChildren(XMLTags.ActionTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + try { + actionList.add(getAction(tempelement, md)); + } catch(MathException | ExpressionException e){ + throw new XmlParseException(e); + } + } + + ParticleJumpProcess jump; + if(isLangevin){ + jump = new LangevinParticleJumpProcess(name, varList, jprd, actionList, processSymmetryFactor); + ((LangevinParticleJumpProcess) jump).setSubtype(subtype); + if(LangevinParticleJumpProcess.ParticleSubtype.TRANSITION == subtype){ + ((LangevinParticleJumpProcess) jump).setTransitionCondition(transitionCondition); + } else if(LangevinParticleJumpProcess.ParticleSubtype.BINDING == subtype){ + ((LangevinParticleJumpProcess) jump).setBondLength(bondLength); + } + } else { + jump = new ParticleJumpProcess(name, varList, jprd, actionList, processSymmetryFactor); + } + return jump; + } + + /** + * This method returns a Kinetics object from a XML Element based on the value of the kinetics type attribute. + * Creation date: (3/19/2001 4:42:04 PM) + * + * @param param Element + * @return cbit.vcell.model.Kinetics + */ + private Kinetics getKinetics(Element param, ReactionStep reaction, Model model) throws XmlParseException{ + VariableHash varHash = new VariableHash(); + addResevedSymbols(varHash, model); + + String type = param.getAttributeValue(XMLTags.KineticsTypeAttrTag); + Kinetics newKinetics = null; + try { + if(type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralKinetics)){ + //create a general kinetics + newKinetics = new GeneralKinetics(reaction); + } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralCurrentKinetics)){ + //Create GeneralCurrentKinetics + newKinetics = new GeneralCurrentKinetics(reaction); + } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeMassAction) && reaction instanceof SimpleReaction){ + //create a Mass Action kinetics + newKinetics = new MassActionKinetics((SimpleReaction) reaction); + } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeNernst) && reaction instanceof FluxReaction){ + // create NernstKinetics + newKinetics = new NernstKinetics((FluxReaction) reaction); + } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeGHK) && reaction instanceof FluxReaction){ + //create GHKKinetics + newKinetics = new GHKKinetics((FluxReaction) reaction); + } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeHMM_Irr) && reaction instanceof SimpleReaction){ + //create HMM_IrrKinetics + newKinetics = new HMM_IRRKinetics((SimpleReaction) reaction); + } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeHMM_Rev) && reaction instanceof SimpleReaction){ + //create HMM_RevKinetics + newKinetics = new HMM_REVKinetics((SimpleReaction) reaction); + } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralTotal_oldname)){ + //create GeneralTotalKinetics + newKinetics = new GeneralLumpedKinetics(reaction); + } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralLumped)){ + //create GeneralLumpedKinetics + newKinetics = new GeneralLumpedKinetics(reaction); + } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralCurrentLumped)){ + //create GeneralCurrentLumpedKinetics + newKinetics = new GeneralCurrentLumpedKinetics(reaction); + } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralPermeability) && reaction instanceof FluxReaction){ + // create GeneralPermeabilityKinetics + newKinetics = new GeneralPermeabilityKinetics((FluxReaction) reaction); + } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeMacroscopic_Irr) && reaction instanceof SimpleReaction){ + // create Macroscopic_IRRKinetics + newKinetics = new Macroscopic_IRRKinetics((SimpleReaction) reaction); + } else if(type.equalsIgnoreCase(XMLTags.KineticsTypeMicroscopic_Irr) && reaction instanceof SimpleReaction){ + // create Microscopic_IRRKinetics + newKinetics = new Microscopic_IRRKinetics((SimpleReaction) reaction); + } else { + throw new XmlParseException("Unknown kinetics type: " + type); + } + } catch(ExpressionException e){ + throw new XmlParseException("Error creating the kinetics for reaction: " + reaction.getName(), e); + } + + try { + newKinetics.reading(true); // transaction begin flag ... yeah, this is a hack + + //Read all of the parameters + List list = param.getChildren(XMLTags.ParameterTag, vcNamespace); + + // add constants that may be used in kinetics. + // VariableHash varHash = getVariablesHash(); + ArrayList reserved = new ArrayList(); + + ReservedSymbol[] reservedSymbols = reaction.getModel().getReservedSymbols(); + for(ReservedSymbol rs : reservedSymbols){ + reserved.add(rs.getName()); + } + + try { + if(reaction.getStructure() instanceof Membrane){ + Membrane membrane = (Membrane) reaction.getStructure(); + varHash.addVariable(new Constant(membrane.getMembraneVoltage().getName(), new Expression(0.0))); + reserved.add(membrane.getMembraneVoltage().getName()); + } + // + // add Reactants, Products, and Catalysts (ReactionParticipants) + // + ReactionParticipant rp[] = reaction.getReactionParticipants(); + for(int i = 0; i < rp.length; i++){ + varHash.addVariable(new Constant(rp[i].getName(), new Expression(0.0))); + } + } catch(MathException e){ + throw new XmlParseException("error reordering parameters according to dependencies: ", e); + } + // + // rename "special" parameters (those that are not "user defined") + // + for(Element xmlParam : list){ + String paramName = unMangle(xmlParam.getAttributeValue(XMLTags.NameAttrTag)); + String role = xmlParam.getAttributeValue(XMLTags.ParamRoleAttrTag); + String paramExpStr = xmlParam.getText(); + Expression paramExp = unMangleExpression(paramExpStr); + try { + if(varHash.getVariable(paramName) == null){ + varHash.addVariable(new Function(paramName, paramExp, null)); + } else { + if(reserved.contains(paramName)){ + varHash.removeVariable(paramName); + varHash.addVariable(new Function(paramName, paramExp, null)); + } + } + } catch(MathException e){ + throw new XmlParseException("error reordering parameters according to dependencies: ", e); + } + Kinetics.KineticsParameter tempParam = null; + if(!role.equals(XMLTags.ParamRoleUserDefinedTag)){ + tempParam = newKinetics.getKineticsParameterFromRole(Kinetics.getParamRoleFromDefaultDesc(role)); + } else { + continue; + } + // hack for bringing in General Total kinetics without breaking. + if(tempParam == null && newKinetics instanceof GeneralLumpedKinetics){ + if(role.equals(Kinetics.GTK_AssumedCompartmentSize_oldname) || role.equals(Kinetics.GTK_ReactionRate_oldname) || role.equals(Kinetics.GTK_CurrentDensity_oldname)){ + continue; + } else if(role.equals(VCMODL.TotalRate_oldname)){ + tempParam = newKinetics.getKineticsParameterFromRole(Kinetics.ROLE_LumpedReactionRate); + } + } + // hack from bringing in chargeValence parameters without breaking + if(tempParam == null && Kinetics.getParamRoleFromDefaultDesc(role) == Kinetics.ROLE_ChargeValence){ + tempParam = newKinetics.getChargeValenceParameter(); + } + + if(tempParam == null){ + throw new XmlParseException("parameter with role '" + role + "' not found in kinetics type '" + type + "'"); + } + // + // custom name for "special" parameter + // + if(!tempParam.getName().equals(paramName)){ + Kinetics.KineticsParameter multNameParam = newKinetics.getKineticsParameter(paramName); + int n = 0; + while (multNameParam != null) { + String tempName = paramName + "_" + n++; + newKinetics.renameParameter(paramName, tempName); + multNameParam = newKinetics.getKineticsParameter(tempName); + } + newKinetics.renameParameter(tempParam.getName(), paramName); + } + } + // + // create unresolved parameters for all unresolved symbols + // + String unresolvedSymbol = varHash.getFirstUnresolvedSymbol(); + while (unresolvedSymbol != null) { + try { + varHash.addVariable(new Function(unresolvedSymbol, new Expression(0.0), null)); // will turn into an UnresolvedParameter. + } catch(MathException e){ + throw new XmlParseException(e); + } + newKinetics.addUnresolvedParameter(unresolvedSymbol); + unresolvedSymbol = varHash.getFirstUnresolvedSymbol(); + } + + Variable sortedVariables[] = varHash.getTopologicallyReorderedVariables(); + ModelUnitSystem modelUnitSystem = reaction.getModel().getUnitSystem(); + for(int i = sortedVariables.length - 1; i >= 0; i--){ + if(sortedVariables[i] instanceof Function){ + Function paramFunction = (Function) sortedVariables[i]; + Element xmlParam = null; + for(int j = 0; j < list.size(); j++){ + Element tempParam = (Element) list.get(j); + if(paramFunction.getName().equals(unMangle(tempParam.getAttributeValue(XMLTags.NameAttrTag)))){ + xmlParam = tempParam; + break; + } + } + if(xmlParam == null){ + + continue; // must have been an unresolved parameter + } + String symbol = xmlParam.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); + VCUnitDefinition unit = null; + if(symbol != null){ + unit = modelUnitSystem.getInstance(symbol); + } + Kinetics.KineticsParameter tempParam = newKinetics.getKineticsParameter(paramFunction.getName()); + if(tempParam == null){ + newKinetics.addUserDefinedKineticsParameter(paramFunction.getName(), paramFunction.getExpression(), unit); + } else { + newKinetics.setParameterValue(tempParam, paramFunction.getExpression()); + tempParam.setUnitDefinition(unit); + } + } + } + } catch(PropertyVetoException | ExpressionException e){ + throw new XmlParseException("Exception while setting parameters for Reaction : " + reaction.getName(), e); + } finally { + newKinetics.reading(false); + } + + return newKinetics; + } + + + /** + * This method returns a MathDescription from a XML element. + * Creation date: (4/26/2001 12:11:14 PM) + * + * @param param Element + * @return cbit.vcell.math.MathDescription + * @throws cbit.vcell.xml.XmlParseException The exception description. + */ + MathDescription getMathDescription(Element param, Geometry geometry) throws XmlParseException{ + MathDescription mathdes = null; + Element tempelement; + + //Retrieve Metadata(Version) + Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace)); + + //Retrieve attributes + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + + //Create new MathDescription + if(version != null){ + mathdes = new MathDescription(version); + } else { + mathdes = new MathDescription(name); + } + + try { + mathdes.setGeometry(geometry); //this step is needed! + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("a PropertyVetoException was fired when setting the Geometry to the Mathdescription in the simContext " + name, e); + } + //set attributes + try { + mathdes.setName(name); + //String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag); + + //if (annotation!=null) { + //mathdes.setDescription(unMangle(annotation)); + //} + //add Annotation + String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace); + if(annotationText != null && annotationText.length() > 0){ + mathdes.setDescription(unMangle(annotationText)); + } + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A PropertyVetoException was fired when setting the name " + name + ", to a new MathDescription!", e); + } + + VariableHash varHash = new VariableHash(); + + //Retrieve Constant + Iterator iterator = param.getChildren(XMLTags.ConstantTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + try { + varHash.addVariable(getConstant(tempelement)); + } catch(MathException e){ + throw new XmlParseException(e); + } + } + + //Retrieve FilamentRegionVariables + iterator = param.getChildren(XMLTags.FilamentRegionVariableTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + try { + varHash.addVariable(getFilamentRegionVariable(tempelement)); + } catch(MathException e){ + throw new XmlParseException(e); + } + } + + //Retrieve FilamentVariables + iterator = param.getChildren(XMLTags.FilamentVariableTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + try { + varHash.addVariable(getFilamentVariable(tempelement)); + } catch(MathException e){ + throw new XmlParseException(e); + } + } + + //retrieve InsideVariables + //**** This variables are for internal USE ****** + + //Retrieve MembraneRegionVariable + iterator = param.getChildren(XMLTags.MembraneRegionVariableTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + try { + varHash.addVariable(getMembraneRegionVariable(tempelement)); + } catch(MathException e){ + throw new XmlParseException(e); + } + + } + + //Retrieve MembraneVariable + iterator = param.getChildren(XMLTags.MembraneVariableTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + try { + varHash.addVariable(getMemVariable(tempelement)); + } catch(MathException e){ + throw new XmlParseException(e); + } + + } + + //Retrieve PointVariable + iterator = param.getChildren(XMLTags.PointVariableTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + try { + varHash.addVariable(getPointVariable(tempelement)); + } catch(MathException e){ + throw new XmlParseException(e); + } + + } + //retrieve OutsideVariables + //**** This variables are for internal USE ****** + + //Retrieve Volume Region variable + iterator = param.getChildren(XMLTags.VolumeRegionVariableTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + try { + varHash.addVariable(getVolumeRegionVariable(tempelement)); + } catch(MathException e){ + throw new XmlParseException(e); + } + + } + + //Retrieve VolumeVariable + iterator = param.getChildren(XMLTags.VolumeVariableTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + try { + varHash.addVariable(getVolVariable(tempelement)); + } catch(MathException e){ + throw new XmlParseException(e); + } + } + + //Retrieve StochVolVariable + iterator = param.getChildren(XMLTags.StochVolVariableTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + try { + varHash.addVariable(getStochVolVariable(tempelement)); + } catch(MathException e){ + throw new XmlParseException(e); + } + } + + //Retrieve all the Functions //This needs to be processed before all the variables are read! + iterator = param.getChildren(XMLTags.FunctionTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + try { + varHash.addVariable(getFunction(tempelement)); + } catch(MathException e){ + throw new XmlParseException(e); + } + } + + iterator = param.getChildren(XMLTags.VolumeRandomVariableTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + try { + varHash.addVariable(getRandomVariable(tempelement)); + } catch(MathException e){ + throw new XmlParseException(e); + } + } + iterator = param.getChildren(XMLTags.MembraneRandomVariableTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + try { + varHash.addVariable(getRandomVariable(tempelement)); + } catch(MathException e){ + throw new XmlParseException(e); + } + } + iterator = param.getChildren(XMLTags.VolumeParticleVariableTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + try { + varHash.addVariable(getVolumeParticalVariable(tempelement)); + } catch(MathException e){ + throw new XmlParseException(e); + } + } + iterator = param.getChildren(XMLTags.MembraneParticleVariableTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + try { + varHash.addVariable(getMembraneParticalVariable(tempelement)); + } catch(MathException e){ + throw new XmlParseException(e); + } + } + + // ParticleMolecularTypeTag getParticleMolecularTypes + // has to be done before VolumeParticleSpeciesPattern and VolumeParticleObservable + iterator = param.getChildren(XMLTags.ParticleMolecularTypeTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + mathdes.addParticleMolecularType(getParticleMolecularType(tempelement, false)); + } + iterator = param.getChildren(XMLTags.LangevinParticleMolecularTypeTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + mathdes.addParticleMolecularType(getParticleMolecularType(tempelement, true)); + } + // VolumeParticleSpeciesPatternTag + iterator = param.getChildren(XMLTags.VolumeParticleSpeciesPatternTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + try { + varHash.addVariable(getVolumeParticleSpeciesPattern(tempelement, mathdes)); + } catch(MathException e){ + throw new XmlParseException(e); + } + } + // VolumeParticleObservableTag getParticleObservables + iterator = param.getChildren(XMLTags.VolumeParticleObservableTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + try { + varHash.addVariable(getVolumeParticleObservable(tempelement, varHash)); + } catch(MathException e){ + throw new XmlParseException(e); + } + } + + // + // add all variables at once + // + try { + mathdes.setAllVariables(varHash.getAlphabeticallyOrderedVariables()); + } catch(MathException | ExpressionBindingException e){ + throw new XmlParseException("Error adding the Function variables to the MathDescription " + name, e); + } + + //Retrieve CompartmentsSubdomains + iterator = param.getChildren(XMLTags.CompartmentSubDomainTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + try { + mathdes.addSubDomain(getCompartmentSubDomain(tempelement, mathdes)); + } catch(MathException e){ + throw new XmlParseException("Error adding a new CompartmentSubDomain to the MathDescription " + name, e); + } + } + + //Retrieve MembraneSubdomains + iterator = param.getChildren(XMLTags.MembraneSubDomainTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + try { + mathdes.addSubDomain(getMembraneSubDomain(tempelement, mathdes)); + } catch(MathException e){ + throw new XmlParseException("Error adding a new MembraneSubDomain to the MathDescription " + name, e); + } + } + + //Retrieve the FilamentSubdomain (if any) + tempelement = param.getChild(XMLTags.FilamentSubDomainTag, vcNamespace); + if(tempelement != null){ + try { + mathdes.addSubDomain(getFilamentSubDomain(tempelement, mathdes)); + } catch(MathException e){ + throw new XmlParseException("Error adding a new FilamentSubDomain to the MathDescription " + name, e); + } + } + + //Retrieve the PointSubdomain (if any) + tempelement = param.getChild(XMLTags.PointSubDomainTag, vcNamespace); + if(tempelement != null){ + try { + mathdes.addSubDomain(getPointSubDomain(tempelement, mathdes)); + } catch(MathException e){ + throw new XmlParseException("Error adding a new PointSubDomain to the MathDescription " + name, e); + } + } + + iterator = param.getChildren(XMLTags.EventTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + Event event = getEvent(mathdes, tempelement); + try { + mathdes.addEvent(event); + } catch(MathException e){ + throw new XmlParseException(e); + } + } + iterator = param.getChildren(XMLTags.PostProcessingBlock, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + getPostProcessingBlock(mathdes, tempelement); + } + + mathdes.refreshDependencies(); + + return mathdes; + } + + private void getPostProcessingBlock(MathDescription mathDesc, Element element) throws XmlParseException{ + Iterator iterator = element.getChildren(XMLTags.ExplicitDataGenerator, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + + ExplicitDataGenerator explicitDataGenerator = getExplicitDataGenerator(tempelement); + try { + mathDesc.getPostProcessingBlock().addDataGenerator(explicitDataGenerator); + } catch(MathException e){ + throw new XmlParseException(e); + } + } + iterator = element.getChildren(XMLTags.ProjectionDataGenerator, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + + ProjectionDataGenerator projectionDataGenerator = getProjectionDataGenerator(tempelement); + try { + mathDesc.getPostProcessingBlock().addDataGenerator(projectionDataGenerator); + } catch(MathException e){ + throw new XmlParseException(e); + } + } + iterator = element.getChildren(XMLTags.ConvolutionDataGenerator, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + + ConvolutionDataGenerator convolutionDataGenerator = getConvolutionDataGenerator(tempelement); + try { + mathDesc.getPostProcessingBlock().addDataGenerator(convolutionDataGenerator); + } catch(MathException e){ + throw new XmlParseException(e); + } + } + } + + private ExplicitDataGenerator getExplicitDataGenerator(Element element){ + String name = unMangle(element.getAttributeValue(XMLTags.NameAttrTag)); + String domainStr = unMangle(element.getAttributeValue(XMLTags.DomainAttrTag)); + Domain domain = null; + if(domainStr != null){ + domain = new Domain(domainStr); + } + String temp = element.getText(); + + Expression exp = unMangleExpression(temp); + ExplicitDataGenerator explicitDataGenerator = new ExplicitDataGenerator(name, domain, exp); + return explicitDataGenerator; + } + + private ConvolutionDataGenerator getConvolutionDataGenerator(Element element){ + String name = unMangle(element.getAttributeValue(XMLTags.NameAttrTag)); + + Expression volumeFunction = null; + Element volumeFunctionElement = element.getChild(XMLTags.FunctionTag, vcNamespace); + if(volumeFunctionElement == null){ + volumeFunctionElement = element.getChild(XMLTags.VolumeFunctionTag, vcNamespace); + } + if(volumeFunctionElement != null){ + String s = volumeFunctionElement.getText(); + volumeFunction = unMangleExpression(s); + } + + Expression membraneFunction = null; + Element membraneFunctionElement = element.getChild(XMLTags.MembraneFunctionTag, vcNamespace); + if(membraneFunctionElement != null){ + String s = membraneFunctionElement.getText(); + membraneFunction = unMangleExpression(s); + } + + ConvolutionDataGeneratorKernel kernel = null; + Element kernelElement = element.getChild(XMLTags.Kernel, vcNamespace); + String kernelType = kernelElement.getAttributeValue(XMLTags.TypeAttrTag); + if(kernelType.equals(XMLTags.KernelType_Gaussian)){ + Element e0 = kernelElement.getChild(XMLTags.KernelGaussianSigmaXY, vcNamespace); + String s = e0.getText(); + Expression sigmaXY = unMangleExpression(s); + + e0 = kernelElement.getChild(XMLTags.KernelGaussianSigmaZ, vcNamespace); + s = e0.getText(); + Expression sigmaZ = unMangleExpression(s); + + kernel = new GaussianConvolutionDataGeneratorKernel(sigmaXY, sigmaZ); + } + + ConvolutionDataGenerator cdg = new ConvolutionDataGenerator(name, kernel, volumeFunction, membraneFunction); + return cdg; + } + + private ProjectionDataGenerator getProjectionDataGenerator(Element element){ + String name = unMangle(element.getAttributeValue(XMLTags.NameAttrTag)); + String domainStr = unMangle(element.getAttributeValue(XMLTags.DomainAttrTag)); + Domain domain = null; + if(domainStr != null){ + domain = new Domain(domainStr); + } + + Element e = element.getChild(XMLTags.ProjectionAxis, vcNamespace); + String axis = e.getText(); +// ProjectionDataGenerator.Axis axis = ProjectionDataGenerator.Axis.valueOf(s); + + e = element.getChild(XMLTags.ProjectionOperation, vcNamespace); + String operation = e.getText(); +// ProjectionDataGenerator.Operation operation = ProjectionDataGenerator.Operation.valueOf(s); + + e = element.getChild(XMLTags.FunctionTag, vcNamespace); + String s = e.getText(); + Expression exp = unMangleExpression(s); + ProjectionDataGenerator projectionDataGenerator = new ProjectionDataGenerator(name, domain, axis, operation, exp); + return projectionDataGenerator; + } + + private RandomVariable getRandomVariable(Element param) throws XmlParseException{ + //get attributes + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + Element element = param.getChild(XMLTags.RandomVariableSeedTag, vcNamespace); + Expression seed = null; + if(element != null){ + seed = unMangleExpression(element.getText()); + } + Distribution dist = null; + element = param.getChild(XMLTags.UniformDistributionTag, vcNamespace); + if(element != null){ + dist = getUniformDistribution(element); + } + element = param.getChild(XMLTags.GaussianDistributionTag, vcNamespace); + if(element != null){ + dist = getGaussianDistribution(element); + } + + String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); + Domain domain = null; + if(domainStr != null){ + domain = new Domain(domainStr); + } + + RandomVariable var = null; + if(param.getName().equals(XMLTags.VolumeRandomVariableTag)){ + var = new VolumeRandomVariable(name, seed, dist, domain); + } else if(param.getName().equals(XMLTags.MembraneRandomVariableTag)){ + var = new MembraneRandomVariable(name, seed, dist, domain); + } else { + throw new XmlParseException(param.getName() + " is not supported!"); + } + transcribeComments(param, var); + return var; + } + + private GaussianDistribution getGaussianDistribution(Element distElement){ + Element element = distElement.getChild(XMLTags.GaussianDistributionMeanTag, vcNamespace); + Expression mu = unMangleExpression(element.getText()); + + element = distElement.getChild(XMLTags.GaussianDistributionStandardDeviationTag, vcNamespace); + Expression sigma = unMangleExpression(element.getText()); + + return new GaussianDistribution(mu, sigma); + } + + private UniformDistribution getUniformDistribution(Element distElement){ + Element element = distElement.getChild(XMLTags.UniformDistributionMinimumTag, vcNamespace); + Expression low = unMangleExpression(element.getText()); + + element = distElement.getChild(XMLTags.UniformDistributionMaximumTag, vcNamespace); + Expression high = unMangleExpression(element.getText()); + + return new UniformDistribution(low, high); + } + + private Event getEvent(MathDescription mathdesc, Element eventElement) throws XmlParseException{ + + String name = unMangle(eventElement.getAttributeValue(XMLTags.NameAttrTag)); + Element element = eventElement.getChild(XMLTags.TriggerTag, vcNamespace); + Expression triggerExp = unMangleExpression(element.getText()); + + element = eventElement.getChild(XMLTags.DelayTag, vcNamespace); + Delay delay = null; + if(element != null){ + boolean useValuesFromTriggerTime = Boolean.valueOf(element.getAttributeValue(XMLTags.UseValuesFromTriggerTimeAttrTag)).booleanValue(); + Expression durationExp = unMangleExpression(element.getText()); + delay = new Delay(useValuesFromTriggerTime, durationExp); + } + + ArrayList eventAssignmentList = new ArrayList(); + Iterator iter = eventElement.getChildren(XMLTags.EventAssignmentTag, vcNamespace).iterator(); + while (iter.hasNext()) { + element = iter.next(); + String varname = element.getAttributeValue(XMLTags.EventAssignmentVariableAttrTag); + Expression assignExp = unMangleExpression(element.getText()); + Variable var = mathdesc.getVariable(varname); + EventAssignment eventAssignment = new EventAssignment(var, assignExp); + eventAssignmentList.add(eventAssignment); + } + + Event event = new Event(name, triggerExp, delay, eventAssignmentList); + transcribeComments(eventElement, event); + return event; + } + + public BioEvent[] getBioEvents(SimulationContext simContext, Element bioEventsElement) throws XmlParseException{ + Iterator bioEventsIterator = bioEventsElement.getChildren(XMLTags.BioEventTag, vcNamespace).iterator(); + Vector bioEventsVector = new Vector(); + while (bioEventsIterator.hasNext()) { + Element bEventElement = (Element) bioEventsIterator.next(); + + BioEvent newBioEvent = null; + String name = unMangle(bEventElement.getAttributeValue(XMLTags.NameAttrTag)); + Element triggerElement = bEventElement.getChild(XMLTags.TriggerTag, vcNamespace); + if(triggerElement != null && triggerElement.getText().length() > 0){ + // + // read legacy VCell 5.3 style trigger and delay elements + // + // (t>3.0) + // 3.0 [optional] + // + Expression triggerExpression = unMangleExpression(triggerElement.getText()); + + // read + Expression delayDurationExpression = null; + boolean useValuesFromTriggerTime = true; + Element delayElement = bEventElement.getChild(XMLTags.DelayTag, vcNamespace); + if(delayElement != null){ + useValuesFromTriggerTime = Boolean.valueOf(delayElement.getAttributeValue(XMLTags.UseValuesFromTriggerTimeAttrTag)).booleanValue(); + delayDurationExpression = unMangleExpression((delayElement.getText())); + } + + newBioEvent = new BioEvent(name, TriggerType.GeneralTrigger, useValuesFromTriggerTime, simContext); + try { + newBioEvent.setParameterValue(BioEventParameterType.GeneralTriggerFunction, triggerExpression); + if(delayDurationExpression != null){ + newBioEvent.setParameterValue(BioEventParameterType.TriggerDelay, delayDurationExpression); + } + } catch(ExpressionBindingException | PropertyVetoException e){ + throw new XmlParseException("failed to read trigger or delay expressions in bioEvent " + name + ": " + e.getMessage(), e); + } + + } else if(triggerElement != null && triggerElement.getText().length() == 0){ + // + // read legacy first-pass VCell 5.4 style trigger and delay elements + // + // + // + // (t > 500.0) + // + // + // 3.0 [optional] + // + final String TriggerParametersTag = "TriggerParameters"; + final String TriggerClassAttrTag = "triggerClass"; + final String TriggerClassAttrValue_TriggerGeneral = "TriggerGeneral"; + + Element triggerParametersElement = triggerElement.getChild(TriggerParametersTag, vcNamespace); + + Expression triggerExpression = null; + + String triggerClass = triggerParametersElement.getAttributeValue(TriggerClassAttrTag); + if(triggerClass.equals(TriggerClassAttrValue_TriggerGeneral)){ + triggerExpression = unMangleExpression(triggerParametersElement.getText()); + } else { + // not general trigger (just make it never happen, user will have to edit "t > -1") + triggerExpression = Expression.relational(">", new Expression(simContext.getModel().getTIME(), simContext.getModel().getNameScope()), new Expression(-1.0)); + } + + // read + Expression delayDurationExpression = null; + boolean useValuesFromTriggerTime = true; + Element delayElement = bEventElement.getChild(XMLTags.DelayTag, vcNamespace); + if(delayElement != null){ + useValuesFromTriggerTime = Boolean.valueOf(delayElement.getAttributeValue(XMLTags.UseValuesFromTriggerTimeAttrTag)).booleanValue(); + delayDurationExpression = unMangleExpression((delayElement.getText())); + } + + newBioEvent = new BioEvent(name, TriggerType.GeneralTrigger, useValuesFromTriggerTime, simContext); + try { + newBioEvent.setParameterValue(BioEventParameterType.GeneralTriggerFunction, triggerExpression); + if(delayDurationExpression != null){ + newBioEvent.setParameterValue(BioEventParameterType.TriggerDelay, delayDurationExpression); + } + } catch(ExpressionBindingException | PropertyVetoException e){ + throw new XmlParseException("failed to read trigger or delay expressions in bioEvent " + name + ": " + e.getMessage(), e); + } + + } else { + // + // VCell 5.4 style bioevent parameters + // + // + TriggerType triggerType = TriggerType.fromXmlName(bEventElement.getAttributeValue(XMLTags.BioEventTriggerTypeAttrTag)); + boolean bUseValuesFromTriggerTime = Boolean.parseBoolean(bEventElement.getAttributeValue(XMLTags.UseValuesFromTriggerTimeAttrTag)); + + newBioEvent = new BioEvent(name, triggerType, bUseValuesFromTriggerTime, simContext); + + Iterator paramElementIter = bEventElement.getChildren(XMLTags.ParameterTag, vcNamespace).iterator(); + ArrayList parameters = new ArrayList(); + + boolean bHasGeneralTriggerParam = false; + + while (paramElementIter.hasNext()) { + Element paramElement = paramElementIter.next(); + + //Get parameter attributes + String paramName = paramElement.getAttributeValue(XMLTags.NameAttrTag); + Expression exp = unMangleExpression(paramElement.getText()); + String roleStr = paramElement.getAttributeValue(XMLTags.ParamRoleAttrTag); + BioEventParameterType parameterType = BioEventParameterType.fromRoleXmlName(roleStr); + if(parameterType == BioEventParameterType.GeneralTriggerFunction){ + bHasGeneralTriggerParam = true; + } + VCUnitDefinition unit = simContext.getModel().getUnitSystem().getInstance_TBD(); + String unitSymbol = paramElement.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); + if(unitSymbol != null){ + unit = simContext.getModel().getUnitSystem().getInstance(unitSymbol); + } + + parameters.add(newBioEvent.createNewParameter(paramName, parameterType, exp, unit)); + } + if(!bHasGeneralTriggerParam){ + parameters.add(newBioEvent.createNewParameter( + BioEventParameterType.GeneralTriggerFunction.getDefaultName(), + BioEventParameterType.GeneralTriggerFunction, + null, // computed as needed + simContext.getModel().getUnitSystem().getInstance_DIMENSIONLESS())); + } + try { + newBioEvent.setParameters(parameters.toArray(new LocalParameter[0])); + } catch(PropertyVetoException | ExpressionBindingException e){ + throw new XmlParseException("failed to read parameters in bioEvent " + name + ": " + e.getMessage(), e); + } + } + + ArrayList eventAssignmentList = new ArrayList(); + Iterator iter = bEventElement.getChildren(XMLTags.EventAssignmentTag, vcNamespace).iterator(); + while (iter.hasNext()) { + Element eventAssignmentElement = iter.next(); + try { + String varname = eventAssignmentElement.getAttributeValue(XMLTags.EventAssignmentVariableAttrTag); + Expression assignExp = unMangleExpression(eventAssignmentElement.getText()); + SymbolTableEntry target = simContext.getEntry(varname); + if(!(target instanceof EditableSymbolTableEntry)){ + throw new XmlParseException("expecting an EditableSymbolTableEntry for event assignment target, found " + target); + } + BioEvent.EventAssignment eventAssignment = newBioEvent.new EventAssignment((EditableSymbolTableEntry) target, assignExp); + eventAssignmentList.add(eventAssignment); + } catch(ExpressionException e){ + throw new XmlParseException(e); + } + } + try { + newBioEvent.setEventAssignmentsList(eventAssignmentList); + } catch(PropertyVetoException e1){ + throw new XmlParseException(e1); + } + try { + newBioEvent.bind(); + } catch(ExpressionBindingException e){ + throw new XmlParseException(e); + } + bioEventsVector.add(newBioEvent); + } + + return bioEventsVector.toArray(BioEvent[]::new); + } + + public SpatialObject[] getSpatialObjects(SimulationContext simContext, Element spatialObjectsElement) throws XmlParseException{ + Iterator spatialObjectElementIterator = spatialObjectsElement.getChildren(XMLTags.SpatialObjectTag, vcNamespace).iterator(); + ArrayList spatialObjectList = new ArrayList(); + while (spatialObjectElementIterator.hasNext()) { + Element spatialObjectElement = (Element) spatialObjectElementIterator.next(); + + SpatialObject spatialObject = null; + String name = unMangle(spatialObjectElement.getAttributeValue(XMLTags.NameAttrTag)); + String type = unMangle(spatialObjectElement.getAttributeValue(XMLTags.SpatialObjectTypeAttrTag)); + switch(type){ + case XMLTags.SpatialObjectTypeAttrValue_Point -> { + spatialObject = new PointObject(name, simContext); + } + case XMLTags.SpatialObjectTypeAttrValue_Surface -> { + String insideSubvolumeName = unMangle(spatialObjectElement.getAttributeValue(XMLTags.SpatialObjectSubVolumeInsideAttrTag)); + String insideRegionIDString = spatialObjectElement.getAttributeValue(XMLTags.SpatialObjectRegionIdInsideAttrTag); + String outsideSubvolumeName = unMangle(spatialObjectElement.getAttributeValue(XMLTags.SpatialObjectSubVolumeOutsideAttrTag)); + String outsideRegionIDString = spatialObjectElement.getAttributeValue(XMLTags.SpatialObjectRegionIdOutsideAttrTag); + SubVolume insideSubvolume = null; + if(insideSubvolumeName != null){ + insideSubvolume = simContext.getGeometry().getGeometrySpec().getSubVolume(insideSubvolumeName); + } + Integer insideRegionID = null; + if(insideRegionIDString != null){ + insideRegionID = Integer.parseUnsignedInt(insideRegionIDString); + } + SubVolume outsideSubvolume = null; + if(outsideSubvolumeName != null){ + outsideSubvolume = simContext.getGeometry().getGeometrySpec().getSubVolume(outsideSubvolumeName); + } + Integer outsideRegionID = null; + if(outsideRegionIDString != null){ + outsideRegionID = Integer.parseUnsignedInt(outsideRegionIDString); + } + spatialObject = new SurfaceRegionObject(name, insideSubvolume, insideRegionID, outsideSubvolume, outsideRegionID, simContext); + } + case XMLTags.SpatialObjectTypeAttrValue_Volume -> { + String subvolumeName = unMangle(spatialObjectElement.getAttributeValue(XMLTags.SpatialObjectSubVolumeAttrTag)); + String regionIDString = spatialObjectElement.getAttributeValue(XMLTags.SpatialObjectRegionIdAttrTag); + SubVolume subvolume = null; + if(subvolumeName != null){ + subvolume = simContext.getGeometry().getGeometrySpec().getSubVolume(subvolumeName); + } + Integer regionID = null; + if(regionIDString != null){ + regionID = Integer.parseUnsignedInt(regionIDString); + } + spatialObject = new VolumeRegionObject(name, subvolume, regionID, simContext); + } + } + + // set Quantity enables + Element quantityCategoryListElement = spatialObjectElement.getChild(XMLTags.QuantityCategoryListTag, vcNamespace); + List quantityCategoryElements = quantityCategoryListElement.getChildren(XMLTags.QuantityCategoryTag, vcNamespace); + for(Element quantityCategoryElement : quantityCategoryElements){ + String quantityCategoryName = unMangle(quantityCategoryElement.getAttributeValue(XMLTags.QuantityCategoryNameAttrTag)); + boolean enabled = Boolean.parseBoolean(quantityCategoryElement.getAttributeValue(XMLTags.QuantityCategoryEnabledAttrTag)); + QuantityCategory category = QuantityCategory.fromXMLName(quantityCategoryName); + spatialObject.setQuantityCategoryEnabled(category, enabled); + } + + spatialObjectList.add(spatialObject); + } + return spatialObjectList.toArray(new SpatialObject[0]); + } + + public SpatialProcess[] getSpatialProcesses(SimulationContext simContext, Element spatialProcessesElement) throws XmlParseException{ + Iterator spatialProcessElementIterator = spatialProcessesElement.getChildren(XMLTags.SpatialProcessTag, vcNamespace).iterator(); + ArrayList spatialProcessList = new ArrayList(); + while (spatialProcessElementIterator.hasNext()) { + Element spatialProcessElement = (Element) spatialProcessElementIterator.next(); + + SpatialProcess spatialProcess = null; + String name = unMangle(spatialProcessElement.getAttributeValue(XMLTags.NameAttrTag)); + String type = unMangle(spatialProcessElement.getAttributeValue(XMLTags.SpatialProcessTypeAttrTag)); + if(type.equals(XMLTags.SpatialProcessTypeAttrValue_PointKinematics)){ + PointKinematics pointKinematics = new PointKinematics(name, simContext); + String pointObjectName = spatialProcessElement.getAttributeValue(XMLTags.SpatialProcessPointObjectAttrTag); + PointObject pointObject = (PointObject) simContext.getSpatialObject(pointObjectName); + pointKinematics.setPointObject(pointObject); + spatialProcess = pointKinematics; + } else if(type.equals(XMLTags.SpatialProcessTypeAttrValue_PointLocation)){ + PointLocation pointLocation = new PointLocation(name, simContext); + String pointObjectName = spatialProcessElement.getAttributeValue(XMLTags.SpatialProcessPointObjectAttrTag); + PointObject pointObject = (PointObject) simContext.getSpatialObject(pointObjectName); + pointLocation.setPointObject(pointObject); + spatialProcess = pointLocation; + } else if(type.equals(XMLTags.SpatialProcessTypeAttrValue_SurfaceKinematics)){ + SurfaceKinematics surfaceKinematics = new SurfaceKinematics(name, simContext); + String surfaceRegionObjectName = spatialProcessElement.getAttributeValue(XMLTags.SpatialProcessSurfaceObjectAttrTag); + SurfaceRegionObject surfaceRegionObject = (SurfaceRegionObject) simContext.getSpatialObject(surfaceRegionObjectName); + surfaceKinematics.setSurfaceRegionObject(surfaceRegionObject); + spatialProcess = surfaceKinematics; + } else if(type.equals(XMLTags.SpatialProcessTypeAttrValue_VolumeKinematics)){ + VolumeKinematics volumeKinematics = new VolumeKinematics(name, simContext); + String volumeRegionObjectName = spatialProcessElement.getAttributeValue(XMLTags.SpatialProcessVolumeObjectAttrTag); + VolumeRegionObject volumeRegionObject = (VolumeRegionObject) simContext.getSpatialObject(volumeRegionObjectName); + volumeKinematics.setVolumeRegionObject(volumeRegionObject); + spatialProcess = volumeKinematics; + } + + // set parameters + Iterator paramElementIter = spatialProcessElement.getChildren(XMLTags.ParameterTag, vcNamespace).iterator(); + ArrayList parameters = new ArrayList(); + + while (paramElementIter.hasNext()) { + Element paramElement = paramElementIter.next(); + + //Get parameter attributes + String paramName = paramElement.getAttributeValue(XMLTags.NameAttrTag); + Expression exp = unMangleExpression(paramElement.getText()); + String roleStr = paramElement.getAttributeValue(XMLTags.ParamRoleAttrTag); + SpatialProcessParameterType parameterType = SpatialProcessParameterType.fromRoleXmlName(roleStr); + VCUnitDefinition unit = simContext.getModel().getUnitSystem().getInstance_TBD(); + String unitSymbol = paramElement.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); + if(unitSymbol != null){ + unit = simContext.getModel().getUnitSystem().getInstance(unitSymbol); + } + parameters.add(spatialProcess.createNewParameter(paramName, parameterType, exp, unit)); + } + try { + spatialProcess.setParameters(parameters.toArray(new LocalParameter[0])); + } catch(PropertyVetoException | ExpressionBindingException e){ + throw new XmlParseException("failed to read parameters in bioEvent " + name + ": " + e.getMessage(), e); + } + + spatialProcessList.add(spatialProcess); + } + return spatialProcessList.toArray(new SpatialProcess[0]); + } + + public RateRule[] getRateRules(SimulationContext simContext, Element rateRulesElement) throws XmlParseException{ + Iterator rateRulesIterator = rateRulesElement.getChildren(XMLTags.RateRuleTag, vcNamespace).iterator(); + Vector rateRulesVector = new Vector(); + while (rateRulesIterator.hasNext()) { + Element rrElement = (Element) rateRulesIterator.next(); + + RateRule newRateRule = null; + try { + String rrName = unMangle(rrElement.getAttributeValue(XMLTags.NameAttrTag)); + String varname = rrElement.getAttributeValue(XMLTags.RateRuleVariableAttrTag); + SymbolTableEntry rrVar = simContext.getEntry(varname); + Expression rrExp = unMangleExpression(rrElement.getText()); + newRateRule = new RateRule(rrName, rrVar, rrExp, simContext); + newRateRule.bind(); + } catch(ExpressionBindingException e){ + throw new XmlParseException(e.getMessage()); + } + rateRulesVector.add(newRateRule); + } + return rateRulesVector.toArray(RateRule[]::new); + } + + public AssignmentRule[] getAssignmentRules(SimulationContext simContext, Element assignmentRulesElement) throws XmlParseException{ + Iterator assignmentRulesIterator = assignmentRulesElement.getChildren(XMLTags.AssignmentRuleTag, vcNamespace).iterator(); + Vector assignmentRulesVector = new Vector(); + while (assignmentRulesIterator.hasNext()) { + Element rrElement = (Element) assignmentRulesIterator.next(); + + AssignmentRule newAssignmentRule = null; + try { + String rrName = unMangle(rrElement.getAttributeValue(XMLTags.NameAttrTag)); + String varname = rrElement.getAttributeValue(XMLTags.AssignmentRuleVariableAttrTag); + SymbolTableEntry rrVar = simContext.getEntry(varname); + Expression rrExp = unMangleExpression(rrElement.getText()); + newAssignmentRule = new AssignmentRule(rrName, rrVar, rrExp, simContext); + newAssignmentRule.bind(); + } catch(ExpressionBindingException e){ + throw new XmlParseException(e.getMessage()); + } + if(newAssignmentRule != null){ + assignmentRulesVector.add(newAssignmentRule); + } + } + return assignmentRulesVector.toArray(AssignmentRule[]::new); + } + + + public ReactionRuleSpec[] getReactionRuleSpecs(SimulationContext simContext, Element reactionRuleSpecsElement) throws XmlParseException{ + List reactionRulesSpecIterator = reactionRuleSpecsElement.getChildren(XMLTags.ReactionRuleSpecTag, vcNamespace); + ArrayList reactionRuleSpecs = new ArrayList(); + for(Element rrElement : reactionRulesSpecIterator){ + String rrName = unMangle(rrElement.getAttributeValue(XMLTags.ReactionRuleRefAttrTag)); + String rrMappingString = rrElement.getAttributeValue(XMLTags.ReactionRuleMappingAttrTag); + ReactionRuleMappingType rrMapping = ReactionRuleMappingType.fromDatabaseName(rrMappingString); + ReactionRule reactionRule = simContext.getModel().getRbmModelContainer().getReactionRule(rrName); + ReactionRuleSpec reactionRuleSpec = new ReactionRuleSpec(reactionRule); + reactionRuleSpec.setReactionRuleMapping(rrMapping); + + if(SimulationContext.Application.SPRINGSALAD == simContext.getApplicationType()){ // Springsalad + // only the bondLength is needed, the subtype and transitionCondition may be used for sanity check against the math (LangevinParticleJumpProcess) + Subtype subtype = Subtype.INCOMPATIBLE; + if(rrElement.getAttribute(XMLTags.SubTypeAttrTag) != null){ + String stString = rrElement.getAttributeValue(XMLTags.SubTypeAttrTag); + subtype = Subtype.fromName(stString); + } + TransitionCondition transitionCondition = null; + double bondLength = 1; // that's the default, even for non-binding rules (we hide it anyway for those) + if(rrElement.getAttribute(XMLTags.BondLengthAttrTag) != null){ + bondLength = Double.valueOf(rrElement.getAttributeValue(XMLTags.BondLengthAttrTag)); + reactionRuleSpec.setFieldBondLength(bondLength); + + } + if(rrElement.getAttribute(XMLTags.TransitionConditionAttrTag) != null){ + String tcString = rrElement.getAttributeValue(XMLTags.TransitionConditionAttrTag); + transitionCondition = TransitionCondition.fromVcellName(tcString); + } + // TODO: (optional) verify consistency of subtype and transitionCondition against Math:CompartmentSubdomain:ParticleJumpProcess + } + reactionRuleSpecs.add(reactionRuleSpec); + } + return reactionRuleSpecs.toArray(new ReactionRuleSpec[0]); + } + + +/* +public RateRuleVariable[] getRateRuleVariables(Element rateRuleVarsElement, Model model) throws XmlParseException { + Iterator rateRuleVarsIterator = rateRuleVarsElement.getChildren(XMLTags.RateRuleVariableTag, vcNamespace).iterator(); + Vector rateRuleVarsVector = new Vector(); + while (rateRuleVarsIterator.hasNext()) { + Element rrvElement = (Element) rateRuleVarsIterator.next(); + + RateRuleVariable newRateRuleVar = null; + try { + String rrvName = unMangle(rrvElement.getAttributeValue(XMLTags.NameAttrTag)); + String rrvStructureName = unMangle(rrvElement.getAttributeValue(XMLTags.StructureAttrTag)); + // structure can be null + Structure rrvStructure = null; + if (rrvStructureName != null) { + rrvStructure = (Structure) model.getStructure(rrvStructureName); + } +// if (structureref == null) { +// throw new XmlParseException("The structure " + rrvStructureName + "could not be resolved!"); +// } + String rrvRoleStr = rrvElement.getAttributeValue(XMLTags.ParamRoleAttrTag); + int rrvRole = RateRuleVariable.getParamRoleFromDesc(rrvRoleStr); + Element rrvParamElement = rrvElement.getChild(XMLTags.ParameterTag, vcNamespace); + ModelParameter rrvParameter = getModelParameter(rrvParamElement, model); + newRateRuleVar = new RateRuleVariable(rrvName, rrvStructure, rrvParameter, rrvRole); + newRateRuleVar.bind(); + } catch (ExpressionBindingException e) { + lg.error(e); + throw new XmlParseException(e.getMessage()); + } + if (newRateRuleVar != null) { + rateRuleVarsVector.add(newRateRuleVar); + } + } + + return ((RateRuleVariable[])BeanUtils.getArray(rateRuleVarsVector, RateRuleVariable.class)); +} +*/ + + /** + * This method returns a MathModel object from a XML Element. + * Creation date: (3/13/2001 12:35:00 PM) + * + * @param param Element + * @return cbit.vcell.mathmodel.MathModel + */ + public MathModel getMathModel(Element param) throws XmlParseException{ + //Create it + //set Metadata (version), if any + Version versionObject = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace)); + MathModel mathmodel = new MathModel(versionObject); + + //Set attributes + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + try { + mathmodel.setName(name); + //String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag); + + //if (annotation!=null) { + //mathmodel.setDescription(unMangle(annotation)); + //} + //Add annotation + String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace); + if(annotationText != null && annotationText.length() > 0){ + mathmodel.setDescription(unMangle(annotationText)); + } + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("An error occurred while trying to set the name " + param.getAttributeValue(XMLTags.NameAttrTag) + "to a MathModel!", e); + } + + //set Geometry (if any) + Element tempElem = param.getChild(XMLTags.GeometryTag, vcNamespace); + Geometry tempGeometry = getGeometry(tempElem); + + + //set MathDescription + tempElem = param.getChild(XMLTags.MathDescriptionTag, vcNamespace); + MathDescription mathDesc = getMathDescription(tempElem, tempGeometry); + + if(tempElem != null){ + mathmodel.setMathDescription(mathDesc); + } else { + throw new XmlParseException("MathDescription missing in this MathModel!"); + } + + // set output functions (outputfunctionContext) + Element outputFunctionsElement = param.getChild(XMLTags.OutputFunctionsTag, vcNamespace); + if(outputFunctionsElement != null){ + ArrayList outputFunctions = getOutputFunctions(outputFunctionsElement); + try { + // construct OutputFnContext from mathmodel and add output functions that were read in from XML. + OutputFunctionContext outputFnContext = mathmodel.getOutputFunctionContext(); + for(AnnotatedFunction outputFunction : outputFunctions){ + outputFnContext.addOutputFunction(outputFunction); + } + } catch(PropertyVetoException e){ + throw new XmlParseException(e); + } + } + + //Set simulations contexts (if any) + List childList = param.getChildren(XMLTags.SimulationTag, vcNamespace); + Simulation[] simList = new Simulation[childList.size()]; + int simCounter = 0; + for(Element simElement : childList){ + simList[simCounter] = getSimulation(simElement, mathDesc, mathmodel); + simCounter++; + } + try { + mathmodel.setSimulations(simList); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A PropertyVetoException occurred when adding the Simulations to the MathModel " + name, e); + } + + return mathmodel; + } + + + /** + * This method returns a MathOverrides object from a XML Element. + * Creation date: (5/21/2001 3:05:17 PM) + * + * @param param Element + * @return cbit.vcell.solver.MathOverrides + */ + private MathOverrides getMathOverrides(Element param, Simulation simulation) throws XmlParseException{ + + MathOverrides mathOverrides; + try { + //Get the constants + Object[] elements = param.getChildren().toArray(); + Vector v1 = new Vector<>(); + Vector v2 = new Vector<>(); + for(Object element : elements){ + Element e = (Element) element; + Attribute array = e.getAttribute(XMLTags.ConstantArraySpec); + if(array != null){ + // collect scan overrides + String name = e.getAttributeValue(XMLTags.NameAttrTag); + int type = array.getIntValue(); + v1.add(ConstantArraySpec.createFromString(name, e.getText(), type)); + } else { + // collect regular overrides + v2.add(getConstant(e)); + } + } + Constant[] constants = v2.toArray(Constant[]::new); + ConstantArraySpec[] specs = v1.toArray(ConstantArraySpec[]::new); + //create new MathOverrides object + mathOverrides = new MathOverrides(simulation, constants, specs); + } catch(ExpressionException | DataConversionException e){ + throw new XmlParseException("failed to add a Constant to the MathOverrides", e); + } + return mathOverrides; + } + + + /** + * This method returns a Membrane object from a XML element. + * Creation date: (4/4/2001 4:17:32 PM) + * + * @param param Element + * @return cbit.vcell.model.Membrane + */ + private Membrane getMembrane(Model model, Element param, List featureList) throws XmlParseException{ + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + Membrane newmembrane = null; + + //retrieve the key if there is one + KeyValue key = null; + String stringkey = param.getAttributeValue(XMLTags.KeyValueAttrTag); + + if(stringkey != null && stringkey.length() > 0 && this.readKeysFlag){ + key = new KeyValue(stringkey); + } + + //try to create new Membrane named "name" + try { + newmembrane = new Membrane(key, name); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException( + "An error occurred while trying to create the Membrane object " + name, e); + } + //set inside feature + String infeaturename = unMangle(param.getAttributeValue(XMLTags.InsideFeatureTag)); + String outfeaturename = unMangle(param.getAttributeValue(XMLTags.OutsideFeatureTag)); + + String posFeatureName = unMangle(param.getAttributeValue(XMLTags.PositiveFeatureTag)); + String negFeatureName = unMangle(param.getAttributeValue(XMLTags.NegativeFeatureTag)); + + Feature infeatureref = null; + Feature outfeatureref = null; + Feature posFeature = null; + Feature negFeature = null; + + for(Structure s : featureList){ + String sname = s.getName(); + if(sname.equals(infeaturename)){ + infeatureref = (Feature) s; + } + if(sname.equals(outfeaturename)){ + outfeatureref = (Feature) s; + } + if(sname.equals(posFeatureName)){ + posFeature = (Feature) s; + } + if(sname.equals(negFeatureName)){ + negFeature = (Feature) s; + } + } + + //set inside and outside features + if(infeatureref != null){ + model.getStructureTopology().setInsideFeature(newmembrane, infeatureref); + } + if(outfeatureref != null){ + model.getStructureTopology().setOutsideFeature(newmembrane, outfeatureref); + } + //set positive & negative features + if(posFeature != null){ + model.getElectricalTopology().setPositiveFeature(newmembrane, posFeature); + } + if(negFeature != null){ + model.getElectricalTopology().setNegativeFeature(newmembrane, negFeature); + } + //set MemVoltName + if(param.getAttribute(XMLTags.MemVoltNameTag) == null){ + throw new XmlParseException("Error reading membrane Voltage Name!"); + } + String memvoltName = unMangle(param.getAttributeValue(XMLTags.MemVoltNameTag)); + try { + newmembrane.getMembraneVoltage().setName(memvoltName); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("Error setting the membrane Voltage Name", e); + } + + return newmembrane; + } + + + /** + * This method retuns a MembraneMapping object from a XML representation. + * Creation date: (5/7/2001 4:12:03 PM) + * + * @param param Element + * @return cbit.vcell.mapping.MembraneMapping + */ + private MembraneMapping getMembraneMapping(Element param, SimulationContext simulationContext) throws XmlParseException{ + //Retrieve attributes + String membranename = unMangle(param.getAttributeValue(XMLTags.MembraneAttrTag)); + + Membrane membraneref = (Membrane) simulationContext.getModel().getStructure(membranename); + if(membraneref == null){ + throw new XmlParseException("The Membrane " + membranename + " could not be resolved!"); + } + + //*** Create new Membrane Mapping **** + MembraneMapping memmap = new MembraneMapping(membraneref, simulationContext, simulationContext.getModel().getUnitSystem()); + + //Set SurfacetoVolumeRatio when it exists, amended Sept. 27th, 2007 + if(param.getAttributeValue(XMLTags.SurfaceToVolumeRatioTag) != null){ + String ratio = unMangle(param.getAttributeValue(XMLTags.SurfaceToVolumeRatioTag)); + try { + memmap.getSurfaceToVolumeParameter().setExpression(unMangleExpression(ratio)); + } catch(ExpressionException e){ + throw new XmlParseException("An expressionException was fired when setting the SurfacetoVolumeRatio Expression " + ratio + " to a membraneMapping!", e); + } + } + + //Set VolumeFraction when it exists, amended Sept. 27th, 2007 + if(param.getAttributeValue(XMLTags.VolumeFractionTag) != null){ + String fraction = unMangle(param.getAttributeValue(XMLTags.VolumeFractionTag)); + try { + memmap.getVolumeFractionParameter().setExpression(unMangleExpression(fraction)); + } catch(ExpressionException e){ + throw new XmlParseException("An expressionException was fired when setting the VolumeFraction Expression " + fraction + " to a membraneMapping!", e); + } + } + + //Set Area/unit_area if it exists, amended Sept. 27th, 2007 + if(param.getAttributeValue(XMLTags.AreaPerUnitAreaTag) != null){ + String ratio = unMangle(param.getAttributeValue(XMLTags.AreaPerUnitAreaTag)); + try { + memmap.getAreaPerUnitAreaParameter().setExpression(unMangleExpression(ratio)); + } catch(ExpressionException e){ + throw new XmlParseException("An expressionException was fired when setting the AreaPerUnitArea Expression " + ratio + " to a membraneMapping!", e); + } + } + + //Set SurfacetoVolumeRatio when it exists, amended Sept. 27th, 2007 + if(param.getAttributeValue(XMLTags.AreaPerUnitVolumeTag) != null){ + String ratio = unMangle(param.getAttributeValue(XMLTags.AreaPerUnitVolumeTag)); + try { + memmap.getAreaPerUnitVolumeParameter().setExpression(unMangleExpression(ratio)); + } catch(ExpressionException e){ + throw new XmlParseException("An expressionException was fired when setting the AreaPerUnitVolume Expression " + ratio + " to a membraneMapping!", e); + } + } + + //Set Size + if(param.getAttributeValue(XMLTags.SizeTag) != null){ + String size = unMangle(param.getAttributeValue(XMLTags.SizeTag)); + try { + memmap.getSizeParameter().setExpression(unMangleExpression(size)); + } catch(ExpressionException e){ + throw new XmlParseException("An expressionException was fired when setting the size Expression " + size + " to a membraneMapping!", e); + } + } else { + try { + memmap.getSizeParameter().setExpression(null); + } catch(Exception e){ + throw new RuntimeException("unexpected exception while setting structure size", e); + } + } + //** Set electrical properties ** + //set specific capacitance + double specificCap = Double.parseDouble(param.getAttributeValue(XMLTags.SpecificCapacitanceTag)); + try { + memmap.getSpecificCapacitanceParameter().setExpression(new Expression(specificCap)); + } catch(ExpressionException e){ + throw new XmlParseException(e); + } + + //set flag calculate voltage + boolean calculateVolt = (Boolean.valueOf(param.getAttributeValue(XMLTags.CalculateVoltageTag))).booleanValue(); + memmap.setCalculateVoltage(calculateVolt); + + //set initial Voltage + String initialVoltString = param.getAttributeValue(XMLTags.InitialVoltageTag); + try { + Expression initialExpr = unMangleExpression(initialVoltString); + memmap.getInitialVoltageParameter().setExpression(initialExpr); + } catch(ExpressionException e){ + throw new XmlParseException(e); + } + + String geometryClassName = param.getAttributeValue(XMLTags.GeometryClassAttrTag); + if(geometryClassName != null){ + geometryClassName = unMangle(geometryClassName); + } + //Retrieve subvolumeref, allow subvolumes to be 'null' + if(geometryClassName != null){ + GeometryClass[] geometryClasses = simulationContext.getGeometry().getGeometryClasses(); + for(int i = 0; i < geometryClasses.length; i++){ + if(geometryClasses[i].getName().equals(geometryClassName)){ + try { + memmap.setGeometryClass(geometryClasses[i]); + } catch(PropertyVetoException e){ + throw new XmlParseException("A propertyVetoException was fired when trying to set the subvolume or surface " + geometryClassName + " to a MembraneMapping!", e); + } + } + } + } + + //Set Boundary conditions + Element tempElement = param.getChild(XMLTags.BoundariesTypesTag, vcNamespace); + if(tempElement != null){ + //Xm + String temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueXm); + BoundaryConditionType bct = new BoundaryConditionType(temp); + memmap.setBoundaryConditionTypeXm(bct); + //Xp + temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueXp); + bct = new BoundaryConditionType(temp); + memmap.setBoundaryConditionTypeXp(bct); + //Ym + temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueYm); + bct = new BoundaryConditionType(temp); + memmap.setBoundaryConditionTypeYm(bct); + //Yp + temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueYp); + bct = new BoundaryConditionType(temp); + memmap.setBoundaryConditionTypeYp(bct); + //Zm + temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueZm); + bct = new BoundaryConditionType(temp); + memmap.setBoundaryConditionTypeZm(bct); + //Zp + temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueZp); + bct = new BoundaryConditionType(temp); + memmap.setBoundaryConditionTypeZp(bct); + } + + return memmap; + } + + + /** + * This method returns a MembraneRegionEquation from a XML Element. + * Creation date: (5/17/2001 3:52:40 PM) + * + * @param param Element + * @return cbit.vcell.math.MembraneRegionEquation + * @throws cbit.vcell.xml.XmlParseException The exception description. + */ + private MembraneRegionEquation getMembraneRegionEquation(Element param, MathDescription mathDesc) throws XmlParseException{ + //get attributes + String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + + //find reference in the dictionnary + //try a MembraneRegionVariable + MembraneRegionVariable varref = (MembraneRegionVariable) mathDesc.getVariable(varname); + if(varref == null){ + throw new XmlParseException("The reference to the MembraneRegion variable " + varname + " could not be resolved!"); + } + + //get Initial condition + String temp = param.getChildText(XMLTags.InitialTag, vcNamespace); + Expression exp; + exp = unMangleExpression(temp); + // ** Create the Equation ** + MembraneRegionEquation memRegEq = new MembraneRegionEquation(varref, exp); + + //set the Uniform Rate + temp = param.getChildText(XMLTags.UniformRateTag, vcNamespace); + exp = unMangleExpression(temp); + memRegEq.setUniformRateExpression(exp); + + //set the Membrane Rate + temp = param.getChildText(XMLTags.MembraneRateTag, vcNamespace); + exp = unMangleExpression(temp); + memRegEq.setMembraneRateExpression(exp); + + //get ExactSolution (if any) +/* temp = param.getChildText(XMLTags.ExactTag); + if (temp !=null) { + try { + Expression expression = new Expression( unMangle( temp) ); + odeEquation.setExactSolution( expression); + } catch (ExpressionException e) { + lg.error(e); + throw new XmlParseException("An ExpressionException was fired when creating the expression: "+ unMangle(temp)+" : "+e.getMessage()); + } + } + //get ConstructedSolution (if any) + temp = param.getChildText(XMLTags.ConstructedTag); + if (temp != null) { + try { + Expression expression = new Expression(unMangle(temp)); + odeEquation.setConstructedSolution( expression ); + } catch (ExpressionException e) { + lg.error(e); + throw new XmlParseException("An ExpressionException was fired when creating the expression: "+ unMangle(temp)+" : "+e.getMessage()); + } + }*/ + + return memRegEq; + } + + private ComputeNormalComponentEquation getComputeNormal(Element param, MathDescription mathDesc) throws XmlParseException{ + //get attributes + String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + + //find reference in the dictionnary + //try a MembraneRegionVariable + MemVariable varref = (MemVariable) mathDesc.getVariable(varname); + if(varref == null){ + throw new XmlParseException("The reference to the Membrane variable " + varname + " could not be resolved!"); + } + + NormalComponent normalComponent = null; + String normalComponentString = param.getAttributeValue(XMLTags.ComputeNormalComponentAttrTag); + if(normalComponentString.equals(XMLTags.ComputeNormalComponentAttrTagValue_X)){ + normalComponent = NormalComponent.X; + } else if(normalComponentString.equals(XMLTags.ComputeNormalComponentAttrTagValue_Y)){ + normalComponent = NormalComponent.Y; + } else if(normalComponentString.equals(XMLTags.ComputeNormalComponentAttrTagValue_Z)){ + normalComponent = NormalComponent.Z; + } + + ComputeNormalComponentEquation computeNormal = new ComputeNormalComponentEquation(varref, normalComponent); + return computeNormal; + } + + private ComputeMembraneMetricEquation getComputeMembraneMetric(Element param, MathDescription mathDesc) throws XmlParseException{ + //get attributes + String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + + //find reference in the dictionnary + //try a MembraneRegionVariable + VolVariable varref = (VolVariable) mathDesc.getVariable(varname); + if(varref == null){ + throw new XmlParseException("The reference to the Volume variable " + varname + " could not be resolved!"); + } + + MembraneMetricComponent normalComponent = null; + String normalComponentString = param.getAttributeValue(XMLTags.ComputeMembraneMetricComponentAttrTag); + if(normalComponentString.equals(XMLTags.ComputeMembraneMetricComponentAttrTagValue_directionX)){ + normalComponent = MembraneMetricComponent.directionToMembraneX; + } else if(normalComponentString.equals(XMLTags.ComputeMembraneMetricComponentAttrTagValue_directionY)){ + normalComponent = MembraneMetricComponent.directionToMembraneY; + } else if(normalComponentString.equals(XMLTags.ComputeMembraneMetricComponentAttrTagValue_directionZ)){ + normalComponent = MembraneMetricComponent.directionToMembraneZ; + } else if(normalComponentString.equals(XMLTags.ComputeMembraneMetricComponentAttrTagValue_distance)){ + normalComponent = MembraneMetricComponent.distanceToMembrane; + } + + ComputeMembraneMetricEquation computeMembraneMetric = new ComputeMembraneMetricEquation(varref, normalComponent); + String membraneName = param.getAttributeValue(XMLTags.ComputeMembraneMetricTargetMembraneAttrTag); + computeMembraneMetric.setTargetMembraneName(membraneName); + return computeMembraneMetric; + } + + private ComputeCentroidComponentEquation getComputeCentroid(Element param, MathDescription mathDesc) throws XmlParseException{ + //get attributes + String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + + //find reference in the dictionnary + //try a MembraneRegionVariable + VolumeRegionVariable varref = (VolumeRegionVariable) mathDesc.getVariable(varname); + if(varref == null){ + throw new XmlParseException("The reference to the Volume Region variable " + varname + " could not be resolved!"); + } + + CentroidComponent normalComponent = null; + String normalComponentString = param.getAttributeValue(XMLTags.ComputeCentroidComponentAttrTag); + if(normalComponentString.equals(XMLTags.ComputeCentroidComponentAttrTagValue_X)){ + normalComponent = CentroidComponent.X; + } else if(normalComponentString.equals(XMLTags.ComputeCentroidComponentAttrTagValue_Y)){ + normalComponent = CentroidComponent.Y; + } else if(normalComponentString.equals(XMLTags.ComputeCentroidComponentAttrTagValue_Z)){ + normalComponent = CentroidComponent.Z; + } + + ComputeCentroidComponentEquation centroid = new ComputeCentroidComponentEquation(varref, normalComponent); + return centroid; + } + + /** + * This method returns a MembraneRegionVariable object from a XML Element. + * Creation date: (5/16/2001 2:56:34 PM) + * + * @param param Element + * @return cbit.vcell.math.MembraneRegionVariable + */ + private MembraneRegionVariable getMembraneRegionVariable(Element param){ + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); + Domain domain = null; + if(domainStr != null){ + domain = new Domain(domainStr); + } + + //-- create new MembraneRegionVariable object + MembraneRegionVariable memRegVariable = new MembraneRegionVariable(name, domain); + transcribeComments(param, memRegVariable); + + return memRegVariable; + } + + + /** + * This method returns a MembraneSubDomain object from a XML Element. + * Creation date: (5/18/2001 4:23:30 PM) + * + * @param param Element + * @return cbit.vcell.math.MembraneSubDomain + * @throws cbit.vcell.xml.XmlParseException The exception description. + */ + @SuppressWarnings("unchecked") + private MembraneSubDomain getMembraneSubDomain(Element param, MathDescription mathDesc) throws XmlParseException{ + + // no need to do anything with the 'Name' attribute : constructor of MembraneSubDomain creates name from inside/outside compartmentSubDomains. +// String msdName = unMangle( param.getAttributeValue(XMLTags.NameAttrTag) ); +// if ( msdName != null) { +// } + + //get compartmentSubDomain references + //inside + String name = unMangle(param.getAttributeValue(XMLTags.InsideCompartmentTag)); + CompartmentSubDomain insideRef = (CompartmentSubDomain) mathDesc.getCompartmentSubDomain(name); + if(insideRef == null){ + throw new XmlParseException("The reference to the inside CompartmentSubDomain " + name + ", could not be resolved!"); + } + //outside + name = unMangle(param.getAttributeValue(XMLTags.OutsideCompartmentTag)); + CompartmentSubDomain outsideRef = (CompartmentSubDomain) mathDesc.getCompartmentSubDomain(name); + if(outsideRef == null){ + throw new XmlParseException("The reference to the outside CompartmentSubDomain " + name + ", could not be resolved!"); + } + //*** create new Membrane SubDomain *** + SubVolume insideSubVolume = mathDesc.getGeometry().getGeometrySpec().getSubVolume(insideRef.getName()); + SubVolume outsideSubVolume = mathDesc.getGeometry().getGeometrySpec().getSubVolume(outsideRef.getName()); + SurfaceClass surfaceClass = mathDesc.getGeometry().getGeometrySurfaceDescription().getSurfaceClass(insideSubVolume, outsideSubVolume); + + MembraneSubDomain subDomain = new MembraneSubDomain(insideRef, outsideRef, surfaceClass.getName()); + transcribeComments(param, subDomain); + + //Process BoundaryConditions + Iterator iterator = param.getChildren(XMLTags.BoundaryTypeTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + + //create BoundaryConditionType + String temp = tempelement.getAttributeValue(XMLTags.BoundaryTypeAttrTag); + BoundaryConditionType bType = new BoundaryConditionType(temp); + + //check where it goes + //Process Xm + if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueXm)){ + subDomain.setBoundaryConditionXm(bType); + } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueXp)){ + //Process Xp + subDomain.setBoundaryConditionXp(bType); + } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueYm)){ + //Process Ym + subDomain.setBoundaryConditionYm(bType); + } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueYp)){ + //Process Yp + subDomain.setBoundaryConditionYp(bType); + } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueZm)){ + //Process Zm + subDomain.setBoundaryConditionZm(bType); + } else if(tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueZp)){ + //Process Zp + subDomain.setBoundaryConditionZp(bType); + } else { + // If not indentified throw an exception!! + throw new XmlParseException("Unknown BoundaryConditionType: " + tempelement.getAttributeValue(XMLTags.BoundaryAttrTag)); + } + } + + //Add OdeEquations + iterator = param.getChildren(XMLTags.OdeEquationTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempElement = (Element) iterator.next(); + OdeEquation odeEquation = getOdeEquation(tempElement, mathDesc); + + try { + subDomain.addEquation(odeEquation); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding an OdeEquation to a MembraneSubDomain!", e); + } + } + + //process PdeEquations + iterator = param.getChildren(XMLTags.PdeEquationTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempElement = (Element) iterator.next(); + + try { + subDomain.addEquation(getPdeEquation(tempElement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding an PdeEquation to the MembraneSubDomain " + name, e); + } + } + + //Add JumpConditions + iterator = param.getChildren(XMLTags.JumpConditionTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempElement = (Element) iterator.next(); + try { + subDomain.addJumpCondition(getJumpCondition(tempElement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding a JumpCondition to a MembraneSubDomain!", e); + } + } + + //Add the FastSystem (if any) + Element tempElement = param.getChild(XMLTags.FastSystemTag, vcNamespace); + if(tempElement != null){ + subDomain.setFastSystem(getFastSystem(tempElement, mathDesc)); + } + + //add MembraneRegionEquation + iterator = param.getChildren(XMLTags.MembraneRegionEquationTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + tempElement = (Element) iterator.next(); + try { + subDomain.addEquation(getMembraneRegionEquation(tempElement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding a MembraneRegionEquation to a MEmbraneSubDomain!", e); + } + } + + iterator = param.getChildren(XMLTags.ParticleJumpProcessTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + try { + subDomain.addParticleJumpProcess(getParticleJumpProcess(tempelement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding a jump process to the MembraneSubDomain " + name, e); + } + } + + iterator = param.getChildren(XMLTags.LangevinParticleJumpProcessTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + try { + subDomain.addParticleJumpProcess(getParticleJumpProcess(tempelement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding a jump process to the MembraneSubDomain " + name, e); + } + } + + iterator = param.getChildren(XMLTags.ParticlePropertiesTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + try { + subDomain.addParticleProperties(getParticleProperties(tempelement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding a jump process to the MembraneSubDomain " + name, e); + } + } + + //process ComputeNormal "equations" + iterator = param.getChildren(XMLTags.ComputeNormalTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element tempelement = (Element) iterator.next(); + + try { + subDomain.addEquation(getComputeNormal(tempelement, mathDesc)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding an ComputeNormal 'equation' to the MembraneSubDomain " + name, e); + } + } + + + Element velElem = param.getChild(XMLTags.VelocityTag, vcNamespace); + setMembraneSubdomainVelocity(velElem, XMLTags.XAttrTag, subDomain::setVelocityX); + setMembraneSubdomainVelocity(velElem, XMLTags.YAttrTag, subDomain::setVelocityY); + + return subDomain; + } + + /** + * MembraneSubDomain velocity + * + * @param vel could be null + * @param tag + * @param dest + * @throws XmlParseException + */ + private void setMembraneSubdomainVelocity(Element vel, String tag, Consumer dest) throws XmlParseException{ + Expression exp = null; + if(vel != null){ + Element e = vel.getChild(tag, vcNamespace); + if(e != null){ + String expStr = e.getValue(); + try { + exp = new Expression(expStr); + } catch(ExpressionException ee){ + throw new XmlParseException("Error parsing " + expStr, ee); + } + } + } + dest.accept(exp); + } + + + /** + * This method returns a MemVariable object from a XML element. + * Creation date: (5/16/2001 3:17:18 PM) + * + * @param param Element + * @return cbit.vcell.math.MemVariable + */ + private MemVariable getMemVariable(Element param){ + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); + Domain domain = null; + if(domainStr != null){ + domain = new Domain(domainStr); + } + + //Create new memVariable + MemVariable memVariable = new MemVariable(name, domain); + transcribeComments(param, memVariable); + + return memVariable; + } + + + private PointVariable getPointVariable(Element param){ + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); + Domain domain = null; + if(domainStr != null){ + domain = new Domain(domainStr); + } + + //Create new memVariable + PointVariable pointVariable = new PointVariable(name, domain); + transcribeComments(param, pointVariable); + + return pointVariable; + } + + + /** + * This method returns a MeshSpecification object from a XML Element. + * Creation date: (5/22/2001 12:05:21 PM) + * + * @param param Element + * @return cbit.vcell.mesh.MeshSpecification + */ + private MeshSpecification getMeshSpecification(Element param, Geometry geometry) throws XmlParseException{ + //*** create new MeshSpecification *** + MeshSpecification meshSpec = new MeshSpecification(geometry); + + //get ISize + Element size = param.getChild(XMLTags.SizeTag, vcNamespace); + int x = Integer.parseInt(size.getAttributeValue(XMLTags.XAttrTag)); + int y = Integer.parseInt(size.getAttributeValue(XMLTags.YAttrTag)); + int z = Integer.parseInt(size.getAttributeValue(XMLTags.ZAttrTag)); + + ISize newsize = new ISize(x, y, z); + + //set ISize + try { + meshSpec.setSamplingSize(newsize); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A PropertyVetoException was fired when setting the ISize object to a new MeshSpecification", e); + } + + return meshSpec; + } + + + /** + * This method creates a Model object from a XML element. + * Creation date: (3/14/2001 6:14:37 PM) + * + * @param param Element + * @return cbit.vcell.model.Model + */ + public Model getModel(Element param) throws XmlParseException{ + if(param == null){ + throw new XmlParseException("Invalid 'NULL' XML 'model' element arrived!"); + } + //Get version, if any + Model newmodel = null; + Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace)); + + // read in unit system + // if forcedModelUnitSystem has been set, ues that (could be overriding unit system for SBML export) + if(forcedModelUnitSystem != null){ + newmodel = new Model(version, forcedModelUnitSystem); + } else { + Element unitSystemNode = param.getChild(XMLTags.ModelUnitSystemTag, vcNamespace); + if(unitSystemNode != null){ + ModelUnitSystem modelUnitSystem = getUnitSystem(unitSystemNode); + newmodel = new Model(version, modelUnitSystem); + } else { + newmodel = new Model(version); + } + } + + try { + //Set attributes + newmodel.setName(unMangle(param.getAttributeValue(XMLTags.NameAttrTag))); + //Add annotation + String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace); + if(annotationText != null && annotationText.length() > 0){ + newmodel.setDescription(unMangle(annotationText)); + } + + // Add global parameters + Element globalParamsElement = param.getChild(XMLTags.ModelParametersTag, vcNamespace); + if(globalParamsElement != null){ + ModelParameter[] modelParams = getModelParams(globalParamsElement, newmodel); + // add global/model param to model - done inside getModelParam by passing newModel + newmodel.setModelParameters(modelParams); + } + + //Add Species (Compounds) + Iterator iterator = param.getChildren(XMLTags.SpeciesTag, vcNamespace).iterator(); + ArrayList speciesList = new ArrayList(); + while (iterator.hasNext()) { + Element temp = (Element) iterator.next(); + speciesList.add(getSpecies(temp)); + } + newmodel.setSpecies(speciesList.toArray(new Species[speciesList.size()])); + //Add Structures + LinkedList newstructures = new LinkedList(); + //(features) + List children = param.getChildren(XMLTags.FeatureTag, vcNamespace); + for(Element featureElement : children){ + newstructures.add(getFeature(featureElement)); + } + //(Membrane) + children = param.getChildren(XMLTags.MembraneTag, vcNamespace); + for(Element memElement : children){ + newstructures.add(getMembrane(newmodel, memElement, newstructures)); + } + if(newstructures.size() > 0){ + Structure[] structarray = new Structure[newstructures.size()]; + newstructures.toArray(structarray); + // Add all the retrieved structures + newmodel.setStructures(structarray); + } + + // retrieve the RbmModelContainer, if present - must be done before we retrieve species context! + Element element = param.getChild(XMLTags.RbmModelContainerTag, vcNamespace); + if(element != null){ + getRbmModelContainer(element, newmodel); + } else { + lg.debug("RbmModelContainer is missing."); + } + + //Add SpeciesContexts + children = param.getChildren(XMLTags.SpeciesContextTag, vcNamespace); + SpeciesContext[] newspeccon = new SpeciesContext[children.size()]; + int scCounter = 0; + for(Element scElement : children){ + newspeccon[scCounter] = getSpeciesContext(scElement, newmodel); + scCounter++; + } + newmodel.setSpeciesContexts(newspeccon); + + // Retrieve rateRules and add to model +// Element rateRuleVarsElement = param.getChild(XMLTags.RateRuleVariablesTag, vcNamespace); +// if(rateRuleVarsElement != null){ +// RateRuleVariable[] rateRuleVars = getRateRuleVariables(rateRuleVarsElement, newmodel); +// newmodel.setRateRuleVariables(rateRuleVars); +// } + + //Add Reaction steps (if available) + + //(Simplereaction) + // Create a varHash with reserved symbols and global parameters, if any, to pass on to Kinetics + // must create new hash for each reaction and flux, since each kinetics uses new variables hash + iterator = param.getChildren(XMLTags.SimpleReactionTag, vcNamespace).iterator(); + ArrayList reactionStepList = new ArrayList(); + while (iterator.hasNext()) { + Element temp = iterator.next(); + reactionStepList.add(getSimpleReaction(temp, newmodel)); + } + //(fluxStep) + iterator = param.getChildren(XMLTags.FluxStepTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + Element temp = iterator.next(); + reactionStepList.add(getFluxReaction(temp, newmodel)); + } + newmodel.setReactionSteps(reactionStepList.toArray(new ReactionStep[reactionStepList.size()])); + //Add Diagrams + children = param.getChildren(XMLTags.DiagramTag, vcNamespace); + if(children.size() > 0){ + Diagram[] newdiagrams = new Diagram[children.size()]; + int diagramCounter = 0; + for(Element diagramElement : children){ + newdiagrams[diagramCounter] = getDiagram(diagramElement, newmodel); + diagramCounter++; + } + reorderDiagramsInPlace_UponRead(docVCellSoftwareVersion, newdiagrams, newmodel.getStructureTopology()); +// if(docVCellSoftwareVersion != null && !docVCellSoftwareVersion.isValid() && docVCellSoftwareVersion.getMajorVersion()<=5 && docVCellSoftwareVersion.getMinorVersion() <=2){ +// //In Vcell 5.2 and previous we need to order diagrams topologically, in 5.3 and later the diagrams are displayed as they are ordered when read from document +// final StructureTopology structureTopology = newmodel.getStructureTopology(); +// Arrays.sort(newdiagrams, new Comparator() { +// @Override +// public int compare(Diagram o1, Diagram o2) { +// return getStructureLevel(o1.getStructure(), structureTopology) - getStructureLevel(o2.getStructure(), structureTopology); +// } +// }); +// } + newmodel.setDiagrams(newdiagrams); + } + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException(e); + } catch(ModelException e){ + lg.error(e); + } + + // model param expresions are not bound when they are read in, since they could be functions of each other or structures/speciesContexts. + // Hence bind the model param exprs at the end, after reading all model level quantities. + ModelParameter[] modelParameters = newmodel.getModelParameters(); + for(int i = 0; modelParameters != null && i < modelParameters.length; i++){ + try { + modelParameters[i].getExpression().bindExpression(newmodel); + } catch(ExpressionBindingException e){ + throw new RuntimeException("Error binding global parameter '" + modelParameters[i].getName() + "' to model." + e.getMessage(), e); + } + } + return newmodel; + } + + @SuppressWarnings("unchecked") + public void getRbmModelContainer(Element param, Model newModel) throws ModelException, PropertyVetoException, XmlParseException{ + Element element = param.getChild(XMLTags.RbmMolecularTypeListTag, vcNamespace); + if(element != null){ + getRbmMolecularTypeList(element, newModel); + } + element = param.getChild(XMLTags.RbmObservableListTag, vcNamespace); + if(element != null){ + getRbmObservableList(element, newModel); + } + element = param.getChild(XMLTags.RbmReactionRuleListTag, vcNamespace); + if(element != null){ + getRbmReactionRuleList(element, newModel); + } + element = param.getChild(XMLTags.RbmNetworkConstraintsTag, vcNamespace); + if(element != null){ + getRbmNetworkConstraints(element, newModel); // one network constraint element + } + } + + private void getRbmMolecularTypeList(Element param, Model newModel){ + RbmModelContainer mc = newModel.getRbmModelContainer(); + List mtl = mc.getMolecularTypeList(); + List children = param.getChildren(XMLTags.RbmMolecularTypeTag, vcNamespace); + for(Element element : children){ + MolecularType t = getRbmMolecularType(element, newModel); + if(t != null){ + mtl.add(t); + } + } + } + + //private void getRbmSeedSpeciesList(Element param, Model newModel) { +// RbmModelContainer mc = newModel.getRbmModelContainer(); +// List ssl = mc.getSeedSpeciesList(); +// List children = param.getChildren(XMLTags.RbmSeedSpeciesTag, vcNamespace); +// for (Element element : children) { +// SeedSpecies s = getRbmSeedSpecies(element, newModel); +// if(s != null) { ssl.add(s); } +// } +//} + private void getRbmObservableList(Element param, Model newModel) throws ModelException, PropertyVetoException{ + RbmModelContainer mc = newModel.getRbmModelContainer(); + List children = new ArrayList(); + children = param.getChildren(XMLTags.RbmObservableTag, vcNamespace); + for(Element element : children){ + RbmObservable o = getRbmObservables(element, newModel); + if(o != null){ + mc.addObservable(o); + } + } + } + + private void getRbmReactionRuleList(Element param, Model newModel) throws XmlParseException{ + RbmModelContainer mc = newModel.getRbmModelContainer(); + List rrl = mc.getReactionRuleList(); + List children = new ArrayList(); + children = param.getChildren(XMLTags.RbmReactionRuleTag, vcNamespace); + for(Element element : children){ + ReactionRule r = getRbmReactionRule(element, newModel); + if(r != null){ + rrl.add(r); + } + } + } + + private MolecularType getRbmMolecularType(Element e, Model newModel){ + String s = e.getAttributeValue(XMLTags.NameAttrTag); + if(s == null || s.isEmpty()){ + System.out.println("XMLReader: getRBMMolecularType: name is missing."); + return null; + } + MolecularType mt = new MolecularType(s, newModel); + + final String attributeValue = e.getAttributeValue(XMLTags.RbmMolecularTypeAnchorAllAttrTag); + if(attributeValue != null){ + boolean anchorAll = Boolean.parseBoolean(attributeValue); + mt.setAnchorAll(anchorAll); + } + List anchors = e.getChildren(XMLTags.RbmMolecularTypeAnchorTag, vcNamespace); + for(Element element : anchors){ + String anchor = element.getAttributeValue(XMLTags.StructureAttrTag); + Structure structure = newModel.getStructure(anchor); + if(structure == null){ + System.out.println("XMLReader: getRbmMolecularType: anchor is missing from the structures list."); + } + if(structure != null){ + mt.addAnchor(structure); + } + } + List children = e.getChildren(XMLTags.RbmMolecularComponentTag, vcNamespace); + for(Element element : children){ + MolecularComponent mc = getRbmMolecularComponent(element, newModel); + if(mc != null){ + mt.addMolecularComponent(mc); + } + } + return mt; + } + + private MolecularComponent getRbmMolecularComponent(Element e, Model newModel){ + String s = e.getAttributeValue(XMLTags.NameAttrTag); + if(s == null || s.isEmpty()){ + System.out.println("XMLReader: getRbmMolecularComponent: name is missing."); + return null; + } + MolecularComponent mc = new MolecularComponent(s); + s = e.getAttributeValue(XMLTags.RbmIndexAttrTag); + if(s == null || s.isEmpty()){ + System.out.println("XMLReader: getRbmMolecularComponent: index is missing."); + return null; + } + int index = Integer.parseInt(s); + mc.setIndex(index); + List children = e.getChildren(XMLTags.RbmMolecularTypeAllowableStateTag, vcNamespace); + for(Element element : children){ + ComponentStateDefinition cs = getRbmComponentStateDefinition(element, newModel); + if(cs != null){ + mc.addComponentStateDefinition(cs); + } + } + return mc; + } + + private ComponentStateDefinition getRbmComponentStateDefinition(Element e, Model newModel){ + String s = e.getAttributeValue(XMLTags.NameAttrTag); + if(s == null || s.isEmpty()){ + System.out.println("XMLReader: getRbmComponentState: name is missing."); + return null; + } + ComponentStateDefinition cs = new ComponentStateDefinition(s); +// s = e.getAttributeValue(XMLTags.RbmMolecularTypeAnyTag); +// if(s!=null && !s.isEmpty()) { +// boolean any = Boolean.parseBoolean(s); +// cs.setAny(any); +// } + return cs; + } + + //private SeedSpecies getRbmSeedSpecies(Element e, Model newModel) { +// String s = e.getAttributeValue(XMLTags.RbmInitialConditionTag); +// if(s == null || s.isEmpty()) { +// System.out.println("XMLReader: getRbmSeedSpecies: initial condition is missing."); +// return null; +// } +// Expression exp = unMangleExpression(s); +// Element element = e.getChild(XMLTags.RbmSpeciesPatternTag, vcNamespace); +// SpeciesPattern sp = getSpeciesPattern(element, newModel); +// if(sp == null) { +// System.out.println("XMLReader: getRbmSeedSpecies: SpeciesPattern is missing."); +// return null; +// } +// SeedSpecies ss = new SeedSpecies(sp, exp); +// return ss; +//} + private SpeciesPattern getSpeciesPattern(Element e, Model newModel){ + + SpeciesPattern sp = new SpeciesPattern(); + List children = e.getChildren(XMLTags.RbmMolecularTypePatternTag, vcNamespace); + for(Element element : children){ + MolecularTypePattern tp = getRbmMolecularTypePattern(element, newModel); + if(tp != null){ + sp.addMolecularTypePattern(tp); + } + } + return sp; + } + + private MolecularTypePattern getRbmMolecularTypePattern(Element e, Model newModel){ + RbmModelContainer mc = newModel.getRbmModelContainer(); + Element e1 = e.getChild(XMLTags.RbmMolecularTypeTag, vcNamespace); + String molecularTypeName = e1.getAttributeValue(XMLTags.NameAttrTag); + MolecularType mt = mc.getMolecularType(molecularTypeName); + if(mt == null){ + System.out.println("XMLReader: getRbmMolecularTypePattern: encountered reference to non-existing MolecularType."); + return null; + } + MolecularTypePattern tp = new MolecularTypePattern(mt, false); // we insert the component patterns below + String index = e.getAttributeValue(XMLTags.RbmIndexAttrTag); + if(index != null && !index.isEmpty()){ + tp.setIndex(Integer.parseInt(index)); + } + String match = e.getAttributeValue(XMLTags.RbmParticipantPatternMatchTag); + if(match != null && !match.isEmpty()){ + tp.setParticipantMatchLabel(match); + } + List cpl = new ArrayList(); + List children = e.getChildren(XMLTags.RbmMolecularComponentPatternTag, vcNamespace); + for(Element e2 : children){ + MolecularComponentPattern cp = getRbmMolecularComponentPattern(e2, tp, mt, newModel); + if(cp != null){ + cpl.add(cp); + } + } + tp.setComponentPatterns(cpl); + return tp; + } + + public static void reorderDiagramsInPlace_UponRead(VCellSoftwareVersion docVCellSoftwareVersion, final Diagram[] diagramArr, final StructureTopology structureTopology){ + if(docVCellSoftwareVersion != null && (docVCellSoftwareVersion.getMajorVersion() < 5 || (docVCellSoftwareVersion.getMajorVersion() == 5 && docVCellSoftwareVersion.getMinorVersion() <= 2))){ + //In Vcell 5.2 and previous we need to order diagrams topologically, in 5.3 and later the diagrams are displayed as they are ordered when read from document + Arrays.sort(diagramArr, new Comparator() { + @Override + public int compare(Diagram o1, Diagram o2){ + return getStructureLevel(o1.getStructure(), structureTopology) - getStructureLevel(o2.getStructure(), structureTopology); + } + }); + } + } + + private static Integer getStructureLevel(Structure s, StructureTopology structureTopology){ + Structure s0 = s; + int level = 0; + while (s0 != null) { + level += 1; + s0 = structureTopology.getParentStructure(s0); + } + return level; + } + + private MolecularComponentPattern getRbmMolecularComponentPattern(Element e, MolecularTypePattern mtp, MolecularType mt, Model newModel){ + RbmModelContainer mc = newModel.getRbmModelContainer(); + String s = e.getAttributeValue(XMLTags.RbmMolecularComponentTag); + if(s == null || s.isEmpty()){ + System.out.println("XMLReader: getRbmMolecularComponentPattern: MolecularComponent name is missing."); + return null; + } + MolecularComponent c = mt.getMolecularComponent(s); + if(c == null){ + System.out.println("XMLReader: getRbmMolecularComponentPattern: encountered reference " + s + " to non-existing MolecularComponent."); + return null; + } + ComponentStatePattern csp = new ComponentStatePattern(); + MolecularComponentPattern mcp = new MolecularComponentPattern(c); + s = e.getAttributeValue(XMLTags.RbmMolecularComponentStatePatternTag); + if(s != null && !s.isEmpty()){ // state may be missing, we set it only if is present + ComponentStateDefinition cs = c.getComponentStateDefinition(s); + if(cs == null){ + System.out.println("XMLReader: getRbmMolecularComponentPattern: encountered reference " + s + " to non-existing MolecularComponentState."); + return null; + } + csp = new ComponentStatePattern(cs); + mcp.setComponentStatePattern(csp); + } +// s = e.getAttributeValue(XMLTags.RbmMolecularTypeAnyTag); +// if(s!=null && !s.isEmpty()) { +// boolean any = Boolean.parseBoolean(s); +// csp.setAny(any); +// } + + s = e.getAttributeValue(XMLTags.RbmBondTypeAttrTag); + BondType bondType = BondType.fromSymbol(s); + if(bondType == BondType.Specified){ + int bondId = Integer.parseInt(s); + mcp.setBondId(bondId); + } + mcp.setBondType(bondType); + // sanity check, we only read the names here and make sure they make sense + Element bondElement = e.getChild(XMLTags.RbmBondTag, vcNamespace); + if(bondElement != null){ + String molecularTypeName = bondElement.getAttributeValue(XMLTags.RbmMolecularTypePatternTag); // it's actually the name of the MolecularType inside this pattern + String molecularComponentName = bondElement.getAttributeValue(XMLTags.RbmMolecularComponentPatternTag); + if(molecularTypeName == null || molecularTypeName.isEmpty()){ + System.out.println("XMLReader: getRbmMolecularComponentPattern: Bond Attribute molecularTypeName missing."); + return mcp; + } + if(molecularComponentName == null || molecularComponentName.isEmpty()){ + System.out.println("XMLReader: getRbmMolecularComponentPattern: Bond Attribute molecularComponentName missing."); + return mcp; + } + Bond bond = new Bond(); // we'll have a bond here, it will be properly initialized during RbmObservable.resolveBonds() call !!! + mcp.setBond(bond); + } + return mcp; + } + + private RbmObservable getRbmObservables(Element e, Model newModel){ + String n = e.getAttributeValue(XMLTags.NameAttrTag); + if(n == null || n.isEmpty()){ + System.out.println("XMLReader: getRbmObservables: name is missing."); + return null; + } + String t = e.getAttributeValue(XMLTags.RbmObservableTypeTag); + if(t == null || t.isEmpty()){ + System.out.println("XMLReader: getRbmObservables: type is missing."); + return null; + } + RbmObservable.ObservableType ot = RbmObservable.ObservableType.Molecules; + if(!t.equals(ot.name())){ + ot = RbmObservable.ObservableType.Species; + } + Structure structure = null; + String structureName = e.getAttributeValue(XMLTags.StructureAttrTag); + if(structureName == null || structureName.isEmpty()){ // the tag is missing + if(newModel.getStructures().length == 1){ + structure = newModel.getStructure(0); // possible old single compartment model where we were not saving the structure for observable + } else { + throw new RuntimeException("XMLReader: structure missing for observable " + n); + } + } else { + structure = newModel.getStructure(structureName); + } + RbmObservable o = new RbmObservable(newModel, n, structure, ot); + + RbmObservable.Sequence se = RbmObservable.Sequence.Multimolecular; // Sequence + String ses = e.getAttributeValue(XMLTags.RbmObservableSequenceAttrTag); + if(ses != null && ses.equals(RbmObservable.Sequence.PolymerLengthEqual.name())){ + se = RbmObservable.Sequence.PolymerLengthEqual; + } else if(ses != null && ses.equals(RbmObservable.Sequence.PolymerLengthGreater.name())){ + se = RbmObservable.Sequence.PolymerLengthGreater; + } + o.setSequence(se); + + String lens = e.getAttributeValue(XMLTags.RbmObservableLenEqualAttrTag); + if(lens != null){ // may be null for older models in which case the observable has default initial values + int len = Integer.parseInt(lens); + o.setSequenceLength(RbmObservable.Sequence.PolymerLengthEqual, len); + } + lens = e.getAttributeValue(XMLTags.RbmObservableLenGreaterAttrTag); + if(lens != null){ + int len = Integer.parseInt(lens); + o.setSequenceLength(RbmObservable.Sequence.PolymerLengthGreater, len); + } + +// Element element = e.getChild(XMLTags.RbmSpeciesPatternTag, vcNamespace); +// SpeciesPattern sp = getSpeciesPattern(element, newModel); + List children = e.getChildren(XMLTags.RbmSpeciesPatternTag, vcNamespace); + for(Element e2 : children){ + SpeciesPattern sp = getSpeciesPattern(e2, newModel); + if(sp != null){ + o.addSpeciesPattern(sp); + } // setSpeciesPattern() will call resolveBonds() + } + return o; + } + + private ReactionRule getRbmReactionRule(Element reactionRuleElement, Model newModel) throws XmlParseException{ + String n = reactionRuleElement.getAttributeValue(XMLTags.NameAttrTag); + if(n == null || n.isEmpty()){ + System.out.println("XMLReader: getRbmReactionRule: name is missing."); + return null; + } + try { + boolean reversible = Boolean.valueOf(reactionRuleElement.getAttributeValue(XMLTags.RbmReactionRuleReversibleTag)); + String structureName = reactionRuleElement.getAttributeValue(XMLTags.StructureAttrTag, newModel.getStructures()[0].getName()); // get 1st structure if attribute missing + Structure structure = newModel.getStructure(structureName); + ReactionRule reactionRule = new ReactionRule(newModel, n, structure, reversible); + String reactionRuleLabel = reactionRuleElement.getAttributeValue(XMLTags.RbmReactionRuleLabelTag); // we ignore this, name and label are the same thing for now + + // + // old style kinetics placed parameter values as attributes + // look for attributes named ("MassActionKf","MassActionKr","MichaelisMentenKcat","MichaelisMentenKm","SaturableKs","SaturableVmax") + String[] oldKineticsAttributes = new String[]{ + XMLTags.RbmMassActionKfAttrTag_DEPRECATED, + XMLTags.RbmMassActionKrAttrTag_DEPRECATED, + XMLTags.RbmMichaelisMentenKcatAttrTag_DEPRECATED, + XMLTags.RbmMichaelisMentenKmAttrTag_DEPRECATED, + XMLTags.RbmSaturableKsAttrTag_DEPRECATED, + XMLTags.RbmSaturableVmaxAttrTag_DEPRECATED + }; + boolean bOldKineticsFound = false; + for(String oldKineticsAttribute : oldKineticsAttributes){ + if(reactionRuleElement.getAttribute(oldKineticsAttribute) != null){ + bOldKineticsFound = true; + } + } + + if(bOldKineticsFound){ + readOldRbmKineticsAttributes(reactionRuleElement, reactionRule); + } else { + Element kineticsElement = reactionRuleElement.getChild(XMLTags.KineticsTag, vcNamespace); + if(kineticsElement != null){ + String kineticLawTypeString = kineticsElement.getAttributeValue(XMLTags.KineticsTypeAttrTag); + RbmKineticLaw.RateLawType rateLawType = null; + if(XMLTags.RbmKineticTypeMassAction.equals(kineticLawTypeString)){ + rateLawType = RateLawType.MassAction; + } else if(XMLTags.RbmKineticTypeMichaelisMenten.equals(kineticLawTypeString)){ + rateLawType = RateLawType.MichaelisMenten; + } else if(XMLTags.RbmKineticTypeSaturable.equals(kineticLawTypeString)){ + rateLawType = RateLawType.Saturable; + } else { + throw new RuntimeException("unexpected rate law type " + kineticLawTypeString); + } + reactionRule.setKineticLaw(new RbmKineticLaw(reactionRule, rateLawType)); + List parameterElements = kineticsElement.getChildren(XMLTags.ParameterTag, vcNamespace); + HashMap roleHash = new HashMap(); + roleHash.put(XMLTags.RbmMassActionKfRole, RbmKineticLawParameterType.MassActionForwardRate); + roleHash.put(XMLTags.RbmMassActionKrRole, RbmKineticLawParameterType.MassActionReverseRate); + roleHash.put(XMLTags.RbmMichaelisMentenVmaxRole, RbmKineticLawParameterType.MichaelisMentenVmax); + roleHash.put(XMLTags.RbmMichaelisMentenKmRole, RbmKineticLawParameterType.MichaelisMentenKm); + roleHash.put(XMLTags.RbmSaturableVmaxRole, RbmKineticLawParameterType.SaturableVmax); + roleHash.put(XMLTags.RbmSaturableKsRole, RbmKineticLawParameterType.SaturableKs); + roleHash.put(XMLTags.RbmUserDefinedRole, RbmKineticLawParameterType.UserDefined); + HashSet xmlRolesToIgnore = new HashSet(); + xmlRolesToIgnore.add(XMLTags.RbmRuleRateRole); + ParameterContext parameterContext = reactionRule.getKineticLaw().getParameterContext(); + readParameters(parameterElements, parameterContext, roleHash, RbmKineticLawParameterType.UserDefined, xmlRolesToIgnore, newModel); + } + } + Element e1 = reactionRuleElement.getChild(XMLTags.RbmReactantPatternsListTag, vcNamespace); + getRbmReactantPatternsList(e1, reactionRule, newModel); + Element e2 = reactionRuleElement.getChild(XMLTags.RbmProductPatternsListTag, vcNamespace); + getRbmProductPatternsList(e2, reactionRule, newModel); + reactionRule.checkMatchConsistency(); + return reactionRule; + } catch(PropertyVetoException | ExpressionException ex){ + throw new RuntimeException("failed to parse kinetics for reaction rule '" + n + "': " + ex.getMessage(), ex); + } + } + + private void readOldRbmKineticsAttributes(Element reactionRuleElement, ReactionRule reactionRule) throws PropertyVetoException, ExpressionException{ + boolean reversible = reactionRule.isReversible(); + + // + // try Mass Action Kinetics attributes + // + { + String massActionForwardRate = reactionRuleElement.getAttributeValue(XMLTags.RbmMassActionKfAttrTag_DEPRECATED); + if(massActionForwardRate != null && !massActionForwardRate.isEmpty()){ + reactionRule.setKineticLaw(new RbmKineticLaw(reactionRule, RateLawType.MassAction)); + Expression massActionKfExp = unMangleExpression(massActionForwardRate); + LocalParameter forwardRateParameter = reactionRule.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate); + reactionRule.getKineticLaw().setParameterValue(forwardRateParameter, massActionKfExp, true); + if(reversible == true){ + String massActionReverseRate = reactionRuleElement.getAttributeValue(XMLTags.RbmMassActionKrAttrTag_DEPRECATED); + if(massActionReverseRate == null || massActionReverseRate.isEmpty()){ + throw new RuntimeException("XMLReader: getRbmReactionRule: Mass Action: Reverse Rate is missing."); + } else { + Expression massActionKrExp = unMangleExpression(massActionReverseRate); + LocalParameter reverseRateParameter = reactionRule.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate); + reactionRule.getKineticLaw().setParameterValue(reverseRateParameter, massActionKrExp, true); + } + } + return; + } + } + + // + // try Michaelis Menten Kinetics attributes + // + { + String MM_Kcat = reactionRuleElement.getAttributeValue(XMLTags.RbmMichaelisMentenKcatAttrTag_DEPRECATED); + if(MM_Kcat != null && !MM_Kcat.isEmpty()){ + reactionRule.setKineticLaw(new RbmKineticLaw(reactionRule, RateLawType.MichaelisMenten)); + Expression MM_Kcat_exp = unMangleExpression(MM_Kcat); + LocalParameter kcatParameter = reactionRule.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MichaelisMentenVmax); + reactionRule.getKineticLaw().setParameterValue(kcatParameter, MM_Kcat_exp, true); + String MM_Km = reactionRuleElement.getAttributeValue(XMLTags.RbmMichaelisMentenKmAttrTag_DEPRECATED); + if(MM_Km == null || MM_Km.isEmpty()){ + System.out.println("XMLReader: getRbmReactionRule: MM_Km is missing."); + } else { + Expression MM_Km_exp = unMangleExpression(MM_Km); + LocalParameter kmParameter = reactionRule.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MichaelisMentenKm); + reactionRule.getKineticLaw().setParameterValue(kmParameter, MM_Km_exp, true); + } + return; + } + } + + // + // try Saturable Kinetics attributes + // + { + String Sat_Ks = reactionRuleElement.getAttributeValue(XMLTags.RbmSaturableKsAttrTag_DEPRECATED); + if(Sat_Ks != null && !Sat_Ks.isEmpty()){ + reactionRule.setKineticLaw(new RbmKineticLaw(reactionRule, RateLawType.Saturable)); + Expression Sat_Ks_exp = unMangleExpression(Sat_Ks); + LocalParameter ksParameter = reactionRule.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.SaturableKs); + reactionRule.getKineticLaw().setParameterValue(ksParameter, Sat_Ks_exp, true); + String Sat_Vmax = reactionRuleElement.getAttributeValue(XMLTags.RbmSaturableVmaxAttrTag_DEPRECATED); + if(Sat_Vmax == null || Sat_Vmax.isEmpty()){ + System.out.println("XMLReader: getRbmReactionRule: Sat_Vmax is missing."); + } else { + Expression Sat_Vmax_exp = unMangleExpression(Sat_Vmax); + LocalParameter vmaxParameter = reactionRule.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.SaturableVmax); + reactionRule.getKineticLaw().setParameterValue(vmaxParameter, Sat_Vmax_exp, true); + } + return; + } + } + + throw new RuntimeException("Kinetic law unsupported or missing. Must be Mass Action, Michaelis Menten or Saturable."); + } + + private void getRbmReactantPatternsList(Element e, ReactionRule r, Model newModel){ + if(e != null){ + List rpChildren = e.getChildren(XMLTags.RbmReactantPatternTag, vcNamespace); + for(Element rpElement : rpChildren){ + Structure structure = null; + String structureName = rpElement.getAttributeValue(XMLTags.StructureAttrTag); + if(structureName == null || structureName.isEmpty()){ // the tag is missing + throw new RuntimeException("XMLReader: structure missing for reaction rule pattern."); + } else { + structure = newModel.getStructure(structureName); + } + Element spe = rpElement.getChild(XMLTags.RbmSpeciesPatternTag, vcNamespace); + SpeciesPattern s = getSpeciesPattern(spe, newModel); + if(s != null){ + r.addReactant(new ReactantPattern(s, structure), false); + } + } + // older models have the species pattern saved directly and using the structure or the rule + List spChildren = e.getChildren(XMLTags.RbmSpeciesPatternTag, vcNamespace); + for(Element element : spChildren){ + SpeciesPattern s = getSpeciesPattern(element, newModel); + if(s != null){ + r.addReactant(new ReactantPattern(s, r.getStructure()), false); + } + } + } + } + + private void getRbmProductPatternsList(Element e, ReactionRule r, Model newModel){ + if(e != null){ + List ppChildren = e.getChildren(XMLTags.RbmProductPatternTag, vcNamespace); + for(Element ppElement : ppChildren){ + Structure structure = null; + String structureName = ppElement.getAttributeValue(XMLTags.StructureAttrTag); + if(structureName == null || structureName.isEmpty()){ // the tag is missing + throw new RuntimeException("XMLReader: structure missing for reaction rule pattern."); + } else { + structure = newModel.getStructure(structureName); + } + Element spe = ppElement.getChild(XMLTags.RbmSpeciesPatternTag, vcNamespace); + SpeciesPattern s = getSpeciesPattern(spe, newModel); + if(s != null){ + r.addProduct(new ProductPattern(s, structure), false); + } + } + // older models have the species pattern saved directly and using the structure or the rule + List spChildren = GenericUtils.convert(e.getChildren(XMLTags.RbmSpeciesPatternTag, vcNamespace), Element.class); + for(Element element : spChildren){ + SpeciesPattern s = getSpeciesPattern(element, newModel); + if(s != null){ + r.addProduct(new ProductPattern(s, r.getStructure()), false); + } + } + } + } + + // +// Legacy NetworkConstraints was the single NetworkConstraints object formerly stored +// in the Model's RbmModelContainer. The NetworkConstraints are now stored in each +// SimulationContext instead (inheriting the "global" NetworkConstraint) upon first +// load. +// +// We read the single BioModel network constraints from legacy Rule-based models +// (pre-release VCell 6.0 models only). +// +// Warning: We will NOT preserve this default NetworkConstraints object for saved BioModels +// where the database cached XML document is lost and must be regenerated. +// This rare condition for few models would have added complexity and been of limited value. +// +// + private NetworkConstraints legacyNetworkConstraints = null; + + private void getRbmNetworkConstraints(Element e, Model newModel){ + RbmModelContainer mc = newModel.getRbmModelContainer(); + NetworkConstraints nc = new NetworkConstraints(); + this.legacyNetworkConstraints = nc; + + String s = e.getAttributeValue(XMLTags.RbmMaxIterationTag); + if(s != null && !s.isEmpty()){ + int maxIteration = Integer.parseInt(s); + nc.setMaxIteration(maxIteration); + } + s = e.getAttributeValue(XMLTags.RbmMaxMoleculesPerSpeciesTag); + if(s != null && !s.isEmpty()){ + int maxMoleculesPerSpecies = Integer.parseInt(s); + nc.setMaxMoleculesPerSpecies(maxMoleculesPerSpecies); + } + /* + * there has never been a species limit or a reaction limit here, so we don't even try to read them + */ + List children = e.getChildren(XMLTags.RbmMaxStoichiometryTag, vcNamespace); + for(Element element : children){ + Integer i = 1; + MolecularType mt = null; + s = element.getAttributeValue(XMLTags.RbmIntegerAttrTag); + if(s != null && !s.isEmpty()){ + i = Integer.valueOf(s); + } + s = element.getAttributeValue(XMLTags.RbmMolecularTypeTag); + if(s != null && !s.isEmpty()){ + mt = mc.getMolecularType(s); + } + if(mt != null){ + nc.setMaxStoichiometry(mt, i); + } + } + } + +// -------------------------------------------------------------------- + + public ModelUnitSystem getUnitSystem(Element unitSystemNode){ + + //Read all the attributes + String volSubsUnit = unMangle(unitSystemNode.getAttributeValue(XMLTags.VolumeSubstanceUnitTag)); + String memSubsUnit = unMangle(unitSystemNode.getAttributeValue(XMLTags.MembraneSubstanceUnitTag)); + String lumpedSubsUnit = unMangle(unitSystemNode.getAttributeValue(XMLTags.LumpedReactionSubstanceUnitTag)); + String volUnit = unMangle(unitSystemNode.getAttributeValue(XMLTags.VolumeUnitTag)); + String areaUnit = unMangle(unitSystemNode.getAttributeValue(XMLTags.AreaUnitTag)); + String lengthUnit = unMangle(unitSystemNode.getAttributeValue(XMLTags.LengthUnitTag)); + String timeUnit = unMangle(unitSystemNode.getAttributeValue(XMLTags.TimeUnitTag)); + + return ModelUnitSystem.createVCModelUnitSystem(volSubsUnit, memSubsUnit, lumpedSubsUnit, volUnit, areaUnit, lengthUnit, timeUnit); + } + + /** + * This method returns a nodeReference onject from a XML representation. + * Creation date: (4/24/2001 5:35:56 PM) + * + * @param param Element + * @return cbit.vcell.model.NodeReference + */ + private NodeReference getNodeReference(Element param) throws XmlParseException{ + String tempname = param.getName(); + NodeReference newNodeRef = null; + + int type = NodeReference.UNKNOWN_NODE; + String name = null; + //determine the type of nodereference to create + if(tempname.equalsIgnoreCase(XMLTags.SpeciesContextShapeTag)){ + type = NodeReference.SPECIES_CONTEXT_NODE; + name = unMangle(param.getAttributeValue(XMLTags.SpeciesContextRefAttrTag)); + } else if(tempname.equalsIgnoreCase(XMLTags.SimpleReactionShapeTag)){ + type = NodeReference.SIMPLE_REACTION_NODE; + name = unMangle(param.getAttributeValue(XMLTags.SimpleReactionRefAttrTag)); + } else if(tempname.equalsIgnoreCase(XMLTags.FluxReactionShapeTag)){ + type = NodeReference.FLUX_REACTION_NODE; + name = unMangle(param.getAttributeValue(XMLTags.FluxReactionRefAttrTag)); + } else if(tempname.equalsIgnoreCase(XMLTags.ReactionRuleShapeTag)){ + type = NodeReference.REACTION_RULE_NODE; + name = unMangle(param.getAttributeValue(XMLTags.ReactionRuleRef2AttrTag)); + } else if(tempname.equalsIgnoreCase(XMLTags.RuleParticipantFullShapeTag) || tempname.equalsIgnoreCase(XMLTags.RuleParticipantShapeTag)){ + type = NodeReference.RULE_PARTICIPANT_SIGNATURE_FULL_NODE; + name = unMangle(param.getAttributeValue(XMLTags.RuleParticipantRefAttrTag)); + } else if(tempname.equalsIgnoreCase(XMLTags.RuleParticipantShortShapeTag)){ + type = NodeReference.RULE_PARTICIPANT_SIGNATURE_SHORT_NODE; + name = unMangle(param.getAttributeValue(XMLTags.RuleParticipantRefAttrTag)); + } else { + throw new XmlParseException("An unknown type was found " + tempname + ",when processing noderefence!"); + } + String modeString = unMangle(param.getAttributeValue(XMLTags.NodeReferenceModeAttrTag)); + NodeReference.Mode mode = NodeReference.Mode.none; + if(modeString != null){ + mode = Mode.fromValue(modeString); + } + java.awt.Point location = new java.awt.Point(Integer.parseInt(param.getAttributeValue(XMLTags.LocationXAttrTag)), Integer.parseInt(param.getAttributeValue(XMLTags.LocationYAttrTag))); + newNodeRef = new NodeReference(mode, type, name, location); + return newNodeRef; + } + + + /** + * This method returns an OdeEquation from a XML Element. + * Creation date: (5/17/2001 3:52:40 PM) + * + * @param param Element + * @return cbit.vcell.math.OdeEquation + * @throws cbit.vcell.xml.XmlParseException The exception description. + */ + private OdeEquation getOdeEquation(Element param, MathDescription mathDesc) throws XmlParseException{ + //get attributes + String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + //find reference in the dictionnary + //try as a VolVariable + Variable varref = mathDesc.getVariable(varname); + + //Make sure that the reference is not empty!!! + if(varref == null){ + throw new XmlParseException("The reference to the variable " + varname + " in a OdeEquation could not be resolved!"); + } + + //get Initial condition + String temp = param.getChildText(XMLTags.InitialTag, vcNamespace); + Expression initialexp = null; + + if(temp != null && temp.length() > 0){ + initialexp = unMangleExpression(temp); + } + + //Get Rate condition + temp = param.getChildText(XMLTags.RateTag, vcNamespace); + Expression rateexp = null; + if(temp != null && temp.length() > 0){ + rateexp = unMangleExpression((temp)); + } + + //--- Create the OdeEquation object --- + OdeEquation odeEquation = new OdeEquation(varref, initialexp, rateexp); + + //add specific solutions expressions + String solType = param.getAttributeValue(XMLTags.SolutionTypeTag); + + if(solType.equalsIgnoreCase(XMLTags.ExactTypeTag)){ + String solutionExp = param.getChildText(XMLTags.SolutionExpressionTag, vcNamespace); + + if(solutionExp != null && solutionExp.length() > 0){ + Expression expression = unMangleExpression(solutionExp); + odeEquation.setExactSolution(expression); + } + } + + return odeEquation; + } + + + public Origin getOrigin(Element parsed){ + double x = Double.parseDouble(parsed.getAttributeValue(XMLTags.XAttrTag)); + double y = Double.parseDouble(parsed.getAttributeValue(XMLTags.YAttrTag)); + double z = Double.parseDouble(parsed.getAttributeValue(XMLTags.ZAttrTag)); + Origin origin = new Origin(x, y, z); + + return origin; + } + + + /** + * This method returns a TimeStep object from a XML Element. + * Creation date: (5/22/2001 11:45:33 AM) + * + * @param param Element + * @return cbit.vcell.solver.TimeStep + */ + private OutputTimeSpec getOutputTimeSpec(Element param){ + if(param != null){ + //get attributes + if(param.getAttributeValue(XMLTags.KeepEveryAttrTag) != null){ + int keepEvery = Integer.parseInt(param.getAttributeValue(XMLTags.KeepEveryAttrTag)); + int keepAtMost = Integer.parseInt(param.getAttributeValue(XMLTags.KeepAtMostAttrTag)); + return new DefaultOutputTimeSpec(keepEvery, keepAtMost); + } else if(param.getAttributeValue(XMLTags.OutputTimeStepAttrTag) != null){ + double outputStep = Double.parseDouble(param.getAttributeValue(XMLTags.OutputTimeStepAttrTag)); + return new UniformOutputTimeSpec(outputStep); + } else if(param.getAttributeValue(XMLTags.OutputTimesAttrTag) != null){ + String line = param.getAttributeValue(XMLTags.OutputTimesAttrTag); + return ExplicitOutputTimeSpec.fromString(line); + } + } + return null; + } + + + /** + * This method returns an OutsideVariable object from a XML Element + * Creation date: (5/18/2001 6:14:42 PM) + * + * @param param Element + * @return cbit.vcell.math.InsideVariable + */ + private OutsideVariable getOutsideVariable(Element param){ + //Get name + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + //get VolVariableRef + String volvarName = unMangle(param.getAttributeValue(XMLTags.VolumeVariableAttrTag)); + + //*** create new OutsideVariable *** + OutsideVariable variable = new OutsideVariable(name, volvarName); + transcribeComments(param, variable); + + return variable; + } + + + /** + * This method returns a PdeEquation from a XML element. + * Creation date: (4/26/2001 12:11:14 PM) + * + * @param param Element + * @return cbit.vcell.math.PdeEquation + * @throws cbit.vcell.xml.XmlParseException The exception description. + */ + + private PdeEquation getPdeEquation(Element param, MathDescription mathDesc) throws XmlParseException{ + //Retrieve the variable reference + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + boolean bSteady = false; + String bSteadyAttr = param.getAttributeValue(XMLTags.SteadyTag); + if(bSteadyAttr != null && bSteadyAttr.equals("1")){ + bSteady = true; + } + Variable varref = mathDesc.getVariable(name); + if(varref == null){ + throw new XmlParseException("The variable " + name + " for a PdeEquation, could not be resolved!"); + } + PdeEquation pdeEquation = null; + + try { + //Retrieve the initial expression + String temp = param.getChildText(XMLTags.InitialTag, vcNamespace); + Expression initialExp = null; + if(temp != null && temp.length() > 0){ + initialExp = unMangleExpression(temp); + } + + //Retrieve the Rate Expression + temp = param.getChildText(XMLTags.RateTag, vcNamespace); + Expression rateExp = null; + if(temp != null && temp.length() > 0){ + rateExp = unMangleExpression(temp); + } + + //Retrieve the diffusion rate expression + temp = param.getChildText(XMLTags.DiffusionTag, vcNamespace); + Expression difExp = null; + if(temp != null && temp.length() > 0){ + difExp = unMangleExpression(temp); + } + + //*** Create new PdeEquation object **** + pdeEquation = new PdeEquation(varref, bSteady, initialExp, rateExp, difExp); + //***** ***** + + //add specific solutions expressions + String solType = param.getAttributeValue(XMLTags.SolutionTypeTag); + + if(solType.equalsIgnoreCase(XMLTags.ExactTypeTag)){ + String solutionExp = param.getChildText(XMLTags.SolutionExpressionTag, vcNamespace); + + if(solutionExp != null && solutionExp.length() > 0){ + Expression expression = unMangleExpression(solutionExp); + pdeEquation.setExactSolution(expression); + } + } + + //Retrieve Boudaries (if any) + Element tempelement = param.getChild(XMLTags.BoundariesTag, vcNamespace); + if(tempelement != null){ + Expression newexp = null; + //Xm + temp = tempelement.getAttributeValue(XMLTags.BoundaryAttrValueXm); + if(temp != null){ + newexp = unMangleExpression(temp); + pdeEquation.setBoundaryXm(newexp); + } + //Xp + temp = tempelement.getAttributeValue(XMLTags.BoundaryAttrValueXp); + if(temp != null){ + newexp = unMangleExpression(temp); + pdeEquation.setBoundaryXp(newexp); + } + //Ym + temp = tempelement.getAttributeValue(XMLTags.BoundaryAttrValueYm); + if(temp != null){ + newexp = unMangleExpression(temp); + pdeEquation.setBoundaryYm(newexp); + } + //Yp + temp = tempelement.getAttributeValue(XMLTags.BoundaryAttrValueYp); + if(temp != null){ + newexp = unMangleExpression(temp); + pdeEquation.setBoundaryYp(newexp); + } + //Zm + temp = tempelement.getAttributeValue(XMLTags.BoundaryAttrValueZm); + if(temp != null){ + newexp = unMangleExpression(temp); + pdeEquation.setBoundaryZm(newexp); + } + //Zp + temp = tempelement.getAttributeValue(XMLTags.BoundaryAttrValueZp); + if(temp != null){ + newexp = unMangleExpression(temp); + pdeEquation.setBoundaryZp(newexp); + } + } + + //process BoundaryConditionValues + { + Iterator iterator = param.getChildren(XMLTags.BoundaryConditionValueTag, vcNamespace).iterator(); + if(iterator != null){ + while (iterator.hasNext()) { + tempelement = (Element) iterator.next(); + try { + pdeEquation.addBoundaryConditionValue(getBoundaryConditionValue(tempelement, pdeEquation)); + } catch(MathException e){ + throw new XmlParseException("A MathException was fired when adding a BoundaryConditionValue to the compartmentSubDomain " + name, e); + } + } + } + } + + { + //add Velocity + Element velocityE = param.getChild(XMLTags.VelocityTag, vcNamespace); + if(velocityE != null){ + String tempStr = null; + boolean dummyVel = true; + tempStr = velocityE.getAttributeValue(XMLTags.XAttrTag); + if(tempStr != null){ + pdeEquation.setVelocityX(unMangleExpression(tempStr)); //all velocity dimensions are optional. + if(dummyVel){ + dummyVel = false; + } + } + tempStr = velocityE.getAttributeValue(XMLTags.YAttrTag); + if(tempStr != null){ + pdeEquation.setVelocityY(unMangleExpression(tempStr)); + if(dummyVel){ + dummyVel = false; + } + } + tempStr = velocityE.getAttributeValue(XMLTags.ZAttrTag); + if(tempStr != null){ + pdeEquation.setVelocityZ(unMangleExpression(tempStr)); + if(dummyVel){ + dummyVel = false; + } + } + if(dummyVel){ + throw new XmlParseException("Void Velocity element found under PDE for: " + name); + } + } + } + { + //add Grad + Element gradElement = param.getChild(XMLTags.GradientTag, vcNamespace); + if(gradElement != null){ + String tempStr = null; + tempStr = gradElement.getAttributeValue(XMLTags.XAttrTag); + if(tempStr != null){ + pdeEquation.setGradientX(unMangleExpression(tempStr)); //all grad dimensions are optional. + } + tempStr = gradElement.getAttributeValue(XMLTags.YAttrTag); + if(tempStr != null){ + pdeEquation.setGradientY(unMangleExpression(tempStr)); + } + tempStr = gradElement.getAttributeValue(XMLTags.ZAttrTag); + if(tempStr != null){ + pdeEquation.setGradientZ(unMangleExpression(tempStr)); + } + } + } + } catch(Exception e){ + throw new XmlParseException(e); + } + + return pdeEquation; + } + + + /** + * This method returns a VCImageRegion from a XML Representation. + * Creation date: (5/2/2001 12:17:05 PM) + * + * @param param Element + * @return cbit.image.VCImageRegion + */ + private VCPixelClass getPixelClass(Element param){ + //Read attributes + String pixelClassName = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + int pixelvalue = Integer.parseInt(param.getAttributeValue(XMLTags.ImagePixelValueTag)); + + //retrieve the key if there is one + KeyValue key = null; + String stringkey = param.getAttributeValue(XMLTags.KeyValueAttrTag); + + if(stringkey != null && stringkey.length() > 0 && this.readKeysFlag){ + key = new KeyValue(stringkey); + } + + return new VCPixelClass(key, pixelClassName, pixelvalue); + } + + + /** + * This method returns a Product object from a XML representation. + * Creation date: (5/4/2001 2:22:56 PM) + * + * @param param Element + * @return cbit.vcell.model.Product + * @throws cbit.vcell.xml.XmlParseException The exception description. + */ + private Product getProduct(Element param, ReactionStep reaction, Model model) throws XmlParseException{ + //retrieve the key if there is one + KeyValue key = null; + String keystring = param.getAttributeValue(XMLTags.KeyValueAttrTag); + + if(keystring != null && keystring.length() > 0 && this.readKeysFlag){ + key = new KeyValue(keystring); + } + + String speccontref = unMangle(param.getAttributeValue(XMLTags.SpeciesContextRefAttrTag)); + SpeciesContext speccont = model.getSpeciesContext(speccontref); + if(speccont == null){ + throw new XmlParseException( + "The reference to the SpecieContext " + + speccontref + + " for a Product could not be resolved!"); + } + //Retrieve Stoichiometry + int stoch = 1; + Attribute tempAttrib = param.getAttribute(XMLTags.StoichiometryAttrTag); + if(tempAttrib != null){ + String temp = tempAttrib.getValue(); + if(temp.length() > 0){ + stoch = Integer.parseInt(temp); + } + } + //int stoch = Integer.parseInt(param.getAttributeValue(XMLTags.StoichiometryAttrTag)); + + return new Product(key, reaction, speccont, stoch); + } + + + /** + * This method returns a Reactant object from a XML representation. + * Creation date: (5/4/2001 2:22:56 PM) + * + * @param param Element + * @return cbit.vcell.model.Reactant + * @throws cbit.vcell.xml.XmlParseException The exception description. + */ + private Reactant getReactant(Element param, ReactionStep reaction, Model model) throws XmlParseException{ + //retrieve the key if there is one + String keystring = param.getAttributeValue(XMLTags.KeyValueAttrTag); + KeyValue key = null; + + if(keystring != null && keystring.length() > 0 && this.readKeysFlag){ + key = new KeyValue(keystring); + } + + String speccontref = unMangle(param.getAttributeValue(XMLTags.SpeciesContextRefAttrTag)); + SpeciesContext speccont = model.getSpeciesContext(speccontref); + if(speccont == null){ + throw new XmlParseException( + "The reference to the SpecieContext " + + speccontref + + " for a SimpleReaction could not be resolved!"); + } + //Retrieve Stoichiometry + int stoch = 1; + Attribute tempArg = param.getAttribute(XMLTags.StoichiometryAttrTag); + if(tempArg != null){ + String tempValue = tempArg.getValue(); + if(tempValue.length() > 0) + stoch = Integer.parseInt(tempValue); + //param.getAttributeValue(XMLTags.StoichiometryAttrTag)); + } + + //return new Reactant(newkey, reaction, speccont, stoch); + return new Reactant(key, reaction, speccont, stoch); + } + + + /** + * Insert the method's description here. + * Creation date: (4/26/2001 4:13:26 PM) + * + * @param param Element + * @return cbit.vcell.mapping.ReactionSpec + */ + private ReactionSpec getReactionSpec(Element param, SimulationContext simulationContext) throws XmlParseException{ + ReactionSpec reactionspec = null; + + //retrieve the reactionstep reference + String reactionstepname = unMangle(param.getAttributeValue(XMLTags.ReactionStepRefAttrTag)); + ReactionStep reactionstepref = (ReactionStep) simulationContext.getModel().getReactionStep(reactionstepname); + + if(reactionstepref == null){ + throw new XmlParseException("The reference to the ReactionStep " + reactionstepname + ", could not be resolved!"); + } + //Create the new SpeciesContextSpec + reactionspec = new ReactionSpec(reactionstepref, simulationContext); + + //set the reactionMapping value + String temp = param.getAttributeValue(XMLTags.ReactionMappingAttrTag); + try { + reactionspec.setReactionMapping(temp); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A PropertyVetoException was fired when setting the reactionMapping value " + temp + ", in a reactionSpec object!", e); + } + + return reactionspec; + } + + + /** + * This method returns a SimpleReaction object from a XML element. + * Creation date: (3/16/2001 11:52:02 AM) + * + * @param param Element + * @return cbit.vcell.model.SimpleReaction + */ + private SimpleReaction getSimpleReaction(Element param, Model model) throws XmlParseException{ + //resolve reference to the structure that it belongs to. + String structureName = unMangle(param.getAttributeValue(XMLTags.StructureAttrTag)); + Structure structureref = (Structure) model.getStructure(structureName); + + if(structureref == null){ + throw new XmlParseException("The structure " + structureName + "could not be resolved!"); + } + + //try to get keValue information + String keystring = param.getAttributeValue(XMLTags.KeyValueAttrTag); + KeyValue key = null; + + if(keystring != null && keystring.length() > 0 && this.readKeysFlag){ + key = new KeyValue(keystring); + } + + //---Instantiate a new Simplereaction--- + SimpleReaction simplereaction = null; + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + + String reversibleAttributeValue = param.getAttributeValue(XMLTags.ReversibleAttrTag); + boolean bReversible = true; + if(reversibleAttributeValue != null){ + if(Boolean.TRUE.toString().equals(reversibleAttributeValue)){ + bReversible = true; + } else if(Boolean.FALSE.toString().equals(reversibleAttributeValue)){ + bReversible = false; + } else { + throw new RuntimeException("unexpected value " + reversibleAttributeValue + " for reversible flag for reaction " + name); + } + } + + try { + simplereaction = new SimpleReaction(model, structureref, key, name, bReversible); + if(param.getAttributeValue(XMLTags.SbmlNameAttrTag) != null){ + simplereaction.setSbmlName(unMangle(param.getAttributeValue(XMLTags.SbmlNameAttrTag))); + } + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("An error occurred while trying to create the simpleReaction " + name, e); + } + //Annotation +// String rsAnnotation = null; +// String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace); +// if (annotationText!=null && annotationText.length()>0) { +// rsAnnotation = unMangle(annotationText); +// } +// simplereaction.setAnnotation(rsAnnotation); + + //set the fluxOption + String fluxOptionString = null; + fluxOptionString = param.getAttributeValue(XMLTags.FluxOptionAttrTag); + + if(fluxOptionString != null && fluxOptionString.length() > 0){ + try { + if(fluxOptionString.equals(XMLTags.FluxOptionElectricalOnly)){ + simplereaction.setPhysicsOptions(SimpleReaction.PHYSICS_ELECTRICAL_ONLY); + } else if(fluxOptionString.equals(XMLTags.FluxOptionMolecularAndElectrical)){ + simplereaction.setPhysicsOptions(SimpleReaction.PHYSICS_MOLECULAR_AND_ELECTRICAL); + } else if(fluxOptionString.equals(XMLTags.FluxOptionMolecularOnly)){ + simplereaction.setPhysicsOptions(SimpleReaction.PHYSICS_MOLECULAR_ONLY); + } + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A propertyVetoException was fired when setting the fluxOption to the flux reaction " + name, e); + } + } + //Add Reactants + try { + Iterator iterator = param.getChildren(XMLTags.ReactantTag, vcNamespace).iterator(); + + while (iterator.hasNext()) { + Element temp = iterator.next(); + + //Add Reactant to this SimpleReaction + simplereaction.addReactionParticipant(getReactant(temp, simplereaction, model)); + } + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("Error adding a reactant to the reaction " + name, e); + } + + //Add Products + try { + Iterator iterator = param.getChildren(XMLTags.ProductTag, vcNamespace).iterator(); + + while (iterator.hasNext()) { + Element temp = iterator.next(); + + //Add Product to this simplereaction + simplereaction.addReactionParticipant(getProduct(temp, simplereaction, model)); + } + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("Error adding a product to the reaction " + name + " : ", e); + } + + //Add Catalyst(Modifiers) + try { + Iterator iterator = param.getChildren(XMLTags.CatalystTag, vcNamespace).iterator(); + + while (iterator.hasNext()) { + Element temp = iterator.next(); + simplereaction.addReactionParticipant(getCatalyst(temp, simplereaction, model)); + } + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("Error adding a catalyst to the reaction " + name, e); + } + + //Add Kinetics + Element tempKinet = param.getChild(XMLTags.KineticsTag, vcNamespace); + + if(tempKinet != null){ + simplereaction.setKinetics(getKinetics(tempKinet, simplereaction, model)); + } + + //set the valence (for legacy support for "chargeCarrierValence" stored with reaction). + String valenceString = null; + try { + valenceString = unMangle(param.getAttributeValue(XMLTags.FluxCarrierValenceAttrTag)); + if(valenceString != null && valenceString.length() > 0){ + KineticsParameter chargeValenceParameter = simplereaction.getKinetics().getChargeValenceParameter(); + if(chargeValenceParameter != null){ + chargeValenceParameter.setExpression(new Expression(Integer.parseInt(unMangle(valenceString)))); + } + } + } catch(NumberFormatException e){ + throw new XmlParseException("A NumberFormatException was fired when setting the (integer) valence '" + valenceString + "' (integer) to the reaction " + name, e); + } + + + return simplereaction; + } + + Simulation getSimulation(Element param, MathDescription mathDesc) throws XmlParseException{ + return getSimulation(param, mathDesc, null); + } + + + Simulation getSimulation(Element param, MathDescription mathDesc, SimulationOwner simulationOwner) throws XmlParseException{ + //retrive metadata (if any) + SimulationVersion simulationVersion = getSimulationVersion(param.getChild(XMLTags.VersionTag, vcNamespace)); + + //create new simulation + Simulation simulation = null; + + if(simulationVersion != null){ + simulation = new Simulation(simulationVersion, mathDesc, simulationOwner); + } else { + simulation = new Simulation(mathDesc, simulationOwner); + } + + //set attributes + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + + try { + simulation.setName(name); + String importedTaskId = param.getAttributeValue(XMLTags.ImportedTaskIdTag); + if(importedTaskId != null){ + simulation.setImportedTaskID(importedTaskId); + } + + //String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag); + //if (annotation!=null) { + //simulation.setDescription(unMangle(annotation)); + //} + //Add Annotation + String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace); + if(annotationText != null && annotationText.length() > 0){ + simulation.setDescription(unMangle(annotationText)); + } + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException(e); + } + + //Retrieve MathOverrides + simulation.setMathOverrides(getMathOverrides(param.getChild(XMLTags.MathOverridesTag, vcNamespace), simulation)); + + //Retrieve SolverTaskDescription + try { + simulation.setSolverTaskDescription(getSolverTaskDescription(param.getChild(XMLTags.SolverTaskDescriptionTag, vcNamespace), simulation)); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A PropertyVetoException was fired when setting the SolverTaskDescroiption object to the Simulation object " + name, e); + } + + Element dataProcessingInstructionsElement = param.getChild(XMLTags.DataProcessingInstructionsTag, vcNamespace); + if(dataProcessingInstructionsElement != null){ + String scriptName = dataProcessingInstructionsElement.getAttributeValue(XMLTags.DataProcessingScriptNameAttrTag); + String scriptInput = dataProcessingInstructionsElement.getText(); + simulation.setDataProcessingInstructions(new DataProcessingInstructions(scriptName, scriptInput)); + } + + //Retrieve MeshEspecification (if any) + Element tempElement = param.getChild(XMLTags.MeshSpecTag, vcNamespace); + + if(tempElement != null){ + try { + simulation.setMeshSpecification(getMeshSpecification(tempElement, mathDesc.getGeometry())); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A ProperyVetoException was fired when setting the MeshSpecification to a new Simulation!", e); + } + } + + return simulation; + } + + //public because it's being called in simcontexttable to read from the app components element + public NetworkConstraints getAppNetworkConstraints(Element e, Model newModel){ + RbmModelContainer mc = newModel.getRbmModelContainer(); + NetworkConstraints nc = new NetworkConstraints(); + String s = e.getAttributeValue(XMLTags.RbmMaxIterationTag); + if(s != null && !s.isEmpty()){ + int maxIteration = Integer.parseInt(s); + nc.setMaxIteration(maxIteration); + } + s = e.getAttributeValue(XMLTags.RbmMaxMoleculesPerSpeciesTag); + if(s != null && !s.isEmpty()){ + int maxMoleculesPerSpecies = Integer.parseInt(s); + nc.setMaxMoleculesPerSpecies(maxMoleculesPerSpecies); + } + s = e.getAttributeValue(XMLTags.RbmSpeciesLimitTag); + if(s != null && !s.isEmpty()){ + int speciesLimit = Integer.parseInt(s); + nc.setSpeciesLimit(speciesLimit); + } + s = e.getAttributeValue(XMLTags.RbmReactionsLimitTag); + if(s != null && !s.isEmpty()){ + int reactionsLimit = Integer.parseInt(s); + nc.setReactionsLimit(reactionsLimit); + } + List children = e.getChildren(XMLTags.RbmMaxStoichiometryTag, vcNamespace); + for(Element element : children){ + Integer i = 1; + MolecularType mt = null; + s = element.getAttributeValue(XMLTags.RbmIntegerAttrTag); + if(s != null && !s.isEmpty()){ + i = Integer.valueOf(s); + } + s = element.getAttributeValue(XMLTags.RbmMolecularTypeTag); + if(s != null && !s.isEmpty()){ + mt = mc.getMolecularType(s); + } + if(mt != null){ + nc.setMaxStoichiometry(mt, i); + } + } + return nc; + } + + /** + * This method returns a SimulationContext from a XML representation. + * Creation date: (4/2/2001 3:19:01 PM) + * + * @param param Element + * @return cbit.vcell.mapping.SimulationContext + */ + private SimulationContext getSimulationContext(Element param, BioModel biomodel) throws XmlParseException{ + //get the attributes + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); //name + boolean bStoch = false; + boolean bRuleBased = false; + boolean bSpringSaLaD = false; + boolean bUseConcentration = true; + boolean bRandomizeInitCondition = false; + boolean bInsufficientIterations = false; + boolean bInsufficientMaxMolecules = false; + boolean bMassConservationModelReduction = true; // default is true for now + + NetworkConstraints nc = null; + Element ncElement = param.getChild(XMLTags.RbmNetworkConstraintsTag, vcNamespace); + if(ncElement != null){ + nc = getAppNetworkConstraints(ncElement, biomodel.getModel()); // one network constraint element + } else { + if(legacyNetworkConstraints != null){ + nc = legacyNetworkConstraints; + } + } + + if((param.getAttributeValue(XMLTags.StochAttrTag) != null) && (param.getAttributeValue(XMLTags.StochAttrTag).equals("true"))){ + bStoch = true; + } + if(bStoch){ + // stochastic and using concentration vs amount + if((param.getAttributeValue(XMLTags.ConcentrationAttrTag) != null) && (param.getAttributeValue(XMLTags.ConcentrationAttrTag).equals("false"))){ + bUseConcentration = false; + } + + // stochastic and randomizing initial conditions or not (for non-spatial) + if((param.getAttributeValue(XMLTags.RandomizeInitConditionTag) != null) && (param.getAttributeValue(XMLTags.RandomizeInitConditionTag).equals("true"))){ + bRandomizeInitCondition = true; + } + } + if((param.getAttributeValue(XMLTags.MassConservationModelReductionTag) != null) && (param.getAttributeValue(XMLTags.MassConservationModelReductionTag).equals("false"))){ + bMassConservationModelReduction = false; + } + if((param.getAttributeValue(XMLTags.InsufficientIterationsTag) != null) && (param.getAttributeValue(XMLTags.InsufficientIterationsTag).equals("true"))){ + bInsufficientIterations = true; + } + if((param.getAttributeValue(XMLTags.InsufficientMaxMoleculesTag) != null) && (param.getAttributeValue(XMLTags.InsufficientMaxMoleculesTag).equals("true"))){ + bInsufficientMaxMolecules = true; + } + if((param.getAttributeValue(XMLTags.RuleBasedAttrTag) != null) && (param.getAttributeValue(XMLTags.RuleBasedAttrTag).equals("true"))){ + bRuleBased = true; + if((param.getAttributeValue(XMLTags.ConcentrationAttrTag) != null) && (param.getAttributeValue(XMLTags.ConcentrationAttrTag).equals("false"))){ + bUseConcentration = false; + } + if((param.getAttributeValue(XMLTags.RandomizeInitConditionTag) != null) && (param.getAttributeValue(XMLTags.RandomizeInitConditionTag).equals("true"))){ + // we propagate the flag but we don't use it for now + bRandomizeInitCondition = true; + } + } else if((param.getAttributeValue(XMLTags.SpringSaLaDAttrTag) != null) && (param.getAttributeValue(XMLTags.SpringSaLaDAttrTag).equals("true"))){ + bSpringSaLaD = true; + if((param.getAttributeValue(XMLTags.ConcentrationAttrTag) != null) && (param.getAttributeValue(XMLTags.ConcentrationAttrTag).equals("false"))){ + bUseConcentration = false; + } + } + + //Retrieve Geometry + Geometry newgeometry = null; + try { + newgeometry = getGeometry(param.getChild(XMLTags.GeometryTag, vcNamespace)); + } catch(Exception e){ + lg.error(e.getMessage(), e); + String stackTrace = null; + try { + java.io.ByteArrayOutputStream bos = new java.io.ByteArrayOutputStream(); + java.io.PrintStream ps = new java.io.PrintStream(bos); + e.printStackTrace(ps); + ps.flush(); + bos.flush(); + stackTrace = new String(bos.toByteArray()); + ps.close(); + bos.close(); + } catch(Exception e2){ + //do Nothing + } + throw new XmlParseException( + "A Problem occurred while retrieving the geometry for the simulationContext " + name, e); + } + + //Retrieve MathDescription(if there is no MathDescription skip it) + MathDescription newmathdesc = null; + Element xmlMathDescription = param.getChild(XMLTags.MathDescriptionTag, vcNamespace); + if(xmlMathDescription != null){ + newmathdesc = getMathDescription(xmlMathDescription, newgeometry); + if(biomodel.getVersion() != null && biomodel.getVersion().getVersionKey() != null){ + Long lpcBMKey = Long.valueOf(biomodel.getVersion().getVersionKey().toString()); + + // MathDescription.originalHasLowPrecisionConstants.remove(lpcBMKey); + try { + Enumeration myenum = newmathdesc.getConstants(); + while (myenum.hasMoreElements()) { + Constant nextElement = myenum.nextElement(); + String name2 = nextElement.getName(); + ReservedSymbol reservedSymbolByName = biomodel.getModel().getReservedSymbolByName(name2); + if(reservedSymbolByName != null && nextElement.getExpression() != null && reservedSymbolByName.getExpression() != null){ + // System.out.println(name2); + boolean equals = nextElement.getExpression().infix().equals(reservedSymbolByName.getExpression().infix()); + // System.out.println("--"+" "+nextElement.getExpression().infix() +" "+reservedSymbolByName.getExpression().infix()+" "+equals); + if(!equals){ + TreeSet treeSet = MathDescription.originalHasLowPrecisionConstants.get(lpcBMKey); + if(treeSet == null){ + treeSet = new TreeSet<>(); + MathDescription.originalHasLowPrecisionConstants.put(lpcBMKey, treeSet); + } + treeSet.add(newmathdesc.getVersion().getVersionKey().toString()); + break; + } + } + } + } catch(Exception e){ + lg.error(e.getMessage(), e); + } + } + } + + //Retrieve Version (Metada) + Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace)); + + //------ Create SimContext ------ + SimulationContext newsimcontext = null; + Application type = Application.NETWORK_DETERMINISTIC; + if(bSpringSaLaD){ + type = Application.SPRINGSALAD; + } else if(bRuleBased){ + type = Application.RULE_BASED_STOCHASTIC; + } else if(bStoch){ + type = Application.NETWORK_STOCHASTIC; + } + try { + newsimcontext = new SimulationContext(biomodel.getModel(), newgeometry, newmathdesc, version, type); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A propertyveto exception was generated when creating the new SimulationContext " + name, e); + } + + //set attributes + try { + newsimcontext.setName(name); + //Add annotation + String annotation = param.getChildText(XMLTags.AnnotationTag, vcNamespace); + if(annotation != null/* && annotation.length()>0*/){ + newsimcontext.setDescription(unMangle(annotation)); + } + //set if using concentration + newsimcontext.setUsingConcentration(bUseConcentration, false); + // set mass conservation model reduction flag + newsimcontext.setUsingMassConservationModelReduction(bMassConservationModelReduction); + // set if randomizing init condition or not (for stochastic applications + if(bStoch){ + newsimcontext.setRandomizeInitConditions(bRandomizeInitCondition); + } + if(bInsufficientIterations){ + newsimcontext.setInsufficientIterations(bInsufficientIterations); + } + if(bInsufficientMaxMolecules){ + newsimcontext.setInsufficientMaxMolecules(bInsufficientMaxMolecules); + } + if(nc != null){ + newsimcontext.setNetworkConstraints(nc); + } + + } catch(Exception e){ + throw new XmlParseException("Exception", e); + } + + String tempchar = param.getAttributeValue(XMLTags.CharacteristicSizeTag); + if(tempchar != null){ + try { + newsimcontext.setCharacteristicSize(Double.valueOf(tempchar)); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A PropertyVetoException was fired when setting the CharacteristicSize " + tempchar, e); + } + } + + // Retrieve DataContext + Element dataContextElement = param.getChild(XMLTags.DataContextTag, vcNamespace); + if(dataContextElement != null){ + DataContext dataContext = newsimcontext.getDataContext(); + ArrayList dataSymbols = getDataSymbols(dataContextElement, dataContext, newsimcontext.getModel().getUnitSystem()); + for(int i = 0; i < dataSymbols.size(); i++){ + dataContext.addDataSymbol(dataSymbols.get(i)); + } + } + + // Retrieve spatialObjects and add to simContext + Element spatialObjectsElement = param.getChild(XMLTags.SpatialObjectsTag, vcNamespace); + if(spatialObjectsElement != null){ + SpatialObject[] spatialObjects = getSpatialObjects(newsimcontext, spatialObjectsElement); + try { + newsimcontext.setSpatialObjects(spatialObjects); + } catch(PropertyVetoException e){ + throw new RuntimeException("Error adding spatialObjects to simulationContext", e); + } + } + + // Retrieve application parameters and add to simContext + Element appParamsElement = param.getChild(XMLTags.ApplicationParametersTag, vcNamespace); + if(appParamsElement != null){ + SimulationContextParameter[] appParameters = getSimulationContextParams(appParamsElement, newsimcontext); + try { + newsimcontext.setSimulationContextParameters(appParameters); + } catch(PropertyVetoException e){ + throw new RuntimeException("Error adding application parameters to simulationContext", e); + } + } + + // + //-Process the GeometryContext- + // + Element tempelement = param.getChild(XMLTags.GeometryContextTag, vcNamespace); + LinkedList maplist = new LinkedList(); + //Retrieve FeatureMappings + Iterator iterator = tempelement.getChildren(XMLTags.FeatureMappingTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + maplist.add(getFeatureMapping((Element) (iterator.next()), newsimcontext)); + } + //Retrieve MembraneMappings + iterator = tempelement.getChildren(XMLTags.MembraneMappingTag, vcNamespace).iterator(); + while (iterator.hasNext()) { + maplist.add(getMembraneMapping((Element) (iterator.next()), newsimcontext)); + } + // Add these mappings to the internal geometryContext of this simcontext + StructureMapping[] structarray = new StructureMapping[maplist.size()]; + maplist.toArray(structarray); + try { + newsimcontext.getGeometryContext().setStructureMappings(structarray); + newsimcontext.getGeometryContext().refreshStructureMappings(); + newsimcontext.refreshSpatialObjects(); + } catch(MappingException | PropertyVetoException e){ + throw new XmlParseException("failed to set the StructureMappings array to the Geometrycontext of the SimContext " + name, e); + } + // + //-Process the ReactionContext- + // + tempelement = param.getChild(XMLTags.ReactionContextTag, vcNamespace); + // Retrieve ReactionSpecs + List children = tempelement.getChildren(XMLTags.ReactionSpecTag, vcNamespace); + if(children.size() != 0){ + if(children.size() != biomodel.getModel().getReactionSteps().length){ + throw new XmlParseException("The number of reactions is not consistent.\n" + "Model reactions=" + biomodel.getModel().getReactionSteps().length + ", Reaction specs=" + children.size()); + } + //*NOTE: Importing a model from other languages does not generates reaction specs. + // A more robust code will read the reactions in the source file and replace the ones created by the default by the VirtualCell framework. + ReactionSpec reactionSpecs[] = new ReactionSpec[children.size()]; + int rSpecCounter = 0; + for(Element rsElement : children){ + reactionSpecs[rSpecCounter] = getReactionSpec(rsElement, newsimcontext); + rSpecCounter++; + } + try { + newsimcontext.getReactionContext().setReactionSpecs(reactionSpecs); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A PropertyVetoException occurred while setting the ReactionSpecs to the SimContext " + name, e); + } + } + + // Retrieve ReactionRuleSpecs + Element reactionRuleSpecsElement = tempelement.getChild(XMLTags.ReactionRuleSpecsTag, vcNamespace); + if(reactionRuleSpecsElement != null){ + ReactionRuleSpec[] reactionRuleSpecs = getReactionRuleSpecs(newsimcontext, reactionRuleSpecsElement); + try { + newsimcontext.getReactionContext().setReactionRuleSpecs(reactionRuleSpecs); + } catch(PropertyVetoException e){ + throw new XmlParseException("A PropertyVetoException occurred while setting the ReactionRuleSpecs to the SimContext " + name, e); + } + } + + children = tempelement.getChildren(XMLTags.SpeciesContextSpecTag, vcNamespace); + getSpeciesContextSpecs(children, newsimcontext.getReactionContext(), biomodel.getModel()); + + // Retrieve output functions + Element outputFunctionsElement = param.getChild(XMLTags.OutputFunctionsTag, vcNamespace); + if(outputFunctionsElement != null){ + ArrayList outputFunctions = getOutputFunctions(outputFunctionsElement); + try { + // construct OutputFnContext from mathDesc in newSimContext and add output functions that were read in from XML. + OutputFunctionContext outputFnContext = newsimcontext.getOutputFunctionContext(); + for(AnnotatedFunction outputFunction : outputFunctions){ + outputFnContext.addOutputFunction(outputFunction); + } + } catch(PropertyVetoException e){ + throw new XmlParseException(e); + } + } + + + //Retrieve Electrical context + Element electElem = param.getChild(XMLTags.ElectricalContextTag, vcNamespace); + //this information is optional! + if(electElem != null){ + if(electElem.getChild(XMLTags.ClampTag, vcNamespace) != null){ + //read clamp + ElectricalStimulus[] electArray = new ElectricalStimulus[1]; + electArray[0] = getElectricalStimulus(electElem.getChild(XMLTags.ClampTag, vcNamespace), newsimcontext); + + try { + newsimcontext.setElectricalStimuli(electArray); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException(e); + } + } + + //read ground electrode + if(electElem.getChild(XMLTags.ElectrodeTag, vcNamespace) != null){ + Electrode groundElectrode = getElectrode(electElem.getChild(XMLTags.ElectrodeTag, vcNamespace), newsimcontext); + + try { + newsimcontext.setGroundElectrode(groundElectrode); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException(e); + } + } + } + + // Retrieve (bio)events and add to simContext + tempelement = param.getChild(XMLTags.BioEventsTag, vcNamespace); + if(tempelement != null){ + BioEvent[] bioEvents = getBioEvents(newsimcontext, tempelement); + try { + newsimcontext.setBioEvents(bioEvents); + } catch(PropertyVetoException e){ + throw new RuntimeException("Error adding events to simulationContext", e); + } + } + + // Retrieve spatialProcesses and add to simContext + tempelement = param.getChild(XMLTags.SpatialProcessesTag, vcNamespace); + if(tempelement != null){ + SpatialProcess[] spatialProcesses = getSpatialProcesses(newsimcontext, tempelement); + try { + newsimcontext.setSpatialProcesses(spatialProcesses); + } catch(PropertyVetoException e){ + throw new RuntimeException("Error adding spatialProcesses to simulationContext", e); + } + } + + // Retrieve rate rules and add to simContext + tempelement = param.getChild(XMLTags.RateRulesTag, vcNamespace); + if(tempelement != null){ + RateRule[] rateRules = getRateRules(newsimcontext, tempelement); + try { + newsimcontext.setRateRules(rateRules); + } catch(PropertyVetoException e){ + throw new RuntimeException("Error adding rate rules to simulationContext", e); + } + } + tempelement = param.getChild(XMLTags.AssignmentRulesTag, vcNamespace); + if(tempelement != null){ + AssignmentRule[] assignmentRules = getAssignmentRules(newsimcontext, tempelement); + try { + newsimcontext.setAssignmentRules(assignmentRules); + } catch(PropertyVetoException e){ + throw new RuntimeException("Error adding assignment rules to simulationContext", e); + } + } + + Element analysisTaskListElement = param.getChild(XMLTags.AnalysisTaskListTag, vcNamespace); + if(analysisTaskListElement != null){ + children = analysisTaskListElement.getChildren(XMLTags.ParameterEstimationTaskTag, vcNamespace); + if(children.size() != 0){ + Vector analysisTaskList = new Vector(); + for(Element parameterEstimationTaskElement : children){ + try { + ParameterEstimationTask parameterEstimationTask = ParameterEstimationTaskXMLPersistence.getParameterEstimationTask(parameterEstimationTaskElement, newsimcontext); + analysisTaskList.add(parameterEstimationTask); + } catch(Exception e){ + throw new XmlParseException("An Exception occurred when parsing AnalysisTasks of SimContext " + name, e); + } + } + try { + newsimcontext.setAnalysisTasks(analysisTaskList.toArray(AnalysisTask[]::new)); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A PropertyVetoException occurred when setting the AnalysisTasks of the SimContext " + name, e); + } + } + } + + // Microscope Measurement + Element element = param.getChild(XMLTags.MicroscopeMeasurement, vcNamespace); + if(element != null){ + getMicroscopeMeasurement(element, newsimcontext); + } + + +// for (GeometryClass gc : newsimcontext.getGeometry().getGeometryClasses()) { +// try { +// StructureSizeSolver.updateUnitStructureSizes(newsimcontext, gc); +// } catch (Exception e) { +// lg.error(e); +// } +// } + + newsimcontext.getGeometryContext().enforceHierarchicalBoundaryConditions(newsimcontext.getModel().getStructureTopology()); + + return newsimcontext; + } + + public void getMicroscopeMeasurement(Element element, SimulationContext simContext){ + MicroscopeMeasurement microscopeMeasurement = simContext.getMicroscopeMeasurement(); + + String name = element.getAttributeValue(XMLTags.NameAttrTag); + microscopeMeasurement.setName(name); + + Element kernelElement = element.getChild(XMLTags.ConvolutionKernel, vcNamespace); + String type = kernelElement.getAttributeValue(XMLTags.TypeAttrTag); + ConvolutionKernel ck = null; + if(type.equals(XMLTags.ConvolutionKernel_Type_ProjectionZKernel)){ + ck = new ProjectionZKernel(); + } else if(type.equals(XMLTags.ConvolutionKernel_Type_GaussianConvolutionKernel)){ + Element e = kernelElement.getChild(XMLTags.KernelGaussianSigmaXY, vcNamespace); + String s = e.getText(); + Expression sigmaXY = unMangleExpression(s); + + e = kernelElement.getChild(XMLTags.KernelGaussianSigmaZ, vcNamespace); + s = e.getText(); + Expression sigmaZ = unMangleExpression(s); + + ck = new GaussianConvolutionKernel(sigmaXY, sigmaZ); + } + microscopeMeasurement.setConvolutionKernel(ck); + List children = element.getChildren(XMLTags.FluorescenceSpecies, vcNamespace); + for(Element c : children){ + String speciesName = c.getAttributeValue(XMLTags.NameAttrTag); + SpeciesContext sc = simContext.getModel().getSpeciesContext(speciesName); + microscopeMeasurement.addFluorescentSpecies(sc); + } + } + + private ArrayList getDataSymbols(Element dataContextElement, DataContext dataContext, ModelUnitSystem modelUnitSystem){ + ArrayList dataSymbolsList = new ArrayList(); + // iterate over fieldDatasymbols. When other dataSymbol types are implemented, repeat this loop. + Iterator dataSymbolsElementIter = dataContextElement.getChildren(XMLTags.FieldDataSymbolTag, vcNamespace).iterator(); + while (dataSymbolsElementIter.hasNext()) { + Element dataSymbolElement = (Element) dataSymbolsElementIter.next(); + String dataSymbolName = unMangle(dataSymbolElement.getAttributeValue(XMLTags.DataSymbolNameTag)); + DataSymbolType dataSymbolType = DataSymbolType.fromDatabaseName(unMangle(dataSymbolElement.getAttributeValue(XMLTags.DataSymbolTypeTag))); + String symbol = dataSymbolElement.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); + VCUnitDefinition vcUnitDefinition = null; + if(symbol != null){ + vcUnitDefinition = modelUnitSystem.getInstance(symbol); + } + // ExternalDataIdentifier dataSetID in FieldDataSymbol + Element dataSetIDElement = dataSymbolElement.getChild(XMLTags.ExternalDataIdentifierTag, vcNamespace); + String name = unMangle(dataSetIDElement.getAttributeValue(XMLTags.NameAttrTag)); + String key = unMangle(dataSetIDElement.getAttributeValue(XMLTags.KeyValueAttrTag)); + String userID = unMangle(dataSetIDElement.getAttributeValue(XMLTags.OwnerNameAttrTag)); + String userKey = unMangle(dataSetIDElement.getAttributeValue(XMLTags.OwnerKeyAttrTag)); + User owner = new User(userID, new KeyValue(userKey)); + ExternalDataIdentifier edi = new ExternalDataIdentifier(new KeyValue(key), owner, name); + // --- + String fieldItemName = unMangle(dataSymbolElement.getAttributeValue(XMLTags.FieldItemNameTag)); + String fieldItemType = unMangle(dataSymbolElement.getAttributeValue(XMLTags.FieldItemTypeTag)); + double fieldItemTime = Double.parseDouble(unMangle(dataSymbolElement.getAttributeValue(XMLTags.FieldItemTimeTag))); + + FieldDataSymbol fds = new FieldDataSymbol(dataSymbolName, dataSymbolType, dataContext, vcUnitDefinition, + edi, fieldItemName, fieldItemType, fieldItemTime); + dataSymbolsList.add(fds); + } + // other while loops for other dataSymbol types; then return cumulative list + // ... + + return dataSymbolsList; + } + + private SimulationVersion getSimulationVersion(Element xmlVersion) throws XmlParseException{ + if(xmlVersion == null){ + return null; + } + + //determine if it should be processed using the 'fromVersionable' + if(xmlVersion.getAttributeValue(XMLTags.FromVersionableTag) == null || Boolean.valueOf(xmlVersion.getAttributeValue(XMLTags.FromVersionableTag)).booleanValue() || this.readKeysFlag == false){ + //this came from a versionable object, so skip! Or it should not explicitly import the information inside the Version + return null; + } + + //Read all the attributes + //*name + String name = unMangle(xmlVersion.getAttributeValue(XMLTags.NameAttrTag)); + //*key + String temp = xmlVersion.getAttributeValue(XMLTags.KeyValueAttrTag); + KeyValue key = new KeyValue(temp); + //*owner + Element tempElement = xmlVersion.getChild(XMLTags.OwnerTag, vcNamespace); + User owner = new User(unMangle(tempElement.getAttributeValue(XMLTags.NameAttrTag)), new KeyValue(tempElement.getAttributeValue(XMLTags.IdentifierAttrTag))); + //*access + GroupAccess groupAccess = getGroupAccess(xmlVersion.getChild(XMLTags.GroupAccessTag, vcNamespace)); + //*Branchpointref + temp = xmlVersion.getAttributeValue(XMLTags.BranchPointRefTag); + KeyValue branchpointref = null; + + if(temp != null){ + branchpointref = new KeyValue(temp); + } + + //*BranchID + java.math.BigDecimal branchId = new java.math.BigDecimal(xmlVersion.getAttributeValue(XMLTags.BranchIdAttrTag)); + //*Flag + temp = xmlVersion.getAttributeValue(XMLTags.FlagAttrTag); + VersionFlag flag = VersionFlag.fromInt(Integer.parseInt(temp)); + //*Date + java.util.Date date = null; + temp = xmlVersion.getAttributeValue(XMLTags.DateAttrTag); + + if(temp != null){ + try { + SimpleDateFormat simpleDateFormat = new SimpleDateFormat(BeanUtils.vcDateFormat, Locale.US); + date = simpleDateFormat.parse(temp); + } catch(java.text.ParseException e){ + throw new XmlParseException("Invalid date:" + temp, e); + } + } + + //*DataSimulationRef + KeyValue parentSimRefKey = null; + tempElement = xmlVersion.getChild(XMLTags.ParentSimRefTag, vcNamespace); + if(tempElement != null){ + parentSimRefKey = new KeyValue(tempElement.getAttributeValue(XMLTags.KeyValueAttrTag)); + } + + //*Annotation + String annotation = null; + String annotationText = xmlVersion.getChildText(XMLTags.AnnotationTag, vcNamespace); + if(annotationText != null && annotationText.length() > 0){ + annotation = unMangle(annotationText); + } + + //Create and return the version object + return new SimulationVersion(key, name, owner, groupAccess, branchpointref, branchId, date, flag, annotation, parentSimRefKey); + } + + + /** + * This method returns a SolverTaskDescription Object from a XML Element. + * Creation date: (5/22/2001 10:51:23 AM) + * + * @param param Element + * @param simulation cbit.vcell.solver.Simulation + * @return cbit.vcell.solver.SolverTaskDescription + */ + private SolverTaskDescription getSolverTaskDescription(Element param, Simulation simulation) throws XmlParseException{ + //*** create new SolverTaskDescription *** + SolverTaskDescription solverTaskDesc = new SolverTaskDescription(simulation); + //Added July 22nd, 2007, used as condition for stochSimOptions or stochHybridOprtions + SolverDescription sd = null; + //Retrieve attributes + String taskType = param.getAttributeValue(XMLTags.TaskTypeTag); + int keepEvery = -1; + int keepAtMost = -1; + if(param.getAttributeValue(XMLTags.KeepEveryTag) != null){ + keepEvery = Integer.parseInt(param.getAttributeValue(XMLTags.KeepEveryTag)); + keepAtMost = Integer.parseInt(param.getAttributeValue(XMLTags.KeepAtMostTag)); + } + boolean useSymJacob = Boolean.parseBoolean(param.getAttributeValue(XMLTags.UseSymbolicJacobianAttrTag)); + String solverName = param.getAttributeValue(XMLTags.SolverNameTag); + //get sentivity parameter + Element sensparamElement = param.getChild(XMLTags.ConstantTag, vcNamespace); + Constant sensitivityparam = null; + + if(sensparamElement != null){ + sensitivityparam = getConstant(sensparamElement); + } + + //set Attributes + try { + //set solver + sd = SolverDescription.fromDatabaseName(solverName); + if(sd == null){ + System.err.println("====================================== couldn't find solver description name =========================================="); + } + solverTaskDesc.setSolverDescription(sd); + + if(taskType.equalsIgnoreCase(XMLTags.UnsteadyTag)){ + solverTaskDesc.setTaskType(SolverTaskDescription.TASK_UNSTEADY); + } else if(taskType.equalsIgnoreCase(XMLTags.SteadyTag)){ + solverTaskDesc.setTaskType(SolverTaskDescription.TASK_STEADY); + } else { + throw new XmlParseException("Unexpected task type: " + taskType); + } + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException("A PropertyVetoException was fired when setting the taskType: " + taskType, e); + } + int numProcessors = parseIntWithDefault(param, XMLTags.NUM_PROCESSORS, 1); + int numTrials = parseIntWithDefault(param, XMLTags.SolverTaskDescriptionNumTrials, 1); + + try { + solverTaskDesc.setNumProcessors(numProcessors); + solverTaskDesc.setNumTrials(numTrials); + solverTaskDesc.setUseSymbolicJacobian(useSymJacob); + //get TimeBound + solverTaskDesc.setTimeBounds(getTimeBounds(param.getChild(XMLTags.TimeBoundTag, vcNamespace))); + //get TimeStep + solverTaskDesc.setTimeStep(getTimeStep(param.getChild(XMLTags.TimeStepTag, vcNamespace))); + //get ErrorTolerance + solverTaskDesc.setErrorTolerance(getErrorTolerance(param.getChild(XMLTags.ErrorToleranceTag, vcNamespace))); + //get StochSimOptions + if(simulation != null && simulation.getMathDescription() != null){ + if(simulation.getMathDescription().isNonSpatialStoch() && param.getChild(XMLTags.StochSimOptionsTag, vcNamespace) != null){ //Amended July 22nd, 2007 to read either stochSimOptions or stochHybridOptions + solverTaskDesc.setStochOpt(getStochSimOptions(param.getChild(XMLTags.StochSimOptionsTag, vcNamespace))); + if(sd != null && !sd.equals(SolverDescription.StochGibson)){ + solverTaskDesc.setStochHybridOpt(getStochHybridOptions(param.getChild(XMLTags.StochSimOptionsTag, vcNamespace))); + } + } + } + //get OutputOptions + if(keepEvery != -1){ + solverTaskDesc.setOutputTimeSpec(new DefaultOutputTimeSpec(keepEvery, keepAtMost)); + } + OutputTimeSpec ots = getOutputTimeSpec(param.getChild(XMLTags.OutputOptionsTag, vcNamespace)); + if(ots != null){ + solverTaskDesc.setOutputTimeSpec(getOutputTimeSpec(param.getChild(XMLTags.OutputOptionsTag, vcNamespace))); + } + //set SensitivityParameter + solverTaskDesc.setSensitivityParameter(sensitivityparam); + + // set StopAtSpatiallyUniform + Element stopSpatiallyElement = param.getChild(XMLTags.StopAtSpatiallyUniform, vcNamespace); + if(stopSpatiallyElement != null){ + Element errTolElement = stopSpatiallyElement.getChild(XMLTags.ErrorToleranceTag, vcNamespace); + if(errTolElement != null){ + solverTaskDesc.setStopAtSpatiallyUniformErrorTolerance(getErrorTolerance(errTolElement)); + } + } + + String runParameterScanSeriallyAttributeValue = param.getAttributeValue(XMLTags.RunParameterScanSerially); + if(runParameterScanSeriallyAttributeValue != null){ + solverTaskDesc.setSerialParameterScan(Boolean.parseBoolean(runParameterScanSeriallyAttributeValue)); + } + String timeoutDisabledAttributeValue = param.getAttributeValue(XMLTags.TimeoutSimulationDisabled); + if(timeoutDisabledAttributeValue != null){ + solverTaskDesc.setTimeoutDisabled(Boolean.parseBoolean(timeoutDisabledAttributeValue)); + } + String borderExtrapolationDisabled = param.getAttributeValue(XMLTags.BorderExtrapolationDisabled); + if(borderExtrapolationDisabled != null){ + solverTaskDesc.setBorderExtrapolationDisabled(Boolean.parseBoolean(borderExtrapolationDisabled)); + } + + Element nfsimSimulationOptionsElement = param.getChild(XMLTags.NFSimSimulationOptions, vcNamespace); + if(nfsimSimulationOptionsElement != null){ + NFsimSimulationOptions nfsimSimulationOptions = getNFSimSimulationOptions(nfsimSimulationOptionsElement); + solverTaskDesc.setNFSimSimulationOptions(nfsimSimulationOptions); + } + Element langevinSimulationOptionsElement = param.getChild(XMLTags.LangevinSimulationOptions, vcNamespace); + if(langevinSimulationOptionsElement != null){ + LangevinSimulationOptions langevinSimulationOptions = getLangevinSimulationOptions(langevinSimulationOptionsElement); + solverTaskDesc.setLangevinSimulationOptions(langevinSimulationOptions); + } + Element smoldySimulationOptionsElement = param.getChild(XMLTags.SmoldynSimulationOptions, vcNamespace); + if(smoldySimulationOptionsElement != null){ + SmoldynSimulationOptions smoldynSimulationOptions = getSmoldySimulationOptions(smoldySimulationOptionsElement); + solverTaskDesc.setSmoldynSimulationOptions(smoldynSimulationOptions); + } + Element sundialsPdeSolverOptionsElement = param.getChild(XMLTags.SundialsSolverOptions, vcNamespace); + if(sundialsPdeSolverOptionsElement != null){ + SundialsPdeSolverOptions sundialsPdeSolverOptions = getSundialsPdeSolverOptions(sundialsPdeSolverOptionsElement); + solverTaskDesc.setSundialsPdeSolverOptions(sundialsPdeSolverOptions); + } + Element chomboElement = param.getChild(XMLTags.ChomboSolverSpec, vcNamespace); + if(chomboElement != null){ + ChomboSolverSpec chombo = getChomboSolverSpec(solverTaskDesc, chomboElement, simulation.getMathDescription().getGeometry().getDimension()); + solverTaskDesc.setChomboSolverSpec(chombo); + } + Element mbElement = param.getChild(XMLTags.MovingBoundarySolverOptionsTag, vcNamespace); + if(mbElement != null){ + MovingBoundarySolverOptions mb = getMovingBoundarySolverOptions(solverTaskDesc, mbElement); + solverTaskDesc.setMovingBoundarySolverOptions(mb); + } + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException(e); + } + + return solverTaskDesc; + } + + private NFsimSimulationOptions getNFSimSimulationOptions(Element nfsimSimulationOptionsElement) throws XmlParseException{ + NFsimSimulationOptions so = new NFsimSimulationOptions(); + String temp = null; + + temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_observableComputationOff, vcNamespace); + if(temp != null){ + so.setObservableComputationOff(Boolean.parseBoolean(temp)); + } + temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_moleculeDistance, vcNamespace); + if(temp != null){ + so.setMoleculeDistance(Integer.parseInt(temp)); + } + temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_aggregateBookkeeping, vcNamespace); + if(temp != null){ + so.setAggregateBookkeeping(Boolean.parseBoolean(temp)); + } + temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_maxMoleculesPerType, vcNamespace); + if(temp != null){ + so.setMaxMoleculesPerType(Integer.parseInt(temp)); + } + temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_equilibrateTime, vcNamespace); + if(temp != null){ + so.setEquilibrateTime(Integer.parseInt(temp)); + } + temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_randomSeed, vcNamespace); + if(temp != null){ + so.setRandomSeed(Integer.parseInt(temp)); + } + temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_preventIntraBonds, vcNamespace); + if(temp != null){ + so.setPreventIntraBonds(Boolean.parseBoolean(temp)); + } + temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_matchComplexes, vcNamespace); + if(temp != null){ + so.setMatchComplexes(Boolean.parseBoolean(temp)); + } + temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_numOfTrials, vcNamespace); + if(temp != null){ + so.setNumOfTrials(Integer.parseInt(temp)); + } + return so; + } + + private LangevinSimulationOptions getLangevinSimulationOptions(Element langevinSimulationOptionsElement) throws XmlParseException{ + LangevinSimulationOptions lo = new LangevinSimulationOptions(); + String temp = null; + temp = langevinSimulationOptionsElement.getChildText(XMLTags.LangevinSO_intervalSpring, vcNamespace); + if(temp != null){ + lo.setIntervalSpring(Double.parseDouble(temp)); + } + temp = langevinSimulationOptionsElement.getChildText(XMLTags.LangevinSO_intervalImage, vcNamespace); + if(temp != null){ + lo.setIntervalImage(Double.parseDouble(temp)); + } + temp = langevinSimulationOptionsElement.getChildText(XMLTags.LangevinSO_Partition_Nx, vcNamespace); + if(temp != null) { + lo.setNPart(0, Integer.parseInt(temp)); + } + temp = langevinSimulationOptionsElement.getChildText(XMLTags.LangevinSO_Partition_Ny, vcNamespace); + if(temp != null) { + lo.setNPart(1, Integer.parseInt(temp)); + } + temp = langevinSimulationOptionsElement.getChildText(XMLTags.LangevinSO_Partition_Nz, vcNamespace); + if(temp != null) { + lo.setNPart(2, Integer.parseInt(temp)); + } + temp = langevinSimulationOptionsElement.getChildText(XMLTags.LangevinSO_totalNumberOfJobs, vcNamespace); + if(temp != null) { + lo.setTotalNumberOfJobs(Integer.parseInt(temp)); + } + temp = langevinSimulationOptionsElement.getChildText(XMLTags.LangevinSO_numberOfConcurrentJobs, vcNamespace); + if(temp != null) { + lo.setNumberOfConcurrentJobs(Integer.parseInt(temp)); + } + temp = langevinSimulationOptionsElement.getChildText(XMLTags.LangevinSO_randomSeed, vcNamespace); + if(temp != null) { + lo.setRandomSeed(new BigInteger(temp)); + } else { + lo.setRandomSeed(null); + } + return lo; + } + + private SmoldynSimulationOptions getSmoldySimulationOptions(Element smoldySimulationOptionsElement) throws XmlParseException{ + + SmoldynSimulationOptions sso = null; + if(smoldySimulationOptionsElement != null){ + sso = new SmoldynSimulationOptions(); + String temp = smoldySimulationOptionsElement.getChildText(XMLTags.SmoldynSimulationOptions_accuracy, vcNamespace); + if(temp != null){ + sso.setAccuracy(Double.parseDouble(temp)); + } + temp = smoldySimulationOptionsElement.getChildText(XMLTags.SmoldynSimulationOptions_randomSeed, vcNamespace); + if(temp != null){ + sso.setRandomSeed(Integer.parseInt(temp)); + } + temp = smoldySimulationOptionsElement.getChildText(XMLTags.SmoldynSimulationOptions_gaussianTableSize, vcNamespace); + if(temp != null){ + try { + sso.setGaussianTableSize(Integer.parseInt(temp)); + } catch(NumberFormatException | PropertyVetoException e){ + throw new XmlParseException(e); + } + } + temp = smoldySimulationOptionsElement.getChildText(XMLTags.SmoldynSimulationOptions_high_res, vcNamespace); + if(temp != null){ + sso.setUseHighResolutionSample(Boolean.parseBoolean(temp)); + } + temp = smoldySimulationOptionsElement.getChildText(XMLTags.SmoldynSimulationOptions_saveParticleFiles, vcNamespace); + if(temp != null){ + sso.setSaveParticleLocations(Boolean.parseBoolean(temp)); + } + temp = smoldySimulationOptionsElement.getChildText(XMLTags.SmoldynSimulationOptions_stepMultiplier, vcNamespace); + if(temp != null){ + sso.setSmoldynStepMultiplier(Integer.parseInt(temp)); + } + } + return sso; + } + + private SundialsPdeSolverOptions getSundialsPdeSolverOptions(Element sundialsPdeSolverOptionsElement) throws XmlParseException{ + + SundialsPdeSolverOptions sundialsPdeSolverOptions = null; + if(sundialsPdeSolverOptionsElement != null){ + String temp = sundialsPdeSolverOptionsElement.getChildText(XMLTags.SundialsSolverOptions_maxOrderAdvection, vcNamespace); + if(temp != null){ + sundialsPdeSolverOptions = new SundialsPdeSolverOptions(Integer.parseInt(temp)); + } + } + return sundialsPdeSolverOptions; + } + + public ModelParameter[] getModelParams(Element globalParams, Model model) throws XmlParseException{ + List parameterElements = globalParams.getChildren(XMLTags.ParameterTag, vcNamespace); + Vector modelParamsVector = new Vector<>(); + for(Element paramElement : parameterElements){ + modelParamsVector.add(getModelParameter(paramElement, model)); + } + return modelParamsVector.toArray(ModelParameter[]::new); + } + + + public ModelParameter getModelParameter(Element paramElement, Model model) throws XmlParseException{ + //get its attributes : name, role and unit definition + String glParamName = unMangle(paramElement.getAttributeValue(XMLTags.NameAttrTag)); + String role = paramElement.getAttributeValue(XMLTags.ParamRoleAttrTag); + ModelUnitSystem modelUnitSystem = model.getUnitSystem(); + int glParamRole = -1; + if(role.equals(XMLTags.ParamRoleUserDefinedTag)){ + glParamRole = Model.ROLE_UserDefined; + } else { + throw new RuntimeException("unknown type of model parameter (not user-defined)"); + } +// +// int glParamRole = -1; +// if (role.equals(XMLTags.ParamRoleUserDefinedTag)) { +// glParamRole = Model.ROLE_UserDefined; +// } else if (role.equals(XMLTags.RoleVariableRateTag)) { +// glParamRole = Model.ROLE_VariableRate; +// } else { +// throw new RuntimeException("unknown type of model parameter (not user-defined or variable rate)"); +// } + String unitSymbol = paramElement.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); + VCUnitDefinition glParamUnit = null; + if(unitSymbol != null){ + glParamUnit = modelUnitSystem.getInstance(unitSymbol); + } + //get parameter contents : expression; annotation, if any. + String glParamExpStr = paramElement.getText(); + Expression glParamExp = unMangleExpression(glParamExpStr); + String glParamAnnotation = null; + String annotationText = paramElement.getChildText(XMLTags.AnnotationTag, vcNamespace); + if(annotationText != null && annotationText.length() > 0){ + glParamAnnotation = unMangle(annotationText); + } + + //create new global parameter + try { + ModelParameter newGlParam = model.new ModelParameter(glParamName, glParamExp, glParamRole, glParamUnit); + if(paramElement.getAttributeValue(XMLTags.SbmlNameAttrTag) != null){ + String sbmlName = unMangle(paramElement.getAttributeValue(XMLTags.SbmlNameAttrTag)); + if(sbmlName != null && !sbmlName.isEmpty()){ + newGlParam.setSbmlName(sbmlName); + } + } + newGlParam.setModelParameterAnnotation(glParamAnnotation); + return newGlParam; + } catch(PropertyVetoException e){ + throw new XmlParseException("An error occurred while trying to create the ModelParameter " + glParamName, e); + } + } + + public SimulationContextParameter[] getSimulationContextParams(Element appParams, SimulationContext simContext) throws XmlParseException{ + Iterator appParamIterator = appParams.getChildren(XMLTags.ParameterTag, vcNamespace).iterator(); + ArrayList appParamsList = new ArrayList(); + while (appParamIterator.hasNext()) { + Element paramElement = (Element) appParamIterator.next(); + appParamsList.add(getSimulationContextParameter(paramElement, simContext)); + } + return appParamsList.toArray(new SimulationContextParameter[0]); + } + + + public SimulationContextParameter getSimulationContextParameter(Element paramElement, SimulationContext simContext){ + //get its attributes : name, role and unit definition + String appParamName = unMangle(paramElement.getAttributeValue(XMLTags.NameAttrTag)); + String role = paramElement.getAttributeValue(XMLTags.ParamRoleAttrTag); + ModelUnitSystem modelUnitSystem = simContext.getModel().getUnitSystem(); + int appParamRole = -1; + if(role.equals(XMLTags.ParamRoleUserDefinedTag)){ + appParamRole = SimulationContext.ROLE_UserDefined; + } else { + throw new RuntimeException("unknown type of application parameter (not user-defined)"); + } + String unitSymbol = paramElement.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag); + VCUnitDefinition appParamUnit = null; + if(unitSymbol != null){ + appParamUnit = modelUnitSystem.getInstance(unitSymbol); + } + //get parameter contents : expression; annotation, if any. + String appParamExpStr = paramElement.getText(); + Expression appParamExp = unMangleExpression(appParamExpStr); +// String appParamAnnotation = null; +// String annotationText = paramElement.getChildText(XMLTags.AnnotationTag, vcNamespace); +// if (annotationText != null && annotationText.length() > 0) { +// appParamAnnotation = unMangle(annotationText); +// } + + //create new global parameter + SimulationContextParameter newAppParam = simContext.new SimulationContextParameter(appParamName, appParamExp, appParamRole, appParamUnit); +// newGlParam.setModelParameterAnnotation(appParamAnnotation); + + return newAppParam; + } + + public ArrayList getOutputFunctions(Element outputFunctionsElement) throws XmlParseException{ + Iterator outputFnsIterator = outputFunctionsElement.getChildren(XMLTags.AnnotatedFunctionTag, vcNamespace).iterator(); + ArrayList outputFunctions = new ArrayList(); + while (outputFnsIterator.hasNext()) { + Element observableElement = (Element) outputFnsIterator.next(); + AnnotatedFunction func = getOutputFunction(observableElement); + outputFunctions.add(func); + } + return (outputFunctions); + } + + /** + * This method creates a Specie (Compound) object from an XML Element. + * Creation date: (3/15/2001 12:57:43 PM) + * + * @param param Element + * @return cbit.vcell.model.Species + */ + private Species getSpecies(Element param) throws XmlParseException{ + //get its data + String specieName = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String specieAnnotation = null; + + //the Annotation paramater can be optional + //String temp = param.getAttributeValue(XMLTags.AnnotationAttrTag); + //if (temp!=null && temp.length()!=0) { + //specieAnnotation = unMangle(temp); + //} + String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace); + if(annotationText != null && annotationText.length() > 0){ + specieAnnotation = unMangle(annotationText); + } + //create new Specie + Species newspecie = new Species(specieName, specieAnnotation); + + //Try to read the DBSpecie data + Element dbspecieElement = param.getChild(XMLTags.DBSpeciesTag, vcNamespace); + + if(dbspecieElement != null && this.readKeysFlag){ + //read the data + try { + newspecie.setDBSpecies(getDBSpecies(dbspecieElement)); + } catch(PropertyVetoException e){ + throw new XmlParseException(e); + } + } + + return newspecie; + } + + /** + * This method returns a Speciecontext object from a XML Element. + * Creation date: (4/16/2001 6:32:23 PM) + * + * @param param Element + * @return cbit.vcell.model.SpeciesContext + */ + private SpeciesContext getSpeciesContext(Element param, Model model) throws XmlParseException{ + //retrieve its information + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String sbmlName = unMangle(param.getAttributeValue(XMLTags.SbmlNameAttrTag)); + String hasOverrideString = param.getAttributeValue(XMLTags.HasOverrideAttrTag); + String speciesName = unMangle(param.getAttributeValue(XMLTags.SpeciesRefAttrTag)); + Species specieref = (Species) model.getSpecies(speciesName); + if(specieref == null){ + throw new XmlParseException("The Species " + speciesName + "could not be resolved!"); + } + + String structureName = unMangle(param.getAttributeValue(XMLTags.StructureAttrTag)); + Structure structureref = (Structure) model.getStructure(structureName); + if(structureref == null){ + //the structure coul not be retrieved, so throw an exception! + throw new XmlParseException("The Structure " + structureName + "could not be resolved!"); + } + + //Try to read KeyValue data + String keystring = param.getAttributeValue(XMLTags.KeyValueAttrTag); + KeyValue key = null; + + if(keystring != null && keystring.length() > 0 && this.readKeysFlag){ + key = new KeyValue(keystring); + } + + SpeciesPattern sp = null; + Element element = param.getChild(XMLTags.RbmSpeciesPatternTag, vcNamespace); + if(element != null){ + sp = getSpeciesPattern(element, model); + sp.resolveBonds(); + if(sp == null){ + throw new XmlParseException("XMLReader: getSpeciesContext: SpeciesPattern is missing."); + } + } + //---try to create the speciesContext--- + SpeciesContext speciecontext = null; + speciecontext = new SpeciesContext(key, name, specieref, structureref, sp); + try { + speciecontext.setSbmlName(sbmlName); + } catch(PropertyVetoException e){ // can't happen here, whatever we saved must have been correct + // throw new XmlParseException("The SbmlName is invalid"); + lg.error(e); + } + return speciecontext; + } + + + private void getSpeciesContextSpecs(List scsChildren, ReactionContext rxnContext, Model model) throws XmlParseException{ + for(int i = 0; i < scsChildren.size(); i++){ + Element scsElement = scsChildren.get(i); + SpeciesContextSpec specspec = null; + //Get Atributes + String speccontname = unMangle(scsElement.getAttributeValue(XMLTags.SpeciesContextRefAttrTag)); + boolean constant = Boolean.valueOf(scsElement.getAttributeValue(XMLTags.ForceConstantAttrTag)).booleanValue(); + //boolean enabledif = Boolean.valueOf(scsElement.getAttributeValue(XMLTags.EnableDiffusionAttrTag)).booleanValue(); + String spatialStr = scsElement.getAttributeValue(XMLTags.SpatialAttrTag); + Boolean spatial = null; + if(spatialStr != null){ + spatial = Boolean.valueOf(spatialStr); + } + + String bWellMixedStr = scsElement.getAttributeValue(XMLTags.WellMixedAttrTag); + Boolean bWellMixed = null; + if(bWellMixedStr != null){ + bWellMixed = Boolean.valueOf(bWellMixedStr); + } + + String bForceContinuousStr = scsElement.getAttributeValue(XMLTags.ForceContinuousAttrTag); + Boolean bForceContinuous = null; + if(bForceContinuousStr != null){ + bForceContinuous = Boolean.valueOf(bForceContinuousStr); + } + + //Retrieve reference + SpeciesContext specref = model.getSpeciesContext(speccontname); + if(specref == null){ + throw new XmlParseException("The SpeciesContext " + speccontname + " refrence could not be resolved!"); + } + + // get SpeciesContextSpec from reactionContext & specRef + specspec = rxnContext.getSpeciesContextSpec(specref); + //set attributes + specspec.setConstant(constant); +// try { +// specspec.setEnableDiffusing( enabledif ); +// } catch (MappingException e) { +// lg.error(e); +// throw new XmlParseException("error setting the 'enableDiffusing' property of a SpeciesContext: "+e.getMessage()); +// } + if(spatial != null){ + specspec.setWellMixed(!spatial); + } + if(bWellMixed != null){ + specspec.setWellMixed(bWellMixed); + } + if(bForceContinuous != null){ + specspec.setForceContinuous(bForceContinuous); + } + //set expressions + //Initial + String tempCon = scsElement.getChildText(XMLTags.InitialConcentrationTag, vcNamespace); + String tempAmt = scsElement.getChildText(XMLTags.InitialAmountTag, vcNamespace); + String temp = scsElement.getChildText(XMLTags.InitialTag, vcNamespace); + try { + if(temp != null)//old model + { + Expression expression = unMangleExpression(temp); + specspec.getInitialConcentrationParameter().setExpression(expression); + specspec.getInitialCountParameter().setExpression(null); + } else //new model + { + if(tempCon != null)//use concentration as initial condition + { + Expression expression = unMangleExpression(tempCon); + specspec.getInitialConcentrationParameter().setExpression(expression); + specspec.getInitialCountParameter().setExpression(null); + } else if(tempAmt != null)//use number of particles as initial condition + { + Expression expression = unMangleExpression(tempAmt); + specspec.getInitialCountParameter().setExpression(expression); + specspec.getInitialConcentrationParameter().setExpression(null); + } else { + throw new XmlParseException("Unrecognizable initial condition when parsing VCML file."); + } + } + + // Expression expression = unMangleExpression(temp); + // specspec.getInitialConditionParameter().setExpression(expression); + } catch(ExpressionException e){ + throw new XmlParseException("An expressionException was fired when setting the InitilaconditionExpression " + temp + ", for a SpeciesContextSpec!", e); + } + //diffusion (if there is no diffusion information skip it) + Element xmlDiffusionElement = scsElement.getChild(XMLTags.DiffusionTag, vcNamespace); + if(xmlDiffusionElement != null){ + temp = xmlDiffusionElement.getText(); + try { + Expression expression = unMangleExpression(temp); + specspec.getDiffusionParameter().setExpression(expression); + } catch(ExpressionException e){ + throw new XmlParseException("An ExpressionException was fired when setting the diffusionExpression " + temp + " to a SpeciesContextSpec!", e); + } + } + + //Get Boundaries if any + Element tempElement = scsElement.getChild(XMLTags.BoundariesTag, vcNamespace); + if(tempElement != null){ + try { + //Xm + temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueXm); + if(temp != null){ + specspec.getBoundaryXmParameter().setExpression(unMangleExpression(temp)); + } + //Xp + temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueXp); + if(temp != null){ + specspec.getBoundaryXpParameter().setExpression(unMangleExpression(temp)); + } + //Ym + temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueYm); + if(temp != null){ + specspec.getBoundaryYmParameter().setExpression(unMangleExpression(temp)); + } + //Yp + temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueYp); + if(temp != null){ + specspec.getBoundaryYpParameter().setExpression(unMangleExpression(temp)); + } + //Zm + temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueZm); + if(temp != null){ + specspec.getBoundaryZmParameter().setExpression(unMangleExpression(temp)); + } + //Zp + temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueZp); + if(temp != null){ + specspec.getBoundaryZpParameter().setExpression(unMangleExpression(temp)); + } + } catch(ExpressionException e){ + throw new XmlParseException("An ExpressionException was fired when Setting the boundary Expression: " + unMangle(temp), e); + } + } + + // Get Velocities if any + Element velocityE = scsElement.getChild(XMLTags.VelocityTag, vcNamespace); + if(velocityE != null){ + String tempStr = null; + boolean dummyVel = true; + try { + tempStr = velocityE.getAttributeValue(XMLTags.XAttrTag); + if(tempStr != null){ + specspec.getVelocityXParameter().setExpression(unMangleExpression(tempStr)); //all velocity dimensions are optional. + if(dummyVel){ + dummyVel = false; + } + } + tempStr = velocityE.getAttributeValue(XMLTags.YAttrTag); + if(tempStr != null){ + specspec.getVelocityYParameter().setExpression(unMangleExpression(tempStr)); + if(dummyVel){ + dummyVel = false; + } + } + tempStr = velocityE.getAttributeValue(XMLTags.ZAttrTag); + if(tempStr != null){ + specspec.getVelocityZParameter().setExpression(unMangleExpression(tempStr)); + if(dummyVel){ + dummyVel = false; + } + } + } catch(ExpressionException e){ + throw new XmlParseException("Error setting Velocity parameter for '" + specspec.getSpeciesContext().getName(), e); + } + if(dummyVel){ + throw new XmlParseException("Void Velocity element found under PDE for: " + specspec.getSpeciesContext().getName()); + } + } + + if(!(SimulationContext.Application.SPRINGSALAD == rxnContext.getSimulationContext().getApplicationType())){ + continue; + } + // we could do extra validation to make sure that sc has a sp, which has exactly one mtp, aso + // but probably it would be superfluous + SpeciesContext sc = specspec.getSpeciesContext(); + SpeciesPattern sp = sc.getSpeciesPattern(); + if(sp == null){ + throw new XmlParseException("Expected non-null SpeciesPattern for " + specspec.getDisplayName()); + } + MolecularTypePattern mtp = sp.getMolecularTypePatterns().get(0); + + // we maintain a map between the names of the LinkNodes (siteRef) which may be MolecularComponentPatterns or + // StructuralSites, so that we could get the right instances once we'll start parsing the InternalLinkSpecs. + Map refToLinkNodeMap = new LinkedHashMap<>(); + // all SpeciesContextSpec objects now have a siteAttributesMap, if the app is not Springsalad it will be empty + Map siteAttributesMap = new LinkedHashMap<>(); + List saSpecs = scsElement.getChildren(XMLTags.SiteAttributesSpecTag, vcNamespace); + for(Element attributeSpec : saSpecs){ // should map to Math's ParticleJumpProcess (1 -> 1) + String moleculeRef = attributeSpec.getAttributeValue(XMLTags.MoleculeRefAttrTag); + if(!mtp.getMolecularType().getName().equals(moleculeRef)) { // sanity check, we need the right mtp for the mcp instance + throw new XmlParseException("Bad SiteAttributeSpec molecular type for " + specspec.getDisplayName()); + } + String siteRef = attributeSpec.getAttributeValue(XMLTags.SiteRefAttrTag); + double radius = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteRadiusAttrTag)); + double diff = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteDiffusionAttrTag)); + String locationName = attributeSpec.getAttributeValue(XMLTags.SiteLocationRefAttrTag); + NamedColor color = Colors.getColorByName(attributeSpec.getAttributeValue(XMLTags.SiteColorAttrTag)); + double x = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteCoordXAttrTag)); + double y = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteCoordYAttrTag)); + double z = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteCoordZAttrTag)); + Coordinate coordinate = new Coordinate(x, y, z); + MolecularComponentPattern mcp = mtp.getMolecularComponentPattern(siteRef); + refToLinkNodeMap.put(siteRef, mcp); + Structure structure = model.getStructure(locationName); + SiteAttributesSpec sas = new SiteAttributesSpec(specspec, mcp, radius, diff, structure, coordinate, color); + siteAttributesMap.put(mcp, sas); + } + specspec.setSiteAttributesMap(siteAttributesMap); + + // all SpeciesContextSpec objects now have a structuralSiteAttributesMap, if the app is not Springsalad it will be empty + Map structuralSiteAttributesMap = new LinkedHashMap<>(); + List ssaSpecs = scsElement.getChildren(XMLTags.StructuralSiteAttributesSpecTag, vcNamespace); + for(Element attributeSpec : ssaSpecs){ // should map to Math's ParticleJumpProcess (1 -> 1) + String moleculeRef = attributeSpec.getAttributeValue(XMLTags.MoleculeRefAttrTag); + if(!mtp.getMolecularType().getName().equals(moleculeRef)) { // sanity check, we don't need it for StructuralSites + throw new XmlParseException("Bad SiteAttributeSpec molecular type for " + specspec.getDisplayName()); + } + String siteRef = attributeSpec.getAttributeValue(XMLTags.SiteRefAttrTag); + double radius = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteRadiusAttrTag)); + double diff = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteDiffusionAttrTag)); + String locationName = attributeSpec.getAttributeValue(XMLTags.SiteLocationRefAttrTag); + NamedColor color = Colors.getColorByName(attributeSpec.getAttributeValue(XMLTags.SiteColorAttrTag)); + double x = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteCoordXAttrTag)); + double y = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteCoordYAttrTag)); + double z = Double.parseDouble(attributeSpec.getAttributeValue(XMLTags.SiteCoordZAttrTag)); + Coordinate coordinate = new Coordinate(x, y, z); + StructuralSite mcp = new StructuralSite(siteRef); + refToLinkNodeMap.put(siteRef, mcp); + Structure structure = model.getStructure(locationName); + SiteAttributesSpec sas = new SiteAttributesSpec(specspec, mcp, radius, diff, structure, coordinate, color); + structuralSiteAttributesMap.put(mcp, sas); + } + specspec.setStructuralSiteAttributesMap(structuralSiteAttributesMap); + + // all SpeciesContextSpec objects now have an internalLinkSet, if the app is not Springsalad it will be empty + Set internalLinkSet = new LinkedHashSet<>(); + List linkSpecs = scsElement.getChildren(XMLTags.InternalLinkSpecTag, vcNamespace); + for(Element linkSpec : linkSpecs){ // should map to Math's ParticleMolecularType (n -> 1) + String oneName = unMangle(linkSpec.getAttributeValue(XMLTags.SiteOneRefAttrTag)); + String twoName = unMangle(linkSpec.getAttributeValue(XMLTags.SiteTwoRefAttrTag)); + LinkNode one = refToLinkNodeMap.get(oneName); + LinkNode two = refToLinkNodeMap.get(twoName); + MolecularInternalLinkSpec internalLink = new MolecularInternalLinkSpec(specspec, one, two); + internalLinkSet.add(internalLink); + } + specspec.setInternalLinkSet(internalLinkSet); + } + } + + /** + * This method returns a TimeStep object from a XML Element. + * Creation date: (5/22/2001 11:45:33 AM) + * + * @param param Element + * @return cbit.vcell.solver.TimeStep + */ + private NonspatialStochSimOptions getStochSimOptions(Element param){ + //get attributes + boolean isUseCustomSeed = Boolean.parseBoolean(param.getAttributeValue(XMLTags.UseCustomSeedAttrTag)); + int customSeed = 0; + if(isUseCustomSeed) + customSeed = Integer.parseInt(param.getAttributeValue(XMLTags.CustomSeedAttrTag)); + int numOfTrials = Integer.parseInt(param.getAttributeValue(XMLTags.NumberOfTrialAttrTag)); + boolean bHistogram = true; // initialize for old style cases when XMLTags.IsHistogram may be missing + if(numOfTrials == 1){ + bHistogram = false; + } + String histAttr = param.getAttributeValue(XMLTags.IsHistogram); + if(histAttr != null && !histAttr.isEmpty()){ + bHistogram = Boolean.parseBoolean(histAttr); + } + + return new NonspatialStochSimOptions(isUseCustomSeed, customSeed, numOfTrials, bHistogram); + } + + + /** + * This method returns a TimeStep object from a XML Element. + * Creation date: (5/22/2001 11:45:33 AM) + * + * @param param Element + * @return cbit.vcell.solver.TimeStep + */ + private NonspatialStochHybridOptions getStochHybridOptions(Element param){ + // StochHybridOptions are immutable, so we grab the default values from the default constructor - and read the options which are stored in XML + NonspatialStochHybridOptions defaultStochHybridOptions = new NonspatialStochHybridOptions(); + double epsilon = defaultStochHybridOptions.getEpsilon(); + double lambda = defaultStochHybridOptions.getLambda(); + double MSRTolerance = defaultStochHybridOptions.getMSRTolerance(); + double SDETDolerance = defaultStochHybridOptions.getSDETolerance(); + if(param.getAttributeValue(XMLTags.HybridEpsilonAttrTag) != null){ + epsilon = Double.parseDouble(param.getAttributeValue(XMLTags.HybridEpsilonAttrTag)); + } + if(param.getAttributeValue(XMLTags.HybridLambdaAttrTag) != null){ + lambda = Double.parseDouble(param.getAttributeValue(XMLTags.HybridLambdaAttrTag)); + } + if(param.getAttributeValue(XMLTags.HybridMSRToleranceAttrTag) != null){ + MSRTolerance = Double.parseDouble(param.getAttributeValue(XMLTags.HybridMSRToleranceAttrTag)); + } + if(param.getAttributeValue(XMLTags.HybridSDEToleranceAttrTag) != null){ + SDETDolerance = Double.parseDouble(param.getAttributeValue(XMLTags.HybridSDEToleranceAttrTag)); + } + //**** create a new StochHybridOptions object and return **** + return new NonspatialStochHybridOptions(epsilon, lambda, MSRTolerance, SDETDolerance); + } + + + /** + * This method returns a Stochasitc volumn variable from a XML element. + * Creation date: (7/24/2006 5:05:51 PM) + * + * @param param Element + * @return cbit.vcell.math.StochVolVariable + */ + private StochVolVariable getStochVolVariable(Element param){ + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + //-- create new StochVolVariable object + StochVolVariable stochVar = new StochVolVariable(name); + transcribeComments(param, stochVar); + + return stochVar; + } + + /** + * This method returns a SubVolume element type from a XML representation. + * Creation date: (4/26/2001 4:14:01 PM) + * + * @param param Element + * @return SubVolume + */ + private SubVolume getSubVolume(Element param) throws XmlParseException{ + String typeString = param.getAttributeValue(XMLTags.TypeAttrTag); + SubVolume newsubvolume = null; + + if(typeString != null){ + //process the subvolume upon the 'type' + if(typeString.equalsIgnoreCase(XMLTags.CompartmentBasedTypeTag)){ + //Process compartmental based + newsubvolume = getCompartmentSubVolume(param); + } else if(typeString.equalsIgnoreCase(XMLTags.AnalyticBasedTypeTag)){ + //Process Analytic based + newsubvolume = getAnalyticSubVolume(param); + } else if(typeString.equalsIgnoreCase(XMLTags.ImageBasedTypeTag)){ + //Process Image based + newsubvolume = getImageSubVolume(param); + } else if(typeString.equalsIgnoreCase(XMLTags.CSGBasedTypeTag)){ + //Process Constructed Solid Geometry based + newsubvolume = getCSGObject(param, null); + } else { + //Throw an exception + throw new XmlParseException("Parse Error! Unknown Subvolume type:" + typeString); + } + + } else { + System.out.println("Invalid VCML format! Error in "); + System.out.println("Valid format is:"); + System.out.println(""); + throw new XmlParseException("Invalid VCML syntax in "); + } + + return newsubvolume; + } + + public CSGObject getCSGObject(Element param, KeyValue keyFromDB) throws XmlParseException{ + //retrieve the attributes + String name = param.getAttributeValue(XMLTags.NameAttrTag); + int handle = Integer.parseInt(param.getAttributeValue(XMLTags.HandleAttrTag)); + + //process the key + KeyValue key = null; + String temp = param.getAttributeValue(XMLTags.KeyValueAttrTag); + + if(temp != null && temp.length() > 0 && this.readKeysFlag){ + key = new KeyValue(temp); + } + if(keyFromDB != null){ + key = keyFromDB; + } + + //Retrieve CSGObject CSGNode - CSGObject element should have one child (the root node of the CSGObject) + Object[] elements = param.getChildren().toArray(); + if(elements.length > 1){ + throw new XmlParseException("CSGObject subvolume element cannot have more than one child element"); + } + CSGNode csgRootNode = getCSGNode((Element) elements[0]); + + //Create the CSGObject + CSGObject newCSGObjectSubvol = new CSGObject(key, name, handle); + newCSGObjectSubvol.setRoot(csgRootNode); + + return newCSGObjectSubvol; + } + + private CSGNode getCSGNode(Element param) throws XmlParseException{ + String nodeNameString = param.getName(); + CSGNode csgNode = null; + + if(nodeNameString != null){ + if(nodeNameString.equalsIgnoreCase(XMLTags.CSGPrimitiveTag)){ + //Process CSGPrimitive + csgNode = getCSGPrimitive(param); + } else if(nodeNameString.equalsIgnoreCase(XMLTags.CSGPseudoPrimitiveTag)){ + //Process CSGPseudoPrimitive + csgNode = getCSGPseudoPrimitive(param); + } else if(nodeNameString.equalsIgnoreCase(XMLTags.CSGSetOperatorTag)){ + //Process CSGSetOperator + csgNode = getCSGSetOperator(param); + } else if(nodeNameString.equalsIgnoreCase(XMLTags.CSGHomogeneousTransformationTag)){ + //Process CSGHomogeneousTransformation + csgNode = getCSGHomogeneousTransformation(param); + } else if(nodeNameString.equalsIgnoreCase(XMLTags.CSGRotationTag)){ + //Process CSGRotation + csgNode = getCSGRotation(param); + } else if(nodeNameString.equalsIgnoreCase(XMLTags.CSGScaleTag)){ + //Process CSGScale + csgNode = getCSGScale(param); + } else if(nodeNameString.equalsIgnoreCase(XMLTags.CSGTranslationTag)){ + //Process CSGTranslation + csgNode = getCSGTranslation(param); + } else { + //Throw an exception + throw new XmlParseException("Parse Error! Unknown CSGNode type : " + nodeNameString); + } + + } else { + throw new XmlParseException("CSGNode : cannot be null"); + } + + return csgNode; + } + + + private CSGPrimitive getCSGPrimitive(Element param){ + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String primitiveTypeStr = unMangle(param.getAttributeValue(XMLTags.CSGPrimitiveTypeTag)); + + //---Create the new CSGPrimitive object --- + PrimitiveType type = CSGPrimitive.PrimitiveType.valueOf(primitiveTypeStr); + CSGPrimitive csgPrimitive = new CSGPrimitive(name, type); + + return csgPrimitive; + } + + private CSGPseudoPrimitive getCSGPseudoPrimitive(Element param) throws XmlParseException{ + throw new XmlParseException("CSGPseudoPrimitive not implemented yet."); + } + + + private CSGSetOperator getCSGSetOperator(Element param) throws XmlParseException{ + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String operatorTypeStr = unMangle(param.getAttributeValue(XMLTags.CSGSetOperatorTypeTag)); + + //---Create the new CSGSetOperator object --- + OperatorType type = CSGSetOperator.OperatorType.valueOf(operatorTypeStr); + CSGSetOperator csgSetOperator = new CSGSetOperator(name, type); + + List children = param.getChildren(); + Iterator iterator = children.iterator(); + int count = 0; + while (iterator.hasNext()) { + Element tempElement = iterator.next(); + CSGNode csgNode = getCSGNode(tempElement); + csgSetOperator.addChild(csgNode); + } + + return csgSetOperator; + } + + private CSGHomogeneousTransformation getCSGHomogeneousTransformation(Element param) throws XmlParseException{ + throw new XmlParseException("CSGHomogeneousTransformation not implemented yet."); + } + + + private CSGRotation getCSGRotation(Element param) throws XmlParseException{ + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String rotateXStr = unMangle(param.getAttributeValue(XMLTags.CSGRotationXTag)); + String rotateYStr = unMangle(param.getAttributeValue(XMLTags.CSGRotationYTag)); + String rotateZStr = unMangle(param.getAttributeValue(XMLTags.CSGRotationZTag)); + String rotationAngleStr = unMangle(param.getAttributeValue(XMLTags.CSGRotationAngleInRadiansTag)); + Vect3d rotationAxis = new Vect3d(Double.parseDouble(rotateXStr), Double.parseDouble(rotateYStr), Double.parseDouble(rotateZStr)); + CSGRotation csgRotation = new CSGRotation(name, rotationAxis, Double.parseDouble(rotationAngleStr)); + + //Retrieve CSGNode - CSGRotation element should have one child + Object[] elements = param.getChildren().toArray(); + if(elements.length > 1){ + throw new XmlParseException("CSGRotation element cannot have more than one child element"); + } + CSGNode csgChildNode = getCSGNode((Element) elements[0]); + + csgRotation.setChild(csgChildNode); + return csgRotation; + } + + + private CSGScale getCSGScale(Element param) throws XmlParseException{ + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String scaleXStr = unMangle(param.getAttributeValue(XMLTags.CSGScaleXTag)); + String scaleYStr = unMangle(param.getAttributeValue(XMLTags.CSGScaleYTag)); + String scaleZStr = unMangle(param.getAttributeValue(XMLTags.CSGScaleZTag)); + Vect3d scaleAxis = new Vect3d(Double.parseDouble(scaleXStr), Double.parseDouble(scaleYStr), Double.parseDouble(scaleZStr)); + CSGScale csgScale = new CSGScale(name, scaleAxis); + + //Retrieve CSGNode - CSGScale element should have one child + Object[] elements = param.getChildren().toArray(); + if(elements.length > 1){ + throw new XmlParseException("CSGScale element cannot have more than one child element"); + } + CSGNode csgChildNode = getCSGNode((Element) elements[0]); + + csgScale.setChild(csgChildNode); + return csgScale; + } + + private CSGTranslation getCSGTranslation(Element param) throws XmlParseException{ + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String translateXStr = unMangle(param.getAttributeValue(XMLTags.CSGTranslationXTag)); + String translateYStr = unMangle(param.getAttributeValue(XMLTags.CSGTranslationYTag)); + String translateZStr = unMangle(param.getAttributeValue(XMLTags.CSGTranslationZTag)); + Vect3d translateAxis = new Vect3d(Double.parseDouble(translateXStr), Double.parseDouble(translateYStr), Double.parseDouble(translateZStr)); + CSGTranslation csgTranslation = new CSGTranslation(name, translateAxis); + + //Retrieve CSGNode - CSGScale element should have one child + Object[] elements = param.getChildren().toArray(); + if(elements.length > 1){ + throw new XmlParseException("CSGScale element cannot have more than one child element"); + } + CSGNode csgChildNode = getCSGNode((Element) elements[0]); + + csgTranslation.setChild(csgChildNode); + return csgTranslation; + } + + + private SurfaceClass getSurfaceClass(Element param, Geometry geom) throws XmlParseException{ + + Set surfaceClassSubVolumeSet = new HashSet(); + KeyValue surfaceClassKey = null; + String surfaceClassName = null; + + surfaceClassName = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String surfaceClassKeyStr = param.getAttributeValue(XMLTags.KeyValueAttrTag); + surfaceClassKey = (surfaceClassKeyStr == null ? null : new KeyValue(surfaceClassKeyStr)); + String subVol1Ref = param.getAttributeValue(XMLTags.SubVolume1RefAttrTag); + String subVol2Ref = param.getAttributeValue(XMLTags.SubVolume2RefAttrTag); + if(subVol1Ref != null){ + SubVolume subVolume = geom.getGeometrySpec().getSubVolume(subVol1Ref); + if(subVolume == null){ + throw new XmlParseException("SurfaceClass missing subvolume '" + subVol1Ref + "'"); + } + surfaceClassSubVolumeSet.add(subVolume); + } + if(subVol2Ref != null){ + SubVolume subVolume = geom.getGeometrySpec().getSubVolume(subVol2Ref); + if(subVolume == null){ + throw new XmlParseException("SurfaceClass missing subvolume '" + subVol2Ref + "'"); + } + surfaceClassSubVolumeSet.add(subVolume); + } + + return new SurfaceClass(surfaceClassSubVolumeSet, surfaceClassKey, surfaceClassName); + } + + /** + * This method returns a TimeBounds object from a XML Element. + * Creation date: (5/22/2001 11:41:04 AM) + * + * @param param Element + * @return cbit.vcell.solver.TimeBounds + */ + private TimeBounds getTimeBounds(Element param){ + //get Attributes + double start = Double.parseDouble(param.getAttributeValue(XMLTags.StartTimeAttrTag)); + double end = Double.parseDouble(param.getAttributeValue(XMLTags.EndTimeAttrTag)); + + //*** create new TimeBounds object **** + TimeBounds timeBounds = new TimeBounds(start, end); + + return timeBounds; + } + + + /** + * This method returns a TimeStep object from a XML Element. + * Creation date: (5/22/2001 11:45:33 AM) + * + * @param param Element + * @return cbit.vcell.solver.TimeStep + */ + private TimeStep getTimeStep(Element param){ + //get attributes + double min = Double.parseDouble(param.getAttributeValue(XMLTags.MinTimeAttrTag)); + double def = Double.parseDouble(param.getAttributeValue(XMLTags.DefaultTimeAttrTag)); + double max = Double.parseDouble(param.getAttributeValue(XMLTags.MaxTimeAttrTag)); + + //**** create new TimeStep object **** + TimeStep timeStep = new TimeStep(min, def, max); + + return timeStep; + } + + + /** + * This methos returns a User object from a XML Element. + * Creation date: (3/16/2001 3:52:30 PM) + * + * @param param Element + * @return cbit.vcell.server.User + */ + private User getUser(Element param){ + User newuser = + new User( + param.getAttributeValue(XMLTags.NameAttrTag), + new KeyValue(param.getAttributeValue(XMLTags.IdentifierAttrTag))); + + return newuser; + } + + private void addResevedSymbols(VariableHash varHash, Model model) throws XmlParseException{ + + // + // add constants that may be used in kinetics. + // + try { + // add reserved symbols + varHash.addVariable(new Constant(model.getPI_CONSTANT().getName(), new Expression(0.0))); + varHash.addVariable(new Constant(model.getFARADAY_CONSTANT().getName(), new Expression(0.0))); + varHash.addVariable(new Constant(model.getFARADAY_CONSTANT_NMOLE().getName(), new Expression(0.0))); + varHash.addVariable(new Constant(model.getGAS_CONSTANT().getName(), new Expression(0.0))); + varHash.addVariable(new Constant(model.getKMILLIVOLTS().getName(), new Expression(0.0))); + varHash.addVariable(new Constant(model.getN_PMOLE().getName(), new Expression(0.0))); + varHash.addVariable(new Constant(model.getKMOLE().getName(), new Expression(0.0))); + varHash.addVariable(new Constant(model.getTEMPERATURE().getName(), new Expression(0.0))); + varHash.addVariable(new Constant(model.getK_GHK().getName(), new Expression(0.0))); + varHash.addVariable(new Constant(model.getTIME().getName(), new Expression(0.0))); + } catch(MathException e){ + throw new XmlParseException("error reordering parameters according to dependencies", e); + } + } + + /** + * This method return a VarIniCondition object from a XML element. + * Creation date: (7/24/2006 5:26:05 PM) + * + * @param param Element + * @return cbit.vcell.math.VarIniCondition + * @throws cbit.vcell.xml.XmlParseException The exception description. + */ + private VarIniCondition getVarIniCount(Element param, MathDescription md) throws XmlParseException, MathException, ExpressionException{ + //retrieve values + Expression exp = unMangleExpression(param.getText()); + + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + Variable var = md.getVariable(name); + if(var == null){ + throw new MathFormatException("variable " + name + " not defined"); + } + if(!(var instanceof StochVolVariable)){ + throw new MathFormatException("variable " + name + " not a Stochastic Volume Variable"); + } + try { + VarIniCondition varIni = new VarIniCount(var, exp); + return varIni; + } catch(Exception e){ + lg.error(e.getMessage(), e); + } + + return null; + } + + + private BoundaryConditionSpec getBoundaryConditionSpec(Element param) throws XmlParseException, MathException{ + //retrieve values + String boundarySubdomainName = unMangle(param.getAttributeValue(XMLTags.BoundarySubdomainNameTag)); + String boundarySubdomainType = unMangle(param.getAttributeValue(XMLTags.BoundaryTypeTag)); + + if(boundarySubdomainName != null && boundarySubdomainType != null){ + BoundaryConditionSpec bcs = new BoundaryConditionSpec(boundarySubdomainName, new BoundaryConditionType(boundarySubdomainType)); + return bcs; + } + return null; + } + + + private BoundaryConditionValue getBoundaryConditionValue(Element param, PdeEquation pde) throws XmlParseException, MathException{ + //retrieve values + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + Expression valueExpr = unMangleExpression(param.getAttributeValue(XMLTags.BoundaryValueExpressionTag)); + + if(name != null && valueExpr != null){ + BoundaryConditionValue bcv = pde.new BoundaryConditionValue(name, valueExpr); + return bcv; + } + return null; + } + + private VarIniCondition getVarIniPoissonExpectedCount(Element param, MathDescription md) throws XmlParseException, MathException, ExpressionException{ + //retrieve values + Expression exp = unMangleExpression(param.getText()); + + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + Variable var = md.getVariable(name); + if(var == null){ + throw new MathFormatException("variable " + name + " not defined"); + } + if(!(var instanceof StochVolVariable)){ + throw new MathFormatException("variable " + name + " not a Stochastic Volume Variable"); + } + try { + VarIniCondition varIni = new VarIniPoissonExpectedCount(var, exp); + return varIni; + } catch(Exception e){ + lg.error(e.getMessage(), e); + } + + return null; + } + + + /** + * This method returns a VCIMage object from a XML representation. + * Creation date: (3/16/2001 3:41:24 PM) + * + * @param param Element + * @return VCImage + */ + VCImage getVCImage(Element param, Extent extent) throws XmlParseException{ + // + // A BioModel repeats its whole , image included, inside every + // , so the same image arrives here once per application. Decoding it + // each time costs a hex decode, an inflate, and a retained copy of the pixels -- for the + // model in #2021 that is 62 MB of pixels per application, eleven times over. + // + // Only the IMAGE is shared, not the Geometry: a VCImage is immutable payload (its + // compressed pixels are final and VCPixelClass is declared Immutable), whereas a Geometry + // is mutable and two applications sharing one would see each other's edits. + // + String digest = imageElementDigest(param); + if(digest != null){ + VCImage alreadyParsed = parsedImagesByDigest.get(digest); + if(alreadyParsed != null){ + return alreadyParsed; + } + } + VCImage image = parseVCImage(param, extent); + if(digest != null){ + parsedImagesByDigest.put(digest, image); + } + return image; + } + + private VCImage parseVCImage(Element param, Extent extent) throws XmlParseException{ + //try to get metadata(version) + Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace)); + + //get the attributes + Element tempelement = param.getChild(XMLTags.ImageDataTag, vcNamespace); + int aNumX = Integer.parseInt(tempelement.getAttributeValue(XMLTags.XAttrTag)); + int aNumY = Integer.parseInt(tempelement.getAttributeValue(XMLTags.YAttrTag)); + int aNumZ = Integer.parseInt(tempelement.getAttributeValue(XMLTags.ZAttrTag)); + + //getpixels + String temp = tempelement.getText(); + byte[] data = Hex.toBytes(temp); //decode + + //create the VCImage object + VCImageCompressed newimage = null; + try { + newimage = new VCImageCompressed(version, data, extent, aNumX, aNumY, aNumZ); + } catch(ImageException e){ + throw new XmlParseException("An imageException occurred while trying to create a VCImage!", e); + } + //set attributes + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + + try { + newimage.setName(name); + //String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag); + //if (annotation!=null) { + //newimage.setDescription(unMangle(annotation)); + //} + + //read the annotation + String annotation = param.getChildText(XMLTags.AnnotationTag, vcNamespace); + if(annotation != null && annotation.length() > 0){ + newimage.setDescription(unMangle(annotation)); + } + + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException(e); + } + + //get PixelClasses + List pixelClassList = param.getChildren(XMLTags.PixelClassTag, vcNamespace); + + if(pixelClassList.size() != 0){ + VCPixelClass[] pixelClassArray = new VCPixelClass[pixelClassList.size()]; + int pixelClassCounter = 0; + for(Element pcElement : pixelClassList){ + pixelClassArray[pixelClassCounter] = getPixelClass(pcElement); + pixelClassCounter++; + } + try { + newimage.setPixelClasses(pixelClassArray); + } catch(java.beans.PropertyVetoException e){ + throw new XmlParseException(e); + } + } else {//Invalid format + System.out.println("Format Error! No references found inside !"); + System.out.println("Valid format for images is:"); + System.out.println(""); + System.out.println(" "); + System.out.println(" ......Image content..."); + System.out.println(" "); + System.out.println(" "); + System.out.println(" ..."); + System.out.println(" "); + System.out.println(" "); + System.out.println(""); + throw new XmlParseException("Invalid VCML format error!\nNo references found inside !"); + } + + return newimage; + } + + + private Version getVersion(Element xmlVersion) throws XmlParseException{ + if(xmlVersion == null){ + return null; + } + + //determine if it should be processed using the 'fromVersionable' + if(xmlVersion.getAttributeValue(XMLTags.FromVersionableTag) == null || Boolean.valueOf(xmlVersion.getAttributeValue(XMLTags.FromVersionableTag)).booleanValue() || this.readKeysFlag == false){ + //this came from a versionable object, so skip! Or it should not explicitly import the information inside the Version + return null; + } + + //Read all the attributes + //*name + String name = unMangle(xmlVersion.getAttributeValue(XMLTags.NameAttrTag)); + //*key + String temp = xmlVersion.getAttributeValue(XMLTags.KeyValueAttrTag); + KeyValue key = new KeyValue(temp); + //*owner + Element tempElement = xmlVersion.getChild(XMLTags.OwnerTag, vcNamespace); + User owner = new User(unMangle(tempElement.getAttributeValue(XMLTags.NameAttrTag)), new KeyValue(tempElement.getAttributeValue(XMLTags.IdentifierAttrTag))); + //*access + GroupAccess groupAccess = getGroupAccess(xmlVersion.getChild(XMLTags.GroupAccessTag, vcNamespace)); + //*Branchpointref + temp = xmlVersion.getAttributeValue(XMLTags.BranchPointRefTag); + KeyValue branchpointref = null; + + if(temp != null){ + branchpointref = new KeyValue(temp); + } + + //*BranchID + java.math.BigDecimal branchId = new java.math.BigDecimal(xmlVersion.getAttributeValue(XMLTags.BranchIdAttrTag)); + //*Flag + temp = xmlVersion.getAttributeValue(XMLTags.FlagAttrTag); + VersionFlag flag = VersionFlag.fromInt(Integer.parseInt(temp)); + //*Date + java.util.Date date = null; + temp = xmlVersion.getAttributeValue(XMLTags.DateAttrTag); + + if(temp != null){ + try { + SimpleDateFormat simpleDateFormat = new SimpleDateFormat(BeanUtils.vcDateFormat, Locale.US); + date = simpleDateFormat.parse(temp); + } catch(java.text.ParseException e){ + throw new XmlParseException("Invalid date:" + temp, e); + } + } + + //*Annotation + String annotation = null; + String annotationText = xmlVersion.getChildText(XMLTags.AnnotationTag, vcNamespace); + if(annotationText != null && annotationText.length() > 0){ + annotation = unMangle(annotationText); + } + + //Create and return the version object + return new Version(key, name, owner, groupAccess, branchpointref, branchId, date, flag, annotation); + } + + + /** + * This method returns a VolumeRegionEquation from a XML Element. + * Creation date: (5/17/2001 3:52:40 PM) + * + * @param param Element + * @return cbit.vcell.math.VolumeRegionEquation + * @throws cbit.vcell.xml.XmlParseException The exception description. + */ + private VolumeRegionEquation getVolumeRegionEquation(Element param, MathDescription mathDesc) throws XmlParseException{ + //get attributes + String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + + //try a VolumeRegionVariable + VolumeRegionVariable varref = (VolumeRegionVariable) mathDesc.getVariable(varname); + if(varref == null){ + throw new XmlParseException("The reference to the VolumeRegion variable " + varname + " could not be resolved!"); + } + + //get Initial condition + String temp = param.getChildText(XMLTags.InitialTag, vcNamespace); + Expression exp = unMangleExpression(temp); + // ** Create the Equation ** + VolumeRegionEquation volRegEq = new VolumeRegionEquation(varref, exp); + + //set the Uniform Rate + temp = param.getChildText(XMLTags.UniformRateTag, vcNamespace); + exp = unMangleExpression(temp); + volRegEq.setUniformRateExpression(exp); + + //Set the Volume Rate + temp = param.getChildText(XMLTags.VolumeRateTag, vcNamespace); + exp = unMangleExpression(temp); + volRegEq.setVolumeRateExpression(exp); + + //get ExactSolution (if any) +/* temp = param.getChildText(XMLTags.ExactTag); + if (temp !=null) { + try { + Expression expression = new Expression( unMangle( temp) ); + odeEquation.setExactSolution( expression); + } catch (ExpressionException e) { + lg.error(e); + throw new XmlParseException("An ExpressionException was fired when creating the expression: "+ unMangle(temp)+" : "+e.getMessage()); + } + } + //get ConstructedSolution (if any) + temp = param.getChildText(XMLTags.ConstructedTag); + if (temp != null) { + try { + Expression expression = new Expression(unMangle(temp)); + odeEquation.setConstructedSolution( expression ); + } catch (ExpressionException e) { + lg.error(e); + throw new XmlParseException("An ExpressionException was fired when creating the expression: "+ unMangle(temp) +" : "+e.getMessage()); + } + }*/ + + return volRegEq; + } + + + /** + * This method returns a VolumeRegionVariable object from a XML Element. + * Creation date: (5/16/2001 2:56:34 PM) + * + * @param param Element + * @return cbit.vcell.math.VolumeRegionVariable + */ + private VolumeRegionVariable getVolumeRegionVariable(Element param){ + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); + Domain domain = null; + if(domainStr != null){ + domain = new Domain(domainStr); + } + //-- create new VolumeRegionVariable object + VolumeRegionVariable volRegVariable = new VolumeRegionVariable(name, domain); + transcribeComments(param, volRegVariable); + + return volRegVariable; + } + + + /** + * This method returns a VolVariable object from a XML Element. + * Creation date: (5/16/2001 2:56:34 PM) + * + * @param param Element + * @return cbit.vcell.math.VolVariable + */ + private VolVariable getVolVariable(Element param){ + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); + Domain domain = null; + if(domainStr != null){ + domain = new Domain(domainStr); + } + + //-- create new VolVariable object + VolVariable volVariable = new VolVariable(name, domain); + transcribeComments(param, volVariable); + + return volVariable; + } + + private VolumeParticleObservable getVolumeParticleObservable(Element param, VariableHash varHash) throws XmlParseException{ + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); + Domain domain = null; + if(domainStr != null){ + domain = new Domain(domainStr); + } + String molecularTypeString = unMangle(param.getAttributeValue(XMLTags.ParticleMolecularTypePatternTag)); + ObservableType observableType = ObservableType.fromString(molecularTypeString); + VolumeParticleObservable var = new VolumeParticleObservable(name, domain, observableType); + String sequenceAttr = param.getAttributeValue(XMLTags.ParticleObservableSequenceTypeAttrTag); + + if(sequenceAttr != null){ + Sequence sequence = Sequence.fromString(sequenceAttr); + String sequenceLength = param.getAttributeValue(XMLTags.ParticleObservableSequenceLengthAttrTag); + var.setSequence(sequence); + if(sequence != Sequence.Multimolecular){ + var.setQuantity(Integer.parseInt(sequenceLength)); + } + } else { + var.setSequence(Sequence.Multimolecular); + } + + Element volumeParticleSpeciesPatternsElement = param.getChild(XMLTags.VolumeParticleSpeciesPatternsTag, vcNamespace); + if(volumeParticleSpeciesPatternsElement != null){ + List volumeParticleSpeciesPatternList = volumeParticleSpeciesPatternsElement.getChildren(XMLTags.VolumeParticleSpeciesPatternTag, vcNamespace); + for(Element volumeParticleSpeciesPattern : volumeParticleSpeciesPatternList){ + String volumeParticleSpeciesPatternName = unMangle(volumeParticleSpeciesPattern.getAttributeValue(XMLTags.NameAttrTag)); + + Variable v = varHash.getVariable(volumeParticleSpeciesPatternName); + if(v == null){ + throw new XmlParseException("failed to find VolumeParticleSpeciesPattern named " + volumeParticleSpeciesPatternName); + } + if(v instanceof ParticleSpeciesPattern){ + var.addParticleSpeciesPattern((ParticleSpeciesPattern) v); + } else { + throw new XmlParseException("Variable " + volumeParticleSpeciesPatternName + " is not a ParticleSpeciesPattern"); + } + } + } + return var; + } + + private ParticleMolecularComponent getParticleMolecularComponent(String pmtName, Element param, boolean isLangevin) throws XmlParseException { + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + ParticleMolecularComponent var; + if(isLangevin){ + var = new LangevinParticleMolecularComponent(pmtName + "_" + name, name); + if(param.getAttributeValue(XMLTags.ParticleMolecularComponentRadiusTag) != null){ + Expression radius; + try { + radius = new Expression(param.getAttributeValue(XMLTags.ParticleMolecularComponentRadiusTag)); + } catch(ExpressionException e){ + throw new XmlParseException("unparseable " + XMLTags.ParticleMolecularComponentRadiusTag, e); + } + ((LangevinParticleMolecularComponent) var).setRadius(radius); + } + if(param.getAttributeValue(XMLTags.ParticleMolecularComponentDiffusionRateTag) != null){ + Expression diff; + try { + diff = new Expression(param.getAttributeValue(XMLTags.ParticleMolecularComponentDiffusionRateTag)); + } catch(ExpressionException e){ + throw new XmlParseException("unparseable " + XMLTags.ParticleMolecularComponentDiffusionRateTag, e); + } + ((LangevinParticleMolecularComponent) var).setDiffusionRate(diff); + } + if(param.getAttributeValue(XMLTags.ParticleMolecularComponentLocationTag) != null){ + String location = param.getAttributeValue(XMLTags.ParticleMolecularComponentLocationTag); + ((LangevinParticleMolecularComponent) var).setLocation(location); + } + double x = 0; + double y = 0; + double z = 0; + if(param.getAttributeValue(XMLTags.ParticleMolecularComponentCoordXAttrTag) != null){ + x = Double.parseDouble(param.getAttributeValue(XMLTags.ParticleMolecularComponentCoordXAttrTag)); + } + if(param.getAttributeValue(XMLTags.ParticleMolecularComponentCoordYAttrTag) != null){ + y = Double.parseDouble(param.getAttributeValue(XMLTags.ParticleMolecularComponentCoordYAttrTag)); + } + if(param.getAttributeValue(XMLTags.ParticleMolecularComponentCoordZAttrTag) != null){ + z = Double.parseDouble(param.getAttributeValue(XMLTags.ParticleMolecularComponentCoordZAttrTag)); + } + ((LangevinParticleMolecularComponent) var).setCoordinate(new Coordinate(x, y, z)); + if(param.getAttributeValue(XMLTags.ParticleMolecularComponentColorTag) != null){ + NamedColor color = Colors.getColorByName(param.getAttributeValue(XMLTags.ParticleMolecularComponentColorTag)); + ((LangevinParticleMolecularComponent) var).setColor(color); + } + } else { + var = new ParticleMolecularComponent(pmtName + "_" + name, name); + } + List componentStateList = param.getChildren(XMLTags.ParticleMolecularTypeAllowableStateTag, vcNamespace); + for(Element componentState : componentStateList){ + String componentStateName = unMangle(componentState.getAttributeValue(XMLTags.NameAttrTag)); + if(!componentStateName.equals("*")){ + ParticleComponentStateDefinition p = var.getComponentStateDefinition(componentStateName); + if(p == null){ + p = new ParticleComponentStateDefinition(componentStateName); + var.addComponentStateDefinition(p); + } + } + } + return var; + } + + private ParticleMolecularType getParticleMolecularType(Element param, boolean isLangevin) throws XmlParseException { + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + ParticleMolecularType var; + if(isLangevin){ + LangevinParticleMolecularType langevinVar = new LangevinParticleMolecularType(name); + if(param.getAttribute(XMLTags.ParticleMolecularTypeIs2DTag) != null){ + langevinVar.setIs2D(Boolean.parseBoolean(param.getAttributeValue(XMLTags.ParticleMolecularTypeIs2DTag))); + } + var = langevinVar; + } else { + var = new ParticleMolecularType(name); + } + List molecularComponentList = param.getChildren(XMLTags.ParticleMolecularComponentPatternTag, vcNamespace); + for(Element molecularComponent : molecularComponentList){ + ParticleMolecularComponent p = getParticleMolecularComponent(name, molecularComponent, isLangevin); + var.addMolecularComponent(p); + } + + if(var instanceof LangevinParticleMolecularType){ + List molecularTypeLinkList = param.getChildren(XMLTags.ParticleMolecularTypeLinksTag, vcNamespace); + Set> internalLinkSet = new LinkedHashSet<>(); + for(Element molecularTypeLink : molecularTypeLinkList){ + Pair internalLink = getInternalLink((LangevinParticleMolecularType) var, molecularTypeLink); + internalLinkSet.add(internalLink); + } + ((LangevinParticleMolecularType) var).setInternalLinkSpec(internalLinkSet); + } + + List anchorList = param.getChildren(XMLTags.ParticleMolecularTypeAnchorTag, vcNamespace); + for(Element anchorElement : anchorList){ + String anchor = unMangle(anchorElement.getAttributeValue(XMLTags.NameAttrTag)); + var.addAnchor(anchor); + } + return var; + } + + private Pair getInternalLink(LangevinParticleMolecularType var, Element param){ + String oneName = unMangle(param.getAttributeValue(XMLTags.LangevinParticleMolecularComponentOneTag)); + String twoName = unMangle(param.getAttributeValue(XMLTags.LangevinParticleMolecularComponentTwoTag)); + // by this time the molecullar components are the correct class LangevinParticleMolecularComponent and won't throw cast exception + LangevinParticleMolecularComponent one = (LangevinParticleMolecularComponent) var.getMolecularComponent(oneName); + LangevinParticleMolecularComponent two = (LangevinParticleMolecularComponent) var.getMolecularComponent(twoName); + Pair pair = new Pair<>(one, two); + return pair; + } + + + private ParticleMolecularComponentPattern getParticleMolecularComponentPattern(Element param, ParticleMolecularType particleMolecularType) throws XmlParseException{ + String molecularComponentName = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + ParticleMolecularComponent particleMolecularComponent = particleMolecularType.getMolecularComponent(molecularComponentName); + if(particleMolecularComponent != null){ + ParticleMolecularComponentPattern var = new ParticleMolecularComponentPattern(particleMolecularComponent); + ParticleComponentStatePattern pcsp = null; + String componentStateName = unMangle(param.getAttributeValue(XMLTags.StateAttrTag)); + if(componentStateName.equals("*")){ + pcsp = new ParticleComponentStatePattern(); + } else { + //ParticleComponentStateDefinition pcsd = new ParticleComponentStateDefinition(componentStateName); // bad?? + ParticleComponentStateDefinition pcsd = particleMolecularComponent.getComponentStateDefinition(componentStateName); + if(pcsd == null){ + throw new XmlParseException("failed to find ParticleComponentStateDefinition named " + molecularComponentName); + } + pcsp = new ParticleComponentStatePattern(pcsd); + } + var.setComponentStatePattern(pcsp); + String bondString = unMangle(param.getAttributeValue(XMLTags.BondAttrTag)); + + ParticleBondType bondType = ParticleBondType.fromSymbol(bondString); + if(bondType == ParticleBondType.Specified){ + int bondId = Integer.parseInt(bondString); + var.setBondId(bondId); + } + var.setBondType(bondType); + return var; + } else { + throw new XmlParseException("failed to find ParticleMolecularComponent named " + molecularComponentName); + } + } + + private ParticleMolecularTypePattern getParticleMolecularTypePattern(Element param, MathDescription mathDescription) throws XmlParseException{ + String molecularTypeName = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String matchLabel = unMangle(param.getAttributeValue(XMLTags.ParticleMolecularTypePatternMatchLabelAttrTag)); + ParticleMolecularType particleMolecularType = mathDescription.getParticleMolecularType(molecularTypeName); + if(particleMolecularType != null){ + ParticleMolecularTypePattern var = new ParticleMolecularTypePattern(particleMolecularType); + if(matchLabel != null){ + var.setMatchLabel(matchLabel); + } + List componentPatternList = param.getChildren(XMLTags.ParticleMolecularComponentPatternTag, vcNamespace); + for(Element componentPattern : componentPatternList){ + ParticleMolecularComponentPattern p = getParticleMolecularComponentPattern(componentPattern, particleMolecularType); + var.addMolecularComponentPattern(p); + } + return var; + } else { + throw new XmlParseException("failed to find ParticleMolecularType named " + molecularTypeName); + } + } + + private VolumeParticleSpeciesPattern getVolumeParticleSpeciesPattern(Element param, MathDescription mathdes) throws XmlParseException{ + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); + Domain domain = null; + if(domainStr != null){ + domain = new Domain(domainStr); + } + String location = unMangle(param.getAttributeValue(XMLTags.LocationAttrTag)); + VolumeParticleSpeciesPattern var = new VolumeParticleSpeciesPattern(name, domain, location); + + List molecularTypeList = param.getChildren(XMLTags.ParticleMolecularTypePatternTag, vcNamespace); + for(Element molecularType : molecularTypeList){ + ParticleMolecularTypePattern p = getParticleMolecularTypePattern(molecularType, mathdes); + var.addMolecularTypePattern(p); + } + +// Element meshRefineElement = param.getChild(XMLTags.ParticleMolecularTypePatternTag, vcNamespace); +// if (meshRefineElement != null) { +// List levelElementList = meshRefineElement.getChildren(XMLTags.RefinementLevelTag, vcNamespace); +// for (Element levelElement : levelElementList) { + return var; + } + + private VolumeParticleVariable getVolumeParticalVariable(Element param){ + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); + Domain domain = null; + if(domainStr != null){ + domain = new Domain(domainStr); + } + + //-- create new VolVariable object + VolumeParticleVariable var = new VolumeParticleVariable(name, domain); + transcribeComments(param, var); + + return var; + } + + private MembraneParticleVariable getMembraneParticalVariable(Element param){ + String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag)); + String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag)); + Domain domain = null; + if(domainStr != null){ + domain = new Domain(domainStr); + } + + //-- create new VolVariable object + MembraneParticleVariable var = new MembraneParticleVariable(name, domain); + transcribeComments(param, var); + return var; + } + + private interface Convert { + T parse(String in); + } + + private Convert convertInt = new Convert() { + public Integer parse(String in){ + return Integer.parseInt(in); + } + }; + + private Convert convertDouble = new Convert() { + public Double parse(String in){ + return Double.parseDouble(in); + } + }; + + private Convert convertBoolean = new Convert() { + public Boolean parse(String in){ + return Boolean.parseBoolean(in); + } + }; + + /** + * parse parent for specified element. Return defaultValue if it's not present + * + * @param parent + * @param tagName + * @param defaultValue + * @param c converter to change string into T + * @return parsed value, if present, default otherwise + */ + private T parseWithDefault(Element parent, String tagName, T defaultValue, Convert c){ + Element child = parent.getChild(tagName, vcNamespace); + if(child != null){ + return c.parse(child.getText()); + } + return defaultValue; + } + + /** + * read integer XML + * + * @see #parseWithDefault(Element, String, Object, Convert) + */ + private int parseIntWithDefault(Element parent, String tagName, int defaultValue){ + return parseWithDefault(parent, tagName, defaultValue, convertInt); + } + + /** + * read double XML + * + * @see #parseWithDefault(Element, String, Object, Convert) + */ + private double parseDoubleWithDefault(Element parent, String tagName, double defaultValue){ + return parseWithDefault(parent, tagName, defaultValue, convertDouble); + } + + /** + * read boolean XML + * + * @see #parseWithDefault(Element, String, Object, Convert) + */ + private boolean parseBooleanWithDefault(Element parent, String tagName, boolean defaultValue){ + return parseWithDefault(parent, tagName, defaultValue, convertBoolean); + } + + private ChomboSolverSpec getChomboSolverSpec(SolverTaskDescription solverTaskDesc, Element element, int dimension) throws XmlParseException{ + int maxBoxSize = parseIntWithDefault(element, XMLTags.MaxBoxSizeTag, ChomboSolverSpec.getDefaultMaxBoxSize(dimension)); + double fillRatio = parseDoubleWithDefault(element, XMLTags.FillRatioTag, ChomboSolverSpec.getDefaultFillRatio()); + boolean bSaveVCellOutput = parseBooleanWithDefault(element, XMLTags.SaveVCellOutput, true); + boolean bSaveChomboOutput = parseBooleanWithDefault(element, XMLTags.SaveChomboOutput, false); + Element childElement = element.getChild(XMLTags.RefineRatios, vcNamespace); + List refineRatioList = null; + if(childElement != null){ + String text = childElement.getText(); + if(text != null && !text.isEmpty()){ + StringTokenizer st = new StringTokenizer(text, ","); + if(st.hasMoreTokens()){ + refineRatioList = new ArrayList(); + while (st.hasMoreElements()) { + String token = st.nextToken(); + if(token != null){ + int n = Integer.parseInt(token); + refineRatioList.add(n); + } + } + } + } + } + Integer viewLevel = null; + try { + ChomboSolverSpec css = new ChomboSolverSpec(maxBoxSize, fillRatio, viewLevel, bSaveVCellOutput, bSaveChomboOutput, refineRatioList); + double smallVolfracThreshold = parseDoubleWithDefault(element, XMLTags.SmallVolfracThreshold, 0); + int blockFactor = parseIntWithDefault(element, XMLTags.BlockFactorTag, ChomboSolverSpec.DEFAULT_BLOCK_FACTOR); + boolean bActivateFeatureUnderDevelopment = parseBooleanWithDefault(element, XMLTags.ActivateFeatureUnderDevelopment, false); + css.setSmallVolfracThreshold(smallVolfracThreshold); + css.setActivateFeatureUnderDevelopment(bActivateFeatureUnderDevelopment); + css.setBlockFactor(blockFactor); + + int tagsGrow = parseIntWithDefault(element, XMLTags.TagsGrowTag, ChomboSolverSpec.defaultTagsGrow); + css.setTagsGrow(tagsGrow); + + Element timeBoundsElement = element.getChild(XMLTags.TimeBoundTag, vcNamespace); + List timeIntervalElementList = null; + boolean noTimeBounds = false; + if(timeBoundsElement == null){ + noTimeBounds = true; + } else { + timeIntervalElementList = timeBoundsElement.getChildren(XMLTags.TimeIntervalTag, vcNamespace); + if(timeIntervalElementList.size() == 0){ + noTimeBounds = true; + } + } + + if(noTimeBounds){ + // old format + double startTime = 0; + double endTime = solverTaskDesc.getTimeBounds().getEndingTime(); + double timeStep = solverTaskDesc.getTimeStep().getDefaultTimeStep(); + double outputTimeStep = ((UniformOutputTimeSpec) solverTaskDesc.getOutputTimeSpec()).getOutputTimeStep(); + try { + TimeInterval ti = new TimeInterval(startTime, endTime, timeStep, outputTimeStep); + css.addTimeInterval(ti); + } catch(IllegalArgumentException ex){ + css.addTimeInterval(TimeInterval.getDefaultTimeInterval()); + } + } else { + for(Element e : timeIntervalElementList){ + String s = e.getAttributeValue(XMLTags.StartTimeAttrTag); + double startTime = Double.valueOf(s); + + s = e.getAttributeValue(XMLTags.EndTimeAttrTag); + double endTime = Double.valueOf(s); + + s = e.getAttributeValue(XMLTags.TimeStepAttrTag); + double timeStep = Double.valueOf(s); + + s = e.getAttributeValue(XMLTags.OutputTimeStepAttrTag); + double outputTimeStep = Double.valueOf(s); + TimeInterval ti = new TimeInterval(startTime, endTime, timeStep, outputTimeStep); + css.addTimeInterval(ti); + } + } + + Element meshRefineElement = element.getChild(XMLTags.MeshRefinementTag, vcNamespace); + if(meshRefineElement != null){ + if(meshRefineElement.getChildren().size() != 0){ + // in old model, if there is no refinement, set view level to finest + // only set viewLevel when meshRefinement has children + Element viewLevelChild = element.getChild(XMLTags.ViewLevelTag, vcNamespace); + if(viewLevelChild != null){ + viewLevel = parseIntWithDefault(element, XMLTags.ViewLevelTag, 0); + css.setViewLevel(viewLevel); + } + } + List levelElementList = meshRefineElement.getChildren(XMLTags.RefinementRoiTag, vcNamespace); + for(Element levelElement : levelElementList){ + String levelStr = levelElement.getAttributeValue(XMLTags.RefineRoiLevelAttrTag); + int level = 1; + if(levelStr != null){ + level = Integer.parseInt(levelStr); + } + String type = levelElement.getAttributeValue(XMLTags.RefinementRoiTypeAttrTag); + RoiType roiType = RoiType.Membrane; + if(type != null){ + try { + roiType = RoiType.valueOf(type); + } catch(Exception ex){ + // ignore + } + } + + Element expElement = levelElement.getChild(XMLTags.ROIExpressionTag, vcNamespace); + String roiExp = null; + if(expElement != null){ + roiExp = expElement.getText(); + RefinementRoi roi = new RefinementRoi(roiType, level, roiExp); + css.addRefinementRoi(roi); + } + } + } + return css; + } catch(ExpressionException e){ + throw new XmlParseException(e); + } + } + + private MovingBoundarySolverOptions getMovingBoundarySolverOptions(SolverTaskDescription solverTaskDesc, + Element mbElement){ + double frontToNodeRatio = parseDoubleWithDefault(mbElement, XMLTags.FrontToNodeRatioTag, + MovingBoundarySolverOptions.DEFAULT_FRONT_TO_NODE_RATIO); + int redistributionFrequency = parseIntWithDefault(mbElement, XMLTags.RedistributionFrequencyTag, + MovingBoundarySolverOptions.DEFAULT_REDISTRIBUTION_FREQUENCY); + + RedistributionMode redistributionMode = RedistributionMode.FULL_REDIST; + Element child = mbElement.getChild(XMLTags.RedistributionModeTag, vcNamespace); + if(child != null){ + String text = child.getText(); + redistributionMode = RedistributionMode.valueOf(text); + } + RedistributionVersion redistributionVersion = RedistributionVersion.EQUI_BOND_REDISTRIBUTE; + child = mbElement.getChild(XMLTags.RedistributionVersionTag, vcNamespace); + if(child != null){ + String text = child.getText(); + redistributionVersion = RedistributionVersion.valueOf(text); + } + ExtrapolationMethod extrapolationMethod = ExtrapolationMethod.NEAREST_NEIGHBOR; + child = mbElement.getChild(XMLTags.ExtrapolationMethodTag, vcNamespace); + if(child != null){ + String text = child.getText(); + extrapolationMethod = ExtrapolationMethod.valueOf(text); + } + MovingBoundarySolverOptions mb = new MovingBoundarySolverOptions(frontToNodeRatio, redistributionMode, redistributionVersion, redistributionFrequency, extrapolationMethod); + return mb; + } +} diff --git a/vcell-core/src/test/java/cbit/vcell/xml/XmlGeometrySharingBenchmark.java b/vcell-core/src/test/java/cbit/vcell/xml/XmlGeometrySharingBenchmark.java new file mode 100644 index 0000000000..d6efd44a23 --- /dev/null +++ b/vcell-core/src/test/java/cbit/vcell/xml/XmlGeometrySharingBenchmark.java @@ -0,0 +1,182 @@ +package cbit.vcell.xml; + +import cbit.image.VCImageUncompressed; +import cbit.vcell.biomodel.BioModel; +import cbit.vcell.geometry.Geometry; +import cbit.vcell.geometry.GeometryThumbnailImageFactoryAWT; +import cbit.vcell.geometry.ImageSubVolume; +import cbit.vcell.geometry.SubVolume; +import cbit.vcell.geometry.SurfaceClass; +import cbit.vcell.mapping.GeometryContext; +import cbit.vcell.mapping.SimulationContext; +import cbit.vcell.model.Model; +import cbit.vcell.model.ModelTest; +import cbit.vcell.model.Structure; +import cbit.vcell.parser.Expression; +import org.vcell.util.Extent; +import org.vcell.util.Origin; + +import java.lang.management.ManagementFactory; +import java.lang.management.MemoryPoolMXBean; +import java.lang.management.MemoryType; +import java.util.ArrayList; +import java.util.List; + +/** + * What sharing identical {@code } elements is worth, measured rather than argued. + * + * Builds a BioModel with N spatial applications over ONE image geometry -- the shape of the model + * in #2021, where Xmlproducer writes a full copy of the geometry inside every SimulationContext -- + * serialises it to VCML, and parses it back with sharing on and off. + * + * Run (after {@code mvn test-compile -pl vcell-core -am}): + * + * 
+ *   mvn -q -pl vcell-core exec:java -Dexec.classpathScope=test \
+ *       -Dexec.mainClass=cbit.vcell.xml.XmlGeometrySharingBenchmark
+ *
+ * + * Args: {@code }, default {@code 128 6}. Pixels is edge². Keep it modest: + * the OFF case is the one that OOMs, which is the whole point. + */ +public class XmlGeometrySharingBenchmark { + + private static final List HEAP_POOLS = new ArrayList<>(); + + static { + for (MemoryPoolMXBean pool : ManagementFactory.getMemoryPoolMXBeans()) { + if (pool.getType() == MemoryType.HEAP) HEAP_POOLS.add(pool); + } + } + + private static void resetPeaks() { + for (MemoryPoolMXBean pool : HEAP_POOLS) pool.resetPeakUsage(); + } + + private static long peakHeap() { + long total = 0; + for (MemoryPoolMXBean pool : HEAP_POOLS) total += pool.getPeakUsage().getUsed(); + return total; + } + + private static long liveBytes() { + for (int i = 0; i < 4; i++) { + System.gc(); + try { + Thread.sleep(60); + } catch (InterruptedException e) { + Thread.currentThread().interrupt(); + } + } + Runtime rt = Runtime.getRuntime(); + return rt.totalMemory() - rt.freeMemory(); + } + + private static String fmt(long bytes) { + if (Math.abs(bytes) > 1024 * 1024) return String.format("%,.1f MB", bytes / (1024.0 * 1024.0)); + if (Math.abs(bytes) > 1024) return String.format("%,.1f KB", bytes / 1024.0); + return bytes + " B"; + } + + /** A 2D two-subvolume image: the cheapest thing that still produces real regions and surfaces. */ + private static Geometry imageGeometry(int edge) throws Exception { + byte[] pixels = new byte[edge * edge]; + for (int y = 0; y < edge; y++) { + for (int x = 0; x < edge; x++) { + pixels[x + edge * y] = (byte) (x > edge / 2 ? 50 : 100); + } + } + VCImageUncompressed image = new VCImageUncompressed(null, pixels, new Extent(10, 10, 1), edge, edge, 1); + Geometry geometry = new Geometry("benchmark_geometry", image); + geometry.getGeometrySpec().setOrigin(new Origin(-5, -5, -5)); + ImageSubVolume cytosol = geometry.getGeometrySpec().getImageSubVolumeFromPixelValue(50); + cytosol.setName("cytosol"); + ImageSubVolume ec = geometry.getGeometrySpec().getImageSubVolumeFromPixelValue(100); + ec.setName("ec"); + geometry.precomputeAll(new GeometryThumbnailImageFactoryAWT(), true, false); + return geometry; + } + + private static String vcmlWithNApplications(int edge, int numApplications) throws Exception { + BioModel bioModel = new BioModel(null); + bioModel.setName("benchmark"); + bioModel.setModel(ModelTest.getExample_Wagner_simple(false)); + Model model = bioModel.getModel(); + Geometry geometry = imageGeometry(edge); + + SubVolume cytosol = geometry.getGeometrySpec().getSubVolume("cytosol"); + SubVolume ec = geometry.getGeometrySpec().getSubVolume("ec"); + SurfaceClass pm = geometry.getGeometrySurfaceDescription().getSurfaceClass(cytosol, ec); + + SimulationContext[] apps = new SimulationContext[numApplications]; + for (int i = 0; i < numApplications; i++) { + SimulationContext simContext = new SimulationContext(model, geometry, null, null, + SimulationContext.Application.NETWORK_DETERMINISTIC); + simContext.setName("application_" + i); + GeometryContext geoContext = simContext.getGeometryContext(); + Structure ecStruct = model.getStructure("extracellular"); + Structure cytStruct = model.getStructure("cytosol"); + Structure pmStruct = model.getStructure("plasmaMembrane"); + geoContext.assignStructure(ecStruct, ec); + geoContext.getStructureMapping(ecStruct).getUnitSizeParameter().setExpression(new Expression(1.0)); + geoContext.assignStructure(cytStruct, cytosol); + geoContext.getStructureMapping(cytStruct).getUnitSizeParameter().setExpression(new Expression(0.5)); + geoContext.assignStructure(pmStruct, pm); + geoContext.getStructureMapping(pmStruct).getUnitSizeParameter().setExpression(new Expression(1.0)); + apps[i] = simContext; + } + bioModel.setSimulationContexts(apps); + return XmlHelper.bioModelToXML(bioModel); + } + + private static void measure(String label, String vcml, boolean shareImages, boolean shareGeometries) + throws Exception { + System.setProperty(XmlReader.PROPERTY_SHARE_IDENTICAL_IMAGES, Boolean.toString(shareImages)); + System.setProperty(XmlReader.PROPERTY_SHARE_IDENTICAL_GEOMETRIES, Boolean.toString(shareGeometries)); + long before = liveBytes(); + resetPeaks(); + long t0 = System.currentTimeMillis(); + + BioModel parsed = XmlHelper.XMLToBioModel(new XMLSource(vcml)); + + long millis = System.currentTimeMillis() - t0; + long peak = peakHeap(); + long retained = liveBytes() - before; + + // Identity counts, not equality counts: the whole question is how many OBJECTS exist. + java.util.IdentityHashMap geometries = new java.util.IdentityHashMap<>(); + java.util.IdentityHashMap images = new java.util.IdentityHashMap<>(); + for (SimulationContext sc : parsed.getSimulationContexts()) { + geometries.put(sc.getGeometry(), null); + if (sc.getGeometry().getGeometrySpec().getImage() != null) { + images.put(sc.getGeometry().getGeometrySpec().getImage(), null); + } + } + + System.out.printf("%-26s peak %11s retained %11s %5d ms Geometry objects: %-3d VCImage objects: %d%n", + label, fmt(peak), fmt(retained), millis, geometries.size(), images.size()); + + if (parsed.hashCode() == Integer.MIN_VALUE) System.out.println(parsed); // keep reachable + } + + public static void main(String[] args) throws Exception { + int edge = args.length > 0 ? Integer.parseInt(args[0]) : 128; + int numApplications = args.length > 1 ? Integer.parseInt(args[1]) : 6; + + String vcml = vcmlWithNApplications(edge, numApplications); + System.out.printf("max heap %s; %d applications over one %d x %d image; VCML %s%n%n", + fmt(Runtime.getRuntime().maxMemory()), numApplications, edge, edge, + fmt(vcml.length())); + + // Warm up class loading and JIT, or the first measured parse absorbs both. + measure("(warmup, ignore)", vcml, false, false); + System.out.println(); + + measure("share nothing (before)", vcml, false, false); + measure("share images only", vcml, true, false); + measure("share whole geometries", vcml, true, true); + + System.clearProperty(XmlReader.PROPERTY_SHARE_IDENTICAL_IMAGES); + System.clearProperty(XmlReader.PROPERTY_SHARE_IDENTICAL_GEOMETRIES); + } +} diff --git a/vcell-core/src/test/java/cbit/vcell/xml/XmlReaderGeometrySharingTest.java b/vcell-core/src/test/java/cbit/vcell/xml/XmlReaderGeometrySharingTest.java new file mode 100644 index 0000000000..c1062c24da --- /dev/null +++ b/vcell-core/src/test/java/cbit/vcell/xml/XmlReaderGeometrySharingTest.java @@ -0,0 +1,208 @@ +package cbit.vcell.xml; + +import cbit.image.VCImage; +import cbit.vcell.biomodel.BioModel; +import cbit.vcell.geometry.Geometry; +import cbit.vcell.geometry.GeometryTest; +import cbit.vcell.geometry.GeometryThumbnailImageFactoryAWT; +import cbit.vcell.geometry.SubVolume; +import cbit.vcell.geometry.SurfaceClass; +import cbit.vcell.mapping.GeometryContext; +import cbit.vcell.mapping.SimulationContext; +import cbit.vcell.model.Model; +import cbit.vcell.model.ModelTest; +import cbit.vcell.model.Structure; +import cbit.vcell.parser.Expression; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.Tag; +import org.junit.jupiter.api.Test; + +import static org.junit.jupiter.api.Assertions.*; + +/** + * A BioModel stores a full copy of its geometry -- image included -- inside EVERY + * {@code } (see {@code Xmlproducer.getXML(SimulationContext)}), so a model with + * N spatial applications on one geometry decodes the same image N times and retains N copies of the + * pixels. For the model in #2021 that is 62 MB of pixels eleven times over, against a 1000 MB heap. + * + * The fix shares the decoded {@link VCImage} and NOT the {@link Geometry}. That distinction is the + * point of this class: a VCImage is immutable payload, while a Geometry is mutable, and five + * applications sharing one Geometry would see each other's subvolume renames and geometry edits. + * Measurement says sharing images alone captures the entire win, so there is nothing to trade. + */ +@Tag("Fast") +public class XmlReaderGeometrySharingTest { + + @AfterEach + public void clearOverrides() { + System.clearProperty(XmlReader.PROPERTY_SHARE_IDENTICAL_IMAGES); + System.clearProperty(XmlReader.PROPERTY_SHARE_IDENTICAL_GEOMETRIES); + } + + /** + * Two applications over one geometry object, which is what makes Xmlproducer write two + * identical {@code } elements -- the shape of the model in #2021. + */ + private static BioModel twoApplicationsOnOneGeometry() throws Exception { + BioModel bioModel = new BioModel(null); + bioModel.setName("twoAppsOneGeometry"); + bioModel.setModel(ModelTest.getExample_Wagner_simple(false)); + Model model = bioModel.getModel(); + + Geometry geometry = GeometryTest.getImageExample2D(); + geometry.setName("shared_image_geometry"); + geometry.precomputeAll(new GeometryThumbnailImageFactoryAWT(), true, false); + + bioModel.setSimulationContexts(new SimulationContext[]{ + newSpatialApplication(model, geometry, "application_one"), + newSpatialApplication(model, geometry, "application_two")}); + return bioModel; + } + + private static SimulationContext newSpatialApplication(Model model, Geometry geometry, String name) + throws Exception { + SimulationContext simContext = new SimulationContext(model, geometry, null, null, + SimulationContext.Application.NETWORK_DETERMINISTIC); + simContext.setName(name); + + SubVolume cytosol = geometry.getGeometrySpec().getSubVolume("cytosol"); + SubVolume ec = geometry.getGeometrySpec().getSubVolume("ec"); + SurfaceClass pm = geometry.getGeometrySurfaceDescription().getSurfaceClass(cytosol, ec); + + GeometryContext geoContext = simContext.getGeometryContext(); + Structure structure_ec = model.getStructure("extracellular"); + Structure structure_cyt = model.getStructure("cytosol"); + Structure structure_pm = model.getStructure("plasmaMembrane"); + + geoContext.assignStructure(structure_ec, ec); + geoContext.getStructureMapping(structure_ec).getUnitSizeParameter().setExpression(new Expression(1.0)); + geoContext.assignStructure(structure_cyt, cytosol); + geoContext.getStructureMapping(structure_cyt).getUnitSizeParameter().setExpression(new Expression(0.5)); + geoContext.assignStructure(structure_pm, pm); + geoContext.getStructureMapping(structure_pm).getUnitSizeParameter().setExpression(new Expression(1.0)); + return simContext; + } + + private static BioModel roundTrip(BioModel bioModel) throws Exception { + return XmlHelper.XMLToBioModel(new XMLSource(XmlHelper.bioModelToXML(bioModel))); + } + + // ---- the default: share the image, never the geometry --------------------------------- + + @Test + public void identicalImagesAreDecodedOnce() throws Exception { + BioModel parsed = roundTrip(twoApplicationsOnOneGeometry()); + assertEquals(2, parsed.getNumSimulationContexts()); + + VCImage first = parsed.getSimulationContext(0).getGeometry().getGeometrySpec().getImage(); + VCImage second = parsed.getSimulationContext(1).getGeometry().getGeometrySpec().getImage(); + + assertSame(first, second, + "two applications over one image must share the decoded VCImage, not each retain a copy"); + } + + /** + * The safety guarantee, and the reason this fix shares images rather than geometries: editing + * one application's geometry must not change another's. If Geometry objects were shared, a + * subvolume rename in one application would silently appear in all of them. + */ + @Test + public void eachApplicationKeepsItsOwnGeometry() throws Exception { + BioModel parsed = roundTrip(twoApplicationsOnOneGeometry()); + Geometry first = parsed.getSimulationContext(0).getGeometry(); + Geometry second = parsed.getSimulationContext(1).getGeometry(); + + assertNotSame(first, second, "applications must NOT share a mutable Geometry by default"); + assertNotSame(first.getGeometrySpec(), second.getGeometrySpec()); + assertNotSame(first.getGeometrySpec().getSubVolume("cytosol"), + second.getGeometrySpec().getSubVolume("cytosol"), + "subvolumes must be private to each application, or renames would leak between them"); + + // Demonstrate it rather than assert it structurally: rename in one, check the other. + first.getGeometrySpec().getSubVolume("cytosol").setName("renamed_in_app_one"); + assertNotNull(second.getGeometrySpec().getSubVolume("cytosol"), + "renaming a subvolume in one application must not rename it in another"); + assertNull(second.getGeometrySpec().getSubVolume("renamed_in_app_one")); + } + + @Test + public void sharingAnImageDoesNotLoseItsContent() throws Exception { + BioModel parsed = roundTrip(twoApplicationsOnOneGeometry()); + // The SECOND application is the one served from the cache, so check that one: a cache + // returning something half-built would show up here and nowhere else. + Geometry geometry = parsed.getSimulationContext(1).getGeometry(); + + assertEquals("shared_image_geometry", geometry.getName()); + assertEquals(2, geometry.getDimension()); + VCImage image = geometry.getGeometrySpec().getImage(); + assertNotNull(image); + assertEquals(100, image.getNumX()); + assertEquals(100, image.getNumY()); + assertEquals(2, image.getNumPixelClasses()); + assertNotNull(geometry.getGeometrySpec().getSubVolume("cytosol")); + assertNotNull(geometry.getGeometrySpec().getSubVolume("ec")); + } + + /** + * The negative control. If this fails while {@link #identicalImagesAreDecodedOnce} passes, the + * cache key has stopped discriminating and unrelated images are being conflated -- far worse + * than the memory problem being solved. + */ + @Test + public void differentImagesAreNotShared() throws Exception { + BioModel bioModel = new BioModel(null); + bioModel.setName("twoAppsTwoGeometries"); + bioModel.setModel(ModelTest.getExample_Wagner_simple(false)); + Model model = bioModel.getModel(); + + Geometry geometryOne = GeometryTest.getImageExample2D(); + geometryOne.setName("geometry_one"); + geometryOne.getGeometrySpec().getImage().setName("image_one"); + geometryOne.precomputeAll(new GeometryThumbnailImageFactoryAWT(), true, false); + + Geometry geometryTwo = GeometryTest.getImageExample2D(); + geometryTwo.setName("geometry_two"); + geometryTwo.getGeometrySpec().getImage().setName("image_two"); + geometryTwo.precomputeAll(new GeometryThumbnailImageFactoryAWT(), true, false); + + bioModel.setSimulationContexts(new SimulationContext[]{ + newSpatialApplication(model, geometryOne, "application_one"), + newSpatialApplication(model, geometryTwo, "application_two")}); + + BioModel parsed = roundTrip(bioModel); + assertNotSame(parsed.getSimulationContext(0).getGeometry().getGeometrySpec().getImage(), + parsed.getSimulationContext(1).getGeometry().getGeometrySpec().getImage(), + "images that differ must NOT be conflated"); + assertEquals("geometry_one", parsed.getSimulationContext(0).getGeometry().getName()); + assertEquals("geometry_two", parsed.getSimulationContext(1).getGeometry().getName()); + } + + @Test + public void imageSharingCanBeSwitchedOff() throws Exception { + System.setProperty(XmlReader.PROPERTY_SHARE_IDENTICAL_IMAGES, "false"); + BioModel parsed = roundTrip(twoApplicationsOnOneGeometry()); + + assertNotSame(parsed.getSimulationContext(0).getGeometry().getGeometrySpec().getImage(), + parsed.getSimulationContext(1).getGeometry().getGeometrySpec().getImage(), + "the escape hatch must restore the old one-VCImage-per-application behaviour"); + } + + // ---- geometry sharing: opt-in only ---------------------------------------------------- + + /** + * Geometry sharing exists for read-only consumers -- a server that parses a document to + * serialise it or to generate math, and never edits it. It must stay OFF unless asked for, + * because a shared Geometry is a shared mutable object. + */ + @Test + public void geometrySharingIsOffUnlessAskedFor() throws Exception { + assertNotSame(roundTrip(twoApplicationsOnOneGeometry()).getSimulationContext(0).getGeometry(), + roundTrip(twoApplicationsOnOneGeometry()).getSimulationContext(1).getGeometry()); + + System.setProperty(XmlReader.PROPERTY_SHARE_IDENTICAL_GEOMETRIES, "true"); + BioModel parsed = roundTrip(twoApplicationsOnOneGeometry()); + assertSame(parsed.getSimulationContext(0).getGeometry(), + parsed.getSimulationContext(1).getGeometry(), + "enabling the property must actually share the Geometry"); + } +}