Examples with Model cbit.vcell.model.Model used on opensource projects

Example 81 with Model

use of cbit.vcell.model.Model in project vcell by virtualcell.

the class BioModelEditorConversionTableModel method createTableRowForTransportParticipant.

private ConversionTableRow createTableRowForTransportParticipant(BioPaxObject bpObject, String interactionId, String interactionLabel, String participantType, double stoich, HashSet<RelationshipObject> relationshipObjects) {
    String location = "";
    ConversionTableRow conversionTableRow = new ConversionTableRow(bpObject);
    conversionTableRow.setInteractionId(interactionId);
    conversionTableRow.setInteractionLabel(interactionLabel);
    conversionTableRow.setParticipantType(participantType);
    // stoichiometry and location
    Model model = bioModel.getModel();
    StructureTopology structTopology = model.getStructureTopology();
    if (participantType.equals("Reactant")) {
        // stoichiometry
        if (stoich != 0)
            conversionTableRow.setStoich(stoich);
        else
            conversionTableRow.setStoich(1.0);
        // else{
        if (model.getMembranes().size() > 0)
            location = structTopology.getOutsideFeature(model.getMembranes().get(0)).getName();
        else
            location = model.getStructures()[0].getName();
        // }
        conversionTableRow.setLocation(location);
    } else if (participantType.equals("Product")) {
        // stoichiometry
        if (stoich != 0)
            conversionTableRow.setStoich(stoich);
        else
            conversionTableRow.setStoich(1.0);
        // else{
        if (model.getMembranes().size() > 0)
            location = structTopology.getInsideFeature(model.getMembranes().get(0)).getName();
        else
            location = model.getStructures()[0].getName();
        // }
        conversionTableRow.setLocation(location);
    } else {
        conversionTableRow.setStoich(1.0);
        // else
        if (bpObject instanceof Transport) {
            if (model.getMembranes().size() > 0)
                location = model.getMembranes().get(0).getName();
            else
                location = model.getStructures()[0].getName();
        } else
            location = model.getStructures()[0].getName();
        conversionTableRow.setLocation(location);
    }
    // id
    if (relationshipObjects == null) {
        if (bpObject instanceof Entity) {
            String id = (BioPAXUtil.getName((Entity) bpObject) + "_" + location).trim();
            if (isValid(id))
                conversionTableRow.setId(id);
            else
                conversionTableRow.setId(changeID(id));
        }
    } else {
        String id = null;
        for (RelationshipObject relationshipObject : relationshipObjects) {
            if (relationshipObject.getBioModelEntityObject().getStructure().getName().equalsIgnoreCase(location)) {
                id = relationshipObject.getBioModelEntityObject().getName();
            }
        }
        if (id != null) {
            // the linked bmObject with the same location will be used
            conversionTableRow.setId(id);
        } else {
            // a new bmObject will be created if no linked bmObject in the same location
            if (bpObject instanceof Entity) {
                id = (BioPAXUtil.getName((Entity) bpObject) + "_" + location).trim();
                if (isValid(id))
                    conversionTableRow.setId(id);
                else
                    conversionTableRow.setId(changeID(id));
            }
        }
    }
    return conversionTableRow;
}

Example 82 with Model

use of cbit.vcell.model.Model in project vcell by virtualcell.

the class BioModelEditorModelPanel method duplicateReactionRule.

private ReactionRule duplicateReactionRule(ReactionRule oldRule, Structure structure) {
    try {
        ReactionRule newRule = ReactionRule.duplicate(oldRule, structure);
        Model m = oldRule.getModel();
        m.getRbmModelContainer().addReactionRule(newRule);
        return newRule;
    } catch (PropertyVetoException | ExpressionBindingException e) {
        e.printStackTrace();
        throw new RuntimeException("Problem duplicating " + ReactionRule.typeName + " " + oldRule.getDisplayName());
    }
}

Example 83 with Model

use of cbit.vcell.model.Model in project vcell by virtualcell.

the class XmlReader method getBioModel.

/**
 * This method returns a Biomodel object from a XML Element.
 * Creation date: (3/13/2001 12:35:00 PM)
 * @return cbit.vcell.biomodel.BioModel
 * @param param org.jdom.Element
 */
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) {
        e.printStackTrace();
        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<Element> children = param.getChildren(XMLTags.SimulationSpecTag, vcNamespace);
    java.util.Iterator<Element> iterator = children.iterator();
    // System.out.println("model-------- "+((double)(l3-l2))/1000);
    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) {
            e.printStackTrace();
            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<Element> simIterator = tempElement.getChildren(XMLTags.SimulationTag, vcNamespace).iterator();
        // System.out.println("simcontext-------- "+((double)(l5-l4))/1000);
        while (simIterator.hasNext()) {
            try {
                biomodel.addSimulation(getSimulation((Element) simIterator.next(), simContext.getMathDescription()));
            } catch (java.beans.PropertyVetoException e) {
                e.printStackTrace();
                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<Element> 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);
            // ??? is this needed ???
            pathwayModel.reconcileReferences(null);
            // 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;
}

Example 84 with Model

use of cbit.vcell.model.Model in project vcell by virtualcell.

the class XmlReader method getModel.

/**
 * This method creates a Model object from a XML element.
 * Creation date: (3/14/2001 6:14:37 PM)
 * @return cbit.vcell.model.Model
 * @param param org.jdom.Element
 */
private 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));
    // 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<Element> iterator = param.getChildren(XMLTags.SpeciesTag, vcNamespace).iterator();
        ArrayList<Species> speciesList = new ArrayList<Species>();
        while (iterator.hasNext()) {
            org.jdom.Element temp = (Element) iterator.next();
            speciesList.add(getSpecies(temp));
        }
        newmodel.setSpecies(speciesList.toArray(new Species[speciesList.size()]));
        // Add Structures
        LinkedList<Structure> newstructures = new LinkedList<Structure>();
        // (features)
        List<Element> 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.info("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<ReactionStep> reactionStepList = new ArrayList<ReactionStep>();
        while (iterator.hasNext()) {
            org.jdom.Element temp = iterator.next();
            reactionStepList.add(getSimpleReaction(temp, newmodel));
        }
        // (fluxStep)
        iterator = param.getChildren(XMLTags.FluxStepTag, vcNamespace).iterator();
        while (iterator.hasNext()) {
            org.jdom.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<Diagram>() {
            // @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) {
        e.printStackTrace();
        throw new XmlParseException(e);
    } catch (ModelException e) {
        e.printStackTrace();
    }
    // 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) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error binding global parameter '" + modelParameters[i].getName() + "' to model." + e.getMessage());
        }
    }
    return newmodel;
}

Example 85 with Model

use of cbit.vcell.model.Model in project vcell by virtualcell.

the class RbmNetworkGenerator method writeBngl_internal.

public static void writeBngl_internal(SimulationContext simulationContext, PrintWriter writer, Map<FakeReactionRuleRateParameter, LocalParameter> kineticsParameterMap, Map<FakeSeedSpeciesInitialConditionsParameter, Pair<SpeciesContext, Expression>> speciesEquivalenceMap, NetworkGenerationRequirements networkGenerationRequirements, CompartmentMode compartmentMode) {
    String callerClassName = new Exception().getStackTrace()[1].getClassName();
    String networkTransformerClassName = NetworkTransformer.class.getName();
    String rulebasedTransformerClassName = RulebasedTransformer.class.getName();
    if (!callerClassName.equals(networkTransformerClassName) && !callerClassName.equals(rulebasedTransformerClassName)) {
        throw new UnsupportedOperationException("This method may only be called from within a " + networkTransformerClassName + " or " + rulebasedTransformerClassName + " instance.");
    }
    Model model = simulationContext.getModel();
    RbmModelContainer rbmModelContainer = model.getRbmModelContainer();
    checkConsistency(model);
    // first we prepare the fake parameters we need to maintain the relationship between the species context and the seed species
    List<FakeSeedSpeciesInitialConditionsParameter> fakeParameterList = new ArrayList<FakeSeedSpeciesInitialConditionsParameter>();
    List<String> seedSpeciesList = new ArrayList<String>();
    SpeciesContext[] speciesContexts = model.getSpeciesContexts();
    for (int i = 0; i < speciesContexts.length; i++) {
        SpeciesContext sc = speciesContexts[i];
        if (!sc.hasSpeciesPattern()) {
            continue;
        }
        SpeciesContextSpec scs = simulationContext.getReactionContext().getSpeciesContextSpec(sc);
        Expression initialConcentration = scs.getParameter(SpeciesContextSpec.ROLE_InitialConcentration).getExpression();
        // fake initial values for the seed species, we need to present them to bngl as parameters
        FakeSeedSpeciesInitialConditionsParameter fakeSeedSpeciesParam = new FakeSeedSpeciesInitialConditionsParameter(sc.getName());
        Pair<SpeciesContext, Expression> p = new Pair<SpeciesContext, Expression>(sc, initialConcentration);
        speciesEquivalenceMap.put(fakeSeedSpeciesParam, p);
        String modified;
        if (compartmentMode == CompartmentMode.show) {
            modified = RbmUtils.toBnglString(sc.getSpeciesPattern(), null, CompartmentMode.hide, 0);
            modified = "@" + sc.getStructure().getName() + ":" + modified;
        } else if (compartmentMode == CompartmentMode.asSite) {
            modified = RbmUtils.toBnglString(sc.getSpeciesPattern(), sc.getStructure(), CompartmentMode.asSite, 0);
        } else {
            // CompartmentMode.hide
            modified = RbmUtils.toBnglString(sc.getSpeciesPattern(), null, CompartmentMode.hide, 0);
        }
        modified += " " + fakeSeedSpeciesParam.fakeParameterName;
        // we label the seed species with the index
        modified = (i + 1) + " " + modified;
        // we build the seed species list now, we write it later (in the BEGIN SPECIES block)
        seedSpeciesList.add(modified);
        fakeParameterList.add(fakeSeedSpeciesParam);
    }
    // second we produce the bngl file
    writer.println(BEGIN_MODEL);
    writer.println();
    for (ReactionRuleSpec rrs : simulationContext.getReactionContext().getReactionRuleSpecs()) {
        if (!rrs.isExcluded()) {
            ReactionRule reactionRule = rrs.getReactionRule();
            RbmKineticLaw kineticLaw = reactionRule.getKineticLaw();
            switch(kineticLaw.getRateLawType()) {
                case MassAction:
                    {
                        FakeReactionRuleRateParameter fakeRateParameterForward = new FakeReactionRuleRateParameter(reactionRule, RbmKineticLawParameterType.MassActionForwardRate);
                        LocalParameter origForwardRateParameter = kineticLaw.getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate);
                        kineticsParameterMap.put(fakeRateParameterForward, origForwardRateParameter);
                        if (reactionRule.isReversible()) {
                            FakeReactionRuleRateParameter fakeRateParameterReverse = new FakeReactionRuleRateParameter(reactionRule, RbmKineticLawParameterType.MassActionReverseRate);
                            LocalParameter origReverseRateParameter = kineticLaw.getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate);
                            kineticsParameterMap.put(fakeRateParameterReverse, origReverseRateParameter);
                        }
                        break;
                    }
                default:
                    {
                        throw new RuntimeException("kinetic law type " + kineticLaw.getRateLawType().name() + " not yet implemented");
                    }
            }
        }
    }
    if (compartmentMode == CompartmentMode.show) {
        RbmNetworkGenerator.writeCompartments(writer, model, simulationContext);
    }
    writer.println(BEGIN_PARAMETERS);
    // the fake parameters used for reaction rule kinetics
    for (FakeReactionRuleRateParameter p : kineticsParameterMap.keySet()) {
        writer.println(p.fakeParameterName + "\t\t1");
    }
    // the fake parameters used at initial values for the seed species
    for (FakeSeedSpeciesInitialConditionsParameter s : fakeParameterList) {
        writer.println(s.fakeParameterName + "\t\t1");
    }
    writer.println(END_PARAMETERS);
    writer.println();
    RbmNetworkGenerator.writeMolecularTypes(writer, model, compartmentMode);
    // write modified version of seed species while maintaining the connection between the species context and the real seed species
    writer.println(BEGIN_SPECIES);
    for (String s : seedSpeciesList) {
        writer.println(s);
    }
    writer.println(END_SPECIES);
    writer.println();
    RbmNetworkGenerator.writeObservables(writer, rbmModelContainer, compartmentMode);
    RbmNetworkGenerator.writeReactions_internal(writer, simulationContext, compartmentMode);
    writer.println(END_MODEL);
    writer.println();
    if (callerClassName.equals(networkTransformerClassName)) {
        RbmNetworkGenerator.writeNetworkConstraints(writer, rbmModelContainer, simulationContext, networkGenerationRequirements);
    } else if (callerClassName.equals(rulebasedTransformerClassName)) {
        writer.println();
        writer.println("writeXML()");
    }
    writer.println();
}