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

Example 76 with Model

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

the class StructureAnalyzer method refreshTotalSpeciesContextMappings.

/**
 * This method was created in VisualAge.
 */
private void refreshTotalSpeciesContextMappings() throws java.beans.PropertyVetoException {
    if (structures == null) {
        return;
    }
    // System.out.println("StructureAnalyzer.refreshSpeciesContextMappings()");
    // GeometryContext geoContext = mathMapping.getSimulationContext().getGeometryContext();
    Model model = mathMapping_4_8.getSimulationContext().getReactionContext().getModel();
    // 
    // note, the order of species is specified such that the first species have priority
    // when the null space is solved for dependent variables.  So the order of priority
    // for elimination are as follows:
    // 
    // 1) Species involved with fast reactions.
    // 2) Species not involved with fast reactions.
    // 
    Vector<SpeciesContextMapping> scmList = new Vector<SpeciesContextMapping>();
    // 
    for (int i = 0; i < structures.length; i++) {
        SpeciesContext[] speciesContexts = model.getSpeciesContexts(structures[i]);
        for (int j = 0; j < speciesContexts.length; j++) {
            SpeciesContext sc = speciesContexts[j];
            SpeciesContextMapping scm = mathMapping_4_8.getSpeciesContextMapping(sc);
            SpeciesContextSpec scs = mathMapping_4_8.getSimulationContext().getReactionContext().getSpeciesContextSpec(sc);
            if (scm.isFastParticipant() && !scs.isConstant()) {
                scmList.addElement(scm);
            }
        }
    }
    // 
    for (int i = 0; i < structures.length; i++) {
        SpeciesContext[] speciesContexts = model.getSpeciesContexts(structures[i]);
        for (int j = 0; j < speciesContexts.length; j++) {
            SpeciesContext sc = speciesContexts[j];
            SpeciesContextMapping scm = mathMapping_4_8.getSpeciesContextMapping(sc);
            SpeciesContextSpec scs = mathMapping_4_8.getSimulationContext().getReactionContext().getSpeciesContextSpec(sc);
            if (!scm.isFastParticipant() && !scs.isConstant()) {
                scmList.addElement(scm);
            }
        }
    }
    if (scmList.size() > 0) {
        speciesContextMappings = new SpeciesContextMapping[scmList.size()];
        scmList.copyInto(speciesContextMappings);
        for (int i = 0; i < speciesContextMappings.length; i++) {
            speciesContextMappings[i].setRate(new Expression(0.0));
        // System.out.println("speciesContextMappings["+i+"] = "+speciesContextMappings[i].getSpeciesContext().getName());
        }
    } else {
        speciesContextMappings = null;
    }
    // System.out.println("StructureAnalyzer.refreshTotalSpeciesContextMapping(), speciesContextMappings.length = "+scmList.size());
    // 
    // get all reactionSteps associated with these structures
    // 
    Vector<ReactionStep> rsList = new Vector<ReactionStep>();
    ReactionSpec[] allReactionSpecs = mathMapping_4_8.getSimulationContext().getReactionContext().getReactionSpecs();
    for (int i = 0; i < allReactionSpecs.length; i++) {
        if (allReactionSpecs[i].isExcluded()) {
            continue;
        }
        ReactionStep rs = allReactionSpecs[i].getReactionStep();
        for (int j = 0; j < structures.length; j++) {
            if (rs.getStructure() == structures[j]) {
                rsList.addElement(rs);
            }
        }
    }
    // 
    for (int i = 0; i < scmList.size(); i++) {
        SpeciesContextMapping scm = (SpeciesContextMapping) scmList.elementAt(i);
        if (scm.isPDERequired()) {
            rsList.addElement(new DiffusionDummyReactionStep("DiffusionDummyReactionStep" + i, model, scm.getSpeciesContext().getStructure(), scm.getSpeciesContext()));
        }
        if (scm.hasEventAssignment()) {
            rsList.addElement(new EventDummyReactionStep("EventDummyReactionStep" + i, model, scm.getSpeciesContext().getStructure(), scm.getSpeciesContext()));
        }
        if (scm.hasHybridReaction()) {
            rsList.addElement(new HybridDummyReactionStep("HybridDummyReactionStep" + i, model, scm.getSpeciesContext().getStructure(), scm.getSpeciesContext()));
        }
        SimulationContext simContext = mathMapping_4_8.getSimulationContext();
        if (simContext.isStoch() && simContext.getGeometry().getDimension() > 0 && !simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext()).isForceContinuous()) {
            rsList.addElement(new ParticleDummyReactionStep("ParticleDummyReactionStep" + i, model, scm.getSpeciesContext().getStructure(), scm.getSpeciesContext()));
        }
    }
    if (rsList.size() > 0) {
        reactionSteps = new ReactionStep[rsList.size()];
        rsList.copyInto(reactionSteps);
    } else {
        reactionSteps = null;
    }
// System.out.println("StructureAnalyzer.refreshTotalSpeciesContextMapping(), reactionSteps.length = "+scmList.size());
}

Example 77 with Model

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

the class GeometryContext method setModel.

/**
 * Sets the model property (cbit.vcell.model.Model) value.
 * @param model The new value for the property.
 * @see #getModel
 */
public void setModel(Model model) throws MappingException {
    Model oldValue = fieldModel;
    fieldModel = model;
    try {
        refreshStructureMappings();
        refreshDependencies();
    } catch (PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new MappingException(e.getMessage());
    }
    firePropertyChange("model", oldValue, model);
}

Example 78 with Model

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

the class ReactionContext method setModel.

/**
 * Sets the model property (cbit.vcell.model.Model) value.
 * @param model The new value for the property.
 * @see #getModel
 */
public void setModel(Model model) throws MappingException, java.beans.PropertyVetoException {
    Model oldValue = fieldModel;
    fieldModel = model;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(this);
        oldValue.removeVetoableChangeListener(this);
    }
    if (fieldModel != null) {
        fieldModel.addPropertyChangeListener(this);
        fieldModel.addVetoableChangeListener(this);
    }
    refreshSpeciesContextSpecs();
    refreshReactionSpecs();
    refreshReactionRuleSpecs();
    firePropertyChange("model", oldValue, model);
}

Example 79 with Model

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

the class RulebasedTransformer method transform.

@Override
public final RulebasedTransformation transform(SimulationContext originalSimContext, MathMappingCallback mathMappingCallback, NetworkGenerationRequirements netGenReq_NOT_USED) {
    SimulationContext transformedSimContext;
    keyMap.clear();
    try {
        transformedSimContext = (SimulationContext) BeanUtils.cloneSerializable(originalSimContext);
        transformedSimContext.getModel().refreshDependencies();
        transformedSimContext.refreshDependencies();
        transformedSimContext.compareEqual(originalSimContext);
    } catch (ClassNotFoundException | IOException e) {
        e.printStackTrace();
        throw new RuntimeException("Unexpected transform exception: " + e.getMessage());
    }
    final Model transformedModel = transformedSimContext.getModel();
    transformedModel.refreshDependencies();
    transformedSimContext.refreshDependencies1(false);
    ArrayList<ModelEntityMapping> entityMappings = new ArrayList<ModelEntityMapping>();
    try {
        transform(originalSimContext, transformedSimContext, entityMappings, mathMappingCallback);
    } catch (PropertyVetoException e) {
        e.printStackTrace();
        throw new RuntimeException("Unexpected transform exception: " + e.getMessage());
    }
    ModelEntityMapping[] modelEntityMappings = entityMappings.toArray(new ModelEntityMapping[0]);
    return new RulebasedTransformation(originalSimContext, transformedSimContext, modelEntityMappings, ruleElementMap, rulesForwardMap, rulesReverseMap);
}

Example 80 with Model

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

the class BioModelEditorModelPanel method addNewReaction.

private void addNewReaction() {
    if (reactionEditorPanel == null) {
        reactionEditorPanel = new ReactionEditorPanel();
    }
    Model model = getModel();
    reactionEditorPanel.setModel(model);
    while (true) {
        int confirm = DialogUtils.showComponentOKCancelDialog(this, reactionEditorPanel, "New Reaction");
        if (confirm == javax.swing.JOptionPane.OK_OPTION) {
            Structure reactionStructure = reactionEditorPanel.getStructure();
            String reactionName = reactionEditorPanel.getReactionName();
            String equationString = reactionEditorPanel.getEquationString();
            try {
                if (reactionName == null || reactionName.trim().length() == 0 || equationString == null || equationString.trim().length() == 0) {
                    throw new RuntimeException("Reaction name or equation cannot be empty.");
                }
                if (getModel().getReactionStep(reactionName) != null) {
                    throw new RuntimeException("Reaction '" + reactionName + "' already exists.");
                }
                ReactionStep simpleReaction = new SimpleReaction(model, reactionStructure, "dummy", true);
                ReactionParticipant[] rpArray = ModelProcessEquation.parseReaction(simpleReaction, getModel(), equationString);
                // StructureTopology structTopology = getModel().getStructureTopology();
                // for (ReactionParticipant reactionParticipant : rpArray) {
                // if (reactionParticipant.getStructure() == reactionStructure) {
                // continue;
                // }
                // if (reactionStructure instanceof Feature) {
                // throw new RuntimeException("Species '" + reactionParticipant.getSpeciesContext().getName() + "' must be in the same volume compartment as reaction.");
                // } else if (reactionStructure instanceof Membrane) {
                // if (structTopology.getInsideFeature((Membrane)reactionStructure) != reactionParticipant.getStructure()
                // && (structTopology.getOutsideFeature((Membrane)reactionStructure)) != reactionParticipant.getStructure()) {
                // throw new RuntimeException("Species '" + reactionParticipant.getSpeciesContext().getName() + "' must be adjacent to " +
                // "or within reaction's structure '" + reactionStructure.getName() + "'.");
                // }
                // }
                // }
                simpleReaction = getModel().createSimpleReaction(reactionStructure);
                for (ReactionParticipant rp : rpArray) {
                    SpeciesContext speciesContext = rp.getSpeciesContext();
                    if (bioModel.getModel().getSpeciesContext(speciesContext.getName()) == null) {
                        bioModel.getModel().addSpecies(speciesContext.getSpecies());
                        bioModel.getModel().addSpeciesContext(speciesContext);
                    }
                }
                simpleReaction.setReactionParticipants(rpArray);
                simpleReaction.setName(reactionName);
                setSelectedObjects(new Object[] { simpleReaction });
                break;
            } catch (Exception e) {
                e.printStackTrace();
                DialogUtils.showErrorDialog(this, e.getMessage());
            }
        } else {
            break;
        }
    }
}