Examples with Simulation cbit.vcell.solver.Simulation used on opensource projects

Example 31 with Simulation

use of cbit.vcell.solver.Simulation in project vcell by virtualcell.

the class BioModel method propertyChange.

/**
 * This method gets called when a bound property is changed.
 * @param evt A PropertyChangeEvent object describing the event source
 *   	and the property that has changed.
 */
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    // 
    if (evt.getSource() instanceof SimulationContext && evt.getPropertyName().equals("mathDescription") && evt.getNewValue() != null) {
        if (fieldSimulations != null) {
            for (int i = 0; i < fieldSimulations.length; i++) {
                if (fieldSimulations[i].getMathDescription() == evt.getOldValue()) {
                    try {
                        fieldSimulations[i].setMathDescription((MathDescription) evt.getNewValue());
                    } catch (PropertyVetoException e) {
                        System.out.println("error propagating math from SimulationContext '" + ((SimulationContext) evt.getSource()).getName() + "' to Simulation '" + fieldSimulations[i].getName());
                        e.printStackTrace(System.out);
                    }
                }
            }
        }
    }
    // 
    if (evt.getSource() == this && evt.getPropertyName().equals(PropertyConstants.PROPERTY_NAME_SIMULATIONS) && evt.getNewValue() != null) {
        // 
        if (evt.getOldValue() != null) {
            Simulation[] simulations = (Simulation[]) evt.getOldValue();
            for (int i = 0; i < simulations.length; i++) {
                simulations[i].removeVetoableChangeListener(this);
                simulations[i].removePropertyChangeListener(this);
            }
        }
        // 
        if (evt.getOldValue() != null) {
            Simulation[] simulations = (Simulation[]) evt.getNewValue();
            for (int i = 0; i < simulations.length; i++) {
                simulations[i].addVetoableChangeListener(this);
                simulations[i].addPropertyChangeListener(this);
            }
        }
    }
    if (evt.getSource() == this && evt.getPropertyName().equals(PROPERTY_NAME_SIMULATION_CONTEXTS) && evt.getNewValue() != null) {
        // 
        if (evt.getOldValue() != null) {
            SimulationContext[] simulationContexts = (SimulationContext[]) evt.getOldValue();
            for (int i = 0; i < simulationContexts.length; i++) {
                simulationContexts[i].removeVetoableChangeListener(this);
                simulationContexts[i].removePropertyChangeListener(this);
            }
        }
        // 
        if (evt.getOldValue() != null) {
            SimulationContext[] simulationContexts = (SimulationContext[]) evt.getNewValue();
            for (int i = 0; i < simulationContexts.length; i++) {
                simulationContexts[i].addVetoableChangeListener(this);
                simulationContexts[i].addPropertyChangeListener(this);
            }
        }
    }
    if (evt.getSource() == fieldModel && (evt.getPropertyName().equals(Model.PROPERTY_NAME_SPECIES_CONTEXTS) || evt.getPropertyName().equals(Model.PROPERTY_NAME_REACTION_STEPS))) {
        // remove the relationship objects if the biomodelEntity objects were removed
        Set<BioModelEntityObject> removedObjects = relationshipModel.getBioModelEntityObjects();
        for (SpeciesContext sc : fieldModel.getSpeciesContexts()) {
            removedObjects.remove(sc);
        }
        for (ReactionStep rs : fieldModel.getReactionSteps()) {
            removedObjects.remove(rs);
        }
        for (MolecularType mt : fieldModel.getRbmModelContainer().getMolecularTypeList()) {
            removedObjects.remove(mt);
        }
        for (ReactionRule rr : fieldModel.getRbmModelContainer().getReactionRuleList()) {
            removedObjects.remove(rr);
        }
        relationshipModel.removeRelationshipObjects(removedObjects);
    }
    // adjust the relationship model when a molecule gets deleted
    if (evt.getSource() == fieldModel && (evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_MOLECULAR_TYPE_LIST))) {
        @SuppressWarnings("unchecked") List<MolecularType> oldListCopy = new ArrayList<MolecularType>((List<MolecularType>) evt.getOldValue());
        @SuppressWarnings("unchecked") List<MolecularType> newList = (List<MolecularType>) evt.getNewValue();
        if (newList != null && oldListCopy != null && oldListCopy.size() > newList.size()) {
            // something got deleted
            oldListCopy.removeAll(newList);
            for (MolecularType removedMt : oldListCopy) {
                relationshipModel.removeRelationshipObject(removedMt);
            }
        }
    }
    if (evt.getSource() == fieldModel && (evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_REACTION_RULE_LIST))) {
        @SuppressWarnings("unchecked") List<ReactionRule> oldListCopy = new ArrayList<ReactionRule>((List<ReactionRule>) evt.getOldValue());
        @SuppressWarnings("unchecked") List<ReactionRule> newList = (List<ReactionRule>) evt.getNewValue();
        if (newList != null && oldListCopy != null && oldListCopy.size() > newList.size()) {
            // something got deleted
            oldListCopy.removeAll(newList);
            for (ReactionRule removedRr : oldListCopy) {
                relationshipModel.removeRelationshipObject(removedRr);
            }
        }
    }
}

Example 32 with Simulation

use of cbit.vcell.solver.Simulation in project vcell by virtualcell.

the class NfsimExtensionFilter method writeBioModel.

@Override
public void writeBioModel(DocumentManager documentManager, BioModel bioModel, File exportFile, SimulationContext simulationContext) throws Exception {
    // TODO: get the first thing we find for now, in the future we'll need to modify ChooseFile
    // to only offer the applications / simulations with bngl content
    // This should be done by creating one or more additional Selector values and add the filtering logic to ChooseFile
    SimulationContext[] simContexts = bioModel.getSimulationContexts();
    Simulation selectedSim = simulationContext.getSimulations(0);
    // Simulation selectedSim = (Simulation)hashTable.get("selectedSimulation");
    SimulationTask simTask = new SimulationTask(new SimulationJob(selectedSim, 0, null), 0);
    // a fixed seed will allow us to run reproducible simulations
    long randomSeed = 0;
    // long randomSeed = System.currentTimeMillis();
    NFsimSimulationOptions nfsimSimulationOptions = new NFsimSimulationOptions();
    // we get the data we need from the math description
    boolean bUseLocationMarks = true;
    Element root = NFsimXMLWriter.writeNFsimXML(simTask, randomSeed, nfsimSimulationOptions, bUseLocationMarks);
    Document doc = new Document();
    doc.setRootElement(root);
    XMLOutputter xmlOut = new XMLOutputter();
    String resultString = xmlOut.outputString(doc);
    FileUtils.writeStringToFile(exportFile, resultString);
}

Example 33 with Simulation

use of cbit.vcell.solver.Simulation in project vcell by virtualcell.

the class SbmlExtensionFilter method askUser.

@Override
public void askUser(ChooseContext c) throws UserCancelException {
    BioModel bioModel = c.chosenContext.getBioModel();
    JFrame currentWindow = c.currentWindow;
    selectedSimWOSBE = null;
    selectedSimContext = c.chosenContext;
    // get user choice of structure and its size and computes absolute sizes of compartments using the StructureSizeSolver.
    Structure[] structures = bioModel.getModel().getStructures();
    // get the nonspatial simulationContexts corresponding to names in applicableAppNameList
    // This is needed in ApplnSelectionAndStructureSizeInputPanel
    String strucName = null;
    double structSize = 1.0;
    int structSelection = -1;
    int option = JOptionPane.CANCEL_OPTION;
    ApplnSelectionAndStructureSizeInputPanel applnStructInputPanel = null;
    while (structSelection < 0) {
        applnStructInputPanel = new ApplnSelectionAndStructureSizeInputPanel();
        applnStructInputPanel.setSimContext(c.chosenContext);
        applnStructInputPanel.setStructures(structures);
        if (applnStructInputPanel.isNeedStructureSizes()) {
            applnStructInputPanel.setPreferredSize(new java.awt.Dimension(350, 400));
            applnStructInputPanel.setMaximumSize(new java.awt.Dimension(350, 400));
            option = DialogUtils.showComponentOKCancelDialog(currentWindow, applnStructInputPanel, "Specify Structure Size to Export:");
            structSelection = applnStructInputPanel.getStructSelectionIndex();
            if (option == JOptionPane.CANCEL_OPTION || option == JOptionPane.CLOSED_OPTION) {
                break;
            } else if (option == JOptionPane.OK_OPTION && structSelection < 0) {
                DialogUtils.showErrorDialog(currentWindow, "Please select a structure and set its size");
            }
        } else {
            // adapt to legacy logic ...
            structSelection = 0;
            option = JOptionPane.OK_OPTION;
        }
    }
    if (option == JOptionPane.OK_OPTION) {
        applnStructInputPanel.applyStructureNameAndSizeValues();
        strucName = applnStructInputPanel.getSelectedStructureName();
        selectedSimContext = applnStructInputPanel.getSelectedSimContext();
        GeometryContext geoContext = selectedSimContext.getGeometryContext();
        if (!isSpatial) {
            // calculate structure Sizes only if appln is not spatial
            structSize = applnStructInputPanel.getStructureSize();
            // Invoke StructureSizeEvaluator to compute absolute sizes of compartments if all sizes are not set
            if ((geoContext.isAllSizeSpecifiedNull() && geoContext.isAllVolFracAndSurfVolSpecifiedNull()) || ((strucName == null || structSize <= 0.0) && (geoContext.isAllSizeSpecifiedNull() && geoContext.isAllVolFracAndSurfVolSpecified())) || (!geoContext.isAllSizeSpecifiedPositive() && geoContext.isAllVolFracAndSurfVolSpecifiedNull()) || (!geoContext.isAllSizeSpecifiedPositive() && !geoContext.isAllVolFracAndSurfVolSpecified()) || (geoContext.isAllSizeSpecifiedNull() && !geoContext.isAllVolFracAndSurfVolSpecified())) {
                DialogUtils.showErrorDialog(currentWindow, "Cannot export to SBML without compartment sizes being set. This can be automatically " + " computed if the absolute size of at least one compartment and the relative sizes (Surface-to-volume-ratio/Volume-fraction) " + " of all compartments are known. Sufficient information is not available to perform this computation." + "\n\nThis can be fixed by going back to the application '" + selectedSimContext.getName() + "' and setting structure sizes in the 'StructureMapping' tab.");
                throw UserCancelException.CANCEL_XML_TRANSLATION;
            }
            if (!geoContext.isAllSizeSpecifiedPositive() && geoContext.isAllVolFracAndSurfVolSpecified()) {
                Structure chosenStructure = selectedSimContext.getModel().getStructure(strucName);
                StructureMapping chosenStructMapping = selectedSimContext.getGeometryContext().getStructureMapping(chosenStructure);
                try {
                    StructureSizeSolver.updateAbsoluteStructureSizes(selectedSimContext, chosenStructure, structSize, chosenStructMapping.getSizeParameter().getUnitDefinition());
                } catch (Exception e) {
                    throw new ProgrammingException("exception updating sizes", e);
                }
            }
        } else {
            if (!geoContext.isAllUnitSizeParameterSetForSpatial()) {
                DialogUtils.showErrorDialog(currentWindow, "Cannot export to SBML without compartment size ratios being set." + "\n\nThis can be fixed by going back to the application '" + selectedSimContext.getName() + "' and setting structure" + " size ratios in the 'StructureMapping' tab.");
                throw UserCancelException.CANCEL_XML_TRANSLATION;
            }
        }
        // Select simulation whose overrides need to be exported
        // If simContext doesn't have simulations, don't pop up simulationSelectionPanel
        Simulation[] sims = bioModel.getSimulations(selectedSimContext);
        // display only those simulations that have overrides in the simulationSelectionPanel.
        Vector<Simulation> orSims = new Vector<Simulation>();
        for (int s = 0; (sims != null) && (s < sims.length); s++) {
            if (sims[s].getMathOverrides().hasOverrides()) {
                orSims.addElement(sims[s]);
            }
        }
        Simulation[] overriddenSims = orSims.toArray(new Simulation[orSims.size()]);
        if (overriddenSims.length > 0) {
            SimulationSelectionPanel simSelectionPanel = new SimulationSelectionPanel();
            simSelectionPanel.setPreferredSize(new java.awt.Dimension(600, 400));
            simSelectionPanel.setMaximumSize(new java.awt.Dimension(600, 400));
            simSelectionPanel.setSimulations(overriddenSims);
            int simOption = DialogUtils.showComponentOKCancelDialog(currentWindow, simSelectionPanel, "Select Simulation whose overrides should be exported:");
            if (simOption == JOptionPane.OK_OPTION) {
                selectedSimWOSBE = simSelectionPanel.getSelectedSimulation();
            // if (chosenSimulation != null) {
            // CARRY						hashTable.put("selectedSimulation", chosenSimulation);
            // }
            } else if (simOption == JOptionPane.CANCEL_OPTION || simOption == JOptionPane.CLOSED_OPTION) {
                // Hence canceling the entire export to SBML operation.
                throw UserCancelException.CANCEL_XML_TRANSLATION;
            }
        }
    } else if (option == JOptionPane.CANCEL_OPTION || option == JOptionPane.CLOSED_OPTION) {
        // Hence canceling the entire export to SBML operation.
        throw UserCancelException.CANCEL_XML_TRANSLATION;
    }
    if (selectedSimWOSBE != null) {
        String selectedFileName = c.filename;
        // rename file to contain exported simulation.
        String ext = FilenameUtils.getExtension(selectedFileName);
        String base = FilenameUtils.getBaseName(selectedFileName);
        String path = FilenameUtils.getPath(selectedFileName);
        base += "_" + TokenMangler.mangleToSName(selectedSimWOSBE.getName());
        selectedFileName = path + base + ext;
        c.selectedFile.renameTo(new File(selectedFileName));
    }
}

Example 34 with Simulation

use of cbit.vcell.solver.Simulation in project vcell by virtualcell.

the class SmoldynExtensionFilter method askUser.

@Override
public void askUser(ChooseContext ctx) throws UserCancelException {
    SimulationContext chosenSimContext = ctx.chosenContext;
    String[] simNames = new String[chosenSimContext.getSimulations().length];
    Simulation[] sims = chosenSimContext.getSimulations();
    for (int i = 0; i < sims.length; i++) {
        simNames[i] = sims[i].getName();
    }
    Object choice = PopupGenerator.showListDialog(ctx.topLevelWindowManager, simNames, "Please select " + chosenSimContext.getName() + " simulation to export");
    if (choice == null) {
        throw UserCancelException.CANCEL_FILE_SELECTION;
    }
    String chosenSimulationName = (String) choice;
    Simulation chosenSimulation = chosenSimContext.getSimulation(chosenSimulationName);
    Objects.requireNonNull(chosenSimulation);
    // PENDING delete
    ctx.hashTable.put(SIM_KEY, chosenSimulation);
    selectedSim = chosenSimulation;
}

Example 35 with Simulation

use of cbit.vcell.solver.Simulation in project vcell by virtualcell.

the class ClientDocumentManager method getMathModel.

/**
 * Insert the method's description here.
 * Creation date: (11/14/00 4:02:44 PM)
 * @return cbit.vcell.biomodel.BioModel
 * @param bioModelInfo cbit.vcell.biomodel.BioModelInfo
 */
public MathModel getMathModel(KeyValue mathModelKey) throws DataAccessException {
    XMLHolder<MathModel> mathModelXML = getMathModelXML(mathModelKey);
    MathModel mathModel = getMathModelFromDatabaseXML(mathModelXML);
    // 
    // preload SimulationJobStatus for all simulations if any missing from hash.
    // 
    Simulation[] simulations = mathModel.getSimulations();
    KeyValue[] simKeys = new KeyValue[simulations.length];
    for (int i = 0; i < simulations.length; i++) {
        VCSimulationIdentifier vcSimulationIdentifier = simulations[i].getSimulationInfo().getAuthoritativeVCSimulationIdentifier();
        simKeys[i] = vcSimulationIdentifier.getSimulationKey();
    }
    preloadSimulationStatus(simKeys);
    return mathModel;
}