Examples with MathModel cbit.vcell.mathmodel.MathModel used on opensource projects

Example 56 with MathModel

use of cbit.vcell.mathmodel.MathModel in project vcell by virtualcell.

the class IssuePanel method invokeHyperlink.

private void invokeHyperlink(Issue issue) {
    if (selectionManager != null) {
        // followHyperlink is no-op if selectionManger null, so no point in proceeding if it is
        IssueContext issueContext = issue.getIssueContext();
        IssueSource object = issue.getSource();
        if (object instanceof DecoratedIssueSource) {
            DecoratedIssueSource dis = (DecoratedIssueSource) object;
            dis.activateView(selectionManager);
        } else if (object instanceof Parameter) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.BIOMODEL_PARAMETERS_NODE, ActiveViewID.parameters_functions), new Object[] { object });
        } else if (object instanceof StructureMapping) {
            StructureMapping structureMapping = (StructureMapping) object;
            StructureMappingNameScope structureMappingNameScope = (StructureMappingNameScope) structureMapping.getNameScope();
            SimulationContext simulationContext = ((SimulationContextNameScope) (structureMappingNameScope.getParent())).getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.structure_mapping), new Object[] { object });
        } else if (object instanceof SpatialObject) {
            SpatialObject spatialObject = (SpatialObject) object;
            SimulationContext simulationContext = spatialObject.getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.spatial_objects), new Object[] { object });
        } else if (object instanceof SpatialProcess) {
            SpatialProcess spatialProcess = (SpatialProcess) object;
            SimulationContext simulationContext = spatialProcess.getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.spatial_processes), new Object[] { object });
        } else if (object instanceof GeometryContext.UnmappedGeometryClass) {
            UnmappedGeometryClass unmappedGeometryClass = (UnmappedGeometryClass) object;
            SimulationContext simulationContext = unmappedGeometryClass.getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.structure_mapping), new Object[] { object });
        } else if (object instanceof MicroscopeMeasurement) {
            SimulationContext simulationContext = ((MicroscopeMeasurement) object).getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.PROTOCOLS_NODE, ActiveViewID.microscope_measuremments), new Object[] { object });
        } else if (object instanceof BioEvent) {
            BioEvent be = (BioEvent) object;
            SimulationContext simulationContext = be.getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.PROTOCOLS_NODE, ActiveViewID.events), new Object[] { object });
        } else if (object instanceof OutputFunctionIssueSource) {
            SimulationOwner simulationOwner = ((OutputFunctionIssueSource) object).getOutputFunctionContext().getSimulationOwner();
            if (simulationOwner instanceof SimulationContext) {
                SimulationContext simulationContext = (SimulationContext) simulationOwner;
                followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.SIMULATIONS_NODE, ActiveViewID.output_functions), new Object[] { ((OutputFunctionIssueSource) object).getAnnotatedFunction() });
            } else if (simulationOwner instanceof MathModel) {
                followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MATH_OUTPUT_FUNCTIONS_NODE, ActiveViewID.math_output_functions), new Object[] { ((OutputFunctionIssueSource) object).getAnnotatedFunction() });
            }
        } else if (object instanceof Simulation) {
            Simulation simulation = (Simulation) object;
            SimulationOwner simulationOwner = simulation.getSimulationOwner();
            if (simulationOwner instanceof SimulationContext) {
                SimulationContext simulationContext = (SimulationContext) simulationOwner;
                followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.SIMULATIONS_NODE, ActiveViewID.simulations), new Object[] { simulation });
            } else if (simulationOwner instanceof MathModel) {
                followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MATH_SIMULATIONS_NODE, ActiveViewID.math_simulations), new Object[] { simulation });
            }
        } else if (object instanceof GeometryContext) {
            setActiveView(new ActiveView(((GeometryContext) object).getSimulationContext(), DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.geometry_definition));
        } else if (object instanceof Structure) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.STRUCTURES_NODE, ActiveViewID.structures), new Object[] { object });
        } else if (object instanceof MolecularType) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MOLECULAR_TYPES_NODE, ActiveViewID.structures), new Object[] { object });
        } else if (object instanceof ReactionStep) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.REACTIONS_NODE, ActiveViewID.reactions), new Object[] { object });
        } else if (object instanceof ReactionRule) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.REACTIONS_NODE, ActiveViewID.reactions), new Object[] { object });
        } else if (object instanceof SpeciesContextSpec) {
            SpeciesContextSpec scs = (SpeciesContextSpec) object;
            ActiveView av = new ActiveView(scs.getSimulationContext(), DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.species_settings);
            followHyperlink(av, new Object[] { object });
        } else if (object instanceof ReactionCombo) {
            ReactionCombo rc = (ReactionCombo) object;
            followHyperlink(new ActiveView(rc.getReactionContext().getSimulationContext(), DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.reaction_setting), new Object[] { ((ReactionCombo) object).getReactionSpec() });
        } else if (object instanceof SpeciesContext) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.SPECIES_NODE, ActiveViewID.species), new Object[] { object });
        } else if (object instanceof RbmObservable) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.OBSERVABLES_NODE, ActiveViewID.observables), new Object[] { object });
        } else if (object instanceof MathDescription) {
            // followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MATH_SIMULATIONS_NODE, ActiveViewID.generated_math), new Object[] {object});
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.structure_mapping), new Object[] { object });
        } else if (object instanceof SpeciesPattern) {
            // if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
            // SpeciesContext thing = (SpeciesContext)issue.getIssueContext().getContextObject(ContextType.SpeciesContext);
            // followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.SPECIES_NODE, ActiveViewID.species), new Object[] {thing});
            // }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
            // ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
            // followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.REACTIONS_NODE, ActiveViewID.reactions), new Object[] {thing});
            // }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
            // RbmObservable thing = (RbmObservable)issue.getIssueContext().getContextObject(ContextType.RbmObservable);
            // followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.OBSERVABLES_NODE, ActiveViewID.observables), new Object[] {thing});
            // } else {
            System.err.println("SpeciesPattern object missing a proper issue context.");
        // }
        } else if (object instanceof SimulationContext) {
            SimulationContext sc = (SimulationContext) object;
            IssueCategory ic = issue.getCategory();
            switch(ic) {
                case RbmNetworkConstraintsBad:
                    NetworkConstraints nc = sc.getNetworkConstraints();
                    if (issue.getMessage() == SimulationContext.IssueInsufficientMolecules) {
                        NetworkConstraintsEntity nce = new NetworkConstraintsEntity(NetworkConstraintsTableModel.sMaxMoleculesName, NetworkConstraintsTableModel.sValueType, nc.getMaxMoleculesPerSpecies() + "");
                        followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.network_setting), new Object[] { nce });
                    } else {
                        NetworkConstraintsEntity nce = new NetworkConstraintsEntity(NetworkConstraintsTableModel.sMaxIterationName, NetworkConstraintsTableModel.sValueType, nc.getMaxIteration() + "");
                        followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.network_setting), new Object[] { nce });
                    }
                    break;
                default:
                    followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.network_setting), new Object[] { object });
                    break;
            }
        } else if (object instanceof Geometry) {
            if (issueContext.hasContextType(ContextType.SimContext)) {
                SimulationContext simContext = (SimulationContext) issueContext.getContextObject(ContextType.SimContext);
                followHyperlink(new ActiveView(simContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.geometry_definition), new Object[] { object });
            } else if (issueContext.hasContextType(ContextType.MathModel)) {
                followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MATH_GEOMETRY_NODE, ActiveViewID.math_geometry), new Object[] { object });
            } else if (issueContext.hasContextType(ContextType.MathDescription)) {
                followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.geometry_definition), new Object[] { object });
            }
        } else {
            System.err.println("unknown object type in IssuePanel.invokeHyperlink(): " + object.getClass() + ", context type: " + issueContext.getContextType());
        }
    }
}

Example 57 with MathModel

use of cbit.vcell.mathmodel.MathModel in project vcell by virtualcell.

the class GeometryViewer method resample.

private void resample() {
    AsynchClientTask precomputeCurrentGeometryTask = new AsynchClientTask("computing surfaces for existing geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (getGeometry().getGeometrySurfaceDescription().getRegionImage() == null) {
                getGeometry().precomputeAll(new GeometryThumbnailImageFactoryAWT(), true, true);
            }
        }
    };
    AsynchClientTask sampleSizeTask = new AsynchClientTask("specify sample size", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            VCImage currSampledImage = getGeometry().getGeometrySpec().getSampledImage().getCurrentValue();
            int currNumSamples = currSampledImage.getNumXYZ();
            ISize currSize = new ISize(currSampledImage.getNumX(), currSampledImage.getNumY(), currSampledImage.getNumZ());
            ISize sampleSize_times_ten = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), currNumSamples * 10);
            ISize sampleSize_div_ten = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), currNumSamples / 10);
            ISize sampleSize_1e2 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e2);
            ISize sampleSize_1e3 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e3);
            ISize sampleSize_1e4 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e4);
            ISize sampleSize_1e5 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e5);
            ISize sampleSize_1e6 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e6);
            ISize sampleSize_1e7 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e7);
            ISize sampleSize_1e8 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e8);
            String[] columnNames = new String[] { "description", "num samples", "(X,Y,Z)" };
            Object[][] rowData = new Object[][] { new Object[] { "same size", new Integer(currSize.getXYZ()), currSize }, new Object[] { "10 times smaller", new Integer(sampleSize_div_ten.getXYZ()), sampleSize_div_ten }, new Object[] { "10 times bigger", new Integer(sampleSize_times_ten.getXYZ()), sampleSize_times_ten }, new Object[] { "        100 samples", new Integer(sampleSize_1e2.getXYZ()), sampleSize_1e2 }, new Object[] { "      1,000 samples", new Integer(sampleSize_1e3.getXYZ()), sampleSize_1e3 }, new Object[] { "     10,000 samples", new Integer(sampleSize_1e4.getXYZ()), sampleSize_1e4 }, new Object[] { "    100,000 samples", new Integer(sampleSize_1e5.getXYZ()), sampleSize_1e5 }, new Object[] { "  1,000,000 samples", new Integer(sampleSize_1e6.getXYZ()), sampleSize_1e6 }, new Object[] { " 10,000,000 samples", new Integer(sampleSize_1e7.getXYZ()), sampleSize_1e7 }, new Object[] { "100,000,000 samples", new Integer(sampleSize_1e8.getXYZ()), sampleSize_1e8 } };
            int[] selectedRows = DialogUtils.showComponentOKCancelTableList(GeometryViewer.this, "sample size", columnNames, rowData, ListSelectionModel.SINGLE_SELECTION);
            ISize sampleSize = (ISize) rowData[selectedRows[0]][2];
            hashTable.put("sampleSize", sampleSize);
        }
    };
    AsynchClientTask resampleTask = new AsynchClientTask("resample geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ISize sampleSize = (ISize) hashTable.get("sampleSize");
            Geometry newGeometry = RayCaster.resampleGeometry(new GeometryThumbnailImageFactoryAWT(), getGeometry(), sampleSize);
            hashTable.put("newGeometry", newGeometry);
        }
    };
    AsynchClientTask setGeometryTask = new AsynchClientTask("loading geometry", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Geometry newGeometry = (Geometry) hashTable.get("newGeometry");
            if (getGeometryOwner() instanceof SimulationContext) {
                ((SimulationContext) getGeometryOwner()).setGeometry(newGeometry);
            } else if (getGeometryOwner() instanceof MathModel) {
                ((MathModel) getGeometryOwner()).getMathDescription().setGeometry(newGeometry);
            } else {
                throw new RuntimeException("unexpected geometry owner, could not set resampled geometry");
            }
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { precomputeCurrentGeometryTask, sampleSizeTask, resampleTask, setGeometryTask }, false);
}

Example 58 with MathModel

use of cbit.vcell.mathmodel.MathModel in project vcell by virtualcell.

the class ChooseFile method showMathModelXMLFileChooser.

/**
 * Insert the method's description here.
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
private File showMathModelXMLFileChooser(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    // for mathmodels:
    MathModel mathModel = (MathModel) hashTable.get("documentToExport");
    JFrame currentWindow = (JFrame) hashTable.get("currentWindow");
    UserPreferences userPreferences = (UserPreferences) hashTable.get("userPreferences");
    TopLevelWindowManager topLevelWindowManager = (TopLevelWindowManager) hashTable.get("topLevelWindowManager");
    if (topLevelWindowManager == null) {
        throw new RuntimeException("toplLevelWindowManager required");
    }
    File defaultPath = userPreferences.getCurrentDialogPath();
    VCFileChooser fileChooser = new VCFileChooser(defaultPath);
    fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
    fileChooser.setMultiSelectionEnabled(false);
    // fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_SBML_21);		// Can export Mathmodel to L2V1 ??
    fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_SBML_23);
    fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_SBML_24);
    // fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_CELLML);
    fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_MATLABV6);
    fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_PDF);
    fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_SMOLDYN_INPUT);
    // remove all selector
    fileChooser.removeChoosableFileFilter(fileChooser.getAcceptAllFileFilter());
    // set the default file filter...
    fileChooser.setFileFilter(FileFilters.FILE_FILTER_VCML);
    fileChooser.setSelectedFile(new java.io.File(TokenMangler.fixTokenStrict(mathModel.getName())));
    fileChooser.setDialogTitle("Export Virtual Cell MathModel As...");
    if (fileChooser.showSaveDialog(currentWindow) != JFileChooser.APPROVE_OPTION) {
        // user didn't choose save
        throw UserCancelException.CANCEL_FILE_SELECTION;
    } else {
        File selectedFile = fileChooser.getSelectedFile();
        javax.swing.filechooser.FileFilter fileFilter = fileChooser.getFileFilter();
        if (selectedFile == null) {
            // no file selected (no name given)
            throw UserCancelException.CANCEL_FILE_SELECTION;
        } else {
            // /
            String selectedFileName = recordAndRemoveExtension(selectedFile.getPath());
            String n = selectedFile.getPath().toLowerCase();
            if (fileFilter == FileFilters.FILE_FILTER_CELLML && !n.endsWith(".xml")) {
                selectedFile = new File(selectedFileName + ".xml");
            } else if (fileFilter == FileFilters.FILE_FILTER_VCML && !n.endsWith(".vcml")) {
                selectedFile = new File(selectedFileName + ".vcml");
            } else if ((fileFilter == FileFilters.FILE_FILTER_SBML_23 || (fileFilter == FileFilters.FILE_FILTER_SBML_24)) && !n.endsWith(".xml")) {
                selectedFile = new File(selectedFileName + ".xml");
            } else if (fileFilter == FileFilters.FILE_FILTER_MATLABV6 && !n.endsWith(".m")) {
                selectedFile = new File(selectedFileName + ".m");
            } else if (fileFilter == FileFilters.FILE_FILTER_PDF && !n.endsWith(".pdf")) {
                selectedFile = new File(selectedFileName + ".pdf");
            } else if (fileFilter == FileFilters.FILE_FILTER_SMOLDYN_INPUT && !(n.endsWith(SMOLDYN_INPUT_FILE_EXTENSION) || (n.endsWith(".txt")))) {
                selectedFile = new File(selectedFileName + SMOLDYN_INPUT_FILE_EXTENSION);
            }
            checkForOverwrites(selectedFile, topLevelWindowManager.getComponent(), userPreferences);
            // put the filter in the hash so the export task knows what to do...
            hashTable.put("fileFilter", fileFilter);
            // only non-spatial math models can be exported to CellML.
            if (fileFilter == FileFilters.FILE_FILTER_CELLML && mathModel.getMathDescription().getGeometry().getDimension() != 0) {
                throw new Exception("No non-spatial applications, can only export to this format the math from a non-spatial application");
            } else // Select a spatial stochastic simulation to export
            if (fileFilter.getDescription().equals(FileFilters.FILE_FILTER_SMOLDYN_INPUT.getDescription())) {
                Simulation[] sims = mathModel.getSimulations();
                if (sims == null || sims.length == 0) {
                    DialogUtils.showWarningDialog(topLevelWindowManager.getComponent(), "MathModel '" + mathModel.getName() + "' has no simulations to export");
                    throw UserCancelException.CANCEL_GENERIC;
                }
                String[][] rowData = new String[sims.length][2];
                for (int i = 0; i < sims.length; i++) {
                    rowData[i][0] = sims[i].getName();
                    rowData[i][1] = sims[i].getSolverTaskDescription().getSolverDescription().getDisplayLabel();
                }
                int[] selectedRow = PopupGenerator.showComponentOKCancelTableList(topLevelWindowManager.getComponent(), "Select a simulation to export", new String[] { "Simulation Name", "Solver" }, rowData, ListSelectionModel.SINGLE_SELECTION);
                if (selectedRow == null) {
                    throw UserCancelException.CANCEL_GENERIC;
                }
                String chosenSimulationName = rowData[selectedRow[0]][0];
                Simulation chosenSimulation = mathModel.getSimulation(chosenSimulationName);
                if (chosenSimulation != null) {
                    hashTable.put("selectedSimulation", chosenSimulation);
                } else {
                    throw new Exception("Couldn't match selection '" + chosenSimulationName + "' with simulation");
                }
            }
            resetPreferredFilePath(selectedFile, userPreferences);
            return selectedFile;
        }
    }
}

Example 59 with MathModel

use of cbit.vcell.mathmodel.MathModel in project vcell by virtualcell.

the class DeleteOldDocument method run.

/**
 * Insert the method's description here.
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
public void run(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    DocumentWindowManager dwm = (DocumentWindowManager) fetch(hashTable, DOCUMENT_WINDOW_MANAGER);
    VCDocument currentDocument = dwm.getVCDocument();
    DocumentManager documentManager = (DocumentManager) fetch(hashTable, DOCUMENT_MANAGER);
    switch(currentDocument.getDocumentType()) {
        case BIOMODEL_DOC:
            {
                // make the info
                BioModel oldBioModel = (BioModel) currentDocument;
                BioModelInfo oldBioModelInfo = documentManager.getBioModelInfo(oldBioModel.getVersion().getVersionKey());
                // delete document
                documentManager.delete(oldBioModelInfo);
                break;
            }
        case MATHMODEL_DOC:
            {
                // make the info
                MathModel oldMathModel = (MathModel) currentDocument;
                MathModelInfo oldMathModelInfo = documentManager.getMathModelInfo(oldMathModel.getVersion().getVersionKey());
                // delete document
                documentManager.delete(oldMathModelInfo);
                break;
            }
        case GEOMETRY_DOC:
            {
                // make the info
                Geometry oldGeometry = (Geometry) currentDocument;
                GeometryInfo oldGeometryInfo = documentManager.getGeometryInfo(oldGeometry.getVersion().getVersionKey());
                // delete document
                documentManager.delete(oldGeometryInfo);
                break;
            }
        default:
            break;
    }
}

Example 60 with MathModel

use of cbit.vcell.mathmodel.MathModel in project vcell by virtualcell.

the class RunSims method run.

/**
 * Insert the method's description here.
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
public void run(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    DocumentWindowManager documentWindowManager = (DocumentWindowManager) hashTable.get(CommonTask.DOCUMENT_WINDOW_MANAGER.name);
    ClientSimManager clientSimManager = (ClientSimManager) hashTable.get("clientSimManager");
    // DocumentManager documentManager = (DocumentManager)hashTable.get(CommonTask.DOCUMENT_MANAGER.name);
    JobManager jobManager = (JobManager) hashTable.get("jobManager");
    Simulation[] simulations = (Simulation[]) hashTable.get("simulations");
    Hashtable<Simulation, Throwable> failures = new Hashtable<Simulation, Throwable>();
    if (simulations != null && simulations.length > 0) {
        // we need to get the new ones if a save occurred...
        if (hashTable.containsKey(SaveDocument.DOC_KEY)) {
            VCDocument savedDocument = (VCDocument) hashTable.get(SaveDocument.DOC_KEY);
            Simulation[] allSims = null;
            if (savedDocument instanceof BioModel) {
                allSims = ((BioModel) savedDocument).getSimulations();
            } else if (savedDocument instanceof MathModel) {
                allSims = ((MathModel) savedDocument).getSimulations();
            }
            Vector<Simulation> v = new Vector<Simulation>();
            for (int i = 0; i < simulations.length; i++) {
                for (int j = 0; j < allSims.length; j++) {
                    if (simulations[i].getName().equals(allSims[j].getName())) {
                        v.add(allSims[j]);
                        break;
                    }
                }
            }
            simulations = (Simulation[]) BeanUtils.getArray(v, Simulation.class);
        }
        for (Simulation sim : simulations) {
            try {
                int dimension = sim.getMathDescription().getGeometry().getDimension();
                if (clientSimManager.getSimulationStatus(sim).isCompleted()) {
                    // completed
                    String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_1, sim.getName());
                    String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                    if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                        continue;
                    }
                }
                DataProcessingInstructions dataProcessingInstructions = sim.getDataProcessingInstructions();
                try {
                    if (dataProcessingInstructions != null) {
                        dataProcessingInstructions.getSampleImageFieldData(sim.getVersion().getOwner());
                    }
                } catch (Exception ex) {
                    DialogUtils.showErrorDialog(documentWindowManager.getComponent(), "Problem found in simulation '" + sim.getName() + "':\n" + ex.getMessage());
                    continue;
                }
                if (dimension > 0) {
                    MeshSpecification meshSpecification = sim.getMeshSpecification();
                    boolean bCellCentered = sim.hasCellCenteredMesh();
                    if (meshSpecification != null && !meshSpecification.isAspectRatioOK(bCellCentered)) {
                        String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_2, sim.getName(), "\u0394x=" + meshSpecification.getDx(bCellCentered) + "\n" + "\u0394y=" + meshSpecification.getDy(bCellCentered) + (dimension < 3 ? "" : "\n\u0394z=" + meshSpecification.getDz(bCellCentered)));
                        String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                        if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                            continue;
                        }
                    }
                    if (sim.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.Smoldyn)) {
                        if (!isSmoldynTimeStepOK(sim)) {
                            double s = smoldynTimestepVars.getSpatialResolution();
                            double dMax = smoldynTimestepVars.getMaxDiffusion();
                            double condn = (s * s) / (2.0 * dMax);
                            String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_3, Double.toString(s), Double.toString(dMax), Double.toString(condn));
                            DialogUtils.showErrorDialog(documentWindowManager.getComponent(), warningMessage);
                            continue;
                        }
                    }
                    // check the number of regions if the simulation mesh is coarser.
                    Geometry mathGeometry = sim.getMathDescription().getGeometry();
                    ISize newSize = meshSpecification.getSamplingSize();
                    ISize defaultSize = mathGeometry.getGeometrySpec().getDefaultSampledImageSize();
                    if (!sim.getSolverTaskDescription().getSolverDescription().isChomboSolver()) {
                        int defaultTotalVolumeElements = mathGeometry.getGeometrySurfaceDescription().getVolumeSampleSize().getXYZ();
                        int newTotalVolumeElements = meshSpecification.getSamplingSize().getXYZ();
                        if (defaultTotalVolumeElements > newTotalVolumeElements) {
                            // coarser
                            Geometry resampledGeometry = (Geometry) BeanUtils.cloneSerializable(mathGeometry);
                            GeometrySurfaceDescription geoSurfaceDesc = resampledGeometry.getGeometrySurfaceDescription();
                            geoSurfaceDesc.setVolumeSampleSize(newSize);
                            geoSurfaceDesc.updateAll();
                            if (mathGeometry.getGeometrySurfaceDescription().getGeometricRegions() == null) {
                                mathGeometry.getGeometrySurfaceDescription().updateAll();
                            }
                            int defaultNumGeometricRegions = mathGeometry.getGeometrySurfaceDescription().getGeometricRegions().length;
                            int numGeometricRegions = geoSurfaceDesc.getGeometricRegions().length;
                            if (numGeometricRegions != defaultNumGeometricRegions) {
                                String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_4, newSize.getX() + (dimension > 1 ? " x " + newSize.getY() : "") + (dimension > 2 ? " x " + newSize.getZ() : ""), sim.getName(), numGeometricRegions, defaultNumGeometricRegions);
                                String result = PopupGenerator.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                                if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                                    continue;
                                }
                            }
                        }
                        if (mathGeometry.getGeometrySpec().hasImage()) {
                            // if it's an image.
                            if (defaultSize.getX() + 1 < newSize.getX() || defaultSize.getY() + 1 < newSize.getY() || defaultSize.getZ() + 1 < newSize.getZ()) {
                                // finer
                                String defaultSizeString = (defaultSize.getX() + 1) + (dimension > 1 ? " x " + (defaultSize.getY() + 1) : "") + (dimension > 2 ? " x " + (defaultSize.getZ() + 1) : "");
                                String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_5, newSize.getX() + (dimension > 1 ? " x " + newSize.getY() : "") + (dimension > 2 ? " x " + newSize.getZ() : ""), sim.getName(), defaultSizeString, defaultSizeString);
                                String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                                if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                                    continue;
                                }
                            }
                        }
                    }
                    boolean bGiveWarning = false;
                    for (int i = 0; i < sim.getScanCount(); i++) {
                        if (sim.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.SundialsPDE)) {
                            SimulationJob simJob = new SimulationJob(sim, i, null);
                            if (simJob.getSimulationSymbolTable().hasTimeVaryingDiffusionOrAdvection()) {
                                bGiveWarning = true;
                                break;
                            }
                        }
                    }
                    if (bGiveWarning) {
                        String warningMessage = VCellErrorMessages.RunSims_6;
                        String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                        if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                            continue;
                        }
                    }
                }
                SimulationInfo simInfo = sim.getSimulationInfo();
                if (simInfo != null) {
                    // 
                    // translate to common ancestral simulation (oldest mathematically equivalent simulation)
                    // 
                    SimulationStatus simulationStatus = jobManager.startSimulation(simInfo.getAuthoritativeVCSimulationIdentifier(), sim.getScanCount());
                    // updateStatus
                    clientSimManager.updateStatusFromStartRequest(sim, simulationStatus);
                } else {
                    // this should really not happen...
                    throw new RuntimeException(">>>>>>>>>> trying to run an unsaved simulation...");
                }
            } catch (Throwable exc) {
                exc.printStackTrace(System.out);
                failures.put(sim, exc);
            }
        }
    }
    // we deal with individual request failures here, passing down only other things (that break the whole thing down) to dispatcher
    if (!failures.isEmpty()) {
        Enumeration<Simulation> en = failures.keys();
        while (en.hasMoreElements()) {
            Simulation sim = en.nextElement();
            Throwable exc = (Throwable) failures.get(sim);
            // // updateStatus
            // SimulationStatus simulationStatus = clientSimManager.updateStatusFromStartRequest(sim, true, exc.getMessage());
            // notify user
            PopupGenerator.showErrorDialog(documentWindowManager, "Failed to start simulation'" + sim.getName() + "'\n" + exc.getMessage());
        }
    }
}