Examples with SimulationContext cbit.vcell.mapping.SimulationContext used on opensource projects

Example 36 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class BioModelEditor method popupMenuActionPerformed.

@Override
protected void popupMenuActionPerformed(DocumentEditorPopupMenuAction action, String actionCommand) {
    Model model = bioModel.getModel();
    final SimulationContext selectedSimulationContext = getSelectedSimulationContext();
    switch(action) {
        case add_new:
            try {
                Object obj = documentEditorTree.getLastSelectedPathComponent();
                if (obj == null || !(obj instanceof BioModelNode)) {
                    return;
                }
                BioModelNode selectedNode = (BioModelNode) obj;
                Object userObject = selectedNode.getUserObject();
                if (userObject instanceof DocumentEditorTreeFolderNode) {
                    DocumentEditorTreeFolderClass folderClass = ((DocumentEditorTreeFolderNode) userObject).getFolderClass();
                    Object newObject = null;
                    switch(folderClass) {
                        case REACTIONS_NODE:
                            // TODO: should add a Add New Rule menu item
                            newObject = model.createSimpleReaction(model.getStructure(0));
                            break;
                        case STRUCTURES_NODE:
                            newObject = model.createFeature();
                            break;
                        case SPECIES_NODE:
                            newObject = model.createSpeciesContext(model.getStructure(0));
                            break;
                        case MOLECULAR_TYPES_NODE:
                            MolecularType mt = model.getRbmModelContainer().createMolecularType();
                            model.getRbmModelContainer().addMolecularType(mt, true);
                            newObject = mt;
                            break;
                        case OBSERVABLES_NODE:
                            if (bioModel.getModel().getRbmModelContainer().getMolecularTypeList().isEmpty()) {
                                PopupGenerator.showInfoDialog(this, VCellErrorMessages.MustBeRuleBased);
                                return;
                            }
                            RbmObservable o = model.getRbmModelContainer().createObservable(RbmObservable.ObservableType.Molecules);
                            model.getRbmModelContainer().addObservable(o);
                            SpeciesPattern sp = new SpeciesPattern();
                            o.addSpeciesPattern(sp);
                            newObject = o;
                            break;
                        case SIMULATIONS_NODE:
                            if (selectedSimulationContext != null) {
                                AsynchClientTask task1 = new AsynchClientTask("new simulation", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                                    @Override
                                    public void run(Hashtable<String, Object> hashTable) throws Exception {
                                        MathMappingCallback callback = new MathMappingCallbackTaskAdapter(getClientTaskStatusSupport());
                                        selectedSimulationContext.refreshMathDescription(callback, NetworkGenerationRequirements.AllowTruncatedStandardTimeout);
                                    }
                                };
                                AsynchClientTask task2 = new AsynchClientTask("new simulation", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

                                    @Override
                                    public void run(Hashtable<String, Object> hashTable) throws Exception {
                                        MathMappingCallback callback = new MathMappingCallbackTaskAdapter(getClientTaskStatusSupport());
                                        Object newsim = selectedSimulationContext.addNewSimulation(SimulationOwner.DEFAULT_SIM_NAME_PREFIX, callback, NetworkGenerationRequirements.AllowTruncatedStandardTimeout);
                                        selectionManager.setSelectedObjects(new Object[] { newsim });
                                    }
                                };
                                ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
                            }
                            break;
                        default:
                            break;
                    }
                    if (newObject != null) {
                        selectionManager.setSelectedObjects(new Object[] { newObject });
                    }
                }
            } catch (Exception ex) {
                DialogUtils.showErrorDialog(this, ex.getMessage());
            }
            break;
        case add_new_app_deterministic:
            newApplication(Application.NETWORK_DETERMINISTIC);
            break;
        case add_new_app_stochastic:
            newApplication(Application.NETWORK_STOCHASTIC);
            break;
        case add_new_app_rulebased:
            {
                // if(model.getStructures().length > 1) {
                // DialogUtils.showErrorDialog(this, VCellErrorMessages.NFSimAppNotAllowedForMultipleStructures);
                // return;
                // }
                newApplication(Application.RULE_BASED_STOCHASTIC);
                break;
            }
        case copyName:
            String name = bioModel.getName();
            StringSelection data = new StringSelection(name);
            Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
            c.setContents(data, data);
            break;
        case copy_app:
            ApplicationActionCommand acc = ApplicationActionCommand.lookup(actionCommand);
            switch(acc.actionType()) {
                case COPY_AS_IS:
                    copyApplication();
                    break;
                case COPY_CHANGE:
                    boolean bothSpatial = acc.isSourceSpatial() && acc.isDestSpatial();
                    // if(acc.getAppType().equals(SimulationContext.Application.RULE_BASED_STOCHASTIC) && model.getStructures().length > 1) {
                    // DialogUtils.showErrorDialog(this, VCellErrorMessages.NFSimAppNotAllowedForMultipleStructures);
                    // return;
                    // }
                    copyApplication(bothSpatial, acc.getAppType());
                    break;
                case CREATE:
                    // not used in this menu
                    throw new UnsupportedOperationException();
            }
            break;
        case app_new_biomodel:
            if (actionCommand.equals(GuiConstants.MENU_TEXT_APP_NEWBIOMODEL)) {
                createNewBiomodelFromApp();
            }
            break;
        case delete:
            try {
                if (selectedSimulationContext != null) {
                    String confirm = PopupGenerator.showOKCancelWarningDialog(this, "Deleting application", "You are going to delete the Application '" + selectedSimulationContext.getName() + "'. Continue?");
                    if (confirm.equals(UserMessage.OPTION_CANCEL)) {
                        return;
                    }
                    deleteSimulationcontexts(new SimulationContext[] { selectedSimulationContext });
                }
            } catch (Exception ex) {
                DialogUtils.showErrorDialog(this, ex.getMessage());
            }
            break;
        case deleteChoose:
            try {
                SimulationContext[] allSimContexts = Arrays.copyOf(getBioModelWindowManager().getVCDocument().getSimulationContexts(), getBioModelWindowManager().getVCDocument().getSimulationContexts().length);
                Arrays.sort(allSimContexts, new Comparator<SimulationContext>() {

                    @Override
                    public int compare(SimulationContext o1, SimulationContext o2) {
                        return o1.getName().compareToIgnoreCase(o2.getName());
                    }
                });
                String[][] rowDataOrig = new String[allSimContexts.length][2];
                for (int i = 0; i < allSimContexts.length; i++) {
                    rowDataOrig[i][0] = allSimContexts[i].getName();
                    rowDataOrig[i][1] = allSimContexts[i].getSimulations().length + "";
                }
                final String DELETE = "Delete";
                final String CANCEL = "Cancel";
                TableListResult result = DialogUtils.showComponentOptionsTableList(this, "Select Applications (and associated Simulations) to delete.", new String[] { "Application", "# of Sims" }, rowDataOrig, ListSelectionModel.MULTIPLE_INTERVAL_SELECTION, null, new String[] { DELETE, CANCEL }, CANCEL, null);
                if (result != null && result.selectedOption != null && result.selectedOption.equals(DELETE) && result.selectedTableRows != null && result.selectedTableRows.length > 0) {
                    ArrayList<SimulationContext> deleteTheseSimcontexts = new ArrayList<SimulationContext>();
                    for (int i = 0; i < result.selectedTableRows.length; i++) {
                        deleteTheseSimcontexts.add(allSimContexts[result.selectedTableRows[i]]);
                    }
                    deleteSimulationcontexts(deleteTheseSimcontexts.toArray(new SimulationContext[0]));
                }
            } catch (Exception ex) {
                DialogUtils.showErrorDialog(this, ex.getMessage());
            }
            break;
        default:
            break;
    }
}

Example 37 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class ApplicationsPropertiesPanel method setBioModel.

/**
 * Sets the speciesContext property (cbit.vcell.model.SpeciesContext) value.
 * @param speciesContext The new value for the property.
 * @see #getSpeciesContext
 */
public void setBioModel(BioModel newValue) {
    if (newValue == bioModel) {
        return;
    }
    BioModel oldValue = bioModel;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(eventHandler);
        for (SimulationContext simContext : oldValue.getSimulationContexts()) {
            simContext.removePropertyChangeListener(eventHandler);
        }
    }
    bioModel = newValue;
    if (newValue != null) {
        newValue.addPropertyChangeListener(eventHandler);
        for (SimulationContext simContext : newValue.getSimulationContexts()) {
            simContext.addPropertyChangeListener(eventHandler);
        }
    }
    updateInterface();
}

Example 38 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class ApplicationsPropertiesPanel method updateInterface.

/**
 * Comment
 */
private void updateInterface() {
    if (bioModel == null) {
        return;
    }
    applicationsPanel.removeAll();
    int gridy = 0;
    SimulationContext[] simulationContexts = bioModel.getSimulationContexts();
    if (simulationContexts != null) {
        for (int i = 0; i < simulationContexts.length; i++) {
            SimulationContext simContext = simulationContexts[i];
            JLabel label = new JLabel(simContext.getName());
            label.setFont(label.getFont().deriveFont(Font.BOLD));
            label.setIcon(simulationContextIcon);
            GridBagConstraints gbc = new java.awt.GridBagConstraints();
            gbc.gridx = 0;
            gbc.gridy = gridy++;
            gbc.weightx = 1.0;
            gbc.fill = GridBagConstraints.HORIZONTAL;
            gbc.anchor = GridBagConstraints.FIRST_LINE_START;
            if (i > 0) {
                gbc.insets = new Insets(4, 0, 0, 0);
            }
            applicationsPanel.add(label, gbc);
            Geometry geometry = simContext.getGeometry();
            String geometryText = "Compartmental geometry";
            if (geometry != null) {
                Version geometryVersion = geometry.getVersion();
                int dimension = geometry.getDimension();
                if (dimension > 0) {
                    String description = geometry.getDimension() + "D " + (geometry.getGeometrySpec().hasImage() ? "image" : "analytic") + " geometry";
                    geometryText = description;
                    if (geometryVersion != null) {
                        geometryText += " - " + geometryVersion.getName();
                    }
                }
            }
            JLabel geometryLabel = new JLabel(geometryText);
            geometryLabel.setIcon(geometryIcon);
            JLabel detStochLabel = new JLabel(simContext.getMathType().getDescription());
            detStochLabel.setIcon(appTypeIcon);
            gbc.insets = new Insets(2, 20, 2, 2);
            gbc.gridy = gridy++;
            applicationsPanel.add(detStochLabel, gbc);
            gbc.gridy = gridy++;
            if (i == simulationContexts.length - 1) {
                gbc.weighty = 1.0;
            }
            applicationsPanel.add(geometryLabel, gbc);
        }
    }
}

Example 39 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class BioModelEditorApplicationsPanel method compareButtonPressed.

private void compareButtonPressed() {
    int[] rows = table.getSelectedRows();
    if (rows == null || rows.length != 2) {
        return;
    }
    try {
        SimulationContext simContext1 = tableModel.getValueAt(rows[0]);
        SimulationContext simContext2 = tableModel.getValueAt(rows[1]);
        BioModel bioModel = simContext1.getBioModel();
        MathMappingCallback callback = new MathMappingCallback() {

            @Override
            public void setProgressFraction(float fractionDone) {
                Thread.dumpStack();
                System.out.println("---> stdout mathMapping: progress = " + (fractionDone * 100.0) + "% done");
            }

            @Override
            public void setMessage(String message) {
                Thread.dumpStack();
                System.out.println("---> stdout mathMapping: message = " + message);
            }

            @Override
            public boolean isInterrupted() {
                return false;
            }
        };
        simContext1.refreshMathDescription(callback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
        simContext2.refreshMathDescription(callback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
        Xmlproducer xmlProducer = new Xmlproducer(false);
        String simContext1XML = XmlUtil.xmlToString(xmlProducer.getXML(simContext1, bioModel));
        String simContext2XML = XmlUtil.xmlToString(xmlProducer.getXML(simContext2, bioModel));
        DiffConfiguration comparisonSetting = DiffConfiguration.COMPARE_DOCS_OTHER;
        XmlTreeDiff diffTree = XmlHelper.compareMerge(simContext1XML, simContext2XML, comparisonSetting, true);
        String baselineDesc = "application " + simContext1.getName();
        String modifiedDesc = "application " + simContext2.getName();
        TMLPanel comparePanel = new TMLPanel();
        comparePanel.setXmlTreeDiff(diffTree);
        comparePanel.setBaselineVersionDescription(baselineDesc);
        comparePanel.setModifiedVersionDescription(modifiedDesc);
        ChildWindowManager childWindowManager = ChildWindowManager.findChildWindowManager(this);
        String title = "comparing application " + simContext1.getName() + " and " + simContext2.getName();
        ChildWindow childWindow = childWindowManager.addChildWindow(comparePanel, diffTree, title, true);
        childWindow.setSize(new Dimension(600, 600));
        childWindow.show();
    } catch (XmlParseException e) {
        e.printStackTrace();
        DialogUtils.showErrorDialog(this, "failed to compare applications: \n\n" + e.getMessage());
    }
}

Example 40 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class BioModelEditorApplicationsPanel method deleteButtonPressed.

protected void deleteButtonPressed() {
    int[] rows = table.getSelectedRows();
    if (rows == null || rows.length == 0) {
        return;
    }
    String confirm = PopupGenerator.showOKCancelWarningDialog(this, "Deleting application(s)", "Are you sure you want to delete selected application(s)?");
    if (confirm.equals(UserMessage.OPTION_CANCEL)) {
        return;
    }
    ArrayList<SimulationContext> deleteList = new ArrayList<SimulationContext>();
    for (int r : rows) {
        SimulationContext simContext = tableModel.getValueAt(r);
        if (simContext != null) {
            deleteList.add(simContext);
        }
    }
    try {
        for (SimulationContext sc : deleteList) {
            deleteApplication(sc);
        }
    } catch (PropertyVetoException ex) {
        ex.printStackTrace();
        DialogUtils.showErrorDialog(BioModelEditorApplicationsPanel.this, ex.getMessage());
    }
}