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

Example 61 with SimulationContext

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

the class BioModelEditorApplicationPanel method setSimulationContext.

public void setSimulationContext(SimulationContext newValue) {
    if (simulationContext == newValue) {
        return;
    }
    final boolean respondingToSelectionManager = selectionManager.isBusy();
    final Object[] selectedObj = selectionManager.getSelectedObjects();
    SimulationContext oldValue = simulationContext;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(eventHandler);
    }
    if (newValue != null) {
        newValue.addPropertyChangeListener(eventHandler);
    }
    simulationContext = newValue;
    AsynchClientTask task1 = new AsynchClientTask("loading application", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            simulationContext.getGeometry().precomputeAll(new GeometryThumbnailImageFactoryAWT());
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("showing application", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            applicationGeometryPanel.setSimulationContext(simulationContext);
            applicationSpecificationsPanel.setSimulationContext(simulationContext);
            applicationProtocolsPanel.setSimulationContext(simulationContext);
            applicationSimulationsPanel.setSimulationContext(simulationContext);
            parameterEstimationPanel.setSelectionManager(null);
            showOrHideFittingPanel();
            parameterEstimationPanel.setSelectionManager(selectionManager);
            // showOrHideProtocolsPanel();
            if (respondingToSelectionManager) {
                selectionManager.setSelectedObjects(new Object[0]);
                selectionManager.setSelectedObjects(selectedObj);
            }
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
}

Example 62 with SimulationContext

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

the class BioModelEditorApplicationsPanel method getJMenuAppCopyAs.

/**
 * Return the JMenuItemCopy property value.
 * @return javax.swing.JMenuItem
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private javax.swing.JMenu getJMenuAppCopyAs() {
    if (menuAppCopyAs == null) {
        try {
            menuAppCopyAs = new javax.swing.JMenu(GuiConstants.MENU_TEXT_APP_COPYAS);
            menuItemAppNonSpatialCopyStochastic = new JMenuItem(GuiConstants.MENU_TEXT_STOCHASTIC_APPLICATION);
            menuItemAppNonSpatialCopyStochastic.setActionCommand(GuiConstants.ACTIONCMD_NON_SPATIAL_COPY_TO_STOCHASTIC_APPLICATION);
            menuItemAppNonSpatialCopyStochastic.addActionListener(eventHandler);
            menuItemNonSpatialCopyDeterministic = new javax.swing.JMenuItem(GuiConstants.MENU_TEXT_DETERMINISTIC_APPLICATION);
            menuItemNonSpatialCopyDeterministic.setActionCommand(GuiConstants.ACTIONCMD_NON_SPATIAL_COPY_TO_DETERMINISTIC_APPLICATION);
            menuItemNonSpatialCopyDeterministic.addActionListener(eventHandler);
            menuItemAppNonSpatialCopyRulebased = new javax.swing.JMenuItem(GuiConstants.MENU_TEXT_RULEBASED_APPLICATION);
            menuItemAppNonSpatialCopyRulebased.setActionCommand(GuiConstants.ACTIONCMD_NON_SPATIAL_COPY_TO_RULEBASED_APPLICATION);
            menuItemAppNonSpatialCopyRulebased.addActionListener(eventHandler);
            menuAppSpatialCopyAsNonSpatial = new JMenu(GuiConstants.MENU_TEXT_NON_SPATIAL_APPLICATION);
            menuItemAppSpatialCopyAsNonSpatialDeterministic = new JMenuItem(GuiConstants.MENU_TEXT_DETERMINISTIC_APPLICATION);
            menuItemAppSpatialCopyAsNonSpatialDeterministic.setActionCommand(GuiConstants.ACTIONCMD_SPATIAL_COPY_TO_NON_SPATIAL_DETERMINISTIC_APPLICATION);
            menuItemAppSpatialCopyAsNonSpatialDeterministic.addActionListener(eventHandler);
            menuItemAppSpatialCopyAsNonSpatialStochastic = new JMenuItem(GuiConstants.MENU_TEXT_STOCHASTIC_APPLICATION);
            menuItemAppSpatialCopyAsNonSpatialStochastic.setActionCommand(GuiConstants.ACTIONCMD_SPATIAL_COPY_TO_NON_SPATIAL_STOCHASTIC_APPLICATION);
            menuItemAppSpatialCopyAsNonSpatialStochastic.addActionListener(eventHandler);
            menuAppSpatialCopyAsNonSpatial.add(menuItemAppSpatialCopyAsNonSpatialDeterministic);
            menuAppSpatialCopyAsNonSpatial.add(menuItemAppSpatialCopyAsNonSpatialStochastic);
            menuAppSpatialCopyAsSpatial = new JMenu(GuiConstants.MENU_TEXT_SPATIAL_APPLICATION);
            menuItemAppSpatialCopyAsSpatialDeterministic = new JMenuItem(GuiConstants.MENU_TEXT_DETERMINISTIC_APPLICATION);
            menuItemAppSpatialCopyAsSpatialDeterministic.setActionCommand(GuiConstants.ACTIONCMD_SPATIAL_COPY_TO_SPATIAL_DETERMINISTIC_APPLICATION);
            menuItemAppSpatialCopyAsSpatialDeterministic.addActionListener(eventHandler);
            menuItemAppSpatialCopyAsSpatialStochastic = new JMenuItem(GuiConstants.MENU_TEXT_STOCHASTIC_APPLICATION);
            menuItemAppSpatialCopyAsSpatialStochastic.setActionCommand(GuiConstants.ACTIONCMD_SPATIAL_COPY_TO_SPATIAL_STOCHASTIC_APPLICATION);
            menuItemAppSpatialCopyAsSpatialStochastic.addActionListener(eventHandler);
            menuAppSpatialCopyAsSpatial.add(menuItemAppSpatialCopyAsSpatialDeterministic);
            menuAppSpatialCopyAsSpatial.add(menuItemAppSpatialCopyAsSpatialStochastic);
        } catch (java.lang.Throwable ivjExc) {
            handleException(ivjExc);
        }
    }
    menuAppCopyAs.removeAll();
    SimulationContext selectedSimContext = getSelectedSimulationContext();
    if (selectedSimContext != null) {
        if (selectedSimContext.getGeometry().getDimension() == 0) {
            menuAppCopyAs.add(menuItemNonSpatialCopyDeterministic);
            menuAppCopyAs.add(menuItemAppNonSpatialCopyStochastic);
            menuAppCopyAs.add(menuItemAppNonSpatialCopyRulebased);
        } else {
            menuAppCopyAs.add(menuAppSpatialCopyAsNonSpatial);
            menuAppCopyAs.add(menuAppSpatialCopyAsSpatial);
        }
    }
    return menuAppCopyAs;
}

Example 63 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());
    }
}

Example 64 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 65 with SimulationContext

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

the class BioModelEditorApplicationsTableModel method bioModelChange.

@Override
protected void bioModelChange(PropertyChangeEvent evt) {
    super.bioModelChange(evt);
    BioModel oldValue = (BioModel) evt.getOldValue();
    if (oldValue != null) {
        for (SimulationContext simulationContext : oldValue.getSimulationContexts()) {
            simulationContext.removePropertyChangeListener(this);
        }
    }
    BioModel newValue = (BioModel) evt.getNewValue();
    if (newValue != null) {
        for (SimulationContext simulationContext : newValue.getSimulationContexts()) {
            simulationContext.addPropertyChangeListener(this);
        }
    }
}