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

Example 41 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 42 with SimulationContext

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

the class BioModelEditor method setRightTopPanel.

private void setRightTopPanel(Object selectedObject, SimulationContext simulationContext) {
    JComponent newTopPanel = emptyPanel;
    // DEFAULT_DIVIDER_LOCATION;
    int dividerLocation = rightSplitPane.getDividerLocation();
    if (selectedObject instanceof Model) {
        newTopPanel = bioModelEditorModelPanel;
    } else if (selectedObject instanceof BioModel || selectedObject instanceof VCMetaData || selectedObject instanceof MiriamResource) {
        newTopPanel = bioModelPropertiesPanel;
        bioModelPropertiesPanel.setBioModel(bioModel);
    } else if (selectedObject instanceof SimulationContext) {
        newTopPanel = bioModelEditorApplicationPanel;
        bioModelEditorApplicationPanel.setSimulationContext(simulationContext);
    } else if (selectedObject instanceof DocumentEditorTreeFolderNode) {
        DocumentEditorTreeFolderNode folderNode = (DocumentEditorTreeFolderNode) selectedObject;
        DocumentEditorTreeFolderClass folderClass = folderNode.getFolderClass();
        if (folderClass == DocumentEditorTreeFolderClass.MODEL_NODE) {
            newTopPanel = bioModelEditorModelPanel;
        } else if (folderClass == DocumentEditorTreeFolderClass.STRUCTURES_NODE || folderClass == DocumentEditorTreeFolderClass.SPECIES_NODE || folderClass == DocumentEditorTreeFolderClass.MOLECULAR_TYPES_NODE || folderClass == DocumentEditorTreeFolderClass.OBSERVABLES_NODE || folderClass == DocumentEditorTreeFolderClass.REACTIONS_NODE || folderClass == DocumentEditorTreeFolderClass.REACTION_DIAGRAM_NODE) // || folderClass == DocumentEditorTreeFolderClass.STRUCTURE_DIAGRAM_NODE
        {
            newTopPanel = bioModelEditorModelPanel;
        } else if (folderClass == DocumentEditorTreeFolderClass.PATHWAY_DIAGRAM_NODE || folderClass == DocumentEditorTreeFolderClass.PATHWAY_OBJECTS_NODE || folderClass == DocumentEditorTreeFolderClass.BIOPAX_SUMMARY_NODE || folderClass == DocumentEditorTreeFolderClass.BIOPAX_TREE_NODE) {
            newTopPanel = bioModelEditorPathwayDiagramPanel;
        } else if (folderClass == DocumentEditorTreeFolderClass.PATHWAY_NODE) {
            newTopPanel = getBioModelEditorPathwayDiagramPanel();
            getBioModelEditorPathwayDiagramPanel().setBioModel(bioModel);
        } else if (folderClass == DocumentEditorTreeFolderClass.BIOMODEL_PARAMETERS_NODE) {
            newTopPanel = bioModelParametersPanel;
        } else if (folderClass == DocumentEditorTreeFolderClass.APPLICATIONS_NODE) {
            newTopPanel = bioModelEditorApplicationsPanel;
        // } else if (folderClass == DocumentEditorTreeFolderClass.DATA_NODE) {
        // newTopPanel = dataSymbolsPanel;
        } else if (folderClass == DocumentEditorTreeFolderClass.SCRIPTING_NODE) {
            newTopPanel = getScriptingPanel();
        } else if (folderClass == DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE || folderClass == DocumentEditorTreeFolderClass.PROTOCOLS_NODE || folderClass == DocumentEditorTreeFolderClass.SIMULATIONS_NODE || folderClass == DocumentEditorTreeFolderClass.GEOMETRY_NODE || folderClass == DocumentEditorTreeFolderClass.PARAMETER_ESTIMATION_NODE) {
            newTopPanel = bioModelEditorApplicationPanel;
            bioModelEditorApplicationPanel.setSimulationContext(simulationContext);
        }
    }
    Component rightTopComponent = rightSplitPane.getTopComponent();
    if (rightTopComponent != newTopPanel) {
        rightSplitPane.setTopComponent(newTopPanel);
    }
    rightSplitPane.setDividerLocation(dividerLocation);
    getSimulationConsolePanel().setSimulationContext(simulationContext);
    if (simulationContext == null) {
        rightBottomTabbedPane.remove(getSimulationConsolePanel());
    } else {
        // show the console only for bionetgen deterministic applications (flattened network)
        if (simulationContext.getApplicationType() == Application.RULE_BASED_STOCHASTIC) {
            // if(simulationContext.isRuleBased() || simulationContext.isStoch()) {
            // if(simulationContext.isStoch()) {
            rightBottomTabbedPane.remove(getSimulationConsolePanel());
            return;
        }
        boolean bHasRules = simulationContext.getModel().getRbmModelContainer().hasRules();
        if (!bHasRules) {
            rightBottomTabbedPane.remove(getSimulationConsolePanel());
            return;
        }
        // rightBottomTabbedPane.addTab("Network Console", new TabCloseIcon(), getSimulationConsolePanel());
        rightBottomTabbedPane.addTab("Network Generation Status", getSimulationConsolePanel());
    }
}

Example 43 with SimulationContext

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

the class BioModelEditorApplicationPanel method onActiveViewChange.

@Override
protected void onActiveViewChange(ActiveView activeView) {
    super.onActiveViewChange(activeView);
    SimulationContext selectedSimContext = activeView.getSimulationContext();
    DocumentEditorTreeFolderClass folderClass = activeView.getDocumentEditorTreeFolderClass();
    if (folderClass == null) {
        return;
    }
    switch(folderClass) {
        case GEOMETRY_NODE:
            selectTab(ApplicationPanelTabID.geometry);
            break;
        case SPECIFICATIONS_NODE:
            selectTab(ApplicationPanelTabID.settings);
            break;
        case PROTOCOLS_NODE:
            selectTab(ApplicationPanelTabID.protocols);
            applicationProtocolsPanel.selectTab(activeView.getActiveViewID());
            break;
        case SIMULATIONS_NODE:
            selectTab(ApplicationPanelTabID.simulations);
            break;
        case PARAMETER_ESTIMATION_NODE:
            selectTab(ApplicationPanelTabID.parameterEstimation);
            setSelectedObjects(new Object[] { parameterEstimationPanel.getParameterEstimationTask() });
            break;
    }
}

Example 44 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);
            if (respondingToSelectionManager) {
                selectionManager.setSelectedObjects(new Object[0]);
                selectionManager.setSelectedObjects(selectedObj);
            }
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
}

Example 45 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);
        }
    }
}