Examples with BioModelNode cbit.vcell.desktop.BioModelNode used on opensource projects

Example 51 with BioModelNode

use of cbit.vcell.desktop.BioModelNode in project vcell by virtualcell.

the class BioModelEditorTreeModel method populateApplicationsNode.

private void populateApplicationsNode(boolean bFromRoot) {
    if (bioModel.getNumSimulationContexts() == 0 && childApplicationsNodeList.size() == 0) {
        return;
    }
    boolean bSelected = false;
    boolean bFoundSelected = false;
    Map<String, Boolean> selectedInSimulationContextMap = new HashMap<String, Boolean>();
    if (selectedBioModelNode != null && applicationsNode.isNodeDescendant(selectedBioModelNode)) {
        bSelected = true;
        for (BioModelNode node : childApplicationsNodeList) {
            Object userObject = node.getUserObject();
            if (userObject instanceof SimulationContext) {
                SimulationContext simContext = (SimulationContext) userObject;
                boolean nodeDescendant = node.isNodeDescendant(selectedBioModelNode);
                selectedInSimulationContextMap.put(simContext.getName(), nodeDescendant);
            }
        }
    }
    applicationsNode.removeAllChildren();
    childApplicationsNodeList.clear();
    SimulationContext[] simulationContexts = bioModel.getSimulationContexts();
    if (simulationContexts != null && simulationContexts.length > 0) {
        simulationContexts = simulationContexts.clone();
        Arrays.sort(simulationContexts, new Comparator<SimulationContext>() {

            public int compare(SimulationContext o1, SimulationContext o2) {
                return o1.getName().compareToIgnoreCase(o2.getName());
            }
        });
        for (SimulationContext simulationContext : simulationContexts) {
            BioModelNode appNode = new BioModelNode(simulationContext, true);
            applicationsNode.add(appNode);
            childApplicationsNodeList.add(appNode);
            Object selectedUserObject = null;
            if (selectedBioModelNode != null) {
                selectedUserObject = selectedBioModelNode.getUserObject();
            }
            if (bSelected && !bFoundSelected && selectedUserObject instanceof SimulationContext && ((SimulationContext) selectedUserObject).getName().equals(((SimulationContext) appNode.getUserObject()).getName())) {
                bFoundSelected = true;
                selectedBioModelNode = appNode;
            }
            Boolean bSelectedInChild = selectedInSimulationContextMap.get(simulationContext.getName());
            boolean bSelectedInSimulationContext = false;
            if (bSelectedInChild != null) {
                bSelectedInSimulationContext = bSelectedInChild;
            }
            BioModelNode geometryNode = new BioModelNode(new DocumentEditorTreeFolderNode(DocumentEditorTreeFolderClass.GEOMETRY_NODE, true), false);
            BioModelNode settingsNode = new BioModelNode(new DocumentEditorTreeFolderNode(DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, true), false);
            BioModelNode protocolsNode = new BioModelNode(new DocumentEditorTreeFolderNode(DocumentEditorTreeFolderClass.PROTOCOLS_NODE, true), false);
            BioModelNode simulationsNode = new BioModelNode(new DocumentEditorTreeFolderNode(DocumentEditorTreeFolderClass.SIMULATIONS_NODE, true), false);
            BioModelNode fittingNode = new BioModelNode(new DocumentEditorTreeFolderNode(DocumentEditorTreeFolderClass.PARAMETER_ESTIMATION_NODE, true), false);
            BioModelNode[] applicationChildNodes = null;
            if (simulationContext.isValidForFitting()) {
                simulationContext.createDefaultParameterEstimationTask();
                applicationChildNodes = new BioModelNode[] { geometryNode, settingsNode, protocolsNode, simulationsNode, fittingNode };
            } else {
                applicationChildNodes = new BioModelNode[] { geometryNode, settingsNode, protocolsNode, simulationsNode };
            }
            for (BioModelNode node : applicationChildNodes) {
                appNode.add(node);
                if (bSelectedInSimulationContext && !bFoundSelected && selectedUserObject instanceof DocumentEditorTreeFolderNode && ((DocumentEditorTreeFolderNode) selectedUserObject).getName().equals(((DocumentEditorTreeFolderNode) node.getUserObject()).getName())) {
                    bFoundSelected = true;
                    selectedBioModelNode = node;
                }
            }
        }
    }
    nodeStructureChanged(applicationsNode);
    ownerTree.expandPath(new TreePath(applicationsNode.getPath()));
    if (bSelected) {
        if (!bFoundSelected) {
            selectedBioModelNode = applicationsNode;
        }
        if (!bFromRoot) {
            restoreTreeSelection();
        }
    }
}

Example 52 with BioModelNode

use of cbit.vcell.desktop.BioModelNode in project vcell by virtualcell.

the class BioModelsNetPanel method importFromBioModelsNet.

public void importFromBioModelsNet() {
    Object obj = tree.getLastSelectedPathComponent();
    if (obj == null || !(obj instanceof BioModelNode)) {
        return;
    }
    BioModelNode selectedNode = (BioModelNode) obj;
    Object userObject = selectedNode.getUserObject();
    if (!(userObject instanceof BioModelsNetModelInfo)) {
        return;
    }
    final BioModelsNetModelInfo bioModelsNetInfo = (BioModelsNetModelInfo) userObject;
    AsynchClientTask task1 = new AsynchClientTask("Importing " + bioModelsNetInfo.getName(), AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            BioModelsWebServicesServiceLocator bioModelsWebServicesServiceLocator = new BioModelsWebServicesServiceLocator();
            BioModelsWebServices bioModelsWebServices = bioModelsWebServicesServiceLocator.getBioModelsWebServices();
            String bioModelSBML = bioModelsWebServices.getModelSBMLById(bioModelsNetInfo.getId());
            ExternalDocInfo externalDocInfo = ExternalDocInfo.createBioModelsNetExternalDocInfo(bioModelSBML, bioModelsNetInfo.getName());
            if (externalDocInfo != null) {
                hashTable.put("externalDocInfo", externalDocInfo);
            }
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("Opening", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ExternalDocInfo externalDocInfo = (ExternalDocInfo) hashTable.get("externalDocInfo");
            if (externalDocInfo == null) {
                return;
            }
            documentWindowManager.getRequestManager().openDocument(externalDocInfo, documentWindowManager, true);
        }
    };
    ClientTaskDispatcher.dispatch(documentWindowManager.getComponent(), new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 }, false);
}

Example 53 with BioModelNode

use of cbit.vcell.desktop.BioModelNode in project vcell by virtualcell.

the class DocumentEditor method selectClickPath.

private void selectClickPath(MouseEvent e) {
    Point mousePoint = e.getPoint();
    TreePath clickPath = documentEditorTree.getPathForLocation(mousePoint.x, mousePoint.y);
    if (clickPath == null) {
        return;
    }
    Object rightClickNode = clickPath.getLastPathComponent();
    if (rightClickNode == null || !(rightClickNode instanceof BioModelNode)) {
        return;
    }
    TreePath[] selectedPaths = documentEditorTree.getSelectionPaths();
    if (selectedPaths == null || selectedPaths.length == 0) {
        return;
    }
    boolean bFound = false;
    for (TreePath tp : selectedPaths) {
        if (tp.equals(clickPath)) {
            bFound = true;
            break;
        }
    }
    if (!bFound) {
        documentEditorTree.setSelectionPath(clickPath);
    }
}

Example 54 with BioModelNode

use of cbit.vcell.desktop.BioModelNode in project vcell by virtualcell.

the class DocumentEditor method construcutPopupMenu.

private void construcutPopupMenu() {
    popupMenu.removeAll();
    TreePath[] selectedPaths = documentEditorTree.getSelectionPaths();
    boolean bRename = false;
    boolean bExpand = true;
    boolean bAddNew = false;
    boolean bAddNewApp = false;
    boolean bCopyApp = false;
    boolean bDelete = false;
    boolean bNewBiomodel = false;
    boolean bRemoveApps = false;
    DocumentEditorTreeFolderClass folderClass = null;
    for (TreePath tp : selectedPaths) {
        Object obj = tp.getLastPathComponent();
        if (obj == null || !(obj instanceof BioModelNode)) {
            continue;
        }
        if (documentEditorTree.getModel().isLeaf(obj)) {
            bExpand = false;
        }
        BioModelNode selectedNode = (BioModelNode) obj;
        Object userObject = selectedNode.getUserObject();
        if (userObject instanceof DocumentEditorTreeFolderNode) {
            folderClass = ((DocumentEditorTreeFolderNode) userObject).getFolderClass();
            if (folderClass == DocumentEditorTreeFolderClass.APPLICATIONS_NODE) {
                bAddNewApp = true;
                if (selectedNode.getChildCount() > 0) {
                    bRemoveApps = true;
                }
            } else if (folderClass == DocumentEditorTreeFolderClass.REACTIONS_NODE || folderClass == DocumentEditorTreeFolderClass.STRUCTURES_NODE || folderClass == DocumentEditorTreeFolderClass.SPECIES_NODE || folderClass == DocumentEditorTreeFolderClass.MOLECULAR_TYPES_NODE || folderClass == DocumentEditorTreeFolderClass.OBSERVABLES_NODE || folderClass == DocumentEditorTreeFolderClass.MATH_SIMULATIONS_NODE) {
                bAddNew = (selectedPaths.length == 1);
                bRename = false;
            }
        } else if (userObject instanceof SimulationContext) {
            bRename = true;
            bCopyApp = true;
            bDelete = true;
            bNewBiomodel = true;
        }
    }
    if (selectedPaths.length != 1) {
        bRename = false;
    }
    if (bAddNewApp) {
        if (addNewAppMenu == null) {
            addNewAppMenu = new JMenu("New Application");
            addNewAppDeterministicMenuItem = new JMenuItem(GuiConstants.MENU_TEXT_DETERMINISTIC_APPLICATION);
            addNewAppDeterministicMenuItem.addActionListener(eventHandler);
            addNewAppStochasticMenuItem = new JMenuItem(GuiConstants.MENU_TEXT_STOCHASTIC_APPLICATION);
            addNewAppStochasticMenuItem.addActionListener(eventHandler);
            addNewAppRulebasedMenuItem = new JMenuItem(GuiConstants.MENU_TEXT_RULEBASED_APPLICATION);
            addNewAppRulebasedMenuItem.addActionListener(eventHandler);
            addNewAppMenu.add(addNewAppDeterministicMenuItem);
            addNewAppMenu.add(addNewAppStochasticMenuItem);
            addNewAppMenu.add(addNewAppRulebasedMenuItem);
        }
        popupMenu.add(addNewAppMenu);
    }
    if (bRemoveApps) {
        if (removeAppsMenu == null) {
            removeAppsMenu = new JMenuItem("Remove Apps...");
            removeAppsMenu.addActionListener(eventHandler);
        }
        popupMenu.add(removeAppsMenu);
    }
    if (bAddNew) {
        String addText = "New";
        if (folderClass == DocumentEditorTreeFolderClass.REACTIONS_NODE) {
            addText += " Reaction";
        } else if (folderClass == DocumentEditorTreeFolderClass.STRUCTURES_NODE) {
            addText += " Compartment";
        } else if (folderClass == DocumentEditorTreeFolderClass.SPECIES_NODE) {
            addText += " Species";
        } else if (folderClass == DocumentEditorTreeFolderClass.MOLECULAR_TYPES_NODE) {
            addText += " Molecule";
        } else if (folderClass == DocumentEditorTreeFolderClass.OBSERVABLES_NODE) {
            addText += " Observable";
        } else if (folderClass == DocumentEditorTreeFolderClass.MATH_SIMULATIONS_NODE) {
            addText += " Simulation";
        }
        addNewMenuItem = new javax.swing.JMenuItem(addText);
        addNewMenuItem.addActionListener(eventHandler);
        popupMenu.add(addNewMenuItem);
    }
    if (bRename) {
        if (renameMenuItem == null) {
            renameMenuItem = new javax.swing.JMenuItem("Rename");
            renameMenuItem.addActionListener(eventHandler);
        }
        popupMenu.add(renameMenuItem);
    }
    if (bDelete) {
        if (deleteMenuItem == null) {
            deleteMenuItem = new javax.swing.JMenuItem("Delete");
            deleteMenuItem.addActionListener(eventHandler);
        }
        popupMenu.add(deleteMenuItem);
    }
    if (bCopyApp) {
        if (menuItemAppCopy == null) {
            menuItemAppCopy = new JMenuItem(GuiConstants.MENU_TEXT_APP_COPY);
            menuItemAppCopy.addActionListener(eventHandler);
            menuItemAppCopy.setActionCommand(GuiConstants.ACTIONCMD_COPY_APPLICATION);
        }
        if (menuAppCopyAs == null) {
            menuAppCopyAs = new JMenu(GuiConstants.MENU_TEXT_APP_COPYAS);
        }
        menuAppCopyAs.removeAll();
        SimulationContext selectedSimContext = getSelectedSimulationContext();
        if (selectedSimContext != null) {
            if (selectedSimContext.getGeometry().getDimension() == 0) {
                if (menuItemNonSpatialCopyDeterministic == null) {
                    menuItemNonSpatialCopyStochastic = new JMenuItem(GuiConstants.MENU_TEXT_STOCHASTIC_APPLICATION);
                    menuItemNonSpatialCopyStochastic.setActionCommand(GuiConstants.ACTIONCMD_NON_SPATIAL_COPY_TO_STOCHASTIC_APPLICATION);
                    menuItemNonSpatialCopyStochastic.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);
                    menuItemNonSpatialCopyRulebased = new javax.swing.JMenuItem(GuiConstants.MENU_TEXT_RULEBASED_APPLICATION);
                    menuItemNonSpatialCopyRulebased.setActionCommand(GuiConstants.ACTIONCMD_NON_SPATIAL_COPY_TO_RULEBASED_APPLICATION);
                    menuItemNonSpatialCopyRulebased.addActionListener(eventHandler);
                }
                menuAppCopyAs.add(menuItemNonSpatialCopyDeterministic);
                menuAppCopyAs.add(menuItemNonSpatialCopyStochastic);
                menuAppCopyAs.add(menuItemNonSpatialCopyRulebased);
            } else {
                if (menuSpatialCopyAsNonSpatial == null) {
                    menuSpatialCopyAsNonSpatial = new JMenu(GuiConstants.MENU_TEXT_NON_SPATIAL_APPLICATION);
                    menuItemSpatialCopyAsNonSpatialDeterministic = new JMenuItem(GuiConstants.MENU_TEXT_DETERMINISTIC_APPLICATION);
                    menuItemSpatialCopyAsNonSpatialDeterministic.setActionCommand(GuiConstants.ACTIONCMD_SPATIAL_COPY_TO_NON_SPATIAL_DETERMINISTIC_APPLICATION);
                    menuItemSpatialCopyAsNonSpatialDeterministic.addActionListener(eventHandler);
                    menuItemSpatialCopyAsNonSpatialStochastic = new JMenuItem(GuiConstants.MENU_TEXT_STOCHASTIC_APPLICATION);
                    menuItemSpatialCopyAsNonSpatialStochastic.setActionCommand(GuiConstants.ACTIONCMD_SPATIAL_COPY_TO_NON_SPATIAL_STOCHASTIC_APPLICATION);
                    menuItemSpatialCopyAsNonSpatialStochastic.addActionListener(eventHandler);
                    menuItemSpatialCopyAsNonSpatialRulebased = new JMenuItem(GuiConstants.MENU_TEXT_RULEBASED_APPLICATION);
                    menuItemSpatialCopyAsNonSpatialRulebased.setActionCommand(GuiConstants.ACTIONCMD_SPATIAL_COPY_TO_NON_SPATIAL_RULEBASED_APPLICATION);
                    menuItemSpatialCopyAsNonSpatialRulebased.addActionListener(eventHandler);
                    menuSpatialCopyAsNonSpatial.add(menuItemSpatialCopyAsNonSpatialDeterministic);
                    menuSpatialCopyAsNonSpatial.add(menuItemSpatialCopyAsNonSpatialStochastic);
                    menuSpatialCopyAsNonSpatial.add(menuItemSpatialCopyAsNonSpatialRulebased);
                    menuSpatialCopyAsSpatial = new JMenu(GuiConstants.MENU_TEXT_SPATIAL_APPLICATION);
                    menuItemSpatialCopyAsSpatialDeterministic = new JMenuItem(GuiConstants.MENU_TEXT_DETERMINISTIC_APPLICATION);
                    menuItemSpatialCopyAsSpatialDeterministic.setActionCommand(GuiConstants.ACTIONCMD_SPATIAL_COPY_TO_SPATIAL_DETERMINISTIC_APPLICATION);
                    menuItemSpatialCopyAsSpatialDeterministic.addActionListener(eventHandler);
                    menuItemSpatialCopyAsSpatialStochastic = new JMenuItem(GuiConstants.MENU_TEXT_STOCHASTIC_APPLICATION);
                    menuItemSpatialCopyAsSpatialStochastic.setActionCommand(GuiConstants.ACTIONCMD_SPATIAL_COPY_TO_SPATIAL_STOCHASTIC_APPLICATION);
                    menuItemSpatialCopyAsSpatialStochastic.addActionListener(eventHandler);
                    menuItemSpatialCopyAsSpatialRulebased = new JMenuItem(GuiConstants.MENU_TEXT_RULEBASED_APPLICATION);
                    menuItemSpatialCopyAsSpatialRulebased.setActionCommand(GuiConstants.ACTIONCMD_SPATIAL_COPY_TO_SPATIAL_RULEBASED_APPLICATION);
                    menuItemSpatialCopyAsSpatialRulebased.addActionListener(eventHandler);
                    menuSpatialCopyAsSpatial.add(menuItemSpatialCopyAsSpatialDeterministic);
                    menuSpatialCopyAsSpatial.add(menuItemSpatialCopyAsSpatialStochastic);
                // menuSpatialCopyAsSpatial.add(menuItemSpatialCopyAsSpatialRulebased);		// not supported yet, uncomment when time comes
                }
                menuAppCopyAs.add(menuSpatialCopyAsNonSpatial);
                menuAppCopyAs.add(menuSpatialCopyAsSpatial);
            }
        }
        if (popupMenu.getComponents().length > 0) {
            popupMenu.add(new JSeparator());
        }
        popupMenu.add(menuItemAppCopy);
        popupMenu.add(menuAppCopyAs);
    }
    if (bNewBiomodel) {
        menuItemNewBiomodelFromApp = new JMenuItem(GuiConstants.MENU_TEXT_APP_NEWBIOMODEL);
        menuItemNewBiomodelFromApp.addActionListener(eventHandler);
        popupMenu.add(menuItemNewBiomodelFromApp);
    }
    if (bExpand) {
        if (expandAllMenuItem == null) {
            popupMenuSeparator = new JSeparator();
            expandAllMenuItem = new javax.swing.JMenuItem("Expand All");
            collapseAllMenuItem = new javax.swing.JMenuItem("Collapse All");
            expandAllMenuItem.addActionListener(eventHandler);
            collapseAllMenuItem.addActionListener(eventHandler);
        }
        if (popupMenu.getComponents().length > 0) {
            popupMenu.add(popupMenuSeparator);
        }
        popupMenu.add(expandAllMenuItem);
        popupMenu.add(collapseAllMenuItem);
    }
}

Example 55 with BioModelNode

use of cbit.vcell.desktop.BioModelNode in project vcell by virtualcell.

the class DocumentEditorTreeModel method valueForPathChanged.

@Override
public void valueForPathChanged(TreePath path, Object newValue) {
    if (!(newValue instanceof String)) {
        return;
    }
    String newName = (String) newValue;
    try {
        if (newName == null || newName.length() == 0) {
            return;
        }
        Object obj = path.getLastPathComponent();
        if (obj == null || !(obj instanceof BioModelNode)) {
            return;
        }
        BioModelNode selectedNode = (BioModelNode) obj;
        Object userObject = selectedNode.getUserObject();
        if (userObject instanceof SimulationContext) {
            ((SimulationContext) userObject).setName(newName);
        }
    } catch (Exception ex) {
        DialogUtils.showErrorDialog(ownerTree, ex.getMessage());
    }
}