Examples with DocumentEditorTreeFolderNode cbit.vcell.client.desktop.biomodel.DocumentEditorTreeModel.DocumentEditorTreeFolderNode used on opensource projects

Example 1 with DocumentEditorTreeFolderNode

use of cbit.vcell.client.desktop.biomodel.DocumentEditorTreeModel.DocumentEditorTreeFolderNode in project vcell by virtualcell.

the class DocumentEditor method treeSelectionChanged0.

private void treeSelectionChanged0(TreeSelectionEvent treeSelectionEvent) {
    try {
        treeSelectionChanged();
        Object selectedNode = documentEditorTree.getLastSelectedPathComponent();
        if (selectedNode != null && (selectedNode instanceof BioModelNode)) {
            Object selectedObject = ((BioModelNode) selectedNode).getUserObject();
            DocumentEditorTreeFolderClass folderClass = null;
            if (selectedObject instanceof DocumentEditorTreeFolderNode) {
                folderClass = ((DocumentEditorTreeFolderNode) selectedObject).getFolderClass();
            }
            ActiveView activeView = new ActiveView(getSelectedSimulationContext(), folderClass, null);
            selectionManager.setActiveView(activeView);
            if (/*selectedObject instanceof SimulationContext 
					|| */
            selectedObject instanceof BioModel || selectedObject instanceof MathModel) {
                selectionManager.setSelectedObjects(new Object[] { selectedObject });
            }
        }
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
    }
}

Example 2 with DocumentEditorTreeFolderNode

use of cbit.vcell.client.desktop.biomodel.DocumentEditorTreeModel.DocumentEditorTreeFolderNode 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 3 with DocumentEditorTreeFolderNode

use of cbit.vcell.client.desktop.biomodel.DocumentEditorTreeModel.DocumentEditorTreeFolderNode in project vcell by virtualcell.

the class BioModelEditor method setRightBottomPanelOnSelection.

@Override
protected void setRightBottomPanelOnSelection(Object[] selections) {
    if (selections == null) {
        return;
    }
    JComponent bottomComponent = rightBottomEmptyPanel;
    int destComponentIndex = DocumentEditorTabID.object_properties.ordinal();
    boolean bShowInDatabaseProperties = false;
    boolean bShowPathway = false;
    if (selections.length == 1) {
        Object singleSelection = selections[0];
        if (singleSelection instanceof ReactionStep) {
            bottomComponent = getReactionPropertiesPanel();
        } else if (singleSelection instanceof ReactionRule) {
            bottomComponent = getReactionRulePropertiesPanel();
        } else if (singleSelection instanceof SpeciesContext) {
            bottomComponent = getSpeciesPropertiesPanel();
        } else if (singleSelection instanceof MolecularType) {
            bottomComponent = getMolecularTypePropertiesPanel();
        } else if (singleSelection instanceof RbmObservable) {
            bottomComponent = getObservablePropertiesPanel();
        } else if (singleSelection instanceof Structure) {
            bottomComponent = getStructurePropertiesPanel();
            getStructurePropertiesPanel().setModel(bioModel.getModel());
        } else if (singleSelection instanceof Parameter) {
            bottomComponent = getParameterPropertiesPanel();
        } else if (singleSelection instanceof SimulationContext) {
            bottomComponent = getApplicationPropertiesPanel();
        } else if (singleSelection instanceof ParameterEstimationTask) {
            bottomComponent = parameterEstimationTaskPropertiesPanel;
        } else if (singleSelection instanceof Product || singleSelection instanceof Reactant) {
            bottomComponent = getReactionParticipantPropertiesPanel();
        } else if (singleSelection instanceof BioModelInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = bioModelMetaDataPanel;
        } else if (singleSelection instanceof MathModelInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = mathModelMetaDataPanel;
        } else if (singleSelection instanceof GeometryInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = geometryMetaDataPanel;
        } else if (singleSelection instanceof SpeciesContextSpec) {
            bottomComponent = getSpeciesContextSpecPanel();
        } else if (singleSelection instanceof ReactionSpec) {
            bottomComponent = getKineticsTypeTemplatePanel();
        } else if (singleSelection instanceof ReactionRuleSpec) {
            // 
            bottomComponent = getReactionRuleSpecPropertiesPanel();
        } else if (singleSelection instanceof BioModelsNetModelInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = getBioModelsNetPropertiesPanel();
        } else if (singleSelection instanceof Simulation) {
            bottomComponent = getSimulationSummaryPanel();
        } else if (singleSelection instanceof DataSymbol) {
            bottomComponent = getDataSymbolsSpecPanel();
        } else if (singleSelection instanceof BioEvent) {
            bottomComponent = getEventPanel();
        } else if (singleSelection instanceof SpatialObject) {
            bottomComponent = getSpatialObjectPropertyPanel();
        } else if (singleSelection instanceof SpatialProcess) {
            bottomComponent = getSpatialProcessPropertyPanel();
        } else if (singleSelection instanceof BioPaxObject) {
            bottomComponent = bioPaxObjectPropertiesPanel;
        } else if (singleSelection instanceof BioModel || singleSelection instanceof VCMetaData) {
            bottomComponent = bioModelEditorAnnotationPanel;
        } else if (singleSelection instanceof PathwayData) {
            bShowPathway = true;
            bottomComponent = getBioModelEditorPathwayPanel();
        } else if (singleSelection instanceof Model) {
        } else if (singleSelection instanceof RuleParticipantSignature) {
            bottomComponent = getReactionRuleParticipantSignaturePropertiesPanel();
        } else if (singleSelection instanceof CSGObject) {
            bottomComponent = csgObjectPropertiesPanel;
            csgObjectPropertiesPanel.setSimulationContext(getSelectedSimulationContext());
        } else if (singleSelection instanceof DocumentEditorTreeFolderNode) {
            DocumentEditorTreeFolderClass folderClass = ((DocumentEditorTreeFolderNode) singleSelection).getFolderClass();
            if ((folderClass == DocumentEditorTreeFolderClass.REACTIONS_NODE) && !(singleSelection instanceof ReactionRule)) {
                bottomComponent = getReactionPropertiesPanel();
            } else if ((folderClass == DocumentEditorTreeFolderClass.REACTIONS_NODE) && (singleSelection instanceof ReactionRule)) {
                bottomComponent = getReactionRulePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.STRUCTURES_NODE) {
                bottomComponent = getStructurePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.SPECIES_NODE) {
                bottomComponent = getSpeciesPropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.MOLECULAR_TYPES_NODE) {
                bottomComponent = getMolecularTypePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.OBSERVABLES_NODE) {
                bottomComponent = getObservablePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.APPLICATIONS_NODE) {
                bottomComponent = getApplicationsPropertiesPanel();
                getApplicationsPropertiesPanel().setBioModel(bioModel);
            } else if (folderClass == DocumentEditorTreeFolderClass.PARAMETER_ESTIMATION_NODE) {
                bottomComponent = parameterEstimationTaskPropertiesPanel;
            }
        }
    }
    if (bShowPathway) {
        for (destComponentIndex = 0; destComponentIndex < rightBottomTabbedPane.getTabCount(); destComponentIndex++) {
            if (rightBottomTabbedPane.getComponentAt(destComponentIndex) == bottomComponent) {
                break;
            }
        }
        String tabTitle = "Pathway Preview";
        if (rightBottomTabbedPane.getTabCount() == destComponentIndex) {
            rightBottomTabbedPane.addTab(tabTitle, new TabCloseIcon(), bottomComponent);
        }
    } else if (bShowInDatabaseProperties) {
        for (destComponentIndex = 0; destComponentIndex < rightBottomTabbedPane.getTabCount(); destComponentIndex++) {
            Component c = rightBottomTabbedPane.getComponentAt(destComponentIndex);
            if (c == bioModelMetaDataPanel || c == mathModelMetaDataPanel || c == geometryMetaDataPanel || c == getBioModelsNetPropertiesPanel()) {
                break;
            }
        }
        if (rightBottomTabbedPane.getTabCount() == destComponentIndex) {
            rightBottomTabbedPane.addTab(DATABASE_PROPERTIES_TAB_TITLE, new TabCloseIcon(), bottomComponent);
        }
    }
    if (rightBottomTabbedPane.getComponentAt(destComponentIndex) != bottomComponent) {
        bottomComponent.setBorder(GuiConstants.TAB_PANEL_BORDER);
        rightBottomTabbedPane.setComponentAt(destComponentIndex, bottomComponent);
        rightSplitPane.repaint();
    }
    if (rightBottomTabbedPane.getSelectedComponent() != bottomComponent) {
        rightBottomTabbedPane.setSelectedComponent(bottomComponent);
    }
}

Example 4 with DocumentEditorTreeFolderNode

use of cbit.vcell.client.desktop.biomodel.DocumentEditorTreeModel.DocumentEditorTreeFolderNode 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 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 5 with DocumentEditorTreeFolderNode

use of cbit.vcell.client.desktop.biomodel.DocumentEditorTreeModel.DocumentEditorTreeFolderNode in project vcell by virtualcell.

the class MathModelEditor method setRightTopPanel.

private void setRightTopPanel(Object selectedObject) {
    JComponent newTopPanel = emptyPanel;
    int dividerLocation = rightSplitPane.getDividerLocation();
    if (selectedObject == mathModel) {
        newTopPanel = mathModelPropertiesPanel;
        mathModelPropertiesPanel.setMathModel(mathModel);
    } else if (selectedObject instanceof DocumentEditorTreeFolderNode) {
        DocumentEditorTreeFolderNode folderNode = (DocumentEditorTreeFolderNode) selectedObject;
        DocumentEditorTreeFolderClass folderClass = folderNode.getFolderClass();
        if (folderClass == DocumentEditorTreeFolderClass.MATH_ANNOTATION_NODE) {
            newTopPanel = mathModelPropertiesPanel;
        } else if (folderClass == DocumentEditorTreeFolderClass.MATH_VCML_NODE) {
            newTopPanel = vcmlEditorPanel;
        } else if (folderClass == DocumentEditorTreeFolderClass.MATH_GEOMETRY_NODE) {
            newTopPanel = geometryViewer;
        } else if (folderClass == DocumentEditorTreeFolderClass.MATH_SIMULATIONS_NODE) {
            newTopPanel = simulationListPanel;
        } else if (folderClass == DocumentEditorTreeFolderClass.MATH_OUTPUT_FUNCTIONS_NODE) {
            newTopPanel = outputFunctionsPanel;
            outputFunctionsPanel.setSimulationWorkspace(mathModelWindowManager.getSimulationWorkspace());
        }
    }
    Component rightTopComponent = rightSplitPane.getTopComponent();
    if (rightTopComponent != newTopPanel) {
        newTopPanel.setBorder(GuiConstants.TAB_PANEL_BORDER);
        rightSplitPane.setTopComponent(newTopPanel);
    }
    rightSplitPane.setDividerLocation(dividerLocation);
}