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

Example 56 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 57 with SimulationContext

use of cbit.vcell.mapping.SimulationContext 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 58 with SimulationContext

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

the class BioModelEditor method createNewBiomodelFromApp.

private void createNewBiomodelFromApp() {
    SimulationContext simulationContext = getSelectedSimulationContext();
    if (simulationContext == null) {
        PopupGenerator.showErrorDialog(this, "Please select an application.");
        return;
    }
    // bioModel.getVCMetaData().cleanupMetadata();
    try {
        String newBMXML = XmlHelper.bioModelToXML(bioModel);
        BioModel newBioModel = XmlHelper.XMLToBioModel(new XMLSource(newBMXML));
        newBioModel.clearVersion();
        SimulationContext[] newBMSimcontexts = newBioModel.getSimulationContexts();
        for (int i = 0; i < newBMSimcontexts.length; i++) {
            if (!newBMSimcontexts[i].getName().equals(simulationContext.getName())) {
                // Remove sims before removing simcontext
                Simulation[] newBMSims = newBMSimcontexts[i].getSimulations();
                for (int j = 0; j < newBMSims.length; j++) {
                    newBMSimcontexts[i].removeSimulation(newBMSims[j]);
                }
                newBioModel.removeSimulationContext(newBMSimcontexts[i]);
            }
        }
        VCDocument.DocumentCreationInfo newBMDocCreateInfo = new VCDocument.DocumentCreationInfo(VCDocumentType.BIOMODEL_DOC, VCDocument.BIO_OPTION_DEFAULT);
        newBMDocCreateInfo.setPreCreatedDocument(newBioModel);
        AsynchClientTask[] newBMTasks = getBioModelWindowManager().newDocument(newBMDocCreateInfo);
        ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), newBMTasks);
    } catch (Exception e) {
        e.printStackTrace();
        PopupGenerator.showErrorDialog(this, "Error creating new BioModel from Application '" + simulationContext.getName() + "'\n" + e.getMessage());
    }
}

Example 59 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 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 60 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);
            break;
        case SIMULATIONS_NODE:
            selectTab(ApplicationPanelTabID.simulations);
            break;
        case PARAMETER_ESTIMATION_NODE:
            selectTab(ApplicationPanelTabID.parameterEstimation);
            setSelectedObjects(new Object[] { parameterEstimationPanel.getParameterEstimationTask() });
            break;
    }
}