Examples with GeometryInfo cbit.vcell.geometry.GeometryInfo used on opensource projects

Example 11 with GeometryInfo

use of cbit.vcell.geometry.GeometryInfo in project vcell by virtualcell.

the class BioModelEditor method setRightBottomPanelOnSelection.

@Override
protected void setRightBottomPanelOnSelection(Object[] selections) {
    if (selections == null) {
        return;
    }
    // TODO: here
    JComponent bottomComponent = rightBottomEmptyPanel;
    JComponent annotationComponent = rightBottomEmptyAnnotationsPanel;
    // properties panel
    int destComponentIndex = DocumentEditorTabID.object_properties.ordinal();
    // annotations panel
    int annComponentIndex = DocumentEditorTabID.annotations.ordinal();
    boolean bShowInDatabaseProperties = false;
    boolean bShowPathway = false;
    if (selections.length == 1) {
        annotationComponent = getAnnotationsPanel();
        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 BioModelNode.PublicationInfoNode) {
            bShowInDatabaseProperties = true;
            bottomComponent = bioModelMetaDataPanel;
        } 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) {
            // only contains Notes, is displayed in the Object Properties Panel
            bottomComponent = bioModelEditorAnnotationPanel;
        } else if (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;
            }
        } else if (singleSelection instanceof SelectionManager.AnnotationNavigator) {
            Object entity = ((SelectionManager.AnnotationNavigator) singleSelection).getEntity();
            if (entity instanceof ReactionStep) {
                bottomComponent = getReactionPropertiesPanel();
            } else if (entity instanceof SpeciesContext) {
                bottomComponent = getSpeciesPropertiesPanel();
            } else if (entity instanceof Structure) {
                // Observables. MolecularType, Structures
                bottomComponent = getStructurePropertiesPanel();
            } else if (entity instanceof MolecularType) {
                bottomComponent = getMolecularTypePropertiesPanel();
            } else if (entity instanceof RbmObservable) {
                bottomComponent = getObservablePropertiesPanel();
            } else {
                bottomComponent = bioModelEditorAnnotationPanel;
            }
        }
    }
    if (bShowPathway) {
        int numTabs = rightBottomTabbedPane.getTabCount();
        for (destComponentIndex = 0; destComponentIndex < numTabs; destComponentIndex++) {
            Component current = rightBottomTabbedPane.getComponentAt(destComponentIndex);
            if (current == 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);
        annotationComponent.setBorder(GuiConstants.TAB_PANEL_BORDER);
        rightBottomTabbedPane.setComponentAt(destComponentIndex, bottomComponent);
        rightBottomTabbedPane.setComponentAt(annComponentIndex, annotationComponent);
        rightSplitPane.repaint();
    }
    Component selectedComponent = rightBottomTabbedPane.getSelectedComponent();
    if (selections.length == 1 && selections[0] instanceof BioModel && bottomComponent instanceof BioModelEditorAnnotationPanel) {
        // if the biomodel name is selected in the upper left tree, we select the Annotations tab
        rightBottomTabbedPane.setSelectedComponent(annotationComponent);
    } else if (selections.length == 1 && selections[0] instanceof SelectionManager.AnnotationNavigator && selections[0] instanceof SelectionManager.AnnotationNavigator) {
        // we want to navigate to the AnnotationPanel
        rightBottomTabbedPane.setSelectedComponent(annotationComponent);
    // } else if(selections.length == 1 && selections[0] instanceof SelectionManager.AnnotationNavigator && bottomComponent instanceof BioModelEditorAnnotationPanel) {
    // // we want to navigate to the AnnotationPanel (old way)
    // rightBottomTabbedPane.setSelectedComponent(annotationComponent);
    } else if (selectedComponent != bottomComponent) /* && rightBottomTabbedPane.getSelectedComponent() != annotationComponent */
    {
        rightBottomTabbedPane.setSelectedComponent(bottomComponent);
    }
}

Example 12 with GeometryInfo

use of cbit.vcell.geometry.GeometryInfo in project vcell by virtualcell.

the class DatabaseWindowPanel method currentDocumentInfo.

/**
 * Comment
 */
private void currentDocumentInfo() {
    VCDocumentInfo selectedDocInfo = null;
    switch(getJTabbedPane1().getSelectedIndex()) {
        case 0:
            {
                // VCDocumentType.BIOMODEL_DOC
                selectedDocInfo = (BioModelInfo) getBioModelDbTreePanel1().getSelectedVersionInfo();
                break;
            }
        case 1:
            {
                // VCDocumentType.MATHMODEL_DOC
                selectedDocInfo = (MathModelInfo) getMathModelDbTreePanel1().getSelectedVersionInfo();
                break;
            }
        case 2:
            {
                // VCDocumentType.GEOMETRY_DOC
                selectedDocInfo = (GeometryInfo) getGeometryTreePanel1().getSelectedVersionInfo();
                break;
            }
    }
    setSelectedDocumentInfo(selectedDocInfo);
}

Example 13 with GeometryInfo

use of cbit.vcell.geometry.GeometryInfo in project vcell by virtualcell.

the class VCDocumentDbTreeModel method initOwners.

protected static synchronized TreeMap<String, BioModelNode> initOwners(VCDocumentInfo[] vcDocumentInfos, User loginUser, VCDocumentDbTreeModel subTreeParent, Method subTreeMethod) {
    // 
    // get list of users (owners)
    // 
    Vector<User> userList = new Vector<User>();
    userList.addElement(loginUser);
    for (int i = 0; i < vcDocumentInfos.length; i++) {
        VCDocumentInfo vcDocumentInfo = vcDocumentInfos[i];
        if (!userList.contains(vcDocumentInfo.getVersion().getOwner())) {
            userList.addElement(vcDocumentInfo.getVersion().getOwner());
        }
    }
    // 
    // for each user
    // 
    TreeMap<String, BioModelNode> treeMap = new TreeMap<String, BioModelNode>(new Comparator<String>() {

        public int compare(String o1, String o2) {
            return o1.compareToIgnoreCase(o2);
        }
    });
    for (int ownerIndex = 0; ownerIndex < userList.size(); ownerIndex++) {
        User owner = (User) userList.elementAt(ownerIndex);
        BioModelNode ownerNode = null;
        try {
            if (vcDocumentInfos instanceof BioModelInfo[]) {
                ownerNode = (BioModelNode) subTreeMethod.invoke(subTreeParent, new Object[] { owner, (BioModelInfo[]) vcDocumentInfos });
            } else if (vcDocumentInfos instanceof MathModelInfo[]) {
                ownerNode = (BioModelNode) subTreeMethod.invoke(subTreeParent, new Object[] { owner, (MathModelInfo[]) vcDocumentInfos });
            } else if (vcDocumentInfos instanceof GeometryInfo[]) {
                ownerNode = (BioModelNode) subTreeMethod.invoke(subTreeParent, new Object[] { owner, (GeometryInfo[]) vcDocumentInfos });
            } else {
                throw new Exception("Unimplemented VCDocumentInfo type=" + vcDocumentInfos.getClass().getName());
            }
        } catch (Exception e) {
            e.printStackTrace();
            ownerNode = new BioModelNode("Error" + e.getMessage());
        }
        if (owner.equals(loginUser) || ownerNode.getChildCount() > 0) {
            treeMap.put(owner.getName(), ownerNode);
        }
    }
    return treeMap;
}

Example 14 with GeometryInfo

use of cbit.vcell.geometry.GeometryInfo in project vcell by virtualcell.

the class GeometryTreePanel method actionsOnClick.

/**
 * Comment
 */
protected void actionsOnClick(MouseEvent mouseEvent) {
    if (mouseEvent.isPopupTrigger()) {
        if (!getPopupMenuDisabled()) {
            TreePath treePath = ((JTree) mouseEvent.getSource()).getPathForLocation(mouseEvent.getX(), mouseEvent.getY());
            ((JTree) mouseEvent.getSource()).setSelectionPath(treePath);
            if (getSelectedVersionInfo() instanceof GeometryInfo) {
                Version version = getSelectedVersionInfo().getVersion();
                boolean isOwner = version.getOwner().compareEqual(getDocumentManager().getUser());
                getJMenuItemPermission().setEnabled(isOwner);
                getJMenuItemDelete().setEnabled(isOwner);
                getJMenuItemGeomRefs().setEnabled(isOwner);
                getGeometryPopupMenu().show(getJTree1(), mouseEvent.getPoint().x, mouseEvent.getPoint().y);
            } else if (treePath != null) {
                BioModelNode bioModelNode = (BioModelNode) treePath.getLastPathComponent();
                Object object = bioModelNode.getUserObject();
                if (object instanceof User) {
                    User selectedUser = (User) object;
                    boolean isOwner = selectedUser.compareEqual(getDocumentManager().getUser());
                    if (isOwner) {
                        JPopupMenu jPopupMenu = new JPopupMenu();
                        jPopupMenu.add(getJMenuItemCreateNewGeometry());
                        jPopupMenu.show(getJTree1(), mouseEvent.getPoint().x, mouseEvent.getPoint().y);
                    }
                }
            }
        }
    } else {
        ifNeedsDoubleClickEvent(mouseEvent, GeometryInfo.class);
    }
}

Example 15 with GeometryInfo

use of cbit.vcell.geometry.GeometryInfo in project vcell by virtualcell.

the class GeometryTreePanel method treeSelection.

/**
 * Comment
 */
protected void treeSelection() {
    TreePath treePath = getJTree1().getSelectionPath();
    if (treePath == null) {
        setSelectedVersionInfo(null);
        return;
    }
    BioModelNode bioModelNode = (BioModelNode) treePath.getLastPathComponent();
    Object object = bioModelNode.getUserObject();
    try {
        BeanUtils.setCursorThroughout(this, java.awt.Cursor.getPredefinedCursor(java.awt.Cursor.WAIT_CURSOR));
        if (object instanceof VersionInfo) {
            setSelectedVersionInfo((VersionInfo) object);
        } else if (object instanceof VCDocumentInfoNode && bioModelNode.getChildCount() > 0 && ((BioModelNode) bioModelNode.getChildAt(0)).getUserObject() instanceof GeometryInfo) {
            GeometryInfo geometryInfo = (GeometryInfo) ((BioModelNode) bioModelNode.getChildAt(0)).getUserObject();
            setSelectedVersionInfo(geometryInfo);
        } else {
            setSelectedVersionInfo(null);
        }
    } catch (Exception exc) {
        handleException(exc);
    } finally {
        BeanUtils.setCursorThroughout(this, java.awt.Cursor.getPredefinedCursor(java.awt.Cursor.DEFAULT_CURSOR));
    }
}