Examples with IdentifiableNode cbit.vcell.xml.gui.MiriamTreeModel.IdentifiableNode used on opensource projects

Example 1 with IdentifiableNode

use of cbit.vcell.xml.gui.MiriamTreeModel.IdentifiableNode in project vcell by virtualcell.

the class MIRIAMAnnotationEditor method removeSelectedRefGroups.

public void removeSelectedRefGroups() {
    Object treeNode = jTreeMIRIAM.getLastSelectedPathComponent();
    if (treeNode instanceof IdentifiableNode) {
        Identifiable identifiable = ((IdentifiableNode) treeNode).getIdentifiable();
        Map<MiriamRefGroup, MIRIAMQualifier> refGroupsToRemove = vcMetaData.getMiriamManager().getAllMiriamRefGroups(identifiable);
        for (MiriamRefGroup refGroup : refGroupsToRemove.keySet()) {
            MIRIAMQualifier qualifier = refGroupsToRemove.get(refGroup);
            try {
                vcMetaData.getMiriamManager().remove(identifiable, qualifier, refGroup);
            } catch (URNParseFailureException e) {
                e.printStackTrace(System.out);
            }
        }
    }
}

Example 2 with IdentifiableNode

use of cbit.vcell.xml.gui.MiriamTreeModel.IdentifiableNode in project vcell by virtualcell.

the class MIRIAMAnnotationEditor method initialize.

/**
 * This method initializes this
 */
private void initialize() {
    GridBagConstraints gridBagConstraints5 = new GridBagConstraints();
    gridBagConstraints5.gridx = 0;
    gridBagConstraints5.fill = GridBagConstraints.NONE;
    gridBagConstraints5.insets = new Insets(4, 4, 4, 4);
    gridBagConstraints5.gridy = 2;
    GridBagConstraints gridBagConstraints1 = new GridBagConstraints();
    gridBagConstraints1.fill = GridBagConstraints.BOTH;
    gridBagConstraints1.weighty = 1.0;
    gridBagConstraints1.gridx = 0;
    gridBagConstraints1.gridy = 0;
    gridBagConstraints1.weightx = 1.0;
    this.setLayout(new GridBagLayout());
    this.setSize(new Dimension(627, 333));
    this.add(getJScrollPane(), gridBagConstraints1);
    this.add(getJPanel(), gridBagConstraints5);
    getJButtonAdd().setEnabled(false);
    getJTreeMIRIAM().addTreeSelectionListener(new TreeSelectionListener() {

        public void valueChanged(TreeSelectionEvent e) {
            getJButtonAdd().setEnabled(((JTree) e.getSource()).getSelectionPath() != null && ((JTree) e.getSource()).getSelectionPath().getLastPathComponent() instanceof IdentifiableNode);
        // getJButtonAdd().setEnabled(e.getPath().getLastPathComponent() instanceof IdentifiableNode);
        }
    });
}

Example 3 with IdentifiableNode

use of cbit.vcell.xml.gui.MiriamTreeModel.IdentifiableNode in project vcell by virtualcell.

the class MIRIAMAnnotationEditor method showEditFreehandText.

private void showEditFreehandText(DefaultMutableTreeNode node) {
    final IdentifiableNode parentIdentifiableNode = (IdentifiableNode) ((BioModelNode) node).getParent();
    final Annotation oldAnnotation = (Annotation) ((BioModelNode) node).getUserObject();
    try {
        String newAnnotation = DialogUtils.showAnnotationDialog(MIRIAMAnnotationEditor.this, oldAnnotation.toString());
        if (BeanUtils.triggersPropertyChangeEvent(oldAnnotation, newAnnotation)) {
            vcMetaData.setFreeTextAnnotation(parentIdentifiableNode.getIdentifiable(), newAnnotation);
        }
    } catch (UtilCancelException uce) {
    // ignore
    } catch (Exception exc) {
        exc.printStackTrace();
        DialogUtils.showErrorDialog(MIRIAMAnnotationEditor.this, "Error editing Annotation:\n" + exc.getMessage(), exc);
    }
}

Example 4 with IdentifiableNode

use of cbit.vcell.xml.gui.MiriamTreeModel.IdentifiableNode in project vcell by virtualcell.

the class MIRIAMAnnotationEditor method showPopup.

private void showPopup(MouseEvent mouseEvent, final TreePath closestMousePath) {
    final DefaultMutableTreeNode lastPathComp = ((DefaultMutableTreeNode) closestMousePath.getLastPathComponent());
    if (mouseEvent.isPopupTrigger()) {
        JPopupMenu jpop = new JPopupMenu();
        if (lastPathComp.getParent() == null) {
            JMenuItem expandJMenuItem = new JMenuItem("Expand all");
            expandJMenuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    expandJTreeNode(jTreeMIRIAM, lastPathComp, 0, 3);
                }
            });
            jpop.add(expandJMenuItem);
        }
        if (lastPathComp instanceof IdentifiableNode) {
            JMenuItem addAnnotationElementMenuItem = new JMenuItem("Add Annotation element");
            addAnnotationElementMenuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    fireActionPerformed(new ActionEvent(MIRIAMAnnotationEditor.this, 0, MIRIAMAnnotationEditor.ACTION_ADD));
                }
            });
            jpop.add(addAnnotationElementMenuItem);
        // JMenuItem addIDentifierJMenuItem = new JMenuItem("Add Identifier...");
        // addIDentifierJMenuItem.addActionListener(new ActionListener() {
        // public void actionPerformed(ActionEvent e) {
        // addIdentifierDialog();
        // }
        // });
        // jpop.add(addIDentifierJMenuItem);
        // 
        // JMenuItem addIDateJMenuItem = new JMenuItem("Add Date...");
        // addIDateJMenuItem.addActionListener(new ActionListener() {
        // public void actionPerformed(ActionEvent e) {
        // addTimeUTCDialog();
        // }
        // });
        // jpop.add(addIDateJMenuItem);
        } else if (isNodeFreeHandTextEditable(lastPathComp)) {
            JMenuItem editFreehandJMenuItem = new JMenuItem("Edit freehand text");
            editFreehandJMenuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    showEditFreehandText(lastPathComp);
                }
            });
            jpop.add(editFreehandJMenuItem);
        } else if (lastPathComp instanceof LinkNode) {
            JMenuItem showLinkJMenuItem = new JMenuItem("Show link in web browser");
            showLinkJMenuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    showBrowseToLink((LinkNode) lastPathComp);
                }
            });
            jpop.add(showLinkJMenuItem);
        }
        jpop.show(jTreeMIRIAM, mouseEvent.getPoint().x, mouseEvent.getPoint().y);
    }
}