- viewId = viewid;
- // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
- // bounds.width,bounds.height);
-
- this.addInternalFrameListener(new InternalFrameAdapter()
- {
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
- {
- closeViewer();
- }
- });
- initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
-
- }
- private void initMenus() {
- seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,
- new ItemListener()
- {
-
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- if (!seqColour.isSelected())
- {
- seqColour.doClick();
- }
- else
- {
- // update the jmol display now.
- seqColour_actionPerformed(null);
- }
- }
- });
- viewMenu.add(seqColourBy);
- final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this,
- _alignwith, handler=new ItemListener()
- {
-
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- alignStructs.setEnabled(_alignwith.size() > 0);
- alignStructs.setToolTipText("Align structures using "
- + _alignwith.size() + " linked alignment views");
- }
- });
- handler.itemStateChanged(null);
- jmolActionMenu.add(alpanels);
- jmolActionMenu.addMenuListener(new MenuListener()
- {
-
- @Override
- public void menuSelected(MenuEvent e)
- {
- handler.itemStateChanged(null);
- }
-
- @Override
- public void menuDeselected(MenuEvent e)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void menuCanceled(MenuEvent e)
- {
- // TODO Auto-generated method stub
-
- }
- });
-
- }
- IProgressIndicator progressBar = null;
-
- public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap)
- {
- progressBar = ap.alignFrame;
- // ////////////////////////////////
- // Is the pdb file already loaded?
- String alreadyMapped = StructureSelectionManager
- .getStructureSelectionManager().alreadyMappedToFile(
- pdbentry.getId());
-
- if (alreadyMapped != null)