userColourSchemes = UserDefinedColours
- .getUserColourSchemes();
- if (userColourSchemes != null)
- {
- for (String userColour : userColourSchemes.keySet())
- {
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
- userColour);
- radioItem.setName("USER_DEFINED");
- radioItem.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Mac
- {
- offerRemoval(radioItem);
- }
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Windows
- {
- offerRemoval(radioItem);
- }
- }
-
- /**
- * @param radioItem
- */
- void offerRemoval(final JRadioButtonMenuItem radioItem)
- {
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- int option = JvOptionPane.showInternalConfirmDialog(
- jalview.gui.Desktop.desktop, MessageManager
- .getString("label.remove_from_default_list"),
- MessageManager
- .getString("label.remove_user_defined_colour"),
- JvOptionPane.YES_NO_OPTION);
- if (option == JvOptionPane.YES_OPTION)
- {
- jalview.gui.UserDefinedColours
- .removeColourFromDefaults(radioItem.getText());
- coloursMenu.remove(radioItem);
- }
- else
- {
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- user_actionPerformed(evt);
- }
- });
- }
- }
- });
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- user_actionPerformed(evt);
- }
- });
- coloursMenu.add(radioItem);
- bg.add(radioItem);
- }
- }
-
- viewMenu.add(wire);
- viewMenu.add(depth);
- viewMenu.add(zbuffer);
- viewMenu.add(allchains);
- }
-
- JMenuBar jMenuBar1 = new JMenuBar();
-
- JMenu fileMenu = new JMenu();
-
- JMenu coloursMenu = new JMenu();
-
- JMenu saveMenu = new JMenu();
-
- JMenuItem png = new JMenuItem();
-
- JMenuItem eps = new JMenuItem();
-
- JMenuItem mapping = new JMenuItem();
-
- JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
-
- JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
-
- JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
-
- JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
-
- JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem user = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
-
- JMenu viewMenu = new JMenu();
-
- JMenuItem background = new JMenuItem();
-
- JMenuItem savePDB = new JMenuItem();
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void eps_actionPerformed(ActionEvent e)
- {
- makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void png_actionPerformed(ActionEvent e)
- {
- makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
- }
-
- void makePDBImage(jalview.util.ImageMaker.TYPE type)
- {
- int width = pdbcanvas.getWidth();
- int height = pdbcanvas.getHeight();
-
- jalview.util.ImageMaker im;
-
- if (type == jalview.util.ImageMaker.TYPE.PNG)
- {
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
- width, height, null, null, null, 0, false);
- }
- else if (type == jalview.util.ImageMaker.TYPE.EPS)
- {
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
- width, height, null, this.getTitle(), null, 0, false);
- }
- else
- {
-
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
- width, height, null, this.getTitle(), null, 0, false);
- }
-
- if (im.getGraphics() != null)
- {
- pdbcanvas.drawAll(im.getGraphics(), width, height);
- im.writeImage();
- }
- }
-
- public void charge_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setChargeColours();
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void hydro_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void chain_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setChainColours();
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void zbuffer_actionPerformed(ActionEvent e)
- {
- pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void molecule_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void depth_actionPerformed(ActionEvent e)
- {
- pdbcanvas.depthcue = !pdbcanvas.depthcue;
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void wire_actionPerformed(ActionEvent e)
- {
- pdbcanvas.wire = !pdbcanvas.wire;
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void seqButton_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = true;
- pdbcanvas.updateSeqColours();
- }
-
- public void mapping_actionPerformed(ActionEvent e)
- {
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- try
- {
- cap.setText(pdbcanvas.mappingDetails.toString());
- Desktop.addInternalFrame(cap,
- MessageManager.getString("label.pdb_sequence_mapping"), 550,
- 600);
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning("Opening sequence to structure mapping report", oom);
- cap.dispose();
- }
- }
-
- public void allchains_itemStateChanged(ItemEvent e)
- {
- pdbcanvas.setAllchainsVisible(allchains.getState());
- }
-
- public void zappo_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new ZappoColourScheme());
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void taylor_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new TaylorColourScheme());
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void helix_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new HelixColourScheme());
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void strand_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new StrandColourScheme());
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void turn_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new TurnColourScheme());
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void buried_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new BuriedColourScheme());
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void user_actionPerformed(ActionEvent e)
- {
- if (e.getActionCommand().equals(
- MessageManager.getString("action.user_defined")))
- {
- // new UserDefinedColours(pdbcanvas, null);
- }
- else
- {
- UserColourScheme udc = UserDefinedColours
- .getUserColourSchemes().get(e.getActionCommand());
-
- pdbcanvas.pdb.setColours(udc);
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
- }
-
- public void background_actionPerformed(ActionEvent e)
- {
- Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_background_colour"),
- pdbcanvas.backgroundColour);
-
- if (col != null)
- {
- pdbcanvas.backgroundColour = col;
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
- }
-
- public void savePDB_actionPerformed(ActionEvent e)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
- chooser.setToolTipText(MessageManager.getString("action.save"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- try
- {
- BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
- File outFile = chooser.getSelectedFile();
-
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
- String data;
- while ((data = in.readLine()) != null)
- {
- if (!(data.indexOf("") > -1 || data.indexOf("
") > -1))
- {
- out.println(data);
- }
- }
- out.close();
- in.close();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- }
-}