- public void userColour_actionPerformed(ActionEvent actionEvent)
- {
- userColour.setSelected(true);
- new UserDefinedColours(this, null);
- }
-
- public void backGround_actionPerformed(ActionEvent actionEvent)
- {
- java.awt.Color col = JColorChooser.showDialog(this,
- "Select Background Colour", null);
- if (col != null)
- {
- jmb.setBackgroundColour(col);
- }
- }
-
- public void jmolHelp_actionPerformed(ActionEvent actionEvent)
- {
- try
- {
- jalview.util.BrowserLauncher
- .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
- } catch (Exception ex)
- {
- }
- }
-
- public void showConsole(boolean showConsole)
- {
-
- if (showConsole)
- {
- if (splitPane == null)
- {
- splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
- splitPane.setTopComponent(renderPanel);
- splitPane.setBottomComponent(scriptWindow);
- this.getContentPane().add(splitPane, BorderLayout.CENTER);
- splitPane.setDividerLocation(getHeight() - 200);
- scriptWindow.setVisible(true);
- scriptWindow.validate();
- splitPane.validate();
- }
-
- }
- else
- {
- if (splitPane != null)
- {
- splitPane.setVisible(false);
- }
-
- splitPane = null;
-
- this.getContentPane().add(renderPanel, BorderLayout.CENTER);
- }
-
- validate();
- }
-
- class RenderPanel extends JPanel
- {
- final Dimension currentSize = new Dimension();
-
- final Rectangle rectClip = new Rectangle();
-
- public void paintComponent(Graphics g)
- {
- getSize(currentSize);
- g.getClipBounds(rectClip);
-
- if (jmb.fileLoadingError != null)
- {
- g.setColor(Color.black);
- g.fillRect(0, 0, currentSize.width, currentSize.height);
- g.setColor(Color.white);
- g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Error loading file...", 20, currentSize.height / 2);
- StringBuffer sb = new StringBuffer();
- int lines = 0;
- for (int e = 0; e < jmb.pdbentry.length; e++)
- {
- sb.append(jmb.pdbentry[e].getId());
- if (e < jmb.pdbentry.length - 1)
- {
- sb.append(",");
- }
-
- if (e == jmb.pdbentry.length - 1 || sb.length() > 20)
- {
- lines++;
- g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
- * g.getFontMetrics().getHeight());
- }
- }
- }
- else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
- {
- g.setColor(Color.black);
- g.fillRect(0, 0, currentSize.width, currentSize.height);
- g.setColor(Color.white);
- g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
- }
- else
- {
- jmb.viewer.renderScreenImage(g, currentSize, rectClip);
- }
- }
- }
-
- String viewId = null;
-
- public String getViewId()
- {
- if (viewId == null)
- {
- viewId = System.currentTimeMillis() + "." + this.hashCode();
- }
- return viewId;
- }
-
- public void updateTitleAndMenus()
- {
- if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
- {
- repaint();
- return;
- }
- setChainMenuItems(jmb.chainNames);
-
- this.setTitle(jmb.getViewerTitle());
- if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
- {
- jmolActionMenu.setVisible(true);
- }
- if (!jmb.isLoadingFromArchive())
- {
- seqColour_actionPerformed(null);
- }
- }
-
- protected void buildJmolActionMenu()
- {
- if (_alignwith == null)
- {
- _alignwith = new Vector<AlignmentPanel>();
- }
- if (_alignwith.size() == 0 && ap != null)
- {
- _alignwith.add(ap);
- }
- ;
- for (Component c : jmolActionMenu.getMenuComponents())
- {
- if (c != alignStructs)
- {
- jmolActionMenu.remove((JMenuItem) c);
- }
- }
- final ItemListener handler;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
- * .ActionEvent)
- */
- @Override
- protected void alignStructs_actionPerformed(ActionEvent actionEvent)
- {
- alignStructs_withAllAlignPanels();
- }
-
- private void alignStructs_withAllAlignPanels()
- {
- if (ap == null)
- {
- return;
- }
- ;
- if (_alignwith.size() == 0)
- {
- _alignwith.add(ap);
- }
- ;
- try
- {
- AlignmentI[] als = new Alignment[_alignwith.size()];
- ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
- int[] alm = new int[_alignwith.size()];
- int a = 0;
-
- for (AlignmentPanel ap : _alignwith)
- {
- als[a] = ap.av.getAlignment();
- alm[a] = -1;
- alc[a++] = ap.av.getColumnSelection();
- }
- jmb.superposeStructures(als, alm, alc);
- } catch (Exception e)
- {
- StringBuffer sp = new StringBuffer();
- for (AlignmentPanel ap : _alignwith)
- {
- sp.append("'" + ap.alignFrame.getTitle() + "' ");
- }
- Cache.log.info("Couldn't align structures with the " + sp.toString()
- + "associated alignment panels.", e);
-
- }
-
- }
-
- public void setJalviewColourScheme(ColourSchemeI ucs)
- {
- jmb.setJalviewColourScheme(ucs);
-
- }
-
- /**
- *
- * @param alignment
- * @return first alignment panel displaying given alignment, or the default
- * alignment panel
- */
- public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
- {
- for (AlignmentPanel ap : getAllAlignmentPanels())
- {
- if (ap.av.getAlignment() == alignment)
- {
- return ap;
- }
- }
- return ap;
- }
-
- /**
- *
- * @param ap2
- * @return true if this Jmol instance is linked with the given alignPanel
- */
- public boolean isLinkedWith(AlignmentPanel ap2)
- {
- return _aps.contains(ap2.av.getSequenceSetId());
- }
-
- public boolean isUsedforaligment(AlignmentPanel ap2)
- {
-
- return (_alignwith != null) && _alignwith.contains(ap2);
- }
-
- public boolean isUsedforcolourby(AlignmentPanel ap2)
- {
- return (_colourwith != null) && _colourwith.contains(ap2);
- }