- throw new Error(
- MessageManager
- .getString("error.png_generation_not_implemented"));
- }
-
- @Override
- public void viewerColour_actionPerformed(ActionEvent actionEvent)
- {
- if (viewerColour.isSelected())
- {
- // disable automatic sequence colouring.
- jmb.setColourBySequence(false);
- }
- }
-
- @Override
- public void seqColour_actionPerformed(ActionEvent actionEvent)
- {
- jmb.setColourBySequence(seqColour.isSelected());
- if (_colourwith == null)
- {
- _colourwith = new Vector<AlignmentPanel>();
- }
- if (jmb.isColourBySequence())
- {
- if (!jmb.isLoadingFromArchive())
- {
- if (_colourwith.size() == 0 && getAlignmentPanel() != null)
- {
- // Make the currently displayed alignment panel the associated view
- _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
- }
- }
- // Set the colour using the current view for the associated alignframe
- for (AlignmentPanel ap : _colourwith)
- {
- jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
- }
- }
- }
-
- @Override
- public void chainColour_actionPerformed(ActionEvent actionEvent)
- {
- chainColour.setSelected(true);
- jmb.colourByChain();
- }
-
- @Override
- public void chargeColour_actionPerformed(ActionEvent actionEvent)
- {
- chargeColour.setSelected(true);
- jmb.colourByCharge();
- }
-
- @Override
- public void zappoColour_actionPerformed(ActionEvent actionEvent)
- {
- zappoColour.setSelected(true);
- jmb.setJalviewColourScheme(new ZappoColourScheme());
- }
-
- @Override
- public void taylorColour_actionPerformed(ActionEvent actionEvent)
- {
- taylorColour.setSelected(true);
- jmb.setJalviewColourScheme(new TaylorColourScheme());
- }
-
- @Override
- public void hydroColour_actionPerformed(ActionEvent actionEvent)
- {
- hydroColour.setSelected(true);
- jmb.setJalviewColourScheme(new HydrophobicColourScheme());
- }
-
- @Override
- public void helixColour_actionPerformed(ActionEvent actionEvent)
- {
- helixColour.setSelected(true);
- jmb.setJalviewColourScheme(new HelixColourScheme());
- }
-
- @Override
- public void strandColour_actionPerformed(ActionEvent actionEvent)
- {
- strandColour.setSelected(true);
- jmb.setJalviewColourScheme(new StrandColourScheme());
- }
-
- @Override
- public void turnColour_actionPerformed(ActionEvent actionEvent)
- {
- turnColour.setSelected(true);
- jmb.setJalviewColourScheme(new TurnColourScheme());
- }
-
- @Override
- public void buriedColour_actionPerformed(ActionEvent actionEvent)
- {
- buriedColour.setSelected(true);
- jmb.setJalviewColourScheme(new BuriedColourScheme());
- }
-
- @Override
- public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new PurinePyrimidineColourScheme());
- }
-
- @Override
- public void userColour_actionPerformed(ActionEvent actionEvent)
- {
- userColour.setSelected(true);
- new UserDefinedColours(this, null);
- }
-
- @Override
- public void backGround_actionPerformed(ActionEvent actionEvent)
- {
- java.awt.Color col = JColorChooser
- .showDialog(this, MessageManager
- .getString("label.select_backgroud_colour"), null);
- if (col != null)
- {
- jmb.setBackgroundColour(col);
- }
- }
-
- @Override
- public void showHelp_actionPerformed(ActionEvent actionEvent)
- {
- try
- {
- jalview.util.BrowserLauncher
- .openURL("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide");
- } catch (Exception ex)
- {
- }
- }
-
- public void updateTitleAndMenus()
- {
- if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
- {
- repaint();
- return;
- }
- setChainMenuItems(jmb.getChainNames());
-
- this.setTitle(jmb.getViewerTitle("Chimera", true));
- if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
- {
- viewerActionMenu.setVisible(true);
- }
- if (!jmb.isLoadingFromArchive())
- {
- seqColour_actionPerformed(null);
- }
- }
-
- /*
- * (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 (getAlignmentPanel() == null)
- {
- return;
- }
- ;
- if (_alignwith.size() == 0)
- {
- _alignwith.add(getAlignmentPanel());
- }
- ;
- 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 getAlignmentPanel();