2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
23 import javax.swing.event.*;
25 import java.awt.event.*;
28 import jalview.jbgui.GStructureViewer;
29 import jalview.api.AlignmentViewPanel;
30 import jalview.api.SequenceStructureBinding;
31 import jalview.bin.Cache;
32 import jalview.datamodel.*;
33 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
34 import jalview.structure.*;
35 import jalview.datamodel.PDBEntry;
37 import jalview.schemes.*;
39 public class AppJmol extends GStructureViewer implements Runnable,
40 SequenceStructureBinding, ViewSetProvider
49 RenderPanel renderPanel;
53 Vector atomsPicked = new Vector();
55 private boolean addingStructures = false;
65 * @deprecated defaults to AppJmol(String[] files, ... , viewid);
67 public AppJmol(String file, String id, SequenceI[] seq,
68 AlignmentPanel ap, String loadStatus, Rectangle bounds)
70 this(file, id, seq, ap, loadStatus, bounds, null);
76 public AppJmol(String file, String id, SequenceI[] seq,
77 AlignmentPanel ap, String loadStatus, Rectangle bounds,
81 { file }, new String[]
82 { id }, new SequenceI[][]
83 { seq }, ap, true, true, false, loadStatus, bounds, viewid);
86 ViewSelectionMenu seqColourBy;
95 * - add the alignment panel to the list used for colouring these
98 * - add the alignment panel to the list used for aligning these
100 * @param leaveColouringToJmol
101 * - do not update the colours from any other source. Jmol is handling them
106 public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,
107 AlignmentPanel ap, boolean usetoColour, boolean useToAlign, boolean leaveColouringToJmol,
108 String loadStatus, Rectangle bounds, String viewid)
110 PDBEntry[] pdbentrys = new PDBEntry[files.length];
111 for (int i = 0; i < pdbentrys.length; i++)
113 PDBEntry pdbentry = new PDBEntry();
114 pdbentry.setFile(files[i]);
115 pdbentry.setId(ids[i]);
116 pdbentrys[i] = pdbentry;
118 // / TODO: check if protocol is needed to be set, and if chains are
120 jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
122 jmb.setLoadingFromArchive(true);
123 addAlignmentPanel(ap);
126 useAlignmentPanelForSuperposition(ap);
128 if (leaveColouringToJmol || !usetoColour)
130 jmb.setColourBySequence(false);
131 seqColour.setSelected(false);
132 jmolColour.setSelected(true);
136 useAlignmentPanelForColourbyseq(ap);
137 jmb.setColourBySequence(true);
138 seqColour.setSelected(true);
139 jmolColour.setSelected(false);
141 this.setBounds(bounds);
144 // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
145 // bounds.width,bounds.height);
147 this.addInternalFrameListener(new InternalFrameAdapter()
149 public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
154 initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
158 private void initMenus()
160 seqColour.setSelected(jmb.isColourBySequence());
161 jmolColour.setSelected(!jmb.isColourBySequence());
162 if (_colourwith==null)
164 _colourwith=new Vector<AlignmentPanel>();
166 if (_alignwith==null)
168 _alignwith=new Vector<AlignmentPanel>();
171 seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,
176 public void itemStateChanged(ItemEvent e)
178 if (!seqColour.isSelected())
184 // update the jmol display now.
185 seqColour_actionPerformed(null);
189 viewMenu.add(seqColourBy);
190 final ItemListener handler;
191 JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this,
192 _alignwith, handler = new ItemListener()
196 public void itemStateChanged(ItemEvent e)
198 alignStructs.setEnabled(_alignwith.size() > 0);
199 alignStructs.setToolTipText("Align structures using "
200 + _alignwith.size() + " linked alignment views");
203 handler.itemStateChanged(null);
204 jmolActionMenu.add(alpanels);
205 jmolActionMenu.addMenuListener(new MenuListener()
209 public void menuSelected(MenuEvent e)
211 handler.itemStateChanged(null);
215 public void menuDeselected(MenuEvent e)
217 // TODO Auto-generated method stub
222 public void menuCanceled(MenuEvent e)
224 // TODO Auto-generated method stub
229 IProgressIndicator progressBar = null;
232 * add a single PDB structure to a new or existing Jmol view
238 public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
239 final AlignmentPanel ap)
241 progressBar = ap.alignFrame;
242 // ////////////////////////////////
243 // Is the pdb file already loaded?
244 String alreadyMapped = ap.getStructureSelectionManager().alreadyMappedToFile(
247 if (alreadyMapped != null)
249 int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
250 pdbentry.getId() + " is already displayed."
251 + "\nDo you want to re-use this viewer ?",
252 "Map Sequences to Visible Window: " + pdbentry.getId(),
253 JOptionPane.YES_NO_OPTION);
255 if (option == JOptionPane.YES_OPTION)
257 // TODO : Fix multiple seq to one chain issue here.
258 ap.getStructureSelectionManager().setMapping(seq, chains, alreadyMapped,
259 AppletFormatAdapter.FILE);
260 if (ap.seqPanel.seqCanvas.fr != null)
262 ap.seqPanel.seqCanvas.fr.featuresAdded();
263 ap.paintAlignment(true);
266 // Now this AppJmol is mapped to new sequences. We must add them to
267 // the exisiting array
268 JInternalFrame[] frames = Desktop.instance.getAllFrames();
270 for (int i = 0; i < frames.length; i++)
272 if (frames[i] instanceof AppJmol)
274 final AppJmol topJmol = ((AppJmol) frames[i]);
275 // JBPNOTE: this looks like a binding routine, rather than a gui
277 for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
279 if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
281 topJmol.jmb.addSequence(pe, seq);
282 topJmol.addAlignmentPanel(ap);
283 // add it to the set used for colouring
284 topJmol.useAlignmentPanelForColourbyseq(ap);
285 topJmol.buildJmolActionMenu();
286 ap.getStructureSelectionManager().sequenceColoursChanged(ap);
296 // /////////////////////////////////
297 // Check if there are other Jmol views involving this alignment
298 // and prompt user about adding this molecule to one of them
299 Vector existingViews = getJmolsFor(ap);
300 if (existingViews.size() > 0)
302 Enumeration jm = existingViews.elements();
303 while (jm.hasMoreElements())
305 AppJmol topJmol = (AppJmol) jm.nextElement();
306 // TODO: highlight topJmol in view somehow
307 int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
308 "Do you want to add " + pdbentry.getId()
309 + " to the view called\n'" + topJmol.getTitle()
310 + "'\n", "Align to existing structure view",
311 JOptionPane.YES_NO_OPTION);
312 if (option == JOptionPane.YES_OPTION)
314 topJmol.useAlignmentPanelForSuperposition(ap);
315 topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
320 // /////////////////////////////////
321 openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
323 private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) {
324 boolean promptUser=pdbentrys.length==1;
325 progressBar = ap.alignFrame;
326 jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
327 addAlignmentPanel(ap);
328 useAlignmentPanelForColourbyseq(ap);
329 if (pdbentrys.length>1)
331 alignAddedStructures=true;
332 useAlignmentPanelForSuperposition(ap);
334 jmb.setColourBySequence(true);
335 setSize(400, 400); // probably should be a configurable/dynamic default here
339 // for (PDBEntry pe: pdbentrys)
341 // if (pe.getFile()==null)
343 addingStructures = false;
344 worker = new Thread(this);
348 // filelist+=" \""+pe.getFile()+"\"";
353 initJmol("load"+(pdbentrys.length>1 ? " APPEND" : "") + filelist);
356 this.addInternalFrameListener(new InternalFrameAdapter()
358 public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
367 * create a new Jmol containing several structures superimposed using the given alignPanel.
372 public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
374 openNewJmol(ap, pe, seqs);
378 * list of sequenceSet ids associated with the view
380 ArrayList<String> _aps = new ArrayList();
382 public AlignmentPanel[] getAllAlignmentPanels()
384 AlignmentPanel[] t, list = new AlignmentPanel[0];
385 for (String setid : _aps)
387 AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
390 t = new AlignmentPanel[list.length + panels.length];
391 System.arraycopy(list, 0, t, 0, list.length);
392 System.arraycopy(panels, 0, t, list.length, panels.length);
401 * list of alignment panels to use for superposition
403 Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
406 * list of alignment panels that are used for colouring structures by aligned
409 Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
412 * set the primary alignmentPanel reference and add another alignPanel to the
413 * list of ones to use for colouring and aligning
417 public void addAlignmentPanel(AlignmentPanel nap)
423 if (!_aps.contains(nap.av.getSequenceSetId()))
425 _aps.add(nap.av.getSequenceSetId());
430 * remove any references held to the given alignment panel
434 public void removeAlignmentPanel(AlignmentPanel nap)
438 _alignwith.remove(nap);
439 _colourwith.remove(nap);
443 for (AlignmentPanel aps : getAllAlignmentPanels())
452 } catch (Exception ex)
457 buildJmolActionMenu();
461 public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
463 addAlignmentPanel(nap);
464 if (!_alignwith.contains(nap))
470 public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
472 if (_alignwith.contains(nap))
474 _alignwith.remove(nap);
478 public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, boolean enableColourBySeq)
480 useAlignmentPanelForColourbyseq(nap);
481 jmb.setColourBySequence(enableColourBySeq);
482 seqColour.setSelected(enableColourBySeq);
483 jmolColour.setSelected(!enableColourBySeq);
485 public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
487 addAlignmentPanel(nap);
488 if (!_colourwith.contains(nap))
490 _colourwith.add(nap);
494 public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
496 if (_colourwith.contains(nap))
498 _colourwith.remove(nap);
503 * pdb retrieval thread.
505 private Thread worker = null;
508 * add a new structure (with associated sequences and chains) to this viewer,
509 * retrieving it if necessary first.
516 * if true, new structure(s) will be align using associated alignment
518 private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
519 final String[] chains, final boolean b,
520 final IProgressIndicator alignFrame)
522 if (pdbentry.getFile() == null)
524 if (worker != null && worker.isAlive())
526 // a retrieval is in progress, wait around and add ourselves to the
528 new Thread(new Runnable()
532 while (worker != null && worker.isAlive() && _started)
536 Thread.sleep(100 + ((int) Math.random() * 100));
538 } catch (Exception e)
543 // and call ourselves again.
544 addStructure(pdbentry, seq, chains, b, alignFrame);
550 // otherwise, start adding the structure.
551 jmb.addSequenceAndChain(new PDBEntry[]
552 { pdbentry }, new SequenceI[][]
553 { seq }, new String[][]
555 addingStructures = true;
557 alignAddedStructures = b;
558 progressBar = alignFrame; // visual indication happens on caller frame.
559 (worker = new Thread(this)).start();
563 private Vector getJmolsFor(AlignmentPanel ap2)
565 Vector otherJmols = new Vector();
566 // Now this AppJmol is mapped to new sequences. We must add them to
567 // the exisiting array
568 JInternalFrame[] frames = Desktop.instance.getAllFrames();
570 for (int i = 0; i < frames.length; i++)
572 if (frames[i] instanceof AppJmol)
574 AppJmol topJmol = ((AppJmol) frames[i]);
575 if (topJmol.isLinkedWith(ap2))
577 otherJmols.addElement(topJmol);
584 void initJmol(String command)
586 jmb.setFinishedInit(false);
587 renderPanel = new RenderPanel();
588 // TODO: consider waiting until the structure/view is fully loaded before
590 this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
591 jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
592 getBounds().width, getBounds().height);
593 if (scriptWindow == null)
595 BorderLayout bl = new BorderLayout();
598 scriptWindow = new JPanel(bl);
599 scriptWindow.setVisible(false);
602 jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
604 jmb.newJmolPopup(true, "Jmol", true);
609 jmb.evalStateCommand(command);
610 jmb.setFinishedInit(true);
613 void setChainMenuItems(Vector chains)
615 chainMenu.removeAll();
620 JMenuItem menuItem = new JMenuItem("All");
621 menuItem.addActionListener(new ActionListener()
623 public void actionPerformed(ActionEvent evt)
625 allChainsSelected = true;
626 for (int i = 0; i < chainMenu.getItemCount(); i++)
628 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
629 ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
632 allChainsSelected = false;
636 chainMenu.add(menuItem);
638 for (int c = 0; c < chains.size(); c++)
640 menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
641 menuItem.addItemListener(new ItemListener()
643 public void itemStateChanged(ItemEvent evt)
645 if (!allChainsSelected)
650 chainMenu.add(menuItem);
654 boolean allChainsSelected = false;
656 private boolean alignAddedStructures = false;
660 Vector toshow = new Vector();
662 int mlength, p, mnum;
663 for (int i = 0; i < chainMenu.getItemCount(); i++)
665 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
667 JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
668 if (item.isSelected())
670 toshow.addElement(item.getText());
674 jmb.centerViewer(toshow);
684 // TODO: check for memory leaks where instance isn't finalised because jmb
685 // holds a reference to the window
690 * state flag for PDB retrieval thread
692 private boolean _started = false;
698 // todo - record which pdbids were successfuly imported.
699 StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
702 String[] curfiles = jmb.getPdbFile(); // files currently in viewer
703 // TODO: replace with reference fetching/transfer code (validate PDBentry
705 jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
706 for (int pi = 0; pi < jmb.pdbentry.length; pi++)
708 String file = jmb.pdbentry[pi].getFile();
711 // retrieve the pdb and store it locally
712 AlignmentI pdbseq = null;
713 pdbid = jmb.pdbentry[pi].getId();
714 long hdl = pdbid.hashCode() - System.currentTimeMillis();
715 if (progressBar != null)
717 progressBar.setProgressBar("Fetching PDB " + pdbid, hdl);
721 pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
723 } catch (OutOfMemoryError oomerror)
725 new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
726 } catch (Exception ex)
728 ex.printStackTrace();
729 errormsgs.append("'" + pdbid + "'");
731 if (progressBar != null)
733 progressBar.setProgressBar("Finished.", hdl);
737 // just transfer the file name from the first sequence's first
739 jmb.pdbentry[pi].setFile(file = ((PDBEntry) pdbseq
740 .getSequenceAt(0).getPDBId().elementAt(0)).getFile());
741 files.append(" \"" + file + "\"");
745 errormsgs.append("'" + pdbid + "' ");
750 if (curfiles != null && curfiles.length > 0)
752 addingStructures = true; // already files loaded.
753 for (int c = 0; c < curfiles.length; c++)
755 if (curfiles[c].equals(file))
764 files.append(" \"" + file + "\"");
768 } catch (OutOfMemoryError oomerror)
770 new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
771 } catch (Exception ex)
773 ex.printStackTrace();
774 errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
777 if (errormsgs.length() > 0)
780 JOptionPane.showInternalMessageDialog(Desktop.desktop,
781 "The following pdb entries could not be retrieved from the PDB:\n"
782 + errormsgs.toString()
783 + "\nPlease try downloading them manually.",
784 "Couldn't load file", JOptionPane.ERROR_MESSAGE);
787 long lastnotify = jmb.getLoadNotifiesHandled();
788 if (files.length() > 0)
790 if (!addingStructures)
795 initJmol("load FILES " + files.toString());
796 } catch (OutOfMemoryError oomerror)
798 new OOMWarning("When trying to open the Jmol viewer!", oomerror);
799 Cache.log.debug("File locations are " + files);
800 } catch (Exception ex)
802 Cache.log.error("Couldn't open Jmol viewer!", ex);
807 StringBuffer cmd = new StringBuffer();
808 cmd.append("loadingJalviewdata=true\nload APPEND ");
809 cmd.append(files.toString());
810 cmd.append("\nloadingJalviewdata=null");
811 final String command = cmd.toString();
813 lastnotify = jmb.getLoadNotifiesHandled();
817 jmb.evalStateCommand(command);
818 } catch (OutOfMemoryError oomerror)
821 "When trying to add structures to the Jmol viewer!",
823 Cache.log.debug("File locations are " + files);
824 } catch (Exception ex)
826 Cache.log.error("Couldn't add files to Jmol viewer!", ex);
830 // need to wait around until script has finished
831 while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
832 : (jmb.isFinishedInit() && jmb.getPdbFile().length!=jmb.pdbentry.length))
836 Cache.log.debug("Waiting around for jmb notify.");
838 } catch (Exception e)
842 // refresh the sequence colours for the new structure(s)
843 for (AlignmentPanel ap : _colourwith)
845 jmb.updateColours(ap);
847 // do superposition if asked to
848 if (alignAddedStructures)
850 javax.swing.SwingUtilities.invokeLater(new Runnable()
854 alignStructs_withAllAlignPanels();
855 // jmb.superposeStructures(ap.av.getAlignment(), -1, null);
858 alignAddedStructures = false;
860 addingStructures = false;
867 public void pdbFile_actionPerformed(ActionEvent actionEvent)
869 JalviewFileChooser chooser = new JalviewFileChooser(
870 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
872 chooser.setFileView(new JalviewFileView());
873 chooser.setDialogTitle("Save PDB File");
874 chooser.setToolTipText("Save");
876 int value = chooser.showSaveDialog(this);
878 if (value == JalviewFileChooser.APPROVE_OPTION)
882 // TODO: cope with multiple PDB files in view
883 BufferedReader in = new BufferedReader(new FileReader(
884 jmb.getPdbFile()[0]));
885 File outFile = chooser.getSelectedFile();
887 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
889 while ((data = in.readLine()) != null)
891 if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
897 } catch (Exception ex)
899 ex.printStackTrace();
904 public void viewMapping_actionPerformed(ActionEvent actionEvent)
906 jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
909 for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
911 cap.appendText(jmb.printMapping(
912 jmb.pdbentry[pdbe].getFile()));
913 cap.appendText("\n");
915 } catch (OutOfMemoryError e)
918 "composing sequence-structure alignments for display in text box.",
923 jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
933 public void eps_actionPerformed(ActionEvent e)
935 makePDBImage(jalview.util.ImageMaker.EPS);
944 public void png_actionPerformed(ActionEvent e)
946 makePDBImage(jalview.util.ImageMaker.PNG);
949 void makePDBImage(int type)
951 int width = getWidth();
952 int height = getHeight();
954 jalview.util.ImageMaker im;
956 if (type == jalview.util.ImageMaker.PNG)
958 im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
959 "Make PNG image from view", width, height, null, null);
963 im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
964 "Make EPS file from view", width, height, null,
968 if (im.getGraphics() != null)
970 Rectangle rect = new Rectangle(width, height);
971 jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
975 public void jmolColour_actionPerformed(ActionEvent actionEvent)
977 if (jmolColour.isSelected()) {
978 // disable automatic sequence colouring.
979 jmb.setColourBySequence(false);
982 public void seqColour_actionPerformed(ActionEvent actionEvent)
984 jmb.setColourBySequence(seqColour.isSelected());
985 if (_colourwith == null)
987 _colourwith = new Vector<AlignmentPanel>();
989 if (jmb.isColourBySequence())
991 if (!jmb.isLoadingFromArchive())
993 if (_colourwith.size()==0 && ap!=null) {
994 // Make the currently displayed alignment panel the associated view
995 _colourwith.add(ap.alignFrame.alignPanel);
998 // Set the colour using the current view for the associated alignframe
999 for (AlignmentPanel ap : _colourwith)
1001 jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
1006 public void chainColour_actionPerformed(ActionEvent actionEvent)
1008 chainColour.setSelected(true);
1009 jmb.colourByChain();
1012 public void chargeColour_actionPerformed(ActionEvent actionEvent)
1014 chargeColour.setSelected(true);
1015 jmb.colourByCharge();
1018 public void zappoColour_actionPerformed(ActionEvent actionEvent)
1020 zappoColour.setSelected(true);
1021 jmb.setJalviewColourScheme(new ZappoColourScheme());
1024 public void taylorColour_actionPerformed(ActionEvent actionEvent)
1026 taylorColour.setSelected(true);
1027 jmb.setJalviewColourScheme(new TaylorColourScheme());
1030 public void hydroColour_actionPerformed(ActionEvent actionEvent)
1032 hydroColour.setSelected(true);
1033 jmb.setJalviewColourScheme(new HydrophobicColourScheme());
1036 public void helixColour_actionPerformed(ActionEvent actionEvent)
1038 helixColour.setSelected(true);
1039 jmb.setJalviewColourScheme(new HelixColourScheme());
1042 public void strandColour_actionPerformed(ActionEvent actionEvent)
1044 strandColour.setSelected(true);
1045 jmb.setJalviewColourScheme(new StrandColourScheme());
1048 public void turnColour_actionPerformed(ActionEvent actionEvent)
1050 turnColour.setSelected(true);
1051 jmb.setJalviewColourScheme(new TurnColourScheme());
1054 public void buriedColour_actionPerformed(ActionEvent actionEvent)
1056 buriedColour.setSelected(true);
1057 jmb.setJalviewColourScheme(new BuriedColourScheme());
1060 public void userColour_actionPerformed(ActionEvent actionEvent)
1062 userColour.setSelected(true);
1063 new UserDefinedColours(this, null);
1066 public void backGround_actionPerformed(ActionEvent actionEvent)
1068 java.awt.Color col = JColorChooser.showDialog(this,
1069 "Select Background Colour", null);
1072 jmb.setBackgroundColour(col);
1076 public void jmolHelp_actionPerformed(ActionEvent actionEvent)
1080 jalview.util.BrowserLauncher
1081 .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
1082 } catch (Exception ex)
1087 public void showConsole(boolean showConsole)
1092 if (splitPane == null)
1094 splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
1095 splitPane.setTopComponent(renderPanel);
1096 splitPane.setBottomComponent(scriptWindow);
1097 this.getContentPane().add(splitPane, BorderLayout.CENTER);
1098 splitPane.setDividerLocation(getHeight() - 200);
1099 scriptWindow.setVisible(true);
1100 scriptWindow.validate();
1101 splitPane.validate();
1107 if (splitPane != null)
1109 splitPane.setVisible(false);
1114 this.getContentPane().add(renderPanel, BorderLayout.CENTER);
1120 class RenderPanel extends JPanel
1122 final Dimension currentSize = new Dimension();
1124 final Rectangle rectClip = new Rectangle();
1126 public void paintComponent(Graphics g)
1128 getSize(currentSize);
1129 g.getClipBounds(rectClip);
1131 if (jmb.fileLoadingError != null)
1133 g.setColor(Color.black);
1134 g.fillRect(0, 0, currentSize.width, currentSize.height);
1135 g.setColor(Color.white);
1136 g.setFont(new Font("Verdana", Font.BOLD, 14));
1137 g.drawString("Error loading file...", 20, currentSize.height / 2);
1138 StringBuffer sb = new StringBuffer();
1140 for (int e = 0; e < jmb.pdbentry.length; e++)
1142 sb.append(jmb.pdbentry[e].getId());
1143 if (e < jmb.pdbentry.length - 1)
1148 if (e == jmb.pdbentry.length - 1 || sb.length() > 20)
1151 g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
1152 * g.getFontMetrics().getHeight());
1156 else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
1158 g.setColor(Color.black);
1159 g.fillRect(0, 0, currentSize.width, currentSize.height);
1160 g.setColor(Color.white);
1161 g.setFont(new Font("Verdana", Font.BOLD, 14));
1162 g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
1166 jmb.viewer.renderScreenImage(g, currentSize, rectClip);
1171 String viewId = null;
1173 public String getViewId()
1177 viewId = System.currentTimeMillis() + "." + this.hashCode();
1182 public void updateTitleAndMenus()
1184 if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
1189 setChainMenuItems(jmb.chainNames);
1191 this.setTitle(jmb.getViewerTitle());
1192 if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
1194 jmolActionMenu.setVisible(true);
1196 if (!jmb.isLoadingFromArchive())
1198 seqColour_actionPerformed(null);
1202 protected void buildJmolActionMenu()
1204 if (_alignwith == null)
1206 _alignwith = new Vector<AlignmentPanel>();
1208 if (_alignwith.size() == 0 && ap != null)
1213 for (Component c : jmolActionMenu.getMenuComponents())
1215 if (c != alignStructs)
1217 jmolActionMenu.remove((JMenuItem) c);
1220 final ItemListener handler;
1227 * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
1231 protected void alignStructs_actionPerformed(ActionEvent actionEvent)
1233 alignStructs_withAllAlignPanels();
1236 private void alignStructs_withAllAlignPanels()
1243 if (_alignwith.size() == 0)
1250 AlignmentI[] als = new Alignment[_alignwith.size()];
1251 ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
1252 int[] alm = new int[_alignwith.size()];
1255 for (AlignmentPanel ap : _alignwith)
1257 als[a] = ap.av.getAlignment();
1259 alc[a++] = ap.av.getColumnSelection();
1261 jmb.superposeStructures(als, alm, alc);
1262 } catch (Exception e)
1264 StringBuffer sp = new StringBuffer();
1265 for (AlignmentPanel ap : _alignwith)
1267 sp.append("'" + ap.alignFrame.getTitle() + "' ");
1269 Cache.log.info("Couldn't align structures with the " + sp.toString()
1270 + "associated alignment panels.", e);
1276 public void setJalviewColourScheme(ColourSchemeI ucs)
1278 jmb.setJalviewColourScheme(ucs);
1285 * @return first alignment panel displaying given alignment, or the default
1288 public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
1290 for (AlignmentPanel ap : getAllAlignmentPanels())
1292 if (ap.av.getAlignment() == alignment)
1303 * @return true if this Jmol instance is linked with the given alignPanel
1305 public boolean isLinkedWith(AlignmentPanel ap2)
1307 return _aps.contains(ap2.av.getSequenceSetId());
1310 public boolean isUsedforaligment(AlignmentPanel ap2)
1313 return (_alignwith != null) && _alignwith.contains(ap2);
1316 public boolean isUsedforcolourby(AlignmentPanel ap2)
1318 return (_colourwith != null) && _colourwith.contains(ap2);
1323 * @return TRUE if the view is NOT being coloured by sequence associations.
1325 public boolean isColouredByJmol()
1327 return !jmb.isColourBySequence();