2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import java.awt.BorderLayout;
24 import java.awt.Color;
25 import java.awt.Dimension;
27 import java.awt.Graphics;
28 import java.awt.Rectangle;
29 import java.awt.event.ActionEvent;
30 import java.awt.event.ActionListener;
31 import java.awt.event.ItemEvent;
32 import java.awt.event.ItemListener;
33 import java.io.BufferedReader;
35 import java.io.FileOutputStream;
36 import java.io.FileReader;
37 import java.io.PrintWriter;
38 import java.util.Enumeration;
39 import java.util.Vector;
41 import javax.swing.JCheckBoxMenuItem;
42 import javax.swing.JColorChooser;
43 import javax.swing.JInternalFrame;
44 import javax.swing.JMenu;
45 import javax.swing.JMenuItem;
46 import javax.swing.JOptionPane;
47 import javax.swing.JPanel;
48 import javax.swing.JSplitPane;
49 import javax.swing.event.InternalFrameAdapter;
50 import javax.swing.event.InternalFrameEvent;
51 import javax.swing.event.MenuEvent;
52 import javax.swing.event.MenuListener;
54 import jalview.bin.Cache;
55 import jalview.datamodel.Alignment;
56 import jalview.datamodel.AlignmentI;
57 import jalview.datamodel.ColumnSelection;
58 import jalview.datamodel.PDBEntry;
59 import jalview.datamodel.SequenceI;
60 import jalview.io.AppletFormatAdapter;
61 import jalview.io.JalviewFileChooser;
62 import jalview.io.JalviewFileView;
63 import jalview.schemes.BuriedColourScheme;
64 import jalview.schemes.ColourSchemeI;
65 import jalview.schemes.HelixColourScheme;
66 import jalview.schemes.HydrophobicColourScheme;
67 import jalview.schemes.PurinePyrimidineColourScheme;
68 import jalview.schemes.StrandColourScheme;
69 import jalview.schemes.TaylorColourScheme;
70 import jalview.schemes.TurnColourScheme;
71 import jalview.schemes.ZappoColourScheme;
72 import jalview.structures.models.AAStructureBindingModel;
73 import jalview.util.MessageManager;
74 import jalview.util.Platform;
76 public class AppJmol extends StructureViewerBase
84 RenderPanel renderPanel;
86 Vector atomsPicked = new Vector();
88 private boolean addingStructures = false;
98 * @deprecated defaults to AppJmol(String[] files, ... , viewid);
101 public AppJmol(String file, String id, SequenceI[] seq,
102 AlignmentPanel ap, String loadStatus, Rectangle bounds)
104 this(file, id, seq, ap, loadStatus, bounds, null);
111 public AppJmol(String file, String id, SequenceI[] seq,
112 AlignmentPanel ap, String loadStatus, Rectangle bounds,
116 { file }, new String[]
117 { id }, new SequenceI[][]
118 { seq }, ap, true, true, false, loadStatus, bounds, viewid);
121 ViewSelectionMenu seqColourBy;
130 * - add the alignment panel to the list used for colouring these
133 * - add the alignment panel to the list used for aligning these
135 * @param leaveColouringToJmol
136 * - do not update the colours from any other source. Jmol is
142 public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,
143 AlignmentPanel ap, boolean usetoColour, boolean useToAlign,
144 boolean leaveColouringToJmol, String loadStatus,
145 Rectangle bounds, String viewid)
147 PDBEntry[] pdbentrys = new PDBEntry[files.length];
148 for (int i = 0; i < pdbentrys.length; i++)
150 // PDBEntry pdbentry = new PDBEntry(files[i], ids[i]);
151 PDBEntry pdbentry = new PDBEntry(ids[i], null, PDBEntry.Type.PDB,
153 pdbentrys[i] = pdbentry;
155 // / TODO: check if protocol is needed to be set, and if chains are
157 jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
158 pdbentrys, seqs, null, null);
160 jmb.setLoadingFromArchive(true);
161 addAlignmentPanel(ap);
164 useAlignmentPanelForSuperposition(ap);
166 if (leaveColouringToJmol || !usetoColour)
168 jmb.setColourBySequence(false);
169 seqColour.setSelected(false);
170 viewerColour.setSelected(true);
172 else if (usetoColour)
174 useAlignmentPanelForColourbyseq(ap);
175 jmb.setColourBySequence(true);
176 seqColour.setSelected(true);
177 viewerColour.setSelected(false);
179 this.setBounds(bounds);
182 // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
183 // bounds.width,bounds.height);
185 this.addInternalFrameListener(new InternalFrameAdapter()
187 public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
192 initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
196 private void initMenus()
198 seqColour.setSelected(jmb.isColourBySequence());
199 viewerColour.setSelected(!jmb.isColourBySequence());
200 if (_colourwith == null)
202 _colourwith = new Vector<AlignmentPanel>();
204 if (_alignwith == null)
206 _alignwith = new Vector<AlignmentPanel>();
209 seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith,
214 public void itemStateChanged(ItemEvent e)
216 if (!seqColour.isSelected())
222 // update the jmol display now.
223 seqColour_actionPerformed(null);
227 viewMenu.add(seqColourBy);
228 final ItemListener handler;
229 JMenu alpanels = new ViewSelectionMenu(MessageManager.getString("label.superpose_with"), this,
230 _alignwith, handler = new ItemListener()
234 public void itemStateChanged(ItemEvent e)
236 alignStructs.setEnabled(_alignwith.size() > 0);
237 alignStructs.setToolTipText(MessageManager
239 "label.align_structures_using_linked_alignment_views",
241 { new Integer(_alignwith.size()).toString() }));
244 handler.itemStateChanged(null);
245 viewerActionMenu.add(alpanels);
246 viewerActionMenu.addMenuListener(new MenuListener()
250 public void menuSelected(MenuEvent e)
252 handler.itemStateChanged(null);
256 public void menuDeselected(MenuEvent e)
258 // TODO Auto-generated method stub
263 public void menuCanceled(MenuEvent e)
265 // TODO Auto-generated method stub
271 IProgressIndicator progressBar = null;
274 * add a single PDB structure to a new or existing Jmol view
281 public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
282 final AlignmentPanel ap)
284 progressBar = ap.alignFrame;
285 // ////////////////////////////////
286 // Is the pdb file already loaded?
287 String alreadyMapped = ap.getStructureSelectionManager()
288 .alreadyMappedToFile(pdbentry.getId());
290 if (alreadyMapped != null)
292 int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
293 MessageManager.formatMessage(
294 "label.pdb_entry_is_already_displayed", new String[]
295 { pdbentry.getId() }), MessageManager.formatMessage(
296 "label.map_sequences_to_visible_window", new String[]
297 { pdbentry.getId() }),
298 JOptionPane.YES_NO_CANCEL_OPTION);
300 if (option == JOptionPane.CANCEL_OPTION)
304 if (option == JOptionPane.YES_OPTION)
306 // TODO : Fix multiple seq to one chain issue here.
307 ap.getStructureSelectionManager().setMapping(seq, chains,
308 alreadyMapped, AppletFormatAdapter.FILE);
309 if (ap.getSeqPanel().seqCanvas.fr != null)
311 ap.getSeqPanel().seqCanvas.fr.featuresAdded();
312 ap.paintAlignment(true);
315 // Now this AppJmol is mapped to new sequences. We must add them to
316 // the exisiting array
317 JInternalFrame[] frames = Desktop.instance.getAllFrames();
319 for (int i = 0; i < frames.length; i++)
321 if (frames[i] instanceof AppJmol)
323 final AppJmol topJmol = ((AppJmol) frames[i]);
324 // JBPNOTE: this looks like a binding routine, rather than a gui
326 for (int pe = 0; pe < topJmol.jmb.getPdbCount(); pe++)
328 if (topJmol.jmb.getPdbEntry(pe).getFile()
329 .equals(alreadyMapped))
331 topJmol.jmb.addSequence(pe, seq);
332 topJmol.addAlignmentPanel(ap);
333 // add it to the set used for colouring
334 topJmol.useAlignmentPanelForColourbyseq(ap);
335 topJmol.buildActionMenu();
336 ap.getStructureSelectionManager()
337 .sequenceColoursChanged(ap);
347 // /////////////////////////////////
348 // Check if there are other Jmol views involving this alignment
349 // and prompt user about adding this molecule to one of them
350 Vector existingViews = getJmolsFor(ap);
351 if (existingViews.size() > 0)
353 Enumeration jm = existingViews.elements();
354 while (jm.hasMoreElements())
356 AppJmol topJmol = (AppJmol) jm.nextElement();
357 // TODO: highlight topJmol in view somehow
358 int option = JOptionPane
359 .showInternalConfirmDialog(
361 MessageManager.formatMessage(
362 "label.add_pdbentry_to_view", new String[]
363 { pdbentry.getId(), topJmol.getTitle() }),
365 .getString("label.align_to_existing_structure_view"),
366 JOptionPane.YES_NO_CANCEL_OPTION);
367 if (option == JOptionPane.CANCEL_OPTION)
371 if (option == JOptionPane.YES_OPTION)
373 topJmol.useAlignmentPanelForSuperposition(ap);
374 topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
379 // /////////////////////////////////
380 openNewJmol(ap, new PDBEntry[]
381 { pdbentry }, new SequenceI[][]
385 private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
388 progressBar = ap.alignFrame;
389 jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
390 pdbentrys, seqs, null, null);
391 addAlignmentPanel(ap);
392 useAlignmentPanelForColourbyseq(ap);
393 if (pdbentrys.length > 1)
395 alignAddedStructures = true;
396 useAlignmentPanelForSuperposition(ap);
398 jmb.setColourBySequence(true);
399 setSize(400, 400); // probably should be a configurable/dynamic default here
403 addingStructures = false;
404 worker = new Thread(this);
407 this.addInternalFrameListener(new InternalFrameAdapter()
409 public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
418 * create a new Jmol containing several structures superimposed using the
425 public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
427 openNewJmol(ap, pe, seqs);
431 * pdb retrieval thread.
433 private Thread worker = null;
436 * add a new structure (with associated sequences and chains) to this viewer,
437 * retrieving it if necessary first.
444 * if true, new structure(s) will be align using associated alignment
446 private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
447 final String[] chains, final boolean b,
448 final IProgressIndicator alignFrame)
450 if (pdbentry.getFile() == null)
452 if (worker != null && worker.isAlive())
454 // a retrieval is in progress, wait around and add ourselves to the
456 new Thread(new Runnable()
460 while (worker != null && worker.isAlive() && _started)
464 Thread.sleep(100 + ((int) Math.random() * 100));
466 } catch (Exception e)
471 // and call ourselves again.
472 addStructure(pdbentry, seq, chains, b, alignFrame);
478 // otherwise, start adding the structure.
479 jmb.addSequenceAndChain(new PDBEntry[]
480 { pdbentry }, new SequenceI[][]
481 { seq }, new String[][]
483 addingStructures = true;
485 alignAddedStructures = b;
486 progressBar = alignFrame; // visual indication happens on caller frame.
487 (worker = new Thread(this)).start();
491 private Vector getJmolsFor(AlignmentPanel apanel)
493 Vector result = new Vector();
494 JInternalFrame[] frames = Desktop.instance.getAllFrames();
496 for (JInternalFrame frame : frames)
498 if (frame instanceof AppJmol)
500 if (((StructureViewerBase) frame).isLinkedWith(apanel))
502 result.addElement(frame);
509 void initJmol(String command)
511 jmb.setFinishedInit(false);
512 renderPanel = new RenderPanel();
513 // TODO: consider waiting until the structure/view is fully loaded before
515 this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
516 jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
517 getBounds().width, getBounds().height);
518 if (scriptWindow == null)
520 BorderLayout bl = new BorderLayout();
523 scriptWindow = new JPanel(bl);
524 scriptWindow.setVisible(false);
527 jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
529 jmb.newJmolPopup(true, "Jmol", true);
534 jmb.evalStateCommand(command);
535 jmb.setFinishedInit(true);
538 void setChainMenuItems(Vector chains)
540 chainMenu.removeAll();
545 JMenuItem menuItem = new JMenuItem(
546 MessageManager.getString("label.all"));
547 menuItem.addActionListener(new ActionListener()
549 public void actionPerformed(ActionEvent evt)
551 allChainsSelected = true;
552 for (int i = 0; i < chainMenu.getItemCount(); i++)
554 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
556 ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
560 allChainsSelected = false;
564 chainMenu.add(menuItem);
566 for (int c = 0; c < chains.size(); c++)
568 menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
569 menuItem.addItemListener(new ItemListener()
571 public void itemStateChanged(ItemEvent evt)
573 if (!allChainsSelected)
580 chainMenu.add(menuItem);
584 boolean allChainsSelected = false;
586 private boolean alignAddedStructures = false;
590 Vector toshow = new Vector();
592 int mlength, p, mnum;
593 for (int i = 0; i < chainMenu.getItemCount(); i++)
595 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
597 JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
598 if (item.isSelected())
600 toshow.addElement(item.getText());
604 jmb.centerViewer(toshow);
607 public void closeViewer(boolean closeExternalViewer)
609 // JMol does not use an external viewer
611 setAlignmentPanel(null);
615 // TODO: check for memory leaks where instance isn't finalised because jmb
616 // holds a reference to the window
621 * state flag for PDB retrieval thread
623 private boolean _started = false;
629 // todo - record which pdbids were successfuly imported.
630 StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
633 String[] curfiles = jmb.getPdbFile(); // files currently in viewer
634 // TODO: replace with reference fetching/transfer code (validate PDBentry
636 jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
637 for (int pi = 0; pi < jmb.getPdbCount(); pi++)
639 String file = jmb.getPdbEntry(pi).getFile();
642 // retrieve the pdb and store it locally
643 AlignmentI pdbseq = null;
644 pdbid = jmb.getPdbEntry(pi).getId();
645 long hdl = pdbid.hashCode() - System.currentTimeMillis();
646 if (progressBar != null)
648 progressBar.setProgressBar(MessageManager.formatMessage("status.fetching_pdb", new String[]{pdbid}), hdl);
652 pdbseq = pdbclient.getSequenceRecords(pdbid);
653 } catch (OutOfMemoryError oomerror)
655 new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
656 } catch (Exception ex)
658 ex.printStackTrace();
659 errormsgs.append("'" + pdbid + "'");
661 if (progressBar != null)
663 progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl);
667 // just transfer the file name from the first sequence's first
669 file = new File(pdbseq.getSequenceAt(0).getPDBId()
670 .elementAt(0).getFile()).getAbsolutePath();
671 jmb.getPdbEntry(pi).setFile(file);
673 files.append(" \"" + Platform.escapeString(file) + "\"");
677 errormsgs.append("'" + pdbid + "' ");
682 if (curfiles != null && curfiles.length > 0)
684 addingStructures = true; // already files loaded.
685 for (int c = 0; c < curfiles.length; c++)
687 if (curfiles[c].equals(file))
696 files.append(" \"" + Platform.escapeString(file) + "\"");
700 } catch (OutOfMemoryError oomerror)
702 new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
703 } catch (Exception ex)
705 ex.printStackTrace();
706 errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
709 if (errormsgs.length() > 0)
712 JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
713 .formatMessage("label.pdb_entries_couldnt_be_retrieved",
715 { errormsgs.toString() }), MessageManager
716 .getString("label.couldnt_load_file"),
717 JOptionPane.ERROR_MESSAGE);
720 long lastnotify = jmb.getLoadNotifiesHandled();
721 if (files.length() > 0)
723 if (!addingStructures)
728 initJmol("load FILES " + files.toString());
729 } catch (OutOfMemoryError oomerror)
731 new OOMWarning("When trying to open the Jmol viewer!", oomerror);
732 Cache.log.debug("File locations are " + files);
733 } catch (Exception ex)
735 Cache.log.error("Couldn't open Jmol viewer!", ex);
740 StringBuffer cmd = new StringBuffer();
741 cmd.append("loadingJalviewdata=true\nload APPEND ");
742 cmd.append(files.toString());
743 cmd.append("\nloadingJalviewdata=null");
744 final String command = cmd.toString();
746 lastnotify = jmb.getLoadNotifiesHandled();
750 jmb.evalStateCommand(command);
751 } catch (OutOfMemoryError oomerror)
754 "When trying to add structures to the Jmol viewer!",
756 Cache.log.debug("File locations are " + files);
757 } catch (Exception ex)
759 Cache.log.error("Couldn't add files to Jmol viewer!", ex);
763 // need to wait around until script has finished
764 while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
765 : (jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
766 .getPdbFile().length != jmb.getPdbCount()))
770 Cache.log.debug("Waiting around for jmb notify.");
772 } catch (Exception e)
776 // refresh the sequence colours for the new structure(s)
777 for (AlignmentPanel ap : _colourwith)
779 jmb.updateColours(ap);
781 // do superposition if asked to
782 if (alignAddedStructures)
784 javax.swing.SwingUtilities.invokeLater(new Runnable()
788 alignStructs_withAllAlignPanels();
789 // jmb.superposeStructures(ap.av.getAlignment(), -1, null);
792 alignAddedStructures = false;
794 addingStructures = false;
802 public void pdbFile_actionPerformed(ActionEvent actionEvent)
804 JalviewFileChooser chooser = new JalviewFileChooser(
805 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
807 chooser.setFileView(new JalviewFileView());
808 chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
809 chooser.setToolTipText(MessageManager.getString("action.save"));
811 int value = chooser.showSaveDialog(this);
813 if (value == JalviewFileChooser.APPROVE_OPTION)
817 // TODO: cope with multiple PDB files in view
818 BufferedReader in = new BufferedReader(new FileReader(
819 jmb.getPdbFile()[0]));
820 File outFile = chooser.getSelectedFile();
822 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
824 while ((data = in.readLine()) != null)
826 if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
832 } catch (Exception ex)
834 ex.printStackTrace();
840 public void viewMapping_actionPerformed(ActionEvent actionEvent)
842 jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
845 cap.appendText(jmb.printMappings());
846 } catch (OutOfMemoryError e)
849 "composing sequence-structure alignments for display in text box.",
854 jalview.gui.Desktop.addInternalFrame(cap,
855 MessageManager.getString("label.pdb_sequence_mapping"), 550,
860 public void eps_actionPerformed(ActionEvent e)
862 makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
866 public void png_actionPerformed(ActionEvent e)
868 makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
871 void makePDBImage(jalview.util.ImageMaker.TYPE type)
873 int width = getWidth();
874 int height = getHeight();
876 jalview.util.ImageMaker im;
878 if (type == jalview.util.ImageMaker.TYPE.PNG)
880 im = new jalview.util.ImageMaker(this,
881 jalview.util.ImageMaker.TYPE.PNG,
882 "Make PNG image from view", width, height, null, null);
884 else if (type == jalview.util.ImageMaker.TYPE.EPS)
886 im = new jalview.util.ImageMaker(this,
887 jalview.util.ImageMaker.TYPE.EPS,
888 "Make EPS file from view", width, height, null,
894 im = new jalview.util.ImageMaker(this,
895 jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
896 width, height, null, this.getTitle());
899 if (im.getGraphics() != null)
901 Rectangle rect = new Rectangle(width, height);
902 jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
908 public void viewerColour_actionPerformed(ActionEvent actionEvent)
910 if (viewerColour.isSelected())
912 // disable automatic sequence colouring.
913 jmb.setColourBySequence(false);
918 public void seqColour_actionPerformed(ActionEvent actionEvent)
920 jmb.setColourBySequence(seqColour.isSelected());
921 if (_colourwith == null)
923 _colourwith = new Vector<AlignmentPanel>();
925 if (jmb.isColourBySequence())
927 if (!jmb.isLoadingFromArchive())
929 if (_colourwith.size() == 0 && getAlignmentPanel() != null)
931 // Make the currently displayed alignment panel the associated view
932 _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
935 // Set the colour using the current view for the associated alignframe
936 for (AlignmentPanel ap : _colourwith)
938 jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
944 public void chainColour_actionPerformed(ActionEvent actionEvent)
946 chainColour.setSelected(true);
951 public void chargeColour_actionPerformed(ActionEvent actionEvent)
953 chargeColour.setSelected(true);
954 jmb.colourByCharge();
958 public void zappoColour_actionPerformed(ActionEvent actionEvent)
960 zappoColour.setSelected(true);
961 jmb.setJalviewColourScheme(new ZappoColourScheme());
965 public void taylorColour_actionPerformed(ActionEvent actionEvent)
967 taylorColour.setSelected(true);
968 jmb.setJalviewColourScheme(new TaylorColourScheme());
972 public void hydroColour_actionPerformed(ActionEvent actionEvent)
974 hydroColour.setSelected(true);
975 jmb.setJalviewColourScheme(new HydrophobicColourScheme());
979 public void helixColour_actionPerformed(ActionEvent actionEvent)
981 helixColour.setSelected(true);
982 jmb.setJalviewColourScheme(new HelixColourScheme());
986 public void strandColour_actionPerformed(ActionEvent actionEvent)
988 strandColour.setSelected(true);
989 jmb.setJalviewColourScheme(new StrandColourScheme());
993 public void turnColour_actionPerformed(ActionEvent actionEvent)
995 turnColour.setSelected(true);
996 jmb.setJalviewColourScheme(new TurnColourScheme());
1000 public void buriedColour_actionPerformed(ActionEvent actionEvent)
1002 buriedColour.setSelected(true);
1003 jmb.setJalviewColourScheme(new BuriedColourScheme());
1007 public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
1009 setJalviewColourScheme(new PurinePyrimidineColourScheme());
1013 public void userColour_actionPerformed(ActionEvent actionEvent)
1015 userColour.setSelected(true);
1016 new UserDefinedColours(this, null);
1020 public void backGround_actionPerformed(ActionEvent actionEvent)
1022 java.awt.Color col = JColorChooser.showDialog(this,
1023 MessageManager.getString("label.select_backgroud_colour"), null);
1026 jmb.setBackgroundColour(col);
1031 public void showHelp_actionPerformed(ActionEvent actionEvent)
1035 jalview.util.BrowserLauncher
1036 .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
1037 } catch (Exception ex)
1042 public void showConsole(boolean showConsole)
1047 if (splitPane == null)
1049 splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
1050 splitPane.setTopComponent(renderPanel);
1051 splitPane.setBottomComponent(scriptWindow);
1052 this.getContentPane().add(splitPane, BorderLayout.CENTER);
1053 splitPane.setDividerLocation(getHeight() - 200);
1054 scriptWindow.setVisible(true);
1055 scriptWindow.validate();
1056 splitPane.validate();
1062 if (splitPane != null)
1064 splitPane.setVisible(false);
1069 this.getContentPane().add(renderPanel, BorderLayout.CENTER);
1075 class RenderPanel extends JPanel
1077 final Dimension currentSize = new Dimension();
1079 final Rectangle rectClip = new Rectangle();
1081 public void paintComponent(Graphics g)
1083 getSize(currentSize);
1084 g.getClipBounds(rectClip);
1086 if (jmb.fileLoadingError != null)
1088 g.setColor(Color.black);
1089 g.fillRect(0, 0, currentSize.width, currentSize.height);
1090 g.setColor(Color.white);
1091 g.setFont(new Font("Verdana", Font.BOLD, 14));
1092 g.drawString(MessageManager.getString("label.error_loading_file")
1093 + "...", 20, currentSize.height / 2);
1094 StringBuffer sb = new StringBuffer();
1096 for (int e = 0; e < jmb.getPdbCount(); e++)
1098 sb.append(jmb.getPdbEntry(e).getId());
1099 if (e < jmb.getPdbCount() - 1)
1104 if (e == jmb.getPdbCount() - 1 || sb.length() > 20)
1107 g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
1108 * g.getFontMetrics().getHeight());
1112 else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
1114 g.setColor(Color.black);
1115 g.fillRect(0, 0, currentSize.width, currentSize.height);
1116 g.setColor(Color.white);
1117 g.setFont(new Font("Verdana", Font.BOLD, 14));
1118 g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
1119 20, currentSize.height / 2);
1123 jmb.viewer.renderScreenImage(g, currentSize, rectClip);
1128 public void updateTitleAndMenus()
1130 if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
1135 setChainMenuItems(jmb.chainNames);
1137 this.setTitle(jmb.getViewerTitle());
1138 if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
1140 viewerActionMenu.setVisible(true);
1142 if (!jmb.isLoadingFromArchive())
1144 seqColour_actionPerformed(null);
1152 * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
1156 protected void alignStructs_actionPerformed(ActionEvent actionEvent)
1158 alignStructs_withAllAlignPanels();
1161 private void alignStructs_withAllAlignPanels()
1163 if (getAlignmentPanel() == null)
1168 if (_alignwith.size() == 0)
1170 _alignwith.add(getAlignmentPanel());
1175 AlignmentI[] als = new Alignment[_alignwith.size()];
1176 ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
1177 int[] alm = new int[_alignwith.size()];
1180 for (AlignmentPanel ap : _alignwith)
1182 als[a] = ap.av.getAlignment();
1184 alc[a++] = ap.av.getColumnSelection();
1186 jmb.superposeStructures(als, alm, alc);
1187 } catch (Exception e)
1189 StringBuffer sp = new StringBuffer();
1190 for (AlignmentPanel ap : _alignwith)
1192 sp.append("'" + ap.alignFrame.getTitle() + "' ");
1194 Cache.log.info("Couldn't align structures with the " + sp.toString()
1195 + "associated alignment panels.", e);
1201 public void setJalviewColourScheme(ColourSchemeI ucs)
1203 jmb.setJalviewColourScheme(ucs);
1210 * @return first alignment panel displaying given alignment, or the default
1213 public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
1215 for (AlignmentPanel ap : getAllAlignmentPanels())
1217 if (ap.av.getAlignment() == alignment)
1222 return getAlignmentPanel();
1226 public AAStructureBindingModel getBinding()
1232 public String getStateInfo()
1234 return jmb == null ? null : jmb.viewer.getStateInfo();