2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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 jalview.bin.Cache;
24 import jalview.datamodel.Alignment;
25 import jalview.datamodel.AlignmentI;
26 import jalview.datamodel.ColumnSelection;
27 import jalview.datamodel.PDBEntry;
28 import jalview.datamodel.SequenceI;
29 import jalview.io.AppletFormatAdapter;
30 import jalview.io.JalviewFileChooser;
31 import jalview.io.JalviewFileView;
32 import jalview.schemes.BuriedColourScheme;
33 import jalview.schemes.ColourSchemeI;
34 import jalview.schemes.HelixColourScheme;
35 import jalview.schemes.HydrophobicColourScheme;
36 import jalview.schemes.PurinePyrimidineColourScheme;
37 import jalview.schemes.StrandColourScheme;
38 import jalview.schemes.TaylorColourScheme;
39 import jalview.schemes.TurnColourScheme;
40 import jalview.schemes.ZappoColourScheme;
41 import jalview.structures.models.AAStructureBindingModel;
42 import jalview.util.MessageManager;
43 import jalview.util.Platform;
45 import java.awt.BorderLayout;
46 import java.awt.Color;
47 import java.awt.Dimension;
49 import java.awt.Graphics;
50 import java.awt.Rectangle;
51 import java.awt.event.ActionEvent;
52 import java.awt.event.ActionListener;
53 import java.awt.event.ItemEvent;
54 import java.awt.event.ItemListener;
55 import java.io.BufferedReader;
57 import java.io.FileOutputStream;
58 import java.io.FileReader;
59 import java.io.PrintWriter;
60 import java.util.Enumeration;
61 import java.util.Vector;
63 import javax.swing.JCheckBoxMenuItem;
64 import javax.swing.JColorChooser;
65 import javax.swing.JInternalFrame;
66 import javax.swing.JMenu;
67 import javax.swing.JMenuItem;
68 import javax.swing.JOptionPane;
69 import javax.swing.JPanel;
70 import javax.swing.JSplitPane;
71 import javax.swing.event.InternalFrameAdapter;
72 import javax.swing.event.InternalFrameEvent;
73 import javax.swing.event.MenuEvent;
74 import javax.swing.event.MenuListener;
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();
151 pdbentry.setFile(files[i]);
152 pdbentry.setId(ids[i]);
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);
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);
430 public AlignmentPanel[] getAllAlignmentPanels()
433 AlignmentPanel[] list = new AlignmentPanel[0];
434 for (String setid : _aps)
436 AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
439 t = new AlignmentPanel[list.length + panels.length];
440 System.arraycopy(list, 0, t, 0, list.length);
441 System.arraycopy(panels, 0, t, list.length, panels.length);
450 * set the primary alignmentPanel reference and add another alignPanel to the
451 * list of ones to use for colouring and aligning
455 public void addAlignmentPanel(AlignmentPanel nap)
457 if (getAlignmentPanel() == null)
459 setAlignmentPanel(nap);
461 if (!_aps.contains(nap.av.getSequenceSetId()))
463 _aps.add(nap.av.getSequenceSetId());
468 * remove any references held to the given alignment panel
472 public void removeAlignmentPanel(AlignmentPanel nap)
476 _alignwith.remove(nap);
477 _colourwith.remove(nap);
478 if (getAlignmentPanel() == nap)
480 setAlignmentPanel(null);
481 for (AlignmentPanel aps : getAllAlignmentPanels())
485 setAlignmentPanel(aps);
490 } catch (Exception ex)
493 if (getAlignmentPanel() != null)
499 public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
501 addAlignmentPanel(nap);
502 if (!_alignwith.contains(nap))
508 public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
510 if (_alignwith.contains(nap))
512 _alignwith.remove(nap);
516 public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,
517 boolean enableColourBySeq)
519 useAlignmentPanelForColourbyseq(nap);
520 getBinding().setColourBySequence(enableColourBySeq);
521 seqColour.setSelected(enableColourBySeq);
522 viewerColour.setSelected(!enableColourBySeq);
525 public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
527 addAlignmentPanel(nap);
528 if (!_colourwith.contains(nap))
530 _colourwith.add(nap);
534 public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
536 if (_colourwith.contains(nap))
538 _colourwith.remove(nap);
543 * pdb retrieval thread.
545 private Thread worker = null;
548 * add a new structure (with associated sequences and chains) to this viewer,
549 * retrieving it if necessary first.
556 * if true, new structure(s) will be align using associated alignment
558 private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
559 final String[] chains, final boolean b,
560 final IProgressIndicator alignFrame)
562 if (pdbentry.getFile() == null)
564 if (worker != null && worker.isAlive())
566 // a retrieval is in progress, wait around and add ourselves to the
568 new Thread(new Runnable()
572 while (worker != null && worker.isAlive() && _started)
576 Thread.sleep(100 + ((int) Math.random() * 100));
578 } catch (Exception e)
583 // and call ourselves again.
584 addStructure(pdbentry, seq, chains, b, alignFrame);
590 // otherwise, start adding the structure.
591 jmb.addSequenceAndChain(new PDBEntry[]
592 { pdbentry }, new SequenceI[][]
593 { seq }, new String[][]
595 addingStructures = true;
597 alignAddedStructures = b;
598 progressBar = alignFrame; // visual indication happens on caller frame.
599 (worker = new Thread(this)).start();
603 private Vector getJmolsFor(AlignmentPanel apanel)
605 Vector result = new Vector();
606 JInternalFrame[] frames = Desktop.instance.getAllFrames();
608 for (JInternalFrame frame : frames)
610 if (frame instanceof AppJmol)
612 if (((StructureViewerBase) frame).isLinkedWith(apanel))
614 result.addElement(frame);
621 void initJmol(String command)
623 jmb.setFinishedInit(false);
624 renderPanel = new RenderPanel();
625 // TODO: consider waiting until the structure/view is fully loaded before
627 this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
628 jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
629 getBounds().width, getBounds().height);
630 if (scriptWindow == null)
632 BorderLayout bl = new BorderLayout();
635 scriptWindow = new JPanel(bl);
636 scriptWindow.setVisible(false);
639 jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
641 jmb.newJmolPopup(true, "Jmol", true);
646 jmb.evalStateCommand(command);
647 jmb.setFinishedInit(true);
650 void setChainMenuItems(Vector chains)
652 chainMenu.removeAll();
657 JMenuItem menuItem = new JMenuItem(
658 MessageManager.getString("label.all"));
659 menuItem.addActionListener(new ActionListener()
661 public void actionPerformed(ActionEvent evt)
663 allChainsSelected = true;
664 for (int i = 0; i < chainMenu.getItemCount(); i++)
666 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
668 ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
672 allChainsSelected = false;
676 chainMenu.add(menuItem);
678 for (int c = 0; c < chains.size(); c++)
680 menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
681 menuItem.addItemListener(new ItemListener()
683 public void itemStateChanged(ItemEvent evt)
685 if (!allChainsSelected)
692 chainMenu.add(menuItem);
696 boolean allChainsSelected = false;
698 private boolean alignAddedStructures = false;
702 Vector toshow = new Vector();
704 int mlength, p, mnum;
705 for (int i = 0; i < chainMenu.getItemCount(); i++)
707 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
709 JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
710 if (item.isSelected())
712 toshow.addElement(item.getText());
716 jmb.centerViewer(toshow);
719 public void closeViewer()
722 setAlignmentPanel(null);
726 // TODO: check for memory leaks where instance isn't finalised because jmb
727 // holds a reference to the window
732 * state flag for PDB retrieval thread
734 private boolean _started = false;
740 // todo - record which pdbids were successfuly imported.
741 StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
744 String[] curfiles = jmb.getPdbFile(); // files currently in viewer
745 // TODO: replace with reference fetching/transfer code (validate PDBentry
747 jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
748 for (int pi = 0; pi < jmb.getPdbCount(); pi++)
750 String file = jmb.getPdbEntry(pi).getFile();
753 // retrieve the pdb and store it locally
754 AlignmentI pdbseq = null;
755 pdbid = jmb.getPdbEntry(pi).getId();
756 long hdl = pdbid.hashCode() - System.currentTimeMillis();
757 if (progressBar != null)
759 progressBar.setProgressBar(MessageManager.formatMessage("status.fetching_pdb", new String[]{pdbid}), hdl);
763 pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.getPdbEntry(
766 } catch (OutOfMemoryError oomerror)
768 new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
769 } catch (Exception ex)
771 ex.printStackTrace();
772 errormsgs.append("'" + pdbid + "'");
774 if (progressBar != null)
776 progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl);
780 // just transfer the file name from the first sequence's first
782 file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
783 .elementAt(0)).getFile()).getAbsolutePath();
784 jmb.getPdbEntry(pi).setFile(file);
786 files.append(" \"" + Platform.escapeString(file) + "\"");
790 errormsgs.append("'" + pdbid + "' ");
795 if (curfiles != null && curfiles.length > 0)
797 addingStructures = true; // already files loaded.
798 for (int c = 0; c < curfiles.length; c++)
800 if (curfiles[c].equals(file))
809 files.append(" \"" + Platform.escapeString(file) + "\"");
813 } catch (OutOfMemoryError oomerror)
815 new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
816 } catch (Exception ex)
818 ex.printStackTrace();
819 errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
822 if (errormsgs.length() > 0)
825 JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
826 .formatMessage("label.pdb_entries_couldnt_be_retrieved",
828 { errormsgs.toString() }), MessageManager
829 .getString("label.couldnt_load_file"),
830 JOptionPane.ERROR_MESSAGE);
833 long lastnotify = jmb.getLoadNotifiesHandled();
834 if (files.length() > 0)
836 if (!addingStructures)
841 initJmol("load FILES " + files.toString());
842 } catch (OutOfMemoryError oomerror)
844 new OOMWarning("When trying to open the Jmol viewer!", oomerror);
845 Cache.log.debug("File locations are " + files);
846 } catch (Exception ex)
848 Cache.log.error("Couldn't open Jmol viewer!", ex);
853 StringBuffer cmd = new StringBuffer();
854 cmd.append("loadingJalviewdata=true\nload APPEND ");
855 cmd.append(files.toString());
856 cmd.append("\nloadingJalviewdata=null");
857 final String command = cmd.toString();
859 lastnotify = jmb.getLoadNotifiesHandled();
863 jmb.evalStateCommand(command);
864 } catch (OutOfMemoryError oomerror)
867 "When trying to add structures to the Jmol viewer!",
869 Cache.log.debug("File locations are " + files);
870 } catch (Exception ex)
872 Cache.log.error("Couldn't add files to Jmol viewer!", ex);
876 // need to wait around until script has finished
877 while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
878 : (jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
879 .getPdbFile().length != jmb.getPdbCount()))
883 Cache.log.debug("Waiting around for jmb notify.");
885 } catch (Exception e)
889 // refresh the sequence colours for the new structure(s)
890 for (AlignmentPanel ap : _colourwith)
892 jmb.updateColours(ap);
894 // do superposition if asked to
895 if (alignAddedStructures)
897 javax.swing.SwingUtilities.invokeLater(new Runnable()
901 alignStructs_withAllAlignPanels();
902 // jmb.superposeStructures(ap.av.getAlignment(), -1, null);
905 alignAddedStructures = false;
907 addingStructures = false;
915 public void pdbFile_actionPerformed(ActionEvent actionEvent)
917 JalviewFileChooser chooser = new JalviewFileChooser(
918 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
920 chooser.setFileView(new JalviewFileView());
921 chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
922 chooser.setToolTipText(MessageManager.getString("action.save"));
924 int value = chooser.showSaveDialog(this);
926 if (value == JalviewFileChooser.APPROVE_OPTION)
930 // TODO: cope with multiple PDB files in view
931 BufferedReader in = new BufferedReader(new FileReader(
932 jmb.getPdbFile()[0]));
933 File outFile = chooser.getSelectedFile();
935 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
937 while ((data = in.readLine()) != null)
939 if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
945 } catch (Exception ex)
947 ex.printStackTrace();
953 public void viewMapping_actionPerformed(ActionEvent actionEvent)
955 jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
958 for (int pdbe = 0; pdbe < jmb.getPdbCount(); pdbe++)
960 cap.appendText(jmb.printMapping(jmb.getPdbEntry(pdbe).getFile()));
961 cap.appendText("\n");
963 } catch (OutOfMemoryError e)
966 "composing sequence-structure alignments for display in text box.",
971 jalview.gui.Desktop.addInternalFrame(cap,
972 MessageManager.getString("label.pdb_sequence_mapping"), 550,
977 public void eps_actionPerformed(ActionEvent e)
979 makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
983 public void png_actionPerformed(ActionEvent e)
985 makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
988 void makePDBImage(jalview.util.ImageMaker.TYPE type)
990 int width = getWidth();
991 int height = getHeight();
993 jalview.util.ImageMaker im;
995 if (type == jalview.util.ImageMaker.TYPE.PNG)
997 im = new jalview.util.ImageMaker(this,
998 jalview.util.ImageMaker.TYPE.PNG,
999 "Make PNG image from view", width, height, null, null);
1001 else if (type == jalview.util.ImageMaker.TYPE.EPS)
1003 im = new jalview.util.ImageMaker(this,
1004 jalview.util.ImageMaker.TYPE.EPS,
1005 "Make EPS file from view", width, height, null,
1011 im = new jalview.util.ImageMaker(this,
1012 jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
1013 width, height, null, this.getTitle());
1016 if (im.getGraphics() != null)
1018 Rectangle rect = new Rectangle(width, height);
1019 jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
1025 public void viewerColour_actionPerformed(ActionEvent actionEvent)
1027 if (viewerColour.isSelected())
1029 // disable automatic sequence colouring.
1030 jmb.setColourBySequence(false);
1035 public void seqColour_actionPerformed(ActionEvent actionEvent)
1037 jmb.setColourBySequence(seqColour.isSelected());
1038 if (_colourwith == null)
1040 _colourwith = new Vector<AlignmentPanel>();
1042 if (jmb.isColourBySequence())
1044 if (!jmb.isLoadingFromArchive())
1046 if (_colourwith.size() == 0 && getAlignmentPanel() != null)
1048 // Make the currently displayed alignment panel the associated view
1049 _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
1052 // Set the colour using the current view for the associated alignframe
1053 for (AlignmentPanel ap : _colourwith)
1055 jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
1061 public void chainColour_actionPerformed(ActionEvent actionEvent)
1063 chainColour.setSelected(true);
1064 jmb.colourByChain();
1068 public void chargeColour_actionPerformed(ActionEvent actionEvent)
1070 chargeColour.setSelected(true);
1071 jmb.colourByCharge();
1075 public void zappoColour_actionPerformed(ActionEvent actionEvent)
1077 zappoColour.setSelected(true);
1078 jmb.setJalviewColourScheme(new ZappoColourScheme());
1082 public void taylorColour_actionPerformed(ActionEvent actionEvent)
1084 taylorColour.setSelected(true);
1085 jmb.setJalviewColourScheme(new TaylorColourScheme());
1089 public void hydroColour_actionPerformed(ActionEvent actionEvent)
1091 hydroColour.setSelected(true);
1092 jmb.setJalviewColourScheme(new HydrophobicColourScheme());
1096 public void helixColour_actionPerformed(ActionEvent actionEvent)
1098 helixColour.setSelected(true);
1099 jmb.setJalviewColourScheme(new HelixColourScheme());
1103 public void strandColour_actionPerformed(ActionEvent actionEvent)
1105 strandColour.setSelected(true);
1106 jmb.setJalviewColourScheme(new StrandColourScheme());
1110 public void turnColour_actionPerformed(ActionEvent actionEvent)
1112 turnColour.setSelected(true);
1113 jmb.setJalviewColourScheme(new TurnColourScheme());
1117 public void buriedColour_actionPerformed(ActionEvent actionEvent)
1119 buriedColour.setSelected(true);
1120 jmb.setJalviewColourScheme(new BuriedColourScheme());
1124 public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
1126 setJalviewColourScheme(new PurinePyrimidineColourScheme());
1130 public void userColour_actionPerformed(ActionEvent actionEvent)
1132 userColour.setSelected(true);
1133 new UserDefinedColours(this, null);
1137 public void backGround_actionPerformed(ActionEvent actionEvent)
1139 java.awt.Color col = JColorChooser.showDialog(this,
1140 MessageManager.getString("label.select_backgroud_colour"), null);
1143 jmb.setBackgroundColour(col);
1148 public void showHelp_actionPerformed(ActionEvent actionEvent)
1152 jalview.util.BrowserLauncher
1153 .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
1154 } catch (Exception ex)
1159 public void showConsole(boolean showConsole)
1164 if (splitPane == null)
1166 splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
1167 splitPane.setTopComponent(renderPanel);
1168 splitPane.setBottomComponent(scriptWindow);
1169 this.getContentPane().add(splitPane, BorderLayout.CENTER);
1170 splitPane.setDividerLocation(getHeight() - 200);
1171 scriptWindow.setVisible(true);
1172 scriptWindow.validate();
1173 splitPane.validate();
1179 if (splitPane != null)
1181 splitPane.setVisible(false);
1186 this.getContentPane().add(renderPanel, BorderLayout.CENTER);
1192 class RenderPanel extends JPanel
1194 final Dimension currentSize = new Dimension();
1196 final Rectangle rectClip = new Rectangle();
1198 public void paintComponent(Graphics g)
1200 getSize(currentSize);
1201 g.getClipBounds(rectClip);
1203 if (jmb.fileLoadingError != null)
1205 g.setColor(Color.black);
1206 g.fillRect(0, 0, currentSize.width, currentSize.height);
1207 g.setColor(Color.white);
1208 g.setFont(new Font("Verdana", Font.BOLD, 14));
1209 g.drawString(MessageManager.getString("label.error_loading_file")
1210 + "...", 20, currentSize.height / 2);
1211 StringBuffer sb = new StringBuffer();
1213 for (int e = 0; e < jmb.getPdbCount(); e++)
1215 sb.append(jmb.getPdbEntry(e).getId());
1216 if (e < jmb.getPdbCount() - 1)
1221 if (e == jmb.getPdbCount() - 1 || sb.length() > 20)
1224 g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
1225 * g.getFontMetrics().getHeight());
1229 else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
1231 g.setColor(Color.black);
1232 g.fillRect(0, 0, currentSize.width, currentSize.height);
1233 g.setColor(Color.white);
1234 g.setFont(new Font("Verdana", Font.BOLD, 14));
1235 g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
1236 20, currentSize.height / 2);
1240 jmb.viewer.renderScreenImage(g, currentSize, rectClip);
1245 public void updateTitleAndMenus()
1247 if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
1252 setChainMenuItems(jmb.chainNames);
1254 this.setTitle(jmb.getViewerTitle());
1255 if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
1257 viewerActionMenu.setVisible(true);
1259 if (!jmb.isLoadingFromArchive())
1261 seqColour_actionPerformed(null);
1269 * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
1273 protected void alignStructs_actionPerformed(ActionEvent actionEvent)
1275 alignStructs_withAllAlignPanels();
1278 private void alignStructs_withAllAlignPanels()
1280 if (getAlignmentPanel() == null)
1285 if (_alignwith.size() == 0)
1287 _alignwith.add(getAlignmentPanel());
1292 AlignmentI[] als = new Alignment[_alignwith.size()];
1293 ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
1294 int[] alm = new int[_alignwith.size()];
1297 for (AlignmentPanel ap : _alignwith)
1299 als[a] = ap.av.getAlignment();
1301 alc[a++] = ap.av.getColumnSelection();
1303 jmb.superposeStructures(als, alm, alc);
1304 } catch (Exception e)
1306 StringBuffer sp = new StringBuffer();
1307 for (AlignmentPanel ap : _alignwith)
1309 sp.append("'" + ap.alignFrame.getTitle() + "' ");
1311 Cache.log.info("Couldn't align structures with the " + sp.toString()
1312 + "associated alignment panels.", e);
1318 public void setJalviewColourScheme(ColourSchemeI ucs)
1320 jmb.setJalviewColourScheme(ucs);
1327 * @return first alignment panel displaying given alignment, or the default
1330 public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
1332 for (AlignmentPanel ap : getAllAlignmentPanels())
1334 if (ap.av.getAlignment() == alignment)
1339 return getAlignmentPanel();
1343 public AAStructureBindingModel getBinding()
1349 public String getStateInfo()
1351 return jmb == null ? null : jmb.viewer.getStateInfo();