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 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.gui.StructureViewer.ViewerType;
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.IOException;
60 import java.io.PrintWriter;
61 import java.util.ArrayList;
62 import java.util.List;
63 import java.util.Vector;
65 import javax.swing.JCheckBoxMenuItem;
66 import javax.swing.JColorChooser;
67 import javax.swing.JInternalFrame;
68 import javax.swing.JMenu;
69 import javax.swing.JMenuItem;
70 import javax.swing.JOptionPane;
71 import javax.swing.JPanel;
72 import javax.swing.JSplitPane;
73 import javax.swing.event.InternalFrameAdapter;
74 import javax.swing.event.InternalFrameEvent;
75 import javax.swing.event.MenuEvent;
76 import javax.swing.event.MenuListener;
78 public class AppJmol extends StructureViewerBase
86 RenderPanel renderPanel;
88 ViewSelectionMenu seqColourBy;
97 * - add the alignment panel to the list used for colouring these
100 * - add the alignment panel to the list used for aligning these
102 * @param leaveColouringToJmol
103 * - do not update the colours from any other source. Jmol is
109 public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,
110 AlignmentPanel ap, boolean usetoColour, boolean useToAlign,
111 boolean leaveColouringToJmol, String loadStatus,
112 Rectangle bounds, String viewid)
114 PDBEntry[] pdbentrys = new PDBEntry[files.length];
115 for (int i = 0; i < pdbentrys.length; i++)
117 // PDBEntry pdbentry = new PDBEntry(files[i], ids[i]);
118 PDBEntry pdbentry = new PDBEntry(ids[i], null, PDBEntry.Type.PDB,
120 pdbentrys[i] = pdbentry;
122 // / TODO: check if protocol is needed to be set, and if chains are
124 jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
125 pdbentrys, seqs, null, null);
127 jmb.setLoadingFromArchive(true);
128 addAlignmentPanel(ap);
131 useAlignmentPanelForSuperposition(ap);
133 if (leaveColouringToJmol || !usetoColour)
135 jmb.setColourBySequence(false);
136 seqColour.setSelected(false);
137 viewerColour.setSelected(true);
139 else if (usetoColour)
141 useAlignmentPanelForColourbyseq(ap);
142 jmb.setColourBySequence(true);
143 seqColour.setSelected(true);
144 viewerColour.setSelected(false);
146 this.setBounds(bounds);
149 // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
150 // bounds.width,bounds.height);
152 this.addInternalFrameListener(new InternalFrameAdapter()
155 public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
160 initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
164 private void initMenus()
166 seqColour.setSelected(jmb.isColourBySequence());
167 viewerColour.setSelected(!jmb.isColourBySequence());
168 if (_colourwith == null)
170 _colourwith = new Vector<AlignmentPanel>();
172 if (_alignwith == null)
174 _alignwith = new Vector<AlignmentPanel>();
177 seqColourBy = new ViewSelectionMenu(
178 MessageManager.getString("label.colour_by"), this, _colourwith,
183 public void itemStateChanged(ItemEvent e)
185 if (!seqColour.isSelected())
191 // update the jmol display now.
192 seqColour_actionPerformed(null);
196 viewMenu.add(seqColourBy);
197 final ItemListener handler;
198 JMenu alpanels = new ViewSelectionMenu(
199 MessageManager.getString("label.superpose_with"), this,
200 _alignwith, handler = new ItemListener()
204 public void itemStateChanged(ItemEvent e)
206 alignStructs.setEnabled(_alignwith.size() > 0);
207 alignStructs.setToolTipText(MessageManager
209 "label.align_structures_using_linked_alignment_views",
210 new String[] { new Integer(_alignwith
211 .size()).toString() }));
214 handler.itemStateChanged(null);
215 viewerActionMenu.add(alpanels);
216 viewerActionMenu.addMenuListener(new MenuListener()
220 public void menuSelected(MenuEvent e)
222 handler.itemStateChanged(null);
226 public void menuDeselected(MenuEvent e)
228 // TODO Auto-generated method stub
233 public void menuCanceled(MenuEvent e)
235 // TODO Auto-generated method stub
241 IProgressIndicator progressBar = null;
244 * add a single PDB structure to a new or existing Jmol view
251 public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
252 final AlignmentPanel ap)
254 progressBar = ap.alignFrame;
255 String pdbId = pdbentry.getId();
258 * If the PDB file is already loaded, the user may just choose to add to an
259 * existing viewer (or cancel)
261 if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
267 * Check if there are other Jmol views involving this alignment and prompt
268 * user about adding this molecule to one of them
270 if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
276 * If the options above are declined or do not apply, open a new viewer
278 openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
282 * Answers true if this viewer already involves the given PDB ID
285 protected boolean hasPdbId(String pdbId)
287 return jmb.hasPdbId(pdbId);
290 private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
293 progressBar = ap.alignFrame;
294 jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
295 pdbentrys, seqs, null, null);
296 addAlignmentPanel(ap);
297 useAlignmentPanelForColourbyseq(ap);
298 if (pdbentrys.length > 1)
300 alignAddedStructures = true;
301 useAlignmentPanelForSuperposition(ap);
303 jmb.setColourBySequence(true);
304 setSize(400, 400); // probably should be a configurable/dynamic default here
308 addingStructures = false;
309 worker = new Thread(this);
312 this.addInternalFrameListener(new InternalFrameAdapter()
315 public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
324 * create a new Jmol containing several structures superimposed using the
331 public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
333 openNewJmol(ap, pe, seqs);
337 * Returns a list of any Jmol viewers. The list is restricted to those linked
338 * to the given alignment panel if it is not null.
341 protected List<StructureViewerBase> getViewersFor(AlignmentPanel apanel)
343 List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
344 JInternalFrame[] frames = Desktop.instance.getAllFrames();
346 for (JInternalFrame frame : frames)
348 if (frame instanceof AppJmol)
351 || ((StructureViewerBase) frame).isLinkedWith(apanel))
353 result.add((StructureViewerBase) frame);
360 void initJmol(String command)
362 jmb.setFinishedInit(false);
363 renderPanel = new RenderPanel();
364 // TODO: consider waiting until the structure/view is fully loaded before
366 this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
367 jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
368 getBounds().width, getBounds().height);
369 if (scriptWindow == null)
371 BorderLayout bl = new BorderLayout();
374 scriptWindow = new JPanel(bl);
375 scriptWindow.setVisible(false);
378 jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
380 // jmb.newJmolPopup("Jmol");
385 jmb.evalStateCommand(command);
386 jmb.evalStateCommand("set hoverDelay=0.1");
387 jmb.setFinishedInit(true);
390 void setChainMenuItems(Vector<String> chains)
392 chainMenu.removeAll();
397 JMenuItem menuItem = new JMenuItem(
398 MessageManager.getString("label.all"));
399 menuItem.addActionListener(new ActionListener()
401 public void actionPerformed(ActionEvent evt)
403 allChainsSelected = true;
404 for (int i = 0; i < chainMenu.getItemCount(); i++)
406 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
408 ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
412 allChainsSelected = false;
416 chainMenu.add(menuItem);
418 for (String chain : chains)
420 menuItem = new JCheckBoxMenuItem(chain, true);
421 menuItem.addItemListener(new ItemListener()
423 public void itemStateChanged(ItemEvent evt)
425 if (!allChainsSelected)
432 chainMenu.add(menuItem);
436 boolean allChainsSelected = false;
440 Vector<String> toshow = new Vector<String>();
441 for (int i = 0; i < chainMenu.getItemCount(); i++)
443 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
445 JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
446 if (item.isSelected())
448 toshow.addElement(item.getText());
452 jmb.centerViewer(toshow);
455 public void closeViewer(boolean closeExternalViewer)
457 // Jmol does not use an external viewer
462 setAlignmentPanel(null);
466 // TODO: check for memory leaks where instance isn't finalised because jmb
467 // holds a reference to the window
475 // todo - record which pdbids were successfuly imported.
476 StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
479 String[] curfiles = jmb.getPdbFile(); // files currently in viewer
480 // TODO: replace with reference fetching/transfer code (validate PDBentry
482 jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
483 for (int pi = 0; pi < jmb.getPdbCount(); pi++)
485 String file = jmb.getPdbEntry(pi).getFile();
488 // retrieve the pdb and store it locally
489 AlignmentI pdbseq = null;
490 pdbid = jmb.getPdbEntry(pi).getId();
491 long hdl = pdbid.hashCode() - System.currentTimeMillis();
492 if (progressBar != null)
494 progressBar.setProgressBar(MessageManager.formatMessage(
495 "status.fetching_pdb", new String[] { pdbid }), hdl);
499 pdbseq = pdbclient.getSequenceRecords(pdbid);
500 } catch (OutOfMemoryError oomerror)
502 new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
503 } catch (Exception ex)
505 ex.printStackTrace();
506 errormsgs.append("'" + pdbid + "'");
508 if (progressBar != null)
510 progressBar.setProgressBar(
511 MessageManager.getString("label.state_completed"), hdl);
515 // just transfer the file name from the first sequence's first
517 file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
518 .elementAt(0).getFile()).getAbsolutePath();
519 jmb.getPdbEntry(pi).setFile(file);
521 files.append(" \"" + Platform.escapeString(file) + "\"");
525 errormsgs.append("'" + pdbid + "' ");
530 if (curfiles != null && curfiles.length > 0)
532 addingStructures = true; // already files loaded.
533 for (int c = 0; c < curfiles.length; c++)
535 if (curfiles[c].equals(file))
544 files.append(" \"" + Platform.escapeString(file) + "\"");
548 } catch (OutOfMemoryError oomerror)
550 new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
551 } catch (Exception ex)
553 ex.printStackTrace();
554 errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
557 if (errormsgs.length() > 0)
560 JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
561 .formatMessage("label.pdb_entries_couldnt_be_retrieved",
562 new String[] { errormsgs.toString() }),
563 MessageManager.getString("label.couldnt_load_file"),
564 JOptionPane.ERROR_MESSAGE);
567 long lastnotify = jmb.getLoadNotifiesHandled();
568 if (files.length() > 0)
570 if (!addingStructures)
575 initJmol("load FILES " + files.toString());
576 } catch (OutOfMemoryError oomerror)
578 new OOMWarning("When trying to open the Jmol viewer!", oomerror);
579 Cache.log.debug("File locations are " + files);
580 } catch (Exception ex)
582 Cache.log.error("Couldn't open Jmol viewer!", ex);
587 StringBuffer cmd = new StringBuffer();
588 cmd.append("loadingJalviewdata=true\nload APPEND ");
589 cmd.append(files.toString());
590 cmd.append("\nloadingJalviewdata=null");
591 final String command = cmd.toString();
593 lastnotify = jmb.getLoadNotifiesHandled();
597 jmb.evalStateCommand(command);
598 } catch (OutOfMemoryError oomerror)
601 "When trying to add structures to the Jmol viewer!",
603 Cache.log.debug("File locations are " + files);
604 } catch (Exception ex)
606 Cache.log.error("Couldn't add files to Jmol viewer!", ex);
610 // need to wait around until script has finished
611 while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
612 : (!jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
613 .getPdbFile().length != jmb.getPdbCount()))
617 Cache.log.debug("Waiting around for jmb notify.");
619 } catch (Exception e)
624 // refresh the sequence colours for the new structure(s)
625 for (AlignmentPanel ap : _colourwith)
627 jmb.updateColours(ap);
629 // do superposition if asked to
630 if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
632 javax.swing.SwingUtilities.invokeLater(new Runnable()
636 if (jmb.viewer.isScriptExecuting())
638 javax.swing.SwingUtilities.invokeLater(this);
642 } catch (InterruptedException q)
650 alignStructs_withAllAlignPanels();
654 alignAddedStructures = false;
656 addingStructures = false;
664 public void pdbFile_actionPerformed(ActionEvent actionEvent)
666 JalviewFileChooser chooser = new JalviewFileChooser(
667 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
669 chooser.setFileView(new JalviewFileView());
670 chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
671 chooser.setToolTipText(MessageManager.getString("action.save"));
673 int value = chooser.showSaveDialog(this);
675 if (value == JalviewFileChooser.APPROVE_OPTION)
677 BufferedReader in = null;
680 // TODO: cope with multiple PDB files in view
681 in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
682 File outFile = chooser.getSelectedFile();
684 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
686 while ((data = in.readLine()) != null)
688 if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
694 } catch (Exception ex)
696 ex.printStackTrace();
704 } catch (IOException e)
714 public void viewMapping_actionPerformed(ActionEvent actionEvent)
716 jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
719 cap.appendText(jmb.printMappings());
720 } catch (OutOfMemoryError e)
723 "composing sequence-structure alignments for display in text box.",
728 jalview.gui.Desktop.addInternalFrame(cap,
729 MessageManager.getString("label.pdb_sequence_mapping"), 550,
734 public void eps_actionPerformed(ActionEvent e)
736 makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
740 public void png_actionPerformed(ActionEvent e)
742 makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
745 void makePDBImage(jalview.util.ImageMaker.TYPE type)
747 int width = getWidth();
748 int height = getHeight();
750 jalview.util.ImageMaker im;
752 if (type == jalview.util.ImageMaker.TYPE.PNG)
754 im = new jalview.util.ImageMaker(this,
755 jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
756 width, height, null, null);
758 else if (type == jalview.util.ImageMaker.TYPE.EPS)
760 im = new jalview.util.ImageMaker(this,
761 jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
762 width, height, null, this.getTitle());
767 im = new jalview.util.ImageMaker(this,
768 jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
769 width, height, null, this.getTitle());
772 if (im.getGraphics() != null)
774 jmb.viewer.renderScreenImage(im.getGraphics(), width, height);
780 public void viewerColour_actionPerformed(ActionEvent actionEvent)
782 if (viewerColour.isSelected())
784 // disable automatic sequence colouring.
785 jmb.setColourBySequence(false);
790 public void seqColour_actionPerformed(ActionEvent actionEvent)
792 jmb.setColourBySequence(seqColour.isSelected());
793 if (_colourwith == null)
795 _colourwith = new Vector<AlignmentPanel>();
797 if (jmb.isColourBySequence())
799 if (!jmb.isLoadingFromArchive())
801 if (_colourwith.size() == 0 && getAlignmentPanel() != null)
803 // Make the currently displayed alignment panel the associated view
804 _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
807 // Set the colour using the current view for the associated alignframe
808 for (AlignmentPanel ap : _colourwith)
810 jmb.colourBySequence(ap);
816 public void chainColour_actionPerformed(ActionEvent actionEvent)
818 chainColour.setSelected(true);
823 public void chargeColour_actionPerformed(ActionEvent actionEvent)
825 chargeColour.setSelected(true);
826 jmb.colourByCharge();
830 public void zappoColour_actionPerformed(ActionEvent actionEvent)
832 zappoColour.setSelected(true);
833 jmb.setJalviewColourScheme(new ZappoColourScheme());
837 public void taylorColour_actionPerformed(ActionEvent actionEvent)
839 taylorColour.setSelected(true);
840 jmb.setJalviewColourScheme(new TaylorColourScheme());
844 public void hydroColour_actionPerformed(ActionEvent actionEvent)
846 hydroColour.setSelected(true);
847 jmb.setJalviewColourScheme(new HydrophobicColourScheme());
851 public void helixColour_actionPerformed(ActionEvent actionEvent)
853 helixColour.setSelected(true);
854 jmb.setJalviewColourScheme(new HelixColourScheme());
858 public void strandColour_actionPerformed(ActionEvent actionEvent)
860 strandColour.setSelected(true);
861 jmb.setJalviewColourScheme(new StrandColourScheme());
865 public void turnColour_actionPerformed(ActionEvent actionEvent)
867 turnColour.setSelected(true);
868 jmb.setJalviewColourScheme(new TurnColourScheme());
872 public void buriedColour_actionPerformed(ActionEvent actionEvent)
874 buriedColour.setSelected(true);
875 jmb.setJalviewColourScheme(new BuriedColourScheme());
879 public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
881 setJalviewColourScheme(new PurinePyrimidineColourScheme());
885 public void userColour_actionPerformed(ActionEvent actionEvent)
887 userColour.setSelected(true);
888 new UserDefinedColours(this, null);
892 public void backGround_actionPerformed(ActionEvent actionEvent)
894 java.awt.Color col = JColorChooser
895 .showDialog(this, MessageManager
896 .getString("label.select_backgroud_colour"), null);
899 jmb.setBackgroundColour(col);
904 public void showHelp_actionPerformed(ActionEvent actionEvent)
908 jalview.util.BrowserLauncher
909 .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
910 } catch (Exception ex)
915 public void showConsole(boolean showConsole)
920 if (splitPane == null)
922 splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
923 splitPane.setTopComponent(renderPanel);
924 splitPane.setBottomComponent(scriptWindow);
925 this.getContentPane().add(splitPane, BorderLayout.CENTER);
926 splitPane.setDividerLocation(getHeight() - 200);
927 scriptWindow.setVisible(true);
928 scriptWindow.validate();
929 splitPane.validate();
935 if (splitPane != null)
937 splitPane.setVisible(false);
942 this.getContentPane().add(renderPanel, BorderLayout.CENTER);
948 class RenderPanel extends JPanel
950 final Dimension currentSize = new Dimension();
953 public void paintComponent(Graphics g)
955 getSize(currentSize);
957 if (jmb != null && jmb.fileLoadingError != null)
959 g.setColor(Color.black);
960 g.fillRect(0, 0, currentSize.width, currentSize.height);
961 g.setColor(Color.white);
962 g.setFont(new Font("Verdana", Font.BOLD, 14));
963 g.drawString(MessageManager.getString("label.error_loading_file")
964 + "...", 20, currentSize.height / 2);
965 StringBuffer sb = new StringBuffer();
967 for (int e = 0; e < jmb.getPdbCount(); e++)
969 sb.append(jmb.getPdbEntry(e).getId());
970 if (e < jmb.getPdbCount() - 1)
975 if (e == jmb.getPdbCount() - 1 || sb.length() > 20)
978 g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
979 * g.getFontMetrics().getHeight());
983 else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
985 g.setColor(Color.black);
986 g.fillRect(0, 0, currentSize.width, currentSize.height);
987 g.setColor(Color.white);
988 g.setFont(new Font("Verdana", Font.BOLD, 14));
989 g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
990 20, currentSize.height / 2);
994 jmb.viewer.renderScreenImage(g, currentSize.width,
1000 public void updateTitleAndMenus()
1002 if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
1007 setChainMenuItems(jmb.chainNames);
1009 this.setTitle(jmb.getViewerTitle());
1010 if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
1012 viewerActionMenu.setVisible(true);
1014 if (!jmb.isLoadingFromArchive())
1016 seqColour_actionPerformed(null);
1024 * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
1028 protected void alignStructs_actionPerformed(ActionEvent actionEvent)
1030 alignStructs_withAllAlignPanels();
1033 private void alignStructs_withAllAlignPanels()
1035 if (getAlignmentPanel() == null)
1040 if (_alignwith.size() == 0)
1042 _alignwith.add(getAlignmentPanel());
1047 AlignmentI[] als = new Alignment[_alignwith.size()];
1048 ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
1049 int[] alm = new int[_alignwith.size()];
1052 for (AlignmentPanel ap : _alignwith)
1054 als[a] = ap.av.getAlignment();
1056 alc[a++] = ap.av.getColumnSelection();
1058 jmb.superposeStructures(als, alm, alc);
1059 } catch (Exception e)
1061 StringBuffer sp = new StringBuffer();
1062 for (AlignmentPanel ap : _alignwith)
1064 sp.append("'" + ap.alignFrame.getTitle() + "' ");
1066 Cache.log.info("Couldn't align structures with the " + sp.toString()
1067 + "associated alignment panels.", e);
1073 public void setJalviewColourScheme(ColourSchemeI ucs)
1075 jmb.setJalviewColourScheme(ucs);
1082 * @return first alignment panel displaying given alignment, or the default
1085 public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
1087 for (AlignmentPanel ap : getAllAlignmentPanels())
1089 if (ap.av.getAlignment() == alignment)
1094 return getAlignmentPanel();
1098 public AAStructureBindingModel getBinding()
1104 public String getStateInfo()
1106 return jmb == null ? null : jmb.viewer.getStateInfo();
1110 public ViewerType getViewerType()
1112 return ViewerType.JMOL;
1116 protected AAStructureBindingModel getBindingModel()