2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
3 * Copyright (C) 2015 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.setFinishedInit(true);
389 void setChainMenuItems(Vector<String> chains)
391 chainMenu.removeAll();
396 JMenuItem menuItem = new JMenuItem(
397 MessageManager.getString("label.all"));
398 menuItem.addActionListener(new ActionListener()
400 public void actionPerformed(ActionEvent evt)
402 allChainsSelected = true;
403 for (int i = 0; i < chainMenu.getItemCount(); i++)
405 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
407 ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
411 allChainsSelected = false;
415 chainMenu.add(menuItem);
417 for (String chain : chains)
419 menuItem = new JCheckBoxMenuItem(chain, true);
420 menuItem.addItemListener(new ItemListener()
422 public void itemStateChanged(ItemEvent evt)
424 if (!allChainsSelected)
431 chainMenu.add(menuItem);
435 boolean allChainsSelected = false;
439 Vector<String> toshow = new Vector<String>();
440 for (int i = 0; i < chainMenu.getItemCount(); i++)
442 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
444 JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
445 if (item.isSelected())
447 toshow.addElement(item.getText());
451 jmb.centerViewer(toshow);
454 public void closeViewer(boolean closeExternalViewer)
456 // Jmol does not use an external viewer
461 setAlignmentPanel(null);
465 // TODO: check for memory leaks where instance isn't finalised because jmb
466 // holds a reference to the window
474 // todo - record which pdbids were successfuly imported.
475 StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
478 String[] curfiles = jmb.getPdbFile(); // files currently in viewer
479 // TODO: replace with reference fetching/transfer code (validate PDBentry
481 jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
482 for (int pi = 0; pi < jmb.getPdbCount(); pi++)
484 String file = jmb.getPdbEntry(pi).getFile();
487 // retrieve the pdb and store it locally
488 AlignmentI pdbseq = null;
489 pdbid = jmb.getPdbEntry(pi).getId();
490 long hdl = pdbid.hashCode() - System.currentTimeMillis();
491 if (progressBar != null)
493 progressBar.setProgressBar(MessageManager.formatMessage(
494 "status.fetching_pdb", new String[] { pdbid }), hdl);
498 pdbseq = pdbclient.getSequenceRecords(pdbid);
499 } catch (OutOfMemoryError oomerror)
501 new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
502 } catch (Exception ex)
504 ex.printStackTrace();
505 errormsgs.append("'" + pdbid + "'");
507 if (progressBar != null)
509 progressBar.setProgressBar(
510 MessageManager.getString("label.state_completed"), hdl);
514 // just transfer the file name from the first sequence's first
516 file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
517 .elementAt(0).getFile()).getAbsolutePath();
518 jmb.getPdbEntry(pi).setFile(file);
520 files.append(" \"" + Platform.escapeString(file) + "\"");
524 errormsgs.append("'" + pdbid + "' ");
529 if (curfiles != null && curfiles.length > 0)
531 addingStructures = true; // already files loaded.
532 for (int c = 0; c < curfiles.length; c++)
534 if (curfiles[c].equals(file))
543 files.append(" \"" + Platform.escapeString(file) + "\"");
547 } catch (OutOfMemoryError oomerror)
549 new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
550 } catch (Exception ex)
552 ex.printStackTrace();
553 errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
556 if (errormsgs.length() > 0)
559 JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
560 .formatMessage("label.pdb_entries_couldnt_be_retrieved",
561 new String[] { errormsgs.toString() }),
562 MessageManager.getString("label.couldnt_load_file"),
563 JOptionPane.ERROR_MESSAGE);
566 long lastnotify = jmb.getLoadNotifiesHandled();
567 if (files.length() > 0)
569 if (!addingStructures)
574 initJmol("load FILES " + files.toString());
575 } catch (OutOfMemoryError oomerror)
577 new OOMWarning("When trying to open the Jmol viewer!", oomerror);
578 Cache.log.debug("File locations are " + files);
579 } catch (Exception ex)
581 Cache.log.error("Couldn't open Jmol viewer!", ex);
586 StringBuffer cmd = new StringBuffer();
587 cmd.append("loadingJalviewdata=true\nload APPEND ");
588 cmd.append(files.toString());
589 cmd.append("\nloadingJalviewdata=null");
590 final String command = cmd.toString();
592 lastnotify = jmb.getLoadNotifiesHandled();
596 jmb.evalStateCommand(command);
597 } catch (OutOfMemoryError oomerror)
600 "When trying to add structures to the Jmol viewer!",
602 Cache.log.debug("File locations are " + files);
603 } catch (Exception ex)
605 Cache.log.error("Couldn't add files to Jmol viewer!", ex);
609 // need to wait around until script has finished
610 while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
611 : (!jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
612 .getPdbFile().length != jmb.getPdbCount()))
616 Cache.log.debug("Waiting around for jmb notify.");
618 } catch (Exception e)
623 // refresh the sequence colours for the new structure(s)
624 for (AlignmentPanel ap : _colourwith)
626 jmb.updateColours(ap);
628 // do superposition if asked to
629 if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
631 javax.swing.SwingUtilities.invokeLater(new Runnable()
635 if (jmb.viewer.isScriptExecuting())
637 javax.swing.SwingUtilities.invokeLater(this);
641 } catch (InterruptedException q)
649 alignStructs_withAllAlignPanels();
653 alignAddedStructures = false;
655 addingStructures = false;
663 public void pdbFile_actionPerformed(ActionEvent actionEvent)
665 JalviewFileChooser chooser = new JalviewFileChooser(
666 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
668 chooser.setFileView(new JalviewFileView());
669 chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
670 chooser.setToolTipText(MessageManager.getString("action.save"));
672 int value = chooser.showSaveDialog(this);
674 if (value == JalviewFileChooser.APPROVE_OPTION)
676 BufferedReader in = null;
679 // TODO: cope with multiple PDB files in view
680 in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
681 File outFile = chooser.getSelectedFile();
683 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
685 while ((data = in.readLine()) != null)
687 if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
693 } catch (Exception ex)
695 ex.printStackTrace();
703 } catch (IOException e)
713 public void viewMapping_actionPerformed(ActionEvent actionEvent)
715 jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
718 cap.appendText(jmb.printMappings());
719 } catch (OutOfMemoryError e)
722 "composing sequence-structure alignments for display in text box.",
727 jalview.gui.Desktop.addInternalFrame(cap,
728 MessageManager.getString("label.pdb_sequence_mapping"), 550,
733 public void eps_actionPerformed(ActionEvent e)
735 makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
739 public void png_actionPerformed(ActionEvent e)
741 makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
744 void makePDBImage(jalview.util.ImageMaker.TYPE type)
746 int width = getWidth();
747 int height = getHeight();
749 jalview.util.ImageMaker im;
751 if (type == jalview.util.ImageMaker.TYPE.PNG)
753 im = new jalview.util.ImageMaker(this,
754 jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
755 width, height, null, null);
757 else if (type == jalview.util.ImageMaker.TYPE.EPS)
759 im = new jalview.util.ImageMaker(this,
760 jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
761 width, height, null, this.getTitle());
766 im = new jalview.util.ImageMaker(this,
767 jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
768 width, height, null, this.getTitle());
771 if (im.getGraphics() != null)
773 jmb.viewer.renderScreenImage(im.getGraphics(), width, height);
779 public void viewerColour_actionPerformed(ActionEvent actionEvent)
781 if (viewerColour.isSelected())
783 // disable automatic sequence colouring.
784 jmb.setColourBySequence(false);
789 public void seqColour_actionPerformed(ActionEvent actionEvent)
791 jmb.setColourBySequence(seqColour.isSelected());
792 if (_colourwith == null)
794 _colourwith = new Vector<AlignmentPanel>();
796 if (jmb.isColourBySequence())
798 if (!jmb.isLoadingFromArchive())
800 if (_colourwith.size() == 0 && getAlignmentPanel() != null)
802 // Make the currently displayed alignment panel the associated view
803 _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
806 // Set the colour using the current view for the associated alignframe
807 for (AlignmentPanel ap : _colourwith)
809 jmb.colourBySequence(ap);
815 public void chainColour_actionPerformed(ActionEvent actionEvent)
817 chainColour.setSelected(true);
822 public void chargeColour_actionPerformed(ActionEvent actionEvent)
824 chargeColour.setSelected(true);
825 jmb.colourByCharge();
829 public void zappoColour_actionPerformed(ActionEvent actionEvent)
831 zappoColour.setSelected(true);
832 jmb.setJalviewColourScheme(new ZappoColourScheme());
836 public void taylorColour_actionPerformed(ActionEvent actionEvent)
838 taylorColour.setSelected(true);
839 jmb.setJalviewColourScheme(new TaylorColourScheme());
843 public void hydroColour_actionPerformed(ActionEvent actionEvent)
845 hydroColour.setSelected(true);
846 jmb.setJalviewColourScheme(new HydrophobicColourScheme());
850 public void helixColour_actionPerformed(ActionEvent actionEvent)
852 helixColour.setSelected(true);
853 jmb.setJalviewColourScheme(new HelixColourScheme());
857 public void strandColour_actionPerformed(ActionEvent actionEvent)
859 strandColour.setSelected(true);
860 jmb.setJalviewColourScheme(new StrandColourScheme());
864 public void turnColour_actionPerformed(ActionEvent actionEvent)
866 turnColour.setSelected(true);
867 jmb.setJalviewColourScheme(new TurnColourScheme());
871 public void buriedColour_actionPerformed(ActionEvent actionEvent)
873 buriedColour.setSelected(true);
874 jmb.setJalviewColourScheme(new BuriedColourScheme());
878 public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
880 setJalviewColourScheme(new PurinePyrimidineColourScheme());
884 public void userColour_actionPerformed(ActionEvent actionEvent)
886 userColour.setSelected(true);
887 new UserDefinedColours(this, null);
891 public void backGround_actionPerformed(ActionEvent actionEvent)
893 java.awt.Color col = JColorChooser
894 .showDialog(this, MessageManager
895 .getString("label.select_backgroud_colour"), null);
898 jmb.setBackgroundColour(col);
903 public void showHelp_actionPerformed(ActionEvent actionEvent)
907 jalview.util.BrowserLauncher
908 .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
909 } catch (Exception ex)
914 public void showConsole(boolean showConsole)
919 if (splitPane == null)
921 splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
922 splitPane.setTopComponent(renderPanel);
923 splitPane.setBottomComponent(scriptWindow);
924 this.getContentPane().add(splitPane, BorderLayout.CENTER);
925 splitPane.setDividerLocation(getHeight() - 200);
926 scriptWindow.setVisible(true);
927 scriptWindow.validate();
928 splitPane.validate();
934 if (splitPane != null)
936 splitPane.setVisible(false);
941 this.getContentPane().add(renderPanel, BorderLayout.CENTER);
947 class RenderPanel extends JPanel
949 final Dimension currentSize = new Dimension();
952 public void paintComponent(Graphics g)
954 getSize(currentSize);
956 if (jmb != null && jmb.fileLoadingError != null)
958 g.setColor(Color.black);
959 g.fillRect(0, 0, currentSize.width, currentSize.height);
960 g.setColor(Color.white);
961 g.setFont(new Font("Verdana", Font.BOLD, 14));
962 g.drawString(MessageManager.getString("label.error_loading_file")
963 + "...", 20, currentSize.height / 2);
964 StringBuffer sb = new StringBuffer();
966 for (int e = 0; e < jmb.getPdbCount(); e++)
968 sb.append(jmb.getPdbEntry(e).getId());
969 if (e < jmb.getPdbCount() - 1)
974 if (e == jmb.getPdbCount() - 1 || sb.length() > 20)
977 g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
978 * g.getFontMetrics().getHeight());
982 else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
984 g.setColor(Color.black);
985 g.fillRect(0, 0, currentSize.width, currentSize.height);
986 g.setColor(Color.white);
987 g.setFont(new Font("Verdana", Font.BOLD, 14));
988 g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
989 20, currentSize.height / 2);
993 jmb.viewer.renderScreenImage(g, currentSize.width,
999 public void updateTitleAndMenus()
1001 if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
1006 setChainMenuItems(jmb.chainNames);
1008 this.setTitle(jmb.getViewerTitle());
1009 if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
1011 viewerActionMenu.setVisible(true);
1013 if (!jmb.isLoadingFromArchive())
1015 seqColour_actionPerformed(null);
1023 * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
1027 protected void alignStructs_actionPerformed(ActionEvent actionEvent)
1029 alignStructs_withAllAlignPanels();
1032 private void alignStructs_withAllAlignPanels()
1034 if (getAlignmentPanel() == null)
1039 if (_alignwith.size() == 0)
1041 _alignwith.add(getAlignmentPanel());
1046 AlignmentI[] als = new Alignment[_alignwith.size()];
1047 ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
1048 int[] alm = new int[_alignwith.size()];
1051 for (AlignmentPanel ap : _alignwith)
1053 als[a] = ap.av.getAlignment();
1055 alc[a++] = ap.av.getColumnSelection();
1057 jmb.superposeStructures(als, alm, alc);
1058 } catch (Exception e)
1060 StringBuffer sp = new StringBuffer();
1061 for (AlignmentPanel ap : _alignwith)
1063 sp.append("'" + ap.alignFrame.getTitle() + "' ");
1065 Cache.log.info("Couldn't align structures with the " + sp.toString()
1066 + "associated alignment panels.", e);
1072 public void setJalviewColourScheme(ColourSchemeI ucs)
1074 jmb.setJalviewColourScheme(ucs);
1081 * @return first alignment panel displaying given alignment, or the default
1084 public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
1086 for (AlignmentPanel ap : getAllAlignmentPanels())
1088 if (ap.av.getAlignment() == alignment)
1093 return getAlignmentPanel();
1097 public AAStructureBindingModel getBinding()
1103 public String getStateInfo()
1105 return jmb == null ? null : jmb.viewer.getStateInfo();
1109 public ViewerType getViewerType()
1111 return ViewerType.JMOL;
1115 protected AAStructureBindingModel getBindingModel()