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.api.AlignmentViewPanel;
24 import jalview.bin.Cache;
25 import jalview.datamodel.Alignment;
26 import jalview.datamodel.AlignmentI;
27 import jalview.datamodel.HiddenColumns;
28 import jalview.datamodel.PDBEntry;
29 import jalview.datamodel.SequenceI;
30 import jalview.gui.StructureViewer.ViewerType;
31 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
32 import jalview.io.DataSourceType;
33 import jalview.io.JalviewFileChooser;
34 import jalview.io.JalviewFileView;
35 import jalview.jbgui.GStructureViewer;
36 import jalview.schemes.ColourSchemeI;
37 import jalview.schemes.ColourSchemes;
38 import jalview.structure.StructureMapping;
39 import jalview.structures.models.AAStructureBindingModel;
40 import jalview.util.MessageManager;
42 import java.awt.Color;
43 import java.awt.Component;
44 import java.awt.event.ActionEvent;
45 import java.awt.event.ActionListener;
46 import java.awt.event.ItemEvent;
47 import java.awt.event.ItemListener;
48 import java.io.BufferedReader;
50 import java.io.FileOutputStream;
51 import java.io.FileReader;
52 import java.io.IOException;
53 import java.io.PrintWriter;
54 import java.util.ArrayList;
55 import java.util.List;
56 import java.util.Vector;
58 import javax.swing.ButtonGroup;
59 import javax.swing.JCheckBoxMenuItem;
60 import javax.swing.JColorChooser;
61 import javax.swing.JMenu;
62 import javax.swing.JMenuItem;
63 import javax.swing.JRadioButtonMenuItem;
64 import javax.swing.event.MenuEvent;
65 import javax.swing.event.MenuListener;
68 * Base class with common functionality for JMol, Chimera or other structure
74 public abstract class StructureViewerBase extends GStructureViewer
75 implements Runnable, ViewSetProvider
78 * names for colour options (additional to Jalview colour schemes)
82 BySequence, ByChain, ChargeCysteine, ByViewer
86 * list of sequenceSet ids associated with the view
88 protected List<String> _aps = new ArrayList<>();
91 * list of alignment panels to use for superposition
93 protected Vector<AlignmentPanel> _alignwith = new Vector<>();
96 * list of alignment panels that are used for colouring structures by aligned
99 protected Vector<AlignmentPanel> _colourwith = new Vector<>();
101 private String viewId = null;
103 private AlignmentPanel ap;
105 protected boolean alignAddedStructures = false;
107 protected volatile boolean _started = false;
109 protected volatile boolean addingStructures = false;
111 protected Thread worker = null;
113 protected boolean allChainsSelected = false;
115 protected JMenu viewSelectionMenu;
118 * set after sequence colouring has been applied for this structure viewer.
119 * used to determine if the final sequence/structure mapping has been
122 protected volatile boolean seqColoursApplied = false;
125 * Default constructor
127 public StructureViewerBase()
133 * @return true if added structures should be aligned to existing one(s)
136 public boolean isAlignAddedStructures()
138 return alignAddedStructures;
144 * if added structures should be aligned to existing one(s)
147 public void setAlignAddedStructures(boolean alignAdded)
149 alignAddedStructures = alignAdded;
155 * @return true if this Jmol instance is linked with the given alignPanel
157 public boolean isLinkedWith(AlignmentPanel ap2)
159 return _aps.contains(ap2.av.getSequenceSetId());
162 public boolean isUsedforaligment(AlignmentPanel ap2)
165 return (_alignwith != null) && _alignwith.contains(ap2);
168 public boolean isUsedforcolourby(AlignmentPanel ap2)
170 return (_colourwith != null) && _colourwith.contains(ap2);
175 * @return TRUE if the view is NOT being coloured by the alignment colours.
177 public boolean isColouredByViewer()
179 return !getBinding().isColourBySequence();
182 public String getViewId()
186 viewId = System.currentTimeMillis() + "." + this.hashCode();
191 protected void setViewId(String viewId)
193 this.viewId = viewId;
196 public abstract String getStateInfo();
198 protected void buildActionMenu()
200 if (_alignwith == null)
202 _alignwith = new Vector<>();
204 if (_alignwith.size() == 0 && ap != null)
209 for (Component c : viewerActionMenu.getMenuComponents())
211 if (c != alignStructs)
213 viewerActionMenu.remove((JMenuItem) c);
218 public AlignmentPanel getAlignmentPanel()
223 protected void setAlignmentPanel(AlignmentPanel alp)
229 public AlignmentPanel[] getAllAlignmentPanels()
231 AlignmentPanel[] t, list = new AlignmentPanel[0];
232 for (String setid : _aps)
234 AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
237 t = new AlignmentPanel[list.length + panels.length];
238 System.arraycopy(list, 0, t, 0, list.length);
239 System.arraycopy(panels, 0, t, list.length, panels.length);
248 * set the primary alignmentPanel reference and add another alignPanel to the
249 * list of ones to use for colouring and aligning
253 public void addAlignmentPanel(AlignmentPanel nap)
255 if (getAlignmentPanel() == null)
257 setAlignmentPanel(nap);
259 if (!_aps.contains(nap.av.getSequenceSetId()))
261 _aps.add(nap.av.getSequenceSetId());
266 * remove any references held to the given alignment panel
270 public void removeAlignmentPanel(AlignmentPanel nap)
274 _alignwith.remove(nap);
275 _colourwith.remove(nap);
276 if (getAlignmentPanel() == nap)
278 setAlignmentPanel(null);
279 for (AlignmentPanel aps : getAllAlignmentPanels())
283 setAlignmentPanel(aps);
288 } catch (Exception ex)
291 if (getAlignmentPanel() != null)
297 public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
299 addAlignmentPanel(nap);
300 if (!_alignwith.contains(nap))
306 public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
308 if (_alignwith.contains(nap))
310 _alignwith.remove(nap);
314 public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,
315 boolean enableColourBySeq)
317 useAlignmentPanelForColourbyseq(nap);
318 getBinding().setColourBySequence(enableColourBySeq);
319 seqColour.setSelected(enableColourBySeq);
320 viewerColour.setSelected(!enableColourBySeq);
323 public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
325 addAlignmentPanel(nap);
326 if (!_colourwith.contains(nap))
328 _colourwith.add(nap);
332 public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
334 if (_colourwith.contains(nap))
336 _colourwith.remove(nap);
340 public abstract ViewerType getViewerType();
342 protected abstract IProgressIndicator getIProgressIndicator();
345 * add a new structure (with associated sequences and chains) to this viewer,
346 * retrieving it if necessary first.
352 * if true, new structure(s) will be aligned using associated
356 protected void addStructure(final PDBEntry pdbentry,
357 final SequenceI[] seqs, final String[] chains,
358 final IProgressIndicator alignFrame)
360 if (pdbentry.getFile() == null)
362 if (worker != null && worker.isAlive())
364 // a retrieval is in progress, wait around and add ourselves to the
366 new Thread(new Runnable()
371 while (worker != null && worker.isAlive() && _started)
375 Thread.sleep(100 + ((int) Math.random() * 100));
377 } catch (Exception e)
381 // and call ourselves again.
382 addStructure(pdbentry, seqs, chains, alignFrame);
388 // otherwise, start adding the structure.
389 getBinding().addSequenceAndChain(new PDBEntry[] { pdbentry },
391 { seqs }, new String[][] { chains });
392 addingStructures = true;
394 worker = new Thread(this);
399 protected boolean hasPdbId(String pdbId)
401 return getBinding().hasPdbId(pdbId);
405 * Returns a list of any viewer of the instantiated type. The list is
406 * restricted to those linked to the given alignment panel if it is not null.
408 protected List<StructureViewerBase> getViewersFor(AlignmentPanel alp)
410 return Desktop.instance.getStructureViewers(alp, this.getClass());
415 * Check for any existing views involving this alignment and give user the
416 * option to add and align this molecule to one of them
423 * @return true if user adds to a view, or cancels entirely, else false
426 public boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
427 String[] chains, final AlignmentViewPanel apanel, String pdbId)
430 * JAL-1742 exclude view with this structure already mapped (don't offer
431 * to align chain B to chain A of the same structure)
437 AlignmentPanel ap = (AlignmentPanel) apanel; // Implementation error if this
439 useAlignmentPanelForSuperposition(ap);
440 addStructure(pdbentry, seq, chains, ap.alignFrame);
445 * Adds mappings for the given sequences to an already opened PDB structure,
446 * and updates any viewers that have the PDB file
453 public void addSequenceMappingsToStructure(SequenceI[] seq,
454 String[] chains, final AlignmentViewPanel alpanel,
457 AlignmentPanel apanel = (AlignmentPanel) alpanel;
459 // TODO : Fix multiple seq to one chain issue here.
461 * create the mappings
463 apanel.getStructureSelectionManager().setMapping(seq, chains,
464 pdbFilename, DataSourceType.FILE, getIProgressIndicator());
467 * alert the FeatureRenderer to show new (PDB RESNUM) features
469 if (apanel.getSeqPanel().seqCanvas.fr != null)
471 apanel.getSeqPanel().seqCanvas.fr.featuresAdded();
472 // note - we don't do a refresh for structure here because we do it
473 // explicitly for all panels later on
474 apanel.paintAlignment(true, false);
478 * add the sequences to any other viewers (of the same type) for this pdb
481 // JBPNOTE: this looks like a binding routine, rather than a gui routine
482 for (StructureViewerBase viewer : getViewersFor(null))
484 AAStructureBindingModel bindingModel = viewer.getBinding();
485 for (int pe = 0; pe < bindingModel.getPdbCount(); pe++)
487 if (bindingModel.getPdbEntry(pe).getFile().equals(pdbFilename))
489 bindingModel.addSequence(pe, seq);
490 viewer.addAlignmentPanel(apanel);
492 * add it to the set of alignments used for colouring structure by
495 viewer.useAlignmentPanelForColourbyseq(apanel);
496 viewer.buildActionMenu();
497 apanel.getStructureSelectionManager()
498 .sequenceColoursChanged(apanel);
506 * Check if the PDB file is already loaded, if so offer to add it to the
513 * @return true if the user chooses to add to a viewer, or to cancel entirely
516 public boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
517 final AlignmentViewPanel apanel, String pdbId)
519 boolean finished = false;
520 String alreadyMapped = apanel.getStructureSelectionManager()
521 .alreadyMappedToFile(pdbId);
523 if (alreadyMapped != null)
526 * the PDB file is already loaded
528 addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
534 void setChainMenuItems(List<String> chainNames)
536 chainMenu.removeAll();
537 if (chainNames == null || chainNames.isEmpty())
541 JMenuItem menuItem = new JMenuItem(
542 MessageManager.getString("label.all"));
543 menuItem.addActionListener(new ActionListener()
546 public void actionPerformed(ActionEvent evt)
548 allChainsSelected = true;
549 for (int i = 0; i < chainMenu.getItemCount(); i++)
551 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
553 ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
556 showSelectedChains();
557 allChainsSelected = false;
561 chainMenu.add(menuItem);
563 for (String chain : chainNames)
565 menuItem = new JCheckBoxMenuItem(chain, true);
566 menuItem.addItemListener(new ItemListener()
569 public void itemStateChanged(ItemEvent evt)
571 if (!allChainsSelected)
573 showSelectedChains();
578 chainMenu.add(menuItem);
582 abstract void showSelectedChains();
585 * Action on selecting one of Jalview's registered colour schemes
588 public void changeColour_actionPerformed(String colourSchemeName)
590 AlignmentI al = getAlignmentPanel().av.getAlignment();
591 ColourSchemeI cs = ColourSchemes.getInstance()
592 .getColourScheme(colourSchemeName, al, null);
593 getBinding().setJalviewColourScheme(cs);
597 * Builds the colour menu
599 protected void buildColourMenu()
601 colourMenu.removeAll();
602 AlignmentI al = getAlignmentPanel().av.getAlignment();
605 * add colour by sequence, by chain, by charge and cysteine
607 colourMenu.add(seqColour);
608 colourMenu.add(chainColour);
609 colourMenu.add(chargeColour);
610 chargeColour.setEnabled(!al.isNucleotide());
613 * add all 'simple' (per-residue) colour schemes registered to Jalview
615 ButtonGroup itemGroup = ColourMenuHelper.addMenuItems(colourMenu, this,
619 * add 'colour by viewer' (menu item text is set in subclasses)
621 viewerColour.setSelected(false);
622 viewerColour.addActionListener(new ActionListener()
625 public void actionPerformed(ActionEvent actionEvent)
627 viewerColour_actionPerformed(actionEvent);
630 colourMenu.add(viewerColour);
633 * add 'set background colour'
635 JMenuItem backGround = new JMenuItem();
637 .setText(MessageManager.getString("action.background_colour"));
638 backGround.addActionListener(new ActionListener()
641 public void actionPerformed(ActionEvent actionEvent)
643 background_actionPerformed(actionEvent);
646 colourMenu.add(backGround);
649 * add colour buttons to a group so their selection is
650 * mutually exclusive (background colour is a separate option)
652 itemGroup.add(seqColour);
653 itemGroup.add(chainColour);
654 itemGroup.add(chargeColour);
655 itemGroup.add(viewerColour);
659 * Construct menu items
661 protected void initMenus()
663 AAStructureBindingModel binding = getBinding();
665 seqColour = new JRadioButtonMenuItem();
666 seqColour.setText(MessageManager.getString("action.by_sequence"));
667 seqColour.setName(ViewerColour.BySequence.name());
668 seqColour.setSelected(binding.isColourBySequence());
669 seqColour.addActionListener(new ActionListener()
672 public void actionPerformed(ActionEvent actionEvent)
674 seqColour_actionPerformed(actionEvent);
678 chainColour = new JRadioButtonMenuItem();
679 chainColour.setText(MessageManager.getString("action.by_chain"));
680 chainColour.setName(ViewerColour.ByChain.name());
681 chainColour.addActionListener(new ActionListener()
684 public void actionPerformed(ActionEvent actionEvent)
686 chainColour_actionPerformed(actionEvent);
690 chargeColour = new JRadioButtonMenuItem();
691 chargeColour.setText(MessageManager.getString("label.charge_cysteine"));
692 chargeColour.setName(ViewerColour.ChargeCysteine.name());
693 chargeColour.addActionListener(new ActionListener()
696 public void actionPerformed(ActionEvent actionEvent)
698 chargeColour_actionPerformed(actionEvent);
702 viewerColour = new JRadioButtonMenuItem();
703 // text is set in overrides of this method
704 viewerColour.setName(ViewerColour.ByViewer.name());
705 viewerColour.setSelected(!binding.isColourBySequence());
707 if (_colourwith == null)
709 _colourwith = new Vector<>();
711 if (_alignwith == null)
713 _alignwith = new Vector<>();
716 ViewSelectionMenu seqColourBy = new ViewSelectionMenu(
717 MessageManager.getString("label.colour_by"), this, _colourwith,
721 public void itemStateChanged(ItemEvent e)
723 if (!seqColour.isSelected())
729 // update the Chimera display now.
730 seqColour_actionPerformed(null);
734 viewMenu.add(seqColourBy);
736 final ItemListener handler = new ItemListener()
739 public void itemStateChanged(ItemEvent e)
741 alignStructs.setEnabled(!_alignwith.isEmpty());
742 alignStructs.setToolTipText(MessageManager.formatMessage(
743 "label.align_structures_using_linked_alignment_views",
747 viewSelectionMenu = new ViewSelectionMenu(
748 MessageManager.getString("label.superpose_with"), this,
749 _alignwith, handler);
750 handler.itemStateChanged(null);
751 viewerActionMenu.add(viewSelectionMenu, 0);
752 viewerActionMenu.addMenuListener(new MenuListener()
755 public void menuSelected(MenuEvent e)
757 handler.itemStateChanged(null);
761 public void menuDeselected(MenuEvent e)
766 public void menuCanceled(MenuEvent e)
775 public void setJalviewColourScheme(ColourSchemeI cs)
777 getBinding().setJalviewColourScheme(cs);
781 * Sends commands to the structure viewer to superimpose structures based on
782 * currently associated alignments. May optionally return an error message for
786 protected String alignStructs_actionPerformed(ActionEvent actionEvent)
788 return alignStructs_withAllAlignPanels();
791 protected String alignStructs_withAllAlignPanels()
793 if (getAlignmentPanel() == null)
798 if (_alignwith.size() == 0)
800 _alignwith.add(getAlignmentPanel());
806 AlignmentI[] als = new Alignment[_alignwith.size()];
807 HiddenColumns[] alc = new HiddenColumns[_alignwith.size()];
808 int[] alm = new int[_alignwith.size()];
811 for (AlignmentPanel ap : _alignwith)
813 als[a] = ap.av.getAlignment();
815 alc[a++] = ap.av.getAlignment().getHiddenColumns();
817 reply = getBinding().superposeStructures(als, alm, alc);
820 String text = MessageManager
821 .formatMessage("error.superposition_failed", reply);
822 statusBar.setText(text);
824 } catch (Exception e)
826 StringBuffer sp = new StringBuffer();
827 for (AlignmentPanel ap : _alignwith)
829 sp.append("'" + ap.alignFrame.getTitle() + "' ");
831 Cache.log.info("Couldn't align structures with the " + sp.toString()
832 + "associated alignment panels.", e);
838 public void background_actionPerformed(ActionEvent actionEvent)
840 Color col = JColorChooser.showDialog(this,
841 MessageManager.getString("label.select_background_colour"),
845 getBinding().setBackgroundColour(col);
850 public void viewerColour_actionPerformed(ActionEvent actionEvent)
852 if (viewerColour.isSelected())
854 // disable automatic sequence colouring.
855 getBinding().setColourBySequence(false);
860 public void chainColour_actionPerformed(ActionEvent actionEvent)
862 chainColour.setSelected(true);
863 getBinding().colourByChain();
867 public void chargeColour_actionPerformed(ActionEvent actionEvent)
869 chargeColour.setSelected(true);
870 getBinding().colourByCharge();
874 public void seqColour_actionPerformed(ActionEvent actionEvent)
876 AAStructureBindingModel binding = getBinding();
877 binding.setColourBySequence(seqColour.isSelected());
878 if (_colourwith == null)
880 _colourwith = new Vector<>();
882 if (binding.isColourBySequence())
884 if (!binding.isLoadingFromArchive())
886 if (_colourwith.size() == 0 && getAlignmentPanel() != null)
888 // Make the currently displayed alignment panel the associated view
889 _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
892 // Set the colour using the current view for the associated alignframe
893 for (AlignmentPanel ap : _colourwith)
895 binding.colourBySequence(ap);
897 seqColoursApplied = true;
902 public void pdbFile_actionPerformed(ActionEvent actionEvent)
904 JalviewFileChooser chooser = new JalviewFileChooser(
905 Cache.getProperty("LAST_DIRECTORY"));
907 chooser.setFileView(new JalviewFileView());
908 chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
909 chooser.setToolTipText(MessageManager.getString("action.save"));
911 int value = chooser.showSaveDialog(this);
913 if (value == JalviewFileChooser.APPROVE_OPTION)
915 BufferedReader in = null;
918 // TODO: cope with multiple PDB files in view
919 in = new BufferedReader(
920 new FileReader(getBinding().getStructureFiles()[0]));
921 File outFile = chooser.getSelectedFile();
923 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
925 while ((data = in.readLine()) != null)
927 if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
933 } catch (Exception ex)
935 ex.printStackTrace();
943 } catch (IOException e)
953 public void viewMapping_actionPerformed(ActionEvent actionEvent)
955 CutAndPasteTransfer cap = new CutAndPasteTransfer();
958 cap.appendText(getBinding().printMappings());
959 } catch (OutOfMemoryError e)
962 "composing sequence-structure alignments for display in text box.",
967 Desktop.addInternalFrame(cap,
968 MessageManager.getString("label.pdb_sequence_mapping"), 550,
972 protected abstract String getViewerName();
975 * Configures the title and menu items of the viewer panel.
978 public void updateTitleAndMenus()
980 AAStructureBindingModel binding = getBinding();
981 if (binding.hasFileLoadingError())
986 setChainMenuItems(binding.getChainNames());
988 this.setTitle(binding.getViewerTitle(getViewerName(), true));
991 * enable 'Superpose with' if more than one mapped structure
993 viewSelectionMenu.setEnabled(false);
994 if (getBinding().getStructureFiles().length > 1
995 && getBinding().getSequence().length > 1)
997 viewSelectionMenu.setEnabled(true);
1001 * Show action menu if it has any enabled items
1003 viewerActionMenu.setVisible(false);
1004 for (int i = 0; i < viewerActionMenu.getItemCount(); i++)
1006 if (viewerActionMenu.getItem(i).isEnabled())
1008 viewerActionMenu.setVisible(true);
1013 if (!binding.isLoadingFromArchive())
1015 seqColour_actionPerformed(null);
1020 public String toString()
1026 public boolean hasMapping()
1028 if (worker != null && (addingStructures || _started))
1032 if (getBinding() == null)
1034 if (_aps == null || _aps.size() == 0)
1036 // viewer has been closed, but we did at some point run.
1041 String[] pdbids = getBinding().getStructureFiles();
1047 for (String pdbid:pdbids) {
1048 StructureMapping sm[] = getBinding().getSsm().getMapping(pdbid);
1049 if (sm!=null && sm.length>0 && sm[0]!=null) {
1053 // only return true if there is a mapping for every structure file we have loaded
1054 if (p == 0 || p != pdbids.length)
1058 // and that coloring has been applied
1059 return seqColoursApplied;