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.HiddenColumns;
27 import jalview.datamodel.PDBEntry;
28 import jalview.datamodel.SequenceI;
29 import jalview.gui.StructureViewer.ViewerType;
30 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
31 import jalview.io.DataSourceType;
32 import jalview.io.JalviewFileChooser;
33 import jalview.io.JalviewFileView;
34 import jalview.jbgui.GStructureViewer;
35 import jalview.schemes.ColourSchemeI;
36 import jalview.schemes.ColourSchemes;
37 import jalview.structures.models.AAStructureBindingModel;
38 import jalview.util.MessageManager;
40 import java.awt.Color;
41 import java.awt.Component;
42 import java.awt.event.ActionEvent;
43 import java.awt.event.ActionListener;
44 import java.awt.event.ItemEvent;
45 import java.awt.event.ItemListener;
46 import java.io.BufferedReader;
48 import java.io.FileOutputStream;
49 import java.io.FileReader;
50 import java.io.IOException;
51 import java.io.PrintWriter;
52 import java.util.ArrayList;
53 import java.util.List;
54 import java.util.Vector;
56 import javax.swing.ButtonGroup;
57 import javax.swing.JCheckBoxMenuItem;
58 import javax.swing.JColorChooser;
59 import javax.swing.JMenu;
60 import javax.swing.JMenuItem;
61 import javax.swing.JRadioButtonMenuItem;
62 import javax.swing.event.MenuEvent;
63 import javax.swing.event.MenuListener;
66 * Base class with common functionality for JMol, Chimera or other structure
72 public abstract class StructureViewerBase extends GStructureViewer
73 implements Runnable, ViewSetProvider
76 * names for colour options (additional to Jalview colour schemes)
80 BySequence, ByChain, ChargeCysteine, ByViewer
84 * list of sequenceSet ids associated with the view
86 protected List<String> _aps = new ArrayList<>();
89 * list of alignment panels to use for superposition
91 protected Vector<AlignmentPanel> _alignwith = new Vector<>();
94 * list of alignment panels that are used for colouring structures by aligned
97 protected Vector<AlignmentPanel> _colourwith = new Vector<>();
99 private String viewId = null;
101 private AlignmentPanel ap;
103 protected boolean alignAddedStructures = false;
105 protected boolean _started = false;
107 protected boolean addingStructures = false;
109 protected Thread worker = null;
111 protected boolean allChainsSelected = false;
113 protected JMenu viewSelectionMenu;
116 * Default constructor
118 public StructureViewerBase()
126 * @return true if this Jmol instance is linked with the given alignPanel
128 public boolean isLinkedWith(AlignmentPanel ap2)
130 return _aps.contains(ap2.av.getSequenceSetId());
133 public boolean isUsedforaligment(AlignmentPanel ap2)
136 return (_alignwith != null) && _alignwith.contains(ap2);
139 public boolean isUsedforcolourby(AlignmentPanel ap2)
141 return (_colourwith != null) && _colourwith.contains(ap2);
146 * @return TRUE if the view is NOT being coloured by the alignment colours.
148 public boolean isColouredByViewer()
150 return !getBinding().isColourBySequence();
153 public String getViewId()
157 viewId = System.currentTimeMillis() + "." + this.hashCode();
162 protected void setViewId(String viewId)
164 this.viewId = viewId;
167 public abstract String getStateInfo();
169 protected void buildActionMenu()
171 if (_alignwith == null)
173 _alignwith = new Vector<>();
175 if (_alignwith.size() == 0 && ap != null)
180 for (Component c : viewerActionMenu.getMenuComponents())
182 if (c != alignStructs)
184 viewerActionMenu.remove((JMenuItem) c);
189 public AlignmentPanel getAlignmentPanel()
194 protected void setAlignmentPanel(AlignmentPanel alp)
200 public AlignmentPanel[] getAllAlignmentPanels()
202 AlignmentPanel[] t, list = new AlignmentPanel[0];
203 for (String setid : _aps)
205 AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
208 t = new AlignmentPanel[list.length + panels.length];
209 System.arraycopy(list, 0, t, 0, list.length);
210 System.arraycopy(panels, 0, t, list.length, panels.length);
219 * set the primary alignmentPanel reference and add another alignPanel to the
220 * list of ones to use for colouring and aligning
224 public void addAlignmentPanel(AlignmentPanel nap)
226 if (getAlignmentPanel() == null)
228 setAlignmentPanel(nap);
230 if (!_aps.contains(nap.av.getSequenceSetId()))
232 _aps.add(nap.av.getSequenceSetId());
237 * remove any references held to the given alignment panel
241 public void removeAlignmentPanel(AlignmentPanel nap)
245 _alignwith.remove(nap);
246 _colourwith.remove(nap);
247 if (getAlignmentPanel() == nap)
249 setAlignmentPanel(null);
250 for (AlignmentPanel aps : getAllAlignmentPanels())
254 setAlignmentPanel(aps);
259 } catch (Exception ex)
262 if (getAlignmentPanel() != null)
268 public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
270 addAlignmentPanel(nap);
271 if (!_alignwith.contains(nap))
277 public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
279 if (_alignwith.contains(nap))
281 _alignwith.remove(nap);
285 public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,
286 boolean enableColourBySeq)
288 useAlignmentPanelForColourbyseq(nap);
289 getBinding().setColourBySequence(enableColourBySeq);
290 seqColour.setSelected(enableColourBySeq);
291 viewerColour.setSelected(!enableColourBySeq);
294 public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
296 addAlignmentPanel(nap);
297 if (!_colourwith.contains(nap))
299 _colourwith.add(nap);
303 public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
305 if (_colourwith.contains(nap))
307 _colourwith.remove(nap);
311 public abstract ViewerType getViewerType();
314 * add a new structure (with associated sequences and chains) to this viewer,
315 * retrieving it if necessary first.
321 * if true, new structure(s) will be aligned using associated
325 protected void addStructure(final PDBEntry pdbentry,
326 final SequenceI[] seqs, final String[] chains,
327 final boolean align, final IProgressIndicator alignFrame)
329 if (pdbentry.getFile() == null)
331 if (worker != null && worker.isAlive())
333 // a retrieval is in progress, wait around and add ourselves to the
335 new Thread(new Runnable()
340 while (worker != null && worker.isAlive() && _started)
344 Thread.sleep(100 + ((int) Math.random() * 100));
346 } catch (Exception e)
350 // and call ourselves again.
351 addStructure(pdbentry, seqs, chains, align, alignFrame);
357 // otherwise, start adding the structure.
358 getBinding().addSequenceAndChain(new PDBEntry[] { pdbentry },
360 { seqs }, new String[][] { chains });
361 addingStructures = true;
363 alignAddedStructures = align;
364 worker = new Thread(this);
370 * Presents a dialog with the option to add an align a structure to an
371 * existing structure view
375 * @return YES, NO or CANCEL JvOptionPane code
377 protected int chooseAlignStructureToViewer(String pdbId,
378 StructureViewerBase view)
380 int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
381 MessageManager.formatMessage("label.add_pdbentry_to_view",
383 { pdbId, view.getTitle() }),
385 .getString("label.align_to_existing_structure_view"),
386 JvOptionPane.YES_NO_CANCEL_OPTION);
390 protected boolean hasPdbId(String pdbId)
392 return getBinding().hasPdbId(pdbId);
395 protected abstract List<StructureViewerBase> getViewersFor(
399 * Check for any existing views involving this alignment and give user the
400 * option to add and align this molecule to one of them
407 * @return true if user adds to a view, or cancels entirely, else false
409 protected boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
410 String[] chains, final AlignmentPanel apanel, String pdbId)
412 for (StructureViewerBase view : getViewersFor(apanel))
414 // TODO: highlight the view somehow
416 * JAL-1742 exclude view with this structure already mapped (don't offer
417 * to align chain B to chain A of the same structure)
419 if (view.hasPdbId(pdbId))
423 int option = chooseAlignStructureToViewer(pdbId, view);
424 if (option == JvOptionPane.CANCEL_OPTION)
428 else if (option == JvOptionPane.YES_OPTION)
430 view.useAlignmentPanelForSuperposition(apanel);
431 view.addStructure(pdbentry, seq, chains, true, apanel.alignFrame);
436 // NO_OPTION - offer the next viewer if any
441 * nothing offered and selected
447 * Adds mappings for the given sequences to an already opened PDB structure,
448 * and updates any viewers that have the PDB file
455 protected void addSequenceMappingsToStructure(SequenceI[] seq,
456 String[] chains, final AlignmentPanel apanel, String pdbFilename)
458 // TODO : Fix multiple seq to one chain issue here.
460 * create the mappings
462 apanel.getStructureSelectionManager().setMapping(seq, chains,
463 pdbFilename, DataSourceType.FILE);
466 * alert the FeatureRenderer to show new (PDB RESNUM) features
468 if (apanel.getSeqPanel().seqCanvas.fr != null)
470 apanel.getSeqPanel().seqCanvas.fr.featuresAdded();
471 // note - we don't do a refresh for structure here because we do it
472 // explicitly for all panels later on
473 apanel.paintAlignment(true, false);
477 * add the sequences to any other viewers (of the same type) for this pdb
480 // JBPNOTE: this looks like a binding routine, rather than a gui routine
481 for (StructureViewerBase viewer : getViewersFor(null))
483 AAStructureBindingModel bindingModel = viewer.getBinding();
484 for (int pe = 0; pe < bindingModel.getPdbCount(); pe++)
486 if (bindingModel.getPdbEntry(pe).getFile().equals(pdbFilename))
488 bindingModel.addSequence(pe, seq);
489 viewer.addAlignmentPanel(apanel);
491 * add it to the set of alignments used for colouring structure by
494 viewer.useAlignmentPanelForColourbyseq(apanel);
495 viewer.buildActionMenu();
496 apanel.getStructureSelectionManager()
497 .sequenceColoursChanged(apanel);
505 * Check if the PDB file is already loaded, if so offer to add it to the
512 * @return true if the user chooses to add to a viewer, or to cancel entirely
514 protected boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
515 final AlignmentPanel apanel, String pdbId)
517 boolean finished = false;
518 String alreadyMapped = apanel.getStructureSelectionManager()
519 .alreadyMappedToFile(pdbId);
521 if (alreadyMapped != null)
524 * the PDB file is already loaded
526 int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
527 MessageManager.formatMessage(
528 "label.pdb_entry_is_already_displayed", new Object[]
530 MessageManager.formatMessage(
531 "label.map_sequences_to_visible_window", new Object[]
533 JvOptionPane.YES_NO_CANCEL_OPTION);
534 if (option == JvOptionPane.CANCEL_OPTION)
538 else if (option == JvOptionPane.YES_OPTION)
540 addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
547 void setChainMenuItems(List<String> chainNames)
549 chainMenu.removeAll();
550 if (chainNames == null || chainNames.isEmpty())
554 JMenuItem menuItem = new JMenuItem(
555 MessageManager.getString("label.all"));
556 menuItem.addActionListener(new ActionListener()
559 public void actionPerformed(ActionEvent evt)
561 allChainsSelected = true;
562 for (int i = 0; i < chainMenu.getItemCount(); i++)
564 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
566 ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
569 showSelectedChains();
570 allChainsSelected = false;
574 chainMenu.add(menuItem);
576 for (String chain : chainNames)
578 menuItem = new JCheckBoxMenuItem(chain, true);
579 menuItem.addItemListener(new ItemListener()
582 public void itemStateChanged(ItemEvent evt)
584 if (!allChainsSelected)
586 showSelectedChains();
591 chainMenu.add(menuItem);
595 abstract void showSelectedChains();
598 * Action on selecting one of Jalview's registered colour schemes
601 public void changeColour_actionPerformed(String colourSchemeName)
603 AlignmentI al = getAlignmentPanel().av.getAlignment();
604 ColourSchemeI cs = ColourSchemes.getInstance()
605 .getColourScheme(colourSchemeName, al, null);
606 getBinding().setJalviewColourScheme(cs);
610 * Builds the colour menu
612 protected void buildColourMenu()
614 colourMenu.removeAll();
615 AlignmentI al = getAlignmentPanel().av.getAlignment();
618 * add colour by sequence, by chain, by charge and cysteine
620 colourMenu.add(seqColour);
621 colourMenu.add(chainColour);
622 colourMenu.add(chargeColour);
623 chargeColour.setEnabled(!al.isNucleotide());
626 * add all 'simple' (per-residue) colour schemes registered to Jalview
628 ButtonGroup itemGroup = ColourMenuHelper.addMenuItems(colourMenu, this,
632 * add 'colour by viewer' (menu item text is set in subclasses)
634 viewerColour.setSelected(false);
635 viewerColour.addActionListener(new ActionListener()
638 public void actionPerformed(ActionEvent actionEvent)
640 viewerColour_actionPerformed(actionEvent);
643 colourMenu.add(viewerColour);
646 * add 'set background colour'
648 JMenuItem backGround = new JMenuItem();
650 .setText(MessageManager.getString("action.background_colour"));
651 backGround.addActionListener(new ActionListener()
654 public void actionPerformed(ActionEvent actionEvent)
656 background_actionPerformed(actionEvent);
659 colourMenu.add(backGround);
662 * add colour buttons to a group so their selection is
663 * mutually exclusive (background colour is a separate option)
665 itemGroup.add(seqColour);
666 itemGroup.add(chainColour);
667 itemGroup.add(chargeColour);
668 itemGroup.add(viewerColour);
672 * Construct menu items
674 protected void initMenus()
676 AAStructureBindingModel binding = getBinding();
678 seqColour = new JRadioButtonMenuItem();
679 seqColour.setText(MessageManager.getString("action.by_sequence"));
680 seqColour.setName(ViewerColour.BySequence.name());
681 seqColour.setSelected(binding.isColourBySequence());
682 seqColour.addActionListener(new ActionListener()
685 public void actionPerformed(ActionEvent actionEvent)
687 seqColour_actionPerformed(actionEvent);
691 chainColour = new JRadioButtonMenuItem();
692 chainColour.setText(MessageManager.getString("action.by_chain"));
693 chainColour.setName(ViewerColour.ByChain.name());
694 chainColour.addActionListener(new ActionListener()
697 public void actionPerformed(ActionEvent actionEvent)
699 chainColour_actionPerformed(actionEvent);
703 chargeColour = new JRadioButtonMenuItem();
704 chargeColour.setText(MessageManager.getString("label.charge_cysteine"));
705 chargeColour.setName(ViewerColour.ChargeCysteine.name());
706 chargeColour.addActionListener(new ActionListener()
709 public void actionPerformed(ActionEvent actionEvent)
711 chargeColour_actionPerformed(actionEvent);
715 viewerColour = new JRadioButtonMenuItem();
716 // text is set in overrides of this method
717 viewerColour.setName(ViewerColour.ByViewer.name());
718 viewerColour.setSelected(!binding.isColourBySequence());
720 if (_colourwith == null)
722 _colourwith = new Vector<>();
724 if (_alignwith == null)
726 _alignwith = new Vector<>();
729 ViewSelectionMenu seqColourBy = new ViewSelectionMenu(
730 MessageManager.getString("label.colour_by"), this, _colourwith,
734 public void itemStateChanged(ItemEvent e)
736 if (!seqColour.isSelected())
742 // update the Chimera display now.
743 seqColour_actionPerformed(null);
747 viewMenu.add(seqColourBy);
749 final ItemListener handler = new ItemListener()
752 public void itemStateChanged(ItemEvent e)
754 alignStructs.setEnabled(!_alignwith.isEmpty());
755 alignStructs.setToolTipText(MessageManager.formatMessage(
756 "label.align_structures_using_linked_alignment_views",
760 viewSelectionMenu = new ViewSelectionMenu(
761 MessageManager.getString("label.superpose_with"), this,
762 _alignwith, handler);
763 handler.itemStateChanged(null);
764 viewerActionMenu.add(viewSelectionMenu, 0);
765 viewerActionMenu.addMenuListener(new MenuListener()
768 public void menuSelected(MenuEvent e)
770 handler.itemStateChanged(null);
774 public void menuDeselected(MenuEvent e)
779 public void menuCanceled(MenuEvent e)
788 public void setJalviewColourScheme(ColourSchemeI cs)
790 getBinding().setJalviewColourScheme(cs);
794 * Sends commands to the structure viewer to superimpose structures based on
795 * currently associated alignments. May optionally return an error message for
799 protected String alignStructs_actionPerformed(ActionEvent actionEvent)
801 return alignStructs_withAllAlignPanels();
804 protected String alignStructs_withAllAlignPanels()
806 if (getAlignmentPanel() == null)
811 if (_alignwith.size() == 0)
813 _alignwith.add(getAlignmentPanel());
819 AlignmentI[] als = new Alignment[_alignwith.size()];
820 HiddenColumns[] alc = new HiddenColumns[_alignwith.size()];
821 int[] alm = new int[_alignwith.size()];
824 for (AlignmentPanel ap : _alignwith)
826 als[a] = ap.av.getAlignment();
828 alc[a++] = ap.av.getAlignment().getHiddenColumns();
830 reply = getBinding().superposeStructures(als, alm, alc);
833 String text = MessageManager
834 .formatMessage("error.superposition_failed", reply);
835 statusBar.setText(text);
837 } catch (Exception e)
839 StringBuffer sp = new StringBuffer();
840 for (AlignmentPanel ap : _alignwith)
842 sp.append("'" + ap.alignFrame.getTitle() + "' ");
844 Cache.log.info("Couldn't align structures with the " + sp.toString()
845 + "associated alignment panels.", e);
851 public void background_actionPerformed(ActionEvent actionEvent)
853 Color col = JColorChooser.showDialog(this,
854 MessageManager.getString("label.select_background_colour"),
858 getBinding().setBackgroundColour(col);
863 public void viewerColour_actionPerformed(ActionEvent actionEvent)
865 if (viewerColour.isSelected())
867 // disable automatic sequence colouring.
868 getBinding().setColourBySequence(false);
873 public void chainColour_actionPerformed(ActionEvent actionEvent)
875 chainColour.setSelected(true);
876 getBinding().colourByChain();
880 public void chargeColour_actionPerformed(ActionEvent actionEvent)
882 chargeColour.setSelected(true);
883 getBinding().colourByCharge();
887 public void seqColour_actionPerformed(ActionEvent actionEvent)
889 AAStructureBindingModel binding = getBinding();
890 binding.setColourBySequence(seqColour.isSelected());
891 if (_colourwith == null)
893 _colourwith = new Vector<>();
895 if (binding.isColourBySequence())
897 if (!binding.isLoadingFromArchive())
899 if (_colourwith.size() == 0 && getAlignmentPanel() != null)
901 // Make the currently displayed alignment panel the associated view
902 _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
905 // Set the colour using the current view for the associated alignframe
906 for (AlignmentPanel ap : _colourwith)
908 binding.colourBySequence(ap);
914 public void pdbFile_actionPerformed(ActionEvent actionEvent)
916 JalviewFileChooser chooser = new JalviewFileChooser(
917 Cache.getProperty("LAST_DIRECTORY"));
919 chooser.setFileView(new JalviewFileView());
920 chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
921 chooser.setToolTipText(MessageManager.getString("action.save"));
923 int value = chooser.showSaveDialog(this);
925 if (value == JalviewFileChooser.APPROVE_OPTION)
927 BufferedReader in = null;
930 // TODO: cope with multiple PDB files in view
931 in = new BufferedReader(
932 new FileReader(getBinding().getStructureFiles()[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();
955 } catch (IOException e)
965 public void viewMapping_actionPerformed(ActionEvent actionEvent)
967 CutAndPasteTransfer cap = new CutAndPasteTransfer();
970 cap.appendText(getBinding().printMappings());
971 } catch (OutOfMemoryError e)
974 "composing sequence-structure alignments for display in text box.",
979 Desktop.addInternalFrame(cap,
980 MessageManager.getString("label.pdb_sequence_mapping"), 550,
984 protected abstract String getViewerName();
987 * Configures the title and menu items of the viewer panel.
989 public void updateTitleAndMenus()
991 AAStructureBindingModel binding = getBinding();
992 if (binding.hasFileLoadingError())
997 setChainMenuItems(binding.getChainNames());
999 this.setTitle(binding.getViewerTitle(getViewerName(), true));
1002 * enable 'Superpose with' if more than one mapped structure
1004 viewSelectionMenu.setEnabled(false);
1005 if (getBinding().getStructureFiles().length > 1
1006 && getBinding().getSequence().length > 1)
1008 viewSelectionMenu.setEnabled(true);
1012 * Show action menu if it has any enabled items
1014 viewerActionMenu.setVisible(false);
1015 for (int i = 0; i < viewerActionMenu.getItemCount(); i++)
1017 if (viewerActionMenu.getItem(i).isEnabled())
1019 viewerActionMenu.setVisible(true);
1024 if (!binding.isLoadingFromArchive())
1026 seqColour_actionPerformed(null);