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.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.ScoreModelI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenSequences;
57 import jalview.datamodel.PDBEntry;
58 import jalview.datamodel.SeqCigar;
59 import jalview.datamodel.Sequence;
60 import jalview.datamodel.SequenceGroup;
61 import jalview.datamodel.SequenceI;
62 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
63 import jalview.io.AlignmentProperties;
64 import jalview.io.AnnotationFile;
65 import jalview.io.BioJsHTMLOutput;
66 import jalview.io.FileLoader;
67 import jalview.io.FormatAdapter;
68 import jalview.io.HtmlSvgOutput;
69 import jalview.io.IdentifyFile;
70 import jalview.io.JalviewFileChooser;
71 import jalview.io.JalviewFileView;
72 import jalview.io.JnetAnnotationMaker;
73 import jalview.io.NewickFile;
74 import jalview.io.TCoffeeScoreFile;
75 import jalview.jbgui.GAlignFrame;
76 import jalview.schemes.Blosum62ColourScheme;
77 import jalview.schemes.BuriedColourScheme;
78 import jalview.schemes.ClustalxColourScheme;
79 import jalview.schemes.ColourSchemeI;
80 import jalview.schemes.ColourSchemeProperty;
81 import jalview.schemes.HelixColourScheme;
82 import jalview.schemes.HydrophobicColourScheme;
83 import jalview.schemes.NucleotideColourScheme;
84 import jalview.schemes.PIDColourScheme;
85 import jalview.schemes.PurinePyrimidineColourScheme;
86 import jalview.schemes.RNAHelicesColourChooser;
87 import jalview.schemes.ResidueProperties;
88 import jalview.schemes.StrandColourScheme;
89 import jalview.schemes.TCoffeeColourScheme;
90 import jalview.schemes.TaylorColourScheme;
91 import jalview.schemes.TurnColourScheme;
92 import jalview.schemes.UserColourScheme;
93 import jalview.schemes.ZappoColourScheme;
94 import jalview.util.MessageManager;
95 import jalview.viewmodel.AlignmentViewport;
96 import jalview.ws.DBRefFetcher;
97 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
98 import jalview.ws.jws1.Discoverer;
99 import jalview.ws.jws2.Jws2Discoverer;
100 import jalview.ws.jws2.jabaws2.Jws2Instance;
101 import jalview.ws.seqfetcher.DbSourceProxy;
103 import java.awt.BorderLayout;
104 import java.awt.Component;
105 import java.awt.Rectangle;
106 import java.awt.Toolkit;
107 import java.awt.datatransfer.Clipboard;
108 import java.awt.datatransfer.DataFlavor;
109 import java.awt.datatransfer.StringSelection;
110 import java.awt.datatransfer.Transferable;
111 import java.awt.dnd.DropTargetDragEvent;
112 import java.awt.dnd.DropTargetDropEvent;
113 import java.awt.dnd.DropTargetEvent;
114 import java.awt.dnd.DropTargetListener;
115 import java.awt.event.ActionEvent;
116 import java.awt.event.ActionListener;
117 import java.awt.event.FocusAdapter;
118 import java.awt.event.FocusEvent;
119 import java.awt.event.ItemEvent;
120 import java.awt.event.ItemListener;
121 import java.awt.event.KeyAdapter;
122 import java.awt.event.KeyEvent;
123 import java.awt.event.MouseAdapter;
124 import java.awt.event.MouseEvent;
125 import java.awt.print.PageFormat;
126 import java.awt.print.PrinterJob;
127 import java.beans.PropertyChangeEvent;
130 import java.util.ArrayList;
131 import java.util.Arrays;
132 import java.util.Deque;
133 import java.util.Enumeration;
134 import java.util.Hashtable;
135 import java.util.List;
136 import java.util.Vector;
138 import javax.swing.JCheckBoxMenuItem;
139 import javax.swing.JEditorPane;
140 import javax.swing.JInternalFrame;
141 import javax.swing.JLayeredPane;
142 import javax.swing.JMenu;
143 import javax.swing.JMenuItem;
144 import javax.swing.JOptionPane;
145 import javax.swing.JRadioButtonMenuItem;
146 import javax.swing.JScrollPane;
147 import javax.swing.SwingUtilities;
153 * @version $Revision$
155 public class AlignFrame extends GAlignFrame implements DropTargetListener,
156 IProgressIndicator, AlignViewControllerGuiI
159 public static final int DEFAULT_WIDTH = 700;
161 public static final int DEFAULT_HEIGHT = 500;
164 * The currently displayed panel (selected tabbed view if more than one)
166 public AlignmentPanel alignPanel;
168 AlignViewport viewport;
170 public AlignViewControllerI avc;
172 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
175 * Last format used to load or save alignments in this window
177 String currentFileFormat = null;
180 * Current filename for this alignment
182 String fileName = null;
185 * Creates a new AlignFrame object with specific width and height.
191 public AlignFrame(AlignmentI al, int width, int height)
193 this(al, null, width, height);
197 * Creates a new AlignFrame object with specific width, height and
203 * @param sequenceSetId
205 public AlignFrame(AlignmentI al, int width, int height,
206 String sequenceSetId)
208 this(al, null, width, height, sequenceSetId);
212 * Creates a new AlignFrame object with specific width, height and
218 * @param sequenceSetId
221 public AlignFrame(AlignmentI al, int width, int height,
222 String sequenceSetId, String viewId)
224 this(al, null, width, height, sequenceSetId, viewId);
228 * new alignment window with hidden columns
232 * @param hiddenColumns
233 * ColumnSelection or null
235 * Width of alignment frame
239 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
240 int width, int height)
242 this(al, hiddenColumns, width, height, null);
246 * Create alignment frame for al with hiddenColumns, a specific width and
247 * height, and specific sequenceId
250 * @param hiddenColumns
253 * @param sequenceSetId
256 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
257 int width, int height, String sequenceSetId)
259 this(al, hiddenColumns, width, height, sequenceSetId, null);
263 * Create alignment frame for al with hiddenColumns, a specific width and
264 * height, and specific sequenceId
267 * @param hiddenColumns
270 * @param sequenceSetId
275 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
276 int width, int height, String sequenceSetId, String viewId)
278 setSize(width, height);
280 if (al.getDataset() == null)
285 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
287 alignPanel = new AlignmentPanel(this, viewport);
289 addAlignmentPanel(alignPanel, true);
293 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
294 ColumnSelection hiddenColumns, int width, int height)
296 setSize(width, height);
298 if (al.getDataset() == null)
303 viewport = new AlignViewport(al, hiddenColumns);
305 if (hiddenSeqs != null && hiddenSeqs.length > 0)
307 viewport.hideSequence(hiddenSeqs);
309 alignPanel = new AlignmentPanel(this, viewport);
310 addAlignmentPanel(alignPanel, true);
315 * Make a new AlignFrame from existing alignmentPanels
322 public AlignFrame(AlignmentPanel ap)
326 addAlignmentPanel(ap, false);
331 * initalise the alignframe from the underlying viewport data and the
336 if (!Jalview.isHeadlessMode())
338 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
341 avc = new jalview.controller.AlignViewController(this, viewport,
343 if (viewport.getAlignmentConservationAnnotation() == null)
345 BLOSUM62Colour.setEnabled(false);
346 conservationMenuItem.setEnabled(false);
347 modifyConservation.setEnabled(false);
348 // PIDColour.setEnabled(false);
349 // abovePIDThreshold.setEnabled(false);
350 // modifyPID.setEnabled(false);
353 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
356 if (sortby.equals("Id"))
358 sortIDMenuItem_actionPerformed(null);
360 else if (sortby.equals("Pairwise Identity"))
362 sortPairwiseMenuItem_actionPerformed(null);
365 if (Desktop.desktop != null)
367 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
368 addServiceListeners();
369 setGUINucleotide(viewport.getAlignment().isNucleotide());
373 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
375 setMenusFromViewport(viewport);
376 buildSortByAnnotationScoresMenu();
379 if (viewport.getWrapAlignment())
381 wrapMenuItem_actionPerformed(null);
384 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
386 this.overviewMenuItem_actionPerformed(null);
391 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
392 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
393 final String menuLabel = MessageManager
394 .getString("label.copy_format_from");
395 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
396 new ViewSetProvider()
400 public AlignmentPanel[] getAllAlignmentPanels()
403 origview.add(alignPanel);
404 // make an array of all alignment panels except for this one
405 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
406 Arrays.asList(Desktop.getAlignmentPanels(null)));
407 aps.remove(AlignFrame.this.alignPanel);
408 return aps.toArray(new AlignmentPanel[aps.size()]);
410 }, selviews, new ItemListener()
414 public void itemStateChanged(ItemEvent e)
416 if (origview.size() > 0)
418 final AlignmentPanel ap = origview.get(0);
421 * Copy the ViewStyle of the selected panel to 'this one'.
422 * Don't change value of 'scaleProteinAsCdna' unless copying
425 ViewStyleI vs = selviews.get(0).getAlignViewport()
427 boolean fromSplitFrame = selviews.get(0)
428 .getAlignViewport().getCodingComplement() != null;
431 vs.setScaleProteinAsCdna(ap.getAlignViewport()
432 .getViewStyle().isScaleProteinAsCdna());
434 ap.getAlignViewport().setViewStyle(vs);
437 * Also rescale ViewStyle of SplitFrame complement if there is
438 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
439 * the whole ViewStyle (allow cDNA protein to have different
442 AlignViewportI complement = ap.getAlignViewport()
443 .getCodingComplement();
444 if (complement != null && vs.isScaleProteinAsCdna())
446 AlignFrame af = Desktop.getAlignFrameFor(complement);
447 ((SplitFrame) af.getSplitViewContainer())
449 af.setMenusForViewport();
453 ap.setSelected(true);
454 ap.alignFrame.setMenusForViewport();
459 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
460 .indexOf("devel") > -1
461 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
462 .indexOf("test") > -1)
464 formatMenu.add(vsel);
466 addFocusListener(new FocusAdapter()
469 public void focusGained(FocusEvent e)
471 Jalview.setCurrentAlignFrame(AlignFrame.this);
478 * Change the filename and format for the alignment, and enable the 'reload'
479 * button functionality.
486 public void setFileName(String file, String format)
489 setFileFormat(format);
490 reload.setEnabled(true);
494 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
497 void addKeyListener()
499 addKeyListener(new KeyAdapter()
502 public void keyPressed(KeyEvent evt)
504 if (viewport.cursorMode
505 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
506 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
507 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
508 && Character.isDigit(evt.getKeyChar()))
510 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
513 switch (evt.getKeyCode())
516 case 27: // escape key
517 deselectAllSequenceMenuItem_actionPerformed(null);
521 case KeyEvent.VK_DOWN:
522 if (evt.isAltDown() || !viewport.cursorMode)
524 moveSelectedSequences(false);
526 if (viewport.cursorMode)
528 alignPanel.getSeqPanel().moveCursor(0, 1);
533 if (evt.isAltDown() || !viewport.cursorMode)
535 moveSelectedSequences(true);
537 if (viewport.cursorMode)
539 alignPanel.getSeqPanel().moveCursor(0, -1);
544 case KeyEvent.VK_LEFT:
545 if (evt.isAltDown() || !viewport.cursorMode)
547 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
551 alignPanel.getSeqPanel().moveCursor(-1, 0);
556 case KeyEvent.VK_RIGHT:
557 if (evt.isAltDown() || !viewport.cursorMode)
559 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
563 alignPanel.getSeqPanel().moveCursor(1, 0);
567 case KeyEvent.VK_SPACE:
568 if (viewport.cursorMode)
570 alignPanel.getSeqPanel().insertGapAtCursor(
571 evt.isControlDown() || evt.isShiftDown()
576 // case KeyEvent.VK_A:
577 // if (viewport.cursorMode)
579 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
580 // //System.out.println("A");
584 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
585 * System.out.println("closing bracket"); } break;
587 case KeyEvent.VK_DELETE:
588 case KeyEvent.VK_BACK_SPACE:
589 if (!viewport.cursorMode)
591 cut_actionPerformed(null);
595 alignPanel.getSeqPanel().deleteGapAtCursor(
596 evt.isControlDown() || evt.isShiftDown()
603 if (viewport.cursorMode)
605 alignPanel.getSeqPanel().setCursorRow();
609 if (viewport.cursorMode && !evt.isControlDown())
611 alignPanel.getSeqPanel().setCursorColumn();
615 if (viewport.cursorMode)
617 alignPanel.getSeqPanel().setCursorPosition();
621 case KeyEvent.VK_ENTER:
622 case KeyEvent.VK_COMMA:
623 if (viewport.cursorMode)
625 alignPanel.getSeqPanel().setCursorRowAndColumn();
630 if (viewport.cursorMode)
632 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
636 if (viewport.cursorMode)
638 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
643 viewport.cursorMode = !viewport.cursorMode;
644 statusBar.setText(MessageManager.formatMessage(
645 "label.keyboard_editing_mode",
646 new String[] { (viewport.cursorMode ? "on" : "off") }));
647 if (viewport.cursorMode)
649 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
650 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
652 alignPanel.getSeqPanel().seqCanvas.repaint();
658 Help.showHelpWindow();
659 } catch (Exception ex)
661 ex.printStackTrace();
666 boolean toggleSeqs = !evt.isControlDown();
667 boolean toggleCols = !evt.isShiftDown();
668 toggleHiddenRegions(toggleSeqs, toggleCols);
671 case KeyEvent.VK_PAGE_UP:
672 if (viewport.getWrapAlignment())
674 alignPanel.scrollUp(true);
678 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
679 - viewport.endSeq + viewport.startSeq);
682 case KeyEvent.VK_PAGE_DOWN:
683 if (viewport.getWrapAlignment())
685 alignPanel.scrollUp(false);
689 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
690 + viewport.endSeq - viewport.startSeq);
697 public void keyReleased(KeyEvent evt)
699 switch (evt.getKeyCode())
701 case KeyEvent.VK_LEFT:
702 if (evt.isAltDown() || !viewport.cursorMode)
704 viewport.firePropertyChange("alignment", null, viewport
705 .getAlignment().getSequences());
709 case KeyEvent.VK_RIGHT:
710 if (evt.isAltDown() || !viewport.cursorMode)
712 viewport.firePropertyChange("alignment", null, viewport
713 .getAlignment().getSequences());
721 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
723 ap.alignFrame = this;
724 avc = new jalview.controller.AlignViewController(this, viewport,
729 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
731 int aSize = alignPanels.size();
733 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
735 if (aSize == 1 && ap.av.viewName == null)
737 this.getContentPane().add(ap, BorderLayout.CENTER);
743 setInitialTabVisible();
746 expandViews.setEnabled(true);
747 gatherViews.setEnabled(true);
748 tabbedPane.addTab(ap.av.viewName, ap);
750 ap.setVisible(false);
755 if (ap.av.isPadGaps())
757 ap.av.getAlignment().padGaps();
759 ap.av.updateConservation(ap);
760 ap.av.updateConsensus(ap);
761 ap.av.updateStrucConsensus(ap);
765 public void setInitialTabVisible()
767 expandViews.setEnabled(true);
768 gatherViews.setEnabled(true);
769 tabbedPane.setVisible(true);
770 AlignmentPanel first = alignPanels.get(0);
771 tabbedPane.addTab(first.av.viewName, first);
772 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
775 public AlignViewport getViewport()
780 /* Set up intrinsic listeners for dynamically generated GUI bits. */
781 private void addServiceListeners()
783 final java.beans.PropertyChangeListener thisListener;
784 Desktop.instance.addJalviewPropertyChangeListener("services",
785 thisListener = new java.beans.PropertyChangeListener()
788 public void propertyChange(PropertyChangeEvent evt)
790 // // System.out.println("Discoverer property change.");
791 // if (evt.getPropertyName().equals("services"))
793 SwingUtilities.invokeLater(new Runnable()
800 .println("Rebuild WS Menu for service change");
801 BuildWebServiceMenu();
808 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
811 public void internalFrameClosed(
812 javax.swing.event.InternalFrameEvent evt)
814 // System.out.println("deregistering discoverer listener");
815 Desktop.instance.removeJalviewPropertyChangeListener("services",
817 closeMenuItem_actionPerformed(true);
820 // Finally, build the menu once to get current service state
821 new Thread(new Runnable()
826 BuildWebServiceMenu();
832 * Configure menu items that vary according to whether the alignment is
833 * nucleotide or protein
837 public void setGUINucleotide(boolean nucleotide)
839 showTranslation.setVisible(nucleotide);
840 showReverse.setVisible(nucleotide);
841 showReverseComplement.setVisible(nucleotide);
842 conservationMenuItem.setEnabled(!nucleotide);
843 modifyConservation.setEnabled(!nucleotide);
844 showGroupConservation.setEnabled(!nucleotide);
845 rnahelicesColour.setEnabled(nucleotide);
846 purinePyrimidineColour.setEnabled(nucleotide);
847 showComplementMenuItem.setText(nucleotide ? MessageManager
848 .getString("label.protein") : MessageManager
849 .getString("label.nucleotide"));
850 setColourSelected(jalview.bin.Cache.getDefault(
851 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
852 : Preferences.DEFAULT_COLOUR_PROT, "None"));
856 * set up menus for the current viewport. This may be called after any
857 * operation that affects the data in the current view (selection changed,
858 * etc) to update the menus to reflect the new state.
861 public void setMenusForViewport()
863 setMenusFromViewport(viewport);
867 * Need to call this method when tabs are selected for multiple views, or when
868 * loading from Jalview2XML.java
873 void setMenusFromViewport(AlignViewport av)
875 padGapsMenuitem.setSelected(av.isPadGaps());
876 colourTextMenuItem.setSelected(av.isShowColourText());
877 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
878 conservationMenuItem.setSelected(av.getConservationSelected());
879 seqLimits.setSelected(av.getShowJVSuffix());
880 idRightAlign.setSelected(av.isRightAlignIds());
881 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
882 renderGapsMenuItem.setSelected(av.isRenderGaps());
883 wrapMenuItem.setSelected(av.getWrapAlignment());
884 scaleAbove.setVisible(av.getWrapAlignment());
885 scaleLeft.setVisible(av.getWrapAlignment());
886 scaleRight.setVisible(av.getWrapAlignment());
887 annotationPanelMenuItem.setState(av.isShowAnnotation());
889 * Show/hide annotations only enabled if annotation panel is shown
891 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
892 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
893 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
894 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
895 viewBoxesMenuItem.setSelected(av.getShowBoxes());
896 viewTextMenuItem.setSelected(av.getShowText());
897 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
898 showGroupConsensus.setSelected(av.isShowGroupConsensus());
899 showGroupConservation.setSelected(av.isShowGroupConservation());
900 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
901 showSequenceLogo.setSelected(av.isShowSequenceLogo());
902 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
904 setColourSelected(ColourSchemeProperty.getColourName(av
905 .getGlobalColourScheme()));
907 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
908 hiddenMarkers.setState(av.getShowHiddenMarkers());
909 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
910 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
911 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
912 autoCalculate.setSelected(av.autoCalculateConsensus);
913 sortByTree.setSelected(av.sortByTree);
914 listenToViewSelections.setSelected(av.followSelection);
915 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
917 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
919 showProducts.setEnabled(canShowProducts());
920 setGroovyEnabled(Desktop.getGroovyConsole() != null);
926 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
930 public void setGroovyEnabled(boolean b)
932 runGroovy.setEnabled(b);
935 private IProgressIndicator progressBar;
940 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
943 public void setProgressBar(String message, long id)
945 progressBar.setProgressBar(message, id);
949 public void registerHandler(final long id,
950 final IProgressIndicatorHandler handler)
952 progressBar.registerHandler(id, handler);
957 * @return true if any progress bars are still active
960 public boolean operationInProgress()
962 return progressBar.operationInProgress();
966 public void setStatus(String text)
968 statusBar.setText(text);
972 * Added so Castor Mapping file can obtain Jalview Version
974 public String getVersion()
976 return jalview.bin.Cache.getProperty("VERSION");
979 public FeatureRenderer getFeatureRenderer()
981 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
985 public void fetchSequence_actionPerformed(ActionEvent e)
987 new jalview.gui.SequenceFetcher(this);
991 public void addFromFile_actionPerformed(ActionEvent e)
993 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
997 public void reload_actionPerformed(ActionEvent e)
999 if (fileName != null)
1001 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1002 // originating file's format
1003 // TODO: work out how to recover feature settings for correct view(s) when
1004 // file is reloaded.
1005 if (currentFileFormat.equals("Jalview"))
1007 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1008 for (int i = 0; i < frames.length; i++)
1010 if (frames[i] instanceof AlignFrame && frames[i] != this
1011 && ((AlignFrame) frames[i]).fileName != null
1012 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1016 frames[i].setSelected(true);
1017 Desktop.instance.closeAssociatedWindows();
1018 } catch (java.beans.PropertyVetoException ex)
1024 Desktop.instance.closeAssociatedWindows();
1026 FileLoader loader = new FileLoader();
1027 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1028 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1032 Rectangle bounds = this.getBounds();
1034 FileLoader loader = new FileLoader();
1035 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1036 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1037 protocol, currentFileFormat);
1039 newframe.setBounds(bounds);
1040 if (featureSettings != null && featureSettings.isShowing())
1042 final Rectangle fspos = featureSettings.frame.getBounds();
1043 // TODO: need a 'show feature settings' function that takes bounds -
1044 // need to refactor Desktop.addFrame
1045 newframe.featureSettings_actionPerformed(null);
1046 final FeatureSettings nfs = newframe.featureSettings;
1047 SwingUtilities.invokeLater(new Runnable()
1052 nfs.frame.setBounds(fspos);
1055 this.featureSettings.close();
1056 this.featureSettings = null;
1058 this.closeMenuItem_actionPerformed(true);
1064 public void addFromText_actionPerformed(ActionEvent e)
1066 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1071 public void addFromURL_actionPerformed(ActionEvent e)
1073 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1077 public void save_actionPerformed(ActionEvent e)
1079 if (fileName == null
1080 || (currentFileFormat == null || !jalview.io.FormatAdapter
1081 .isValidIOFormat(currentFileFormat, true))
1082 || fileName.startsWith("http"))
1084 saveAs_actionPerformed(null);
1088 saveAlignment(fileName, currentFileFormat);
1099 public void saveAs_actionPerformed(ActionEvent e)
1101 JalviewFileChooser chooser = new JalviewFileChooser(
1102 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1103 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1104 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1105 currentFileFormat, false);
1107 chooser.setFileView(new JalviewFileView());
1108 chooser.setDialogTitle(MessageManager
1109 .getString("label.save_alignment_to_file"));
1110 chooser.setToolTipText(MessageManager.getString("action.save"));
1112 int value = chooser.showSaveDialog(this);
1114 if (value == JalviewFileChooser.APPROVE_OPTION)
1116 currentFileFormat = chooser.getSelectedFormat();
1117 while (currentFileFormat == null)
1120 .showInternalMessageDialog(
1123 .getString("label.select_file_format_before_saving"),
1125 .getString("label.file_format_not_specified"),
1126 JOptionPane.WARNING_MESSAGE);
1127 currentFileFormat = chooser.getSelectedFormat();
1128 value = chooser.showSaveDialog(this);
1129 if (value != JalviewFileChooser.APPROVE_OPTION)
1135 fileName = chooser.getSelectedFile().getPath();
1137 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1140 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1141 if (currentFileFormat.indexOf(" ") > -1)
1143 currentFileFormat = currentFileFormat.substring(0,
1144 currentFileFormat.indexOf(" "));
1146 saveAlignment(fileName, currentFileFormat);
1150 public boolean saveAlignment(String file, String format)
1152 boolean success = true;
1154 if (format.equalsIgnoreCase("Jalview"))
1156 String shortName = title;
1158 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1160 shortName = shortName.substring(shortName
1161 .lastIndexOf(java.io.File.separatorChar) + 1);
1164 success = new Jalview2XML().saveAlignment(this, file, shortName);
1166 statusBar.setText(MessageManager.formatMessage(
1167 "label.successfully_saved_to_file_in_format", new Object[] {
1168 fileName, format }));
1173 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1175 warningMessage("Cannot save file " + fileName + " using format "
1176 + format, "Alignment output format not supported");
1177 if (!Jalview.isHeadlessMode())
1179 saveAs_actionPerformed(null);
1184 AlignmentExportData exportData = getAlignmentForExport(format,
1186 if (exportData.getSettings().isCancelled())
1190 FormatAdapter f = new FormatAdapter(alignPanel,
1191 exportData.getSettings());
1192 String output = f.formatSequences(
1194 exportData.getAlignment(), // class cast exceptions will
1195 // occur in the distant future
1196 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1197 f.getCacheSuffixDefault(format),
1198 viewport.getColumnSelection());
1208 java.io.PrintWriter out = new java.io.PrintWriter(
1209 new java.io.FileWriter(file));
1213 this.setTitle(file);
1214 statusBar.setText(MessageManager.formatMessage(
1215 "label.successfully_saved_to_file_in_format",
1216 new Object[] { fileName, format }));
1217 } catch (Exception ex)
1220 ex.printStackTrace();
1227 JOptionPane.showInternalMessageDialog(this, MessageManager
1228 .formatMessage("label.couldnt_save_file",
1229 new Object[] { fileName }), MessageManager
1230 .getString("label.error_saving_file"),
1231 JOptionPane.WARNING_MESSAGE);
1237 private void warningMessage(String warning, String title)
1239 if (new jalview.util.Platform().isHeadless())
1241 System.err.println("Warning: " + title + "\nWarning: " + warning);
1246 JOptionPane.showInternalMessageDialog(this, warning, title,
1247 JOptionPane.WARNING_MESSAGE);
1259 protected void outputText_actionPerformed(ActionEvent e)
1262 AlignmentExportData exportData = getAlignmentForExport(
1263 e.getActionCommand(), viewport, null);
1264 if (exportData.getSettings().isCancelled())
1268 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1269 cap.setForInput(null);
1272 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1273 .formatSequences(e.getActionCommand(),
1274 exportData.getAlignment(),
1275 exportData.getOmitHidden(),
1276 exportData.getStartEndPostions(),
1277 viewport.getColumnSelection()));
1278 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1279 "label.alignment_output_command",
1280 new Object[] { e.getActionCommand() }), 600, 500);
1281 } catch (OutOfMemoryError oom)
1283 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1289 public static AlignmentExportData getAlignmentForExport(
1290 String exportFormat, AlignViewportI viewport,
1291 AlignExportSettingI exportSettings)
1293 AlignmentI alignmentToExport = null;
1294 AlignExportSettingI settings = exportSettings;
1295 String[] omitHidden = null;
1297 HiddenSequences hiddenSeqs = viewport.getAlignment()
1298 .getHiddenSequences();
1300 alignmentToExport = viewport.getAlignment();
1302 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1303 if (settings == null)
1305 settings = new AlignExportSettings(hasHiddenSeqs,
1306 viewport.hasHiddenColumns(), exportFormat);
1308 // settings.isExportAnnotations();
1310 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1312 omitHidden = viewport.getViewAsString(false,
1313 settings.isExportHiddenSequences());
1316 int[] alignmentStartEnd = new int[2];
1317 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1319 alignmentToExport = hiddenSeqs.getFullAlignment();
1323 alignmentToExport = viewport.getAlignment();
1325 alignmentStartEnd = alignmentToExport
1326 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1327 .getHiddenColumns());
1328 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1329 omitHidden, alignmentStartEnd, settings);
1340 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1342 new HtmlSvgOutput(null, alignPanel);
1346 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1348 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1349 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1352 public void createImageMap(File file, String image)
1354 alignPanel.makePNGImageMap(file, image);
1364 public void createPNG(File f)
1366 alignPanel.makePNG(f);
1376 public void createEPS(File f)
1378 alignPanel.makeEPS(f);
1382 public void createSVG(File f)
1384 alignPanel.makeSVG(f);
1388 public void pageSetup_actionPerformed(ActionEvent e)
1390 PrinterJob printJob = PrinterJob.getPrinterJob();
1391 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1401 public void printMenuItem_actionPerformed(ActionEvent e)
1403 // Putting in a thread avoids Swing painting problems
1404 PrintThread thread = new PrintThread(alignPanel);
1409 public void exportFeatures_actionPerformed(ActionEvent e)
1411 new AnnotationExporter().exportFeatures(alignPanel);
1415 public void exportAnnotations_actionPerformed(ActionEvent e)
1417 new AnnotationExporter().exportAnnotations(alignPanel);
1421 public void associatedData_actionPerformed(ActionEvent e)
1423 // Pick the tree file
1424 JalviewFileChooser chooser = new JalviewFileChooser(
1425 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1426 chooser.setFileView(new JalviewFileView());
1427 chooser.setDialogTitle(MessageManager
1428 .getString("label.load_jalview_annotations"));
1429 chooser.setToolTipText(MessageManager
1430 .getString("label.load_jalview_annotations"));
1432 int value = chooser.showOpenDialog(null);
1434 if (value == JalviewFileChooser.APPROVE_OPTION)
1436 String choice = chooser.getSelectedFile().getPath();
1437 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1438 loadJalviewDataFile(choice, null, null, null);
1444 * Close the current view or all views in the alignment frame. If the frame
1445 * only contains one view then the alignment will be removed from memory.
1447 * @param closeAllTabs
1450 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1452 if (alignPanels != null && alignPanels.size() < 2)
1454 closeAllTabs = true;
1459 if (alignPanels != null)
1463 if (this.isClosed())
1465 // really close all the windows - otherwise wait till
1466 // setClosed(true) is called
1467 for (int i = 0; i < alignPanels.size(); i++)
1469 AlignmentPanel ap = alignPanels.get(i);
1476 closeView(alignPanel);
1483 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1484 * be called recursively, with the frame now in 'closed' state
1486 this.setClosed(true);
1488 } catch (Exception ex)
1490 ex.printStackTrace();
1495 * Close the specified panel and close up tabs appropriately.
1497 * @param panelToClose
1499 public void closeView(AlignmentPanel panelToClose)
1501 int index = tabbedPane.getSelectedIndex();
1502 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1503 alignPanels.remove(panelToClose);
1504 panelToClose.closePanel();
1505 panelToClose = null;
1507 tabbedPane.removeTabAt(closedindex);
1508 tabbedPane.validate();
1510 if (index > closedindex || index == tabbedPane.getTabCount())
1512 // modify currently selected tab index if necessary.
1516 this.tabSelectionChanged(index);
1522 void updateEditMenuBar()
1525 if (viewport.getHistoryList().size() > 0)
1527 undoMenuItem.setEnabled(true);
1528 CommandI command = viewport.getHistoryList().peek();
1529 undoMenuItem.setText(MessageManager.formatMessage(
1530 "label.undo_command",
1531 new Object[] { command.getDescription() }));
1535 undoMenuItem.setEnabled(false);
1536 undoMenuItem.setText(MessageManager.getString("action.undo"));
1539 if (viewport.getRedoList().size() > 0)
1541 redoMenuItem.setEnabled(true);
1543 CommandI command = viewport.getRedoList().peek();
1544 redoMenuItem.setText(MessageManager.formatMessage(
1545 "label.redo_command",
1546 new Object[] { command.getDescription() }));
1550 redoMenuItem.setEnabled(false);
1551 redoMenuItem.setText(MessageManager.getString("action.redo"));
1556 public void addHistoryItem(CommandI command)
1558 if (command.getSize() > 0)
1560 viewport.addToHistoryList(command);
1561 viewport.clearRedoList();
1562 updateEditMenuBar();
1563 viewport.updateHiddenColumns();
1564 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1565 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1566 // viewport.getColumnSelection()
1567 // .getHiddenColumns().size() > 0);
1573 * @return alignment objects for all views
1575 AlignmentI[] getViewAlignments()
1577 if (alignPanels != null)
1579 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1581 for (AlignmentPanel ap : alignPanels)
1583 als[i++] = ap.av.getAlignment();
1587 if (viewport != null)
1589 return new AlignmentI[] { viewport.getAlignment() };
1601 protected void undoMenuItem_actionPerformed(ActionEvent e)
1603 if (viewport.getHistoryList().isEmpty())
1607 CommandI command = viewport.getHistoryList().pop();
1608 viewport.addToRedoList(command);
1609 command.undoCommand(getViewAlignments());
1611 AlignmentViewport originalSource = getOriginatingSource(command);
1612 updateEditMenuBar();
1614 if (originalSource != null)
1616 if (originalSource != viewport)
1619 .warn("Implementation worry: mismatch of viewport origin for undo");
1621 originalSource.updateHiddenColumns();
1622 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1624 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1625 // viewport.getColumnSelection()
1626 // .getHiddenColumns().size() > 0);
1627 originalSource.firePropertyChange("alignment", null, originalSource
1628 .getAlignment().getSequences());
1639 protected void redoMenuItem_actionPerformed(ActionEvent e)
1641 if (viewport.getRedoList().size() < 1)
1646 CommandI command = viewport.getRedoList().pop();
1647 viewport.addToHistoryList(command);
1648 command.doCommand(getViewAlignments());
1650 AlignmentViewport originalSource = getOriginatingSource(command);
1651 updateEditMenuBar();
1653 if (originalSource != null)
1656 if (originalSource != viewport)
1659 .warn("Implementation worry: mismatch of viewport origin for redo");
1661 originalSource.updateHiddenColumns();
1662 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1664 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1665 // viewport.getColumnSelection()
1666 // .getHiddenColumns().size() > 0);
1667 originalSource.firePropertyChange("alignment", null, originalSource
1668 .getAlignment().getSequences());
1672 AlignmentViewport getOriginatingSource(CommandI command)
1674 AlignmentViewport originalSource = null;
1675 // For sequence removal and addition, we need to fire
1676 // the property change event FROM the viewport where the
1677 // original alignment was altered
1678 AlignmentI al = null;
1679 if (command instanceof EditCommand)
1681 EditCommand editCommand = (EditCommand) command;
1682 al = editCommand.getAlignment();
1683 List<Component> comps = PaintRefresher.components.get(viewport
1684 .getSequenceSetId());
1686 for (Component comp : comps)
1688 if (comp instanceof AlignmentPanel)
1690 if (al == ((AlignmentPanel) comp).av.getAlignment())
1692 originalSource = ((AlignmentPanel) comp).av;
1699 if (originalSource == null)
1701 // The original view is closed, we must validate
1702 // the current view against the closed view first
1705 PaintRefresher.validateSequences(al, viewport.getAlignment());
1708 originalSource = viewport;
1711 return originalSource;
1720 public void moveSelectedSequences(boolean up)
1722 SequenceGroup sg = viewport.getSelectionGroup();
1728 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1729 viewport.getHiddenRepSequences(), up);
1730 alignPanel.paintAlignment(true);
1733 synchronized void slideSequences(boolean right, int size)
1735 List<SequenceI> sg = new ArrayList<SequenceI>();
1736 if (viewport.cursorMode)
1738 sg.add(viewport.getAlignment().getSequenceAt(
1739 alignPanel.getSeqPanel().seqCanvas.cursorY));
1741 else if (viewport.getSelectionGroup() != null
1742 && viewport.getSelectionGroup().getSize() != viewport
1743 .getAlignment().getHeight())
1745 sg = viewport.getSelectionGroup().getSequences(
1746 viewport.getHiddenRepSequences());
1754 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1756 for (SequenceI seq : viewport.getAlignment().getSequences())
1758 if (!sg.contains(seq))
1760 invertGroup.add(seq);
1764 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1766 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1767 for (int i = 0; i < invertGroup.size(); i++)
1769 seqs2[i] = invertGroup.get(i);
1772 SlideSequencesCommand ssc;
1775 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1776 size, viewport.getGapCharacter());
1780 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1781 size, viewport.getGapCharacter());
1784 int groupAdjustment = 0;
1785 if (ssc.getGapsInsertedBegin() && right)
1787 if (viewport.cursorMode)
1789 alignPanel.getSeqPanel().moveCursor(size, 0);
1793 groupAdjustment = size;
1796 else if (!ssc.getGapsInsertedBegin() && !right)
1798 if (viewport.cursorMode)
1800 alignPanel.getSeqPanel().moveCursor(-size, 0);
1804 groupAdjustment = -size;
1808 if (groupAdjustment != 0)
1810 viewport.getSelectionGroup().setStartRes(
1811 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1812 viewport.getSelectionGroup().setEndRes(
1813 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1817 * just extend the last slide command if compatible; but not if in
1818 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1820 boolean appendHistoryItem = false;
1821 Deque<CommandI> historyList = viewport.getHistoryList();
1822 boolean inSplitFrame = getSplitViewContainer() != null;
1823 if (!inSplitFrame && historyList != null && historyList.size() > 0
1824 && historyList.peek() instanceof SlideSequencesCommand)
1826 appendHistoryItem = ssc
1827 .appendSlideCommand((SlideSequencesCommand) historyList
1831 if (!appendHistoryItem)
1833 addHistoryItem(ssc);
1846 protected void copy_actionPerformed(ActionEvent e)
1849 if (viewport.getSelectionGroup() == null)
1853 // TODO: preserve the ordering of displayed alignment annotation in any
1854 // internal paste (particularly sequence associated annotation)
1855 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1856 String[] omitHidden = null;
1858 if (viewport.hasHiddenColumns())
1860 omitHidden = viewport.getViewAsString(true);
1863 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1866 StringSelection ss = new StringSelection(output);
1870 jalview.gui.Desktop.internalCopy = true;
1871 // Its really worth setting the clipboard contents
1872 // to empty before setting the large StringSelection!!
1873 Toolkit.getDefaultToolkit().getSystemClipboard()
1874 .setContents(new StringSelection(""), null);
1876 Toolkit.getDefaultToolkit().getSystemClipboard()
1877 .setContents(ss, Desktop.instance);
1878 } catch (OutOfMemoryError er)
1880 new OOMWarning("copying region", er);
1884 ArrayList<int[]> hiddenColumns = null;
1885 if (viewport.hasHiddenColumns())
1887 hiddenColumns = new ArrayList<int[]>();
1888 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1889 .getSelectionGroup().getEndRes();
1890 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1892 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1894 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1895 region[1] - hiddenOffset });
1900 Desktop.jalviewClipboard = new Object[] { seqs,
1901 viewport.getAlignment().getDataset(), hiddenColumns };
1902 statusBar.setText(MessageManager.formatMessage(
1903 "label.copied_sequences_to_clipboard", new Object[] { Integer
1904 .valueOf(seqs.length).toString() }));
1914 protected void pasteNew_actionPerformed(ActionEvent e)
1926 protected void pasteThis_actionPerformed(ActionEvent e)
1932 * Paste contents of Jalview clipboard
1934 * @param newAlignment
1935 * true to paste to a new alignment, otherwise add to this.
1937 void paste(boolean newAlignment)
1939 boolean externalPaste = true;
1942 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1943 Transferable contents = c.getContents(this);
1945 if (contents == null)
1953 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1954 if (str.length() < 1)
1959 format = new IdentifyFile().identify(str, "Paste");
1961 } catch (OutOfMemoryError er)
1963 new OOMWarning("Out of memory pasting sequences!!", er);
1967 SequenceI[] sequences;
1968 boolean annotationAdded = false;
1969 AlignmentI alignment = null;
1971 if (Desktop.jalviewClipboard != null)
1973 // The clipboard was filled from within Jalview, we must use the
1975 // And dataset from the copied alignment
1976 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1977 // be doubly sure that we create *new* sequence objects.
1978 sequences = new SequenceI[newseq.length];
1979 for (int i = 0; i < newseq.length; i++)
1981 sequences[i] = new Sequence(newseq[i]);
1983 alignment = new Alignment(sequences);
1984 externalPaste = false;
1988 // parse the clipboard as an alignment.
1989 alignment = new FormatAdapter().readFile(str, "Paste", format);
1990 sequences = alignment.getSequencesArray();
1994 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2000 if (Desktop.jalviewClipboard != null)
2002 // dataset is inherited
2003 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2007 // new dataset is constructed
2008 alignment.setDataset(null);
2010 alwidth = alignment.getWidth() + 1;
2014 AlignmentI pastedal = alignment; // preserve pasted alignment object
2015 // Add pasted sequences and dataset into existing alignment.
2016 alignment = viewport.getAlignment();
2017 alwidth = alignment.getWidth() + 1;
2018 // decide if we need to import sequences from an existing dataset
2019 boolean importDs = Desktop.jalviewClipboard != null
2020 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2021 // importDs==true instructs us to copy over new dataset sequences from
2022 // an existing alignment
2023 Vector newDs = (importDs) ? new Vector() : null; // used to create
2024 // minimum dataset set
2026 for (int i = 0; i < sequences.length; i++)
2030 newDs.addElement(null);
2032 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2034 if (importDs && ds != null)
2036 if (!newDs.contains(ds))
2038 newDs.setElementAt(ds, i);
2039 ds = new Sequence(ds);
2040 // update with new dataset sequence
2041 sequences[i].setDatasetSequence(ds);
2045 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2050 // copy and derive new dataset sequence
2051 sequences[i] = sequences[i].deriveSequence();
2052 alignment.getDataset().addSequence(
2053 sequences[i].getDatasetSequence());
2054 // TODO: avoid creation of duplicate dataset sequences with a
2055 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2057 alignment.addSequence(sequences[i]); // merges dataset
2061 newDs.clear(); // tidy up
2063 if (alignment.getAlignmentAnnotation() != null)
2065 for (AlignmentAnnotation alan : alignment
2066 .getAlignmentAnnotation())
2068 if (alan.graphGroup > fgroup)
2070 fgroup = alan.graphGroup;
2074 if (pastedal.getAlignmentAnnotation() != null)
2076 // Add any annotation attached to alignment.
2077 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2078 for (int i = 0; i < alann.length; i++)
2080 annotationAdded = true;
2081 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2083 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2084 if (newann.graphGroup > -1)
2086 if (newGraphGroups.size() <= newann.graphGroup
2087 || newGraphGroups.get(newann.graphGroup) == null)
2089 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2091 newGraphGroups.add(q, null);
2093 newGraphGroups.set(newann.graphGroup, new Integer(
2096 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2100 newann.padAnnotation(alwidth);
2101 alignment.addAnnotation(newann);
2111 addHistoryItem(new EditCommand(
2112 MessageManager.getString("label.add_sequences"),
2113 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2115 // Add any annotations attached to sequences
2116 for (int i = 0; i < sequences.length; i++)
2118 if (sequences[i].getAnnotation() != null)
2120 AlignmentAnnotation newann;
2121 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2123 annotationAdded = true;
2124 newann = sequences[i].getAnnotation()[a];
2125 newann.adjustForAlignment();
2126 newann.padAnnotation(alwidth);
2127 if (newann.graphGroup > -1)
2129 if (newann.graphGroup > -1)
2131 if (newGraphGroups.size() <= newann.graphGroup
2132 || newGraphGroups.get(newann.graphGroup) == null)
2134 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2136 newGraphGroups.add(q, null);
2138 newGraphGroups.set(newann.graphGroup, new Integer(
2141 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2145 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2150 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2157 // propagate alignment changed.
2158 viewport.setEndSeq(alignment.getHeight());
2159 if (annotationAdded)
2161 // Duplicate sequence annotation in all views.
2162 AlignmentI[] alview = this.getViewAlignments();
2163 for (int i = 0; i < sequences.length; i++)
2165 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2170 for (int avnum = 0; avnum < alview.length; avnum++)
2172 if (alview[avnum] != alignment)
2174 // duplicate in a view other than the one with input focus
2175 int avwidth = alview[avnum].getWidth() + 1;
2176 // this relies on sann being preserved after we
2177 // modify the sequence's annotation array for each duplication
2178 for (int a = 0; a < sann.length; a++)
2180 AlignmentAnnotation newann = new AlignmentAnnotation(
2182 sequences[i].addAlignmentAnnotation(newann);
2183 newann.padAnnotation(avwidth);
2184 alview[avnum].addAnnotation(newann); // annotation was
2185 // duplicated earlier
2186 // TODO JAL-1145 graphGroups are not updated for sequence
2187 // annotation added to several views. This may cause
2189 alview[avnum].setAnnotationIndex(newann, a);
2194 buildSortByAnnotationScoresMenu();
2196 viewport.firePropertyChange("alignment", null,
2197 alignment.getSequences());
2198 if (alignPanels != null)
2200 for (AlignmentPanel ap : alignPanels)
2202 ap.validateAnnotationDimensions(false);
2207 alignPanel.validateAnnotationDimensions(false);
2213 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2215 String newtitle = new String("Copied sequences");
2217 if (Desktop.jalviewClipboard != null
2218 && Desktop.jalviewClipboard[2] != null)
2220 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2221 for (int[] region : hc)
2223 af.viewport.hideColumns(region[0], region[1]);
2227 // >>>This is a fix for the moment, until a better solution is
2229 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2231 alignPanel.getSeqPanel().seqCanvas
2232 .getFeatureRenderer());
2234 // TODO: maintain provenance of an alignment, rather than just make the
2235 // title a concatenation of operations.
2238 if (title.startsWith("Copied sequences"))
2244 newtitle = newtitle.concat("- from " + title);
2249 newtitle = new String("Pasted sequences");
2252 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2257 } catch (Exception ex)
2259 ex.printStackTrace();
2260 System.out.println("Exception whilst pasting: " + ex);
2261 // could be anything being pasted in here
2267 protected void expand_newalign(ActionEvent e)
2271 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2272 .getAlignment(), -1);
2273 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2275 String newtitle = new String("Flanking alignment");
2277 if (Desktop.jalviewClipboard != null
2278 && Desktop.jalviewClipboard[2] != null)
2280 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2281 for (int region[] : hc)
2283 af.viewport.hideColumns(region[0], region[1]);
2287 // >>>This is a fix for the moment, until a better solution is
2289 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2291 alignPanel.getSeqPanel().seqCanvas
2292 .getFeatureRenderer());
2294 // TODO: maintain provenance of an alignment, rather than just make the
2295 // title a concatenation of operations.
2297 if (title.startsWith("Copied sequences"))
2303 newtitle = newtitle.concat("- from " + title);
2307 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2309 } catch (Exception ex)
2311 ex.printStackTrace();
2312 System.out.println("Exception whilst pasting: " + ex);
2313 // could be anything being pasted in here
2314 } catch (OutOfMemoryError oom)
2316 new OOMWarning("Viewing flanking region of alignment", oom);
2327 protected void cut_actionPerformed(ActionEvent e)
2329 copy_actionPerformed(null);
2330 delete_actionPerformed(null);
2340 protected void delete_actionPerformed(ActionEvent evt)
2343 SequenceGroup sg = viewport.getSelectionGroup();
2350 * If the cut affects all sequences, warn, remove highlighted columns
2352 if (sg.getSize() == viewport.getAlignment().getHeight())
2354 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2355 .getAlignment().getWidth()) ? true : false;
2356 if (isEntireAlignWidth)
2358 int confirm = JOptionPane.showConfirmDialog(this,
2359 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2360 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2361 JOptionPane.OK_CANCEL_OPTION);
2363 if (confirm == JOptionPane.CANCEL_OPTION
2364 || confirm == JOptionPane.CLOSED_OPTION)
2369 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2370 sg.getEndRes() + 1);
2372 SequenceI[] cut = sg.getSequences()
2373 .toArray(new SequenceI[sg.getSize()]);
2375 addHistoryItem(new EditCommand(
2376 MessageManager.getString("label.cut_sequences"), Action.CUT,
2377 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2378 viewport.getAlignment()));
2380 viewport.setSelectionGroup(null);
2381 viewport.sendSelection();
2382 viewport.getAlignment().deleteGroup(sg);
2384 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2386 if (viewport.getAlignment().getHeight() < 1)
2390 this.setClosed(true);
2391 } catch (Exception ex)
2404 protected void deleteGroups_actionPerformed(ActionEvent e)
2406 if (avc.deleteGroups())
2408 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2409 alignPanel.updateAnnotation();
2410 alignPanel.paintAlignment(true);
2421 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2423 SequenceGroup sg = new SequenceGroup();
2425 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2427 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2430 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2431 viewport.setSelectionGroup(sg);
2432 viewport.sendSelection();
2433 // JAL-2034 - should delegate to
2434 // alignPanel to decide if overview needs
2436 alignPanel.paintAlignment(false);
2437 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2447 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2449 if (viewport.cursorMode)
2451 alignPanel.getSeqPanel().keyboardNo1 = null;
2452 alignPanel.getSeqPanel().keyboardNo2 = null;
2454 viewport.setSelectionGroup(null);
2455 viewport.getColumnSelection().clear();
2456 viewport.setSelectionGroup(null);
2457 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2458 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2459 // JAL-2034 - should delegate to
2460 // alignPanel to decide if overview needs
2462 alignPanel.paintAlignment(false);
2463 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2464 viewport.sendSelection();
2474 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2476 SequenceGroup sg = viewport.getSelectionGroup();
2480 selectAllSequenceMenuItem_actionPerformed(null);
2485 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2487 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2489 // JAL-2034 - should delegate to
2490 // alignPanel to decide if overview needs
2493 alignPanel.paintAlignment(true);
2494 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2495 viewport.sendSelection();
2499 public void invertColSel_actionPerformed(ActionEvent e)
2501 viewport.invertColumnSelection();
2502 alignPanel.paintAlignment(true);
2503 viewport.sendSelection();
2513 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2515 trimAlignment(true);
2525 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2527 trimAlignment(false);
2530 void trimAlignment(boolean trimLeft)
2532 ColumnSelection colSel = viewport.getColumnSelection();
2535 if (!colSel.isEmpty())
2539 column = colSel.getMin();
2543 column = colSel.getMax();
2547 if (viewport.getSelectionGroup() != null)
2549 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2550 viewport.getHiddenRepSequences());
2554 seqs = viewport.getAlignment().getSequencesArray();
2557 TrimRegionCommand trimRegion;
2560 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2561 column, viewport.getAlignment());
2562 viewport.setStartRes(0);
2566 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2567 column, viewport.getAlignment());
2570 statusBar.setText(MessageManager.formatMessage(
2571 "label.removed_columns",
2572 new String[] { Integer.valueOf(trimRegion.getSize())
2575 addHistoryItem(trimRegion);
2577 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2579 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2580 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2582 viewport.getAlignment().deleteGroup(sg);
2586 viewport.firePropertyChange("alignment", null, viewport
2587 .getAlignment().getSequences());
2598 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2600 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2603 if (viewport.getSelectionGroup() != null)
2605 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2606 viewport.getHiddenRepSequences());
2607 start = viewport.getSelectionGroup().getStartRes();
2608 end = viewport.getSelectionGroup().getEndRes();
2612 seqs = viewport.getAlignment().getSequencesArray();
2615 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2616 "Remove Gapped Columns", seqs, start, end,
2617 viewport.getAlignment());
2619 addHistoryItem(removeGapCols);
2621 statusBar.setText(MessageManager.formatMessage(
2622 "label.removed_empty_columns",
2623 new Object[] { Integer.valueOf(removeGapCols.getSize())
2626 // This is to maintain viewport position on first residue
2627 // of first sequence
2628 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2629 int startRes = seq.findPosition(viewport.startRes);
2630 // ShiftList shifts;
2631 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2632 // edit.alColumnChanges=shifts.getInverse();
2633 // if (viewport.hasHiddenColumns)
2634 // viewport.getColumnSelection().compensateForEdits(shifts);
2635 viewport.setStartRes(seq.findIndex(startRes) - 1);
2636 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2648 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2650 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2653 if (viewport.getSelectionGroup() != null)
2655 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2656 viewport.getHiddenRepSequences());
2657 start = viewport.getSelectionGroup().getStartRes();
2658 end = viewport.getSelectionGroup().getEndRes();
2662 seqs = viewport.getAlignment().getSequencesArray();
2665 // This is to maintain viewport position on first residue
2666 // of first sequence
2667 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2668 int startRes = seq.findPosition(viewport.startRes);
2670 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2671 viewport.getAlignment()));
2673 viewport.setStartRes(seq.findIndex(startRes) - 1);
2675 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2687 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2689 viewport.setPadGaps(padGapsMenuitem.isSelected());
2690 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2701 public void findMenuItem_actionPerformed(ActionEvent e)
2707 * Create a new view of the current alignment.
2710 public void newView_actionPerformed(ActionEvent e)
2712 newView(null, true);
2716 * Creates and shows a new view of the current alignment.
2719 * title of newly created view; if null, one will be generated
2720 * @param copyAnnotation
2721 * if true then duplicate all annnotation, groups and settings
2722 * @return new alignment panel, already displayed.
2724 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2727 * Create a new AlignmentPanel (with its own, new Viewport)
2729 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2731 if (!copyAnnotation)
2734 * remove all groups and annotation except for the automatic stuff
2736 newap.av.getAlignment().deleteAllGroups();
2737 newap.av.getAlignment().deleteAllAnnotations(false);
2740 newap.av.setGatherViewsHere(false);
2742 if (viewport.viewName == null)
2744 viewport.viewName = MessageManager
2745 .getString("label.view_name_original");
2749 * Views share the same edits undo and redo stacks
2751 newap.av.setHistoryList(viewport.getHistoryList());
2752 newap.av.setRedoList(viewport.getRedoList());
2755 * Views share the same mappings; need to deregister any new mappings
2756 * created by copyAlignPanel, and register the new reference to the shared
2759 newap.av.replaceMappings(viewport.getAlignment());
2761 newap.av.viewName = getNewViewName(viewTitle);
2763 addAlignmentPanel(newap, true);
2764 newap.alignmentChanged();
2766 if (alignPanels.size() == 2)
2768 viewport.setGatherViewsHere(true);
2770 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2775 * Make a new name for the view, ensuring it is unique within the current
2776 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2777 * these now use viewId. Unique view names are still desirable for usability.)
2782 protected String getNewViewName(String viewTitle)
2784 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2785 boolean addFirstIndex = false;
2786 if (viewTitle == null || viewTitle.trim().length() == 0)
2788 viewTitle = MessageManager.getString("action.view");
2789 addFirstIndex = true;
2793 index = 1;// we count from 1 if given a specific name
2795 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2797 List<Component> comps = PaintRefresher.components.get(viewport
2798 .getSequenceSetId());
2800 List<String> existingNames = getExistingViewNames(comps);
2802 while (existingNames.contains(newViewName))
2804 newViewName = viewTitle + " " + (++index);
2810 * Returns a list of distinct view names found in the given list of
2811 * components. View names are held on the viewport of an AlignmentPanel.
2816 protected List<String> getExistingViewNames(List<Component> comps)
2818 List<String> existingNames = new ArrayList<String>();
2819 for (Component comp : comps)
2821 if (comp instanceof AlignmentPanel)
2823 AlignmentPanel ap = (AlignmentPanel) comp;
2824 if (!existingNames.contains(ap.av.viewName))
2826 existingNames.add(ap.av.viewName);
2830 return existingNames;
2834 * Explode tabbed views into separate windows.
2837 public void expandViews_actionPerformed(ActionEvent e)
2839 Desktop.explodeViews(this);
2843 * Gather views in separate windows back into a tabbed presentation.
2846 public void gatherViews_actionPerformed(ActionEvent e)
2848 Desktop.instance.gatherViews(this);
2858 public void font_actionPerformed(ActionEvent e)
2860 new FontChooser(alignPanel);
2870 protected void seqLimit_actionPerformed(ActionEvent e)
2872 viewport.setShowJVSuffix(seqLimits.isSelected());
2874 alignPanel.getIdPanel().getIdCanvas()
2875 .setPreferredSize(alignPanel.calculateIdWidth());
2876 alignPanel.paintAlignment(true);
2880 public void idRightAlign_actionPerformed(ActionEvent e)
2882 viewport.setRightAlignIds(idRightAlign.isSelected());
2883 alignPanel.paintAlignment(true);
2887 public void centreColumnLabels_actionPerformed(ActionEvent e)
2889 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2890 alignPanel.paintAlignment(true);
2896 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2899 protected void followHighlight_actionPerformed()
2902 * Set the 'follow' flag on the Viewport (and scroll to position if now
2905 final boolean state = this.followHighlightMenuItem.getState();
2906 viewport.setFollowHighlight(state);
2909 alignPanel.scrollToPosition(
2910 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2921 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2923 viewport.setColourText(colourTextMenuItem.isSelected());
2924 alignPanel.paintAlignment(true);
2934 public void wrapMenuItem_actionPerformed(ActionEvent e)
2936 scaleAbove.setVisible(wrapMenuItem.isSelected());
2937 scaleLeft.setVisible(wrapMenuItem.isSelected());
2938 scaleRight.setVisible(wrapMenuItem.isSelected());
2939 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2940 alignPanel.updateLayout();
2944 public void showAllSeqs_actionPerformed(ActionEvent e)
2946 viewport.showAllHiddenSeqs();
2950 public void showAllColumns_actionPerformed(ActionEvent e)
2952 viewport.showAllHiddenColumns();
2954 viewport.sendSelection();
2958 public void hideSelSequences_actionPerformed(ActionEvent e)
2960 viewport.hideAllSelectedSeqs();
2961 // alignPanel.paintAlignment(true);
2965 * called by key handler and the hide all/show all menu items
2970 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2973 boolean hide = false;
2974 SequenceGroup sg = viewport.getSelectionGroup();
2975 if (!toggleSeqs && !toggleCols)
2977 // Hide everything by the current selection - this is a hack - we do the
2978 // invert and then hide
2979 // first check that there will be visible columns after the invert.
2980 if (viewport.hasSelectedColumns()
2981 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2984 // now invert the sequence set, if required - empty selection implies
2985 // that no hiding is required.
2988 invertSequenceMenuItem_actionPerformed(null);
2989 sg = viewport.getSelectionGroup();
2993 viewport.expandColSelection(sg, true);
2994 // finally invert the column selection and get the new sequence
2996 invertColSel_actionPerformed(null);
3003 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3005 hideSelSequences_actionPerformed(null);
3008 else if (!(toggleCols && viewport.hasSelectedColumns()))
3010 showAllSeqs_actionPerformed(null);
3016 if (viewport.hasSelectedColumns())
3018 hideSelColumns_actionPerformed(null);
3021 viewport.setSelectionGroup(sg);
3026 showAllColumns_actionPerformed(null);
3035 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3036 * event.ActionEvent)
3039 public void hideAllButSelection_actionPerformed(ActionEvent e)
3041 toggleHiddenRegions(false, false);
3042 viewport.sendSelection();
3049 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3053 public void hideAllSelection_actionPerformed(ActionEvent e)
3055 SequenceGroup sg = viewport.getSelectionGroup();
3056 viewport.expandColSelection(sg, false);
3057 viewport.hideAllSelectedSeqs();
3058 viewport.hideSelectedColumns();
3059 alignPanel.paintAlignment(true);
3060 viewport.sendSelection();
3067 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3071 public void showAllhidden_actionPerformed(ActionEvent e)
3073 viewport.showAllHiddenColumns();
3074 viewport.showAllHiddenSeqs();
3075 alignPanel.paintAlignment(true);
3076 viewport.sendSelection();
3080 public void hideSelColumns_actionPerformed(ActionEvent e)
3082 viewport.hideSelectedColumns();
3083 alignPanel.paintAlignment(true);
3084 viewport.sendSelection();
3088 public void hiddenMarkers_actionPerformed(ActionEvent e)
3090 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3101 protected void scaleAbove_actionPerformed(ActionEvent e)
3103 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3104 alignPanel.paintAlignment(true);
3114 protected void scaleLeft_actionPerformed(ActionEvent e)
3116 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3117 alignPanel.paintAlignment(true);
3127 protected void scaleRight_actionPerformed(ActionEvent e)
3129 viewport.setScaleRightWrapped(scaleRight.isSelected());
3130 alignPanel.paintAlignment(true);
3140 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3142 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3143 alignPanel.paintAlignment(true);
3153 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3155 viewport.setShowText(viewTextMenuItem.isSelected());
3156 alignPanel.paintAlignment(true);
3166 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3168 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3169 alignPanel.paintAlignment(true);
3172 public FeatureSettings featureSettings;
3175 public FeatureSettingsControllerI getFeatureSettingsUI()
3177 return featureSettings;
3181 public void featureSettings_actionPerformed(ActionEvent e)
3183 if (featureSettings != null)
3185 featureSettings.close();
3186 featureSettings = null;
3188 if (!showSeqFeatures.isSelected())
3190 // make sure features are actually displayed
3191 showSeqFeatures.setSelected(true);
3192 showSeqFeatures_actionPerformed(null);
3194 featureSettings = new FeatureSettings(this);
3198 * Set or clear 'Show Sequence Features'
3204 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3206 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3207 alignPanel.paintAlignment(true);
3208 if (alignPanel.getOverviewPanel() != null)
3210 alignPanel.getOverviewPanel().updateOverviewImage();
3215 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3216 * the annotations panel as a whole.
3218 * The options to show/hide all annotations should be enabled when the panel
3219 * is shown, and disabled when the panel is hidden.
3224 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3226 final boolean setVisible = annotationPanelMenuItem.isSelected();
3227 viewport.setShowAnnotation(setVisible);
3228 this.showAllSeqAnnotations.setEnabled(setVisible);
3229 this.hideAllSeqAnnotations.setEnabled(setVisible);
3230 this.showAllAlAnnotations.setEnabled(setVisible);
3231 this.hideAllAlAnnotations.setEnabled(setVisible);
3232 alignPanel.updateLayout();
3236 public void alignmentProperties()
3238 JEditorPane editPane = new JEditorPane("text/html", "");
3239 editPane.setEditable(false);
3240 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3242 editPane.setText(MessageManager.formatMessage("label.html_content",
3243 new Object[] { contents.toString() }));
3244 JInternalFrame frame = new JInternalFrame();
3245 frame.getContentPane().add(new JScrollPane(editPane));
3247 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3248 "label.alignment_properties", new Object[] { getTitle() }),
3259 public void overviewMenuItem_actionPerformed(ActionEvent e)
3261 if (alignPanel.overviewPanel != null)
3266 JInternalFrame frame = new JInternalFrame();
3267 OverviewPanel overview = new OverviewPanel(alignPanel);
3268 frame.setContentPane(overview);
3269 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3270 "label.overview_params", new Object[] { this.getTitle() }),
3271 frame.getWidth(), frame.getHeight());
3273 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3274 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3277 public void internalFrameClosed(
3278 javax.swing.event.InternalFrameEvent evt)
3280 alignPanel.setOverviewPanel(null);
3284 alignPanel.setOverviewPanel(overview);
3288 public void textColour_actionPerformed(ActionEvent e)
3290 new TextColourChooser().chooseColour(alignPanel, null);
3300 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3312 public void clustalColour_actionPerformed(ActionEvent e)
3314 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3315 viewport.getHiddenRepSequences()));
3325 public void zappoColour_actionPerformed(ActionEvent e)
3327 changeColour(new ZappoColourScheme());
3337 public void taylorColour_actionPerformed(ActionEvent e)
3339 changeColour(new TaylorColourScheme());
3349 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3351 changeColour(new HydrophobicColourScheme());
3361 public void helixColour_actionPerformed(ActionEvent e)
3363 changeColour(new HelixColourScheme());
3373 public void strandColour_actionPerformed(ActionEvent e)
3375 changeColour(new StrandColourScheme());
3385 public void turnColour_actionPerformed(ActionEvent e)
3387 changeColour(new TurnColourScheme());
3397 public void buriedColour_actionPerformed(ActionEvent e)
3399 changeColour(new BuriedColourScheme());
3409 public void nucleotideColour_actionPerformed(ActionEvent e)
3411 changeColour(new NucleotideColourScheme());
3415 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3417 changeColour(new PurinePyrimidineColourScheme());
3421 * public void covariationColour_actionPerformed(ActionEvent e) {
3423 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3427 public void annotationColour_actionPerformed(ActionEvent e)
3429 new AnnotationColourChooser(viewport, alignPanel);
3433 public void annotationColumn_actionPerformed(ActionEvent e)
3435 new AnnotationColumnChooser(viewport, alignPanel);
3439 public void rnahelicesColour_actionPerformed(ActionEvent e)
3441 new RNAHelicesColourChooser(viewport, alignPanel);
3451 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3453 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3463 public void changeColour(ColourSchemeI cs)
3465 // TODO: pull up to controller method
3469 // Make sure viewport is up to date w.r.t. any sliders
3470 if (viewport.getAbovePIDThreshold())
3472 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3474 viewport.setThreshold(threshold);
3477 if (viewport.getConservationSelected())
3479 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3482 if (cs instanceof TCoffeeColourScheme)
3484 tcoffeeColour.setEnabled(true);
3485 tcoffeeColour.setSelected(true);
3489 viewport.setGlobalColourScheme(cs);
3491 alignPanel.paintAlignment(true);
3501 protected void modifyPID_actionPerformed(ActionEvent e)
3503 if (viewport.getAbovePIDThreshold()
3504 && viewport.getGlobalColourScheme() != null)
3506 SliderPanel.setPIDSliderSource(alignPanel,
3507 viewport.getGlobalColourScheme(), "Background");
3508 SliderPanel.showPIDSlider();
3519 protected void modifyConservation_actionPerformed(ActionEvent e)
3521 if (viewport.getConservationSelected()
3522 && viewport.getGlobalColourScheme() != null)
3524 SliderPanel.setConservationSlider(alignPanel,
3525 viewport.getGlobalColourScheme(), "Background");
3526 SliderPanel.showConservationSlider();
3537 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3539 viewport.setConservationSelected(conservationMenuItem.isSelected());
3541 viewport.setAbovePIDThreshold(false);
3542 abovePIDThreshold.setSelected(false);
3544 changeColour(viewport.getGlobalColourScheme());
3546 modifyConservation_actionPerformed(null);
3556 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3558 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3560 conservationMenuItem.setSelected(false);
3561 viewport.setConservationSelected(false);
3563 changeColour(viewport.getGlobalColourScheme());
3565 modifyPID_actionPerformed(null);
3575 public void userDefinedColour_actionPerformed(ActionEvent e)
3577 if (e.getActionCommand().equals(
3578 MessageManager.getString("action.user_defined")))
3580 new UserDefinedColours(alignPanel, null);
3584 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3585 .getUserColourSchemes().get(e.getActionCommand());
3591 public void updateUserColourMenu()
3594 Component[] menuItems = colourMenu.getMenuComponents();
3595 int iSize = menuItems.length;
3596 for (int i = 0; i < iSize; i++)
3598 if (menuItems[i].getName() != null
3599 && menuItems[i].getName().equals("USER_DEFINED"))
3601 colourMenu.remove(menuItems[i]);
3605 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3607 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3608 .getUserColourSchemes().keys();
3610 while (userColours.hasMoreElements())
3612 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3613 userColours.nextElement().toString());
3614 radioItem.setName("USER_DEFINED");
3615 radioItem.addMouseListener(new MouseAdapter()
3618 public void mousePressed(MouseEvent evt)
3620 if (evt.isPopupTrigger()) // Mac
3622 offerRemoval(radioItem);
3627 public void mouseReleased(MouseEvent evt)
3629 if (evt.isPopupTrigger()) // Windows
3631 offerRemoval(radioItem);
3638 void offerRemoval(final JRadioButtonMenuItem radioItem)
3640 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3642 int option = JOptionPane.showInternalConfirmDialog(
3643 jalview.gui.Desktop.desktop,
3645 .getString("label.remove_from_default_list"),
3647 .getString("label.remove_user_defined_colour"),
3648 JOptionPane.YES_NO_OPTION);
3649 if (option == JOptionPane.YES_OPTION)
3651 jalview.gui.UserDefinedColours
3652 .removeColourFromDefaults(radioItem.getText());
3653 colourMenu.remove(radioItem);
3657 radioItem.addActionListener(new ActionListener()
3660 public void actionPerformed(ActionEvent evt)
3662 userDefinedColour_actionPerformed(evt);
3668 radioItem.addActionListener(new ActionListener()
3671 public void actionPerformed(ActionEvent evt)
3673 userDefinedColour_actionPerformed(evt);
3677 colourMenu.insert(radioItem, 15);
3678 colours.add(radioItem);
3690 public void PIDColour_actionPerformed(ActionEvent e)
3692 changeColour(new PIDColourScheme());
3702 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3704 changeColour(new Blosum62ColourScheme());
3714 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3716 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3717 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3718 .getAlignment().getSequenceAt(0), null);
3719 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3720 viewport.getAlignment()));
3721 alignPanel.paintAlignment(true);
3731 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3733 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3734 AlignmentSorter.sortByID(viewport.getAlignment());
3735 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3736 viewport.getAlignment()));
3737 alignPanel.paintAlignment(true);
3747 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3749 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3750 AlignmentSorter.sortByLength(viewport.getAlignment());
3751 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3752 viewport.getAlignment()));
3753 alignPanel.paintAlignment(true);
3763 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3765 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3766 AlignmentSorter.sortByGroup(viewport.getAlignment());
3767 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3768 viewport.getAlignment()));
3770 alignPanel.paintAlignment(true);
3780 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3782 new RedundancyPanel(alignPanel, this);
3792 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3794 if ((viewport.getSelectionGroup() == null)
3795 || (viewport.getSelectionGroup().getSize() < 2))
3797 JOptionPane.showInternalMessageDialog(this, MessageManager
3798 .getString("label.you_must_select_least_two_sequences"),
3799 MessageManager.getString("label.invalid_selection"),
3800 JOptionPane.WARNING_MESSAGE);
3804 JInternalFrame frame = new JInternalFrame();
3805 frame.setContentPane(new PairwiseAlignPanel(viewport));
3806 Desktop.addInternalFrame(frame,
3807 MessageManager.getString("action.pairwise_alignment"), 600,
3819 public void PCAMenuItem_actionPerformed(ActionEvent e)
3821 if (((viewport.getSelectionGroup() != null)
3822 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3823 .getSelectionGroup().getSize() > 0))
3824 || (viewport.getAlignment().getHeight() < 4))
3827 .showInternalMessageDialog(
3830 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3832 .getString("label.sequence_selection_insufficient"),
3833 JOptionPane.WARNING_MESSAGE);
3838 new PCAPanel(alignPanel);
3842 public void autoCalculate_actionPerformed(ActionEvent e)
3844 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3845 if (viewport.autoCalculateConsensus)
3847 viewport.firePropertyChange("alignment", null, viewport
3848 .getAlignment().getSequences());
3853 public void sortByTreeOption_actionPerformed(ActionEvent e)
3855 viewport.sortByTree = sortByTree.isSelected();
3859 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3861 viewport.followSelection = listenToViewSelections.isSelected();
3871 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3873 newTreePanel("AV", "PID", "Average distance tree using PID");
3883 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3885 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3895 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3897 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3907 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3909 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3922 void newTreePanel(String type, String pwType, String title)
3926 if (viewport.getSelectionGroup() != null
3927 && viewport.getSelectionGroup().getSize() > 0)
3929 if (viewport.getSelectionGroup().getSize() < 3)
3935 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3937 .getString("label.not_enough_sequences"),
3938 JOptionPane.WARNING_MESSAGE);
3942 SequenceGroup sg = viewport.getSelectionGroup();
3944 /* Decide if the selection is a column region */
3945 for (SequenceI _s : sg.getSequences())
3947 if (_s.getLength() < sg.getEndRes())
3953 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3955 .getString("label.sequences_selection_not_aligned"),
3956 JOptionPane.WARNING_MESSAGE);
3962 title = title + " on region";
3963 tp = new TreePanel(alignPanel, type, pwType);
3967 // are the visible sequences aligned?
3968 if (!viewport.getAlignment().isAligned(false))
3974 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3976 .getString("label.sequences_not_aligned"),
3977 JOptionPane.WARNING_MESSAGE);
3982 if (viewport.getAlignment().getHeight() < 2)
3987 tp = new TreePanel(alignPanel, type, pwType);
3992 if (viewport.viewName != null)
3994 title += viewport.viewName + " of ";
3997 title += this.title;
3999 Desktop.addInternalFrame(tp, title, 600, 500);
4010 public void addSortByOrderMenuItem(String title,
4011 final AlignmentOrder order)
4013 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4014 "action.by_title_param", new Object[] { title }));
4016 item.addActionListener(new java.awt.event.ActionListener()
4019 public void actionPerformed(ActionEvent e)
4021 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4023 // TODO: JBPNote - have to map order entries to curent SequenceI
4025 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4027 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4030 alignPanel.paintAlignment(true);
4036 * Add a new sort by annotation score menu item
4039 * the menu to add the option to
4041 * the label used to retrieve scores for each sequence on the
4044 public void addSortByAnnotScoreMenuItem(JMenu sort,
4045 final String scoreLabel)
4047 final JMenuItem item = new JMenuItem(scoreLabel);
4049 item.addActionListener(new java.awt.event.ActionListener()
4052 public void actionPerformed(ActionEvent e)
4054 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4055 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4056 viewport.getAlignment());// ,viewport.getSelectionGroup());
4057 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4058 viewport.getAlignment()));
4059 alignPanel.paintAlignment(true);
4065 * last hash for alignment's annotation array - used to minimise cost of
4068 protected int _annotationScoreVectorHash;
4071 * search the alignment and rebuild the sort by annotation score submenu the
4072 * last alignment annotation vector hash is stored to minimize cost of
4073 * rebuilding in subsequence calls.
4077 public void buildSortByAnnotationScoresMenu()
4079 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4084 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4086 sortByAnnotScore.removeAll();
4087 // almost certainly a quicker way to do this - but we keep it simple
4088 Hashtable scoreSorts = new Hashtable();
4089 AlignmentAnnotation aann[];
4090 for (SequenceI sqa : viewport.getAlignment().getSequences())
4092 aann = sqa.getAnnotation();
4093 for (int i = 0; aann != null && i < aann.length; i++)
4095 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4097 scoreSorts.put(aann[i].label, aann[i].label);
4101 Enumeration labels = scoreSorts.keys();
4102 while (labels.hasMoreElements())
4104 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4105 (String) labels.nextElement());
4107 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4110 _annotationScoreVectorHash = viewport.getAlignment()
4111 .getAlignmentAnnotation().hashCode();
4116 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4117 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4118 * call. Listeners are added to remove the menu item when the treePanel is
4119 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4123 * Displayed tree window.
4125 * SortBy menu item title.
4128 public void buildTreeMenu()
4130 calculateTree.removeAll();
4131 // build the calculate menu
4133 for (final String type : new String[] { "NJ", "AV" })
4135 String treecalcnm = MessageManager.getString("label.tree_calc_"
4136 + type.toLowerCase());
4137 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4139 JMenuItem tm = new JMenuItem();
4140 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4141 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4142 || sm.isProtein() == !viewport.getAlignment()
4145 String smn = MessageManager.getStringOrReturn(
4146 "label.score_model_", sm.getName());
4147 final String title = MessageManager.formatMessage(
4148 "label.treecalc_title", treecalcnm, smn);
4149 tm.setText(title);//
4150 tm.addActionListener(new java.awt.event.ActionListener()
4153 public void actionPerformed(ActionEvent e)
4155 newTreePanel(type, pwtype, title);
4158 calculateTree.add(tm);
4163 sortByTreeMenu.removeAll();
4165 List<Component> comps = PaintRefresher.components.get(viewport
4166 .getSequenceSetId());
4167 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4168 for (Component comp : comps)
4170 if (comp instanceof TreePanel)
4172 treePanels.add((TreePanel) comp);
4176 if (treePanels.size() < 1)
4178 sortByTreeMenu.setVisible(false);
4182 sortByTreeMenu.setVisible(true);
4184 for (final TreePanel tp : treePanels)
4186 final JMenuItem item = new JMenuItem(tp.getTitle());
4187 item.addActionListener(new java.awt.event.ActionListener()
4190 public void actionPerformed(ActionEvent e)
4192 tp.sortByTree_actionPerformed();
4193 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4198 sortByTreeMenu.add(item);
4202 public boolean sortBy(AlignmentOrder alorder, String undoname)
4204 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4205 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4206 if (undoname != null)
4208 addHistoryItem(new OrderCommand(undoname, oldOrder,
4209 viewport.getAlignment()));
4211 alignPanel.paintAlignment(true);
4216 * Work out whether the whole set of sequences or just the selected set will
4217 * be submitted for multiple alignment.
4220 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4222 // Now, check we have enough sequences
4223 AlignmentView msa = null;
4225 if ((viewport.getSelectionGroup() != null)
4226 && (viewport.getSelectionGroup().getSize() > 1))
4228 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4229 // some common interface!
4231 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4232 * SequenceI[sz = seqs.getSize(false)];
4234 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4235 * seqs.getSequenceAt(i); }
4237 msa = viewport.getAlignmentView(true);
4239 else if (viewport.getSelectionGroup() != null
4240 && viewport.getSelectionGroup().getSize() == 1)
4242 int option = JOptionPane.showConfirmDialog(this,
4243 MessageManager.getString("warn.oneseq_msainput_selection"),
4244 MessageManager.getString("label.invalid_selection"),
4245 JOptionPane.OK_CANCEL_OPTION);
4246 if (option == JOptionPane.OK_OPTION)
4248 msa = viewport.getAlignmentView(false);
4253 msa = viewport.getAlignmentView(false);
4259 * Decides what is submitted to a secondary structure prediction service: the
4260 * first sequence in the alignment, or in the current selection, or, if the
4261 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4262 * region or the whole alignment. (where the first sequence in the set is the
4263 * one that the prediction will be for).
4265 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4267 AlignmentView seqs = null;
4269 if ((viewport.getSelectionGroup() != null)
4270 && (viewport.getSelectionGroup().getSize() > 0))
4272 seqs = viewport.getAlignmentView(true);
4276 seqs = viewport.getAlignmentView(false);
4278 // limit sequences - JBPNote in future - could spawn multiple prediction
4280 // TODO: viewport.getAlignment().isAligned is a global state - the local
4281 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4282 if (!viewport.getAlignment().isAligned(false))
4284 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4285 // TODO: if seqs.getSequences().length>1 then should really have warned
4299 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4301 // Pick the tree file
4302 JalviewFileChooser chooser = new JalviewFileChooser(
4303 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4304 chooser.setFileView(new JalviewFileView());
4305 chooser.setDialogTitle(MessageManager
4306 .getString("label.select_newick_like_tree_file"));
4307 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4309 int value = chooser.showOpenDialog(null);
4311 if (value == JalviewFileChooser.APPROVE_OPTION)
4313 String choice = chooser.getSelectedFile().getPath();
4314 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4315 jalview.io.NewickFile fin = null;
4318 fin = new jalview.io.NewickFile(choice, "File");
4319 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4320 } catch (Exception ex)
4327 .getString("label.problem_reading_tree_file"),
4328 JOptionPane.WARNING_MESSAGE);
4329 ex.printStackTrace();
4331 if (fin != null && fin.hasWarningMessage())
4333 JOptionPane.showMessageDialog(Desktop.desktop, fin
4334 .getWarningMessage(), MessageManager
4335 .getString("label.possible_problem_with_tree_file"),
4336 JOptionPane.WARNING_MESSAGE);
4342 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4344 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4347 public TreePanel ShowNewickTree(NewickFile nf, String title)
4349 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4352 public TreePanel ShowNewickTree(NewickFile nf, String title,
4353 AlignmentView input)
4355 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4358 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4359 int h, int x, int y)
4361 return ShowNewickTree(nf, title, null, w, h, x, y);
4365 * Add a treeviewer for the tree extracted from a newick file object to the
4366 * current alignment view
4373 * Associated alignment input data (or null)
4382 * @return TreePanel handle
4384 public TreePanel ShowNewickTree(NewickFile nf, String title,
4385 AlignmentView input, int w, int h, int x, int y)
4387 TreePanel tp = null;
4393 if (nf.getTree() != null)
4395 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4401 tp.setLocation(x, y);
4404 Desktop.addInternalFrame(tp, title, w, h);
4406 } catch (Exception ex)
4408 ex.printStackTrace();
4414 private boolean buildingMenu = false;
4417 * Generates menu items and listener event actions for web service clients
4420 public void BuildWebServiceMenu()
4422 while (buildingMenu)
4426 System.err.println("Waiting for building menu to finish.");
4428 } catch (Exception e)
4432 final AlignFrame me = this;
4433 buildingMenu = true;
4434 new Thread(new Runnable()
4439 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4442 // System.err.println("Building ws menu again "
4443 // + Thread.currentThread());
4444 // TODO: add support for context dependent disabling of services based
4446 // alignment and current selection
4447 // TODO: add additional serviceHandle parameter to specify abstract
4449 // class independently of AbstractName
4450 // TODO: add in rediscovery GUI function to restart discoverer
4451 // TODO: group services by location as well as function and/or
4453 // object broker mechanism.
4454 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4455 final IProgressIndicator af = me;
4458 * do not i18n these strings - they are hard-coded in class
4459 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4460 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4462 final JMenu msawsmenu = new JMenu("Alignment");
4463 final JMenu secstrmenu = new JMenu(
4464 "Secondary Structure Prediction");
4465 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4466 final JMenu analymenu = new JMenu("Analysis");
4467 final JMenu dismenu = new JMenu("Protein Disorder");
4468 // JAL-940 - only show secondary structure prediction services from
4469 // the legacy server
4470 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4472 Discoverer.services != null && (Discoverer.services.size() > 0))
4474 // TODO: refactor to allow list of AbstractName/Handler bindings to
4476 // stored or retrieved from elsewhere
4477 // No MSAWS used any more:
4478 // Vector msaws = null; // (Vector)
4479 // Discoverer.services.get("MsaWS");
4480 Vector secstrpr = (Vector) Discoverer.services
4482 if (secstrpr != null)
4484 // Add any secondary structure prediction services
4485 for (int i = 0, j = secstrpr.size(); i < j; i++)
4487 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4489 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4490 .getServiceClient(sh);
4491 int p = secstrmenu.getItemCount();
4492 impl.attachWSMenuEntry(secstrmenu, me);
4493 int q = secstrmenu.getItemCount();
4494 for (int litm = p; litm < q; litm++)
4496 legacyItems.add(secstrmenu.getItem(litm));
4502 // Add all submenus in the order they should appear on the web
4504 wsmenu.add(msawsmenu);
4505 wsmenu.add(secstrmenu);
4506 wsmenu.add(dismenu);
4507 wsmenu.add(analymenu);
4508 // No search services yet
4509 // wsmenu.add(seqsrchmenu);
4511 javax.swing.SwingUtilities.invokeLater(new Runnable()
4518 webService.removeAll();
4519 // first, add discovered services onto the webservices menu
4520 if (wsmenu.size() > 0)
4522 for (int i = 0, j = wsmenu.size(); i < j; i++)
4524 webService.add(wsmenu.get(i));
4529 webService.add(me.webServiceNoServices);
4531 // TODO: move into separate menu builder class.
4532 boolean new_sspred = false;
4533 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4535 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4536 if (jws2servs != null)
4538 if (jws2servs.hasServices())
4540 jws2servs.attachWSMenuEntry(webService, me);
4541 for (Jws2Instance sv : jws2servs.getServices())
4543 if (sv.description.toLowerCase().contains("jpred"))
4545 for (JMenuItem jmi : legacyItems)
4547 jmi.setVisible(false);
4553 if (jws2servs.isRunning())
4555 JMenuItem tm = new JMenuItem(
4556 "Still discovering JABA Services");
4557 tm.setEnabled(false);
4562 build_urlServiceMenu(me.webService);
4563 build_fetchdbmenu(webService);
4564 for (JMenu item : wsmenu)
4566 if (item.getItemCount() == 0)
4568 item.setEnabled(false);
4572 item.setEnabled(true);
4575 } catch (Exception e)
4578 .debug("Exception during web service menu building process.",
4583 } catch (Exception e)
4586 buildingMenu = false;
4593 * construct any groupURL type service menu entries.
4597 private void build_urlServiceMenu(JMenu webService)
4599 // TODO: remove this code when 2.7 is released
4600 // DEBUG - alignmentView
4602 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4603 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4605 * @Override public void actionPerformed(ActionEvent e) {
4606 * jalview.datamodel.AlignmentView
4607 * .testSelectionViews(af.viewport.getAlignment(),
4608 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4610 * }); webService.add(testAlView);
4612 // TODO: refactor to RestClient discoverer and merge menu entries for
4613 // rest-style services with other types of analysis/calculation service
4614 // SHmmr test client - still being implemented.
4615 // DEBUG - alignmentView
4617 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4620 client.attachWSMenuEntry(
4621 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4627 * Searches the alignment sequences for xRefs and builds the Show
4628 * Cross-References menu (formerly called Show Products), with database
4629 * sources for which cross-references are found (protein sources for a
4630 * nucleotide alignment and vice versa)
4632 * @return true if Show Cross-references menu should be enabled
4634 public boolean canShowProducts()
4636 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4637 AlignmentI dataset = viewport.getAlignment().getDataset();
4639 showProducts.removeAll();
4640 final boolean dna = viewport.getAlignment().isNucleotide();
4642 if (seqs == null || seqs.length == 0)
4644 // nothing to see here.
4648 boolean showp = false;
4651 List<String> ptypes = new CrossRef(seqs, dataset)
4652 .findXrefSourcesForSequences(dna);
4654 for (final String source : ptypes)
4657 final AlignFrame af = this;
4658 JMenuItem xtype = new JMenuItem(source);
4659 xtype.addActionListener(new ActionListener()
4662 public void actionPerformed(ActionEvent e)
4664 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4667 showProducts.add(xtype);
4669 showProducts.setVisible(showp);
4670 showProducts.setEnabled(showp);
4671 } catch (Exception e)
4674 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4682 * Finds and displays cross-references for the selected sequences (protein
4683 * products for nucleotide sequences, dna coding sequences for peptides).
4686 * the sequences to show cross-references for
4688 * true if from a nucleotide alignment (so showing proteins)
4690 * the database to show cross-references for
4692 protected void showProductsFor(final SequenceI[] sel,
4693 final boolean _odna, final String source)
4695 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4700 * Construct and display a new frame containing the translation of this
4701 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4704 public void showTranslation_actionPerformed(ActionEvent e)
4706 AlignmentI al = null;
4709 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4711 al = dna.translateCdna();
4712 } catch (Exception ex)
4714 jalview.bin.Cache.log.error(
4715 "Exception during translation. Please report this !", ex);
4716 final String msg = MessageManager
4717 .getString("label.error_when_translating_sequences_submit_bug_report");
4718 final String errorTitle = MessageManager
4719 .getString("label.implementation_error")
4720 + MessageManager.getString("label.translation_failed");
4721 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4722 JOptionPane.ERROR_MESSAGE);
4725 if (al == null || al.getHeight() == 0)
4727 final String msg = MessageManager
4728 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4729 final String errorTitle = MessageManager
4730 .getString("label.translation_failed");
4731 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4732 JOptionPane.WARNING_MESSAGE);
4736 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4737 af.setFileFormat(this.currentFileFormat);
4738 final String newTitle = MessageManager.formatMessage(
4739 "label.translation_of_params",
4740 new Object[] { this.getTitle() });
4741 af.setTitle(newTitle);
4742 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4744 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4745 viewport.openSplitFrame(af, new Alignment(seqs));
4749 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4756 * Set the file format
4760 public void setFileFormat(String fileFormat)
4762 this.currentFileFormat = fileFormat;
4766 * Try to load a features file onto the alignment.
4769 * contents or path to retrieve file
4771 * access mode of file (see jalview.io.AlignFile)
4772 * @return true if features file was parsed correctly.
4774 public boolean parseFeaturesFile(String file, String type)
4776 return avc.parseFeaturesFile(file, type,
4777 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4782 public void refreshFeatureUI(boolean enableIfNecessary)
4784 // note - currently this is only still here rather than in the controller
4785 // because of the featureSettings hard reference that is yet to be
4787 if (enableIfNecessary)
4789 viewport.setShowSequenceFeatures(true);
4790 showSeqFeatures.setSelected(true);
4796 public void dragEnter(DropTargetDragEvent evt)
4801 public void dragExit(DropTargetEvent evt)
4806 public void dragOver(DropTargetDragEvent evt)
4811 public void dropActionChanged(DropTargetDragEvent evt)
4816 public void drop(DropTargetDropEvent evt)
4818 Transferable t = evt.getTransferable();
4819 java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
4823 Desktop.transferFromDropTarget(files, protocols, evt, t);
4824 } catch (Exception e)
4826 e.printStackTrace();
4832 // check to see if any of these files have names matching sequences in
4834 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4835 .getAlignment().getSequencesArray());
4837 * Object[] { String,SequenceI}
4839 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4840 ArrayList<String> filesnotmatched = new ArrayList<String>();
4841 for (int i = 0; i < files.size(); i++)
4843 String file = files.get(i).toString();
4845 String protocol = FormatAdapter.checkProtocol(file);
4846 if (protocol == jalview.io.FormatAdapter.FILE)
4848 File fl = new File(file);
4849 pdbfn = fl.getName();
4851 else if (protocol == jalview.io.FormatAdapter.URL)
4853 URL url = new URL(file);
4854 pdbfn = url.getFile();
4856 if (pdbfn.length() > 0)
4858 // attempt to find a match in the alignment
4859 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4860 int l = 0, c = pdbfn.indexOf(".");
4861 while (mtch == null && c != -1)
4866 } while ((c = pdbfn.indexOf(".", l)) > l);
4869 pdbfn = pdbfn.substring(0, l);
4871 mtch = idm.findAllIdMatches(pdbfn);
4878 type = new IdentifyFile().identify(file, protocol);
4879 } catch (Exception ex)
4885 if (type.equalsIgnoreCase("PDB"))
4887 filesmatched.add(new Object[] { file, protocol, mtch });
4892 // File wasn't named like one of the sequences or wasn't a PDB file.
4893 filesnotmatched.add(file);
4897 if (filesmatched.size() > 0)
4899 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4905 "label.automatically_associate_pdb_files_with_sequences_same_name",
4906 new Object[] { Integer
4912 .getString("label.automatically_associate_pdb_files_by_name"),
4913 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4916 for (Object[] fm : filesmatched)
4918 // try and associate
4919 // TODO: may want to set a standard ID naming formalism for
4920 // associating PDB files which have no IDs.
4921 for (SequenceI toassoc : (SequenceI[]) fm[2])
4923 PDBEntry pe = new AssociatePdbFileWithSeq()
4924 .associatePdbWithSeq((String) fm[0],
4925 (String) fm[1], toassoc, false,
4929 System.err.println("Associated file : "
4930 + ((String) fm[0]) + " with "
4931 + toassoc.getDisplayId(true));
4935 alignPanel.paintAlignment(true);
4939 if (filesnotmatched.size() > 0)
4942 && (Cache.getDefault(
4943 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4949 "label.ignore_unmatched_dropped_files_info",
4950 new Object[] { Integer
4957 .getString("label.ignore_unmatched_dropped_files"),
4958 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4962 for (String fn : filesnotmatched)
4964 loadJalviewDataFile(fn, null, null, null);
4968 } catch (Exception ex)
4970 ex.printStackTrace();
4976 * Attempt to load a "dropped" file or URL string: First by testing whether
4977 * it's an Annotation file, then a JNet file, and finally a features file. If
4978 * all are false then the user may have dropped an alignment file onto this
4982 * either a filename or a URL string.
4984 public void loadJalviewDataFile(String file, String protocol,
4985 String format, SequenceI assocSeq)
4989 if (protocol == null)
4991 protocol = FormatAdapter.checkProtocol(file);
4993 // if the file isn't identified, or not positively identified as some
4994 // other filetype (PFAM is default unidentified alignment file type) then
4995 // try to parse as annotation.
4996 boolean isAnnotation = (format == null || format
4997 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
4998 .annotateAlignmentView(viewport, file, protocol) : false;
5002 // first see if its a T-COFFEE score file
5003 TCoffeeScoreFile tcf = null;
5006 tcf = new TCoffeeScoreFile(file, protocol);
5009 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5011 tcoffeeColour.setEnabled(true);
5012 tcoffeeColour.setSelected(true);
5013 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5014 isAnnotation = true;
5016 .setText(MessageManager
5017 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5021 // some problem - if no warning its probable that the ID matching
5022 // process didn't work
5026 tcf.getWarningMessage() == null ? MessageManager
5027 .getString("label.check_file_matches_sequence_ids_alignment")
5028 : tcf.getWarningMessage(),
5030 .getString("label.problem_reading_tcoffee_score_file"),
5031 JOptionPane.WARNING_MESSAGE);
5038 } catch (Exception x)
5041 .debug("Exception when processing data source as T-COFFEE score file",
5047 // try to see if its a JNet 'concise' style annotation file *before*
5049 // try to parse it as a features file
5052 format = new IdentifyFile().identify(file, protocol);
5054 if (format.equalsIgnoreCase("JnetFile"))
5056 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5058 new JnetAnnotationMaker();
5059 JnetAnnotationMaker.add_annotation(predictions,
5060 viewport.getAlignment(), 0, false);
5061 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5062 viewport.getAlignment().setSeqrep(repseq);
5063 ColumnSelection cs = new ColumnSelection();
5064 cs.hideInsertionsFor(repseq);
5065 viewport.setColumnSelection(cs);
5066 isAnnotation = true;
5068 else if (IdentifyFile.FeaturesFile.equals(format))
5070 if (parseFeaturesFile(file, protocol))
5072 alignPanel.paintAlignment(true);
5077 new FileLoader().LoadFile(viewport, file, protocol, format);
5084 alignPanel.adjustAnnotationHeight();
5085 viewport.updateSequenceIdColours();
5086 buildSortByAnnotationScoresMenu();
5087 alignPanel.paintAlignment(true);
5089 } catch (Exception ex)
5091 ex.printStackTrace();
5092 } catch (OutOfMemoryError oom)
5097 } catch (Exception x)
5102 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5103 : "using " + protocol + " from " + file)
5105 + (format != null ? "(parsing as '" + format
5106 + "' file)" : ""), oom, Desktop.desktop);
5111 * Method invoked by the ChangeListener on the tabbed pane, in other words
5112 * when a different tabbed pane is selected by the user or programmatically.
5115 public void tabSelectionChanged(int index)
5119 alignPanel = alignPanels.get(index);
5120 viewport = alignPanel.av;
5121 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5122 setMenusFromViewport(viewport);
5126 * If there is a frame linked to this one in a SplitPane, switch it to the
5127 * same view tab index. No infinite recursion of calls should happen, since
5128 * tabSelectionChanged() should not get invoked on setting the selected
5129 * index to an unchanged value. Guard against setting an invalid index
5130 * before the new view peer tab has been created.
5132 final AlignViewportI peer = viewport.getCodingComplement();
5135 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5136 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5138 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5144 * On right mouse click on view tab, prompt for and set new view name.
5147 public void tabbedPane_mousePressed(MouseEvent e)
5149 if (e.isPopupTrigger())
5151 String msg = MessageManager.getString("label.enter_view_name");
5152 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5153 JOptionPane.QUESTION_MESSAGE);
5157 viewport.viewName = reply;
5158 // TODO warn if reply is in getExistingViewNames()?
5159 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5164 public AlignViewport getCurrentView()
5170 * Open the dialog for regex description parsing.
5173 protected void extractScores_actionPerformed(ActionEvent e)
5175 ParseProperties pp = new jalview.analysis.ParseProperties(
5176 viewport.getAlignment());
5177 // TODO: verify regex and introduce GUI dialog for version 2.5
5178 // if (pp.getScoresFromDescription("col", "score column ",
5179 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5181 if (pp.getScoresFromDescription("description column",
5182 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5184 buildSortByAnnotationScoresMenu();
5192 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5196 protected void showDbRefs_actionPerformed(ActionEvent e)
5198 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5204 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5208 protected void showNpFeats_actionPerformed(ActionEvent e)
5210 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5214 * find the viewport amongst the tabs in this alignment frame and close that
5219 public boolean closeView(AlignViewportI av)
5223 this.closeMenuItem_actionPerformed(false);
5226 Component[] comp = tabbedPane.getComponents();
5227 for (int i = 0; comp != null && i < comp.length; i++)
5229 if (comp[i] instanceof AlignmentPanel)
5231 if (((AlignmentPanel) comp[i]).av == av)
5234 closeView((AlignmentPanel) comp[i]);
5242 protected void build_fetchdbmenu(JMenu webService)
5244 // Temporary hack - DBRef Fetcher always top level ws entry.
5245 // TODO We probably want to store a sequence database checklist in
5246 // preferences and have checkboxes.. rather than individual sources selected
5248 final JMenu rfetch = new JMenu(
5249 MessageManager.getString("action.fetch_db_references"));
5250 rfetch.setToolTipText(MessageManager
5251 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5252 webService.add(rfetch);
5254 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5255 MessageManager.getString("option.trim_retrieved_seqs"));
5256 trimrs.setToolTipText(MessageManager
5257 .getString("label.trim_retrieved_sequences"));
5258 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5259 trimrs.addActionListener(new ActionListener()
5262 public void actionPerformed(ActionEvent e)
5264 trimrs.setSelected(trimrs.isSelected());
5265 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5266 Boolean.valueOf(trimrs.isSelected()).toString());
5270 JMenuItem fetchr = new JMenuItem(
5271 MessageManager.getString("label.standard_databases"));
5272 fetchr.setToolTipText(MessageManager
5273 .getString("label.fetch_embl_uniprot"));
5274 fetchr.addActionListener(new ActionListener()
5278 public void actionPerformed(ActionEvent e)
5280 new Thread(new Runnable()
5285 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5286 .getAlignment().isNucleotide();
5287 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5288 .getSequenceSelection(), alignPanel.alignFrame, null,
5289 alignPanel.alignFrame.featureSettings, isNucleotide);
5290 dbRefFetcher.addListener(new FetchFinishedListenerI()
5293 public void finished()
5295 AlignFrame.this.setMenusForViewport();
5298 dbRefFetcher.fetchDBRefs(false);
5306 final AlignFrame me = this;
5307 new Thread(new Runnable()
5312 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5313 .getSequenceFetcherSingleton(me);
5314 javax.swing.SwingUtilities.invokeLater(new Runnable()
5319 String[] dbclasses = sf.getOrderedSupportedSources();
5320 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5321 // jalview.util.QuickSort.sort(otherdb, otherdb);
5322 List<DbSourceProxy> otherdb;
5323 JMenu dfetch = new JMenu();
5324 JMenu ifetch = new JMenu();
5325 JMenuItem fetchr = null;
5326 int comp = 0, icomp = 0, mcomp = 15;
5327 String mname = null;
5329 for (String dbclass : dbclasses)
5331 otherdb = sf.getSourceProxy(dbclass);
5332 // add a single entry for this class, or submenu allowing 'fetch
5334 if (otherdb == null || otherdb.size() < 1)
5338 // List<DbSourceProxy> dbs=otherdb;
5339 // otherdb=new ArrayList<DbSourceProxy>();
5340 // for (DbSourceProxy db:dbs)
5342 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5346 mname = "From " + dbclass;
5348 if (otherdb.size() == 1)
5350 final DbSourceProxy[] dassource = otherdb
5351 .toArray(new DbSourceProxy[0]);
5352 DbSourceProxy src = otherdb.get(0);
5353 fetchr = new JMenuItem(src.getDbSource());
5354 fetchr.addActionListener(new ActionListener()
5358 public void actionPerformed(ActionEvent e)
5360 new Thread(new Runnable()
5366 boolean isNucleotide = alignPanel.alignFrame
5367 .getViewport().getAlignment()
5369 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5370 alignPanel.av.getSequenceSelection(),
5371 alignPanel.alignFrame, dassource,
5372 alignPanel.alignFrame.featureSettings,
5375 .addListener(new FetchFinishedListenerI()
5378 public void finished()
5380 AlignFrame.this.setMenusForViewport();
5383 dbRefFetcher.fetchDBRefs(false);
5389 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5390 MessageManager.formatMessage(
5391 "label.fetch_retrieve_from",
5392 new Object[] { src.getDbName() })));
5398 final DbSourceProxy[] dassource = otherdb
5399 .toArray(new DbSourceProxy[0]);
5401 DbSourceProxy src = otherdb.get(0);
5402 fetchr = new JMenuItem(MessageManager.formatMessage(
5403 "label.fetch_all_param",
5404 new Object[] { src.getDbSource() }));
5405 fetchr.addActionListener(new ActionListener()
5408 public void actionPerformed(ActionEvent e)
5410 new Thread(new Runnable()
5416 boolean isNucleotide = alignPanel.alignFrame
5417 .getViewport().getAlignment()
5419 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5420 alignPanel.av.getSequenceSelection(),
5421 alignPanel.alignFrame, dassource,
5422 alignPanel.alignFrame.featureSettings,
5425 .addListener(new FetchFinishedListenerI()
5428 public void finished()
5430 AlignFrame.this.setMenusForViewport();
5433 dbRefFetcher.fetchDBRefs(false);
5439 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5440 MessageManager.formatMessage(
5441 "label.fetch_retrieve_from_all_sources",
5443 Integer.valueOf(otherdb.size())
5444 .toString(), src.getDbSource(),
5445 src.getDbName() })));
5448 // and then build the rest of the individual menus
5449 ifetch = new JMenu(MessageManager.formatMessage(
5450 "label.source_from_db_source",
5451 new Object[] { src.getDbSource() }));
5453 String imname = null;
5455 for (DbSourceProxy sproxy : otherdb)
5457 String dbname = sproxy.getDbName();
5458 String sname = dbname.length() > 5 ? dbname.substring(0,
5459 5) + "..." : dbname;
5460 String msname = dbname.length() > 10 ? dbname.substring(
5461 0, 10) + "..." : dbname;
5464 imname = MessageManager.formatMessage(
5465 "label.from_msname", new Object[] { sname });
5467 fetchr = new JMenuItem(msname);
5468 final DbSourceProxy[] dassrc = { sproxy };
5469 fetchr.addActionListener(new ActionListener()
5473 public void actionPerformed(ActionEvent e)
5475 new Thread(new Runnable()
5481 boolean isNucleotide = alignPanel.alignFrame
5482 .getViewport().getAlignment()
5484 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5485 alignPanel.av.getSequenceSelection(),
5486 alignPanel.alignFrame, dassrc,
5487 alignPanel.alignFrame.featureSettings,
5490 .addListener(new FetchFinishedListenerI()
5493 public void finished()
5495 AlignFrame.this.setMenusForViewport();
5498 dbRefFetcher.fetchDBRefs(false);
5504 fetchr.setToolTipText("<html>"
5505 + MessageManager.formatMessage(
5506 "label.fetch_retrieve_from", new Object[]
5510 if (++icomp >= mcomp || i == (otherdb.size()))
5512 ifetch.setText(MessageManager.formatMessage(
5513 "label.source_to_target", imname, sname));
5515 ifetch = new JMenu();
5523 if (comp >= mcomp || dbi >= (dbclasses.length))
5525 dfetch.setText(MessageManager.formatMessage(
5526 "label.source_to_target", mname, dbclass));
5528 dfetch = new JMenu();
5541 * Left justify the whole alignment.
5544 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5546 AlignmentI al = viewport.getAlignment();
5548 viewport.firePropertyChange("alignment", null, al);
5552 * Right justify the whole alignment.
5555 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5557 AlignmentI al = viewport.getAlignment();
5559 viewport.firePropertyChange("alignment", null, al);
5563 public void setShowSeqFeatures(boolean b)
5565 showSeqFeatures.setSelected(b);
5566 viewport.setShowSequenceFeatures(b);
5573 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5574 * awt.event.ActionEvent)
5577 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5579 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5580 alignPanel.paintAlignment(true);
5587 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5591 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5593 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5594 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5602 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5603 * .event.ActionEvent)
5606 protected void showGroupConservation_actionPerformed(ActionEvent e)
5608 viewport.setShowGroupConservation(showGroupConservation.getState());
5609 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5616 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5617 * .event.ActionEvent)
5620 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5622 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5623 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5630 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5631 * .event.ActionEvent)
5634 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5636 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5637 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5641 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5643 showSequenceLogo.setState(true);
5644 viewport.setShowSequenceLogo(true);
5645 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5646 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5650 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5652 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5659 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5660 * .event.ActionEvent)
5663 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5665 if (avc.makeGroupsFromSelection())
5667 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5668 alignPanel.updateAnnotation();
5669 alignPanel.paintAlignment(true);
5673 public void clearAlignmentSeqRep()
5675 // TODO refactor alignmentseqrep to controller
5676 if (viewport.getAlignment().hasSeqrep())
5678 viewport.getAlignment().setSeqrep(null);
5679 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5680 alignPanel.updateAnnotation();
5681 alignPanel.paintAlignment(true);
5686 protected void createGroup_actionPerformed(ActionEvent e)
5688 if (avc.createGroup())
5690 alignPanel.alignmentChanged();
5695 protected void unGroup_actionPerformed(ActionEvent e)
5699 alignPanel.alignmentChanged();
5704 * make the given alignmentPanel the currently selected tab
5706 * @param alignmentPanel
5708 public void setDisplayedView(AlignmentPanel alignmentPanel)
5710 if (!viewport.getSequenceSetId().equals(
5711 alignmentPanel.av.getSequenceSetId()))
5715 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5717 if (tabbedPane != null
5718 && tabbedPane.getTabCount() > 0
5719 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5720 .getSelectedIndex())
5722 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5727 * Action on selection of menu options to Show or Hide annotations.
5730 * @param forSequences
5731 * update sequence-related annotations
5732 * @param forAlignment
5733 * update non-sequence-related annotations
5736 protected void setAnnotationsVisibility(boolean visible,
5737 boolean forSequences, boolean forAlignment)
5739 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5740 .getAlignmentAnnotation();
5745 for (AlignmentAnnotation aa : anns)
5748 * don't display non-positional annotations on an alignment
5750 if (aa.annotations == null)
5754 boolean apply = (aa.sequenceRef == null && forAlignment)
5755 || (aa.sequenceRef != null && forSequences);
5758 aa.visible = visible;
5761 alignPanel.validateAnnotationDimensions(true);
5762 alignPanel.alignmentChanged();
5766 * Store selected annotation sort order for the view and repaint.
5769 protected void sortAnnotations_actionPerformed()
5771 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5773 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5774 alignPanel.paintAlignment(true);
5779 * @return alignment panels in this alignment frame
5781 public List<? extends AlignmentViewPanel> getAlignPanels()
5783 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5787 * Open a new alignment window, with the cDNA associated with this (protein)
5788 * alignment, aligned as is the protein.
5790 protected void viewAsCdna_actionPerformed()
5792 // TODO no longer a menu action - refactor as required
5793 final AlignmentI alignment = getViewport().getAlignment();
5794 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5795 if (mappings == null)
5799 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5800 for (SequenceI aaSeq : alignment.getSequences())
5802 for (AlignedCodonFrame acf : mappings)
5804 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5808 * There is a cDNA mapping for this protein sequence - add to new
5809 * alignment. It will share the same dataset sequence as other mapped
5810 * cDNA (no new mappings need to be created).
5812 final Sequence newSeq = new Sequence(dnaSeq);
5813 newSeq.setDatasetSequence(dnaSeq);
5814 cdnaSeqs.add(newSeq);
5818 if (cdnaSeqs.size() == 0)
5820 // show a warning dialog no mapped cDNA
5823 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5825 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5826 AlignFrame.DEFAULT_HEIGHT);
5827 cdna.alignAs(alignment);
5828 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5830 Desktop.addInternalFrame(alignFrame, newtitle,
5831 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5835 * Set visibility of dna/protein complement view (available when shown in a
5841 protected void showComplement_actionPerformed(boolean show)
5843 SplitContainerI sf = getSplitViewContainer();
5846 sf.setComplementVisible(this, show);
5851 * Generate the reverse (optionally complemented) of the selected sequences,
5852 * and add them to the alignment
5855 protected void showReverse_actionPerformed(boolean complement)
5857 AlignmentI al = null;
5860 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5861 al = dna.reverseCdna(complement);
5862 viewport.addAlignment(al, "");
5863 addHistoryItem(new EditCommand(
5864 MessageManager.getString("label.add_sequences"),
5865 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5866 viewport.getAlignment()));
5867 } catch (Exception ex)
5869 System.err.println(ex.getMessage());
5875 * Try to run a script in the Groovy console, having first ensured that this
5876 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5877 * be targeted at this alignment.
5880 protected void runGroovy_actionPerformed()
5882 Jalview.setCurrentAlignFrame(this);
5883 groovy.ui.Console console = Desktop.getGroovyConsole();
5884 if (console != null)
5888 console.runScript();
5889 } catch (Exception ex)
5891 System.err.println((ex.toString()));
5893 .showInternalMessageDialog(Desktop.desktop, MessageManager
5894 .getString("label.couldnt_run_groovy_script"),
5896 .getString("label.groovy_support_failed"),
5897 JOptionPane.ERROR_MESSAGE);
5902 System.err.println("Can't run Groovy script as console not found");
5907 * Hides columns containing (or not containing) a specified feature, provided
5908 * that would not leave all columns hidden
5910 * @param featureType
5911 * @param columnsContaining
5914 public boolean hideFeatureColumns(String featureType,
5915 boolean columnsContaining)
5917 boolean notForHiding = avc.markColumnsContainingFeatures(
5918 columnsContaining, false, false, featureType);
5921 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5922 false, featureType))
5924 getViewport().hideSelectedColumns();
5932 class PrintThread extends Thread
5936 public PrintThread(AlignmentPanel ap)
5941 static PageFormat pf;
5946 PrinterJob printJob = PrinterJob.getPrinterJob();
5950 printJob.setPrintable(ap, pf);
5954 printJob.setPrintable(ap);
5957 if (printJob.printDialog())
5962 } catch (Exception PrintException)
5964 PrintException.printStackTrace();