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.DataSourceType;
67 import jalview.io.FileFormat;
68 import jalview.io.FileFormatI;
69 import jalview.io.FileFormats;
70 import jalview.io.FileLoader;
71 import jalview.io.FormatAdapter;
72 import jalview.io.HtmlSvgOutput;
73 import jalview.io.IdentifyFile;
74 import jalview.io.JPredFile;
75 import jalview.io.JalviewFileChooser;
76 import jalview.io.JalviewFileView;
77 import jalview.io.JnetAnnotationMaker;
78 import jalview.io.NewickFile;
79 import jalview.io.TCoffeeScoreFile;
80 import jalview.jbgui.GAlignFrame;
81 import jalview.schemes.Blosum62ColourScheme;
82 import jalview.schemes.BuriedColourScheme;
83 import jalview.schemes.ClustalxColourScheme;
84 import jalview.schemes.ColourSchemeI;
85 import jalview.schemes.ColourSchemeProperty;
86 import jalview.schemes.HelixColourScheme;
87 import jalview.schemes.HydrophobicColourScheme;
88 import jalview.schemes.NucleotideColourScheme;
89 import jalview.schemes.PIDColourScheme;
90 import jalview.schemes.PurinePyrimidineColourScheme;
91 import jalview.schemes.RNAHelicesColourChooser;
92 import jalview.schemes.ResidueProperties;
93 import jalview.schemes.StrandColourScheme;
94 import jalview.schemes.TCoffeeColourScheme;
95 import jalview.schemes.TaylorColourScheme;
96 import jalview.schemes.TurnColourScheme;
97 import jalview.schemes.UserColourScheme;
98 import jalview.schemes.ZappoColourScheme;
99 import jalview.util.MessageManager;
100 import jalview.viewmodel.AlignmentViewport;
101 import jalview.ws.DBRefFetcher;
102 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
103 import jalview.ws.jws1.Discoverer;
104 import jalview.ws.jws2.Jws2Discoverer;
105 import jalview.ws.jws2.jabaws2.Jws2Instance;
106 import jalview.ws.seqfetcher.DbSourceProxy;
108 import java.awt.BorderLayout;
109 import java.awt.Component;
110 import java.awt.Rectangle;
111 import java.awt.Toolkit;
112 import java.awt.datatransfer.Clipboard;
113 import java.awt.datatransfer.DataFlavor;
114 import java.awt.datatransfer.StringSelection;
115 import java.awt.datatransfer.Transferable;
116 import java.awt.dnd.DnDConstants;
117 import java.awt.dnd.DropTargetDragEvent;
118 import java.awt.dnd.DropTargetDropEvent;
119 import java.awt.dnd.DropTargetEvent;
120 import java.awt.dnd.DropTargetListener;
121 import java.awt.event.ActionEvent;
122 import java.awt.event.ActionListener;
123 import java.awt.event.FocusAdapter;
124 import java.awt.event.FocusEvent;
125 import java.awt.event.ItemEvent;
126 import java.awt.event.ItemListener;
127 import java.awt.event.KeyAdapter;
128 import java.awt.event.KeyEvent;
129 import java.awt.event.MouseAdapter;
130 import java.awt.event.MouseEvent;
131 import java.awt.print.PageFormat;
132 import java.awt.print.PrinterJob;
133 import java.beans.PropertyChangeEvent;
135 import java.io.FileWriter;
136 import java.io.PrintWriter;
138 import java.util.ArrayList;
139 import java.util.Arrays;
140 import java.util.Deque;
141 import java.util.Enumeration;
142 import java.util.Hashtable;
143 import java.util.List;
144 import java.util.Vector;
146 import javax.swing.JCheckBoxMenuItem;
147 import javax.swing.JEditorPane;
148 import javax.swing.JInternalFrame;
149 import javax.swing.JLayeredPane;
150 import javax.swing.JMenu;
151 import javax.swing.JMenuItem;
152 import javax.swing.JRadioButtonMenuItem;
153 import javax.swing.JScrollPane;
154 import javax.swing.SwingUtilities;
160 * @version $Revision$
162 public class AlignFrame extends GAlignFrame implements DropTargetListener,
163 IProgressIndicator, AlignViewControllerGuiI
166 public static final int DEFAULT_WIDTH = 700;
168 public static final int DEFAULT_HEIGHT = 500;
171 * The currently displayed panel (selected tabbed view if more than one)
173 public AlignmentPanel alignPanel;
175 AlignViewport viewport;
177 public AlignViewControllerI avc;
179 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
182 * Last format used to load or save alignments in this window
184 FileFormatI currentFileFormat = null;
187 * Current filename for this alignment
189 String fileName = null;
192 * Creates a new AlignFrame object with specific width and height.
198 public AlignFrame(AlignmentI al, int width, int height)
200 this(al, null, width, height);
204 * Creates a new AlignFrame object with specific width, height and
210 * @param sequenceSetId
212 public AlignFrame(AlignmentI al, int width, int height,
213 String sequenceSetId)
215 this(al, null, width, height, sequenceSetId);
219 * Creates a new AlignFrame object with specific width, height and
225 * @param sequenceSetId
228 public AlignFrame(AlignmentI al, int width, int height,
229 String sequenceSetId, String viewId)
231 this(al, null, width, height, sequenceSetId, viewId);
235 * new alignment window with hidden columns
239 * @param hiddenColumns
240 * ColumnSelection or null
242 * Width of alignment frame
246 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
247 int width, int height)
249 this(al, hiddenColumns, width, height, null);
253 * Create alignment frame for al with hiddenColumns, a specific width and
254 * height, and specific sequenceId
257 * @param hiddenColumns
260 * @param sequenceSetId
263 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
264 int width, int height, String sequenceSetId)
266 this(al, hiddenColumns, width, height, sequenceSetId, null);
270 * Create alignment frame for al with hiddenColumns, a specific width and
271 * height, and specific sequenceId
274 * @param hiddenColumns
277 * @param sequenceSetId
282 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
283 int width, int height, String sequenceSetId, String viewId)
285 setSize(width, height);
287 if (al.getDataset() == null)
292 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
294 alignPanel = new AlignmentPanel(this, viewport);
296 addAlignmentPanel(alignPanel, true);
300 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
301 ColumnSelection hiddenColumns, int width, int height)
303 setSize(width, height);
305 if (al.getDataset() == null)
310 viewport = new AlignViewport(al, hiddenColumns);
312 if (hiddenSeqs != null && hiddenSeqs.length > 0)
314 viewport.hideSequence(hiddenSeqs);
316 alignPanel = new AlignmentPanel(this, viewport);
317 addAlignmentPanel(alignPanel, true);
322 * Make a new AlignFrame from existing alignmentPanels
329 public AlignFrame(AlignmentPanel ap)
333 addAlignmentPanel(ap, false);
338 * initalise the alignframe from the underlying viewport data and the
343 if (!Jalview.isHeadlessMode())
345 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
348 avc = new jalview.controller.AlignViewController(this, viewport,
350 if (viewport.getAlignmentConservationAnnotation() == null)
352 BLOSUM62Colour.setEnabled(false);
353 conservationMenuItem.setEnabled(false);
354 modifyConservation.setEnabled(false);
355 // PIDColour.setEnabled(false);
356 // abovePIDThreshold.setEnabled(false);
357 // modifyPID.setEnabled(false);
360 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
363 if (sortby.equals("Id"))
365 sortIDMenuItem_actionPerformed(null);
367 else if (sortby.equals("Pairwise Identity"))
369 sortPairwiseMenuItem_actionPerformed(null);
372 if (Desktop.desktop != null)
374 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
375 addServiceListeners();
376 setGUINucleotide(viewport.getAlignment().isNucleotide());
380 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
382 setMenusFromViewport(viewport);
383 buildSortByAnnotationScoresMenu();
386 if (viewport.getWrapAlignment())
388 wrapMenuItem_actionPerformed(null);
391 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
393 this.overviewMenuItem_actionPerformed(null);
398 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
399 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
400 final String menuLabel = MessageManager
401 .getString("label.copy_format_from");
402 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
403 new ViewSetProvider()
407 public AlignmentPanel[] getAllAlignmentPanels()
410 origview.add(alignPanel);
411 // make an array of all alignment panels except for this one
412 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
413 Arrays.asList(Desktop.getAlignmentPanels(null)));
414 aps.remove(AlignFrame.this.alignPanel);
415 return aps.toArray(new AlignmentPanel[aps.size()]);
417 }, selviews, new ItemListener()
421 public void itemStateChanged(ItemEvent e)
423 if (origview.size() > 0)
425 final AlignmentPanel ap = origview.get(0);
428 * Copy the ViewStyle of the selected panel to 'this one'.
429 * Don't change value of 'scaleProteinAsCdna' unless copying
432 ViewStyleI vs = selviews.get(0).getAlignViewport()
434 boolean fromSplitFrame = selviews.get(0)
435 .getAlignViewport().getCodingComplement() != null;
438 vs.setScaleProteinAsCdna(ap.getAlignViewport()
439 .getViewStyle().isScaleProteinAsCdna());
441 ap.getAlignViewport().setViewStyle(vs);
444 * Also rescale ViewStyle of SplitFrame complement if there is
445 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
446 * the whole ViewStyle (allow cDNA protein to have different
449 AlignViewportI complement = ap.getAlignViewport()
450 .getCodingComplement();
451 if (complement != null && vs.isScaleProteinAsCdna())
453 AlignFrame af = Desktop.getAlignFrameFor(complement);
454 ((SplitFrame) af.getSplitViewContainer())
456 af.setMenusForViewport();
460 ap.setSelected(true);
461 ap.alignFrame.setMenusForViewport();
466 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
467 .indexOf("devel") > -1
468 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
469 .indexOf("test") > -1)
471 formatMenu.add(vsel);
473 addFocusListener(new FocusAdapter()
476 public void focusGained(FocusEvent e)
478 Jalview.setCurrentAlignFrame(AlignFrame.this);
485 * Change the filename and format for the alignment, and enable the 'reload'
486 * button functionality.
493 public void setFileName(String file, FileFormatI format)
496 setFileFormat(format);
497 reload.setEnabled(true);
501 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
504 void addKeyListener()
506 addKeyListener(new KeyAdapter()
509 public void keyPressed(KeyEvent evt)
511 if (viewport.cursorMode
512 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
513 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
514 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
515 && Character.isDigit(evt.getKeyChar()))
517 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
520 switch (evt.getKeyCode())
523 case 27: // escape key
524 deselectAllSequenceMenuItem_actionPerformed(null);
528 case KeyEvent.VK_DOWN:
529 if (evt.isAltDown() || !viewport.cursorMode)
531 moveSelectedSequences(false);
533 if (viewport.cursorMode)
535 alignPanel.getSeqPanel().moveCursor(0, 1);
540 if (evt.isAltDown() || !viewport.cursorMode)
542 moveSelectedSequences(true);
544 if (viewport.cursorMode)
546 alignPanel.getSeqPanel().moveCursor(0, -1);
551 case KeyEvent.VK_LEFT:
552 if (evt.isAltDown() || !viewport.cursorMode)
554 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
558 alignPanel.getSeqPanel().moveCursor(-1, 0);
563 case KeyEvent.VK_RIGHT:
564 if (evt.isAltDown() || !viewport.cursorMode)
566 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
570 alignPanel.getSeqPanel().moveCursor(1, 0);
574 case KeyEvent.VK_SPACE:
575 if (viewport.cursorMode)
577 alignPanel.getSeqPanel().insertGapAtCursor(
578 evt.isControlDown() || evt.isShiftDown()
583 // case KeyEvent.VK_A:
584 // if (viewport.cursorMode)
586 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
587 // //System.out.println("A");
591 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
592 * System.out.println("closing bracket"); } break;
594 case KeyEvent.VK_DELETE:
595 case KeyEvent.VK_BACK_SPACE:
596 if (!viewport.cursorMode)
598 cut_actionPerformed(null);
602 alignPanel.getSeqPanel().deleteGapAtCursor(
603 evt.isControlDown() || evt.isShiftDown()
610 if (viewport.cursorMode)
612 alignPanel.getSeqPanel().setCursorRow();
616 if (viewport.cursorMode && !evt.isControlDown())
618 alignPanel.getSeqPanel().setCursorColumn();
622 if (viewport.cursorMode)
624 alignPanel.getSeqPanel().setCursorPosition();
628 case KeyEvent.VK_ENTER:
629 case KeyEvent.VK_COMMA:
630 if (viewport.cursorMode)
632 alignPanel.getSeqPanel().setCursorRowAndColumn();
637 if (viewport.cursorMode)
639 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
643 if (viewport.cursorMode)
645 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
650 viewport.cursorMode = !viewport.cursorMode;
651 statusBar.setText(MessageManager.formatMessage(
652 "label.keyboard_editing_mode",
653 new String[] { (viewport.cursorMode ? "on" : "off") }));
654 if (viewport.cursorMode)
656 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
657 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
659 alignPanel.getSeqPanel().seqCanvas.repaint();
665 Help.showHelpWindow();
666 } catch (Exception ex)
668 ex.printStackTrace();
673 boolean toggleSeqs = !evt.isControlDown();
674 boolean toggleCols = !evt.isShiftDown();
675 toggleHiddenRegions(toggleSeqs, toggleCols);
680 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
681 boolean modifyExisting = true; // always modify, don't clear
682 // evt.isShiftDown();
683 boolean invertHighlighted = evt.isAltDown();
684 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
688 case KeyEvent.VK_PAGE_UP:
689 if (viewport.getWrapAlignment())
691 alignPanel.scrollUp(true);
695 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
696 - viewport.endSeq + viewport.startSeq);
699 case KeyEvent.VK_PAGE_DOWN:
700 if (viewport.getWrapAlignment())
702 alignPanel.scrollUp(false);
706 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
707 + viewport.endSeq - viewport.startSeq);
714 public void keyReleased(KeyEvent evt)
716 switch (evt.getKeyCode())
718 case KeyEvent.VK_LEFT:
719 if (evt.isAltDown() || !viewport.cursorMode)
721 viewport.firePropertyChange("alignment", null, viewport
722 .getAlignment().getSequences());
726 case KeyEvent.VK_RIGHT:
727 if (evt.isAltDown() || !viewport.cursorMode)
729 viewport.firePropertyChange("alignment", null, viewport
730 .getAlignment().getSequences());
738 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
740 ap.alignFrame = this;
741 avc = new jalview.controller.AlignViewController(this, viewport,
746 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
748 int aSize = alignPanels.size();
750 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
752 if (aSize == 1 && ap.av.viewName == null)
754 this.getContentPane().add(ap, BorderLayout.CENTER);
760 setInitialTabVisible();
763 expandViews.setEnabled(true);
764 gatherViews.setEnabled(true);
765 tabbedPane.addTab(ap.av.viewName, ap);
767 ap.setVisible(false);
772 if (ap.av.isPadGaps())
774 ap.av.getAlignment().padGaps();
776 ap.av.updateConservation(ap);
777 ap.av.updateConsensus(ap);
778 ap.av.updateStrucConsensus(ap);
782 public void setInitialTabVisible()
784 expandViews.setEnabled(true);
785 gatherViews.setEnabled(true);
786 tabbedPane.setVisible(true);
787 AlignmentPanel first = alignPanels.get(0);
788 tabbedPane.addTab(first.av.viewName, first);
789 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
792 public AlignViewport getViewport()
797 /* Set up intrinsic listeners for dynamically generated GUI bits. */
798 private void addServiceListeners()
800 final java.beans.PropertyChangeListener thisListener;
801 Desktop.instance.addJalviewPropertyChangeListener("services",
802 thisListener = new java.beans.PropertyChangeListener()
805 public void propertyChange(PropertyChangeEvent evt)
807 // // System.out.println("Discoverer property change.");
808 // if (evt.getPropertyName().equals("services"))
810 SwingUtilities.invokeLater(new Runnable()
817 .println("Rebuild WS Menu for service change");
818 BuildWebServiceMenu();
825 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
828 public void internalFrameClosed(
829 javax.swing.event.InternalFrameEvent evt)
831 // System.out.println("deregistering discoverer listener");
832 Desktop.instance.removeJalviewPropertyChangeListener("services",
834 closeMenuItem_actionPerformed(true);
837 // Finally, build the menu once to get current service state
838 new Thread(new Runnable()
843 BuildWebServiceMenu();
849 * Configure menu items that vary according to whether the alignment is
850 * nucleotide or protein
854 public void setGUINucleotide(boolean nucleotide)
856 showTranslation.setVisible(nucleotide);
857 showReverse.setVisible(nucleotide);
858 showReverseComplement.setVisible(nucleotide);
859 conservationMenuItem.setEnabled(!nucleotide);
860 modifyConservation.setEnabled(!nucleotide);
861 showGroupConservation.setEnabled(!nucleotide);
862 rnahelicesColour.setEnabled(nucleotide);
863 nucleotideColour.setEnabled(nucleotide);
864 purinePyrimidineColour.setEnabled(nucleotide);
865 RNAInteractionColour.setEnabled(nucleotide);
866 showComplementMenuItem.setText(nucleotide ? MessageManager
867 .getString("label.protein") : MessageManager
868 .getString("label.nucleotide"));
869 setColourSelected(jalview.bin.Cache.getDefault(
870 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
871 : Preferences.DEFAULT_COLOUR_PROT, "None"));
875 * set up menus for the current viewport. This may be called after any
876 * operation that affects the data in the current view (selection changed,
877 * etc) to update the menus to reflect the new state.
880 public void setMenusForViewport()
882 setMenusFromViewport(viewport);
886 * Need to call this method when tabs are selected for multiple views, or when
887 * loading from Jalview2XML.java
892 void setMenusFromViewport(AlignViewport av)
894 padGapsMenuitem.setSelected(av.isPadGaps());
895 colourTextMenuItem.setSelected(av.isShowColourText());
896 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
897 modifyPID.setEnabled(abovePIDThreshold.isSelected());
898 conservationMenuItem.setSelected(av.getConservationSelected());
899 modifyConservation.setEnabled(conservationMenuItem.isSelected());
900 seqLimits.setSelected(av.getShowJVSuffix());
901 idRightAlign.setSelected(av.isRightAlignIds());
902 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
903 renderGapsMenuItem.setSelected(av.isRenderGaps());
904 wrapMenuItem.setSelected(av.getWrapAlignment());
905 scaleAbove.setVisible(av.getWrapAlignment());
906 scaleLeft.setVisible(av.getWrapAlignment());
907 scaleRight.setVisible(av.getWrapAlignment());
908 annotationPanelMenuItem.setState(av.isShowAnnotation());
910 * Show/hide annotations only enabled if annotation panel is shown
912 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
913 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
914 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
915 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
916 viewBoxesMenuItem.setSelected(av.getShowBoxes());
917 viewTextMenuItem.setSelected(av.getShowText());
918 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
919 showGroupConsensus.setSelected(av.isShowGroupConsensus());
920 showGroupConservation.setSelected(av.isShowGroupConservation());
921 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
922 showSequenceLogo.setSelected(av.isShowSequenceLogo());
923 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
925 setColourSelected(ColourSchemeProperty.getColourName(av
926 .getGlobalColourScheme()));
928 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
929 hiddenMarkers.setState(av.getShowHiddenMarkers());
930 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
931 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
932 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
933 autoCalculate.setSelected(av.autoCalculateConsensus);
934 sortByTree.setSelected(av.sortByTree);
935 listenToViewSelections.setSelected(av.followSelection);
936 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
938 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
940 showProducts.setEnabled(canShowProducts());
941 setGroovyEnabled(Desktop.getGroovyConsole() != null);
947 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
951 public void setGroovyEnabled(boolean b)
953 runGroovy.setEnabled(b);
956 private IProgressIndicator progressBar;
961 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
964 public void setProgressBar(String message, long id)
966 progressBar.setProgressBar(message, id);
970 public void registerHandler(final long id,
971 final IProgressIndicatorHandler handler)
973 progressBar.registerHandler(id, handler);
978 * @return true if any progress bars are still active
981 public boolean operationInProgress()
983 return progressBar.operationInProgress();
987 public void setStatus(String text)
989 statusBar.setText(text);
993 * Added so Castor Mapping file can obtain Jalview Version
995 public String getVersion()
997 return jalview.bin.Cache.getProperty("VERSION");
1000 public FeatureRenderer getFeatureRenderer()
1002 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1006 public void fetchSequence_actionPerformed(ActionEvent e)
1008 new jalview.gui.SequenceFetcher(this);
1012 public void addFromFile_actionPerformed(ActionEvent e)
1014 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1018 public void reload_actionPerformed(ActionEvent e)
1020 if (fileName != null)
1022 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1023 // originating file's format
1024 // TODO: work out how to recover feature settings for correct view(s) when
1025 // file is reloaded.
1026 if (FileFormat.Jalview.equals(currentFileFormat))
1028 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1029 for (int i = 0; i < frames.length; i++)
1031 if (frames[i] instanceof AlignFrame && frames[i] != this
1032 && ((AlignFrame) frames[i]).fileName != null
1033 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1037 frames[i].setSelected(true);
1038 Desktop.instance.closeAssociatedWindows();
1039 } catch (java.beans.PropertyVetoException ex)
1045 Desktop.instance.closeAssociatedWindows();
1047 FileLoader loader = new FileLoader();
1048 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1049 : DataSourceType.FILE;
1050 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1054 Rectangle bounds = this.getBounds();
1056 FileLoader loader = new FileLoader();
1057 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1058 : DataSourceType.FILE;
1059 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1060 protocol, currentFileFormat);
1062 newframe.setBounds(bounds);
1063 if (featureSettings != null && featureSettings.isShowing())
1065 final Rectangle fspos = featureSettings.frame.getBounds();
1066 // TODO: need a 'show feature settings' function that takes bounds -
1067 // need to refactor Desktop.addFrame
1068 newframe.featureSettings_actionPerformed(null);
1069 final FeatureSettings nfs = newframe.featureSettings;
1070 SwingUtilities.invokeLater(new Runnable()
1075 nfs.frame.setBounds(fspos);
1078 this.featureSettings.close();
1079 this.featureSettings = null;
1081 this.closeMenuItem_actionPerformed(true);
1087 public void addFromText_actionPerformed(ActionEvent e)
1089 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1094 public void addFromURL_actionPerformed(ActionEvent e)
1096 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1100 public void save_actionPerformed(ActionEvent e)
1102 if (fileName == null || (currentFileFormat == null)
1103 || fileName.startsWith("http"))
1105 saveAs_actionPerformed(null);
1109 saveAlignment(fileName, currentFileFormat);
1120 public void saveAs_actionPerformed(ActionEvent e)
1122 String format = currentFileFormat == null ? null : currentFileFormat
1124 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1125 Cache.getProperty("LAST_DIRECTORY"), format);
1127 chooser.setFileView(new JalviewFileView());
1128 chooser.setDialogTitle(MessageManager
1129 .getString("label.save_alignment_to_file"));
1130 chooser.setToolTipText(MessageManager.getString("action.save"));
1132 int value = chooser.showSaveDialog(this);
1134 if (value == JalviewFileChooser.APPROVE_OPTION)
1136 currentFileFormat = chooser.getSelectedFormat();
1137 while (currentFileFormat == null)
1140 .showInternalMessageDialog(
1143 .getString("label.select_file_format_before_saving"),
1145 .getString("label.file_format_not_specified"),
1146 JvOptionPane.WARNING_MESSAGE);
1147 currentFileFormat = chooser.getSelectedFormat();
1148 value = chooser.showSaveDialog(this);
1149 if (value != JalviewFileChooser.APPROVE_OPTION)
1155 fileName = chooser.getSelectedFile().getPath();
1157 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1159 Cache.setProperty("LAST_DIRECTORY", fileName);
1160 saveAlignment(fileName, currentFileFormat);
1164 public boolean saveAlignment(String file, FileFormatI format)
1166 boolean success = true;
1168 if (FileFormat.Jalview.equals(format))
1170 String shortName = title;
1172 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1174 shortName = shortName.substring(shortName
1175 .lastIndexOf(java.io.File.separatorChar) + 1);
1178 success = new Jalview2XML().saveAlignment(this, file, shortName);
1180 statusBar.setText(MessageManager.formatMessage(
1181 "label.successfully_saved_to_file_in_format", new Object[] {
1182 fileName, format }));
1187 AlignmentExportData exportData = getAlignmentForExport(format,
1189 if (exportData.getSettings().isCancelled())
1193 FormatAdapter f = new FormatAdapter(alignPanel,
1194 exportData.getSettings());
1195 String output = f.formatSequences(
1197 exportData.getAlignment(), // class cast exceptions will
1198 // occur in the distant future
1199 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1200 f.getCacheSuffixDefault(format),
1201 viewport.getColumnSelection());
1211 PrintWriter out = new PrintWriter(new FileWriter(file));
1215 this.setTitle(file);
1216 statusBar.setText(MessageManager.formatMessage(
1217 "label.successfully_saved_to_file_in_format",
1218 new Object[] { fileName, format.getName() }));
1219 } catch (Exception ex)
1222 ex.printStackTrace();
1229 JvOptionPane.showInternalMessageDialog(this, MessageManager
1230 .formatMessage("label.couldnt_save_file",
1231 new Object[] { fileName }), MessageManager
1232 .getString("label.error_saving_file"),
1233 JvOptionPane.WARNING_MESSAGE);
1239 private void warningMessage(String warning, String title)
1241 if (new jalview.util.Platform().isHeadless())
1243 System.err.println("Warning: " + title + "\nWarning: " + warning);
1248 JvOptionPane.showInternalMessageDialog(this, warning, title,
1249 JvOptionPane.WARNING_MESSAGE);
1261 protected void outputText_actionPerformed(ActionEvent e)
1263 FileFormatI fileFormat = FileFormats.getInstance().forName(
1264 e.getActionCommand());
1265 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1267 if (exportData.getSettings().isCancelled())
1271 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1272 cap.setForInput(null);
1275 FileFormatI format = fileFormat;
1276 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1277 .formatSequences(format,
1278 exportData.getAlignment(),
1279 exportData.getOmitHidden(),
1280 exportData.getStartEndPostions(),
1281 viewport.getColumnSelection()));
1282 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1283 "label.alignment_output_command",
1284 new Object[] { e.getActionCommand() }), 600, 500);
1285 } catch (OutOfMemoryError oom)
1287 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1293 public static AlignmentExportData getAlignmentForExport(
1294 FileFormatI format, AlignViewportI viewport,
1295 AlignExportSettingI exportSettings)
1297 AlignmentI alignmentToExport = null;
1298 AlignExportSettingI settings = exportSettings;
1299 String[] omitHidden = null;
1301 HiddenSequences hiddenSeqs = viewport.getAlignment()
1302 .getHiddenSequences();
1304 alignmentToExport = viewport.getAlignment();
1306 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1307 if (settings == null)
1309 settings = new AlignExportSettings(hasHiddenSeqs,
1310 viewport.hasHiddenColumns(), format);
1312 // settings.isExportAnnotations();
1314 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1316 omitHidden = viewport.getViewAsString(false,
1317 settings.isExportHiddenSequences());
1320 int[] alignmentStartEnd = new int[2];
1321 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1323 alignmentToExport = hiddenSeqs.getFullAlignment();
1327 alignmentToExport = viewport.getAlignment();
1329 alignmentStartEnd = alignmentToExport
1330 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1331 .getHiddenColumns());
1332 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1333 omitHidden, alignmentStartEnd, settings);
1344 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1346 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1347 htmlSVG.exportHTML(null);
1351 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1353 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1354 bjs.exportHTML(null);
1357 public void createImageMap(File file, String image)
1359 alignPanel.makePNGImageMap(file, image);
1369 public void createPNG(File f)
1371 alignPanel.makePNG(f);
1381 public void createEPS(File f)
1383 alignPanel.makeEPS(f);
1387 public void createSVG(File f)
1389 alignPanel.makeSVG(f);
1393 public void pageSetup_actionPerformed(ActionEvent e)
1395 PrinterJob printJob = PrinterJob.getPrinterJob();
1396 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1406 public void printMenuItem_actionPerformed(ActionEvent e)
1408 // Putting in a thread avoids Swing painting problems
1409 PrintThread thread = new PrintThread(alignPanel);
1414 public void exportFeatures_actionPerformed(ActionEvent e)
1416 new AnnotationExporter().exportFeatures(alignPanel);
1420 public void exportAnnotations_actionPerformed(ActionEvent e)
1422 new AnnotationExporter().exportAnnotations(alignPanel);
1426 public void associatedData_actionPerformed(ActionEvent e)
1428 // Pick the tree file
1429 JalviewFileChooser chooser = new JalviewFileChooser(
1430 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1431 chooser.setFileView(new JalviewFileView());
1432 chooser.setDialogTitle(MessageManager
1433 .getString("label.load_jalview_annotations"));
1434 chooser.setToolTipText(MessageManager
1435 .getString("label.load_jalview_annotations"));
1437 int value = chooser.showOpenDialog(null);
1439 if (value == JalviewFileChooser.APPROVE_OPTION)
1441 String choice = chooser.getSelectedFile().getPath();
1442 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1443 loadJalviewDataFile(choice, null, null, null);
1449 * Close the current view or all views in the alignment frame. If the frame
1450 * only contains one view then the alignment will be removed from memory.
1452 * @param closeAllTabs
1455 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1457 if (alignPanels != null && alignPanels.size() < 2)
1459 closeAllTabs = true;
1464 if (alignPanels != null)
1468 if (this.isClosed())
1470 // really close all the windows - otherwise wait till
1471 // setClosed(true) is called
1472 for (int i = 0; i < alignPanels.size(); i++)
1474 AlignmentPanel ap = alignPanels.get(i);
1481 closeView(alignPanel);
1488 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1489 * be called recursively, with the frame now in 'closed' state
1491 this.setClosed(true);
1493 } catch (Exception ex)
1495 ex.printStackTrace();
1500 * Close the specified panel and close up tabs appropriately.
1502 * @param panelToClose
1504 public void closeView(AlignmentPanel panelToClose)
1506 int index = tabbedPane.getSelectedIndex();
1507 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1508 alignPanels.remove(panelToClose);
1509 panelToClose.closePanel();
1510 panelToClose = null;
1512 tabbedPane.removeTabAt(closedindex);
1513 tabbedPane.validate();
1515 if (index > closedindex || index == tabbedPane.getTabCount())
1517 // modify currently selected tab index if necessary.
1521 this.tabSelectionChanged(index);
1527 void updateEditMenuBar()
1530 if (viewport.getHistoryList().size() > 0)
1532 undoMenuItem.setEnabled(true);
1533 CommandI command = viewport.getHistoryList().peek();
1534 undoMenuItem.setText(MessageManager.formatMessage(
1535 "label.undo_command",
1536 new Object[] { command.getDescription() }));
1540 undoMenuItem.setEnabled(false);
1541 undoMenuItem.setText(MessageManager.getString("action.undo"));
1544 if (viewport.getRedoList().size() > 0)
1546 redoMenuItem.setEnabled(true);
1548 CommandI command = viewport.getRedoList().peek();
1549 redoMenuItem.setText(MessageManager.formatMessage(
1550 "label.redo_command",
1551 new Object[] { command.getDescription() }));
1555 redoMenuItem.setEnabled(false);
1556 redoMenuItem.setText(MessageManager.getString("action.redo"));
1561 public void addHistoryItem(CommandI command)
1563 if (command.getSize() > 0)
1565 viewport.addToHistoryList(command);
1566 viewport.clearRedoList();
1567 updateEditMenuBar();
1568 viewport.updateHiddenColumns();
1569 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1570 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1571 // viewport.getColumnSelection()
1572 // .getHiddenColumns().size() > 0);
1578 * @return alignment objects for all views
1580 AlignmentI[] getViewAlignments()
1582 if (alignPanels != null)
1584 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1586 for (AlignmentPanel ap : alignPanels)
1588 als[i++] = ap.av.getAlignment();
1592 if (viewport != null)
1594 return new AlignmentI[] { viewport.getAlignment() };
1606 protected void undoMenuItem_actionPerformed(ActionEvent e)
1608 if (viewport.getHistoryList().isEmpty())
1612 CommandI command = viewport.getHistoryList().pop();
1613 viewport.addToRedoList(command);
1614 command.undoCommand(getViewAlignments());
1616 AlignmentViewport originalSource = getOriginatingSource(command);
1617 updateEditMenuBar();
1619 if (originalSource != null)
1621 if (originalSource != viewport)
1624 .warn("Implementation worry: mismatch of viewport origin for undo");
1626 originalSource.updateHiddenColumns();
1627 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1629 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1630 // viewport.getColumnSelection()
1631 // .getHiddenColumns().size() > 0);
1632 originalSource.firePropertyChange("alignment", null, originalSource
1633 .getAlignment().getSequences());
1644 protected void redoMenuItem_actionPerformed(ActionEvent e)
1646 if (viewport.getRedoList().size() < 1)
1651 CommandI command = viewport.getRedoList().pop();
1652 viewport.addToHistoryList(command);
1653 command.doCommand(getViewAlignments());
1655 AlignmentViewport originalSource = getOriginatingSource(command);
1656 updateEditMenuBar();
1658 if (originalSource != null)
1661 if (originalSource != viewport)
1664 .warn("Implementation worry: mismatch of viewport origin for redo");
1666 originalSource.updateHiddenColumns();
1667 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1669 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1670 // viewport.getColumnSelection()
1671 // .getHiddenColumns().size() > 0);
1672 originalSource.firePropertyChange("alignment", null, originalSource
1673 .getAlignment().getSequences());
1677 AlignmentViewport getOriginatingSource(CommandI command)
1679 AlignmentViewport originalSource = null;
1680 // For sequence removal and addition, we need to fire
1681 // the property change event FROM the viewport where the
1682 // original alignment was altered
1683 AlignmentI al = null;
1684 if (command instanceof EditCommand)
1686 EditCommand editCommand = (EditCommand) command;
1687 al = editCommand.getAlignment();
1688 List<Component> comps = PaintRefresher.components.get(viewport
1689 .getSequenceSetId());
1691 for (Component comp : comps)
1693 if (comp instanceof AlignmentPanel)
1695 if (al == ((AlignmentPanel) comp).av.getAlignment())
1697 originalSource = ((AlignmentPanel) comp).av;
1704 if (originalSource == null)
1706 // The original view is closed, we must validate
1707 // the current view against the closed view first
1710 PaintRefresher.validateSequences(al, viewport.getAlignment());
1713 originalSource = viewport;
1716 return originalSource;
1725 public void moveSelectedSequences(boolean up)
1727 SequenceGroup sg = viewport.getSelectionGroup();
1733 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1734 viewport.getHiddenRepSequences(), up);
1735 alignPanel.paintAlignment(true);
1738 synchronized void slideSequences(boolean right, int size)
1740 List<SequenceI> sg = new ArrayList<SequenceI>();
1741 if (viewport.cursorMode)
1743 sg.add(viewport.getAlignment().getSequenceAt(
1744 alignPanel.getSeqPanel().seqCanvas.cursorY));
1746 else if (viewport.getSelectionGroup() != null
1747 && viewport.getSelectionGroup().getSize() != viewport
1748 .getAlignment().getHeight())
1750 sg = viewport.getSelectionGroup().getSequences(
1751 viewport.getHiddenRepSequences());
1759 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1761 for (SequenceI seq : viewport.getAlignment().getSequences())
1763 if (!sg.contains(seq))
1765 invertGroup.add(seq);
1769 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1771 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1772 for (int i = 0; i < invertGroup.size(); i++)
1774 seqs2[i] = invertGroup.get(i);
1777 SlideSequencesCommand ssc;
1780 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1781 size, viewport.getGapCharacter());
1785 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1786 size, viewport.getGapCharacter());
1789 int groupAdjustment = 0;
1790 if (ssc.getGapsInsertedBegin() && right)
1792 if (viewport.cursorMode)
1794 alignPanel.getSeqPanel().moveCursor(size, 0);
1798 groupAdjustment = size;
1801 else if (!ssc.getGapsInsertedBegin() && !right)
1803 if (viewport.cursorMode)
1805 alignPanel.getSeqPanel().moveCursor(-size, 0);
1809 groupAdjustment = -size;
1813 if (groupAdjustment != 0)
1815 viewport.getSelectionGroup().setStartRes(
1816 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1817 viewport.getSelectionGroup().setEndRes(
1818 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1822 * just extend the last slide command if compatible; but not if in
1823 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1825 boolean appendHistoryItem = false;
1826 Deque<CommandI> historyList = viewport.getHistoryList();
1827 boolean inSplitFrame = getSplitViewContainer() != null;
1828 if (!inSplitFrame && historyList != null && historyList.size() > 0
1829 && historyList.peek() instanceof SlideSequencesCommand)
1831 appendHistoryItem = ssc
1832 .appendSlideCommand((SlideSequencesCommand) historyList
1836 if (!appendHistoryItem)
1838 addHistoryItem(ssc);
1851 protected void copy_actionPerformed(ActionEvent e)
1854 if (viewport.getSelectionGroup() == null)
1858 // TODO: preserve the ordering of displayed alignment annotation in any
1859 // internal paste (particularly sequence associated annotation)
1860 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1861 String[] omitHidden = null;
1863 if (viewport.hasHiddenColumns())
1865 omitHidden = viewport.getViewAsString(true);
1868 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1872 StringSelection ss = new StringSelection(output);
1876 jalview.gui.Desktop.internalCopy = true;
1877 // Its really worth setting the clipboard contents
1878 // to empty before setting the large StringSelection!!
1879 Toolkit.getDefaultToolkit().getSystemClipboard()
1880 .setContents(new StringSelection(""), null);
1882 Toolkit.getDefaultToolkit().getSystemClipboard()
1883 .setContents(ss, Desktop.instance);
1884 } catch (OutOfMemoryError er)
1886 new OOMWarning("copying region", er);
1890 ArrayList<int[]> hiddenColumns = null;
1891 if (viewport.hasHiddenColumns())
1893 hiddenColumns = new ArrayList<int[]>();
1894 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1895 .getSelectionGroup().getEndRes();
1896 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1898 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1900 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1901 region[1] - hiddenOffset });
1906 Desktop.jalviewClipboard = new Object[] { seqs,
1907 viewport.getAlignment().getDataset(), hiddenColumns };
1908 statusBar.setText(MessageManager.formatMessage(
1909 "label.copied_sequences_to_clipboard", new Object[] { Integer
1910 .valueOf(seqs.length).toString() }));
1920 protected void pasteNew_actionPerformed(ActionEvent e)
1932 protected void pasteThis_actionPerformed(ActionEvent e)
1938 * Paste contents of Jalview clipboard
1940 * @param newAlignment
1941 * true to paste to a new alignment, otherwise add to this.
1943 void paste(boolean newAlignment)
1945 boolean externalPaste = true;
1948 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1949 Transferable contents = c.getContents(this);
1951 if (contents == null)
1960 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1961 if (str.length() < 1)
1966 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1968 } catch (OutOfMemoryError er)
1970 new OOMWarning("Out of memory pasting sequences!!", er);
1974 SequenceI[] sequences;
1975 boolean annotationAdded = false;
1976 AlignmentI alignment = null;
1978 if (Desktop.jalviewClipboard != null)
1980 // The clipboard was filled from within Jalview, we must use the
1982 // And dataset from the copied alignment
1983 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1984 // be doubly sure that we create *new* sequence objects.
1985 sequences = new SequenceI[newseq.length];
1986 for (int i = 0; i < newseq.length; i++)
1988 sequences[i] = new Sequence(newseq[i]);
1990 alignment = new Alignment(sequences);
1991 externalPaste = false;
1995 // parse the clipboard as an alignment.
1996 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1998 sequences = alignment.getSequencesArray();
2002 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2008 if (Desktop.jalviewClipboard != null)
2010 // dataset is inherited
2011 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2015 // new dataset is constructed
2016 alignment.setDataset(null);
2018 alwidth = alignment.getWidth() + 1;
2022 AlignmentI pastedal = alignment; // preserve pasted alignment object
2023 // Add pasted sequences and dataset into existing alignment.
2024 alignment = viewport.getAlignment();
2025 alwidth = alignment.getWidth() + 1;
2026 // decide if we need to import sequences from an existing dataset
2027 boolean importDs = Desktop.jalviewClipboard != null
2028 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2029 // importDs==true instructs us to copy over new dataset sequences from
2030 // an existing alignment
2031 Vector newDs = (importDs) ? new Vector() : null; // used to create
2032 // minimum dataset set
2034 for (int i = 0; i < sequences.length; i++)
2038 newDs.addElement(null);
2040 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2042 if (importDs && ds != null)
2044 if (!newDs.contains(ds))
2046 newDs.setElementAt(ds, i);
2047 ds = new Sequence(ds);
2048 // update with new dataset sequence
2049 sequences[i].setDatasetSequence(ds);
2053 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2058 // copy and derive new dataset sequence
2059 sequences[i] = sequences[i].deriveSequence();
2060 alignment.getDataset().addSequence(
2061 sequences[i].getDatasetSequence());
2062 // TODO: avoid creation of duplicate dataset sequences with a
2063 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2065 alignment.addSequence(sequences[i]); // merges dataset
2069 newDs.clear(); // tidy up
2071 if (alignment.getAlignmentAnnotation() != null)
2073 for (AlignmentAnnotation alan : alignment
2074 .getAlignmentAnnotation())
2076 if (alan.graphGroup > fgroup)
2078 fgroup = alan.graphGroup;
2082 if (pastedal.getAlignmentAnnotation() != null)
2084 // Add any annotation attached to alignment.
2085 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2086 for (int i = 0; i < alann.length; i++)
2088 annotationAdded = true;
2089 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2091 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2092 if (newann.graphGroup > -1)
2094 if (newGraphGroups.size() <= newann.graphGroup
2095 || newGraphGroups.get(newann.graphGroup) == null)
2097 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2099 newGraphGroups.add(q, null);
2101 newGraphGroups.set(newann.graphGroup, new Integer(
2104 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2108 newann.padAnnotation(alwidth);
2109 alignment.addAnnotation(newann);
2119 addHistoryItem(new EditCommand(
2120 MessageManager.getString("label.add_sequences"),
2121 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2123 // Add any annotations attached to sequences
2124 for (int i = 0; i < sequences.length; i++)
2126 if (sequences[i].getAnnotation() != null)
2128 AlignmentAnnotation newann;
2129 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2131 annotationAdded = true;
2132 newann = sequences[i].getAnnotation()[a];
2133 newann.adjustForAlignment();
2134 newann.padAnnotation(alwidth);
2135 if (newann.graphGroup > -1)
2137 if (newann.graphGroup > -1)
2139 if (newGraphGroups.size() <= newann.graphGroup
2140 || newGraphGroups.get(newann.graphGroup) == null)
2142 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2144 newGraphGroups.add(q, null);
2146 newGraphGroups.set(newann.graphGroup, new Integer(
2149 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2153 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2158 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2165 // propagate alignment changed.
2166 viewport.setEndSeq(alignment.getHeight());
2167 if (annotationAdded)
2169 // Duplicate sequence annotation in all views.
2170 AlignmentI[] alview = this.getViewAlignments();
2171 for (int i = 0; i < sequences.length; i++)
2173 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2178 for (int avnum = 0; avnum < alview.length; avnum++)
2180 if (alview[avnum] != alignment)
2182 // duplicate in a view other than the one with input focus
2183 int avwidth = alview[avnum].getWidth() + 1;
2184 // this relies on sann being preserved after we
2185 // modify the sequence's annotation array for each duplication
2186 for (int a = 0; a < sann.length; a++)
2188 AlignmentAnnotation newann = new AlignmentAnnotation(
2190 sequences[i].addAlignmentAnnotation(newann);
2191 newann.padAnnotation(avwidth);
2192 alview[avnum].addAnnotation(newann); // annotation was
2193 // duplicated earlier
2194 // TODO JAL-1145 graphGroups are not updated for sequence
2195 // annotation added to several views. This may cause
2197 alview[avnum].setAnnotationIndex(newann, a);
2202 buildSortByAnnotationScoresMenu();
2204 viewport.firePropertyChange("alignment", null,
2205 alignment.getSequences());
2206 if (alignPanels != null)
2208 for (AlignmentPanel ap : alignPanels)
2210 ap.validateAnnotationDimensions(false);
2215 alignPanel.validateAnnotationDimensions(false);
2221 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2223 String newtitle = new String("Copied sequences");
2225 if (Desktop.jalviewClipboard != null
2226 && Desktop.jalviewClipboard[2] != null)
2228 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2229 for (int[] region : hc)
2231 af.viewport.hideColumns(region[0], region[1]);
2235 // >>>This is a fix for the moment, until a better solution is
2237 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2239 alignPanel.getSeqPanel().seqCanvas
2240 .getFeatureRenderer());
2242 // TODO: maintain provenance of an alignment, rather than just make the
2243 // title a concatenation of operations.
2246 if (title.startsWith("Copied sequences"))
2252 newtitle = newtitle.concat("- from " + title);
2257 newtitle = new String("Pasted sequences");
2260 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2265 } catch (Exception ex)
2267 ex.printStackTrace();
2268 System.out.println("Exception whilst pasting: " + ex);
2269 // could be anything being pasted in here
2275 protected void expand_newalign(ActionEvent e)
2279 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2280 .getAlignment(), -1);
2281 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2283 String newtitle = new String("Flanking alignment");
2285 if (Desktop.jalviewClipboard != null
2286 && Desktop.jalviewClipboard[2] != null)
2288 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2289 for (int region[] : hc)
2291 af.viewport.hideColumns(region[0], region[1]);
2295 // >>>This is a fix for the moment, until a better solution is
2297 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2299 alignPanel.getSeqPanel().seqCanvas
2300 .getFeatureRenderer());
2302 // TODO: maintain provenance of an alignment, rather than just make the
2303 // title a concatenation of operations.
2305 if (title.startsWith("Copied sequences"))
2311 newtitle = newtitle.concat("- from " + title);
2315 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2317 } catch (Exception ex)
2319 ex.printStackTrace();
2320 System.out.println("Exception whilst pasting: " + ex);
2321 // could be anything being pasted in here
2322 } catch (OutOfMemoryError oom)
2324 new OOMWarning("Viewing flanking region of alignment", oom);
2335 protected void cut_actionPerformed(ActionEvent e)
2337 copy_actionPerformed(null);
2338 delete_actionPerformed(null);
2348 protected void delete_actionPerformed(ActionEvent evt)
2351 SequenceGroup sg = viewport.getSelectionGroup();
2358 * If the cut affects all sequences, warn, remove highlighted columns
2360 if (sg.getSize() == viewport.getAlignment().getHeight())
2362 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2363 .getAlignment().getWidth()) ? true : false;
2364 if (isEntireAlignWidth)
2366 int confirm = JvOptionPane.showConfirmDialog(this,
2367 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2368 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2369 JvOptionPane.OK_CANCEL_OPTION);
2371 if (confirm == JvOptionPane.CANCEL_OPTION
2372 || confirm == JvOptionPane.CLOSED_OPTION)
2377 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2378 sg.getEndRes() + 1);
2380 SequenceI[] cut = sg.getSequences()
2381 .toArray(new SequenceI[sg.getSize()]);
2383 addHistoryItem(new EditCommand(
2384 MessageManager.getString("label.cut_sequences"), Action.CUT,
2385 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2386 viewport.getAlignment()));
2388 viewport.setSelectionGroup(null);
2389 viewport.sendSelection();
2390 viewport.getAlignment().deleteGroup(sg);
2392 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2394 if (viewport.getAlignment().getHeight() < 1)
2398 this.setClosed(true);
2399 } catch (Exception ex)
2412 protected void deleteGroups_actionPerformed(ActionEvent e)
2414 if (avc.deleteGroups())
2416 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2417 alignPanel.updateAnnotation();
2418 alignPanel.paintAlignment(true);
2429 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2431 SequenceGroup sg = new SequenceGroup();
2433 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2435 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2438 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2439 viewport.setSelectionGroup(sg);
2440 viewport.sendSelection();
2441 // JAL-2034 - should delegate to
2442 // alignPanel to decide if overview needs
2444 alignPanel.paintAlignment(false);
2445 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2455 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2457 if (viewport.cursorMode)
2459 alignPanel.getSeqPanel().keyboardNo1 = null;
2460 alignPanel.getSeqPanel().keyboardNo2 = null;
2462 viewport.setSelectionGroup(null);
2463 viewport.getColumnSelection().clear();
2464 viewport.setSelectionGroup(null);
2465 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2466 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2467 // JAL-2034 - should delegate to
2468 // alignPanel to decide if overview needs
2470 alignPanel.paintAlignment(false);
2471 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2472 viewport.sendSelection();
2482 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2484 SequenceGroup sg = viewport.getSelectionGroup();
2488 selectAllSequenceMenuItem_actionPerformed(null);
2493 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2495 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2497 // JAL-2034 - should delegate to
2498 // alignPanel to decide if overview needs
2501 alignPanel.paintAlignment(true);
2502 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2503 viewport.sendSelection();
2507 public void invertColSel_actionPerformed(ActionEvent e)
2509 viewport.invertColumnSelection();
2510 alignPanel.paintAlignment(true);
2511 viewport.sendSelection();
2521 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2523 trimAlignment(true);
2533 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2535 trimAlignment(false);
2538 void trimAlignment(boolean trimLeft)
2540 ColumnSelection colSel = viewport.getColumnSelection();
2543 if (!colSel.isEmpty())
2547 column = colSel.getMin();
2551 column = colSel.getMax();
2555 if (viewport.getSelectionGroup() != null)
2557 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2558 viewport.getHiddenRepSequences());
2562 seqs = viewport.getAlignment().getSequencesArray();
2565 TrimRegionCommand trimRegion;
2568 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2569 column, viewport.getAlignment());
2570 viewport.setStartRes(0);
2574 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2575 column, viewport.getAlignment());
2578 statusBar.setText(MessageManager.formatMessage(
2579 "label.removed_columns",
2580 new String[] { Integer.valueOf(trimRegion.getSize())
2583 addHistoryItem(trimRegion);
2585 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2587 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2588 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2590 viewport.getAlignment().deleteGroup(sg);
2594 viewport.firePropertyChange("alignment", null, viewport
2595 .getAlignment().getSequences());
2606 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2608 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2611 if (viewport.getSelectionGroup() != null)
2613 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2614 viewport.getHiddenRepSequences());
2615 start = viewport.getSelectionGroup().getStartRes();
2616 end = viewport.getSelectionGroup().getEndRes();
2620 seqs = viewport.getAlignment().getSequencesArray();
2623 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2624 "Remove Gapped Columns", seqs, start, end,
2625 viewport.getAlignment());
2627 addHistoryItem(removeGapCols);
2629 statusBar.setText(MessageManager.formatMessage(
2630 "label.removed_empty_columns",
2631 new Object[] { Integer.valueOf(removeGapCols.getSize())
2634 // This is to maintain viewport position on first residue
2635 // of first sequence
2636 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2637 int startRes = seq.findPosition(viewport.startRes);
2638 // ShiftList shifts;
2639 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2640 // edit.alColumnChanges=shifts.getInverse();
2641 // if (viewport.hasHiddenColumns)
2642 // viewport.getColumnSelection().compensateForEdits(shifts);
2643 viewport.setStartRes(seq.findIndex(startRes) - 1);
2644 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2656 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2658 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2661 if (viewport.getSelectionGroup() != null)
2663 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2664 viewport.getHiddenRepSequences());
2665 start = viewport.getSelectionGroup().getStartRes();
2666 end = viewport.getSelectionGroup().getEndRes();
2670 seqs = viewport.getAlignment().getSequencesArray();
2673 // This is to maintain viewport position on first residue
2674 // of first sequence
2675 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2676 int startRes = seq.findPosition(viewport.startRes);
2678 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2679 viewport.getAlignment()));
2681 viewport.setStartRes(seq.findIndex(startRes) - 1);
2683 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2695 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2697 viewport.setPadGaps(padGapsMenuitem.isSelected());
2698 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2709 public void findMenuItem_actionPerformed(ActionEvent e)
2715 * Create a new view of the current alignment.
2718 public void newView_actionPerformed(ActionEvent e)
2720 newView(null, true);
2724 * Creates and shows a new view of the current alignment.
2727 * title of newly created view; if null, one will be generated
2728 * @param copyAnnotation
2729 * if true then duplicate all annnotation, groups and settings
2730 * @return new alignment panel, already displayed.
2732 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2735 * Create a new AlignmentPanel (with its own, new Viewport)
2737 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2739 if (!copyAnnotation)
2742 * remove all groups and annotation except for the automatic stuff
2744 newap.av.getAlignment().deleteAllGroups();
2745 newap.av.getAlignment().deleteAllAnnotations(false);
2748 newap.av.setGatherViewsHere(false);
2750 if (viewport.viewName == null)
2752 viewport.viewName = MessageManager
2753 .getString("label.view_name_original");
2757 * Views share the same edits undo and redo stacks
2759 newap.av.setHistoryList(viewport.getHistoryList());
2760 newap.av.setRedoList(viewport.getRedoList());
2763 * Views share the same mappings; need to deregister any new mappings
2764 * created by copyAlignPanel, and register the new reference to the shared
2767 newap.av.replaceMappings(viewport.getAlignment());
2769 newap.av.viewName = getNewViewName(viewTitle);
2771 addAlignmentPanel(newap, true);
2772 newap.alignmentChanged();
2774 if (alignPanels.size() == 2)
2776 viewport.setGatherViewsHere(true);
2778 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2783 * Make a new name for the view, ensuring it is unique within the current
2784 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2785 * these now use viewId. Unique view names are still desirable for usability.)
2790 protected String getNewViewName(String viewTitle)
2792 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2793 boolean addFirstIndex = false;
2794 if (viewTitle == null || viewTitle.trim().length() == 0)
2796 viewTitle = MessageManager.getString("action.view");
2797 addFirstIndex = true;
2801 index = 1;// we count from 1 if given a specific name
2803 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2805 List<Component> comps = PaintRefresher.components.get(viewport
2806 .getSequenceSetId());
2808 List<String> existingNames = getExistingViewNames(comps);
2810 while (existingNames.contains(newViewName))
2812 newViewName = viewTitle + " " + (++index);
2818 * Returns a list of distinct view names found in the given list of
2819 * components. View names are held on the viewport of an AlignmentPanel.
2824 protected List<String> getExistingViewNames(List<Component> comps)
2826 List<String> existingNames = new ArrayList<String>();
2827 for (Component comp : comps)
2829 if (comp instanceof AlignmentPanel)
2831 AlignmentPanel ap = (AlignmentPanel) comp;
2832 if (!existingNames.contains(ap.av.viewName))
2834 existingNames.add(ap.av.viewName);
2838 return existingNames;
2842 * Explode tabbed views into separate windows.
2845 public void expandViews_actionPerformed(ActionEvent e)
2847 Desktop.explodeViews(this);
2851 * Gather views in separate windows back into a tabbed presentation.
2854 public void gatherViews_actionPerformed(ActionEvent e)
2856 Desktop.instance.gatherViews(this);
2866 public void font_actionPerformed(ActionEvent e)
2868 new FontChooser(alignPanel);
2878 protected void seqLimit_actionPerformed(ActionEvent e)
2880 viewport.setShowJVSuffix(seqLimits.isSelected());
2882 alignPanel.getIdPanel().getIdCanvas()
2883 .setPreferredSize(alignPanel.calculateIdWidth());
2884 alignPanel.paintAlignment(true);
2888 public void idRightAlign_actionPerformed(ActionEvent e)
2890 viewport.setRightAlignIds(idRightAlign.isSelected());
2891 alignPanel.paintAlignment(true);
2895 public void centreColumnLabels_actionPerformed(ActionEvent e)
2897 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2898 alignPanel.paintAlignment(true);
2904 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2907 protected void followHighlight_actionPerformed()
2910 * Set the 'follow' flag on the Viewport (and scroll to position if now
2913 final boolean state = this.followHighlightMenuItem.getState();
2914 viewport.setFollowHighlight(state);
2917 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2928 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2930 viewport.setColourText(colourTextMenuItem.isSelected());
2931 alignPanel.paintAlignment(true);
2941 public void wrapMenuItem_actionPerformed(ActionEvent e)
2943 scaleAbove.setVisible(wrapMenuItem.isSelected());
2944 scaleLeft.setVisible(wrapMenuItem.isSelected());
2945 scaleRight.setVisible(wrapMenuItem.isSelected());
2946 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2947 alignPanel.updateLayout();
2951 public void showAllSeqs_actionPerformed(ActionEvent e)
2953 viewport.showAllHiddenSeqs();
2957 public void showAllColumns_actionPerformed(ActionEvent e)
2959 viewport.showAllHiddenColumns();
2961 viewport.sendSelection();
2965 public void hideSelSequences_actionPerformed(ActionEvent e)
2967 viewport.hideAllSelectedSeqs();
2968 // alignPanel.paintAlignment(true);
2972 * called by key handler and the hide all/show all menu items
2977 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2980 boolean hide = false;
2981 SequenceGroup sg = viewport.getSelectionGroup();
2982 if (!toggleSeqs && !toggleCols)
2984 // Hide everything by the current selection - this is a hack - we do the
2985 // invert and then hide
2986 // first check that there will be visible columns after the invert.
2987 if (viewport.hasSelectedColumns()
2988 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2991 // now invert the sequence set, if required - empty selection implies
2992 // that no hiding is required.
2995 invertSequenceMenuItem_actionPerformed(null);
2996 sg = viewport.getSelectionGroup();
3000 viewport.expandColSelection(sg, true);
3001 // finally invert the column selection and get the new sequence
3003 invertColSel_actionPerformed(null);
3010 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3012 hideSelSequences_actionPerformed(null);
3015 else if (!(toggleCols && viewport.hasSelectedColumns()))
3017 showAllSeqs_actionPerformed(null);
3023 if (viewport.hasSelectedColumns())
3025 hideSelColumns_actionPerformed(null);
3028 viewport.setSelectionGroup(sg);
3033 showAllColumns_actionPerformed(null);
3042 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3043 * event.ActionEvent)
3046 public void hideAllButSelection_actionPerformed(ActionEvent e)
3048 toggleHiddenRegions(false, false);
3049 viewport.sendSelection();
3056 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3060 public void hideAllSelection_actionPerformed(ActionEvent e)
3062 SequenceGroup sg = viewport.getSelectionGroup();
3063 viewport.expandColSelection(sg, false);
3064 viewport.hideAllSelectedSeqs();
3065 viewport.hideSelectedColumns();
3066 alignPanel.paintAlignment(true);
3067 viewport.sendSelection();
3074 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3078 public void showAllhidden_actionPerformed(ActionEvent e)
3080 viewport.showAllHiddenColumns();
3081 viewport.showAllHiddenSeqs();
3082 alignPanel.paintAlignment(true);
3083 viewport.sendSelection();
3087 public void hideSelColumns_actionPerformed(ActionEvent e)
3089 viewport.hideSelectedColumns();
3090 alignPanel.paintAlignment(true);
3091 viewport.sendSelection();
3095 public void hiddenMarkers_actionPerformed(ActionEvent e)
3097 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3108 protected void scaleAbove_actionPerformed(ActionEvent e)
3110 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3111 alignPanel.paintAlignment(true);
3121 protected void scaleLeft_actionPerformed(ActionEvent e)
3123 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3124 alignPanel.paintAlignment(true);
3134 protected void scaleRight_actionPerformed(ActionEvent e)
3136 viewport.setScaleRightWrapped(scaleRight.isSelected());
3137 alignPanel.paintAlignment(true);
3147 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3149 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3150 alignPanel.paintAlignment(true);
3160 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3162 viewport.setShowText(viewTextMenuItem.isSelected());
3163 alignPanel.paintAlignment(true);
3173 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3175 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3176 alignPanel.paintAlignment(true);
3179 public FeatureSettings featureSettings;
3182 public FeatureSettingsControllerI getFeatureSettingsUI()
3184 return featureSettings;
3188 public void featureSettings_actionPerformed(ActionEvent e)
3190 if (featureSettings != null)
3192 featureSettings.close();
3193 featureSettings = null;
3195 if (!showSeqFeatures.isSelected())
3197 // make sure features are actually displayed
3198 showSeqFeatures.setSelected(true);
3199 showSeqFeatures_actionPerformed(null);
3201 featureSettings = new FeatureSettings(this);
3205 * Set or clear 'Show Sequence Features'
3211 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3213 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3214 alignPanel.paintAlignment(true);
3215 if (alignPanel.getOverviewPanel() != null)
3217 alignPanel.getOverviewPanel().updateOverviewImage();
3222 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3223 * the annotations panel as a whole.
3225 * The options to show/hide all annotations should be enabled when the panel
3226 * is shown, and disabled when the panel is hidden.
3231 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3233 final boolean setVisible = annotationPanelMenuItem.isSelected();
3234 viewport.setShowAnnotation(setVisible);
3235 this.showAllSeqAnnotations.setEnabled(setVisible);
3236 this.hideAllSeqAnnotations.setEnabled(setVisible);
3237 this.showAllAlAnnotations.setEnabled(setVisible);
3238 this.hideAllAlAnnotations.setEnabled(setVisible);
3239 alignPanel.updateLayout();
3243 public void alignmentProperties()
3245 JEditorPane editPane = new JEditorPane("text/html", "");
3246 editPane.setEditable(false);
3247 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3249 editPane.setText(MessageManager.formatMessage("label.html_content",
3250 new Object[] { contents.toString() }));
3251 JInternalFrame frame = new JInternalFrame();
3252 frame.getContentPane().add(new JScrollPane(editPane));
3254 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3255 "label.alignment_properties", new Object[] { getTitle() }),
3266 public void overviewMenuItem_actionPerformed(ActionEvent e)
3268 if (alignPanel.overviewPanel != null)
3273 JInternalFrame frame = new JInternalFrame();
3274 OverviewPanel overview = new OverviewPanel(alignPanel);
3275 frame.setContentPane(overview);
3276 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3277 "label.overview_params", new Object[] { this.getTitle() }),
3278 frame.getWidth(), frame.getHeight());
3280 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3281 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3284 public void internalFrameClosed(
3285 javax.swing.event.InternalFrameEvent evt)
3287 alignPanel.setOverviewPanel(null);
3291 alignPanel.setOverviewPanel(overview);
3295 public void textColour_actionPerformed(ActionEvent e)
3297 new TextColourChooser().chooseColour(alignPanel, null);
3307 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3319 public void clustalColour_actionPerformed(ActionEvent e)
3321 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3322 viewport.getHiddenRepSequences()));
3332 public void zappoColour_actionPerformed(ActionEvent e)
3334 changeColour(new ZappoColourScheme());
3344 public void taylorColour_actionPerformed(ActionEvent e)
3346 changeColour(new TaylorColourScheme());
3356 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3358 changeColour(new HydrophobicColourScheme());
3368 public void helixColour_actionPerformed(ActionEvent e)
3370 changeColour(new HelixColourScheme());
3380 public void strandColour_actionPerformed(ActionEvent e)
3382 changeColour(new StrandColourScheme());
3392 public void turnColour_actionPerformed(ActionEvent e)
3394 changeColour(new TurnColourScheme());
3404 public void buriedColour_actionPerformed(ActionEvent e)
3406 changeColour(new BuriedColourScheme());
3416 public void nucleotideColour_actionPerformed(ActionEvent e)
3418 changeColour(new NucleotideColourScheme());
3422 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3424 changeColour(new PurinePyrimidineColourScheme());
3428 * public void covariationColour_actionPerformed(ActionEvent e) {
3430 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3434 public void annotationColour_actionPerformed(ActionEvent e)
3436 new AnnotationColourChooser(viewport, alignPanel);
3440 public void annotationColumn_actionPerformed(ActionEvent e)
3442 new AnnotationColumnChooser(viewport, alignPanel);
3446 public void rnahelicesColour_actionPerformed(ActionEvent e)
3448 new RNAHelicesColourChooser(viewport, alignPanel);
3458 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3460 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3470 public void changeColour(ColourSchemeI cs)
3472 // TODO: pull up to controller method
3476 // Make sure viewport is up to date w.r.t. any sliders
3477 if (viewport.getAbovePIDThreshold())
3479 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3481 viewport.setThreshold(threshold);
3484 if (viewport.getConservationSelected())
3486 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3489 if (cs instanceof TCoffeeColourScheme)
3491 tcoffeeColour.setEnabled(true);
3492 tcoffeeColour.setSelected(true);
3496 viewport.setGlobalColourScheme(cs);
3498 alignPanel.paintAlignment(true);
3505 protected void modifyPID_actionPerformed()
3507 if (viewport.getAbovePIDThreshold()
3508 && viewport.getGlobalColourScheme() != null)
3510 SliderPanel.setPIDSliderSource(alignPanel,
3511 viewport.getGlobalColourScheme(), "Background");
3512 SliderPanel.showPIDSlider();
3520 protected void modifyConservation_actionPerformed()
3522 if (viewport.getConservationSelected()
3523 && viewport.getGlobalColourScheme() != null)
3525 SliderPanel.setConservationSlider(alignPanel,
3526 viewport.getGlobalColourScheme(), "Background");
3527 SliderPanel.showConservationSlider();
3532 * Action on selecting or deselecting (Colour) By Conservation
3535 protected void conservationMenuItem_actionPerformed()
3537 boolean selected = conservationMenuItem.isSelected();
3538 modifyConservation.setEnabled(selected);
3539 viewport.setConservationSelected(selected);
3541 changeColour(viewport.getGlobalColourScheme());
3544 modifyConservation_actionPerformed();
3548 SliderPanel.hideConservationSlider();
3553 * Action on selecting or deselecting (Colour) Above PID Threshold
3556 public void abovePIDThreshold_actionPerformed()
3558 boolean selected = abovePIDThreshold.isSelected();
3559 modifyPID.setEnabled(selected);
3560 viewport.setAbovePIDThreshold(selected);
3562 changeColour(viewport.getGlobalColourScheme());
3565 modifyPID_actionPerformed();
3569 SliderPanel.hidePIDSlider();
3580 public void userDefinedColour_actionPerformed(ActionEvent e)
3582 if (e.getActionCommand().equals(
3583 MessageManager.getString("action.user_defined")))
3585 new UserDefinedColours(alignPanel, null);
3589 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3590 .getUserColourSchemes().get(e.getActionCommand());
3596 public void updateUserColourMenu()
3599 Component[] menuItems = colourMenu.getMenuComponents();
3600 int iSize = menuItems.length;
3601 for (int i = 0; i < iSize; i++)
3603 if (menuItems[i].getName() != null
3604 && menuItems[i].getName().equals("USER_DEFINED"))
3606 colourMenu.remove(menuItems[i]);
3610 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3612 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3613 .getUserColourSchemes().keys();
3615 while (userColours.hasMoreElements())
3617 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3618 userColours.nextElement().toString());
3619 radioItem.setName("USER_DEFINED");
3620 radioItem.addMouseListener(new MouseAdapter()
3623 public void mousePressed(MouseEvent evt)
3625 if (evt.isPopupTrigger()) // Mac
3627 offerRemoval(radioItem);
3632 public void mouseReleased(MouseEvent evt)
3634 if (evt.isPopupTrigger()) // Windows
3636 offerRemoval(radioItem);
3643 void offerRemoval(final JRadioButtonMenuItem radioItem)
3645 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3647 int option = JvOptionPane.showInternalConfirmDialog(
3648 jalview.gui.Desktop.desktop, MessageManager
3649 .getString("label.remove_from_default_list"),
3651 .getString("label.remove_user_defined_colour"),
3652 JvOptionPane.YES_NO_OPTION);
3653 if (option == JvOptionPane.YES_OPTION)
3655 jalview.gui.UserDefinedColours
3656 .removeColourFromDefaults(radioItem.getText());
3657 colourMenu.remove(radioItem);
3661 radioItem.addActionListener(new ActionListener()
3664 public void actionPerformed(ActionEvent evt)
3666 userDefinedColour_actionPerformed(evt);
3672 radioItem.addActionListener(new ActionListener()
3675 public void actionPerformed(ActionEvent evt)
3677 userDefinedColour_actionPerformed(evt);
3681 colourMenu.insert(radioItem, 15);
3682 colours.add(radioItem);
3694 public void PIDColour_actionPerformed(ActionEvent e)
3696 changeColour(new PIDColourScheme());
3706 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3708 changeColour(new Blosum62ColourScheme());
3718 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3720 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3721 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3722 .getAlignment().getSequenceAt(0), null);
3723 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3724 viewport.getAlignment()));
3725 alignPanel.paintAlignment(true);
3735 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3737 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3738 AlignmentSorter.sortByID(viewport.getAlignment());
3739 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3740 viewport.getAlignment()));
3741 alignPanel.paintAlignment(true);
3751 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3753 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3754 AlignmentSorter.sortByLength(viewport.getAlignment());
3755 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3756 viewport.getAlignment()));
3757 alignPanel.paintAlignment(true);
3767 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3769 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3770 AlignmentSorter.sortByGroup(viewport.getAlignment());
3771 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3772 viewport.getAlignment()));
3774 alignPanel.paintAlignment(true);
3784 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3786 new RedundancyPanel(alignPanel, this);
3796 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3798 if ((viewport.getSelectionGroup() == null)
3799 || (viewport.getSelectionGroup().getSize() < 2))
3801 JvOptionPane.showInternalMessageDialog(this, MessageManager
3802 .getString("label.you_must_select_least_two_sequences"),
3803 MessageManager.getString("label.invalid_selection"),
3804 JvOptionPane.WARNING_MESSAGE);
3808 JInternalFrame frame = new JInternalFrame();
3809 frame.setContentPane(new PairwiseAlignPanel(viewport));
3810 Desktop.addInternalFrame(frame,
3811 MessageManager.getString("action.pairwise_alignment"), 600,
3823 public void PCAMenuItem_actionPerformed(ActionEvent e)
3825 if (((viewport.getSelectionGroup() != null)
3826 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3827 .getSelectionGroup().getSize() > 0))
3828 || (viewport.getAlignment().getHeight() < 4))
3831 .showInternalMessageDialog(
3834 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3836 .getString("label.sequence_selection_insufficient"),
3837 JvOptionPane.WARNING_MESSAGE);
3842 new PCAPanel(alignPanel);
3846 public void autoCalculate_actionPerformed(ActionEvent e)
3848 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3849 if (viewport.autoCalculateConsensus)
3851 viewport.firePropertyChange("alignment", null, viewport
3852 .getAlignment().getSequences());
3857 public void sortByTreeOption_actionPerformed(ActionEvent e)
3859 viewport.sortByTree = sortByTree.isSelected();
3863 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3865 viewport.followSelection = listenToViewSelections.isSelected();
3875 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3877 newTreePanel("AV", "PID", "Average distance tree using PID");
3887 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3889 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3899 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3901 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3911 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3913 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3926 void newTreePanel(String type, String pwType, String title)
3930 if (viewport.getSelectionGroup() != null
3931 && viewport.getSelectionGroup().getSize() > 0)
3933 if (viewport.getSelectionGroup().getSize() < 3)
3939 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3941 .getString("label.not_enough_sequences"),
3942 JvOptionPane.WARNING_MESSAGE);
3946 SequenceGroup sg = viewport.getSelectionGroup();
3948 /* Decide if the selection is a column region */
3949 for (SequenceI _s : sg.getSequences())
3951 if (_s.getLength() < sg.getEndRes())
3957 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3959 .getString("label.sequences_selection_not_aligned"),
3960 JvOptionPane.WARNING_MESSAGE);
3966 title = title + " on region";
3967 tp = new TreePanel(alignPanel, type, pwType);
3971 // are the visible sequences aligned?
3972 if (!viewport.getAlignment().isAligned(false))
3978 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3980 .getString("label.sequences_not_aligned"),
3981 JvOptionPane.WARNING_MESSAGE);
3986 if (viewport.getAlignment().getHeight() < 2)
3991 tp = new TreePanel(alignPanel, type, pwType);
3996 if (viewport.viewName != null)
3998 title += viewport.viewName + " of ";
4001 title += this.title;
4003 Desktop.addInternalFrame(tp, title, 600, 500);
4014 public void addSortByOrderMenuItem(String title,
4015 final AlignmentOrder order)
4017 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4018 "action.by_title_param", new Object[] { title }));
4020 item.addActionListener(new java.awt.event.ActionListener()
4023 public void actionPerformed(ActionEvent e)
4025 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4027 // TODO: JBPNote - have to map order entries to curent SequenceI
4029 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4031 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4034 alignPanel.paintAlignment(true);
4040 * Add a new sort by annotation score menu item
4043 * the menu to add the option to
4045 * the label used to retrieve scores for each sequence on the
4048 public void addSortByAnnotScoreMenuItem(JMenu sort,
4049 final String scoreLabel)
4051 final JMenuItem item = new JMenuItem(scoreLabel);
4053 item.addActionListener(new java.awt.event.ActionListener()
4056 public void actionPerformed(ActionEvent e)
4058 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4059 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4060 viewport.getAlignment());// ,viewport.getSelectionGroup());
4061 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4062 viewport.getAlignment()));
4063 alignPanel.paintAlignment(true);
4069 * last hash for alignment's annotation array - used to minimise cost of
4072 protected int _annotationScoreVectorHash;
4075 * search the alignment and rebuild the sort by annotation score submenu the
4076 * last alignment annotation vector hash is stored to minimize cost of
4077 * rebuilding in subsequence calls.
4081 public void buildSortByAnnotationScoresMenu()
4083 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4088 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4090 sortByAnnotScore.removeAll();
4091 // almost certainly a quicker way to do this - but we keep it simple
4092 Hashtable scoreSorts = new Hashtable();
4093 AlignmentAnnotation aann[];
4094 for (SequenceI sqa : viewport.getAlignment().getSequences())
4096 aann = sqa.getAnnotation();
4097 for (int i = 0; aann != null && i < aann.length; i++)
4099 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4101 scoreSorts.put(aann[i].label, aann[i].label);
4105 Enumeration labels = scoreSorts.keys();
4106 while (labels.hasMoreElements())
4108 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4109 (String) labels.nextElement());
4111 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4114 _annotationScoreVectorHash = viewport.getAlignment()
4115 .getAlignmentAnnotation().hashCode();
4120 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4121 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4122 * call. Listeners are added to remove the menu item when the treePanel is
4123 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4127 * Displayed tree window.
4129 * SortBy menu item title.
4132 public void buildTreeMenu()
4134 calculateTree.removeAll();
4135 // build the calculate menu
4137 for (final String type : new String[] { "NJ", "AV" })
4139 String treecalcnm = MessageManager.getString("label.tree_calc_"
4140 + type.toLowerCase());
4141 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4143 JMenuItem tm = new JMenuItem();
4144 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4145 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4146 || sm.isProtein() == !viewport.getAlignment()
4149 String smn = MessageManager.getStringOrReturn(
4150 "label.score_model_", sm.getName());
4151 final String title = MessageManager.formatMessage(
4152 "label.treecalc_title", treecalcnm, smn);
4153 tm.setText(title);//
4154 tm.addActionListener(new java.awt.event.ActionListener()
4157 public void actionPerformed(ActionEvent e)
4159 newTreePanel(type, pwtype, title);
4162 calculateTree.add(tm);
4167 sortByTreeMenu.removeAll();
4169 List<Component> comps = PaintRefresher.components.get(viewport
4170 .getSequenceSetId());
4171 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4172 for (Component comp : comps)
4174 if (comp instanceof TreePanel)
4176 treePanels.add((TreePanel) comp);
4180 if (treePanels.size() < 1)
4182 sortByTreeMenu.setVisible(false);
4186 sortByTreeMenu.setVisible(true);
4188 for (final TreePanel tp : treePanels)
4190 final JMenuItem item = new JMenuItem(tp.getTitle());
4191 item.addActionListener(new java.awt.event.ActionListener()
4194 public void actionPerformed(ActionEvent e)
4196 tp.sortByTree_actionPerformed();
4197 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4202 sortByTreeMenu.add(item);
4206 public boolean sortBy(AlignmentOrder alorder, String undoname)
4208 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4209 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4210 if (undoname != null)
4212 addHistoryItem(new OrderCommand(undoname, oldOrder,
4213 viewport.getAlignment()));
4215 alignPanel.paintAlignment(true);
4220 * Work out whether the whole set of sequences or just the selected set will
4221 * be submitted for multiple alignment.
4224 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4226 // Now, check we have enough sequences
4227 AlignmentView msa = null;
4229 if ((viewport.getSelectionGroup() != null)
4230 && (viewport.getSelectionGroup().getSize() > 1))
4232 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4233 // some common interface!
4235 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4236 * SequenceI[sz = seqs.getSize(false)];
4238 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4239 * seqs.getSequenceAt(i); }
4241 msa = viewport.getAlignmentView(true);
4243 else if (viewport.getSelectionGroup() != null
4244 && viewport.getSelectionGroup().getSize() == 1)
4246 int option = JvOptionPane.showConfirmDialog(this,
4247 MessageManager.getString("warn.oneseq_msainput_selection"),
4248 MessageManager.getString("label.invalid_selection"),
4249 JvOptionPane.OK_CANCEL_OPTION);
4250 if (option == JvOptionPane.OK_OPTION)
4252 msa = viewport.getAlignmentView(false);
4257 msa = viewport.getAlignmentView(false);
4263 * Decides what is submitted to a secondary structure prediction service: the
4264 * first sequence in the alignment, or in the current selection, or, if the
4265 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4266 * region or the whole alignment. (where the first sequence in the set is the
4267 * one that the prediction will be for).
4269 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4271 AlignmentView seqs = null;
4273 if ((viewport.getSelectionGroup() != null)
4274 && (viewport.getSelectionGroup().getSize() > 0))
4276 seqs = viewport.getAlignmentView(true);
4280 seqs = viewport.getAlignmentView(false);
4282 // limit sequences - JBPNote in future - could spawn multiple prediction
4284 // TODO: viewport.getAlignment().isAligned is a global state - the local
4285 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4286 if (!viewport.getAlignment().isAligned(false))
4288 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4289 // TODO: if seqs.getSequences().length>1 then should really have warned
4303 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4305 // Pick the tree file
4306 JalviewFileChooser chooser = new JalviewFileChooser(
4307 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4308 chooser.setFileView(new JalviewFileView());
4309 chooser.setDialogTitle(MessageManager
4310 .getString("label.select_newick_like_tree_file"));
4311 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4313 int value = chooser.showOpenDialog(null);
4315 if (value == JalviewFileChooser.APPROVE_OPTION)
4317 String choice = chooser.getSelectedFile().getPath();
4318 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4319 jalview.io.NewickFile fin = null;
4322 fin = new NewickFile(choice, DataSourceType.FILE);
4323 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4324 } catch (Exception ex)
4331 .getString("label.problem_reading_tree_file"),
4332 JvOptionPane.WARNING_MESSAGE);
4333 ex.printStackTrace();
4335 if (fin != null && fin.hasWarningMessage())
4337 JvOptionPane.showMessageDialog(Desktop.desktop, fin
4338 .getWarningMessage(), MessageManager
4339 .getString("label.possible_problem_with_tree_file"),
4340 JvOptionPane.WARNING_MESSAGE);
4346 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4348 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4351 public TreePanel ShowNewickTree(NewickFile nf, String title)
4353 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4356 public TreePanel ShowNewickTree(NewickFile nf, String title,
4357 AlignmentView input)
4359 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4362 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4363 int h, int x, int y)
4365 return ShowNewickTree(nf, title, null, w, h, x, y);
4369 * Add a treeviewer for the tree extracted from a newick file object to the
4370 * current alignment view
4377 * Associated alignment input data (or null)
4386 * @return TreePanel handle
4388 public TreePanel ShowNewickTree(NewickFile nf, String title,
4389 AlignmentView input, int w, int h, int x, int y)
4391 TreePanel tp = null;
4397 if (nf.getTree() != null)
4399 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4405 tp.setLocation(x, y);
4408 Desktop.addInternalFrame(tp, title, w, h);
4410 } catch (Exception ex)
4412 ex.printStackTrace();
4418 private boolean buildingMenu = false;
4421 * Generates menu items and listener event actions for web service clients
4424 public void BuildWebServiceMenu()
4426 while (buildingMenu)
4430 System.err.println("Waiting for building menu to finish.");
4432 } catch (Exception e)
4436 final AlignFrame me = this;
4437 buildingMenu = true;
4438 new Thread(new Runnable()
4443 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4446 // System.err.println("Building ws menu again "
4447 // + Thread.currentThread());
4448 // TODO: add support for context dependent disabling of services based
4450 // alignment and current selection
4451 // TODO: add additional serviceHandle parameter to specify abstract
4453 // class independently of AbstractName
4454 // TODO: add in rediscovery GUI function to restart discoverer
4455 // TODO: group services by location as well as function and/or
4457 // object broker mechanism.
4458 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4459 final IProgressIndicator af = me;
4462 * do not i18n these strings - they are hard-coded in class
4463 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4464 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4466 final JMenu msawsmenu = new JMenu("Alignment");
4467 final JMenu secstrmenu = new JMenu(
4468 "Secondary Structure Prediction");
4469 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4470 final JMenu analymenu = new JMenu("Analysis");
4471 final JMenu dismenu = new JMenu("Protein Disorder");
4472 // JAL-940 - only show secondary structure prediction services from
4473 // the legacy server
4474 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4476 Discoverer.services != null && (Discoverer.services.size() > 0))
4478 // TODO: refactor to allow list of AbstractName/Handler bindings to
4480 // stored or retrieved from elsewhere
4481 // No MSAWS used any more:
4482 // Vector msaws = null; // (Vector)
4483 // Discoverer.services.get("MsaWS");
4484 Vector secstrpr = (Vector) Discoverer.services
4486 if (secstrpr != null)
4488 // Add any secondary structure prediction services
4489 for (int i = 0, j = secstrpr.size(); i < j; i++)
4491 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4493 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4494 .getServiceClient(sh);
4495 int p = secstrmenu.getItemCount();
4496 impl.attachWSMenuEntry(secstrmenu, me);
4497 int q = secstrmenu.getItemCount();
4498 for (int litm = p; litm < q; litm++)
4500 legacyItems.add(secstrmenu.getItem(litm));
4506 // Add all submenus in the order they should appear on the web
4508 wsmenu.add(msawsmenu);
4509 wsmenu.add(secstrmenu);
4510 wsmenu.add(dismenu);
4511 wsmenu.add(analymenu);
4512 // No search services yet
4513 // wsmenu.add(seqsrchmenu);
4515 javax.swing.SwingUtilities.invokeLater(new Runnable()
4522 webService.removeAll();
4523 // first, add discovered services onto the webservices menu
4524 if (wsmenu.size() > 0)
4526 for (int i = 0, j = wsmenu.size(); i < j; i++)
4528 webService.add(wsmenu.get(i));
4533 webService.add(me.webServiceNoServices);
4535 // TODO: move into separate menu builder class.
4536 boolean new_sspred = false;
4537 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4539 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4540 if (jws2servs != null)
4542 if (jws2servs.hasServices())
4544 jws2servs.attachWSMenuEntry(webService, me);
4545 for (Jws2Instance sv : jws2servs.getServices())
4547 if (sv.description.toLowerCase().contains("jpred"))
4549 for (JMenuItem jmi : legacyItems)
4551 jmi.setVisible(false);
4557 if (jws2servs.isRunning())
4559 JMenuItem tm = new JMenuItem(
4560 "Still discovering JABA Services");
4561 tm.setEnabled(false);
4566 build_urlServiceMenu(me.webService);
4567 build_fetchdbmenu(webService);
4568 for (JMenu item : wsmenu)
4570 if (item.getItemCount() == 0)
4572 item.setEnabled(false);
4576 item.setEnabled(true);
4579 } catch (Exception e)
4582 .debug("Exception during web service menu building process.",
4587 } catch (Exception e)
4590 buildingMenu = false;
4597 * construct any groupURL type service menu entries.
4601 private void build_urlServiceMenu(JMenu webService)
4603 // TODO: remove this code when 2.7 is released
4604 // DEBUG - alignmentView
4606 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4607 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4609 * @Override public void actionPerformed(ActionEvent e) {
4610 * jalview.datamodel.AlignmentView
4611 * .testSelectionViews(af.viewport.getAlignment(),
4612 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4614 * }); webService.add(testAlView);
4616 // TODO: refactor to RestClient discoverer and merge menu entries for
4617 // rest-style services with other types of analysis/calculation service
4618 // SHmmr test client - still being implemented.
4619 // DEBUG - alignmentView
4621 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4624 client.attachWSMenuEntry(
4625 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4631 * Searches the alignment sequences for xRefs and builds the Show
4632 * Cross-References menu (formerly called Show Products), with database
4633 * sources for which cross-references are found (protein sources for a
4634 * nucleotide alignment and vice versa)
4636 * @return true if Show Cross-references menu should be enabled
4638 public boolean canShowProducts()
4640 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4641 AlignmentI dataset = viewport.getAlignment().getDataset();
4643 showProducts.removeAll();
4644 final boolean dna = viewport.getAlignment().isNucleotide();
4646 if (seqs == null || seqs.length == 0)
4648 // nothing to see here.
4652 boolean showp = false;
4655 List<String> ptypes = new CrossRef(seqs, dataset)
4656 .findXrefSourcesForSequences(dna);
4658 for (final String source : ptypes)
4661 final AlignFrame af = this;
4662 JMenuItem xtype = new JMenuItem(source);
4663 xtype.addActionListener(new ActionListener()
4666 public void actionPerformed(ActionEvent e)
4668 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4671 showProducts.add(xtype);
4673 showProducts.setVisible(showp);
4674 showProducts.setEnabled(showp);
4675 } catch (Exception e)
4678 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4686 * Finds and displays cross-references for the selected sequences (protein
4687 * products for nucleotide sequences, dna coding sequences for peptides).
4690 * the sequences to show cross-references for
4692 * true if from a nucleotide alignment (so showing proteins)
4694 * the database to show cross-references for
4696 protected void showProductsFor(final SequenceI[] sel,
4697 final boolean _odna, final String source)
4699 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4704 * Construct and display a new frame containing the translation of this
4705 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4708 public void showTranslation_actionPerformed(ActionEvent e)
4710 AlignmentI al = null;
4713 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4715 al = dna.translateCdna();
4716 } catch (Exception ex)
4718 jalview.bin.Cache.log.error(
4719 "Exception during translation. Please report this !", ex);
4720 final String msg = MessageManager
4721 .getString("label.error_when_translating_sequences_submit_bug_report");
4722 final String errorTitle = MessageManager
4723 .getString("label.implementation_error")
4724 + MessageManager.getString("label.translation_failed");
4725 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4726 JvOptionPane.ERROR_MESSAGE);
4729 if (al == null || al.getHeight() == 0)
4731 final String msg = MessageManager
4732 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4733 final String errorTitle = MessageManager
4734 .getString("label.translation_failed");
4735 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4736 JvOptionPane.WARNING_MESSAGE);
4740 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4741 af.setFileFormat(this.currentFileFormat);
4742 final String newTitle = MessageManager.formatMessage(
4743 "label.translation_of_params",
4744 new Object[] { this.getTitle() });
4745 af.setTitle(newTitle);
4746 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4748 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4749 viewport.openSplitFrame(af, new Alignment(seqs));
4753 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4760 * Set the file format
4764 public void setFileFormat(FileFormatI format)
4766 this.currentFileFormat = format;
4770 * Try to load a features file onto the alignment.
4773 * contents or path to retrieve file
4775 * access mode of file (see jalview.io.AlignFile)
4776 * @return true if features file was parsed correctly.
4778 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4780 return avc.parseFeaturesFile(file, sourceType,
4781 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4786 public void refreshFeatureUI(boolean enableIfNecessary)
4788 // note - currently this is only still here rather than in the controller
4789 // because of the featureSettings hard reference that is yet to be
4791 if (enableIfNecessary)
4793 viewport.setShowSequenceFeatures(true);
4794 showSeqFeatures.setSelected(true);
4800 public void dragEnter(DropTargetDragEvent evt)
4805 public void dragExit(DropTargetEvent evt)
4810 public void dragOver(DropTargetDragEvent evt)
4815 public void dropActionChanged(DropTargetDragEvent evt)
4820 public void drop(DropTargetDropEvent evt)
4822 // JAL-1552 - acceptDrop required before getTransferable call for
4823 // Java's Transferable for native dnd
4824 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4825 Transferable t = evt.getTransferable();
4826 List<String> files = new ArrayList<String>();
4827 List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4831 Desktop.transferFromDropTarget(files, protocols, evt, t);
4832 } catch (Exception e)
4834 e.printStackTrace();
4840 // check to see if any of these files have names matching sequences in
4842 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4843 .getAlignment().getSequencesArray());
4845 * Object[] { String,SequenceI}
4847 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4848 ArrayList<String> filesnotmatched = new ArrayList<String>();
4849 for (int i = 0; i < files.size(); i++)
4851 String file = files.get(i).toString();
4853 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4854 if (protocol == DataSourceType.FILE)
4856 File fl = new File(file);
4857 pdbfn = fl.getName();
4859 else if (protocol == DataSourceType.URL)
4861 URL url = new URL(file);
4862 pdbfn = url.getFile();
4864 if (pdbfn.length() > 0)
4866 // attempt to find a match in the alignment
4867 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4868 int l = 0, c = pdbfn.indexOf(".");
4869 while (mtch == null && c != -1)
4874 } while ((c = pdbfn.indexOf(".", l)) > l);
4877 pdbfn = pdbfn.substring(0, l);
4879 mtch = idm.findAllIdMatches(pdbfn);
4883 FileFormatI type = null;
4886 type = new IdentifyFile().identify(file, protocol);
4887 } catch (Exception ex)
4891 if (type != null && type.isStructureFile())
4893 filesmatched.add(new Object[] { file, protocol, mtch });
4897 // File wasn't named like one of the sequences or wasn't a PDB file.
4898 filesnotmatched.add(file);
4902 if (filesmatched.size() > 0)
4904 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4910 "label.automatically_associate_structure_files_with_sequences_same_name",
4911 new Object[] { Integer
4917 .getString("label.automatically_associate_structure_files_by_name"),
4918 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4921 for (Object[] fm : filesmatched)
4923 // try and associate
4924 // TODO: may want to set a standard ID naming formalism for
4925 // associating PDB files which have no IDs.
4926 for (SequenceI toassoc : (SequenceI[]) fm[2])
4928 PDBEntry pe = new AssociatePdbFileWithSeq()
4929 .associatePdbWithSeq((String) fm[0],
4930 (DataSourceType) fm[1], toassoc, false,
4934 System.err.println("Associated file : "
4935 + ((String) fm[0]) + " with "
4936 + toassoc.getDisplayId(true));
4940 alignPanel.paintAlignment(true);
4944 if (filesnotmatched.size() > 0)
4947 && (Cache.getDefault(
4948 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4954 "label.ignore_unmatched_dropped_files_info",
4955 new Object[] { Integer
4962 .getString("label.ignore_unmatched_dropped_files"),
4963 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4967 for (String fn : filesnotmatched)
4969 loadJalviewDataFile(fn, null, null, null);
4973 } catch (Exception ex)
4975 ex.printStackTrace();
4981 * Attempt to load a "dropped" file or URL string: First by testing whether
4982 * it's an Annotation file, then a JNet file, and finally a features file. If
4983 * all are false then the user may have dropped an alignment file onto this
4987 * either a filename or a URL string.
4989 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4990 FileFormatI format, SequenceI assocSeq)
4994 if (sourceType == null)
4996 sourceType = FormatAdapter.checkProtocol(file);
4998 // if the file isn't identified, or not positively identified as some
4999 // other filetype (PFAM is default unidentified alignment file type) then
5000 // try to parse as annotation.
5001 boolean isAnnotation = (format == null || FileFormat.Pfam
5002 .equals(format)) ? new AnnotationFile()
5003 .annotateAlignmentView(viewport, file, sourceType) : false;
5007 // first see if its a T-COFFEE score file
5008 TCoffeeScoreFile tcf = null;
5011 tcf = new TCoffeeScoreFile(file, sourceType);
5014 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5016 tcoffeeColour.setEnabled(true);
5017 tcoffeeColour.setSelected(true);
5018 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5019 isAnnotation = true;
5021 .setText(MessageManager
5022 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5026 // some problem - if no warning its probable that the ID matching
5027 // process didn't work
5031 tcf.getWarningMessage() == null ? MessageManager
5032 .getString("label.check_file_matches_sequence_ids_alignment")
5033 : tcf.getWarningMessage(),
5035 .getString("label.problem_reading_tcoffee_score_file"),
5036 JvOptionPane.WARNING_MESSAGE);
5043 } catch (Exception x)
5046 .debug("Exception when processing data source as T-COFFEE score file",
5052 // try to see if its a JNet 'concise' style annotation file *before*
5054 // try to parse it as a features file
5057 format = new IdentifyFile().identify(file, sourceType);
5059 if (FileFormat.Jnet.equals(format))
5061 JPredFile predictions = new JPredFile(
5063 new JnetAnnotationMaker();
5064 JnetAnnotationMaker.add_annotation(predictions,
5065 viewport.getAlignment(), 0, false);
5066 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5067 viewport.getAlignment().setSeqrep(repseq);
5068 ColumnSelection cs = new ColumnSelection();
5069 cs.hideInsertionsFor(repseq);
5070 viewport.setColumnSelection(cs);
5071 isAnnotation = true;
5073 // else if (IdentifyFile.FeaturesFile.equals(format))
5074 else if (FileFormat.Features.equals(format))
5076 if (parseFeaturesFile(file, sourceType))
5078 alignPanel.paintAlignment(true);
5083 new FileLoader().LoadFile(viewport, file, sourceType, format);
5090 alignPanel.adjustAnnotationHeight();
5091 viewport.updateSequenceIdColours();
5092 buildSortByAnnotationScoresMenu();
5093 alignPanel.paintAlignment(true);
5095 } catch (Exception ex)
5097 ex.printStackTrace();
5098 } catch (OutOfMemoryError oom)
5103 } catch (Exception x)
5108 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
5109 : "using " + sourceType + " from " + file)
5111 + (format != null ? "(parsing as '" + format
5112 + "' file)" : ""), oom, Desktop.desktop);
5117 * Method invoked by the ChangeListener on the tabbed pane, in other words
5118 * when a different tabbed pane is selected by the user or programmatically.
5121 public void tabSelectionChanged(int index)
5125 alignPanel = alignPanels.get(index);
5126 viewport = alignPanel.av;
5127 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5128 setMenusFromViewport(viewport);
5132 * If there is a frame linked to this one in a SplitPane, switch it to the
5133 * same view tab index. No infinite recursion of calls should happen, since
5134 * tabSelectionChanged() should not get invoked on setting the selected
5135 * index to an unchanged value. Guard against setting an invalid index
5136 * before the new view peer tab has been created.
5138 final AlignViewportI peer = viewport.getCodingComplement();
5141 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5142 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5144 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5150 * On right mouse click on view tab, prompt for and set new view name.
5153 public void tabbedPane_mousePressed(MouseEvent e)
5155 if (e.isPopupTrigger())
5157 String msg = MessageManager.getString("label.enter_view_name");
5158 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
5159 JvOptionPane.QUESTION_MESSAGE);
5163 viewport.viewName = reply;
5164 // TODO warn if reply is in getExistingViewNames()?
5165 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5170 public AlignViewport getCurrentView()
5176 * Open the dialog for regex description parsing.
5179 protected void extractScores_actionPerformed(ActionEvent e)
5181 ParseProperties pp = new jalview.analysis.ParseProperties(
5182 viewport.getAlignment());
5183 // TODO: verify regex and introduce GUI dialog for version 2.5
5184 // if (pp.getScoresFromDescription("col", "score column ",
5185 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5187 if (pp.getScoresFromDescription("description column",
5188 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5190 buildSortByAnnotationScoresMenu();
5198 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5202 protected void showDbRefs_actionPerformed(ActionEvent e)
5204 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5210 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5214 protected void showNpFeats_actionPerformed(ActionEvent e)
5216 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5220 * find the viewport amongst the tabs in this alignment frame and close that
5225 public boolean closeView(AlignViewportI av)
5229 this.closeMenuItem_actionPerformed(false);
5232 Component[] comp = tabbedPane.getComponents();
5233 for (int i = 0; comp != null && i < comp.length; i++)
5235 if (comp[i] instanceof AlignmentPanel)
5237 if (((AlignmentPanel) comp[i]).av == av)
5240 closeView((AlignmentPanel) comp[i]);
5248 protected void build_fetchdbmenu(JMenu webService)
5250 // Temporary hack - DBRef Fetcher always top level ws entry.
5251 // TODO We probably want to store a sequence database checklist in
5252 // preferences and have checkboxes.. rather than individual sources selected
5254 final JMenu rfetch = new JMenu(
5255 MessageManager.getString("action.fetch_db_references"));
5256 rfetch.setToolTipText(MessageManager
5257 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5258 webService.add(rfetch);
5260 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5261 MessageManager.getString("option.trim_retrieved_seqs"));
5262 trimrs.setToolTipText(MessageManager
5263 .getString("label.trim_retrieved_sequences"));
5264 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5265 trimrs.addActionListener(new ActionListener()
5268 public void actionPerformed(ActionEvent e)
5270 trimrs.setSelected(trimrs.isSelected());
5271 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5272 Boolean.valueOf(trimrs.isSelected()).toString());
5276 JMenuItem fetchr = new JMenuItem(
5277 MessageManager.getString("label.standard_databases"));
5278 fetchr.setToolTipText(MessageManager
5279 .getString("label.fetch_embl_uniprot"));
5280 fetchr.addActionListener(new ActionListener()
5284 public void actionPerformed(ActionEvent e)
5286 new Thread(new Runnable()
5291 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5292 .getAlignment().isNucleotide();
5293 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5294 .getSequenceSelection(), alignPanel.alignFrame, null,
5295 alignPanel.alignFrame.featureSettings, isNucleotide);
5296 dbRefFetcher.addListener(new FetchFinishedListenerI()
5299 public void finished()
5301 AlignFrame.this.setMenusForViewport();
5304 dbRefFetcher.fetchDBRefs(false);
5312 final AlignFrame me = this;
5313 new Thread(new Runnable()
5318 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5319 .getSequenceFetcherSingleton(me);
5320 javax.swing.SwingUtilities.invokeLater(new Runnable()
5325 String[] dbclasses = sf.getOrderedSupportedSources();
5326 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5327 // jalview.util.QuickSort.sort(otherdb, otherdb);
5328 List<DbSourceProxy> otherdb;
5329 JMenu dfetch = new JMenu();
5330 JMenu ifetch = new JMenu();
5331 JMenuItem fetchr = null;
5332 int comp = 0, icomp = 0, mcomp = 15;
5333 String mname = null;
5335 for (String dbclass : dbclasses)
5337 otherdb = sf.getSourceProxy(dbclass);
5338 // add a single entry for this class, or submenu allowing 'fetch
5340 if (otherdb == null || otherdb.size() < 1)
5344 // List<DbSourceProxy> dbs=otherdb;
5345 // otherdb=new ArrayList<DbSourceProxy>();
5346 // for (DbSourceProxy db:dbs)
5348 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5352 mname = "From " + dbclass;
5354 if (otherdb.size() == 1)
5356 final DbSourceProxy[] dassource = otherdb
5357 .toArray(new DbSourceProxy[0]);
5358 DbSourceProxy src = otherdb.get(0);
5359 fetchr = new JMenuItem(src.getDbSource());
5360 fetchr.addActionListener(new ActionListener()
5364 public void actionPerformed(ActionEvent e)
5366 new Thread(new Runnable()
5372 boolean isNucleotide = alignPanel.alignFrame
5373 .getViewport().getAlignment()
5375 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5376 alignPanel.av.getSequenceSelection(),
5377 alignPanel.alignFrame, dassource,
5378 alignPanel.alignFrame.featureSettings,
5381 .addListener(new FetchFinishedListenerI()
5384 public void finished()
5386 AlignFrame.this.setMenusForViewport();
5389 dbRefFetcher.fetchDBRefs(false);
5395 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5396 MessageManager.formatMessage(
5397 "label.fetch_retrieve_from",
5398 new Object[] { src.getDbName() })));
5404 final DbSourceProxy[] dassource = otherdb
5405 .toArray(new DbSourceProxy[0]);
5407 DbSourceProxy src = otherdb.get(0);
5408 fetchr = new JMenuItem(MessageManager.formatMessage(
5409 "label.fetch_all_param",
5410 new Object[] { src.getDbSource() }));
5411 fetchr.addActionListener(new ActionListener()
5414 public void actionPerformed(ActionEvent e)
5416 new Thread(new Runnable()
5422 boolean isNucleotide = alignPanel.alignFrame
5423 .getViewport().getAlignment()
5425 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5426 alignPanel.av.getSequenceSelection(),
5427 alignPanel.alignFrame, dassource,
5428 alignPanel.alignFrame.featureSettings,
5431 .addListener(new FetchFinishedListenerI()
5434 public void finished()
5436 AlignFrame.this.setMenusForViewport();
5439 dbRefFetcher.fetchDBRefs(false);
5445 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5446 MessageManager.formatMessage(
5447 "label.fetch_retrieve_from_all_sources",
5449 Integer.valueOf(otherdb.size())
5450 .toString(), src.getDbSource(),
5451 src.getDbName() })));
5454 // and then build the rest of the individual menus
5455 ifetch = new JMenu(MessageManager.formatMessage(
5456 "label.source_from_db_source",
5457 new Object[] { src.getDbSource() }));
5459 String imname = null;
5461 for (DbSourceProxy sproxy : otherdb)
5463 String dbname = sproxy.getDbName();
5464 String sname = dbname.length() > 5 ? dbname.substring(0,
5465 5) + "..." : dbname;
5466 String msname = dbname.length() > 10 ? dbname.substring(
5467 0, 10) + "..." : dbname;
5470 imname = MessageManager.formatMessage(
5471 "label.from_msname", new Object[] { sname });
5473 fetchr = new JMenuItem(msname);
5474 final DbSourceProxy[] dassrc = { sproxy };
5475 fetchr.addActionListener(new ActionListener()
5479 public void actionPerformed(ActionEvent e)
5481 new Thread(new Runnable()
5487 boolean isNucleotide = alignPanel.alignFrame
5488 .getViewport().getAlignment()
5490 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5491 alignPanel.av.getSequenceSelection(),
5492 alignPanel.alignFrame, dassrc,
5493 alignPanel.alignFrame.featureSettings,
5496 .addListener(new FetchFinishedListenerI()
5499 public void finished()
5501 AlignFrame.this.setMenusForViewport();
5504 dbRefFetcher.fetchDBRefs(false);
5510 fetchr.setToolTipText("<html>"
5511 + MessageManager.formatMessage(
5512 "label.fetch_retrieve_from", new Object[]
5516 if (++icomp >= mcomp || i == (otherdb.size()))
5518 ifetch.setText(MessageManager.formatMessage(
5519 "label.source_to_target", imname, sname));
5521 ifetch = new JMenu();
5529 if (comp >= mcomp || dbi >= (dbclasses.length))
5531 dfetch.setText(MessageManager.formatMessage(
5532 "label.source_to_target", mname, dbclass));
5534 dfetch = new JMenu();
5547 * Left justify the whole alignment.
5550 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5552 AlignmentI al = viewport.getAlignment();
5554 viewport.firePropertyChange("alignment", null, al);
5558 * Right justify the whole alignment.
5561 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5563 AlignmentI al = viewport.getAlignment();
5565 viewport.firePropertyChange("alignment", null, al);
5569 public void setShowSeqFeatures(boolean b)
5571 showSeqFeatures.setSelected(b);
5572 viewport.setShowSequenceFeatures(b);
5579 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5580 * awt.event.ActionEvent)
5583 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5585 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5586 alignPanel.paintAlignment(true);
5593 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5597 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5599 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5600 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5608 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5609 * .event.ActionEvent)
5612 protected void showGroupConservation_actionPerformed(ActionEvent e)
5614 viewport.setShowGroupConservation(showGroupConservation.getState());
5615 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5622 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5623 * .event.ActionEvent)
5626 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5628 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5629 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5636 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5637 * .event.ActionEvent)
5640 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5642 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5643 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5647 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5649 showSequenceLogo.setState(true);
5650 viewport.setShowSequenceLogo(true);
5651 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5652 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5656 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5658 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5665 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5666 * .event.ActionEvent)
5669 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5671 if (avc.makeGroupsFromSelection())
5673 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5674 alignPanel.updateAnnotation();
5675 alignPanel.paintAlignment(true);
5679 public void clearAlignmentSeqRep()
5681 // TODO refactor alignmentseqrep to controller
5682 if (viewport.getAlignment().hasSeqrep())
5684 viewport.getAlignment().setSeqrep(null);
5685 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5686 alignPanel.updateAnnotation();
5687 alignPanel.paintAlignment(true);
5692 protected void createGroup_actionPerformed(ActionEvent e)
5694 if (avc.createGroup())
5696 alignPanel.alignmentChanged();
5701 protected void unGroup_actionPerformed(ActionEvent e)
5705 alignPanel.alignmentChanged();
5710 * make the given alignmentPanel the currently selected tab
5712 * @param alignmentPanel
5714 public void setDisplayedView(AlignmentPanel alignmentPanel)
5716 if (!viewport.getSequenceSetId().equals(
5717 alignmentPanel.av.getSequenceSetId()))
5721 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5723 if (tabbedPane != null
5724 && tabbedPane.getTabCount() > 0
5725 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5726 .getSelectedIndex())
5728 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5733 * Action on selection of menu options to Show or Hide annotations.
5736 * @param forSequences
5737 * update sequence-related annotations
5738 * @param forAlignment
5739 * update non-sequence-related annotations
5742 protected void setAnnotationsVisibility(boolean visible,
5743 boolean forSequences, boolean forAlignment)
5745 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5746 .getAlignmentAnnotation();
5751 for (AlignmentAnnotation aa : anns)
5754 * don't display non-positional annotations on an alignment
5756 if (aa.annotations == null)
5760 boolean apply = (aa.sequenceRef == null && forAlignment)
5761 || (aa.sequenceRef != null && forSequences);
5764 aa.visible = visible;
5767 alignPanel.validateAnnotationDimensions(true);
5768 alignPanel.alignmentChanged();
5772 * Store selected annotation sort order for the view and repaint.
5775 protected void sortAnnotations_actionPerformed()
5777 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5779 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5780 alignPanel.paintAlignment(true);
5785 * @return alignment panels in this alignment frame
5787 public List<? extends AlignmentViewPanel> getAlignPanels()
5789 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5793 * Open a new alignment window, with the cDNA associated with this (protein)
5794 * alignment, aligned as is the protein.
5796 protected void viewAsCdna_actionPerformed()
5798 // TODO no longer a menu action - refactor as required
5799 final AlignmentI alignment = getViewport().getAlignment();
5800 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5801 if (mappings == null)
5805 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5806 for (SequenceI aaSeq : alignment.getSequences())
5808 for (AlignedCodonFrame acf : mappings)
5810 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5814 * There is a cDNA mapping for this protein sequence - add to new
5815 * alignment. It will share the same dataset sequence as other mapped
5816 * cDNA (no new mappings need to be created).
5818 final Sequence newSeq = new Sequence(dnaSeq);
5819 newSeq.setDatasetSequence(dnaSeq);
5820 cdnaSeqs.add(newSeq);
5824 if (cdnaSeqs.size() == 0)
5826 // show a warning dialog no mapped cDNA
5829 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5831 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5832 AlignFrame.DEFAULT_HEIGHT);
5833 cdna.alignAs(alignment);
5834 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5836 Desktop.addInternalFrame(alignFrame, newtitle,
5837 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5841 * Set visibility of dna/protein complement view (available when shown in a
5847 protected void showComplement_actionPerformed(boolean show)
5849 SplitContainerI sf = getSplitViewContainer();
5852 sf.setComplementVisible(this, show);
5857 * Generate the reverse (optionally complemented) of the selected sequences,
5858 * and add them to the alignment
5861 protected void showReverse_actionPerformed(boolean complement)
5863 AlignmentI al = null;
5866 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5867 al = dna.reverseCdna(complement);
5868 viewport.addAlignment(al, "");
5869 addHistoryItem(new EditCommand(
5870 MessageManager.getString("label.add_sequences"),
5871 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5872 viewport.getAlignment()));
5873 } catch (Exception ex)
5875 System.err.println(ex.getMessage());
5881 * Try to run a script in the Groovy console, having first ensured that this
5882 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5883 * be targeted at this alignment.
5886 protected void runGroovy_actionPerformed()
5888 Jalview.setCurrentAlignFrame(this);
5889 groovy.ui.Console console = Desktop.getGroovyConsole();
5890 if (console != null)
5894 console.runScript();
5895 } catch (Exception ex)
5897 System.err.println((ex.toString()));
5899 .showInternalMessageDialog(Desktop.desktop, MessageManager
5900 .getString("label.couldnt_run_groovy_script"),
5902 .getString("label.groovy_support_failed"),
5903 JvOptionPane.ERROR_MESSAGE);
5908 System.err.println("Can't run Groovy script as console not found");
5913 * Hides columns containing (or not containing) a specified feature, provided
5914 * that would not leave all columns hidden
5916 * @param featureType
5917 * @param columnsContaining
5920 public boolean hideFeatureColumns(String featureType,
5921 boolean columnsContaining)
5923 boolean notForHiding = avc.markColumnsContainingFeatures(
5924 columnsContaining, false, false, featureType);
5927 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5928 false, featureType))
5930 getViewport().hideSelectedColumns();
5938 protected void selectHighlightedColumns_actionPerformed(
5939 ActionEvent actionEvent)
5941 // include key modifier check in case user selects from menu
5942 avc.markHighlightedColumns(
5943 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5945 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5949 class PrintThread extends Thread
5953 public PrintThread(AlignmentPanel ap)
5958 static PageFormat pf;
5963 PrinterJob printJob = PrinterJob.getPrinterJob();
5967 printJob.setPrintable(ap, pf);
5971 printJob.setPrintable(ap);
5974 if (printJob.printDialog())
5979 } catch (Exception PrintException)
5981 PrintException.printStackTrace();