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.FileLoader;
70 import jalview.io.FormatAdapter;
71 import jalview.io.HtmlSvgOutput;
72 import jalview.io.IdentifyFile;
73 import jalview.io.JPredFile;
74 import jalview.io.JalviewFileChooser;
75 import jalview.io.JalviewFileView;
76 import jalview.io.JnetAnnotationMaker;
77 import jalview.io.NewickFile;
78 import jalview.io.TCoffeeScoreFile;
79 import jalview.jbgui.GAlignFrame;
80 import jalview.schemes.Blosum62ColourScheme;
81 import jalview.schemes.BuriedColourScheme;
82 import jalview.schemes.ClustalxColourScheme;
83 import jalview.schemes.ColourSchemeI;
84 import jalview.schemes.ColourSchemeProperty;
85 import jalview.schemes.HelixColourScheme;
86 import jalview.schemes.HydrophobicColourScheme;
87 import jalview.schemes.NucleotideColourScheme;
88 import jalview.schemes.PIDColourScheme;
89 import jalview.schemes.PurinePyrimidineColourScheme;
90 import jalview.schemes.RNAHelicesColourChooser;
91 import jalview.schemes.ResidueProperties;
92 import jalview.schemes.StrandColourScheme;
93 import jalview.schemes.TCoffeeColourScheme;
94 import jalview.schemes.TaylorColourScheme;
95 import jalview.schemes.TurnColourScheme;
96 import jalview.schemes.UserColourScheme;
97 import jalview.schemes.ZappoColourScheme;
98 import jalview.util.MessageManager;
99 import jalview.viewmodel.AlignmentViewport;
100 import jalview.ws.DBRefFetcher;
101 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
102 import jalview.ws.jws1.Discoverer;
103 import jalview.ws.jws2.Jws2Discoverer;
104 import jalview.ws.jws2.jabaws2.Jws2Instance;
105 import jalview.ws.seqfetcher.DbSourceProxy;
107 import java.awt.BorderLayout;
108 import java.awt.Component;
109 import java.awt.Rectangle;
110 import java.awt.Toolkit;
111 import java.awt.datatransfer.Clipboard;
112 import java.awt.datatransfer.DataFlavor;
113 import java.awt.datatransfer.StringSelection;
114 import java.awt.datatransfer.Transferable;
115 import java.awt.dnd.DnDConstants;
116 import java.awt.dnd.DropTargetDragEvent;
117 import java.awt.dnd.DropTargetDropEvent;
118 import java.awt.dnd.DropTargetEvent;
119 import java.awt.dnd.DropTargetListener;
120 import java.awt.event.ActionEvent;
121 import java.awt.event.ActionListener;
122 import java.awt.event.FocusAdapter;
123 import java.awt.event.FocusEvent;
124 import java.awt.event.ItemEvent;
125 import java.awt.event.ItemListener;
126 import java.awt.event.KeyAdapter;
127 import java.awt.event.KeyEvent;
128 import java.awt.event.MouseAdapter;
129 import java.awt.event.MouseEvent;
130 import java.awt.print.PageFormat;
131 import java.awt.print.PrinterJob;
132 import java.beans.PropertyChangeEvent;
135 import java.util.ArrayList;
136 import java.util.Arrays;
137 import java.util.Deque;
138 import java.util.Enumeration;
139 import java.util.Hashtable;
140 import java.util.List;
141 import java.util.Vector;
143 import javax.swing.JCheckBoxMenuItem;
144 import javax.swing.JEditorPane;
145 import javax.swing.JInternalFrame;
146 import javax.swing.JLayeredPane;
147 import javax.swing.JMenu;
148 import javax.swing.JMenuItem;
149 import javax.swing.JRadioButtonMenuItem;
150 import javax.swing.JScrollPane;
151 import javax.swing.SwingUtilities;
157 * @version $Revision$
159 public class AlignFrame extends GAlignFrame implements DropTargetListener,
160 IProgressIndicator, AlignViewControllerGuiI
163 public static final int DEFAULT_WIDTH = 700;
165 public static final int DEFAULT_HEIGHT = 500;
168 * The currently displayed panel (selected tabbed view if more than one)
170 public AlignmentPanel alignPanel;
172 AlignViewport viewport;
174 public AlignViewControllerI avc;
176 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
179 * Last format used to load or save alignments in this window
181 FileFormatI currentFileFormat = null;
184 * Current filename for this alignment
186 String fileName = null;
189 * Creates a new AlignFrame object with specific width and height.
195 public AlignFrame(AlignmentI al, int width, int height)
197 this(al, null, width, height);
201 * Creates a new AlignFrame object with specific width, height and
207 * @param sequenceSetId
209 public AlignFrame(AlignmentI al, int width, int height,
210 String sequenceSetId)
212 this(al, null, width, height, sequenceSetId);
216 * Creates a new AlignFrame object with specific width, height and
222 * @param sequenceSetId
225 public AlignFrame(AlignmentI al, int width, int height,
226 String sequenceSetId, String viewId)
228 this(al, null, width, height, sequenceSetId, viewId);
232 * new alignment window with hidden columns
236 * @param hiddenColumns
237 * ColumnSelection or null
239 * Width of alignment frame
243 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
244 int width, int height)
246 this(al, hiddenColumns, width, height, null);
250 * Create alignment frame for al with hiddenColumns, a specific width and
251 * height, and specific sequenceId
254 * @param hiddenColumns
257 * @param sequenceSetId
260 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
261 int width, int height, String sequenceSetId)
263 this(al, hiddenColumns, width, height, sequenceSetId, null);
267 * Create alignment frame for al with hiddenColumns, a specific width and
268 * height, and specific sequenceId
271 * @param hiddenColumns
274 * @param sequenceSetId
279 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
280 int width, int height, String sequenceSetId, String viewId)
282 setSize(width, height);
284 if (al.getDataset() == null)
289 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
291 alignPanel = new AlignmentPanel(this, viewport);
293 addAlignmentPanel(alignPanel, true);
297 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
298 ColumnSelection hiddenColumns, int width, int height)
300 setSize(width, height);
302 if (al.getDataset() == null)
307 viewport = new AlignViewport(al, hiddenColumns);
309 if (hiddenSeqs != null && hiddenSeqs.length > 0)
311 viewport.hideSequence(hiddenSeqs);
313 alignPanel = new AlignmentPanel(this, viewport);
314 addAlignmentPanel(alignPanel, true);
319 * Make a new AlignFrame from existing alignmentPanels
326 public AlignFrame(AlignmentPanel ap)
330 addAlignmentPanel(ap, false);
335 * initalise the alignframe from the underlying viewport data and the
340 if (!Jalview.isHeadlessMode())
342 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
345 avc = new jalview.controller.AlignViewController(this, viewport,
347 if (viewport.getAlignmentConservationAnnotation() == null)
349 BLOSUM62Colour.setEnabled(false);
350 conservationMenuItem.setEnabled(false);
351 modifyConservation.setEnabled(false);
352 // PIDColour.setEnabled(false);
353 // abovePIDThreshold.setEnabled(false);
354 // modifyPID.setEnabled(false);
357 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
360 if (sortby.equals("Id"))
362 sortIDMenuItem_actionPerformed(null);
364 else if (sortby.equals("Pairwise Identity"))
366 sortPairwiseMenuItem_actionPerformed(null);
369 if (Desktop.desktop != null)
371 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
372 addServiceListeners();
373 setGUINucleotide(viewport.getAlignment().isNucleotide());
377 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
379 setMenusFromViewport(viewport);
380 buildSortByAnnotationScoresMenu();
383 if (viewport.getWrapAlignment())
385 wrapMenuItem_actionPerformed(null);
388 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
390 this.overviewMenuItem_actionPerformed(null);
395 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
396 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
397 final String menuLabel = MessageManager
398 .getString("label.copy_format_from");
399 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
400 new ViewSetProvider()
404 public AlignmentPanel[] getAllAlignmentPanels()
407 origview.add(alignPanel);
408 // make an array of all alignment panels except for this one
409 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
410 Arrays.asList(Desktop.getAlignmentPanels(null)));
411 aps.remove(AlignFrame.this.alignPanel);
412 return aps.toArray(new AlignmentPanel[aps.size()]);
414 }, selviews, new ItemListener()
418 public void itemStateChanged(ItemEvent e)
420 if (origview.size() > 0)
422 final AlignmentPanel ap = origview.get(0);
425 * Copy the ViewStyle of the selected panel to 'this one'.
426 * Don't change value of 'scaleProteinAsCdna' unless copying
429 ViewStyleI vs = selviews.get(0).getAlignViewport()
431 boolean fromSplitFrame = selviews.get(0)
432 .getAlignViewport().getCodingComplement() != null;
435 vs.setScaleProteinAsCdna(ap.getAlignViewport()
436 .getViewStyle().isScaleProteinAsCdna());
438 ap.getAlignViewport().setViewStyle(vs);
441 * Also rescale ViewStyle of SplitFrame complement if there is
442 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
443 * the whole ViewStyle (allow cDNA protein to have different
446 AlignViewportI complement = ap.getAlignViewport()
447 .getCodingComplement();
448 if (complement != null && vs.isScaleProteinAsCdna())
450 AlignFrame af = Desktop.getAlignFrameFor(complement);
451 ((SplitFrame) af.getSplitViewContainer())
453 af.setMenusForViewport();
457 ap.setSelected(true);
458 ap.alignFrame.setMenusForViewport();
463 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
464 .indexOf("devel") > -1
465 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
466 .indexOf("test") > -1)
468 formatMenu.add(vsel);
470 addFocusListener(new FocusAdapter()
473 public void focusGained(FocusEvent e)
475 Jalview.setCurrentAlignFrame(AlignFrame.this);
482 * Change the filename and format for the alignment, and enable the 'reload'
483 * button functionality.
490 public void setFileName(String file, FileFormatI format)
493 setFileFormat(format);
494 reload.setEnabled(true);
498 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
501 void addKeyListener()
503 addKeyListener(new KeyAdapter()
506 public void keyPressed(KeyEvent evt)
508 if (viewport.cursorMode
509 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
510 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
511 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
512 && Character.isDigit(evt.getKeyChar()))
514 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
517 switch (evt.getKeyCode())
520 case 27: // escape key
521 deselectAllSequenceMenuItem_actionPerformed(null);
525 case KeyEvent.VK_DOWN:
526 if (evt.isAltDown() || !viewport.cursorMode)
528 moveSelectedSequences(false);
530 if (viewport.cursorMode)
532 alignPanel.getSeqPanel().moveCursor(0, 1);
537 if (evt.isAltDown() || !viewport.cursorMode)
539 moveSelectedSequences(true);
541 if (viewport.cursorMode)
543 alignPanel.getSeqPanel().moveCursor(0, -1);
548 case KeyEvent.VK_LEFT:
549 if (evt.isAltDown() || !viewport.cursorMode)
551 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
555 alignPanel.getSeqPanel().moveCursor(-1, 0);
560 case KeyEvent.VK_RIGHT:
561 if (evt.isAltDown() || !viewport.cursorMode)
563 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
567 alignPanel.getSeqPanel().moveCursor(1, 0);
571 case KeyEvent.VK_SPACE:
572 if (viewport.cursorMode)
574 alignPanel.getSeqPanel().insertGapAtCursor(
575 evt.isControlDown() || evt.isShiftDown()
580 // case KeyEvent.VK_A:
581 // if (viewport.cursorMode)
583 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
584 // //System.out.println("A");
588 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
589 * System.out.println("closing bracket"); } break;
591 case KeyEvent.VK_DELETE:
592 case KeyEvent.VK_BACK_SPACE:
593 if (!viewport.cursorMode)
595 cut_actionPerformed(null);
599 alignPanel.getSeqPanel().deleteGapAtCursor(
600 evt.isControlDown() || evt.isShiftDown()
607 if (viewport.cursorMode)
609 alignPanel.getSeqPanel().setCursorRow();
613 if (viewport.cursorMode && !evt.isControlDown())
615 alignPanel.getSeqPanel().setCursorColumn();
619 if (viewport.cursorMode)
621 alignPanel.getSeqPanel().setCursorPosition();
625 case KeyEvent.VK_ENTER:
626 case KeyEvent.VK_COMMA:
627 if (viewport.cursorMode)
629 alignPanel.getSeqPanel().setCursorRowAndColumn();
634 if (viewport.cursorMode)
636 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
640 if (viewport.cursorMode)
642 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
647 viewport.cursorMode = !viewport.cursorMode;
648 statusBar.setText(MessageManager.formatMessage(
649 "label.keyboard_editing_mode",
650 new String[] { (viewport.cursorMode ? "on" : "off") }));
651 if (viewport.cursorMode)
653 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
654 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
656 alignPanel.getSeqPanel().seqCanvas.repaint();
662 Help.showHelpWindow();
663 } catch (Exception ex)
665 ex.printStackTrace();
670 boolean toggleSeqs = !evt.isControlDown();
671 boolean toggleCols = !evt.isShiftDown();
672 toggleHiddenRegions(toggleSeqs, toggleCols);
677 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
678 boolean modifyExisting = true; // always modify, don't clear
679 // evt.isShiftDown();
680 boolean invertHighlighted = evt.isAltDown();
681 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
685 case KeyEvent.VK_PAGE_UP:
686 if (viewport.getWrapAlignment())
688 alignPanel.scrollUp(true);
692 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
693 - viewport.endSeq + viewport.startSeq);
696 case KeyEvent.VK_PAGE_DOWN:
697 if (viewport.getWrapAlignment())
699 alignPanel.scrollUp(false);
703 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
704 + viewport.endSeq - viewport.startSeq);
711 public void keyReleased(KeyEvent evt)
713 switch (evt.getKeyCode())
715 case KeyEvent.VK_LEFT:
716 if (evt.isAltDown() || !viewport.cursorMode)
718 viewport.firePropertyChange("alignment", null, viewport
719 .getAlignment().getSequences());
723 case KeyEvent.VK_RIGHT:
724 if (evt.isAltDown() || !viewport.cursorMode)
726 viewport.firePropertyChange("alignment", null, viewport
727 .getAlignment().getSequences());
735 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
737 ap.alignFrame = this;
738 avc = new jalview.controller.AlignViewController(this, viewport,
743 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
745 int aSize = alignPanels.size();
747 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
749 if (aSize == 1 && ap.av.viewName == null)
751 this.getContentPane().add(ap, BorderLayout.CENTER);
757 setInitialTabVisible();
760 expandViews.setEnabled(true);
761 gatherViews.setEnabled(true);
762 tabbedPane.addTab(ap.av.viewName, ap);
764 ap.setVisible(false);
769 if (ap.av.isPadGaps())
771 ap.av.getAlignment().padGaps();
773 ap.av.updateConservation(ap);
774 ap.av.updateConsensus(ap);
775 ap.av.updateStrucConsensus(ap);
779 public void setInitialTabVisible()
781 expandViews.setEnabled(true);
782 gatherViews.setEnabled(true);
783 tabbedPane.setVisible(true);
784 AlignmentPanel first = alignPanels.get(0);
785 tabbedPane.addTab(first.av.viewName, first);
786 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
789 public AlignViewport getViewport()
794 /* Set up intrinsic listeners for dynamically generated GUI bits. */
795 private void addServiceListeners()
797 final java.beans.PropertyChangeListener thisListener;
798 Desktop.instance.addJalviewPropertyChangeListener("services",
799 thisListener = new java.beans.PropertyChangeListener()
802 public void propertyChange(PropertyChangeEvent evt)
804 // // System.out.println("Discoverer property change.");
805 // if (evt.getPropertyName().equals("services"))
807 SwingUtilities.invokeLater(new Runnable()
814 .println("Rebuild WS Menu for service change");
815 BuildWebServiceMenu();
822 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
825 public void internalFrameClosed(
826 javax.swing.event.InternalFrameEvent evt)
828 // System.out.println("deregistering discoverer listener");
829 Desktop.instance.removeJalviewPropertyChangeListener("services",
831 closeMenuItem_actionPerformed(true);
834 // Finally, build the menu once to get current service state
835 new Thread(new Runnable()
840 BuildWebServiceMenu();
846 * Configure menu items that vary according to whether the alignment is
847 * nucleotide or protein
851 public void setGUINucleotide(boolean nucleotide)
853 showTranslation.setVisible(nucleotide);
854 showReverse.setVisible(nucleotide);
855 showReverseComplement.setVisible(nucleotide);
856 conservationMenuItem.setEnabled(!nucleotide);
857 modifyConservation.setEnabled(!nucleotide);
858 showGroupConservation.setEnabled(!nucleotide);
859 rnahelicesColour.setEnabled(nucleotide);
860 purinePyrimidineColour.setEnabled(nucleotide);
861 showComplementMenuItem.setText(nucleotide ? MessageManager
862 .getString("label.protein") : MessageManager
863 .getString("label.nucleotide"));
864 setColourSelected(jalview.bin.Cache.getDefault(
865 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
866 : Preferences.DEFAULT_COLOUR_PROT, "None"));
870 * set up menus for the current viewport. This may be called after any
871 * operation that affects the data in the current view (selection changed,
872 * etc) to update the menus to reflect the new state.
875 public void setMenusForViewport()
877 setMenusFromViewport(viewport);
881 * Need to call this method when tabs are selected for multiple views, or when
882 * loading from Jalview2XML.java
887 void setMenusFromViewport(AlignViewport av)
889 padGapsMenuitem.setSelected(av.isPadGaps());
890 colourTextMenuItem.setSelected(av.isShowColourText());
891 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
892 conservationMenuItem.setSelected(av.getConservationSelected());
893 seqLimits.setSelected(av.getShowJVSuffix());
894 idRightAlign.setSelected(av.isRightAlignIds());
895 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
896 renderGapsMenuItem.setSelected(av.isRenderGaps());
897 wrapMenuItem.setSelected(av.getWrapAlignment());
898 scaleAbove.setVisible(av.getWrapAlignment());
899 scaleLeft.setVisible(av.getWrapAlignment());
900 scaleRight.setVisible(av.getWrapAlignment());
901 annotationPanelMenuItem.setState(av.isShowAnnotation());
903 * Show/hide annotations only enabled if annotation panel is shown
905 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
906 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
907 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
908 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
909 viewBoxesMenuItem.setSelected(av.getShowBoxes());
910 viewTextMenuItem.setSelected(av.getShowText());
911 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
912 showGroupConsensus.setSelected(av.isShowGroupConsensus());
913 showGroupConservation.setSelected(av.isShowGroupConservation());
914 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
915 showSequenceLogo.setSelected(av.isShowSequenceLogo());
916 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
918 setColourSelected(ColourSchemeProperty.getColourName(av
919 .getGlobalColourScheme()));
921 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
922 hiddenMarkers.setState(av.getShowHiddenMarkers());
923 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
924 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
925 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
926 autoCalculate.setSelected(av.autoCalculateConsensus);
927 sortByTree.setSelected(av.sortByTree);
928 listenToViewSelections.setSelected(av.followSelection);
929 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
931 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
933 showProducts.setEnabled(canShowProducts());
934 setGroovyEnabled(Desktop.getGroovyConsole() != null);
940 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
944 public void setGroovyEnabled(boolean b)
946 runGroovy.setEnabled(b);
949 private IProgressIndicator progressBar;
954 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
957 public void setProgressBar(String message, long id)
959 progressBar.setProgressBar(message, id);
963 public void registerHandler(final long id,
964 final IProgressIndicatorHandler handler)
966 progressBar.registerHandler(id, handler);
971 * @return true if any progress bars are still active
974 public boolean operationInProgress()
976 return progressBar.operationInProgress();
980 public void setStatus(String text)
982 statusBar.setText(text);
986 * Added so Castor Mapping file can obtain Jalview Version
988 public String getVersion()
990 return jalview.bin.Cache.getProperty("VERSION");
993 public FeatureRenderer getFeatureRenderer()
995 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
999 public void fetchSequence_actionPerformed(ActionEvent e)
1001 new jalview.gui.SequenceFetcher(this);
1005 public void addFromFile_actionPerformed(ActionEvent e)
1007 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1011 public void reload_actionPerformed(ActionEvent e)
1013 if (fileName != null)
1015 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1016 // originating file's format
1017 // TODO: work out how to recover feature settings for correct view(s) when
1018 // file is reloaded.
1019 if (FileFormat.Jalview.equals(currentFileFormat))
1021 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1022 for (int i = 0; i < frames.length; i++)
1024 if (frames[i] instanceof AlignFrame && frames[i] != this
1025 && ((AlignFrame) frames[i]).fileName != null
1026 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1030 frames[i].setSelected(true);
1031 Desktop.instance.closeAssociatedWindows();
1032 } catch (java.beans.PropertyVetoException ex)
1038 Desktop.instance.closeAssociatedWindows();
1040 FileLoader loader = new FileLoader();
1041 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1042 : DataSourceType.FILE;
1043 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1047 Rectangle bounds = this.getBounds();
1049 FileLoader loader = new FileLoader();
1050 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1051 : DataSourceType.FILE;
1052 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1053 protocol, currentFileFormat);
1055 newframe.setBounds(bounds);
1056 if (featureSettings != null && featureSettings.isShowing())
1058 final Rectangle fspos = featureSettings.frame.getBounds();
1059 // TODO: need a 'show feature settings' function that takes bounds -
1060 // need to refactor Desktop.addFrame
1061 newframe.featureSettings_actionPerformed(null);
1062 final FeatureSettings nfs = newframe.featureSettings;
1063 SwingUtilities.invokeLater(new Runnable()
1068 nfs.frame.setBounds(fspos);
1071 this.featureSettings.close();
1072 this.featureSettings = null;
1074 this.closeMenuItem_actionPerformed(true);
1080 public void addFromText_actionPerformed(ActionEvent e)
1082 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1087 public void addFromURL_actionPerformed(ActionEvent e)
1089 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1093 public void save_actionPerformed(ActionEvent e)
1095 if (fileName == null || (currentFileFormat == null)
1096 || fileName.startsWith("http"))
1098 saveAs_actionPerformed(null);
1102 saveAlignment(fileName, currentFileFormat);
1113 public void saveAs_actionPerformed(ActionEvent e)
1115 String format = currentFileFormat == null ? null : currentFileFormat
1117 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1118 Cache.getProperty("LAST_DIRECTORY"), format);
1120 chooser.setFileView(new JalviewFileView());
1121 chooser.setDialogTitle(MessageManager
1122 .getString("label.save_alignment_to_file"));
1123 chooser.setToolTipText(MessageManager.getString("action.save"));
1125 int value = chooser.showSaveDialog(this);
1127 if (value == JalviewFileChooser.APPROVE_OPTION)
1129 currentFileFormat = chooser.getSelectedFormat();
1130 while (currentFileFormat == null)
1133 .showInternalMessageDialog(
1136 .getString("label.select_file_format_before_saving"),
1138 .getString("label.file_format_not_specified"),
1139 JvOptionPane.WARNING_MESSAGE);
1140 currentFileFormat = chooser.getSelectedFormat();
1141 value = chooser.showSaveDialog(this);
1142 if (value != JalviewFileChooser.APPROVE_OPTION)
1148 fileName = chooser.getSelectedFile().getPath();
1150 Cache.setProperty("DEFAULT_FILE_FORMAT",
1151 currentFileFormat.toString());
1153 Cache.setProperty("LAST_DIRECTORY", fileName);
1154 saveAlignment(fileName, currentFileFormat);
1158 public boolean saveAlignment(String file, FileFormatI format)
1160 boolean success = true;
1162 if (FileFormat.Jalview.equals(format))
1164 String shortName = title;
1166 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1168 shortName = shortName.substring(shortName
1169 .lastIndexOf(java.io.File.separatorChar) + 1);
1172 success = new Jalview2XML().saveAlignment(this, file, shortName);
1174 statusBar.setText(MessageManager.formatMessage(
1175 "label.successfully_saved_to_file_in_format", new Object[] {
1176 fileName, format }));
1181 // if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1183 // warningMessage("Cannot save file " + fileName + " using format "
1184 // + format, "Alignment output format not supported");
1185 // if (!Jalview.isHeadlessMode())
1187 // saveAs_actionPerformed(null);
1192 AlignmentExportData exportData = getAlignmentForExport(format,
1194 if (exportData.getSettings().isCancelled())
1198 FormatAdapter f = new FormatAdapter(alignPanel,
1199 exportData.getSettings());
1200 String output = f.formatSequences(
1202 exportData.getAlignment(), // class cast exceptions will
1203 // occur in the distant future
1204 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1205 f.getCacheSuffixDefault(format),
1206 viewport.getColumnSelection());
1216 java.io.PrintWriter out = new java.io.PrintWriter(
1217 new java.io.FileWriter(file));
1221 this.setTitle(file);
1222 statusBar.setText(MessageManager.formatMessage(
1223 "label.successfully_saved_to_file_in_format",
1224 new Object[] { fileName, format }));
1225 } catch (Exception ex)
1228 ex.printStackTrace();
1235 JvOptionPane.showInternalMessageDialog(this, MessageManager
1236 .formatMessage("label.couldnt_save_file",
1237 new Object[] { fileName }), MessageManager
1238 .getString("label.error_saving_file"),
1239 JvOptionPane.WARNING_MESSAGE);
1245 private void warningMessage(String warning, String title)
1247 if (new jalview.util.Platform().isHeadless())
1249 System.err.println("Warning: " + title + "\nWarning: " + warning);
1254 JvOptionPane.showInternalMessageDialog(this, warning, title,
1255 JvOptionPane.WARNING_MESSAGE);
1267 protected void outputText_actionPerformed(ActionEvent e)
1270 FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
1271 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1273 if (exportData.getSettings().isCancelled())
1277 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1278 cap.setForInput(null);
1281 FileFormatI format = fileFormat;
1282 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1283 .formatSequences(format,
1284 exportData.getAlignment(),
1285 exportData.getOmitHidden(),
1286 exportData.getStartEndPostions(),
1287 viewport.getColumnSelection()));
1288 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1289 "label.alignment_output_command",
1290 new Object[] { e.getActionCommand() }), 600, 500);
1291 } catch (OutOfMemoryError oom)
1293 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1299 public static AlignmentExportData getAlignmentForExport(
1300 FileFormatI format, AlignViewportI viewport,
1301 AlignExportSettingI exportSettings)
1303 AlignmentI alignmentToExport = null;
1304 AlignExportSettingI settings = exportSettings;
1305 String[] omitHidden = null;
1307 HiddenSequences hiddenSeqs = viewport.getAlignment()
1308 .getHiddenSequences();
1310 alignmentToExport = viewport.getAlignment();
1312 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1313 if (settings == null)
1315 settings = new AlignExportSettings(hasHiddenSeqs,
1316 viewport.hasHiddenColumns(), format);
1318 // settings.isExportAnnotations();
1320 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1322 omitHidden = viewport.getViewAsString(false,
1323 settings.isExportHiddenSequences());
1326 int[] alignmentStartEnd = new int[2];
1327 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1329 alignmentToExport = hiddenSeqs.getFullAlignment();
1333 alignmentToExport = viewport.getAlignment();
1335 alignmentStartEnd = alignmentToExport
1336 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1337 .getHiddenColumns());
1338 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1339 omitHidden, alignmentStartEnd, settings);
1350 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1352 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1353 htmlSVG.exportHTML(null);
1357 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1359 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1360 bjs.exportHTML(null);
1363 public void createImageMap(File file, String image)
1365 alignPanel.makePNGImageMap(file, image);
1375 public void createPNG(File f)
1377 alignPanel.makePNG(f);
1387 public void createEPS(File f)
1389 alignPanel.makeEPS(f);
1393 public void createSVG(File f)
1395 alignPanel.makeSVG(f);
1399 public void pageSetup_actionPerformed(ActionEvent e)
1401 PrinterJob printJob = PrinterJob.getPrinterJob();
1402 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1412 public void printMenuItem_actionPerformed(ActionEvent e)
1414 // Putting in a thread avoids Swing painting problems
1415 PrintThread thread = new PrintThread(alignPanel);
1420 public void exportFeatures_actionPerformed(ActionEvent e)
1422 new AnnotationExporter().exportFeatures(alignPanel);
1426 public void exportAnnotations_actionPerformed(ActionEvent e)
1428 new AnnotationExporter().exportAnnotations(alignPanel);
1432 public void associatedData_actionPerformed(ActionEvent e)
1434 // Pick the tree file
1435 JalviewFileChooser chooser = new JalviewFileChooser(
1436 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1437 chooser.setFileView(new JalviewFileView());
1438 chooser.setDialogTitle(MessageManager
1439 .getString("label.load_jalview_annotations"));
1440 chooser.setToolTipText(MessageManager
1441 .getString("label.load_jalview_annotations"));
1443 int value = chooser.showOpenDialog(null);
1445 if (value == JalviewFileChooser.APPROVE_OPTION)
1447 String choice = chooser.getSelectedFile().getPath();
1448 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1449 loadJalviewDataFile(choice, null, null, null);
1455 * Close the current view or all views in the alignment frame. If the frame
1456 * only contains one view then the alignment will be removed from memory.
1458 * @param closeAllTabs
1461 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1463 if (alignPanels != null && alignPanels.size() < 2)
1465 closeAllTabs = true;
1470 if (alignPanels != null)
1474 if (this.isClosed())
1476 // really close all the windows - otherwise wait till
1477 // setClosed(true) is called
1478 for (int i = 0; i < alignPanels.size(); i++)
1480 AlignmentPanel ap = alignPanels.get(i);
1487 closeView(alignPanel);
1494 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1495 * be called recursively, with the frame now in 'closed' state
1497 this.setClosed(true);
1499 } catch (Exception ex)
1501 ex.printStackTrace();
1506 * Close the specified panel and close up tabs appropriately.
1508 * @param panelToClose
1510 public void closeView(AlignmentPanel panelToClose)
1512 int index = tabbedPane.getSelectedIndex();
1513 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1514 alignPanels.remove(panelToClose);
1515 panelToClose.closePanel();
1516 panelToClose = null;
1518 tabbedPane.removeTabAt(closedindex);
1519 tabbedPane.validate();
1521 if (index > closedindex || index == tabbedPane.getTabCount())
1523 // modify currently selected tab index if necessary.
1527 this.tabSelectionChanged(index);
1533 void updateEditMenuBar()
1536 if (viewport.getHistoryList().size() > 0)
1538 undoMenuItem.setEnabled(true);
1539 CommandI command = viewport.getHistoryList().peek();
1540 undoMenuItem.setText(MessageManager.formatMessage(
1541 "label.undo_command",
1542 new Object[] { command.getDescription() }));
1546 undoMenuItem.setEnabled(false);
1547 undoMenuItem.setText(MessageManager.getString("action.undo"));
1550 if (viewport.getRedoList().size() > 0)
1552 redoMenuItem.setEnabled(true);
1554 CommandI command = viewport.getRedoList().peek();
1555 redoMenuItem.setText(MessageManager.formatMessage(
1556 "label.redo_command",
1557 new Object[] { command.getDescription() }));
1561 redoMenuItem.setEnabled(false);
1562 redoMenuItem.setText(MessageManager.getString("action.redo"));
1567 public void addHistoryItem(CommandI command)
1569 if (command.getSize() > 0)
1571 viewport.addToHistoryList(command);
1572 viewport.clearRedoList();
1573 updateEditMenuBar();
1574 viewport.updateHiddenColumns();
1575 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1576 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1577 // viewport.getColumnSelection()
1578 // .getHiddenColumns().size() > 0);
1584 * @return alignment objects for all views
1586 AlignmentI[] getViewAlignments()
1588 if (alignPanels != null)
1590 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1592 for (AlignmentPanel ap : alignPanels)
1594 als[i++] = ap.av.getAlignment();
1598 if (viewport != null)
1600 return new AlignmentI[] { viewport.getAlignment() };
1612 protected void undoMenuItem_actionPerformed(ActionEvent e)
1614 if (viewport.getHistoryList().isEmpty())
1618 CommandI command = viewport.getHistoryList().pop();
1619 viewport.addToRedoList(command);
1620 command.undoCommand(getViewAlignments());
1622 AlignmentViewport originalSource = getOriginatingSource(command);
1623 updateEditMenuBar();
1625 if (originalSource != null)
1627 if (originalSource != viewport)
1630 .warn("Implementation worry: mismatch of viewport origin for undo");
1632 originalSource.updateHiddenColumns();
1633 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1635 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1636 // viewport.getColumnSelection()
1637 // .getHiddenColumns().size() > 0);
1638 originalSource.firePropertyChange("alignment", null, originalSource
1639 .getAlignment().getSequences());
1650 protected void redoMenuItem_actionPerformed(ActionEvent e)
1652 if (viewport.getRedoList().size() < 1)
1657 CommandI command = viewport.getRedoList().pop();
1658 viewport.addToHistoryList(command);
1659 command.doCommand(getViewAlignments());
1661 AlignmentViewport originalSource = getOriginatingSource(command);
1662 updateEditMenuBar();
1664 if (originalSource != null)
1667 if (originalSource != viewport)
1670 .warn("Implementation worry: mismatch of viewport origin for redo");
1672 originalSource.updateHiddenColumns();
1673 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1675 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1676 // viewport.getColumnSelection()
1677 // .getHiddenColumns().size() > 0);
1678 originalSource.firePropertyChange("alignment", null, originalSource
1679 .getAlignment().getSequences());
1683 AlignmentViewport getOriginatingSource(CommandI command)
1685 AlignmentViewport originalSource = null;
1686 // For sequence removal and addition, we need to fire
1687 // the property change event FROM the viewport where the
1688 // original alignment was altered
1689 AlignmentI al = null;
1690 if (command instanceof EditCommand)
1692 EditCommand editCommand = (EditCommand) command;
1693 al = editCommand.getAlignment();
1694 List<Component> comps = PaintRefresher.components.get(viewport
1695 .getSequenceSetId());
1697 for (Component comp : comps)
1699 if (comp instanceof AlignmentPanel)
1701 if (al == ((AlignmentPanel) comp).av.getAlignment())
1703 originalSource = ((AlignmentPanel) comp).av;
1710 if (originalSource == null)
1712 // The original view is closed, we must validate
1713 // the current view against the closed view first
1716 PaintRefresher.validateSequences(al, viewport.getAlignment());
1719 originalSource = viewport;
1722 return originalSource;
1731 public void moveSelectedSequences(boolean up)
1733 SequenceGroup sg = viewport.getSelectionGroup();
1739 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1740 viewport.getHiddenRepSequences(), up);
1741 alignPanel.paintAlignment(true);
1744 synchronized void slideSequences(boolean right, int size)
1746 List<SequenceI> sg = new ArrayList<SequenceI>();
1747 if (viewport.cursorMode)
1749 sg.add(viewport.getAlignment().getSequenceAt(
1750 alignPanel.getSeqPanel().seqCanvas.cursorY));
1752 else if (viewport.getSelectionGroup() != null
1753 && viewport.getSelectionGroup().getSize() != viewport
1754 .getAlignment().getHeight())
1756 sg = viewport.getSelectionGroup().getSequences(
1757 viewport.getHiddenRepSequences());
1765 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1767 for (SequenceI seq : viewport.getAlignment().getSequences())
1769 if (!sg.contains(seq))
1771 invertGroup.add(seq);
1775 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1777 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1778 for (int i = 0; i < invertGroup.size(); i++)
1780 seqs2[i] = invertGroup.get(i);
1783 SlideSequencesCommand ssc;
1786 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1787 size, viewport.getGapCharacter());
1791 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1792 size, viewport.getGapCharacter());
1795 int groupAdjustment = 0;
1796 if (ssc.getGapsInsertedBegin() && right)
1798 if (viewport.cursorMode)
1800 alignPanel.getSeqPanel().moveCursor(size, 0);
1804 groupAdjustment = size;
1807 else if (!ssc.getGapsInsertedBegin() && !right)
1809 if (viewport.cursorMode)
1811 alignPanel.getSeqPanel().moveCursor(-size, 0);
1815 groupAdjustment = -size;
1819 if (groupAdjustment != 0)
1821 viewport.getSelectionGroup().setStartRes(
1822 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1823 viewport.getSelectionGroup().setEndRes(
1824 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1828 * just extend the last slide command if compatible; but not if in
1829 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1831 boolean appendHistoryItem = false;
1832 Deque<CommandI> historyList = viewport.getHistoryList();
1833 boolean inSplitFrame = getSplitViewContainer() != null;
1834 if (!inSplitFrame && historyList != null && historyList.size() > 0
1835 && historyList.peek() instanceof SlideSequencesCommand)
1837 appendHistoryItem = ssc
1838 .appendSlideCommand((SlideSequencesCommand) historyList
1842 if (!appendHistoryItem)
1844 addHistoryItem(ssc);
1857 protected void copy_actionPerformed(ActionEvent e)
1860 if (viewport.getSelectionGroup() == null)
1864 // TODO: preserve the ordering of displayed alignment annotation in any
1865 // internal paste (particularly sequence associated annotation)
1866 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1867 String[] omitHidden = null;
1869 if (viewport.hasHiddenColumns())
1871 omitHidden = viewport.getViewAsString(true);
1874 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1878 StringSelection ss = new StringSelection(output);
1882 jalview.gui.Desktop.internalCopy = true;
1883 // Its really worth setting the clipboard contents
1884 // to empty before setting the large StringSelection!!
1885 Toolkit.getDefaultToolkit().getSystemClipboard()
1886 .setContents(new StringSelection(""), null);
1888 Toolkit.getDefaultToolkit().getSystemClipboard()
1889 .setContents(ss, Desktop.instance);
1890 } catch (OutOfMemoryError er)
1892 new OOMWarning("copying region", er);
1896 ArrayList<int[]> hiddenColumns = null;
1897 if (viewport.hasHiddenColumns())
1899 hiddenColumns = new ArrayList<int[]>();
1900 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1901 .getSelectionGroup().getEndRes();
1902 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1904 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1906 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1907 region[1] - hiddenOffset });
1912 Desktop.jalviewClipboard = new Object[] { seqs,
1913 viewport.getAlignment().getDataset(), hiddenColumns };
1914 statusBar.setText(MessageManager.formatMessage(
1915 "label.copied_sequences_to_clipboard", new Object[] { Integer
1916 .valueOf(seqs.length).toString() }));
1926 protected void pasteNew_actionPerformed(ActionEvent e)
1938 protected void pasteThis_actionPerformed(ActionEvent e)
1944 * Paste contents of Jalview clipboard
1946 * @param newAlignment
1947 * true to paste to a new alignment, otherwise add to this.
1949 void paste(boolean newAlignment)
1951 boolean externalPaste = true;
1954 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1955 Transferable contents = c.getContents(this);
1957 if (contents == null)
1966 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1967 if (str.length() < 1)
1972 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1974 } catch (OutOfMemoryError er)
1976 new OOMWarning("Out of memory pasting sequences!!", er);
1980 SequenceI[] sequences;
1981 boolean annotationAdded = false;
1982 AlignmentI alignment = null;
1984 if (Desktop.jalviewClipboard != null)
1986 // The clipboard was filled from within Jalview, we must use the
1988 // And dataset from the copied alignment
1989 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1990 // be doubly sure that we create *new* sequence objects.
1991 sequences = new SequenceI[newseq.length];
1992 for (int i = 0; i < newseq.length; i++)
1994 sequences[i] = new Sequence(newseq[i]);
1996 alignment = new Alignment(sequences);
1997 externalPaste = false;
2001 // parse the clipboard as an alignment.
2002 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2004 sequences = alignment.getSequencesArray();
2008 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2014 if (Desktop.jalviewClipboard != null)
2016 // dataset is inherited
2017 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2021 // new dataset is constructed
2022 alignment.setDataset(null);
2024 alwidth = alignment.getWidth() + 1;
2028 AlignmentI pastedal = alignment; // preserve pasted alignment object
2029 // Add pasted sequences and dataset into existing alignment.
2030 alignment = viewport.getAlignment();
2031 alwidth = alignment.getWidth() + 1;
2032 // decide if we need to import sequences from an existing dataset
2033 boolean importDs = Desktop.jalviewClipboard != null
2034 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2035 // importDs==true instructs us to copy over new dataset sequences from
2036 // an existing alignment
2037 Vector newDs = (importDs) ? new Vector() : null; // used to create
2038 // minimum dataset set
2040 for (int i = 0; i < sequences.length; i++)
2044 newDs.addElement(null);
2046 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2048 if (importDs && ds != null)
2050 if (!newDs.contains(ds))
2052 newDs.setElementAt(ds, i);
2053 ds = new Sequence(ds);
2054 // update with new dataset sequence
2055 sequences[i].setDatasetSequence(ds);
2059 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2064 // copy and derive new dataset sequence
2065 sequences[i] = sequences[i].deriveSequence();
2066 alignment.getDataset().addSequence(
2067 sequences[i].getDatasetSequence());
2068 // TODO: avoid creation of duplicate dataset sequences with a
2069 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2071 alignment.addSequence(sequences[i]); // merges dataset
2075 newDs.clear(); // tidy up
2077 if (alignment.getAlignmentAnnotation() != null)
2079 for (AlignmentAnnotation alan : alignment
2080 .getAlignmentAnnotation())
2082 if (alan.graphGroup > fgroup)
2084 fgroup = alan.graphGroup;
2088 if (pastedal.getAlignmentAnnotation() != null)
2090 // Add any annotation attached to alignment.
2091 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2092 for (int i = 0; i < alann.length; i++)
2094 annotationAdded = true;
2095 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2097 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2098 if (newann.graphGroup > -1)
2100 if (newGraphGroups.size() <= newann.graphGroup
2101 || newGraphGroups.get(newann.graphGroup) == null)
2103 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2105 newGraphGroups.add(q, null);
2107 newGraphGroups.set(newann.graphGroup, new Integer(
2110 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2114 newann.padAnnotation(alwidth);
2115 alignment.addAnnotation(newann);
2125 addHistoryItem(new EditCommand(
2126 MessageManager.getString("label.add_sequences"),
2127 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2129 // Add any annotations attached to sequences
2130 for (int i = 0; i < sequences.length; i++)
2132 if (sequences[i].getAnnotation() != null)
2134 AlignmentAnnotation newann;
2135 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2137 annotationAdded = true;
2138 newann = sequences[i].getAnnotation()[a];
2139 newann.adjustForAlignment();
2140 newann.padAnnotation(alwidth);
2141 if (newann.graphGroup > -1)
2143 if (newann.graphGroup > -1)
2145 if (newGraphGroups.size() <= newann.graphGroup
2146 || newGraphGroups.get(newann.graphGroup) == null)
2148 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2150 newGraphGroups.add(q, null);
2152 newGraphGroups.set(newann.graphGroup, new Integer(
2155 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2159 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2164 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2171 // propagate alignment changed.
2172 viewport.setEndSeq(alignment.getHeight());
2173 if (annotationAdded)
2175 // Duplicate sequence annotation in all views.
2176 AlignmentI[] alview = this.getViewAlignments();
2177 for (int i = 0; i < sequences.length; i++)
2179 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2184 for (int avnum = 0; avnum < alview.length; avnum++)
2186 if (alview[avnum] != alignment)
2188 // duplicate in a view other than the one with input focus
2189 int avwidth = alview[avnum].getWidth() + 1;
2190 // this relies on sann being preserved after we
2191 // modify the sequence's annotation array for each duplication
2192 for (int a = 0; a < sann.length; a++)
2194 AlignmentAnnotation newann = new AlignmentAnnotation(
2196 sequences[i].addAlignmentAnnotation(newann);
2197 newann.padAnnotation(avwidth);
2198 alview[avnum].addAnnotation(newann); // annotation was
2199 // duplicated earlier
2200 // TODO JAL-1145 graphGroups are not updated for sequence
2201 // annotation added to several views. This may cause
2203 alview[avnum].setAnnotationIndex(newann, a);
2208 buildSortByAnnotationScoresMenu();
2210 viewport.firePropertyChange("alignment", null,
2211 alignment.getSequences());
2212 if (alignPanels != null)
2214 for (AlignmentPanel ap : alignPanels)
2216 ap.validateAnnotationDimensions(false);
2221 alignPanel.validateAnnotationDimensions(false);
2227 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2229 String newtitle = new String("Copied sequences");
2231 if (Desktop.jalviewClipboard != null
2232 && Desktop.jalviewClipboard[2] != null)
2234 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2235 for (int[] region : hc)
2237 af.viewport.hideColumns(region[0], region[1]);
2241 // >>>This is a fix for the moment, until a better solution is
2243 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2245 alignPanel.getSeqPanel().seqCanvas
2246 .getFeatureRenderer());
2248 // TODO: maintain provenance of an alignment, rather than just make the
2249 // title a concatenation of operations.
2252 if (title.startsWith("Copied sequences"))
2258 newtitle = newtitle.concat("- from " + title);
2263 newtitle = new String("Pasted sequences");
2266 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2271 } catch (Exception ex)
2273 ex.printStackTrace();
2274 System.out.println("Exception whilst pasting: " + ex);
2275 // could be anything being pasted in here
2281 protected void expand_newalign(ActionEvent e)
2285 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2286 .getAlignment(), -1);
2287 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2289 String newtitle = new String("Flanking alignment");
2291 if (Desktop.jalviewClipboard != null
2292 && Desktop.jalviewClipboard[2] != null)
2294 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2295 for (int region[] : hc)
2297 af.viewport.hideColumns(region[0], region[1]);
2301 // >>>This is a fix for the moment, until a better solution is
2303 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2305 alignPanel.getSeqPanel().seqCanvas
2306 .getFeatureRenderer());
2308 // TODO: maintain provenance of an alignment, rather than just make the
2309 // title a concatenation of operations.
2311 if (title.startsWith("Copied sequences"))
2317 newtitle = newtitle.concat("- from " + title);
2321 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2323 } catch (Exception ex)
2325 ex.printStackTrace();
2326 System.out.println("Exception whilst pasting: " + ex);
2327 // could be anything being pasted in here
2328 } catch (OutOfMemoryError oom)
2330 new OOMWarning("Viewing flanking region of alignment", oom);
2341 protected void cut_actionPerformed(ActionEvent e)
2343 copy_actionPerformed(null);
2344 delete_actionPerformed(null);
2354 protected void delete_actionPerformed(ActionEvent evt)
2357 SequenceGroup sg = viewport.getSelectionGroup();
2364 * If the cut affects all sequences, warn, remove highlighted columns
2366 if (sg.getSize() == viewport.getAlignment().getHeight())
2368 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2369 .getAlignment().getWidth()) ? true : false;
2370 if (isEntireAlignWidth)
2372 int confirm = JvOptionPane.showConfirmDialog(this,
2373 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2374 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2375 JvOptionPane.OK_CANCEL_OPTION);
2377 if (confirm == JvOptionPane.CANCEL_OPTION
2378 || confirm == JvOptionPane.CLOSED_OPTION)
2383 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2384 sg.getEndRes() + 1);
2386 SequenceI[] cut = sg.getSequences()
2387 .toArray(new SequenceI[sg.getSize()]);
2389 addHistoryItem(new EditCommand(
2390 MessageManager.getString("label.cut_sequences"), Action.CUT,
2391 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2392 viewport.getAlignment()));
2394 viewport.setSelectionGroup(null);
2395 viewport.sendSelection();
2396 viewport.getAlignment().deleteGroup(sg);
2398 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2400 if (viewport.getAlignment().getHeight() < 1)
2404 this.setClosed(true);
2405 } catch (Exception ex)
2418 protected void deleteGroups_actionPerformed(ActionEvent e)
2420 if (avc.deleteGroups())
2422 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2423 alignPanel.updateAnnotation();
2424 alignPanel.paintAlignment(true);
2435 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2437 SequenceGroup sg = new SequenceGroup();
2439 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2441 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2444 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2445 viewport.setSelectionGroup(sg);
2446 viewport.sendSelection();
2447 // JAL-2034 - should delegate to
2448 // alignPanel to decide if overview needs
2450 alignPanel.paintAlignment(false);
2451 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2461 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2463 if (viewport.cursorMode)
2465 alignPanel.getSeqPanel().keyboardNo1 = null;
2466 alignPanel.getSeqPanel().keyboardNo2 = null;
2468 viewport.setSelectionGroup(null);
2469 viewport.getColumnSelection().clear();
2470 viewport.setSelectionGroup(null);
2471 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2472 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2473 // JAL-2034 - should delegate to
2474 // alignPanel to decide if overview needs
2476 alignPanel.paintAlignment(false);
2477 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2478 viewport.sendSelection();
2488 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2490 SequenceGroup sg = viewport.getSelectionGroup();
2494 selectAllSequenceMenuItem_actionPerformed(null);
2499 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2501 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2503 // JAL-2034 - should delegate to
2504 // alignPanel to decide if overview needs
2507 alignPanel.paintAlignment(true);
2508 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2509 viewport.sendSelection();
2513 public void invertColSel_actionPerformed(ActionEvent e)
2515 viewport.invertColumnSelection();
2516 alignPanel.paintAlignment(true);
2517 viewport.sendSelection();
2527 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2529 trimAlignment(true);
2539 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2541 trimAlignment(false);
2544 void trimAlignment(boolean trimLeft)
2546 ColumnSelection colSel = viewport.getColumnSelection();
2549 if (!colSel.isEmpty())
2553 column = colSel.getMin();
2557 column = colSel.getMax();
2561 if (viewport.getSelectionGroup() != null)
2563 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2564 viewport.getHiddenRepSequences());
2568 seqs = viewport.getAlignment().getSequencesArray();
2571 TrimRegionCommand trimRegion;
2574 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2575 column, viewport.getAlignment());
2576 viewport.setStartRes(0);
2580 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2581 column, viewport.getAlignment());
2584 statusBar.setText(MessageManager.formatMessage(
2585 "label.removed_columns",
2586 new String[] { Integer.valueOf(trimRegion.getSize())
2589 addHistoryItem(trimRegion);
2591 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2593 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2594 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2596 viewport.getAlignment().deleteGroup(sg);
2600 viewport.firePropertyChange("alignment", null, viewport
2601 .getAlignment().getSequences());
2612 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2614 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2617 if (viewport.getSelectionGroup() != null)
2619 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2620 viewport.getHiddenRepSequences());
2621 start = viewport.getSelectionGroup().getStartRes();
2622 end = viewport.getSelectionGroup().getEndRes();
2626 seqs = viewport.getAlignment().getSequencesArray();
2629 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2630 "Remove Gapped Columns", seqs, start, end,
2631 viewport.getAlignment());
2633 addHistoryItem(removeGapCols);
2635 statusBar.setText(MessageManager.formatMessage(
2636 "label.removed_empty_columns",
2637 new Object[] { Integer.valueOf(removeGapCols.getSize())
2640 // This is to maintain viewport position on first residue
2641 // of first sequence
2642 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2643 int startRes = seq.findPosition(viewport.startRes);
2644 // ShiftList shifts;
2645 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2646 // edit.alColumnChanges=shifts.getInverse();
2647 // if (viewport.hasHiddenColumns)
2648 // viewport.getColumnSelection().compensateForEdits(shifts);
2649 viewport.setStartRes(seq.findIndex(startRes) - 1);
2650 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2662 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2664 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2667 if (viewport.getSelectionGroup() != null)
2669 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2670 viewport.getHiddenRepSequences());
2671 start = viewport.getSelectionGroup().getStartRes();
2672 end = viewport.getSelectionGroup().getEndRes();
2676 seqs = viewport.getAlignment().getSequencesArray();
2679 // This is to maintain viewport position on first residue
2680 // of first sequence
2681 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2682 int startRes = seq.findPosition(viewport.startRes);
2684 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2685 viewport.getAlignment()));
2687 viewport.setStartRes(seq.findIndex(startRes) - 1);
2689 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2701 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2703 viewport.setPadGaps(padGapsMenuitem.isSelected());
2704 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2715 public void findMenuItem_actionPerformed(ActionEvent e)
2721 * Create a new view of the current alignment.
2724 public void newView_actionPerformed(ActionEvent e)
2726 newView(null, true);
2730 * Creates and shows a new view of the current alignment.
2733 * title of newly created view; if null, one will be generated
2734 * @param copyAnnotation
2735 * if true then duplicate all annnotation, groups and settings
2736 * @return new alignment panel, already displayed.
2738 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2741 * Create a new AlignmentPanel (with its own, new Viewport)
2743 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2745 if (!copyAnnotation)
2748 * remove all groups and annotation except for the automatic stuff
2750 newap.av.getAlignment().deleteAllGroups();
2751 newap.av.getAlignment().deleteAllAnnotations(false);
2754 newap.av.setGatherViewsHere(false);
2756 if (viewport.viewName == null)
2758 viewport.viewName = MessageManager
2759 .getString("label.view_name_original");
2763 * Views share the same edits undo and redo stacks
2765 newap.av.setHistoryList(viewport.getHistoryList());
2766 newap.av.setRedoList(viewport.getRedoList());
2769 * Views share the same mappings; need to deregister any new mappings
2770 * created by copyAlignPanel, and register the new reference to the shared
2773 newap.av.replaceMappings(viewport.getAlignment());
2775 newap.av.viewName = getNewViewName(viewTitle);
2777 addAlignmentPanel(newap, true);
2778 newap.alignmentChanged();
2780 if (alignPanels.size() == 2)
2782 viewport.setGatherViewsHere(true);
2784 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2789 * Make a new name for the view, ensuring it is unique within the current
2790 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2791 * these now use viewId. Unique view names are still desirable for usability.)
2796 protected String getNewViewName(String viewTitle)
2798 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2799 boolean addFirstIndex = false;
2800 if (viewTitle == null || viewTitle.trim().length() == 0)
2802 viewTitle = MessageManager.getString("action.view");
2803 addFirstIndex = true;
2807 index = 1;// we count from 1 if given a specific name
2809 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2811 List<Component> comps = PaintRefresher.components.get(viewport
2812 .getSequenceSetId());
2814 List<String> existingNames = getExistingViewNames(comps);
2816 while (existingNames.contains(newViewName))
2818 newViewName = viewTitle + " " + (++index);
2824 * Returns a list of distinct view names found in the given list of
2825 * components. View names are held on the viewport of an AlignmentPanel.
2830 protected List<String> getExistingViewNames(List<Component> comps)
2832 List<String> existingNames = new ArrayList<String>();
2833 for (Component comp : comps)
2835 if (comp instanceof AlignmentPanel)
2837 AlignmentPanel ap = (AlignmentPanel) comp;
2838 if (!existingNames.contains(ap.av.viewName))
2840 existingNames.add(ap.av.viewName);
2844 return existingNames;
2848 * Explode tabbed views into separate windows.
2851 public void expandViews_actionPerformed(ActionEvent e)
2853 Desktop.explodeViews(this);
2857 * Gather views in separate windows back into a tabbed presentation.
2860 public void gatherViews_actionPerformed(ActionEvent e)
2862 Desktop.instance.gatherViews(this);
2872 public void font_actionPerformed(ActionEvent e)
2874 new FontChooser(alignPanel);
2884 protected void seqLimit_actionPerformed(ActionEvent e)
2886 viewport.setShowJVSuffix(seqLimits.isSelected());
2888 alignPanel.getIdPanel().getIdCanvas()
2889 .setPreferredSize(alignPanel.calculateIdWidth());
2890 alignPanel.paintAlignment(true);
2894 public void idRightAlign_actionPerformed(ActionEvent e)
2896 viewport.setRightAlignIds(idRightAlign.isSelected());
2897 alignPanel.paintAlignment(true);
2901 public void centreColumnLabels_actionPerformed(ActionEvent e)
2903 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2904 alignPanel.paintAlignment(true);
2910 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2913 protected void followHighlight_actionPerformed()
2916 * Set the 'follow' flag on the Viewport (and scroll to position if now
2919 final boolean state = this.followHighlightMenuItem.getState();
2920 viewport.setFollowHighlight(state);
2923 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2934 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2936 viewport.setColourText(colourTextMenuItem.isSelected());
2937 alignPanel.paintAlignment(true);
2947 public void wrapMenuItem_actionPerformed(ActionEvent e)
2949 scaleAbove.setVisible(wrapMenuItem.isSelected());
2950 scaleLeft.setVisible(wrapMenuItem.isSelected());
2951 scaleRight.setVisible(wrapMenuItem.isSelected());
2952 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2953 alignPanel.updateLayout();
2957 public void showAllSeqs_actionPerformed(ActionEvent e)
2959 viewport.showAllHiddenSeqs();
2963 public void showAllColumns_actionPerformed(ActionEvent e)
2965 viewport.showAllHiddenColumns();
2967 viewport.sendSelection();
2971 public void hideSelSequences_actionPerformed(ActionEvent e)
2973 viewport.hideAllSelectedSeqs();
2974 // alignPanel.paintAlignment(true);
2978 * called by key handler and the hide all/show all menu items
2983 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2986 boolean hide = false;
2987 SequenceGroup sg = viewport.getSelectionGroup();
2988 if (!toggleSeqs && !toggleCols)
2990 // Hide everything by the current selection - this is a hack - we do the
2991 // invert and then hide
2992 // first check that there will be visible columns after the invert.
2993 if (viewport.hasSelectedColumns()
2994 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2997 // now invert the sequence set, if required - empty selection implies
2998 // that no hiding is required.
3001 invertSequenceMenuItem_actionPerformed(null);
3002 sg = viewport.getSelectionGroup();
3006 viewport.expandColSelection(sg, true);
3007 // finally invert the column selection and get the new sequence
3009 invertColSel_actionPerformed(null);
3016 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3018 hideSelSequences_actionPerformed(null);
3021 else if (!(toggleCols && viewport.hasSelectedColumns()))
3023 showAllSeqs_actionPerformed(null);
3029 if (viewport.hasSelectedColumns())
3031 hideSelColumns_actionPerformed(null);
3034 viewport.setSelectionGroup(sg);
3039 showAllColumns_actionPerformed(null);
3048 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3049 * event.ActionEvent)
3052 public void hideAllButSelection_actionPerformed(ActionEvent e)
3054 toggleHiddenRegions(false, false);
3055 viewport.sendSelection();
3062 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3066 public void hideAllSelection_actionPerformed(ActionEvent e)
3068 SequenceGroup sg = viewport.getSelectionGroup();
3069 viewport.expandColSelection(sg, false);
3070 viewport.hideAllSelectedSeqs();
3071 viewport.hideSelectedColumns();
3072 alignPanel.paintAlignment(true);
3073 viewport.sendSelection();
3080 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3084 public void showAllhidden_actionPerformed(ActionEvent e)
3086 viewport.showAllHiddenColumns();
3087 viewport.showAllHiddenSeqs();
3088 alignPanel.paintAlignment(true);
3089 viewport.sendSelection();
3093 public void hideSelColumns_actionPerformed(ActionEvent e)
3095 viewport.hideSelectedColumns();
3096 alignPanel.paintAlignment(true);
3097 viewport.sendSelection();
3101 public void hiddenMarkers_actionPerformed(ActionEvent e)
3103 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3114 protected void scaleAbove_actionPerformed(ActionEvent e)
3116 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3117 alignPanel.paintAlignment(true);
3127 protected void scaleLeft_actionPerformed(ActionEvent e)
3129 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3130 alignPanel.paintAlignment(true);
3140 protected void scaleRight_actionPerformed(ActionEvent e)
3142 viewport.setScaleRightWrapped(scaleRight.isSelected());
3143 alignPanel.paintAlignment(true);
3153 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3155 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3156 alignPanel.paintAlignment(true);
3166 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3168 viewport.setShowText(viewTextMenuItem.isSelected());
3169 alignPanel.paintAlignment(true);
3179 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3181 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3182 alignPanel.paintAlignment(true);
3185 public FeatureSettings featureSettings;
3188 public FeatureSettingsControllerI getFeatureSettingsUI()
3190 return featureSettings;
3194 public void featureSettings_actionPerformed(ActionEvent e)
3196 if (featureSettings != null)
3198 featureSettings.close();
3199 featureSettings = null;
3201 if (!showSeqFeatures.isSelected())
3203 // make sure features are actually displayed
3204 showSeqFeatures.setSelected(true);
3205 showSeqFeatures_actionPerformed(null);
3207 featureSettings = new FeatureSettings(this);
3211 * Set or clear 'Show Sequence Features'
3217 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3219 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3220 alignPanel.paintAlignment(true);
3221 if (alignPanel.getOverviewPanel() != null)
3223 alignPanel.getOverviewPanel().updateOverviewImage();
3228 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3229 * the annotations panel as a whole.
3231 * The options to show/hide all annotations should be enabled when the panel
3232 * is shown, and disabled when the panel is hidden.
3237 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3239 final boolean setVisible = annotationPanelMenuItem.isSelected();
3240 viewport.setShowAnnotation(setVisible);
3241 this.showAllSeqAnnotations.setEnabled(setVisible);
3242 this.hideAllSeqAnnotations.setEnabled(setVisible);
3243 this.showAllAlAnnotations.setEnabled(setVisible);
3244 this.hideAllAlAnnotations.setEnabled(setVisible);
3245 alignPanel.updateLayout();
3249 public void alignmentProperties()
3251 JEditorPane editPane = new JEditorPane("text/html", "");
3252 editPane.setEditable(false);
3253 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3255 editPane.setText(MessageManager.formatMessage("label.html_content",
3256 new Object[] { contents.toString() }));
3257 JInternalFrame frame = new JInternalFrame();
3258 frame.getContentPane().add(new JScrollPane(editPane));
3260 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3261 "label.alignment_properties", new Object[] { getTitle() }),
3272 public void overviewMenuItem_actionPerformed(ActionEvent e)
3274 if (alignPanel.overviewPanel != null)
3279 JInternalFrame frame = new JInternalFrame();
3280 OverviewPanel overview = new OverviewPanel(alignPanel);
3281 frame.setContentPane(overview);
3282 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3283 "label.overview_params", new Object[] { this.getTitle() }),
3284 frame.getWidth(), frame.getHeight());
3286 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3287 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3290 public void internalFrameClosed(
3291 javax.swing.event.InternalFrameEvent evt)
3293 alignPanel.setOverviewPanel(null);
3297 alignPanel.setOverviewPanel(overview);
3301 public void textColour_actionPerformed(ActionEvent e)
3303 new TextColourChooser().chooseColour(alignPanel, null);
3313 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3325 public void clustalColour_actionPerformed(ActionEvent e)
3327 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3328 viewport.getHiddenRepSequences()));
3338 public void zappoColour_actionPerformed(ActionEvent e)
3340 changeColour(new ZappoColourScheme());
3350 public void taylorColour_actionPerformed(ActionEvent e)
3352 changeColour(new TaylorColourScheme());
3362 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3364 changeColour(new HydrophobicColourScheme());
3374 public void helixColour_actionPerformed(ActionEvent e)
3376 changeColour(new HelixColourScheme());
3386 public void strandColour_actionPerformed(ActionEvent e)
3388 changeColour(new StrandColourScheme());
3398 public void turnColour_actionPerformed(ActionEvent e)
3400 changeColour(new TurnColourScheme());
3410 public void buriedColour_actionPerformed(ActionEvent e)
3412 changeColour(new BuriedColourScheme());
3422 public void nucleotideColour_actionPerformed(ActionEvent e)
3424 changeColour(new NucleotideColourScheme());
3428 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3430 changeColour(new PurinePyrimidineColourScheme());
3434 * public void covariationColour_actionPerformed(ActionEvent e) {
3436 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3440 public void annotationColour_actionPerformed(ActionEvent e)
3442 new AnnotationColourChooser(viewport, alignPanel);
3446 public void annotationColumn_actionPerformed(ActionEvent e)
3448 new AnnotationColumnChooser(viewport, alignPanel);
3452 public void rnahelicesColour_actionPerformed(ActionEvent e)
3454 new RNAHelicesColourChooser(viewport, alignPanel);
3464 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3466 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3476 public void changeColour(ColourSchemeI cs)
3478 // TODO: pull up to controller method
3482 // Make sure viewport is up to date w.r.t. any sliders
3483 if (viewport.getAbovePIDThreshold())
3485 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3487 viewport.setThreshold(threshold);
3490 if (viewport.getConservationSelected())
3492 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3495 if (cs instanceof TCoffeeColourScheme)
3497 tcoffeeColour.setEnabled(true);
3498 tcoffeeColour.setSelected(true);
3502 viewport.setGlobalColourScheme(cs);
3504 alignPanel.paintAlignment(true);
3514 protected void modifyPID_actionPerformed(ActionEvent e)
3516 if (viewport.getAbovePIDThreshold()
3517 && viewport.getGlobalColourScheme() != null)
3519 SliderPanel.setPIDSliderSource(alignPanel,
3520 viewport.getGlobalColourScheme(), "Background");
3521 SliderPanel.showPIDSlider();
3532 protected void modifyConservation_actionPerformed(ActionEvent e)
3534 if (viewport.getConservationSelected()
3535 && viewport.getGlobalColourScheme() != null)
3537 SliderPanel.setConservationSlider(alignPanel,
3538 viewport.getGlobalColourScheme(), "Background");
3539 SliderPanel.showConservationSlider();
3550 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3552 viewport.setConservationSelected(conservationMenuItem.isSelected());
3554 viewport.setAbovePIDThreshold(false);
3555 abovePIDThreshold.setSelected(false);
3557 changeColour(viewport.getGlobalColourScheme());
3559 modifyConservation_actionPerformed(null);
3569 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3571 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3573 conservationMenuItem.setSelected(false);
3574 viewport.setConservationSelected(false);
3576 changeColour(viewport.getGlobalColourScheme());
3578 modifyPID_actionPerformed(null);
3588 public void userDefinedColour_actionPerformed(ActionEvent e)
3590 if (e.getActionCommand().equals(
3591 MessageManager.getString("action.user_defined")))
3593 new UserDefinedColours(alignPanel, null);
3597 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3598 .getUserColourSchemes().get(e.getActionCommand());
3604 public void updateUserColourMenu()
3607 Component[] menuItems = colourMenu.getMenuComponents();
3608 int iSize = menuItems.length;
3609 for (int i = 0; i < iSize; i++)
3611 if (menuItems[i].getName() != null
3612 && menuItems[i].getName().equals("USER_DEFINED"))
3614 colourMenu.remove(menuItems[i]);
3618 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3620 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3621 .getUserColourSchemes().keys();
3623 while (userColours.hasMoreElements())
3625 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3626 userColours.nextElement().toString());
3627 radioItem.setName("USER_DEFINED");
3628 radioItem.addMouseListener(new MouseAdapter()
3631 public void mousePressed(MouseEvent evt)
3633 if (evt.isPopupTrigger()) // Mac
3635 offerRemoval(radioItem);
3640 public void mouseReleased(MouseEvent evt)
3642 if (evt.isPopupTrigger()) // Windows
3644 offerRemoval(radioItem);
3651 void offerRemoval(final JRadioButtonMenuItem radioItem)
3653 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3655 int option = JvOptionPane.showInternalConfirmDialog(
3656 jalview.gui.Desktop.desktop, MessageManager
3657 .getString("label.remove_from_default_list"),
3659 .getString("label.remove_user_defined_colour"),
3660 JvOptionPane.YES_NO_OPTION);
3661 if (option == JvOptionPane.YES_OPTION)
3663 jalview.gui.UserDefinedColours
3664 .removeColourFromDefaults(radioItem.getText());
3665 colourMenu.remove(radioItem);
3669 radioItem.addActionListener(new ActionListener()
3672 public void actionPerformed(ActionEvent evt)
3674 userDefinedColour_actionPerformed(evt);
3680 radioItem.addActionListener(new ActionListener()
3683 public void actionPerformed(ActionEvent evt)
3685 userDefinedColour_actionPerformed(evt);
3689 colourMenu.insert(radioItem, 15);
3690 colours.add(radioItem);
3702 public void PIDColour_actionPerformed(ActionEvent e)
3704 changeColour(new PIDColourScheme());
3714 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3716 changeColour(new Blosum62ColourScheme());
3726 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3728 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3729 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3730 .getAlignment().getSequenceAt(0), null);
3731 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3732 viewport.getAlignment()));
3733 alignPanel.paintAlignment(true);
3743 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3745 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3746 AlignmentSorter.sortByID(viewport.getAlignment());
3747 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3748 viewport.getAlignment()));
3749 alignPanel.paintAlignment(true);
3759 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3761 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3762 AlignmentSorter.sortByLength(viewport.getAlignment());
3763 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3764 viewport.getAlignment()));
3765 alignPanel.paintAlignment(true);
3775 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3777 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3778 AlignmentSorter.sortByGroup(viewport.getAlignment());
3779 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3780 viewport.getAlignment()));
3782 alignPanel.paintAlignment(true);
3792 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3794 new RedundancyPanel(alignPanel, this);
3804 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3806 if ((viewport.getSelectionGroup() == null)
3807 || (viewport.getSelectionGroup().getSize() < 2))
3809 JvOptionPane.showInternalMessageDialog(this, MessageManager
3810 .getString("label.you_must_select_least_two_sequences"),
3811 MessageManager.getString("label.invalid_selection"),
3812 JvOptionPane.WARNING_MESSAGE);
3816 JInternalFrame frame = new JInternalFrame();
3817 frame.setContentPane(new PairwiseAlignPanel(viewport));
3818 Desktop.addInternalFrame(frame,
3819 MessageManager.getString("action.pairwise_alignment"), 600,
3831 public void PCAMenuItem_actionPerformed(ActionEvent e)
3833 if (((viewport.getSelectionGroup() != null)
3834 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3835 .getSelectionGroup().getSize() > 0))
3836 || (viewport.getAlignment().getHeight() < 4))
3839 .showInternalMessageDialog(
3842 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3844 .getString("label.sequence_selection_insufficient"),
3845 JvOptionPane.WARNING_MESSAGE);
3850 new PCAPanel(alignPanel);
3854 public void autoCalculate_actionPerformed(ActionEvent e)
3856 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3857 if (viewport.autoCalculateConsensus)
3859 viewport.firePropertyChange("alignment", null, viewport
3860 .getAlignment().getSequences());
3865 public void sortByTreeOption_actionPerformed(ActionEvent e)
3867 viewport.sortByTree = sortByTree.isSelected();
3871 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3873 viewport.followSelection = listenToViewSelections.isSelected();
3883 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3885 newTreePanel("AV", "PID", "Average distance tree using PID");
3895 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3897 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3907 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3909 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3919 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3921 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3934 void newTreePanel(String type, String pwType, String title)
3938 if (viewport.getSelectionGroup() != null
3939 && viewport.getSelectionGroup().getSize() > 0)
3941 if (viewport.getSelectionGroup().getSize() < 3)
3947 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3949 .getString("label.not_enough_sequences"),
3950 JvOptionPane.WARNING_MESSAGE);
3954 SequenceGroup sg = viewport.getSelectionGroup();
3956 /* Decide if the selection is a column region */
3957 for (SequenceI _s : sg.getSequences())
3959 if (_s.getLength() < sg.getEndRes())
3965 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3967 .getString("label.sequences_selection_not_aligned"),
3968 JvOptionPane.WARNING_MESSAGE);
3974 title = title + " on region";
3975 tp = new TreePanel(alignPanel, type, pwType);
3979 // are the visible sequences aligned?
3980 if (!viewport.getAlignment().isAligned(false))
3986 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3988 .getString("label.sequences_not_aligned"),
3989 JvOptionPane.WARNING_MESSAGE);
3994 if (viewport.getAlignment().getHeight() < 2)
3999 tp = new TreePanel(alignPanel, type, pwType);
4004 if (viewport.viewName != null)
4006 title += viewport.viewName + " of ";
4009 title += this.title;
4011 Desktop.addInternalFrame(tp, title, 600, 500);
4022 public void addSortByOrderMenuItem(String title,
4023 final AlignmentOrder order)
4025 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4026 "action.by_title_param", new Object[] { title }));
4028 item.addActionListener(new java.awt.event.ActionListener()
4031 public void actionPerformed(ActionEvent e)
4033 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4035 // TODO: JBPNote - have to map order entries to curent SequenceI
4037 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4039 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4042 alignPanel.paintAlignment(true);
4048 * Add a new sort by annotation score menu item
4051 * the menu to add the option to
4053 * the label used to retrieve scores for each sequence on the
4056 public void addSortByAnnotScoreMenuItem(JMenu sort,
4057 final String scoreLabel)
4059 final JMenuItem item = new JMenuItem(scoreLabel);
4061 item.addActionListener(new java.awt.event.ActionListener()
4064 public void actionPerformed(ActionEvent e)
4066 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4067 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4068 viewport.getAlignment());// ,viewport.getSelectionGroup());
4069 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4070 viewport.getAlignment()));
4071 alignPanel.paintAlignment(true);
4077 * last hash for alignment's annotation array - used to minimise cost of
4080 protected int _annotationScoreVectorHash;
4083 * search the alignment and rebuild the sort by annotation score submenu the
4084 * last alignment annotation vector hash is stored to minimize cost of
4085 * rebuilding in subsequence calls.
4089 public void buildSortByAnnotationScoresMenu()
4091 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4096 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4098 sortByAnnotScore.removeAll();
4099 // almost certainly a quicker way to do this - but we keep it simple
4100 Hashtable scoreSorts = new Hashtable();
4101 AlignmentAnnotation aann[];
4102 for (SequenceI sqa : viewport.getAlignment().getSequences())
4104 aann = sqa.getAnnotation();
4105 for (int i = 0; aann != null && i < aann.length; i++)
4107 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4109 scoreSorts.put(aann[i].label, aann[i].label);
4113 Enumeration labels = scoreSorts.keys();
4114 while (labels.hasMoreElements())
4116 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4117 (String) labels.nextElement());
4119 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4122 _annotationScoreVectorHash = viewport.getAlignment()
4123 .getAlignmentAnnotation().hashCode();
4128 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4129 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4130 * call. Listeners are added to remove the menu item when the treePanel is
4131 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4135 * Displayed tree window.
4137 * SortBy menu item title.
4140 public void buildTreeMenu()
4142 calculateTree.removeAll();
4143 // build the calculate menu
4145 for (final String type : new String[] { "NJ", "AV" })
4147 String treecalcnm = MessageManager.getString("label.tree_calc_"
4148 + type.toLowerCase());
4149 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4151 JMenuItem tm = new JMenuItem();
4152 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4153 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4154 || sm.isProtein() == !viewport.getAlignment()
4157 String smn = MessageManager.getStringOrReturn(
4158 "label.score_model_", sm.getName());
4159 final String title = MessageManager.formatMessage(
4160 "label.treecalc_title", treecalcnm, smn);
4161 tm.setText(title);//
4162 tm.addActionListener(new java.awt.event.ActionListener()
4165 public void actionPerformed(ActionEvent e)
4167 newTreePanel(type, pwtype, title);
4170 calculateTree.add(tm);
4175 sortByTreeMenu.removeAll();
4177 List<Component> comps = PaintRefresher.components.get(viewport
4178 .getSequenceSetId());
4179 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4180 for (Component comp : comps)
4182 if (comp instanceof TreePanel)
4184 treePanels.add((TreePanel) comp);
4188 if (treePanels.size() < 1)
4190 sortByTreeMenu.setVisible(false);
4194 sortByTreeMenu.setVisible(true);
4196 for (final TreePanel tp : treePanels)
4198 final JMenuItem item = new JMenuItem(tp.getTitle());
4199 item.addActionListener(new java.awt.event.ActionListener()
4202 public void actionPerformed(ActionEvent e)
4204 tp.sortByTree_actionPerformed();
4205 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4210 sortByTreeMenu.add(item);
4214 public boolean sortBy(AlignmentOrder alorder, String undoname)
4216 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4217 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4218 if (undoname != null)
4220 addHistoryItem(new OrderCommand(undoname, oldOrder,
4221 viewport.getAlignment()));
4223 alignPanel.paintAlignment(true);
4228 * Work out whether the whole set of sequences or just the selected set will
4229 * be submitted for multiple alignment.
4232 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4234 // Now, check we have enough sequences
4235 AlignmentView msa = null;
4237 if ((viewport.getSelectionGroup() != null)
4238 && (viewport.getSelectionGroup().getSize() > 1))
4240 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4241 // some common interface!
4243 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4244 * SequenceI[sz = seqs.getSize(false)];
4246 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4247 * seqs.getSequenceAt(i); }
4249 msa = viewport.getAlignmentView(true);
4251 else if (viewport.getSelectionGroup() != null
4252 && viewport.getSelectionGroup().getSize() == 1)
4254 int option = JvOptionPane.showConfirmDialog(this,
4255 MessageManager.getString("warn.oneseq_msainput_selection"),
4256 MessageManager.getString("label.invalid_selection"),
4257 JvOptionPane.OK_CANCEL_OPTION);
4258 if (option == JvOptionPane.OK_OPTION)
4260 msa = viewport.getAlignmentView(false);
4265 msa = viewport.getAlignmentView(false);
4271 * Decides what is submitted to a secondary structure prediction service: the
4272 * first sequence in the alignment, or in the current selection, or, if the
4273 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4274 * region or the whole alignment. (where the first sequence in the set is the
4275 * one that the prediction will be for).
4277 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4279 AlignmentView seqs = null;
4281 if ((viewport.getSelectionGroup() != null)
4282 && (viewport.getSelectionGroup().getSize() > 0))
4284 seqs = viewport.getAlignmentView(true);
4288 seqs = viewport.getAlignmentView(false);
4290 // limit sequences - JBPNote in future - could spawn multiple prediction
4292 // TODO: viewport.getAlignment().isAligned is a global state - the local
4293 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4294 if (!viewport.getAlignment().isAligned(false))
4296 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4297 // TODO: if seqs.getSequences().length>1 then should really have warned
4311 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4313 // Pick the tree file
4314 JalviewFileChooser chooser = new JalviewFileChooser(
4315 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4316 chooser.setFileView(new JalviewFileView());
4317 chooser.setDialogTitle(MessageManager
4318 .getString("label.select_newick_like_tree_file"));
4319 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4321 int value = chooser.showOpenDialog(null);
4323 if (value == JalviewFileChooser.APPROVE_OPTION)
4325 String choice = chooser.getSelectedFile().getPath();
4326 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4327 jalview.io.NewickFile fin = null;
4330 fin = new NewickFile(choice, DataSourceType.FILE);
4331 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4332 } catch (Exception ex)
4339 .getString("label.problem_reading_tree_file"),
4340 JvOptionPane.WARNING_MESSAGE);
4341 ex.printStackTrace();
4343 if (fin != null && fin.hasWarningMessage())
4345 JvOptionPane.showMessageDialog(Desktop.desktop, fin
4346 .getWarningMessage(), MessageManager
4347 .getString("label.possible_problem_with_tree_file"),
4348 JvOptionPane.WARNING_MESSAGE);
4354 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4356 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4359 public TreePanel ShowNewickTree(NewickFile nf, String title)
4361 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4364 public TreePanel ShowNewickTree(NewickFile nf, String title,
4365 AlignmentView input)
4367 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4370 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4371 int h, int x, int y)
4373 return ShowNewickTree(nf, title, null, w, h, x, y);
4377 * Add a treeviewer for the tree extracted from a newick file object to the
4378 * current alignment view
4385 * Associated alignment input data (or null)
4394 * @return TreePanel handle
4396 public TreePanel ShowNewickTree(NewickFile nf, String title,
4397 AlignmentView input, int w, int h, int x, int y)
4399 TreePanel tp = null;
4405 if (nf.getTree() != null)
4407 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4413 tp.setLocation(x, y);
4416 Desktop.addInternalFrame(tp, title, w, h);
4418 } catch (Exception ex)
4420 ex.printStackTrace();
4426 private boolean buildingMenu = false;
4429 * Generates menu items and listener event actions for web service clients
4432 public void BuildWebServiceMenu()
4434 while (buildingMenu)
4438 System.err.println("Waiting for building menu to finish.");
4440 } catch (Exception e)
4444 final AlignFrame me = this;
4445 buildingMenu = true;
4446 new Thread(new Runnable()
4451 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4454 // System.err.println("Building ws menu again "
4455 // + Thread.currentThread());
4456 // TODO: add support for context dependent disabling of services based
4458 // alignment and current selection
4459 // TODO: add additional serviceHandle parameter to specify abstract
4461 // class independently of AbstractName
4462 // TODO: add in rediscovery GUI function to restart discoverer
4463 // TODO: group services by location as well as function and/or
4465 // object broker mechanism.
4466 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4467 final IProgressIndicator af = me;
4470 * do not i18n these strings - they are hard-coded in class
4471 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4472 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4474 final JMenu msawsmenu = new JMenu("Alignment");
4475 final JMenu secstrmenu = new JMenu(
4476 "Secondary Structure Prediction");
4477 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4478 final JMenu analymenu = new JMenu("Analysis");
4479 final JMenu dismenu = new JMenu("Protein Disorder");
4480 // JAL-940 - only show secondary structure prediction services from
4481 // the legacy server
4482 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4484 Discoverer.services != null && (Discoverer.services.size() > 0))
4486 // TODO: refactor to allow list of AbstractName/Handler bindings to
4488 // stored or retrieved from elsewhere
4489 // No MSAWS used any more:
4490 // Vector msaws = null; // (Vector)
4491 // Discoverer.services.get("MsaWS");
4492 Vector secstrpr = (Vector) Discoverer.services
4494 if (secstrpr != null)
4496 // Add any secondary structure prediction services
4497 for (int i = 0, j = secstrpr.size(); i < j; i++)
4499 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4501 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4502 .getServiceClient(sh);
4503 int p = secstrmenu.getItemCount();
4504 impl.attachWSMenuEntry(secstrmenu, me);
4505 int q = secstrmenu.getItemCount();
4506 for (int litm = p; litm < q; litm++)
4508 legacyItems.add(secstrmenu.getItem(litm));
4514 // Add all submenus in the order they should appear on the web
4516 wsmenu.add(msawsmenu);
4517 wsmenu.add(secstrmenu);
4518 wsmenu.add(dismenu);
4519 wsmenu.add(analymenu);
4520 // No search services yet
4521 // wsmenu.add(seqsrchmenu);
4523 javax.swing.SwingUtilities.invokeLater(new Runnable()
4530 webService.removeAll();
4531 // first, add discovered services onto the webservices menu
4532 if (wsmenu.size() > 0)
4534 for (int i = 0, j = wsmenu.size(); i < j; i++)
4536 webService.add(wsmenu.get(i));
4541 webService.add(me.webServiceNoServices);
4543 // TODO: move into separate menu builder class.
4544 boolean new_sspred = false;
4545 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4547 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4548 if (jws2servs != null)
4550 if (jws2servs.hasServices())
4552 jws2servs.attachWSMenuEntry(webService, me);
4553 for (Jws2Instance sv : jws2servs.getServices())
4555 if (sv.description.toLowerCase().contains("jpred"))
4557 for (JMenuItem jmi : legacyItems)
4559 jmi.setVisible(false);
4565 if (jws2servs.isRunning())
4567 JMenuItem tm = new JMenuItem(
4568 "Still discovering JABA Services");
4569 tm.setEnabled(false);
4574 build_urlServiceMenu(me.webService);
4575 build_fetchdbmenu(webService);
4576 for (JMenu item : wsmenu)
4578 if (item.getItemCount() == 0)
4580 item.setEnabled(false);
4584 item.setEnabled(true);
4587 } catch (Exception e)
4590 .debug("Exception during web service menu building process.",
4595 } catch (Exception e)
4598 buildingMenu = false;
4605 * construct any groupURL type service menu entries.
4609 private void build_urlServiceMenu(JMenu webService)
4611 // TODO: remove this code when 2.7 is released
4612 // DEBUG - alignmentView
4614 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4615 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4617 * @Override public void actionPerformed(ActionEvent e) {
4618 * jalview.datamodel.AlignmentView
4619 * .testSelectionViews(af.viewport.getAlignment(),
4620 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4622 * }); webService.add(testAlView);
4624 // TODO: refactor to RestClient discoverer and merge menu entries for
4625 // rest-style services with other types of analysis/calculation service
4626 // SHmmr test client - still being implemented.
4627 // DEBUG - alignmentView
4629 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4632 client.attachWSMenuEntry(
4633 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4639 * Searches the alignment sequences for xRefs and builds the Show
4640 * Cross-References menu (formerly called Show Products), with database
4641 * sources for which cross-references are found (protein sources for a
4642 * nucleotide alignment and vice versa)
4644 * @return true if Show Cross-references menu should be enabled
4646 public boolean canShowProducts()
4648 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4649 AlignmentI dataset = viewport.getAlignment().getDataset();
4651 showProducts.removeAll();
4652 final boolean dna = viewport.getAlignment().isNucleotide();
4654 if (seqs == null || seqs.length == 0)
4656 // nothing to see here.
4660 boolean showp = false;
4663 List<String> ptypes = new CrossRef(seqs, dataset)
4664 .findXrefSourcesForSequences(dna);
4666 for (final String source : ptypes)
4669 final AlignFrame af = this;
4670 JMenuItem xtype = new JMenuItem(source);
4671 xtype.addActionListener(new ActionListener()
4674 public void actionPerformed(ActionEvent e)
4676 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4679 showProducts.add(xtype);
4681 showProducts.setVisible(showp);
4682 showProducts.setEnabled(showp);
4683 } catch (Exception e)
4686 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4694 * Finds and displays cross-references for the selected sequences (protein
4695 * products for nucleotide sequences, dna coding sequences for peptides).
4698 * the sequences to show cross-references for
4700 * true if from a nucleotide alignment (so showing proteins)
4702 * the database to show cross-references for
4704 protected void showProductsFor(final SequenceI[] sel,
4705 final boolean _odna, final String source)
4707 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4712 * Construct and display a new frame containing the translation of this
4713 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4716 public void showTranslation_actionPerformed(ActionEvent e)
4718 AlignmentI al = null;
4721 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4723 al = dna.translateCdna();
4724 } catch (Exception ex)
4726 jalview.bin.Cache.log.error(
4727 "Exception during translation. Please report this !", ex);
4728 final String msg = MessageManager
4729 .getString("label.error_when_translating_sequences_submit_bug_report");
4730 final String errorTitle = MessageManager
4731 .getString("label.implementation_error")
4732 + MessageManager.getString("label.translation_failed");
4733 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4734 JvOptionPane.ERROR_MESSAGE);
4737 if (al == null || al.getHeight() == 0)
4739 final String msg = MessageManager
4740 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4741 final String errorTitle = MessageManager
4742 .getString("label.translation_failed");
4743 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4744 JvOptionPane.WARNING_MESSAGE);
4748 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4749 af.setFileFormat(this.currentFileFormat);
4750 final String newTitle = MessageManager.formatMessage(
4751 "label.translation_of_params",
4752 new Object[] { this.getTitle() });
4753 af.setTitle(newTitle);
4754 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4756 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4757 viewport.openSplitFrame(af, new Alignment(seqs));
4761 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4768 * Set the file format
4772 public void setFileFormat(FileFormatI format)
4774 this.currentFileFormat = format;
4778 * Try to load a features file onto the alignment.
4781 * contents or path to retrieve file
4783 * access mode of file (see jalview.io.AlignFile)
4784 * @return true if features file was parsed correctly.
4786 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4788 return avc.parseFeaturesFile(file, sourceType,
4789 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4794 public void refreshFeatureUI(boolean enableIfNecessary)
4796 // note - currently this is only still here rather than in the controller
4797 // because of the featureSettings hard reference that is yet to be
4799 if (enableIfNecessary)
4801 viewport.setShowSequenceFeatures(true);
4802 showSeqFeatures.setSelected(true);
4808 public void dragEnter(DropTargetDragEvent evt)
4813 public void dragExit(DropTargetEvent evt)
4818 public void dragOver(DropTargetDragEvent evt)
4823 public void dropActionChanged(DropTargetDragEvent evt)
4828 public void drop(DropTargetDropEvent evt)
4830 // JAL-1552 - acceptDrop required before getTransferable call for
4831 // Java's Transferable for native dnd
4832 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4833 Transferable t = evt.getTransferable();
4834 List<String> files = new ArrayList<String>();
4835 List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4839 Desktop.transferFromDropTarget(files, protocols, evt, t);
4840 } catch (Exception e)
4842 e.printStackTrace();
4848 // check to see if any of these files have names matching sequences in
4850 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4851 .getAlignment().getSequencesArray());
4853 * Object[] { String,SequenceI}
4855 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4856 ArrayList<String> filesnotmatched = new ArrayList<String>();
4857 for (int i = 0; i < files.size(); i++)
4859 String file = files.get(i).toString();
4861 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4862 if (protocol == DataSourceType.FILE)
4864 File fl = new File(file);
4865 pdbfn = fl.getName();
4867 else if (protocol == DataSourceType.URL)
4869 URL url = new URL(file);
4870 pdbfn = url.getFile();
4872 if (pdbfn.length() > 0)
4874 // attempt to find a match in the alignment
4875 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4876 int l = 0, c = pdbfn.indexOf(".");
4877 while (mtch == null && c != -1)
4882 } while ((c = pdbfn.indexOf(".", l)) > l);
4885 pdbfn = pdbfn.substring(0, l);
4887 mtch = idm.findAllIdMatches(pdbfn);
4891 FileFormatI type = null;
4894 type = new IdentifyFile().identify(file, protocol);
4895 } catch (Exception ex)
4899 if (type != null && type.isStructureFile())
4901 filesmatched.add(new Object[] { file, protocol, mtch });
4905 // File wasn't named like one of the sequences or wasn't a PDB file.
4906 filesnotmatched.add(file);
4910 if (filesmatched.size() > 0)
4912 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4918 "label.automatically_associate_structure_files_with_sequences_same_name",
4919 new Object[] { Integer
4925 .getString("label.automatically_associate_structure_files_by_name"),
4926 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4929 for (Object[] fm : filesmatched)
4931 // try and associate
4932 // TODO: may want to set a standard ID naming formalism for
4933 // associating PDB files which have no IDs.
4934 for (SequenceI toassoc : (SequenceI[]) fm[2])
4936 PDBEntry pe = new AssociatePdbFileWithSeq()
4937 .associatePdbWithSeq((String) fm[0],
4938 (DataSourceType) fm[1], toassoc, false,
4942 System.err.println("Associated file : "
4943 + ((String) fm[0]) + " with "
4944 + toassoc.getDisplayId(true));
4948 alignPanel.paintAlignment(true);
4952 if (filesnotmatched.size() > 0)
4955 && (Cache.getDefault(
4956 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4962 "label.ignore_unmatched_dropped_files_info",
4963 new Object[] { Integer
4970 .getString("label.ignore_unmatched_dropped_files"),
4971 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4975 for (String fn : filesnotmatched)
4977 loadJalviewDataFile(fn, null, null, null);
4981 } catch (Exception ex)
4983 ex.printStackTrace();
4989 * Attempt to load a "dropped" file or URL string: First by testing whether
4990 * it's an Annotation file, then a JNet file, and finally a features file. If
4991 * all are false then the user may have dropped an alignment file onto this
4995 * either a filename or a URL string.
4997 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4998 FileFormatI format, SequenceI assocSeq)
5002 if (sourceType == null)
5004 sourceType = FormatAdapter.checkProtocol(file);
5006 // if the file isn't identified, or not positively identified as some
5007 // other filetype (PFAM is default unidentified alignment file type) then
5008 // try to parse as annotation.
5009 boolean isAnnotation = (format == null || FileFormat.Pfam
5010 .equals(format)) ? new AnnotationFile()
5011 .annotateAlignmentView(viewport, file, sourceType) : false;
5015 // first see if its a T-COFFEE score file
5016 TCoffeeScoreFile tcf = null;
5019 tcf = new TCoffeeScoreFile(file, sourceType);
5022 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5024 tcoffeeColour.setEnabled(true);
5025 tcoffeeColour.setSelected(true);
5026 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5027 isAnnotation = true;
5029 .setText(MessageManager
5030 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5034 // some problem - if no warning its probable that the ID matching
5035 // process didn't work
5039 tcf.getWarningMessage() == null ? MessageManager
5040 .getString("label.check_file_matches_sequence_ids_alignment")
5041 : tcf.getWarningMessage(),
5043 .getString("label.problem_reading_tcoffee_score_file"),
5044 JvOptionPane.WARNING_MESSAGE);
5051 } catch (Exception x)
5054 .debug("Exception when processing data source as T-COFFEE score file",
5060 // try to see if its a JNet 'concise' style annotation file *before*
5062 // try to parse it as a features file
5065 format = new IdentifyFile().identify(file, sourceType);
5067 if (FileFormat.Jnet.equals(format))
5069 JPredFile predictions = new JPredFile(
5071 new JnetAnnotationMaker();
5072 JnetAnnotationMaker.add_annotation(predictions,
5073 viewport.getAlignment(), 0, false);
5074 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5075 viewport.getAlignment().setSeqrep(repseq);
5076 ColumnSelection cs = new ColumnSelection();
5077 cs.hideInsertionsFor(repseq);
5078 viewport.setColumnSelection(cs);
5079 isAnnotation = true;
5081 // else if (IdentifyFile.FeaturesFile.equals(format))
5082 else if (FileFormat.Features.equals(format))
5084 if (parseFeaturesFile(file, sourceType))
5086 alignPanel.paintAlignment(true);
5091 new FileLoader().LoadFile(viewport, file, sourceType, format);
5098 alignPanel.adjustAnnotationHeight();
5099 viewport.updateSequenceIdColours();
5100 buildSortByAnnotationScoresMenu();
5101 alignPanel.paintAlignment(true);
5103 } catch (Exception ex)
5105 ex.printStackTrace();
5106 } catch (OutOfMemoryError oom)
5111 } catch (Exception x)
5116 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
5117 : "using " + sourceType + " from " + file)
5119 + (format != null ? "(parsing as '" + format
5120 + "' file)" : ""), oom, Desktop.desktop);
5125 * Method invoked by the ChangeListener on the tabbed pane, in other words
5126 * when a different tabbed pane is selected by the user or programmatically.
5129 public void tabSelectionChanged(int index)
5133 alignPanel = alignPanels.get(index);
5134 viewport = alignPanel.av;
5135 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5136 setMenusFromViewport(viewport);
5140 * If there is a frame linked to this one in a SplitPane, switch it to the
5141 * same view tab index. No infinite recursion of calls should happen, since
5142 * tabSelectionChanged() should not get invoked on setting the selected
5143 * index to an unchanged value. Guard against setting an invalid index
5144 * before the new view peer tab has been created.
5146 final AlignViewportI peer = viewport.getCodingComplement();
5149 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5150 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5152 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5158 * On right mouse click on view tab, prompt for and set new view name.
5161 public void tabbedPane_mousePressed(MouseEvent e)
5163 if (e.isPopupTrigger())
5165 String msg = MessageManager.getString("label.enter_view_name");
5166 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
5167 JvOptionPane.QUESTION_MESSAGE);
5171 viewport.viewName = reply;
5172 // TODO warn if reply is in getExistingViewNames()?
5173 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5178 public AlignViewport getCurrentView()
5184 * Open the dialog for regex description parsing.
5187 protected void extractScores_actionPerformed(ActionEvent e)
5189 ParseProperties pp = new jalview.analysis.ParseProperties(
5190 viewport.getAlignment());
5191 // TODO: verify regex and introduce GUI dialog for version 2.5
5192 // if (pp.getScoresFromDescription("col", "score column ",
5193 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5195 if (pp.getScoresFromDescription("description column",
5196 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5198 buildSortByAnnotationScoresMenu();
5206 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5210 protected void showDbRefs_actionPerformed(ActionEvent e)
5212 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5218 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5222 protected void showNpFeats_actionPerformed(ActionEvent e)
5224 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5228 * find the viewport amongst the tabs in this alignment frame and close that
5233 public boolean closeView(AlignViewportI av)
5237 this.closeMenuItem_actionPerformed(false);
5240 Component[] comp = tabbedPane.getComponents();
5241 for (int i = 0; comp != null && i < comp.length; i++)
5243 if (comp[i] instanceof AlignmentPanel)
5245 if (((AlignmentPanel) comp[i]).av == av)
5248 closeView((AlignmentPanel) comp[i]);
5256 protected void build_fetchdbmenu(JMenu webService)
5258 // Temporary hack - DBRef Fetcher always top level ws entry.
5259 // TODO We probably want to store a sequence database checklist in
5260 // preferences and have checkboxes.. rather than individual sources selected
5262 final JMenu rfetch = new JMenu(
5263 MessageManager.getString("action.fetch_db_references"));
5264 rfetch.setToolTipText(MessageManager
5265 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5266 webService.add(rfetch);
5268 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5269 MessageManager.getString("option.trim_retrieved_seqs"));
5270 trimrs.setToolTipText(MessageManager
5271 .getString("label.trim_retrieved_sequences"));
5272 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5273 trimrs.addActionListener(new ActionListener()
5276 public void actionPerformed(ActionEvent e)
5278 trimrs.setSelected(trimrs.isSelected());
5279 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5280 Boolean.valueOf(trimrs.isSelected()).toString());
5284 JMenuItem fetchr = new JMenuItem(
5285 MessageManager.getString("label.standard_databases"));
5286 fetchr.setToolTipText(MessageManager
5287 .getString("label.fetch_embl_uniprot"));
5288 fetchr.addActionListener(new ActionListener()
5292 public void actionPerformed(ActionEvent e)
5294 new Thread(new Runnable()
5299 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5300 .getAlignment().isNucleotide();
5301 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5302 .getSequenceSelection(), alignPanel.alignFrame, null,
5303 alignPanel.alignFrame.featureSettings, isNucleotide);
5304 dbRefFetcher.addListener(new FetchFinishedListenerI()
5307 public void finished()
5309 AlignFrame.this.setMenusForViewport();
5312 dbRefFetcher.fetchDBRefs(false);
5320 final AlignFrame me = this;
5321 new Thread(new Runnable()
5326 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5327 .getSequenceFetcherSingleton(me);
5328 javax.swing.SwingUtilities.invokeLater(new Runnable()
5333 String[] dbclasses = sf.getOrderedSupportedSources();
5334 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5335 // jalview.util.QuickSort.sort(otherdb, otherdb);
5336 List<DbSourceProxy> otherdb;
5337 JMenu dfetch = new JMenu();
5338 JMenu ifetch = new JMenu();
5339 JMenuItem fetchr = null;
5340 int comp = 0, icomp = 0, mcomp = 15;
5341 String mname = null;
5343 for (String dbclass : dbclasses)
5345 otherdb = sf.getSourceProxy(dbclass);
5346 // add a single entry for this class, or submenu allowing 'fetch
5348 if (otherdb == null || otherdb.size() < 1)
5352 // List<DbSourceProxy> dbs=otherdb;
5353 // otherdb=new ArrayList<DbSourceProxy>();
5354 // for (DbSourceProxy db:dbs)
5356 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5360 mname = "From " + dbclass;
5362 if (otherdb.size() == 1)
5364 final DbSourceProxy[] dassource = otherdb
5365 .toArray(new DbSourceProxy[0]);
5366 DbSourceProxy src = otherdb.get(0);
5367 fetchr = new JMenuItem(src.getDbSource());
5368 fetchr.addActionListener(new ActionListener()
5372 public void actionPerformed(ActionEvent e)
5374 new Thread(new Runnable()
5380 boolean isNucleotide = alignPanel.alignFrame
5381 .getViewport().getAlignment()
5383 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5384 alignPanel.av.getSequenceSelection(),
5385 alignPanel.alignFrame, dassource,
5386 alignPanel.alignFrame.featureSettings,
5389 .addListener(new FetchFinishedListenerI()
5392 public void finished()
5394 AlignFrame.this.setMenusForViewport();
5397 dbRefFetcher.fetchDBRefs(false);
5403 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5404 MessageManager.formatMessage(
5405 "label.fetch_retrieve_from",
5406 new Object[] { src.getDbName() })));
5412 final DbSourceProxy[] dassource = otherdb
5413 .toArray(new DbSourceProxy[0]);
5415 DbSourceProxy src = otherdb.get(0);
5416 fetchr = new JMenuItem(MessageManager.formatMessage(
5417 "label.fetch_all_param",
5418 new Object[] { src.getDbSource() }));
5419 fetchr.addActionListener(new ActionListener()
5422 public void actionPerformed(ActionEvent e)
5424 new Thread(new Runnable()
5430 boolean isNucleotide = alignPanel.alignFrame
5431 .getViewport().getAlignment()
5433 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5434 alignPanel.av.getSequenceSelection(),
5435 alignPanel.alignFrame, dassource,
5436 alignPanel.alignFrame.featureSettings,
5439 .addListener(new FetchFinishedListenerI()
5442 public void finished()
5444 AlignFrame.this.setMenusForViewport();
5447 dbRefFetcher.fetchDBRefs(false);
5453 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5454 MessageManager.formatMessage(
5455 "label.fetch_retrieve_from_all_sources",
5457 Integer.valueOf(otherdb.size())
5458 .toString(), src.getDbSource(),
5459 src.getDbName() })));
5462 // and then build the rest of the individual menus
5463 ifetch = new JMenu(MessageManager.formatMessage(
5464 "label.source_from_db_source",
5465 new Object[] { src.getDbSource() }));
5467 String imname = null;
5469 for (DbSourceProxy sproxy : otherdb)
5471 String dbname = sproxy.getDbName();
5472 String sname = dbname.length() > 5 ? dbname.substring(0,
5473 5) + "..." : dbname;
5474 String msname = dbname.length() > 10 ? dbname.substring(
5475 0, 10) + "..." : dbname;
5478 imname = MessageManager.formatMessage(
5479 "label.from_msname", new Object[] { sname });
5481 fetchr = new JMenuItem(msname);
5482 final DbSourceProxy[] dassrc = { sproxy };
5483 fetchr.addActionListener(new ActionListener()
5487 public void actionPerformed(ActionEvent e)
5489 new Thread(new Runnable()
5495 boolean isNucleotide = alignPanel.alignFrame
5496 .getViewport().getAlignment()
5498 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5499 alignPanel.av.getSequenceSelection(),
5500 alignPanel.alignFrame, dassrc,
5501 alignPanel.alignFrame.featureSettings,
5504 .addListener(new FetchFinishedListenerI()
5507 public void finished()
5509 AlignFrame.this.setMenusForViewport();
5512 dbRefFetcher.fetchDBRefs(false);
5518 fetchr.setToolTipText("<html>"
5519 + MessageManager.formatMessage(
5520 "label.fetch_retrieve_from", new Object[]
5524 if (++icomp >= mcomp || i == (otherdb.size()))
5526 ifetch.setText(MessageManager.formatMessage(
5527 "label.source_to_target", imname, sname));
5529 ifetch = new JMenu();
5537 if (comp >= mcomp || dbi >= (dbclasses.length))
5539 dfetch.setText(MessageManager.formatMessage(
5540 "label.source_to_target", mname, dbclass));
5542 dfetch = new JMenu();
5555 * Left justify the whole alignment.
5558 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5560 AlignmentI al = viewport.getAlignment();
5562 viewport.firePropertyChange("alignment", null, al);
5566 * Right justify the whole alignment.
5569 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5571 AlignmentI al = viewport.getAlignment();
5573 viewport.firePropertyChange("alignment", null, al);
5577 public void setShowSeqFeatures(boolean b)
5579 showSeqFeatures.setSelected(b);
5580 viewport.setShowSequenceFeatures(b);
5587 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5588 * awt.event.ActionEvent)
5591 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5593 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5594 alignPanel.paintAlignment(true);
5601 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5605 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5607 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5608 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5616 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5617 * .event.ActionEvent)
5620 protected void showGroupConservation_actionPerformed(ActionEvent e)
5622 viewport.setShowGroupConservation(showGroupConservation.getState());
5623 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5630 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5631 * .event.ActionEvent)
5634 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5636 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5637 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5644 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5645 * .event.ActionEvent)
5648 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5650 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5651 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5655 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5657 showSequenceLogo.setState(true);
5658 viewport.setShowSequenceLogo(true);
5659 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5660 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5664 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5666 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5673 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5674 * .event.ActionEvent)
5677 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5679 if (avc.makeGroupsFromSelection())
5681 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5682 alignPanel.updateAnnotation();
5683 alignPanel.paintAlignment(true);
5687 public void clearAlignmentSeqRep()
5689 // TODO refactor alignmentseqrep to controller
5690 if (viewport.getAlignment().hasSeqrep())
5692 viewport.getAlignment().setSeqrep(null);
5693 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5694 alignPanel.updateAnnotation();
5695 alignPanel.paintAlignment(true);
5700 protected void createGroup_actionPerformed(ActionEvent e)
5702 if (avc.createGroup())
5704 alignPanel.alignmentChanged();
5709 protected void unGroup_actionPerformed(ActionEvent e)
5713 alignPanel.alignmentChanged();
5718 * make the given alignmentPanel the currently selected tab
5720 * @param alignmentPanel
5722 public void setDisplayedView(AlignmentPanel alignmentPanel)
5724 if (!viewport.getSequenceSetId().equals(
5725 alignmentPanel.av.getSequenceSetId()))
5729 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5731 if (tabbedPane != null
5732 && tabbedPane.getTabCount() > 0
5733 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5734 .getSelectedIndex())
5736 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5741 * Action on selection of menu options to Show or Hide annotations.
5744 * @param forSequences
5745 * update sequence-related annotations
5746 * @param forAlignment
5747 * update non-sequence-related annotations
5750 protected void setAnnotationsVisibility(boolean visible,
5751 boolean forSequences, boolean forAlignment)
5753 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5754 .getAlignmentAnnotation();
5759 for (AlignmentAnnotation aa : anns)
5762 * don't display non-positional annotations on an alignment
5764 if (aa.annotations == null)
5768 boolean apply = (aa.sequenceRef == null && forAlignment)
5769 || (aa.sequenceRef != null && forSequences);
5772 aa.visible = visible;
5775 alignPanel.validateAnnotationDimensions(true);
5776 alignPanel.alignmentChanged();
5780 * Store selected annotation sort order for the view and repaint.
5783 protected void sortAnnotations_actionPerformed()
5785 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5787 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5788 alignPanel.paintAlignment(true);
5793 * @return alignment panels in this alignment frame
5795 public List<? extends AlignmentViewPanel> getAlignPanels()
5797 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5801 * Open a new alignment window, with the cDNA associated with this (protein)
5802 * alignment, aligned as is the protein.
5804 protected void viewAsCdna_actionPerformed()
5806 // TODO no longer a menu action - refactor as required
5807 final AlignmentI alignment = getViewport().getAlignment();
5808 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5809 if (mappings == null)
5813 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5814 for (SequenceI aaSeq : alignment.getSequences())
5816 for (AlignedCodonFrame acf : mappings)
5818 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5822 * There is a cDNA mapping for this protein sequence - add to new
5823 * alignment. It will share the same dataset sequence as other mapped
5824 * cDNA (no new mappings need to be created).
5826 final Sequence newSeq = new Sequence(dnaSeq);
5827 newSeq.setDatasetSequence(dnaSeq);
5828 cdnaSeqs.add(newSeq);
5832 if (cdnaSeqs.size() == 0)
5834 // show a warning dialog no mapped cDNA
5837 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5839 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5840 AlignFrame.DEFAULT_HEIGHT);
5841 cdna.alignAs(alignment);
5842 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5844 Desktop.addInternalFrame(alignFrame, newtitle,
5845 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5849 * Set visibility of dna/protein complement view (available when shown in a
5855 protected void showComplement_actionPerformed(boolean show)
5857 SplitContainerI sf = getSplitViewContainer();
5860 sf.setComplementVisible(this, show);
5865 * Generate the reverse (optionally complemented) of the selected sequences,
5866 * and add them to the alignment
5869 protected void showReverse_actionPerformed(boolean complement)
5871 AlignmentI al = null;
5874 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5875 al = dna.reverseCdna(complement);
5876 viewport.addAlignment(al, "");
5877 addHistoryItem(new EditCommand(
5878 MessageManager.getString("label.add_sequences"),
5879 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5880 viewport.getAlignment()));
5881 } catch (Exception ex)
5883 System.err.println(ex.getMessage());
5889 * Try to run a script in the Groovy console, having first ensured that this
5890 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5891 * be targeted at this alignment.
5894 protected void runGroovy_actionPerformed()
5896 Jalview.setCurrentAlignFrame(this);
5897 groovy.ui.Console console = Desktop.getGroovyConsole();
5898 if (console != null)
5902 console.runScript();
5903 } catch (Exception ex)
5905 System.err.println((ex.toString()));
5907 .showInternalMessageDialog(Desktop.desktop, MessageManager
5908 .getString("label.couldnt_run_groovy_script"),
5910 .getString("label.groovy_support_failed"),
5911 JvOptionPane.ERROR_MESSAGE);
5916 System.err.println("Can't run Groovy script as console not found");
5921 * Hides columns containing (or not containing) a specified feature, provided
5922 * that would not leave all columns hidden
5924 * @param featureType
5925 * @param columnsContaining
5928 public boolean hideFeatureColumns(String featureType,
5929 boolean columnsContaining)
5931 boolean notForHiding = avc.markColumnsContainingFeatures(
5932 columnsContaining, false, false, featureType);
5935 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5936 false, featureType))
5938 getViewport().hideSelectedColumns();
5946 protected void selectHighlightedColumns_actionPerformed(
5947 ActionEvent actionEvent)
5949 // include key modifier check in case user selects from menu
5950 avc.markHighlightedColumns(
5951 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5953 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5957 class PrintThread extends Thread
5961 public PrintThread(AlignmentPanel ap)
5966 static PageFormat pf;
5971 PrinterJob printJob = PrinterJob.getPrinterJob();
5975 printJob.setPrintable(ap, pf);
5979 printJob.setPrintable(ap);
5982 if (printJob.printDialog())
5987 } catch (Exception PrintException)
5989 PrintException.printStackTrace();