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.MouseEvent;
129 import java.awt.print.PageFormat;
130 import java.awt.print.PrinterJob;
131 import java.beans.PropertyChangeEvent;
134 import java.util.ArrayList;
135 import java.util.Arrays;
136 import java.util.Deque;
137 import java.util.Enumeration;
138 import java.util.Hashtable;
139 import java.util.List;
140 import java.util.Vector;
142 import javax.swing.JCheckBoxMenuItem;
143 import javax.swing.JEditorPane;
144 import javax.swing.JInternalFrame;
145 import javax.swing.JLayeredPane;
146 import javax.swing.JMenu;
147 import javax.swing.JMenuItem;
148 import javax.swing.JScrollPane;
149 import javax.swing.SwingUtilities;
155 * @version $Revision$
157 public class AlignFrame extends GAlignFrame implements DropTargetListener,
158 IProgressIndicator, AlignViewControllerGuiI
161 public static final int DEFAULT_WIDTH = 700;
163 public static final int DEFAULT_HEIGHT = 500;
166 * The currently displayed panel (selected tabbed view if more than one)
168 public AlignmentPanel alignPanel;
170 AlignViewport viewport;
172 public AlignViewControllerI avc;
174 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
177 * Last format used to load or save alignments in this window
179 FileFormatI currentFileFormat = null;
182 * Current filename for this alignment
184 String fileName = null;
187 * Creates a new AlignFrame object with specific width and height.
193 public AlignFrame(AlignmentI al, int width, int height)
195 this(al, null, width, height);
199 * Creates a new AlignFrame object with specific width, height and
205 * @param sequenceSetId
207 public AlignFrame(AlignmentI al, int width, int height,
208 String sequenceSetId)
210 this(al, null, width, height, sequenceSetId);
214 * Creates a new AlignFrame object with specific width, height and
220 * @param sequenceSetId
223 public AlignFrame(AlignmentI al, int width, int height,
224 String sequenceSetId, String viewId)
226 this(al, null, width, height, sequenceSetId, viewId);
230 * new alignment window with hidden columns
234 * @param hiddenColumns
235 * ColumnSelection or null
237 * Width of alignment frame
241 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
242 int width, int height)
244 this(al, hiddenColumns, width, height, null);
248 * Create alignment frame for al with hiddenColumns, a specific width and
249 * height, and specific sequenceId
252 * @param hiddenColumns
255 * @param sequenceSetId
258 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
259 int width, int height, String sequenceSetId)
261 this(al, hiddenColumns, width, height, sequenceSetId, null);
265 * Create alignment frame for al with hiddenColumns, a specific width and
266 * height, and specific sequenceId
269 * @param hiddenColumns
272 * @param sequenceSetId
277 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
278 int width, int height, String sequenceSetId, String viewId)
280 setSize(width, height);
282 if (al.getDataset() == null)
287 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
289 alignPanel = new AlignmentPanel(this, viewport);
291 addAlignmentPanel(alignPanel, true);
295 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
296 ColumnSelection hiddenColumns, int width, int height)
298 setSize(width, height);
300 if (al.getDataset() == null)
305 viewport = new AlignViewport(al, hiddenColumns);
307 if (hiddenSeqs != null && hiddenSeqs.length > 0)
309 viewport.hideSequence(hiddenSeqs);
311 alignPanel = new AlignmentPanel(this, viewport);
312 addAlignmentPanel(alignPanel, true);
317 * Make a new AlignFrame from existing alignmentPanels
324 public AlignFrame(AlignmentPanel ap)
328 addAlignmentPanel(ap, false);
333 * initalise the alignframe from the underlying viewport data and the
338 if (!Jalview.isHeadlessMode())
340 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
343 avc = new jalview.controller.AlignViewController(this, viewport,
345 if (viewport.getAlignmentConservationAnnotation() == null)
347 BLOSUM62Colour.setEnabled(false);
348 conservationMenuItem.setEnabled(false);
349 modifyConservation.setEnabled(false);
350 // PIDColour.setEnabled(false);
351 // abovePIDThreshold.setEnabled(false);
352 // modifyPID.setEnabled(false);
355 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
358 if (sortby.equals("Id"))
360 sortIDMenuItem_actionPerformed(null);
362 else if (sortby.equals("Pairwise Identity"))
364 sortPairwiseMenuItem_actionPerformed(null);
367 if (Desktop.desktop != null)
369 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
370 addServiceListeners();
371 setGUINucleotide(viewport.getAlignment().isNucleotide());
375 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
377 setMenusFromViewport(viewport);
378 buildSortByAnnotationScoresMenu();
381 if (viewport.getWrapAlignment())
383 wrapMenuItem_actionPerformed(null);
386 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
388 this.overviewMenuItem_actionPerformed(null);
393 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
394 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
395 final String menuLabel = MessageManager
396 .getString("label.copy_format_from");
397 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
398 new ViewSetProvider()
402 public AlignmentPanel[] getAllAlignmentPanels()
405 origview.add(alignPanel);
406 // make an array of all alignment panels except for this one
407 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
408 Arrays.asList(Desktop.getAlignmentPanels(null)));
409 aps.remove(AlignFrame.this.alignPanel);
410 return aps.toArray(new AlignmentPanel[aps.size()]);
412 }, selviews, new ItemListener()
416 public void itemStateChanged(ItemEvent e)
418 if (origview.size() > 0)
420 final AlignmentPanel ap = origview.get(0);
423 * Copy the ViewStyle of the selected panel to 'this one'.
424 * Don't change value of 'scaleProteinAsCdna' unless copying
427 ViewStyleI vs = selviews.get(0).getAlignViewport()
429 boolean fromSplitFrame = selviews.get(0)
430 .getAlignViewport().getCodingComplement() != null;
433 vs.setScaleProteinAsCdna(ap.getAlignViewport()
434 .getViewStyle().isScaleProteinAsCdna());
436 ap.getAlignViewport().setViewStyle(vs);
439 * Also rescale ViewStyle of SplitFrame complement if there is
440 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
441 * the whole ViewStyle (allow cDNA protein to have different
444 AlignViewportI complement = ap.getAlignViewport()
445 .getCodingComplement();
446 if (complement != null && vs.isScaleProteinAsCdna())
448 AlignFrame af = Desktop.getAlignFrameFor(complement);
449 ((SplitFrame) af.getSplitViewContainer())
451 af.setMenusForViewport();
455 ap.setSelected(true);
456 ap.alignFrame.setMenusForViewport();
461 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
462 .indexOf("devel") > -1
463 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
464 .indexOf("test") > -1)
466 formatMenu.add(vsel);
468 addFocusListener(new FocusAdapter()
471 public void focusGained(FocusEvent e)
473 Jalview.setCurrentAlignFrame(AlignFrame.this);
480 * Change the filename and format for the alignment, and enable the 'reload'
481 * button functionality.
488 public void setFileName(String file, FileFormatI format)
491 setFileFormat(format);
492 reload.setEnabled(true);
496 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
499 void addKeyListener()
501 addKeyListener(new KeyAdapter()
504 public void keyPressed(KeyEvent evt)
506 if (viewport.cursorMode
507 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
508 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
509 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
510 && Character.isDigit(evt.getKeyChar()))
512 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
515 switch (evt.getKeyCode())
518 case 27: // escape key
519 deselectAllSequenceMenuItem_actionPerformed(null);
523 case KeyEvent.VK_DOWN:
524 if (evt.isAltDown() || !viewport.cursorMode)
526 moveSelectedSequences(false);
528 if (viewport.cursorMode)
530 alignPanel.getSeqPanel().moveCursor(0, 1);
535 if (evt.isAltDown() || !viewport.cursorMode)
537 moveSelectedSequences(true);
539 if (viewport.cursorMode)
541 alignPanel.getSeqPanel().moveCursor(0, -1);
546 case KeyEvent.VK_LEFT:
547 if (evt.isAltDown() || !viewport.cursorMode)
549 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
553 alignPanel.getSeqPanel().moveCursor(-1, 0);
558 case KeyEvent.VK_RIGHT:
559 if (evt.isAltDown() || !viewport.cursorMode)
561 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
565 alignPanel.getSeqPanel().moveCursor(1, 0);
569 case KeyEvent.VK_SPACE:
570 if (viewport.cursorMode)
572 alignPanel.getSeqPanel().insertGapAtCursor(
573 evt.isControlDown() || evt.isShiftDown()
578 // case KeyEvent.VK_A:
579 // if (viewport.cursorMode)
581 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
582 // //System.out.println("A");
586 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
587 * System.out.println("closing bracket"); } break;
589 case KeyEvent.VK_DELETE:
590 case KeyEvent.VK_BACK_SPACE:
591 if (!viewport.cursorMode)
593 cut_actionPerformed(null);
597 alignPanel.getSeqPanel().deleteGapAtCursor(
598 evt.isControlDown() || evt.isShiftDown()
605 if (viewport.cursorMode)
607 alignPanel.getSeqPanel().setCursorRow();
611 if (viewport.cursorMode && !evt.isControlDown())
613 alignPanel.getSeqPanel().setCursorColumn();
617 if (viewport.cursorMode)
619 alignPanel.getSeqPanel().setCursorPosition();
623 case KeyEvent.VK_ENTER:
624 case KeyEvent.VK_COMMA:
625 if (viewport.cursorMode)
627 alignPanel.getSeqPanel().setCursorRowAndColumn();
632 if (viewport.cursorMode)
634 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
638 if (viewport.cursorMode)
640 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
645 viewport.cursorMode = !viewport.cursorMode;
646 statusBar.setText(MessageManager.formatMessage(
647 "label.keyboard_editing_mode",
648 new String[] { (viewport.cursorMode ? "on" : "off") }));
649 if (viewport.cursorMode)
651 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
652 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
654 alignPanel.getSeqPanel().seqCanvas.repaint();
660 Help.showHelpWindow();
661 } catch (Exception ex)
663 ex.printStackTrace();
668 boolean toggleSeqs = !evt.isControlDown();
669 boolean toggleCols = !evt.isShiftDown();
670 toggleHiddenRegions(toggleSeqs, toggleCols);
675 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
676 boolean modifyExisting = true; // always modify, don't clear
677 // evt.isShiftDown();
678 boolean invertHighlighted = evt.isAltDown();
679 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
683 case KeyEvent.VK_PAGE_UP:
684 if (viewport.getWrapAlignment())
686 alignPanel.scrollUp(true);
690 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
691 - viewport.endSeq + viewport.startSeq);
694 case KeyEvent.VK_PAGE_DOWN:
695 if (viewport.getWrapAlignment())
697 alignPanel.scrollUp(false);
701 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
702 + viewport.endSeq - viewport.startSeq);
709 public void keyReleased(KeyEvent evt)
711 switch (evt.getKeyCode())
713 case KeyEvent.VK_LEFT:
714 if (evt.isAltDown() || !viewport.cursorMode)
716 viewport.firePropertyChange("alignment", null, viewport
717 .getAlignment().getSequences());
721 case KeyEvent.VK_RIGHT:
722 if (evt.isAltDown() || !viewport.cursorMode)
724 viewport.firePropertyChange("alignment", null, viewport
725 .getAlignment().getSequences());
733 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
735 ap.alignFrame = this;
736 avc = new jalview.controller.AlignViewController(this, viewport,
741 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
743 int aSize = alignPanels.size();
745 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
747 if (aSize == 1 && ap.av.viewName == null)
749 this.getContentPane().add(ap, BorderLayout.CENTER);
755 setInitialTabVisible();
758 expandViews.setEnabled(true);
759 gatherViews.setEnabled(true);
760 tabbedPane.addTab(ap.av.viewName, ap);
762 ap.setVisible(false);
767 if (ap.av.isPadGaps())
769 ap.av.getAlignment().padGaps();
771 ap.av.updateConservation(ap);
772 ap.av.updateConsensus(ap);
773 ap.av.updateStrucConsensus(ap);
777 public void setInitialTabVisible()
779 expandViews.setEnabled(true);
780 gatherViews.setEnabled(true);
781 tabbedPane.setVisible(true);
782 AlignmentPanel first = alignPanels.get(0);
783 tabbedPane.addTab(first.av.viewName, first);
784 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
787 public AlignViewport getViewport()
792 /* Set up intrinsic listeners for dynamically generated GUI bits. */
793 private void addServiceListeners()
795 final java.beans.PropertyChangeListener thisListener;
796 Desktop.instance.addJalviewPropertyChangeListener("services",
797 thisListener = new java.beans.PropertyChangeListener()
800 public void propertyChange(PropertyChangeEvent evt)
802 // // System.out.println("Discoverer property change.");
803 // if (evt.getPropertyName().equals("services"))
805 SwingUtilities.invokeLater(new Runnable()
812 .println("Rebuild WS Menu for service change");
813 BuildWebServiceMenu();
820 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
823 public void internalFrameClosed(
824 javax.swing.event.InternalFrameEvent evt)
826 // System.out.println("deregistering discoverer listener");
827 Desktop.instance.removeJalviewPropertyChangeListener("services",
829 closeMenuItem_actionPerformed(true);
832 // Finally, build the menu once to get current service state
833 new Thread(new Runnable()
838 BuildWebServiceMenu();
844 * Configure menu items that vary according to whether the alignment is
845 * nucleotide or protein
849 public void setGUINucleotide(boolean nucleotide)
851 showTranslation.setVisible(nucleotide);
852 showReverse.setVisible(nucleotide);
853 showReverseComplement.setVisible(nucleotide);
854 conservationMenuItem.setEnabled(!nucleotide);
855 modifyConservation.setEnabled(!nucleotide);
856 showGroupConservation.setEnabled(!nucleotide);
857 clustalColour.setEnabled(!nucleotide);
858 zappoColour.setEnabled(!nucleotide);
859 taylorColour.setEnabled(!nucleotide);
860 hydrophobicityColour.setEnabled(!nucleotide);
861 helixColour.setEnabled(!nucleotide);
862 strandColour.setEnabled(!nucleotide);
863 turnColour.setEnabled(!nucleotide);
864 buriedColour.setEnabled(!nucleotide);
865 rnahelicesColour.setEnabled(nucleotide);
866 nucleotideColour.setEnabled(nucleotide);
867 purinePyrimidineColour.setEnabled(nucleotide);
868 RNAInteractionColour.setEnabled(nucleotide);
869 showComplementMenuItem.setText(nucleotide ? MessageManager
870 .getString("label.protein") : MessageManager
871 .getString("label.nucleotide"));
872 String selectedColourScheme = Cache.getDefault(
873 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
874 : Preferences.DEFAULT_COLOUR_PROT, "None");
875 setColourSelected(selectedColourScheme);
879 * set up menus for the current viewport. This may be called after any
880 * operation that affects the data in the current view (selection changed,
881 * etc) to update the menus to reflect the new state.
884 public void setMenusForViewport()
886 setMenusFromViewport(viewport);
890 * Need to call this method when tabs are selected for multiple views, or when
891 * loading from Jalview2XML.java
896 void setMenusFromViewport(AlignViewport av)
898 padGapsMenuitem.setSelected(av.isPadGaps());
899 colourTextMenuItem.setSelected(av.isShowColourText());
900 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
901 conservationMenuItem.setSelected(av.getConservationSelected());
902 seqLimits.setSelected(av.getShowJVSuffix());
903 idRightAlign.setSelected(av.isRightAlignIds());
904 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
905 renderGapsMenuItem.setSelected(av.isRenderGaps());
906 wrapMenuItem.setSelected(av.getWrapAlignment());
907 scaleAbove.setVisible(av.getWrapAlignment());
908 scaleLeft.setVisible(av.getWrapAlignment());
909 scaleRight.setVisible(av.getWrapAlignment());
910 annotationPanelMenuItem.setState(av.isShowAnnotation());
912 * Show/hide annotations only enabled if annotation panel is shown
914 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
915 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
916 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
917 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
918 viewBoxesMenuItem.setSelected(av.getShowBoxes());
919 viewTextMenuItem.setSelected(av.getShowText());
920 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
921 showGroupConsensus.setSelected(av.isShowGroupConsensus());
922 showGroupConservation.setSelected(av.isShowGroupConservation());
923 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
924 showSequenceLogo.setSelected(av.isShowSequenceLogo());
925 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
927 setColourSelected(ColourSchemeProperty.getColourName(av
928 .getGlobalColourScheme()));
930 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
931 hiddenMarkers.setState(av.getShowHiddenMarkers());
932 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
933 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
934 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
935 autoCalculate.setSelected(av.autoCalculateConsensus);
936 sortByTree.setSelected(av.sortByTree);
937 listenToViewSelections.setSelected(av.followSelection);
938 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
940 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
942 showProducts.setEnabled(canShowProducts());
943 setGroovyEnabled(Desktop.getGroovyConsole() != null);
949 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
953 public void setGroovyEnabled(boolean b)
955 runGroovy.setEnabled(b);
958 private IProgressIndicator progressBar;
963 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
966 public void setProgressBar(String message, long id)
968 progressBar.setProgressBar(message, id);
972 public void registerHandler(final long id,
973 final IProgressIndicatorHandler handler)
975 progressBar.registerHandler(id, handler);
980 * @return true if any progress bars are still active
983 public boolean operationInProgress()
985 return progressBar.operationInProgress();
989 public void setStatus(String text)
991 statusBar.setText(text);
995 * Added so Castor Mapping file can obtain Jalview Version
997 public String getVersion()
999 return jalview.bin.Cache.getProperty("VERSION");
1002 public FeatureRenderer getFeatureRenderer()
1004 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1008 public void fetchSequence_actionPerformed(ActionEvent e)
1010 new jalview.gui.SequenceFetcher(this);
1014 public void addFromFile_actionPerformed(ActionEvent e)
1016 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1020 public void reload_actionPerformed(ActionEvent e)
1022 if (fileName != null)
1024 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1025 // originating file's format
1026 // TODO: work out how to recover feature settings for correct view(s) when
1027 // file is reloaded.
1028 if (FileFormat.Jalview.equals(currentFileFormat))
1030 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1031 for (int i = 0; i < frames.length; i++)
1033 if (frames[i] instanceof AlignFrame && frames[i] != this
1034 && ((AlignFrame) frames[i]).fileName != null
1035 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1039 frames[i].setSelected(true);
1040 Desktop.instance.closeAssociatedWindows();
1041 } catch (java.beans.PropertyVetoException ex)
1047 Desktop.instance.closeAssociatedWindows();
1049 FileLoader loader = new FileLoader();
1050 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1051 : DataSourceType.FILE;
1052 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1056 Rectangle bounds = this.getBounds();
1058 FileLoader loader = new FileLoader();
1059 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1060 : DataSourceType.FILE;
1061 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1062 protocol, currentFileFormat);
1064 newframe.setBounds(bounds);
1065 if (featureSettings != null && featureSettings.isShowing())
1067 final Rectangle fspos = featureSettings.frame.getBounds();
1068 // TODO: need a 'show feature settings' function that takes bounds -
1069 // need to refactor Desktop.addFrame
1070 newframe.featureSettings_actionPerformed(null);
1071 final FeatureSettings nfs = newframe.featureSettings;
1072 SwingUtilities.invokeLater(new Runnable()
1077 nfs.frame.setBounds(fspos);
1080 this.featureSettings.close();
1081 this.featureSettings = null;
1083 this.closeMenuItem_actionPerformed(true);
1089 public void addFromText_actionPerformed(ActionEvent e)
1091 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1096 public void addFromURL_actionPerformed(ActionEvent e)
1098 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1102 public void save_actionPerformed(ActionEvent e)
1104 if (fileName == null || (currentFileFormat == null)
1105 || fileName.startsWith("http"))
1107 saveAs_actionPerformed(null);
1111 saveAlignment(fileName, currentFileFormat);
1122 public void saveAs_actionPerformed(ActionEvent e)
1124 String format = currentFileFormat == null ? null : currentFileFormat
1126 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1127 Cache.getProperty("LAST_DIRECTORY"), format);
1129 chooser.setFileView(new JalviewFileView());
1130 chooser.setDialogTitle(MessageManager
1131 .getString("label.save_alignment_to_file"));
1132 chooser.setToolTipText(MessageManager.getString("action.save"));
1134 int value = chooser.showSaveDialog(this);
1136 if (value == JalviewFileChooser.APPROVE_OPTION)
1138 currentFileFormat = chooser.getSelectedFormat();
1139 while (currentFileFormat == null)
1142 .showInternalMessageDialog(
1145 .getString("label.select_file_format_before_saving"),
1147 .getString("label.file_format_not_specified"),
1148 JvOptionPane.WARNING_MESSAGE);
1149 currentFileFormat = chooser.getSelectedFormat();
1150 value = chooser.showSaveDialog(this);
1151 if (value != JalviewFileChooser.APPROVE_OPTION)
1157 fileName = chooser.getSelectedFile().getPath();
1159 Cache.setProperty("DEFAULT_FILE_FORMAT",
1160 currentFileFormat.toString());
1162 Cache.setProperty("LAST_DIRECTORY", fileName);
1163 saveAlignment(fileName, currentFileFormat);
1167 public boolean saveAlignment(String file, FileFormatI format)
1169 boolean success = true;
1171 if (FileFormat.Jalview.equals(format))
1173 String shortName = title;
1175 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1177 shortName = shortName.substring(shortName
1178 .lastIndexOf(java.io.File.separatorChar) + 1);
1181 success = new Jalview2XML().saveAlignment(this, file, shortName);
1183 statusBar.setText(MessageManager.formatMessage(
1184 "label.successfully_saved_to_file_in_format", new Object[] {
1185 fileName, format }));
1190 // if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1192 // warningMessage("Cannot save file " + fileName + " using format "
1193 // + format, "Alignment output format not supported");
1194 // if (!Jalview.isHeadlessMode())
1196 // saveAs_actionPerformed(null);
1201 AlignmentExportData exportData = getAlignmentForExport(format,
1203 if (exportData.getSettings().isCancelled())
1207 FormatAdapter f = new FormatAdapter(alignPanel,
1208 exportData.getSettings());
1209 String output = f.formatSequences(
1211 exportData.getAlignment(), // class cast exceptions will
1212 // occur in the distant future
1213 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1214 f.getCacheSuffixDefault(format),
1215 viewport.getColumnSelection());
1225 java.io.PrintWriter out = new java.io.PrintWriter(
1226 new java.io.FileWriter(file));
1230 this.setTitle(file);
1231 statusBar.setText(MessageManager.formatMessage(
1232 "label.successfully_saved_to_file_in_format",
1233 new Object[] { fileName, format }));
1234 } catch (Exception ex)
1237 ex.printStackTrace();
1244 JvOptionPane.showInternalMessageDialog(this, MessageManager
1245 .formatMessage("label.couldnt_save_file",
1246 new Object[] { fileName }), MessageManager
1247 .getString("label.error_saving_file"),
1248 JvOptionPane.WARNING_MESSAGE);
1254 private void warningMessage(String warning, String title)
1256 if (new jalview.util.Platform().isHeadless())
1258 System.err.println("Warning: " + title + "\nWarning: " + warning);
1263 JvOptionPane.showInternalMessageDialog(this, warning, title,
1264 JvOptionPane.WARNING_MESSAGE);
1276 protected void outputText_actionPerformed(ActionEvent e)
1279 FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
1280 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1282 if (exportData.getSettings().isCancelled())
1286 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1287 cap.setForInput(null);
1290 FileFormatI format = fileFormat;
1291 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1292 .formatSequences(format,
1293 exportData.getAlignment(),
1294 exportData.getOmitHidden(),
1295 exportData.getStartEndPostions(),
1296 viewport.getColumnSelection()));
1297 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1298 "label.alignment_output_command",
1299 new Object[] { e.getActionCommand() }), 600, 500);
1300 } catch (OutOfMemoryError oom)
1302 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1308 public static AlignmentExportData getAlignmentForExport(
1309 FileFormatI format, AlignViewportI viewport,
1310 AlignExportSettingI exportSettings)
1312 AlignmentI alignmentToExport = null;
1313 AlignExportSettingI settings = exportSettings;
1314 String[] omitHidden = null;
1316 HiddenSequences hiddenSeqs = viewport.getAlignment()
1317 .getHiddenSequences();
1319 alignmentToExport = viewport.getAlignment();
1321 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1322 if (settings == null)
1324 settings = new AlignExportSettings(hasHiddenSeqs,
1325 viewport.hasHiddenColumns(), format);
1327 // settings.isExportAnnotations();
1329 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1331 omitHidden = viewport.getViewAsString(false,
1332 settings.isExportHiddenSequences());
1335 int[] alignmentStartEnd = new int[2];
1336 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1338 alignmentToExport = hiddenSeqs.getFullAlignment();
1342 alignmentToExport = viewport.getAlignment();
1344 alignmentStartEnd = alignmentToExport
1345 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1346 .getHiddenColumns());
1347 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1348 omitHidden, alignmentStartEnd, settings);
1359 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1361 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1362 htmlSVG.exportHTML(null);
1366 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1368 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1369 bjs.exportHTML(null);
1372 public void createImageMap(File file, String image)
1374 alignPanel.makePNGImageMap(file, image);
1384 public void createPNG(File f)
1386 alignPanel.makePNG(f);
1396 public void createEPS(File f)
1398 alignPanel.makeEPS(f);
1402 public void createSVG(File f)
1404 alignPanel.makeSVG(f);
1408 public void pageSetup_actionPerformed(ActionEvent e)
1410 PrinterJob printJob = PrinterJob.getPrinterJob();
1411 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1421 public void printMenuItem_actionPerformed(ActionEvent e)
1423 // Putting in a thread avoids Swing painting problems
1424 PrintThread thread = new PrintThread(alignPanel);
1429 public void exportFeatures_actionPerformed(ActionEvent e)
1431 new AnnotationExporter().exportFeatures(alignPanel);
1435 public void exportAnnotations_actionPerformed(ActionEvent e)
1437 new AnnotationExporter().exportAnnotations(alignPanel);
1441 public void associatedData_actionPerformed(ActionEvent e)
1443 // Pick the tree file
1444 JalviewFileChooser chooser = new JalviewFileChooser(
1445 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1446 chooser.setFileView(new JalviewFileView());
1447 chooser.setDialogTitle(MessageManager
1448 .getString("label.load_jalview_annotations"));
1449 chooser.setToolTipText(MessageManager
1450 .getString("label.load_jalview_annotations"));
1452 int value = chooser.showOpenDialog(null);
1454 if (value == JalviewFileChooser.APPROVE_OPTION)
1456 String choice = chooser.getSelectedFile().getPath();
1457 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1458 loadJalviewDataFile(choice, null, null, null);
1464 * Close the current view or all views in the alignment frame. If the frame
1465 * only contains one view then the alignment will be removed from memory.
1467 * @param closeAllTabs
1470 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1472 if (alignPanels != null && alignPanels.size() < 2)
1474 closeAllTabs = true;
1479 if (alignPanels != null)
1483 if (this.isClosed())
1485 // really close all the windows - otherwise wait till
1486 // setClosed(true) is called
1487 for (int i = 0; i < alignPanels.size(); i++)
1489 AlignmentPanel ap = alignPanels.get(i);
1496 closeView(alignPanel);
1503 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1504 * be called recursively, with the frame now in 'closed' state
1506 this.setClosed(true);
1508 } catch (Exception ex)
1510 ex.printStackTrace();
1515 * Close the specified panel and close up tabs appropriately.
1517 * @param panelToClose
1519 public void closeView(AlignmentPanel panelToClose)
1521 int index = tabbedPane.getSelectedIndex();
1522 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1523 alignPanels.remove(panelToClose);
1524 panelToClose.closePanel();
1525 panelToClose = null;
1527 tabbedPane.removeTabAt(closedindex);
1528 tabbedPane.validate();
1530 if (index > closedindex || index == tabbedPane.getTabCount())
1532 // modify currently selected tab index if necessary.
1536 this.tabSelectionChanged(index);
1542 void updateEditMenuBar()
1545 if (viewport.getHistoryList().size() > 0)
1547 undoMenuItem.setEnabled(true);
1548 CommandI command = viewport.getHistoryList().peek();
1549 undoMenuItem.setText(MessageManager.formatMessage(
1550 "label.undo_command",
1551 new Object[] { command.getDescription() }));
1555 undoMenuItem.setEnabled(false);
1556 undoMenuItem.setText(MessageManager.getString("action.undo"));
1559 if (viewport.getRedoList().size() > 0)
1561 redoMenuItem.setEnabled(true);
1563 CommandI command = viewport.getRedoList().peek();
1564 redoMenuItem.setText(MessageManager.formatMessage(
1565 "label.redo_command",
1566 new Object[] { command.getDescription() }));
1570 redoMenuItem.setEnabled(false);
1571 redoMenuItem.setText(MessageManager.getString("action.redo"));
1576 public void addHistoryItem(CommandI command)
1578 if (command.getSize() > 0)
1580 viewport.addToHistoryList(command);
1581 viewport.clearRedoList();
1582 updateEditMenuBar();
1583 viewport.updateHiddenColumns();
1584 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1585 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1586 // viewport.getColumnSelection()
1587 // .getHiddenColumns().size() > 0);
1593 * @return alignment objects for all views
1595 AlignmentI[] getViewAlignments()
1597 if (alignPanels != null)
1599 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1601 for (AlignmentPanel ap : alignPanels)
1603 als[i++] = ap.av.getAlignment();
1607 if (viewport != null)
1609 return new AlignmentI[] { viewport.getAlignment() };
1621 protected void undoMenuItem_actionPerformed(ActionEvent e)
1623 if (viewport.getHistoryList().isEmpty())
1627 CommandI command = viewport.getHistoryList().pop();
1628 viewport.addToRedoList(command);
1629 command.undoCommand(getViewAlignments());
1631 AlignmentViewport originalSource = getOriginatingSource(command);
1632 updateEditMenuBar();
1634 if (originalSource != null)
1636 if (originalSource != viewport)
1639 .warn("Implementation worry: mismatch of viewport origin for undo");
1641 originalSource.updateHiddenColumns();
1642 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1644 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1645 // viewport.getColumnSelection()
1646 // .getHiddenColumns().size() > 0);
1647 originalSource.firePropertyChange("alignment", null, originalSource
1648 .getAlignment().getSequences());
1659 protected void redoMenuItem_actionPerformed(ActionEvent e)
1661 if (viewport.getRedoList().size() < 1)
1666 CommandI command = viewport.getRedoList().pop();
1667 viewport.addToHistoryList(command);
1668 command.doCommand(getViewAlignments());
1670 AlignmentViewport originalSource = getOriginatingSource(command);
1671 updateEditMenuBar();
1673 if (originalSource != null)
1676 if (originalSource != viewport)
1679 .warn("Implementation worry: mismatch of viewport origin for redo");
1681 originalSource.updateHiddenColumns();
1682 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1684 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1685 // viewport.getColumnSelection()
1686 // .getHiddenColumns().size() > 0);
1687 originalSource.firePropertyChange("alignment", null, originalSource
1688 .getAlignment().getSequences());
1692 AlignmentViewport getOriginatingSource(CommandI command)
1694 AlignmentViewport originalSource = null;
1695 // For sequence removal and addition, we need to fire
1696 // the property change event FROM the viewport where the
1697 // original alignment was altered
1698 AlignmentI al = null;
1699 if (command instanceof EditCommand)
1701 EditCommand editCommand = (EditCommand) command;
1702 al = editCommand.getAlignment();
1703 List<Component> comps = PaintRefresher.components.get(viewport
1704 .getSequenceSetId());
1706 for (Component comp : comps)
1708 if (comp instanceof AlignmentPanel)
1710 if (al == ((AlignmentPanel) comp).av.getAlignment())
1712 originalSource = ((AlignmentPanel) comp).av;
1719 if (originalSource == null)
1721 // The original view is closed, we must validate
1722 // the current view against the closed view first
1725 PaintRefresher.validateSequences(al, viewport.getAlignment());
1728 originalSource = viewport;
1731 return originalSource;
1740 public void moveSelectedSequences(boolean up)
1742 SequenceGroup sg = viewport.getSelectionGroup();
1748 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1749 viewport.getHiddenRepSequences(), up);
1750 alignPanel.paintAlignment(true);
1753 synchronized void slideSequences(boolean right, int size)
1755 List<SequenceI> sg = new ArrayList<SequenceI>();
1756 if (viewport.cursorMode)
1758 sg.add(viewport.getAlignment().getSequenceAt(
1759 alignPanel.getSeqPanel().seqCanvas.cursorY));
1761 else if (viewport.getSelectionGroup() != null
1762 && viewport.getSelectionGroup().getSize() != viewport
1763 .getAlignment().getHeight())
1765 sg = viewport.getSelectionGroup().getSequences(
1766 viewport.getHiddenRepSequences());
1774 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1776 for (SequenceI seq : viewport.getAlignment().getSequences())
1778 if (!sg.contains(seq))
1780 invertGroup.add(seq);
1784 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1786 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1787 for (int i = 0; i < invertGroup.size(); i++)
1789 seqs2[i] = invertGroup.get(i);
1792 SlideSequencesCommand ssc;
1795 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1796 size, viewport.getGapCharacter());
1800 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1801 size, viewport.getGapCharacter());
1804 int groupAdjustment = 0;
1805 if (ssc.getGapsInsertedBegin() && right)
1807 if (viewport.cursorMode)
1809 alignPanel.getSeqPanel().moveCursor(size, 0);
1813 groupAdjustment = size;
1816 else if (!ssc.getGapsInsertedBegin() && !right)
1818 if (viewport.cursorMode)
1820 alignPanel.getSeqPanel().moveCursor(-size, 0);
1824 groupAdjustment = -size;
1828 if (groupAdjustment != 0)
1830 viewport.getSelectionGroup().setStartRes(
1831 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1832 viewport.getSelectionGroup().setEndRes(
1833 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1837 * just extend the last slide command if compatible; but not if in
1838 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1840 boolean appendHistoryItem = false;
1841 Deque<CommandI> historyList = viewport.getHistoryList();
1842 boolean inSplitFrame = getSplitViewContainer() != null;
1843 if (!inSplitFrame && historyList != null && historyList.size() > 0
1844 && historyList.peek() instanceof SlideSequencesCommand)
1846 appendHistoryItem = ssc
1847 .appendSlideCommand((SlideSequencesCommand) historyList
1851 if (!appendHistoryItem)
1853 addHistoryItem(ssc);
1866 protected void copy_actionPerformed(ActionEvent e)
1869 if (viewport.getSelectionGroup() == null)
1873 // TODO: preserve the ordering of displayed alignment annotation in any
1874 // internal paste (particularly sequence associated annotation)
1875 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1876 String[] omitHidden = null;
1878 if (viewport.hasHiddenColumns())
1880 omitHidden = viewport.getViewAsString(true);
1883 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1887 StringSelection ss = new StringSelection(output);
1891 jalview.gui.Desktop.internalCopy = true;
1892 // Its really worth setting the clipboard contents
1893 // to empty before setting the large StringSelection!!
1894 Toolkit.getDefaultToolkit().getSystemClipboard()
1895 .setContents(new StringSelection(""), null);
1897 Toolkit.getDefaultToolkit().getSystemClipboard()
1898 .setContents(ss, Desktop.instance);
1899 } catch (OutOfMemoryError er)
1901 new OOMWarning("copying region", er);
1905 ArrayList<int[]> hiddenColumns = null;
1906 if (viewport.hasHiddenColumns())
1908 hiddenColumns = new ArrayList<int[]>();
1909 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1910 .getSelectionGroup().getEndRes();
1911 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1913 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1915 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1916 region[1] - hiddenOffset });
1921 Desktop.jalviewClipboard = new Object[] { seqs,
1922 viewport.getAlignment().getDataset(), hiddenColumns };
1923 statusBar.setText(MessageManager.formatMessage(
1924 "label.copied_sequences_to_clipboard", new Object[] { Integer
1925 .valueOf(seqs.length).toString() }));
1935 protected void pasteNew_actionPerformed(ActionEvent e)
1947 protected void pasteThis_actionPerformed(ActionEvent e)
1953 * Paste contents of Jalview clipboard
1955 * @param newAlignment
1956 * true to paste to a new alignment, otherwise add to this.
1958 void paste(boolean newAlignment)
1960 boolean externalPaste = true;
1963 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1964 Transferable contents = c.getContents(this);
1966 if (contents == null)
1975 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1976 if (str.length() < 1)
1981 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1983 } catch (OutOfMemoryError er)
1985 new OOMWarning("Out of memory pasting sequences!!", er);
1989 SequenceI[] sequences;
1990 boolean annotationAdded = false;
1991 AlignmentI alignment = null;
1993 if (Desktop.jalviewClipboard != null)
1995 // The clipboard was filled from within Jalview, we must use the
1997 // And dataset from the copied alignment
1998 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1999 // be doubly sure that we create *new* sequence objects.
2000 sequences = new SequenceI[newseq.length];
2001 for (int i = 0; i < newseq.length; i++)
2003 sequences[i] = new Sequence(newseq[i]);
2005 alignment = new Alignment(sequences);
2006 externalPaste = false;
2010 // parse the clipboard as an alignment.
2011 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2013 sequences = alignment.getSequencesArray();
2017 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2023 if (Desktop.jalviewClipboard != null)
2025 // dataset is inherited
2026 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2030 // new dataset is constructed
2031 alignment.setDataset(null);
2033 alwidth = alignment.getWidth() + 1;
2037 AlignmentI pastedal = alignment; // preserve pasted alignment object
2038 // Add pasted sequences and dataset into existing alignment.
2039 alignment = viewport.getAlignment();
2040 alwidth = alignment.getWidth() + 1;
2041 // decide if we need to import sequences from an existing dataset
2042 boolean importDs = Desktop.jalviewClipboard != null
2043 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2044 // importDs==true instructs us to copy over new dataset sequences from
2045 // an existing alignment
2046 Vector newDs = (importDs) ? new Vector() : null; // used to create
2047 // minimum dataset set
2049 for (int i = 0; i < sequences.length; i++)
2053 newDs.addElement(null);
2055 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2057 if (importDs && ds != null)
2059 if (!newDs.contains(ds))
2061 newDs.setElementAt(ds, i);
2062 ds = new Sequence(ds);
2063 // update with new dataset sequence
2064 sequences[i].setDatasetSequence(ds);
2068 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2073 // copy and derive new dataset sequence
2074 sequences[i] = sequences[i].deriveSequence();
2075 alignment.getDataset().addSequence(
2076 sequences[i].getDatasetSequence());
2077 // TODO: avoid creation of duplicate dataset sequences with a
2078 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2080 alignment.addSequence(sequences[i]); // merges dataset
2084 newDs.clear(); // tidy up
2086 if (alignment.getAlignmentAnnotation() != null)
2088 for (AlignmentAnnotation alan : alignment
2089 .getAlignmentAnnotation())
2091 if (alan.graphGroup > fgroup)
2093 fgroup = alan.graphGroup;
2097 if (pastedal.getAlignmentAnnotation() != null)
2099 // Add any annotation attached to alignment.
2100 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2101 for (int i = 0; i < alann.length; i++)
2103 annotationAdded = true;
2104 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2106 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2107 if (newann.graphGroup > -1)
2109 if (newGraphGroups.size() <= newann.graphGroup
2110 || newGraphGroups.get(newann.graphGroup) == null)
2112 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2114 newGraphGroups.add(q, null);
2116 newGraphGroups.set(newann.graphGroup, new Integer(
2119 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2123 newann.padAnnotation(alwidth);
2124 alignment.addAnnotation(newann);
2134 addHistoryItem(new EditCommand(
2135 MessageManager.getString("label.add_sequences"),
2136 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2138 // Add any annotations attached to sequences
2139 for (int i = 0; i < sequences.length; i++)
2141 if (sequences[i].getAnnotation() != null)
2143 AlignmentAnnotation newann;
2144 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2146 annotationAdded = true;
2147 newann = sequences[i].getAnnotation()[a];
2148 newann.adjustForAlignment();
2149 newann.padAnnotation(alwidth);
2150 if (newann.graphGroup > -1)
2152 if (newann.graphGroup > -1)
2154 if (newGraphGroups.size() <= newann.graphGroup
2155 || newGraphGroups.get(newann.graphGroup) == null)
2157 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2159 newGraphGroups.add(q, null);
2161 newGraphGroups.set(newann.graphGroup, new Integer(
2164 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2168 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2173 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2180 // propagate alignment changed.
2181 viewport.setEndSeq(alignment.getHeight());
2182 if (annotationAdded)
2184 // Duplicate sequence annotation in all views.
2185 AlignmentI[] alview = this.getViewAlignments();
2186 for (int i = 0; i < sequences.length; i++)
2188 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2193 for (int avnum = 0; avnum < alview.length; avnum++)
2195 if (alview[avnum] != alignment)
2197 // duplicate in a view other than the one with input focus
2198 int avwidth = alview[avnum].getWidth() + 1;
2199 // this relies on sann being preserved after we
2200 // modify the sequence's annotation array for each duplication
2201 for (int a = 0; a < sann.length; a++)
2203 AlignmentAnnotation newann = new AlignmentAnnotation(
2205 sequences[i].addAlignmentAnnotation(newann);
2206 newann.padAnnotation(avwidth);
2207 alview[avnum].addAnnotation(newann); // annotation was
2208 // duplicated earlier
2209 // TODO JAL-1145 graphGroups are not updated for sequence
2210 // annotation added to several views. This may cause
2212 alview[avnum].setAnnotationIndex(newann, a);
2217 buildSortByAnnotationScoresMenu();
2219 viewport.firePropertyChange("alignment", null,
2220 alignment.getSequences());
2221 if (alignPanels != null)
2223 for (AlignmentPanel ap : alignPanels)
2225 ap.validateAnnotationDimensions(false);
2230 alignPanel.validateAnnotationDimensions(false);
2236 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2238 String newtitle = new String("Copied sequences");
2240 if (Desktop.jalviewClipboard != null
2241 && Desktop.jalviewClipboard[2] != null)
2243 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2244 for (int[] region : hc)
2246 af.viewport.hideColumns(region[0], region[1]);
2250 // >>>This is a fix for the moment, until a better solution is
2252 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2254 alignPanel.getSeqPanel().seqCanvas
2255 .getFeatureRenderer());
2257 // TODO: maintain provenance of an alignment, rather than just make the
2258 // title a concatenation of operations.
2261 if (title.startsWith("Copied sequences"))
2267 newtitle = newtitle.concat("- from " + title);
2272 newtitle = new String("Pasted sequences");
2275 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2280 } catch (Exception ex)
2282 ex.printStackTrace();
2283 System.out.println("Exception whilst pasting: " + ex);
2284 // could be anything being pasted in here
2290 protected void expand_newalign(ActionEvent e)
2294 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2295 .getAlignment(), -1);
2296 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2298 String newtitle = new String("Flanking alignment");
2300 if (Desktop.jalviewClipboard != null
2301 && Desktop.jalviewClipboard[2] != null)
2303 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2304 for (int region[] : hc)
2306 af.viewport.hideColumns(region[0], region[1]);
2310 // >>>This is a fix for the moment, until a better solution is
2312 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2314 alignPanel.getSeqPanel().seqCanvas
2315 .getFeatureRenderer());
2317 // TODO: maintain provenance of an alignment, rather than just make the
2318 // title a concatenation of operations.
2320 if (title.startsWith("Copied sequences"))
2326 newtitle = newtitle.concat("- from " + title);
2330 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2332 } catch (Exception ex)
2334 ex.printStackTrace();
2335 System.out.println("Exception whilst pasting: " + ex);
2336 // could be anything being pasted in here
2337 } catch (OutOfMemoryError oom)
2339 new OOMWarning("Viewing flanking region of alignment", oom);
2350 protected void cut_actionPerformed(ActionEvent e)
2352 copy_actionPerformed(null);
2353 delete_actionPerformed(null);
2363 protected void delete_actionPerformed(ActionEvent evt)
2366 SequenceGroup sg = viewport.getSelectionGroup();
2373 * If the cut affects all sequences, warn, remove highlighted columns
2375 if (sg.getSize() == viewport.getAlignment().getHeight())
2377 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2378 .getAlignment().getWidth()) ? true : false;
2379 if (isEntireAlignWidth)
2381 int confirm = JvOptionPane.showConfirmDialog(this,
2382 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2383 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2384 JvOptionPane.OK_CANCEL_OPTION);
2386 if (confirm == JvOptionPane.CANCEL_OPTION
2387 || confirm == JvOptionPane.CLOSED_OPTION)
2392 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2393 sg.getEndRes() + 1);
2395 SequenceI[] cut = sg.getSequences()
2396 .toArray(new SequenceI[sg.getSize()]);
2398 addHistoryItem(new EditCommand(
2399 MessageManager.getString("label.cut_sequences"), Action.CUT,
2400 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2401 viewport.getAlignment()));
2403 viewport.setSelectionGroup(null);
2404 viewport.sendSelection();
2405 viewport.getAlignment().deleteGroup(sg);
2407 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2409 if (viewport.getAlignment().getHeight() < 1)
2413 this.setClosed(true);
2414 } catch (Exception ex)
2427 protected void deleteGroups_actionPerformed(ActionEvent e)
2429 if (avc.deleteGroups())
2431 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2432 alignPanel.updateAnnotation();
2433 alignPanel.paintAlignment(true);
2444 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2446 SequenceGroup sg = new SequenceGroup();
2448 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2450 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2453 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2454 viewport.setSelectionGroup(sg);
2455 viewport.sendSelection();
2456 // JAL-2034 - should delegate to
2457 // alignPanel to decide if overview needs
2459 alignPanel.paintAlignment(false);
2460 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2470 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2472 if (viewport.cursorMode)
2474 alignPanel.getSeqPanel().keyboardNo1 = null;
2475 alignPanel.getSeqPanel().keyboardNo2 = null;
2477 viewport.setSelectionGroup(null);
2478 viewport.getColumnSelection().clear();
2479 viewport.setSelectionGroup(null);
2480 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2481 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2482 // JAL-2034 - should delegate to
2483 // alignPanel to decide if overview needs
2485 alignPanel.paintAlignment(false);
2486 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2487 viewport.sendSelection();
2497 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2499 SequenceGroup sg = viewport.getSelectionGroup();
2503 selectAllSequenceMenuItem_actionPerformed(null);
2508 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2510 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2512 // JAL-2034 - should delegate to
2513 // alignPanel to decide if overview needs
2516 alignPanel.paintAlignment(true);
2517 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2518 viewport.sendSelection();
2522 public void invertColSel_actionPerformed(ActionEvent e)
2524 viewport.invertColumnSelection();
2525 alignPanel.paintAlignment(true);
2526 viewport.sendSelection();
2536 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2538 trimAlignment(true);
2548 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2550 trimAlignment(false);
2553 void trimAlignment(boolean trimLeft)
2555 ColumnSelection colSel = viewport.getColumnSelection();
2558 if (!colSel.isEmpty())
2562 column = colSel.getMin();
2566 column = colSel.getMax();
2570 if (viewport.getSelectionGroup() != null)
2572 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2573 viewport.getHiddenRepSequences());
2577 seqs = viewport.getAlignment().getSequencesArray();
2580 TrimRegionCommand trimRegion;
2583 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2584 column, viewport.getAlignment());
2585 viewport.setStartRes(0);
2589 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2590 column, viewport.getAlignment());
2593 statusBar.setText(MessageManager.formatMessage(
2594 "label.removed_columns",
2595 new String[] { Integer.valueOf(trimRegion.getSize())
2598 addHistoryItem(trimRegion);
2600 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2602 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2603 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2605 viewport.getAlignment().deleteGroup(sg);
2609 viewport.firePropertyChange("alignment", null, viewport
2610 .getAlignment().getSequences());
2621 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2623 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2626 if (viewport.getSelectionGroup() != null)
2628 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2629 viewport.getHiddenRepSequences());
2630 start = viewport.getSelectionGroup().getStartRes();
2631 end = viewport.getSelectionGroup().getEndRes();
2635 seqs = viewport.getAlignment().getSequencesArray();
2638 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2639 "Remove Gapped Columns", seqs, start, end,
2640 viewport.getAlignment());
2642 addHistoryItem(removeGapCols);
2644 statusBar.setText(MessageManager.formatMessage(
2645 "label.removed_empty_columns",
2646 new Object[] { Integer.valueOf(removeGapCols.getSize())
2649 // This is to maintain viewport position on first residue
2650 // of first sequence
2651 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2652 int startRes = seq.findPosition(viewport.startRes);
2653 // ShiftList shifts;
2654 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2655 // edit.alColumnChanges=shifts.getInverse();
2656 // if (viewport.hasHiddenColumns)
2657 // viewport.getColumnSelection().compensateForEdits(shifts);
2658 viewport.setStartRes(seq.findIndex(startRes) - 1);
2659 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2671 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2673 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2676 if (viewport.getSelectionGroup() != null)
2678 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2679 viewport.getHiddenRepSequences());
2680 start = viewport.getSelectionGroup().getStartRes();
2681 end = viewport.getSelectionGroup().getEndRes();
2685 seqs = viewport.getAlignment().getSequencesArray();
2688 // This is to maintain viewport position on first residue
2689 // of first sequence
2690 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2691 int startRes = seq.findPosition(viewport.startRes);
2693 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2694 viewport.getAlignment()));
2696 viewport.setStartRes(seq.findIndex(startRes) - 1);
2698 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2710 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2712 viewport.setPadGaps(padGapsMenuitem.isSelected());
2713 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2724 public void findMenuItem_actionPerformed(ActionEvent e)
2730 * Create a new view of the current alignment.
2733 public void newView_actionPerformed(ActionEvent e)
2735 newView(null, true);
2739 * Creates and shows a new view of the current alignment.
2742 * title of newly created view; if null, one will be generated
2743 * @param copyAnnotation
2744 * if true then duplicate all annnotation, groups and settings
2745 * @return new alignment panel, already displayed.
2747 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2750 * Create a new AlignmentPanel (with its own, new Viewport)
2752 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2754 if (!copyAnnotation)
2757 * remove all groups and annotation except for the automatic stuff
2759 newap.av.getAlignment().deleteAllGroups();
2760 newap.av.getAlignment().deleteAllAnnotations(false);
2763 newap.av.setGatherViewsHere(false);
2765 if (viewport.viewName == null)
2767 viewport.viewName = MessageManager
2768 .getString("label.view_name_original");
2772 * Views share the same edits undo and redo stacks
2774 newap.av.setHistoryList(viewport.getHistoryList());
2775 newap.av.setRedoList(viewport.getRedoList());
2778 * Views share the same mappings; need to deregister any new mappings
2779 * created by copyAlignPanel, and register the new reference to the shared
2782 newap.av.replaceMappings(viewport.getAlignment());
2784 newap.av.viewName = getNewViewName(viewTitle);
2786 addAlignmentPanel(newap, true);
2787 newap.alignmentChanged();
2789 if (alignPanels.size() == 2)
2791 viewport.setGatherViewsHere(true);
2793 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2798 * Make a new name for the view, ensuring it is unique within the current
2799 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2800 * these now use viewId. Unique view names are still desirable for usability.)
2805 protected String getNewViewName(String viewTitle)
2807 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2808 boolean addFirstIndex = false;
2809 if (viewTitle == null || viewTitle.trim().length() == 0)
2811 viewTitle = MessageManager.getString("action.view");
2812 addFirstIndex = true;
2816 index = 1;// we count from 1 if given a specific name
2818 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2820 List<Component> comps = PaintRefresher.components.get(viewport
2821 .getSequenceSetId());
2823 List<String> existingNames = getExistingViewNames(comps);
2825 while (existingNames.contains(newViewName))
2827 newViewName = viewTitle + " " + (++index);
2833 * Returns a list of distinct view names found in the given list of
2834 * components. View names are held on the viewport of an AlignmentPanel.
2839 protected List<String> getExistingViewNames(List<Component> comps)
2841 List<String> existingNames = new ArrayList<String>();
2842 for (Component comp : comps)
2844 if (comp instanceof AlignmentPanel)
2846 AlignmentPanel ap = (AlignmentPanel) comp;
2847 if (!existingNames.contains(ap.av.viewName))
2849 existingNames.add(ap.av.viewName);
2853 return existingNames;
2857 * Explode tabbed views into separate windows.
2860 public void expandViews_actionPerformed(ActionEvent e)
2862 Desktop.explodeViews(this);
2866 * Gather views in separate windows back into a tabbed presentation.
2869 public void gatherViews_actionPerformed(ActionEvent e)
2871 Desktop.instance.gatherViews(this);
2881 public void font_actionPerformed(ActionEvent e)
2883 new FontChooser(alignPanel);
2893 protected void seqLimit_actionPerformed(ActionEvent e)
2895 viewport.setShowJVSuffix(seqLimits.isSelected());
2897 alignPanel.getIdPanel().getIdCanvas()
2898 .setPreferredSize(alignPanel.calculateIdWidth());
2899 alignPanel.paintAlignment(true);
2903 public void idRightAlign_actionPerformed(ActionEvent e)
2905 viewport.setRightAlignIds(idRightAlign.isSelected());
2906 alignPanel.paintAlignment(true);
2910 public void centreColumnLabels_actionPerformed(ActionEvent e)
2912 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2913 alignPanel.paintAlignment(true);
2919 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2922 protected void followHighlight_actionPerformed()
2925 * Set the 'follow' flag on the Viewport (and scroll to position if now
2928 final boolean state = this.followHighlightMenuItem.getState();
2929 viewport.setFollowHighlight(state);
2932 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2943 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2945 viewport.setColourText(colourTextMenuItem.isSelected());
2946 alignPanel.paintAlignment(true);
2956 public void wrapMenuItem_actionPerformed(ActionEvent e)
2958 scaleAbove.setVisible(wrapMenuItem.isSelected());
2959 scaleLeft.setVisible(wrapMenuItem.isSelected());
2960 scaleRight.setVisible(wrapMenuItem.isSelected());
2961 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2962 alignPanel.updateLayout();
2966 public void showAllSeqs_actionPerformed(ActionEvent e)
2968 viewport.showAllHiddenSeqs();
2972 public void showAllColumns_actionPerformed(ActionEvent e)
2974 viewport.showAllHiddenColumns();
2976 viewport.sendSelection();
2980 public void hideSelSequences_actionPerformed(ActionEvent e)
2982 viewport.hideAllSelectedSeqs();
2983 // alignPanel.paintAlignment(true);
2987 * called by key handler and the hide all/show all menu items
2992 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2995 boolean hide = false;
2996 SequenceGroup sg = viewport.getSelectionGroup();
2997 if (!toggleSeqs && !toggleCols)
2999 // Hide everything by the current selection - this is a hack - we do the
3000 // invert and then hide
3001 // first check that there will be visible columns after the invert.
3002 if (viewport.hasSelectedColumns()
3003 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3006 // now invert the sequence set, if required - empty selection implies
3007 // that no hiding is required.
3010 invertSequenceMenuItem_actionPerformed(null);
3011 sg = viewport.getSelectionGroup();
3015 viewport.expandColSelection(sg, true);
3016 // finally invert the column selection and get the new sequence
3018 invertColSel_actionPerformed(null);
3025 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3027 hideSelSequences_actionPerformed(null);
3030 else if (!(toggleCols && viewport.hasSelectedColumns()))
3032 showAllSeqs_actionPerformed(null);
3038 if (viewport.hasSelectedColumns())
3040 hideSelColumns_actionPerformed(null);
3043 viewport.setSelectionGroup(sg);
3048 showAllColumns_actionPerformed(null);
3057 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3058 * event.ActionEvent)
3061 public void hideAllButSelection_actionPerformed(ActionEvent e)
3063 toggleHiddenRegions(false, false);
3064 viewport.sendSelection();
3071 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3075 public void hideAllSelection_actionPerformed(ActionEvent e)
3077 SequenceGroup sg = viewport.getSelectionGroup();
3078 viewport.expandColSelection(sg, false);
3079 viewport.hideAllSelectedSeqs();
3080 viewport.hideSelectedColumns();
3081 alignPanel.paintAlignment(true);
3082 viewport.sendSelection();
3089 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3093 public void showAllhidden_actionPerformed(ActionEvent e)
3095 viewport.showAllHiddenColumns();
3096 viewport.showAllHiddenSeqs();
3097 alignPanel.paintAlignment(true);
3098 viewport.sendSelection();
3102 public void hideSelColumns_actionPerformed(ActionEvent e)
3104 viewport.hideSelectedColumns();
3105 alignPanel.paintAlignment(true);
3106 viewport.sendSelection();
3110 public void hiddenMarkers_actionPerformed(ActionEvent e)
3112 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3123 protected void scaleAbove_actionPerformed(ActionEvent e)
3125 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3126 alignPanel.paintAlignment(true);
3136 protected void scaleLeft_actionPerformed(ActionEvent e)
3138 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3139 alignPanel.paintAlignment(true);
3149 protected void scaleRight_actionPerformed(ActionEvent e)
3151 viewport.setScaleRightWrapped(scaleRight.isSelected());
3152 alignPanel.paintAlignment(true);
3162 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3164 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3165 alignPanel.paintAlignment(true);
3175 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3177 viewport.setShowText(viewTextMenuItem.isSelected());
3178 alignPanel.paintAlignment(true);
3188 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3190 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3191 alignPanel.paintAlignment(true);
3194 public FeatureSettings featureSettings;
3197 public FeatureSettingsControllerI getFeatureSettingsUI()
3199 return featureSettings;
3203 public void featureSettings_actionPerformed(ActionEvent e)
3205 if (featureSettings != null)
3207 featureSettings.close();
3208 featureSettings = null;
3210 if (!showSeqFeatures.isSelected())
3212 // make sure features are actually displayed
3213 showSeqFeatures.setSelected(true);
3214 showSeqFeatures_actionPerformed(null);
3216 featureSettings = new FeatureSettings(this);
3220 * Set or clear 'Show Sequence Features'
3226 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3228 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3229 alignPanel.paintAlignment(true);
3230 if (alignPanel.getOverviewPanel() != null)
3232 alignPanel.getOverviewPanel().updateOverviewImage();
3237 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3238 * the annotations panel as a whole.
3240 * The options to show/hide all annotations should be enabled when the panel
3241 * is shown, and disabled when the panel is hidden.
3246 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3248 final boolean setVisible = annotationPanelMenuItem.isSelected();
3249 viewport.setShowAnnotation(setVisible);
3250 this.showAllSeqAnnotations.setEnabled(setVisible);
3251 this.hideAllSeqAnnotations.setEnabled(setVisible);
3252 this.showAllAlAnnotations.setEnabled(setVisible);
3253 this.hideAllAlAnnotations.setEnabled(setVisible);
3254 alignPanel.updateLayout();
3258 public void alignmentProperties()
3260 JEditorPane editPane = new JEditorPane("text/html", "");
3261 editPane.setEditable(false);
3262 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3264 editPane.setText(MessageManager.formatMessage("label.html_content",
3265 new Object[] { contents.toString() }));
3266 JInternalFrame frame = new JInternalFrame();
3267 frame.getContentPane().add(new JScrollPane(editPane));
3269 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3270 "label.alignment_properties", new Object[] { getTitle() }),
3281 public void overviewMenuItem_actionPerformed(ActionEvent e)
3283 if (alignPanel.overviewPanel != null)
3288 JInternalFrame frame = new JInternalFrame();
3289 OverviewPanel overview = new OverviewPanel(alignPanel);
3290 frame.setContentPane(overview);
3291 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3292 "label.overview_params", new Object[] { this.getTitle() }),
3293 frame.getWidth(), frame.getHeight());
3295 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3296 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3299 public void internalFrameClosed(
3300 javax.swing.event.InternalFrameEvent evt)
3302 alignPanel.setOverviewPanel(null);
3306 alignPanel.setOverviewPanel(overview);
3310 public void textColour_actionPerformed()
3312 new TextColourChooser().chooseColour(alignPanel, null);
3322 protected void noColourmenuItem_actionPerformed()
3334 public void clustalColour_actionPerformed()
3336 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3337 viewport.getHiddenRepSequences()));
3347 public void zappoColour_actionPerformed()
3349 changeColour(new ZappoColourScheme());
3359 public void taylorColour_actionPerformed()
3361 changeColour(new TaylorColourScheme());
3371 public void hydrophobicityColour_actionPerformed()
3373 changeColour(new HydrophobicColourScheme());
3383 public void helixColour_actionPerformed()
3385 changeColour(new HelixColourScheme());
3395 public void strandColour_actionPerformed()
3397 changeColour(new StrandColourScheme());
3407 public void turnColour_actionPerformed()
3409 changeColour(new TurnColourScheme());
3419 public void buriedColour_actionPerformed()
3421 changeColour(new BuriedColourScheme());
3431 public void nucleotideColour_actionPerformed()
3433 changeColour(new NucleotideColourScheme());
3437 public void purinePyrimidineColour_actionPerformed()
3439 changeColour(new PurinePyrimidineColourScheme());
3443 * public void covariationColour_actionPerformed() {
3445 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3449 public void annotationColour_actionPerformed()
3451 new AnnotationColourChooser(viewport, alignPanel);
3455 public void annotationColumn_actionPerformed(ActionEvent e)
3457 new AnnotationColumnChooser(viewport, alignPanel);
3461 public void rnahelicesColour_actionPerformed()
3463 new RNAHelicesColourChooser(viewport, alignPanel);
3471 protected void applyToAllGroups_actionPerformed()
3473 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3483 public void changeColour(ColourSchemeI cs)
3485 // TODO: pull up to controller method
3489 // Make sure viewport is up to date w.r.t. any sliders
3490 if (viewport.getAbovePIDThreshold())
3492 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3494 viewport.setThreshold(threshold);
3497 if (viewport.getConservationSelected())
3499 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3502 if (cs instanceof TCoffeeColourScheme)
3504 tcoffeeColour.setEnabled(true);
3505 tcoffeeColour.setSelected(true);
3509 viewport.setGlobalColourScheme(cs);
3511 alignPanel.paintAlignment(true);
3521 protected void modifyPID_actionPerformed()
3523 if (viewport.getAbovePIDThreshold()
3524 && viewport.getGlobalColourScheme() != null)
3526 SliderPanel.setPIDSliderSource(alignPanel,
3527 viewport.getGlobalColourScheme(), "Background");
3528 SliderPanel.showPIDSlider();
3539 protected void modifyConservation_actionPerformed()
3541 if (viewport.getConservationSelected()
3542 && viewport.getGlobalColourScheme() != null)
3544 SliderPanel.setConservationSlider(alignPanel,
3545 viewport.getGlobalColourScheme(), "Background");
3546 SliderPanel.showConservationSlider();
3557 protected void conservationMenuItem_actionPerformed()
3559 viewport.setConservationSelected(conservationMenuItem.isSelected());
3561 viewport.setAbovePIDThreshold(false);
3562 abovePIDThreshold.setSelected(false);
3564 changeColour(viewport.getGlobalColourScheme());
3566 modifyConservation_actionPerformed();
3576 public void abovePIDThreshold_actionPerformed()
3578 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3580 conservationMenuItem.setSelected(false);
3581 viewport.setConservationSelected(false);
3583 changeColour(viewport.getGlobalColourScheme());
3585 modifyPID_actionPerformed();
3595 public void userDefinedColour_actionPerformed(ActionEvent e)
3597 if (e.getActionCommand().equals(
3598 MessageManager.getString("action.user_defined")))
3600 new UserDefinedColours(alignPanel, null);
3604 UserColourScheme udc = UserDefinedColours
3605 .getUserColourSchemes().get(e.getActionCommand());
3618 public void PIDColour_actionPerformed()
3620 changeColour(new PIDColourScheme());
3630 public void BLOSUM62Colour_actionPerformed()
3632 changeColour(new Blosum62ColourScheme());
3642 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3644 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3645 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3646 .getAlignment().getSequenceAt(0), null);
3647 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3648 viewport.getAlignment()));
3649 alignPanel.paintAlignment(true);
3659 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3661 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3662 AlignmentSorter.sortByID(viewport.getAlignment());
3663 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3664 viewport.getAlignment()));
3665 alignPanel.paintAlignment(true);
3675 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3677 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3678 AlignmentSorter.sortByLength(viewport.getAlignment());
3679 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3680 viewport.getAlignment()));
3681 alignPanel.paintAlignment(true);
3691 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3693 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3694 AlignmentSorter.sortByGroup(viewport.getAlignment());
3695 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3696 viewport.getAlignment()));
3698 alignPanel.paintAlignment(true);
3708 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3710 new RedundancyPanel(alignPanel, this);
3720 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3722 if ((viewport.getSelectionGroup() == null)
3723 || (viewport.getSelectionGroup().getSize() < 2))
3725 JvOptionPane.showInternalMessageDialog(this, MessageManager
3726 .getString("label.you_must_select_least_two_sequences"),
3727 MessageManager.getString("label.invalid_selection"),
3728 JvOptionPane.WARNING_MESSAGE);
3732 JInternalFrame frame = new JInternalFrame();
3733 frame.setContentPane(new PairwiseAlignPanel(viewport));
3734 Desktop.addInternalFrame(frame,
3735 MessageManager.getString("action.pairwise_alignment"), 600,
3747 public void PCAMenuItem_actionPerformed(ActionEvent e)
3749 if (((viewport.getSelectionGroup() != null)
3750 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3751 .getSelectionGroup().getSize() > 0))
3752 || (viewport.getAlignment().getHeight() < 4))
3755 .showInternalMessageDialog(
3758 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3760 .getString("label.sequence_selection_insufficient"),
3761 JvOptionPane.WARNING_MESSAGE);
3766 new PCAPanel(alignPanel);
3770 public void autoCalculate_actionPerformed(ActionEvent e)
3772 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3773 if (viewport.autoCalculateConsensus)
3775 viewport.firePropertyChange("alignment", null, viewport
3776 .getAlignment().getSequences());
3781 public void sortByTreeOption_actionPerformed(ActionEvent e)
3783 viewport.sortByTree = sortByTree.isSelected();
3787 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3789 viewport.followSelection = listenToViewSelections.isSelected();
3799 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3801 newTreePanel("AV", "PID", "Average distance tree using PID");
3811 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3813 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3823 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3825 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3835 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3837 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3850 void newTreePanel(String type, String pwType, String title)
3854 if (viewport.getSelectionGroup() != null
3855 && viewport.getSelectionGroup().getSize() > 0)
3857 if (viewport.getSelectionGroup().getSize() < 3)
3863 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3865 .getString("label.not_enough_sequences"),
3866 JvOptionPane.WARNING_MESSAGE);
3870 SequenceGroup sg = viewport.getSelectionGroup();
3872 /* Decide if the selection is a column region */
3873 for (SequenceI _s : sg.getSequences())
3875 if (_s.getLength() < sg.getEndRes())
3881 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3883 .getString("label.sequences_selection_not_aligned"),
3884 JvOptionPane.WARNING_MESSAGE);
3890 title = title + " on region";
3891 tp = new TreePanel(alignPanel, type, pwType);
3895 // are the visible sequences aligned?
3896 if (!viewport.getAlignment().isAligned(false))
3902 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3904 .getString("label.sequences_not_aligned"),
3905 JvOptionPane.WARNING_MESSAGE);
3910 if (viewport.getAlignment().getHeight() < 2)
3915 tp = new TreePanel(alignPanel, type, pwType);
3920 if (viewport.viewName != null)
3922 title += viewport.viewName + " of ";
3925 title += this.title;
3927 Desktop.addInternalFrame(tp, title, 600, 500);
3938 public void addSortByOrderMenuItem(String title,
3939 final AlignmentOrder order)
3941 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3942 "action.by_title_param", new Object[] { title }));
3944 item.addActionListener(new java.awt.event.ActionListener()
3947 public void actionPerformed(ActionEvent e)
3949 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3951 // TODO: JBPNote - have to map order entries to curent SequenceI
3953 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3955 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3958 alignPanel.paintAlignment(true);
3964 * Add a new sort by annotation score menu item
3967 * the menu to add the option to
3969 * the label used to retrieve scores for each sequence on the
3972 public void addSortByAnnotScoreMenuItem(JMenu sort,
3973 final String scoreLabel)
3975 final JMenuItem item = new JMenuItem(scoreLabel);
3977 item.addActionListener(new java.awt.event.ActionListener()
3980 public void actionPerformed(ActionEvent e)
3982 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3983 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3984 viewport.getAlignment());// ,viewport.getSelectionGroup());
3985 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3986 viewport.getAlignment()));
3987 alignPanel.paintAlignment(true);
3993 * last hash for alignment's annotation array - used to minimise cost of
3996 protected int _annotationScoreVectorHash;
3999 * search the alignment and rebuild the sort by annotation score submenu the
4000 * last alignment annotation vector hash is stored to minimize cost of
4001 * rebuilding in subsequence calls.
4005 public void buildSortByAnnotationScoresMenu()
4007 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4012 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4014 sortByAnnotScore.removeAll();
4015 // almost certainly a quicker way to do this - but we keep it simple
4016 Hashtable scoreSorts = new Hashtable();
4017 AlignmentAnnotation aann[];
4018 for (SequenceI sqa : viewport.getAlignment().getSequences())
4020 aann = sqa.getAnnotation();
4021 for (int i = 0; aann != null && i < aann.length; i++)
4023 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4025 scoreSorts.put(aann[i].label, aann[i].label);
4029 Enumeration labels = scoreSorts.keys();
4030 while (labels.hasMoreElements())
4032 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4033 (String) labels.nextElement());
4035 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4038 _annotationScoreVectorHash = viewport.getAlignment()
4039 .getAlignmentAnnotation().hashCode();
4044 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4045 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4046 * call. Listeners are added to remove the menu item when the treePanel is
4047 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4051 * Displayed tree window.
4053 * SortBy menu item title.
4056 public void buildTreeMenu()
4058 calculateTree.removeAll();
4059 // build the calculate menu
4061 for (final String type : new String[] { "NJ", "AV" })
4063 String treecalcnm = MessageManager.getString("label.tree_calc_"
4064 + type.toLowerCase());
4065 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4067 JMenuItem tm = new JMenuItem();
4068 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4069 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4070 || sm.isProtein() == !viewport.getAlignment()
4073 String smn = MessageManager.getStringOrReturn(
4074 "label.score_model_", sm.getName());
4075 final String title = MessageManager.formatMessage(
4076 "label.treecalc_title", treecalcnm, smn);
4077 tm.setText(title);//
4078 tm.addActionListener(new java.awt.event.ActionListener()
4081 public void actionPerformed(ActionEvent e)
4083 newTreePanel(type, pwtype, title);
4086 calculateTree.add(tm);
4091 sortByTreeMenu.removeAll();
4093 List<Component> comps = PaintRefresher.components.get(viewport
4094 .getSequenceSetId());
4095 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4096 for (Component comp : comps)
4098 if (comp instanceof TreePanel)
4100 treePanels.add((TreePanel) comp);
4104 if (treePanels.size() < 1)
4106 sortByTreeMenu.setVisible(false);
4110 sortByTreeMenu.setVisible(true);
4112 for (final TreePanel tp : treePanels)
4114 final JMenuItem item = new JMenuItem(tp.getTitle());
4115 item.addActionListener(new java.awt.event.ActionListener()
4118 public void actionPerformed(ActionEvent e)
4120 tp.sortByTree_actionPerformed();
4121 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4126 sortByTreeMenu.add(item);
4130 public boolean sortBy(AlignmentOrder alorder, String undoname)
4132 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4133 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4134 if (undoname != null)
4136 addHistoryItem(new OrderCommand(undoname, oldOrder,
4137 viewport.getAlignment()));
4139 alignPanel.paintAlignment(true);
4144 * Work out whether the whole set of sequences or just the selected set will
4145 * be submitted for multiple alignment.
4148 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4150 // Now, check we have enough sequences
4151 AlignmentView msa = null;
4153 if ((viewport.getSelectionGroup() != null)
4154 && (viewport.getSelectionGroup().getSize() > 1))
4156 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4157 // some common interface!
4159 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4160 * SequenceI[sz = seqs.getSize(false)];
4162 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4163 * seqs.getSequenceAt(i); }
4165 msa = viewport.getAlignmentView(true);
4167 else if (viewport.getSelectionGroup() != null
4168 && viewport.getSelectionGroup().getSize() == 1)
4170 int option = JvOptionPane.showConfirmDialog(this,
4171 MessageManager.getString("warn.oneseq_msainput_selection"),
4172 MessageManager.getString("label.invalid_selection"),
4173 JvOptionPane.OK_CANCEL_OPTION);
4174 if (option == JvOptionPane.OK_OPTION)
4176 msa = viewport.getAlignmentView(false);
4181 msa = viewport.getAlignmentView(false);
4187 * Decides what is submitted to a secondary structure prediction service: the
4188 * first sequence in the alignment, or in the current selection, or, if the
4189 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4190 * region or the whole alignment. (where the first sequence in the set is the
4191 * one that the prediction will be for).
4193 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4195 AlignmentView seqs = null;
4197 if ((viewport.getSelectionGroup() != null)
4198 && (viewport.getSelectionGroup().getSize() > 0))
4200 seqs = viewport.getAlignmentView(true);
4204 seqs = viewport.getAlignmentView(false);
4206 // limit sequences - JBPNote in future - could spawn multiple prediction
4208 // TODO: viewport.getAlignment().isAligned is a global state - the local
4209 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4210 if (!viewport.getAlignment().isAligned(false))
4212 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4213 // TODO: if seqs.getSequences().length>1 then should really have warned
4227 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4229 // Pick the tree file
4230 JalviewFileChooser chooser = new JalviewFileChooser(
4231 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4232 chooser.setFileView(new JalviewFileView());
4233 chooser.setDialogTitle(MessageManager
4234 .getString("label.select_newick_like_tree_file"));
4235 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4237 int value = chooser.showOpenDialog(null);
4239 if (value == JalviewFileChooser.APPROVE_OPTION)
4241 String choice = chooser.getSelectedFile().getPath();
4242 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4243 jalview.io.NewickFile fin = null;
4246 fin = new NewickFile(choice, DataSourceType.FILE);
4247 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4248 } catch (Exception ex)
4255 .getString("label.problem_reading_tree_file"),
4256 JvOptionPane.WARNING_MESSAGE);
4257 ex.printStackTrace();
4259 if (fin != null && fin.hasWarningMessage())
4261 JvOptionPane.showMessageDialog(Desktop.desktop, fin
4262 .getWarningMessage(), MessageManager
4263 .getString("label.possible_problem_with_tree_file"),
4264 JvOptionPane.WARNING_MESSAGE);
4270 protected void tcoffeeColorScheme_actionPerformed()
4272 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4275 public TreePanel ShowNewickTree(NewickFile nf, String title)
4277 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4280 public TreePanel ShowNewickTree(NewickFile nf, String title,
4281 AlignmentView input)
4283 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4286 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4287 int h, int x, int y)
4289 return ShowNewickTree(nf, title, null, w, h, x, y);
4293 * Add a treeviewer for the tree extracted from a newick file object to the
4294 * current alignment view
4301 * Associated alignment input data (or null)
4310 * @return TreePanel handle
4312 public TreePanel ShowNewickTree(NewickFile nf, String title,
4313 AlignmentView input, int w, int h, int x, int y)
4315 TreePanel tp = null;
4321 if (nf.getTree() != null)
4323 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4329 tp.setLocation(x, y);
4332 Desktop.addInternalFrame(tp, title, w, h);
4334 } catch (Exception ex)
4336 ex.printStackTrace();
4342 private boolean buildingMenu = false;
4345 * Generates menu items and listener event actions for web service clients
4348 public void BuildWebServiceMenu()
4350 while (buildingMenu)
4354 System.err.println("Waiting for building menu to finish.");
4356 } catch (Exception e)
4360 final AlignFrame me = this;
4361 buildingMenu = true;
4362 new Thread(new Runnable()
4367 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4370 // System.err.println("Building ws menu again "
4371 // + Thread.currentThread());
4372 // TODO: add support for context dependent disabling of services based
4374 // alignment and current selection
4375 // TODO: add additional serviceHandle parameter to specify abstract
4377 // class independently of AbstractName
4378 // TODO: add in rediscovery GUI function to restart discoverer
4379 // TODO: group services by location as well as function and/or
4381 // object broker mechanism.
4382 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4383 final IProgressIndicator af = me;
4386 * do not i18n these strings - they are hard-coded in class
4387 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4388 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4390 final JMenu msawsmenu = new JMenu("Alignment");
4391 final JMenu secstrmenu = new JMenu(
4392 "Secondary Structure Prediction");
4393 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4394 final JMenu analymenu = new JMenu("Analysis");
4395 final JMenu dismenu = new JMenu("Protein Disorder");
4396 // JAL-940 - only show secondary structure prediction services from
4397 // the legacy server
4398 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4400 Discoverer.services != null && (Discoverer.services.size() > 0))
4402 // TODO: refactor to allow list of AbstractName/Handler bindings to
4404 // stored or retrieved from elsewhere
4405 // No MSAWS used any more:
4406 // Vector msaws = null; // (Vector)
4407 // Discoverer.services.get("MsaWS");
4408 Vector secstrpr = (Vector) Discoverer.services
4410 if (secstrpr != null)
4412 // Add any secondary structure prediction services
4413 for (int i = 0, j = secstrpr.size(); i < j; i++)
4415 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4417 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4418 .getServiceClient(sh);
4419 int p = secstrmenu.getItemCount();
4420 impl.attachWSMenuEntry(secstrmenu, me);
4421 int q = secstrmenu.getItemCount();
4422 for (int litm = p; litm < q; litm++)
4424 legacyItems.add(secstrmenu.getItem(litm));
4430 // Add all submenus in the order they should appear on the web
4432 wsmenu.add(msawsmenu);
4433 wsmenu.add(secstrmenu);
4434 wsmenu.add(dismenu);
4435 wsmenu.add(analymenu);
4436 // No search services yet
4437 // wsmenu.add(seqsrchmenu);
4439 javax.swing.SwingUtilities.invokeLater(new Runnable()
4446 webService.removeAll();
4447 // first, add discovered services onto the webservices menu
4448 if (wsmenu.size() > 0)
4450 for (int i = 0, j = wsmenu.size(); i < j; i++)
4452 webService.add(wsmenu.get(i));
4457 webService.add(me.webServiceNoServices);
4459 // TODO: move into separate menu builder class.
4460 boolean new_sspred = false;
4461 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4463 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4464 if (jws2servs != null)
4466 if (jws2servs.hasServices())
4468 jws2servs.attachWSMenuEntry(webService, me);
4469 for (Jws2Instance sv : jws2servs.getServices())
4471 if (sv.description.toLowerCase().contains("jpred"))
4473 for (JMenuItem jmi : legacyItems)
4475 jmi.setVisible(false);
4481 if (jws2servs.isRunning())
4483 JMenuItem tm = new JMenuItem(
4484 "Still discovering JABA Services");
4485 tm.setEnabled(false);
4490 build_urlServiceMenu(me.webService);
4491 build_fetchdbmenu(webService);
4492 for (JMenu item : wsmenu)
4494 if (item.getItemCount() == 0)
4496 item.setEnabled(false);
4500 item.setEnabled(true);
4503 } catch (Exception e)
4506 .debug("Exception during web service menu building process.",
4511 } catch (Exception e)
4514 buildingMenu = false;
4521 * construct any groupURL type service menu entries.
4525 private void build_urlServiceMenu(JMenu webService)
4527 // TODO: remove this code when 2.7 is released
4528 // DEBUG - alignmentView
4530 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4531 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4533 * @Override public void actionPerformed(ActionEvent e) {
4534 * jalview.datamodel.AlignmentView
4535 * .testSelectionViews(af.viewport.getAlignment(),
4536 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4538 * }); webService.add(testAlView);
4540 // TODO: refactor to RestClient discoverer and merge menu entries for
4541 // rest-style services with other types of analysis/calculation service
4542 // SHmmr test client - still being implemented.
4543 // DEBUG - alignmentView
4545 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4548 client.attachWSMenuEntry(
4549 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4555 * Searches the alignment sequences for xRefs and builds the Show
4556 * Cross-References menu (formerly called Show Products), with database
4557 * sources for which cross-references are found (protein sources for a
4558 * nucleotide alignment and vice versa)
4560 * @return true if Show Cross-references menu should be enabled
4562 public boolean canShowProducts()
4564 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4565 AlignmentI dataset = viewport.getAlignment().getDataset();
4567 showProducts.removeAll();
4568 final boolean dna = viewport.getAlignment().isNucleotide();
4570 if (seqs == null || seqs.length == 0)
4572 // nothing to see here.
4576 boolean showp = false;
4579 List<String> ptypes = new CrossRef(seqs, dataset)
4580 .findXrefSourcesForSequences(dna);
4582 for (final String source : ptypes)
4585 final AlignFrame af = this;
4586 JMenuItem xtype = new JMenuItem(source);
4587 xtype.addActionListener(new ActionListener()
4590 public void actionPerformed(ActionEvent e)
4592 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4595 showProducts.add(xtype);
4597 showProducts.setVisible(showp);
4598 showProducts.setEnabled(showp);
4599 } catch (Exception e)
4602 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4610 * Finds and displays cross-references for the selected sequences (protein
4611 * products for nucleotide sequences, dna coding sequences for peptides).
4614 * the sequences to show cross-references for
4616 * true if from a nucleotide alignment (so showing proteins)
4618 * the database to show cross-references for
4620 protected void showProductsFor(final SequenceI[] sel,
4621 final boolean _odna, final String source)
4623 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4628 * Construct and display a new frame containing the translation of this
4629 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4632 public void showTranslation_actionPerformed(ActionEvent e)
4634 AlignmentI al = null;
4637 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4639 al = dna.translateCdna();
4640 } catch (Exception ex)
4642 jalview.bin.Cache.log.error(
4643 "Exception during translation. Please report this !", ex);
4644 final String msg = MessageManager
4645 .getString("label.error_when_translating_sequences_submit_bug_report");
4646 final String errorTitle = MessageManager
4647 .getString("label.implementation_error")
4648 + MessageManager.getString("label.translation_failed");
4649 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4650 JvOptionPane.ERROR_MESSAGE);
4653 if (al == null || al.getHeight() == 0)
4655 final String msg = MessageManager
4656 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4657 final String errorTitle = MessageManager
4658 .getString("label.translation_failed");
4659 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4660 JvOptionPane.WARNING_MESSAGE);
4664 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4665 af.setFileFormat(this.currentFileFormat);
4666 final String newTitle = MessageManager.formatMessage(
4667 "label.translation_of_params",
4668 new Object[] { this.getTitle() });
4669 af.setTitle(newTitle);
4670 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4672 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4673 viewport.openSplitFrame(af, new Alignment(seqs));
4677 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4684 * Set the file format
4688 public void setFileFormat(FileFormatI format)
4690 this.currentFileFormat = format;
4694 * Try to load a features file onto the alignment.
4697 * contents or path to retrieve file
4699 * access mode of file (see jalview.io.AlignFile)
4700 * @return true if features file was parsed correctly.
4702 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4704 return avc.parseFeaturesFile(file, sourceType,
4705 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4710 public void refreshFeatureUI(boolean enableIfNecessary)
4712 // note - currently this is only still here rather than in the controller
4713 // because of the featureSettings hard reference that is yet to be
4715 if (enableIfNecessary)
4717 viewport.setShowSequenceFeatures(true);
4718 showSeqFeatures.setSelected(true);
4724 public void dragEnter(DropTargetDragEvent evt)
4729 public void dragExit(DropTargetEvent evt)
4734 public void dragOver(DropTargetDragEvent evt)
4739 public void dropActionChanged(DropTargetDragEvent evt)
4744 public void drop(DropTargetDropEvent evt)
4746 // JAL-1552 - acceptDrop required before getTransferable call for
4747 // Java's Transferable for native dnd
4748 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4749 Transferable t = evt.getTransferable();
4750 List<String> files = new ArrayList<String>();
4751 List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4755 Desktop.transferFromDropTarget(files, protocols, evt, t);
4756 } catch (Exception e)
4758 e.printStackTrace();
4764 // check to see if any of these files have names matching sequences in
4766 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4767 .getAlignment().getSequencesArray());
4769 * Object[] { String,SequenceI}
4771 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4772 ArrayList<String> filesnotmatched = new ArrayList<String>();
4773 for (int i = 0; i < files.size(); i++)
4775 String file = files.get(i).toString();
4777 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4778 if (protocol == DataSourceType.FILE)
4780 File fl = new File(file);
4781 pdbfn = fl.getName();
4783 else if (protocol == DataSourceType.URL)
4785 URL url = new URL(file);
4786 pdbfn = url.getFile();
4788 if (pdbfn.length() > 0)
4790 // attempt to find a match in the alignment
4791 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4792 int l = 0, c = pdbfn.indexOf(".");
4793 while (mtch == null && c != -1)
4798 } while ((c = pdbfn.indexOf(".", l)) > l);
4801 pdbfn = pdbfn.substring(0, l);
4803 mtch = idm.findAllIdMatches(pdbfn);
4807 FileFormatI type = null;
4810 type = new IdentifyFile().identify(file, protocol);
4811 } catch (Exception ex)
4815 if (type != null && type.isStructureFile())
4817 filesmatched.add(new Object[] { file, protocol, mtch });
4821 // File wasn't named like one of the sequences or wasn't a PDB file.
4822 filesnotmatched.add(file);
4826 if (filesmatched.size() > 0)
4828 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4834 "label.automatically_associate_structure_files_with_sequences_same_name",
4835 new Object[] { Integer
4841 .getString("label.automatically_associate_structure_files_by_name"),
4842 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4845 for (Object[] fm : filesmatched)
4847 // try and associate
4848 // TODO: may want to set a standard ID naming formalism for
4849 // associating PDB files which have no IDs.
4850 for (SequenceI toassoc : (SequenceI[]) fm[2])
4852 PDBEntry pe = new AssociatePdbFileWithSeq()
4853 .associatePdbWithSeq((String) fm[0],
4854 (DataSourceType) fm[1], toassoc, false,
4858 System.err.println("Associated file : "
4859 + ((String) fm[0]) + " with "
4860 + toassoc.getDisplayId(true));
4864 alignPanel.paintAlignment(true);
4868 if (filesnotmatched.size() > 0)
4871 && (Cache.getDefault(
4872 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4878 "label.ignore_unmatched_dropped_files_info",
4879 new Object[] { Integer
4886 .getString("label.ignore_unmatched_dropped_files"),
4887 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4891 for (String fn : filesnotmatched)
4893 loadJalviewDataFile(fn, null, null, null);
4897 } catch (Exception ex)
4899 ex.printStackTrace();
4905 * Attempt to load a "dropped" file or URL string: First by testing whether
4906 * it's an Annotation file, then a JNet file, and finally a features file. If
4907 * all are false then the user may have dropped an alignment file onto this
4911 * either a filename or a URL string.
4913 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4914 FileFormatI format, SequenceI assocSeq)
4918 if (sourceType == null)
4920 sourceType = FormatAdapter.checkProtocol(file);
4922 // if the file isn't identified, or not positively identified as some
4923 // other filetype (PFAM is default unidentified alignment file type) then
4924 // try to parse as annotation.
4925 boolean isAnnotation = (format == null || FileFormat.Pfam
4926 .equals(format)) ? new AnnotationFile()
4927 .annotateAlignmentView(viewport, file, sourceType) : false;
4931 // first see if its a T-COFFEE score file
4932 TCoffeeScoreFile tcf = null;
4935 tcf = new TCoffeeScoreFile(file, sourceType);
4938 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4940 tcoffeeColour.setEnabled(true);
4941 tcoffeeColour.setSelected(true);
4942 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4943 isAnnotation = true;
4945 .setText(MessageManager
4946 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4950 // some problem - if no warning its probable that the ID matching
4951 // process didn't work
4955 tcf.getWarningMessage() == null ? MessageManager
4956 .getString("label.check_file_matches_sequence_ids_alignment")
4957 : tcf.getWarningMessage(),
4959 .getString("label.problem_reading_tcoffee_score_file"),
4960 JvOptionPane.WARNING_MESSAGE);
4967 } catch (Exception x)
4970 .debug("Exception when processing data source as T-COFFEE score file",
4976 // try to see if its a JNet 'concise' style annotation file *before*
4978 // try to parse it as a features file
4981 format = new IdentifyFile().identify(file, sourceType);
4983 if (FileFormat.Jnet.equals(format))
4985 JPredFile predictions = new JPredFile(
4987 new JnetAnnotationMaker();
4988 JnetAnnotationMaker.add_annotation(predictions,
4989 viewport.getAlignment(), 0, false);
4990 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4991 viewport.getAlignment().setSeqrep(repseq);
4992 ColumnSelection cs = new ColumnSelection();
4993 cs.hideInsertionsFor(repseq);
4994 viewport.setColumnSelection(cs);
4995 isAnnotation = true;
4997 // else if (IdentifyFile.FeaturesFile.equals(format))
4998 else if (FileFormat.Features.equals(format))
5000 if (parseFeaturesFile(file, sourceType))
5002 alignPanel.paintAlignment(true);
5007 new FileLoader().LoadFile(viewport, file, sourceType, format);
5014 alignPanel.adjustAnnotationHeight();
5015 viewport.updateSequenceIdColours();
5016 buildSortByAnnotationScoresMenu();
5017 alignPanel.paintAlignment(true);
5019 } catch (Exception ex)
5021 ex.printStackTrace();
5022 } catch (OutOfMemoryError oom)
5027 } catch (Exception x)
5032 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
5033 : "using " + sourceType + " from " + file)
5035 + (format != null ? "(parsing as '" + format
5036 + "' file)" : ""), oom, Desktop.desktop);
5041 * Method invoked by the ChangeListener on the tabbed pane, in other words
5042 * when a different tabbed pane is selected by the user or programmatically.
5045 public void tabSelectionChanged(int index)
5049 alignPanel = alignPanels.get(index);
5050 viewport = alignPanel.av;
5051 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5052 setMenusFromViewport(viewport);
5056 * If there is a frame linked to this one in a SplitPane, switch it to the
5057 * same view tab index. No infinite recursion of calls should happen, since
5058 * tabSelectionChanged() should not get invoked on setting the selected
5059 * index to an unchanged value. Guard against setting an invalid index
5060 * before the new view peer tab has been created.
5062 final AlignViewportI peer = viewport.getCodingComplement();
5065 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5066 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5068 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5074 * On right mouse click on view tab, prompt for and set new view name.
5077 public void tabbedPane_mousePressed(MouseEvent e)
5079 if (e.isPopupTrigger())
5081 String msg = MessageManager.getString("label.enter_view_name");
5082 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
5083 JvOptionPane.QUESTION_MESSAGE);
5087 viewport.viewName = reply;
5088 // TODO warn if reply is in getExistingViewNames()?
5089 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5094 public AlignViewport getCurrentView()
5100 * Open the dialog for regex description parsing.
5103 protected void extractScores_actionPerformed(ActionEvent e)
5105 ParseProperties pp = new jalview.analysis.ParseProperties(
5106 viewport.getAlignment());
5107 // TODO: verify regex and introduce GUI dialog for version 2.5
5108 // if (pp.getScoresFromDescription("col", "score column ",
5109 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5111 if (pp.getScoresFromDescription("description column",
5112 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5114 buildSortByAnnotationScoresMenu();
5122 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5126 protected void showDbRefs_actionPerformed(ActionEvent e)
5128 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5134 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5138 protected void showNpFeats_actionPerformed(ActionEvent e)
5140 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5144 * find the viewport amongst the tabs in this alignment frame and close that
5149 public boolean closeView(AlignViewportI av)
5153 this.closeMenuItem_actionPerformed(false);
5156 Component[] comp = tabbedPane.getComponents();
5157 for (int i = 0; comp != null && i < comp.length; i++)
5159 if (comp[i] instanceof AlignmentPanel)
5161 if (((AlignmentPanel) comp[i]).av == av)
5164 closeView((AlignmentPanel) comp[i]);
5172 protected void build_fetchdbmenu(JMenu webService)
5174 // Temporary hack - DBRef Fetcher always top level ws entry.
5175 // TODO We probably want to store a sequence database checklist in
5176 // preferences and have checkboxes.. rather than individual sources selected
5178 final JMenu rfetch = new JMenu(
5179 MessageManager.getString("action.fetch_db_references"));
5180 rfetch.setToolTipText(MessageManager
5181 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5182 webService.add(rfetch);
5184 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5185 MessageManager.getString("option.trim_retrieved_seqs"));
5186 trimrs.setToolTipText(MessageManager
5187 .getString("label.trim_retrieved_sequences"));
5188 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5189 trimrs.addActionListener(new ActionListener()
5192 public void actionPerformed(ActionEvent e)
5194 trimrs.setSelected(trimrs.isSelected());
5195 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5196 Boolean.valueOf(trimrs.isSelected()).toString());
5200 JMenuItem fetchr = new JMenuItem(
5201 MessageManager.getString("label.standard_databases"));
5202 fetchr.setToolTipText(MessageManager
5203 .getString("label.fetch_embl_uniprot"));
5204 fetchr.addActionListener(new ActionListener()
5208 public void actionPerformed(ActionEvent e)
5210 new Thread(new Runnable()
5215 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5216 .getAlignment().isNucleotide();
5217 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5218 .getSequenceSelection(), alignPanel.alignFrame, null,
5219 alignPanel.alignFrame.featureSettings, isNucleotide);
5220 dbRefFetcher.addListener(new FetchFinishedListenerI()
5223 public void finished()
5225 AlignFrame.this.setMenusForViewport();
5228 dbRefFetcher.fetchDBRefs(false);
5236 final AlignFrame me = this;
5237 new Thread(new Runnable()
5242 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5243 .getSequenceFetcherSingleton(me);
5244 javax.swing.SwingUtilities.invokeLater(new Runnable()
5249 String[] dbclasses = sf.getOrderedSupportedSources();
5250 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5251 // jalview.util.QuickSort.sort(otherdb, otherdb);
5252 List<DbSourceProxy> otherdb;
5253 JMenu dfetch = new JMenu();
5254 JMenu ifetch = new JMenu();
5255 JMenuItem fetchr = null;
5256 int comp = 0, icomp = 0, mcomp = 15;
5257 String mname = null;
5259 for (String dbclass : dbclasses)
5261 otherdb = sf.getSourceProxy(dbclass);
5262 // add a single entry for this class, or submenu allowing 'fetch
5264 if (otherdb == null || otherdb.size() < 1)
5268 // List<DbSourceProxy> dbs=otherdb;
5269 // otherdb=new ArrayList<DbSourceProxy>();
5270 // for (DbSourceProxy db:dbs)
5272 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5276 mname = "From " + dbclass;
5278 if (otherdb.size() == 1)
5280 final DbSourceProxy[] dassource = otherdb
5281 .toArray(new DbSourceProxy[0]);
5282 DbSourceProxy src = otherdb.get(0);
5283 fetchr = new JMenuItem(src.getDbSource());
5284 fetchr.addActionListener(new ActionListener()
5288 public void actionPerformed(ActionEvent e)
5290 new Thread(new Runnable()
5296 boolean isNucleotide = alignPanel.alignFrame
5297 .getViewport().getAlignment()
5299 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5300 alignPanel.av.getSequenceSelection(),
5301 alignPanel.alignFrame, dassource,
5302 alignPanel.alignFrame.featureSettings,
5305 .addListener(new FetchFinishedListenerI()
5308 public void finished()
5310 AlignFrame.this.setMenusForViewport();
5313 dbRefFetcher.fetchDBRefs(false);
5319 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5320 MessageManager.formatMessage(
5321 "label.fetch_retrieve_from",
5322 new Object[] { src.getDbName() })));
5328 final DbSourceProxy[] dassource = otherdb
5329 .toArray(new DbSourceProxy[0]);
5331 DbSourceProxy src = otherdb.get(0);
5332 fetchr = new JMenuItem(MessageManager.formatMessage(
5333 "label.fetch_all_param",
5334 new Object[] { src.getDbSource() }));
5335 fetchr.addActionListener(new ActionListener()
5338 public void actionPerformed(ActionEvent e)
5340 new Thread(new Runnable()
5346 boolean isNucleotide = alignPanel.alignFrame
5347 .getViewport().getAlignment()
5349 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5350 alignPanel.av.getSequenceSelection(),
5351 alignPanel.alignFrame, dassource,
5352 alignPanel.alignFrame.featureSettings,
5355 .addListener(new FetchFinishedListenerI()
5358 public void finished()
5360 AlignFrame.this.setMenusForViewport();
5363 dbRefFetcher.fetchDBRefs(false);
5369 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5370 MessageManager.formatMessage(
5371 "label.fetch_retrieve_from_all_sources",
5373 Integer.valueOf(otherdb.size())
5374 .toString(), src.getDbSource(),
5375 src.getDbName() })));
5378 // and then build the rest of the individual menus
5379 ifetch = new JMenu(MessageManager.formatMessage(
5380 "label.source_from_db_source",
5381 new Object[] { src.getDbSource() }));
5383 String imname = null;
5385 for (DbSourceProxy sproxy : otherdb)
5387 String dbname = sproxy.getDbName();
5388 String sname = dbname.length() > 5 ? dbname.substring(0,
5389 5) + "..." : dbname;
5390 String msname = dbname.length() > 10 ? dbname.substring(
5391 0, 10) + "..." : dbname;
5394 imname = MessageManager.formatMessage(
5395 "label.from_msname", new Object[] { sname });
5397 fetchr = new JMenuItem(msname);
5398 final DbSourceProxy[] dassrc = { sproxy };
5399 fetchr.addActionListener(new ActionListener()
5403 public void actionPerformed(ActionEvent e)
5405 new Thread(new Runnable()
5411 boolean isNucleotide = alignPanel.alignFrame
5412 .getViewport().getAlignment()
5414 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5415 alignPanel.av.getSequenceSelection(),
5416 alignPanel.alignFrame, dassrc,
5417 alignPanel.alignFrame.featureSettings,
5420 .addListener(new FetchFinishedListenerI()
5423 public void finished()
5425 AlignFrame.this.setMenusForViewport();
5428 dbRefFetcher.fetchDBRefs(false);
5434 fetchr.setToolTipText("<html>"
5435 + MessageManager.formatMessage(
5436 "label.fetch_retrieve_from", new Object[]
5440 if (++icomp >= mcomp || i == (otherdb.size()))
5442 ifetch.setText(MessageManager.formatMessage(
5443 "label.source_to_target", imname, sname));
5445 ifetch = new JMenu();
5453 if (comp >= mcomp || dbi >= (dbclasses.length))
5455 dfetch.setText(MessageManager.formatMessage(
5456 "label.source_to_target", mname, dbclass));
5458 dfetch = new JMenu();
5471 * Left justify the whole alignment.
5474 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5476 AlignmentI al = viewport.getAlignment();
5478 viewport.firePropertyChange("alignment", null, al);
5482 * Right justify the whole alignment.
5485 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5487 AlignmentI al = viewport.getAlignment();
5489 viewport.firePropertyChange("alignment", null, al);
5493 public void setShowSeqFeatures(boolean b)
5495 showSeqFeatures.setSelected(b);
5496 viewport.setShowSequenceFeatures(b);
5503 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5504 * awt.event.ActionEvent)
5507 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5509 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5510 alignPanel.paintAlignment(true);
5517 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5521 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5523 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5524 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5532 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5533 * .event.ActionEvent)
5536 protected void showGroupConservation_actionPerformed(ActionEvent e)
5538 viewport.setShowGroupConservation(showGroupConservation.getState());
5539 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5546 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5547 * .event.ActionEvent)
5550 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5552 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5553 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5560 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5561 * .event.ActionEvent)
5564 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5566 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5567 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5571 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5573 showSequenceLogo.setState(true);
5574 viewport.setShowSequenceLogo(true);
5575 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5576 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5580 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5582 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5589 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5590 * .event.ActionEvent)
5593 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5595 if (avc.makeGroupsFromSelection())
5597 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5598 alignPanel.updateAnnotation();
5599 alignPanel.paintAlignment(true);
5603 public void clearAlignmentSeqRep()
5605 // TODO refactor alignmentseqrep to controller
5606 if (viewport.getAlignment().hasSeqrep())
5608 viewport.getAlignment().setSeqrep(null);
5609 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5610 alignPanel.updateAnnotation();
5611 alignPanel.paintAlignment(true);
5616 protected void createGroup_actionPerformed(ActionEvent e)
5618 if (avc.createGroup())
5620 alignPanel.alignmentChanged();
5625 protected void unGroup_actionPerformed(ActionEvent e)
5629 alignPanel.alignmentChanged();
5634 * make the given alignmentPanel the currently selected tab
5636 * @param alignmentPanel
5638 public void setDisplayedView(AlignmentPanel alignmentPanel)
5640 if (!viewport.getSequenceSetId().equals(
5641 alignmentPanel.av.getSequenceSetId()))
5645 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5647 if (tabbedPane != null
5648 && tabbedPane.getTabCount() > 0
5649 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5650 .getSelectedIndex())
5652 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5657 * Action on selection of menu options to Show or Hide annotations.
5660 * @param forSequences
5661 * update sequence-related annotations
5662 * @param forAlignment
5663 * update non-sequence-related annotations
5666 protected void setAnnotationsVisibility(boolean visible,
5667 boolean forSequences, boolean forAlignment)
5669 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5670 .getAlignmentAnnotation();
5675 for (AlignmentAnnotation aa : anns)
5678 * don't display non-positional annotations on an alignment
5680 if (aa.annotations == null)
5684 boolean apply = (aa.sequenceRef == null && forAlignment)
5685 || (aa.sequenceRef != null && forSequences);
5688 aa.visible = visible;
5691 alignPanel.validateAnnotationDimensions(true);
5692 alignPanel.alignmentChanged();
5696 * Store selected annotation sort order for the view and repaint.
5699 protected void sortAnnotations_actionPerformed()
5701 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5703 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5704 alignPanel.paintAlignment(true);
5709 * @return alignment panels in this alignment frame
5711 public List<? extends AlignmentViewPanel> getAlignPanels()
5713 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5717 * Open a new alignment window, with the cDNA associated with this (protein)
5718 * alignment, aligned as is the protein.
5720 protected void viewAsCdna_actionPerformed()
5722 // TODO no longer a menu action - refactor as required
5723 final AlignmentI alignment = getViewport().getAlignment();
5724 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5725 if (mappings == null)
5729 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5730 for (SequenceI aaSeq : alignment.getSequences())
5732 for (AlignedCodonFrame acf : mappings)
5734 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5738 * There is a cDNA mapping for this protein sequence - add to new
5739 * alignment. It will share the same dataset sequence as other mapped
5740 * cDNA (no new mappings need to be created).
5742 final Sequence newSeq = new Sequence(dnaSeq);
5743 newSeq.setDatasetSequence(dnaSeq);
5744 cdnaSeqs.add(newSeq);
5748 if (cdnaSeqs.size() == 0)
5750 // show a warning dialog no mapped cDNA
5753 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5755 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5756 AlignFrame.DEFAULT_HEIGHT);
5757 cdna.alignAs(alignment);
5758 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5760 Desktop.addInternalFrame(alignFrame, newtitle,
5761 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5765 * Set visibility of dna/protein complement view (available when shown in a
5771 protected void showComplement_actionPerformed(boolean show)
5773 SplitContainerI sf = getSplitViewContainer();
5776 sf.setComplementVisible(this, show);
5781 * Generate the reverse (optionally complemented) of the selected sequences,
5782 * and add them to the alignment
5785 protected void showReverse_actionPerformed(boolean complement)
5787 AlignmentI al = null;
5790 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5791 al = dna.reverseCdna(complement);
5792 viewport.addAlignment(al, "");
5793 addHistoryItem(new EditCommand(
5794 MessageManager.getString("label.add_sequences"),
5795 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5796 viewport.getAlignment()));
5797 } catch (Exception ex)
5799 System.err.println(ex.getMessage());
5805 * Try to run a script in the Groovy console, having first ensured that this
5806 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5807 * be targeted at this alignment.
5810 protected void runGroovy_actionPerformed()
5812 Jalview.setCurrentAlignFrame(this);
5813 groovy.ui.Console console = Desktop.getGroovyConsole();
5814 if (console != null)
5818 console.runScript();
5819 } catch (Exception ex)
5821 System.err.println((ex.toString()));
5823 .showInternalMessageDialog(Desktop.desktop, MessageManager
5824 .getString("label.couldnt_run_groovy_script"),
5826 .getString("label.groovy_support_failed"),
5827 JvOptionPane.ERROR_MESSAGE);
5832 System.err.println("Can't run Groovy script as console not found");
5837 * Hides columns containing (or not containing) a specified feature, provided
5838 * that would not leave all columns hidden
5840 * @param featureType
5841 * @param columnsContaining
5844 public boolean hideFeatureColumns(String featureType,
5845 boolean columnsContaining)
5847 boolean notForHiding = avc.markColumnsContainingFeatures(
5848 columnsContaining, false, false, featureType);
5851 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5852 false, featureType))
5854 getViewport().hideSelectedColumns();
5862 protected void selectHighlightedColumns_actionPerformed(
5863 ActionEvent actionEvent)
5865 // include key modifier check in case user selects from menu
5866 avc.markHighlightedColumns(
5867 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5869 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5873 class PrintThread extends Thread
5877 public PrintThread(AlignmentPanel ap)
5882 static PageFormat pf;
5887 PrinterJob printJob = PrinterJob.getPrinterJob();
5891 printJob.setPrintable(ap, pf);
5895 printJob.setPrintable(ap);
5898 if (printJob.printDialog())
5903 } catch (Exception PrintException)
5905 PrintException.printStackTrace();