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.HiddenColumns;
57 import jalview.datamodel.HiddenSequences;
58 import jalview.datamodel.PDBEntry;
59 import jalview.datamodel.SeqCigar;
60 import jalview.datamodel.Sequence;
61 import jalview.datamodel.SequenceGroup;
62 import jalview.datamodel.SequenceI;
63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.DataSourceType;
69 import jalview.io.FileFormat;
70 import jalview.io.FileFormatI;
71 import jalview.io.FileFormats;
72 import jalview.io.FileLoader;
73 import jalview.io.FormatAdapter;
74 import jalview.io.HtmlSvgOutput;
75 import jalview.io.IdentifyFile;
76 import jalview.io.JPredFile;
77 import jalview.io.JalviewFileChooser;
78 import jalview.io.JalviewFileView;
79 import jalview.io.JnetAnnotationMaker;
80 import jalview.io.NewickFile;
81 import jalview.io.TCoffeeScoreFile;
82 import jalview.jbgui.GAlignFrame;
83 import jalview.schemes.ColourSchemeI;
84 import jalview.schemes.ColourSchemes;
85 import jalview.schemes.ResidueColourScheme;
86 import jalview.schemes.ResidueProperties;
87 import jalview.schemes.TCoffeeColourScheme;
88 import jalview.util.MessageManager;
89 import jalview.viewmodel.AlignmentViewport;
90 import jalview.viewmodel.ViewportRanges;
91 import jalview.ws.DBRefFetcher;
92 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
93 import jalview.ws.jws1.Discoverer;
94 import jalview.ws.jws2.Jws2Discoverer;
95 import jalview.ws.jws2.jabaws2.Jws2Instance;
96 import jalview.ws.seqfetcher.DbSourceProxy;
98 import java.awt.BorderLayout;
99 import java.awt.Component;
100 import java.awt.Rectangle;
101 import java.awt.Toolkit;
102 import java.awt.datatransfer.Clipboard;
103 import java.awt.datatransfer.DataFlavor;
104 import java.awt.datatransfer.StringSelection;
105 import java.awt.datatransfer.Transferable;
106 import java.awt.dnd.DnDConstants;
107 import java.awt.dnd.DropTargetDragEvent;
108 import java.awt.dnd.DropTargetDropEvent;
109 import java.awt.dnd.DropTargetEvent;
110 import java.awt.dnd.DropTargetListener;
111 import java.awt.event.ActionEvent;
112 import java.awt.event.ActionListener;
113 import java.awt.event.FocusAdapter;
114 import java.awt.event.FocusEvent;
115 import java.awt.event.ItemEvent;
116 import java.awt.event.ItemListener;
117 import java.awt.event.KeyAdapter;
118 import java.awt.event.KeyEvent;
119 import java.awt.event.MouseEvent;
120 import java.awt.print.PageFormat;
121 import java.awt.print.PrinterJob;
122 import java.beans.PropertyChangeEvent;
124 import java.io.FileWriter;
125 import java.io.PrintWriter;
127 import java.util.ArrayList;
128 import java.util.Arrays;
129 import java.util.Deque;
130 import java.util.Enumeration;
131 import java.util.Hashtable;
132 import java.util.List;
133 import java.util.Vector;
135 import javax.swing.JCheckBoxMenuItem;
136 import javax.swing.JEditorPane;
137 import javax.swing.JInternalFrame;
138 import javax.swing.JLayeredPane;
139 import javax.swing.JMenu;
140 import javax.swing.JMenuItem;
141 import javax.swing.JScrollPane;
142 import javax.swing.SwingUtilities;
148 * @version $Revision$
150 public class AlignFrame extends GAlignFrame implements DropTargetListener,
151 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
154 public static final int DEFAULT_WIDTH = 700;
156 public static final int DEFAULT_HEIGHT = 500;
159 * The currently displayed panel (selected tabbed view if more than one)
161 public AlignmentPanel alignPanel;
163 AlignViewport viewport;
165 ViewportRanges vpRanges;
167 public AlignViewControllerI avc;
169 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
172 * Last format used to load or save alignments in this window
174 FileFormatI currentFileFormat = null;
177 * Current filename for this alignment
179 String fileName = null;
182 * Creates a new AlignFrame object with specific width and height.
188 public AlignFrame(AlignmentI al, int width, int height)
190 this(al, null, width, height);
194 * Creates a new AlignFrame object with specific width, height and
200 * @param sequenceSetId
202 public AlignFrame(AlignmentI al, int width, int height,
203 String sequenceSetId)
205 this(al, null, width, height, sequenceSetId);
209 * Creates a new AlignFrame object with specific width, height and
215 * @param sequenceSetId
218 public AlignFrame(AlignmentI al, int width, int height,
219 String sequenceSetId, String viewId)
221 this(al, null, width, height, sequenceSetId, viewId);
225 * new alignment window with hidden columns
229 * @param hiddenColumns
230 * ColumnSelection or null
232 * Width of alignment frame
236 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
237 int width, int height)
239 this(al, hiddenColumns, width, height, null);
243 * Create alignment frame for al with hiddenColumns, a specific width and
244 * height, and specific sequenceId
247 * @param hiddenColumns
250 * @param sequenceSetId
253 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
254 int width, int height, String sequenceSetId)
256 this(al, hiddenColumns, width, height, sequenceSetId, null);
260 * Create alignment frame for al with hiddenColumns, a specific width and
261 * height, and specific sequenceId
264 * @param hiddenColumns
267 * @param sequenceSetId
272 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
273 int width, int height, String sequenceSetId, String viewId)
275 setSize(width, height);
277 if (al.getDataset() == null)
282 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
284 alignPanel = new AlignmentPanel(this, viewport);
286 addAlignmentPanel(alignPanel, true);
290 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
291 HiddenColumns hiddenColumns, int width, int height)
293 setSize(width, height);
295 if (al.getDataset() == null)
300 viewport = new AlignViewport(al, hiddenColumns);
302 if (hiddenSeqs != null && hiddenSeqs.length > 0)
304 viewport.hideSequence(hiddenSeqs);
306 alignPanel = new AlignmentPanel(this, viewport);
307 addAlignmentPanel(alignPanel, true);
312 * Make a new AlignFrame from existing alignmentPanels
319 public AlignFrame(AlignmentPanel ap)
323 addAlignmentPanel(ap, false);
328 * initalise the alignframe from the underlying viewport data and the
333 if (!Jalview.isHeadlessMode())
335 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
338 vpRanges = viewport.getRanges();
339 avc = new jalview.controller.AlignViewController(this, viewport,
341 if (viewport.getAlignmentConservationAnnotation() == null)
343 // BLOSUM62Colour.setEnabled(false);
344 conservationMenuItem.setEnabled(false);
345 modifyConservation.setEnabled(false);
346 // PIDColour.setEnabled(false);
347 // abovePIDThreshold.setEnabled(false);
348 // modifyPID.setEnabled(false);
351 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
354 if (sortby.equals("Id"))
356 sortIDMenuItem_actionPerformed(null);
358 else if (sortby.equals("Pairwise Identity"))
360 sortPairwiseMenuItem_actionPerformed(null);
364 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
366 setMenusFromViewport(viewport);
367 buildSortByAnnotationScoresMenu();
371 if (Desktop.desktop != null)
373 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
374 addServiceListeners();
378 if (viewport.getWrapAlignment())
380 wrapMenuItem_actionPerformed(null);
383 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
385 this.overviewMenuItem_actionPerformed(null);
390 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
391 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
392 final String menuLabel = MessageManager
393 .getString("label.copy_format_from");
394 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
395 new ViewSetProvider()
399 public AlignmentPanel[] getAllAlignmentPanels()
402 origview.add(alignPanel);
403 // make an array of all alignment panels except for this one
404 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
405 Arrays.asList(Desktop.getAlignmentPanels(null)));
406 aps.remove(AlignFrame.this.alignPanel);
407 return aps.toArray(new AlignmentPanel[aps.size()]);
409 }, selviews, new ItemListener()
413 public void itemStateChanged(ItemEvent e)
415 if (origview.size() > 0)
417 final AlignmentPanel ap = origview.get(0);
420 * Copy the ViewStyle of the selected panel to 'this one'.
421 * Don't change value of 'scaleProteinAsCdna' unless copying
424 ViewStyleI vs = selviews.get(0).getAlignViewport()
426 boolean fromSplitFrame = selviews.get(0)
427 .getAlignViewport().getCodingComplement() != null;
430 vs.setScaleProteinAsCdna(ap.getAlignViewport()
431 .getViewStyle().isScaleProteinAsCdna());
433 ap.getAlignViewport().setViewStyle(vs);
436 * Also rescale ViewStyle of SplitFrame complement if there is
437 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
438 * the whole ViewStyle (allow cDNA protein to have different
441 AlignViewportI complement = ap.getAlignViewport()
442 .getCodingComplement();
443 if (complement != null && vs.isScaleProteinAsCdna())
445 AlignFrame af = Desktop.getAlignFrameFor(complement);
446 ((SplitFrame) af.getSplitViewContainer())
448 af.setMenusForViewport();
452 ap.setSelected(true);
453 ap.alignFrame.setMenusForViewport();
458 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
459 .indexOf("devel") > -1
460 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
461 .indexOf("test") > -1)
463 formatMenu.add(vsel);
465 addFocusListener(new FocusAdapter()
468 public void focusGained(FocusEvent e)
470 Jalview.setCurrentAlignFrame(AlignFrame.this);
477 * Change the filename and format for the alignment, and enable the 'reload'
478 * button functionality.
485 public void setFileName(String file, FileFormatI format)
488 setFileFormat(format);
489 reload.setEnabled(true);
493 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
496 void addKeyListener()
498 addKeyListener(new KeyAdapter()
501 public void keyPressed(KeyEvent evt)
503 if (viewport.cursorMode
504 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
505 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
506 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
507 && Character.isDigit(evt.getKeyChar()))
509 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
512 switch (evt.getKeyCode())
515 case 27: // escape key
516 deselectAllSequenceMenuItem_actionPerformed(null);
520 case KeyEvent.VK_DOWN:
521 if (evt.isAltDown() || !viewport.cursorMode)
523 moveSelectedSequences(false);
525 if (viewport.cursorMode)
527 alignPanel.getSeqPanel().moveCursor(0, 1);
532 if (evt.isAltDown() || !viewport.cursorMode)
534 moveSelectedSequences(true);
536 if (viewport.cursorMode)
538 alignPanel.getSeqPanel().moveCursor(0, -1);
543 case KeyEvent.VK_LEFT:
544 if (evt.isAltDown() || !viewport.cursorMode)
546 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
550 alignPanel.getSeqPanel().moveCursor(-1, 0);
555 case KeyEvent.VK_RIGHT:
556 if (evt.isAltDown() || !viewport.cursorMode)
558 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
562 alignPanel.getSeqPanel().moveCursor(1, 0);
566 case KeyEvent.VK_SPACE:
567 if (viewport.cursorMode)
569 alignPanel.getSeqPanel().insertGapAtCursor(
570 evt.isControlDown() || evt.isShiftDown()
575 // case KeyEvent.VK_A:
576 // if (viewport.cursorMode)
578 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
579 // //System.out.println("A");
583 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
584 * System.out.println("closing bracket"); } break;
586 case KeyEvent.VK_DELETE:
587 case KeyEvent.VK_BACK_SPACE:
588 if (!viewport.cursorMode)
590 cut_actionPerformed(null);
594 alignPanel.getSeqPanel().deleteGapAtCursor(
595 evt.isControlDown() || evt.isShiftDown()
602 if (viewport.cursorMode)
604 alignPanel.getSeqPanel().setCursorRow();
608 if (viewport.cursorMode && !evt.isControlDown())
610 alignPanel.getSeqPanel().setCursorColumn();
614 if (viewport.cursorMode)
616 alignPanel.getSeqPanel().setCursorPosition();
620 case KeyEvent.VK_ENTER:
621 case KeyEvent.VK_COMMA:
622 if (viewport.cursorMode)
624 alignPanel.getSeqPanel().setCursorRowAndColumn();
629 if (viewport.cursorMode)
631 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
635 if (viewport.cursorMode)
637 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
642 viewport.cursorMode = !viewport.cursorMode;
643 statusBar.setText(MessageManager.formatMessage(
644 "label.keyboard_editing_mode",
645 new String[] { (viewport.cursorMode ? "on" : "off") }));
646 if (viewport.cursorMode)
648 alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
650 alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
653 alignPanel.getSeqPanel().seqCanvas.repaint();
659 Help.showHelpWindow();
660 } catch (Exception ex)
662 ex.printStackTrace();
667 boolean toggleSeqs = !evt.isControlDown();
668 boolean toggleCols = !evt.isShiftDown();
669 toggleHiddenRegions(toggleSeqs, toggleCols);
674 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
675 boolean modifyExisting = true; // always modify, don't clear
676 // evt.isShiftDown();
677 boolean invertHighlighted = evt.isAltDown();
678 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
682 case KeyEvent.VK_PAGE_UP:
683 if (viewport.getWrapAlignment())
685 alignPanel.scrollUp(true);
689 alignPanel.setScrollValues(vpRanges.getStartRes(),
690 2 * vpRanges.getStartSeq() - vpRanges.getEndSeq());
693 case KeyEvent.VK_PAGE_DOWN:
694 if (viewport.getWrapAlignment())
696 alignPanel.scrollUp(false);
700 alignPanel.setScrollValues(vpRanges.getStartRes(),
701 vpRanges.getEndSeq());
708 public void keyReleased(KeyEvent evt)
710 switch (evt.getKeyCode())
712 case KeyEvent.VK_LEFT:
713 if (evt.isAltDown() || !viewport.cursorMode)
715 viewport.firePropertyChange("alignment", null, viewport
716 .getAlignment().getSequences());
720 case KeyEvent.VK_RIGHT:
721 if (evt.isAltDown() || !viewport.cursorMode)
723 viewport.firePropertyChange("alignment", null, viewport
724 .getAlignment().getSequences());
732 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
734 ap.alignFrame = this;
735 avc = new jalview.controller.AlignViewController(this, viewport,
740 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
742 int aSize = alignPanels.size();
744 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
746 if (aSize == 1 && ap.av.viewName == null)
748 this.getContentPane().add(ap, BorderLayout.CENTER);
754 setInitialTabVisible();
757 expandViews.setEnabled(true);
758 gatherViews.setEnabled(true);
759 tabbedPane.addTab(ap.av.viewName, ap);
761 ap.setVisible(false);
766 if (ap.av.isPadGaps())
768 ap.av.getAlignment().padGaps();
770 ap.av.updateConservation(ap);
771 ap.av.updateConsensus(ap);
772 ap.av.updateStrucConsensus(ap);
776 public void setInitialTabVisible()
778 expandViews.setEnabled(true);
779 gatherViews.setEnabled(true);
780 tabbedPane.setVisible(true);
781 AlignmentPanel first = alignPanels.get(0);
782 tabbedPane.addTab(first.av.viewName, first);
783 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
786 public AlignViewport getViewport()
791 /* Set up intrinsic listeners for dynamically generated GUI bits. */
792 private void addServiceListeners()
794 final java.beans.PropertyChangeListener thisListener;
795 Desktop.instance.addJalviewPropertyChangeListener("services",
796 thisListener = new java.beans.PropertyChangeListener()
799 public void propertyChange(PropertyChangeEvent evt)
801 // // System.out.println("Discoverer property change.");
802 // if (evt.getPropertyName().equals("services"))
804 SwingUtilities.invokeLater(new Runnable()
811 .println("Rebuild WS Menu for service change");
812 BuildWebServiceMenu();
819 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
822 public void internalFrameClosed(
823 javax.swing.event.InternalFrameEvent evt)
825 // System.out.println("deregistering discoverer listener");
826 Desktop.instance.removeJalviewPropertyChangeListener("services",
828 closeMenuItem_actionPerformed(true);
831 // Finally, build the menu once to get current service state
832 new Thread(new Runnable()
837 BuildWebServiceMenu();
843 * Configure menu items that vary according to whether the alignment is
844 * nucleotide or protein
846 public void setGUINucleotide()
848 AlignmentI al = getViewport().getAlignment();
849 boolean nucleotide = al.isNucleotide();
851 showTranslation.setVisible(nucleotide);
852 showReverse.setVisible(nucleotide);
853 showReverseComplement.setVisible(nucleotide);
854 conservationMenuItem.setEnabled(!nucleotide);
855 modifyConservation.setEnabled(!nucleotide
856 && conservationMenuItem.isSelected());
857 showGroupConservation.setEnabled(!nucleotide);
859 showComplementMenuItem.setText(nucleotide ? MessageManager
860 .getString("label.protein") : MessageManager
861 .getString("label.nucleotide"));
865 * set up menus for the current viewport. This may be called after any
866 * operation that affects the data in the current view (selection changed,
867 * etc) to update the menus to reflect the new state.
870 public void setMenusForViewport()
872 setMenusFromViewport(viewport);
876 * Need to call this method when tabs are selected for multiple views, or when
877 * loading from Jalview2XML.java
882 void setMenusFromViewport(AlignViewport av)
884 padGapsMenuitem.setSelected(av.isPadGaps());
885 colourTextMenuItem.setSelected(av.isShowColourText());
886 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
887 modifyPID.setEnabled(abovePIDThreshold.isSelected());
888 conservationMenuItem.setSelected(av.getConservationSelected());
889 modifyConservation.setEnabled(conservationMenuItem.isSelected());
890 seqLimits.setSelected(av.getShowJVSuffix());
891 idRightAlign.setSelected(av.isRightAlignIds());
892 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
893 renderGapsMenuItem.setSelected(av.isRenderGaps());
894 wrapMenuItem.setSelected(av.getWrapAlignment());
895 scaleAbove.setVisible(av.getWrapAlignment());
896 scaleLeft.setVisible(av.getWrapAlignment());
897 scaleRight.setVisible(av.getWrapAlignment());
898 annotationPanelMenuItem.setState(av.isShowAnnotation());
900 * Show/hide annotations only enabled if annotation panel is shown
902 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
903 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
904 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
905 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
906 viewBoxesMenuItem.setSelected(av.getShowBoxes());
907 viewTextMenuItem.setSelected(av.getShowText());
908 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
909 showGroupConsensus.setSelected(av.isShowGroupConsensus());
910 showGroupConservation.setSelected(av.isShowGroupConservation());
911 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
912 showSequenceLogo.setSelected(av.isShowSequenceLogo());
913 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
915 ColourMenuHelper.setColourSelected(colourMenu,
916 av.getGlobalColourScheme());
918 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
919 hiddenMarkers.setState(av.getShowHiddenMarkers());
920 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
921 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
922 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
923 autoCalculate.setSelected(av.autoCalculateConsensus);
924 sortByTree.setSelected(av.sortByTree);
925 listenToViewSelections.setSelected(av.followSelection);
927 showProducts.setEnabled(canShowProducts());
928 setGroovyEnabled(Desktop.getGroovyConsole() != null);
934 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
938 public void setGroovyEnabled(boolean b)
940 runGroovy.setEnabled(b);
943 private IProgressIndicator progressBar;
948 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
951 public void setProgressBar(String message, long id)
953 progressBar.setProgressBar(message, id);
957 public void registerHandler(final long id,
958 final IProgressIndicatorHandler handler)
960 progressBar.registerHandler(id, handler);
965 * @return true if any progress bars are still active
968 public boolean operationInProgress()
970 return progressBar.operationInProgress();
974 public void setStatus(String text)
976 statusBar.setText(text);
980 * Added so Castor Mapping file can obtain Jalview Version
982 public String getVersion()
984 return jalview.bin.Cache.getProperty("VERSION");
987 public FeatureRenderer getFeatureRenderer()
989 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
993 public void fetchSequence_actionPerformed(ActionEvent e)
995 new jalview.gui.SequenceFetcher(this);
999 public void addFromFile_actionPerformed(ActionEvent e)
1001 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1005 public void reload_actionPerformed(ActionEvent e)
1007 if (fileName != null)
1009 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1010 // originating file's format
1011 // TODO: work out how to recover feature settings for correct view(s) when
1012 // file is reloaded.
1013 if (FileFormat.Jalview.equals(currentFileFormat))
1015 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1016 for (int i = 0; i < frames.length; i++)
1018 if (frames[i] instanceof AlignFrame && frames[i] != this
1019 && ((AlignFrame) frames[i]).fileName != null
1020 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1024 frames[i].setSelected(true);
1025 Desktop.instance.closeAssociatedWindows();
1026 } catch (java.beans.PropertyVetoException ex)
1032 Desktop.instance.closeAssociatedWindows();
1034 FileLoader loader = new FileLoader();
1035 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1036 : DataSourceType.FILE;
1037 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1041 Rectangle bounds = this.getBounds();
1043 FileLoader loader = new FileLoader();
1044 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1045 : DataSourceType.FILE;
1046 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1047 protocol, currentFileFormat);
1049 newframe.setBounds(bounds);
1050 if (featureSettings != null && featureSettings.isShowing())
1052 final Rectangle fspos = featureSettings.frame.getBounds();
1053 // TODO: need a 'show feature settings' function that takes bounds -
1054 // need to refactor Desktop.addFrame
1055 newframe.featureSettings_actionPerformed(null);
1056 final FeatureSettings nfs = newframe.featureSettings;
1057 SwingUtilities.invokeLater(new Runnable()
1062 nfs.frame.setBounds(fspos);
1065 this.featureSettings.close();
1066 this.featureSettings = null;
1068 this.closeMenuItem_actionPerformed(true);
1074 public void addFromText_actionPerformed(ActionEvent e)
1076 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1081 public void addFromURL_actionPerformed(ActionEvent e)
1083 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1087 public void save_actionPerformed(ActionEvent e)
1089 if (fileName == null || (currentFileFormat == null)
1090 || fileName.startsWith("http"))
1092 saveAs_actionPerformed(null);
1096 saveAlignment(fileName, currentFileFormat);
1107 public void saveAs_actionPerformed(ActionEvent e)
1109 String format = currentFileFormat == null ? null : currentFileFormat
1111 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1112 Cache.getProperty("LAST_DIRECTORY"), format);
1114 chooser.setFileView(new JalviewFileView());
1115 chooser.setDialogTitle(MessageManager
1116 .getString("label.save_alignment_to_file"));
1117 chooser.setToolTipText(MessageManager.getString("action.save"));
1119 int value = chooser.showSaveDialog(this);
1121 if (value == JalviewFileChooser.APPROVE_OPTION)
1123 currentFileFormat = chooser.getSelectedFormat();
1124 while (currentFileFormat == null)
1127 .showInternalMessageDialog(
1130 .getString("label.select_file_format_before_saving"),
1132 .getString("label.file_format_not_specified"),
1133 JvOptionPane.WARNING_MESSAGE);
1134 currentFileFormat = chooser.getSelectedFormat();
1135 value = chooser.showSaveDialog(this);
1136 if (value != JalviewFileChooser.APPROVE_OPTION)
1142 fileName = chooser.getSelectedFile().getPath();
1144 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1146 Cache.setProperty("LAST_DIRECTORY", fileName);
1147 saveAlignment(fileName, currentFileFormat);
1151 public boolean saveAlignment(String file, FileFormatI format)
1153 boolean success = true;
1155 if (FileFormat.Jalview.equals(format))
1157 String shortName = title;
1159 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1161 shortName = shortName.substring(shortName
1162 .lastIndexOf(java.io.File.separatorChar) + 1);
1165 success = new Jalview2XML().saveAlignment(this, file, shortName);
1167 statusBar.setText(MessageManager.formatMessage(
1168 "label.successfully_saved_to_file_in_format", new Object[] {
1169 fileName, format }));
1174 AlignmentExportData exportData = getAlignmentForExport(format,
1176 if (exportData.getSettings().isCancelled())
1180 FormatAdapter f = new FormatAdapter(alignPanel,
1181 exportData.getSettings());
1182 String output = f.formatSequences(
1184 exportData.getAlignment(), // class cast exceptions will
1185 // occur in the distant future
1186 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1187 f.getCacheSuffixDefault(format), viewport.getAlignment()
1188 .getHiddenColumns());
1198 PrintWriter out = new PrintWriter(new FileWriter(file));
1202 this.setTitle(file);
1203 statusBar.setText(MessageManager.formatMessage(
1204 "label.successfully_saved_to_file_in_format",
1205 new Object[] { fileName, format.getName() }));
1206 } catch (Exception ex)
1209 ex.printStackTrace();
1216 JvOptionPane.showInternalMessageDialog(this, MessageManager
1217 .formatMessage("label.couldnt_save_file",
1218 new Object[] { fileName }), MessageManager
1219 .getString("label.error_saving_file"),
1220 JvOptionPane.WARNING_MESSAGE);
1226 private void warningMessage(String warning, String title)
1228 if (new jalview.util.Platform().isHeadless())
1230 System.err.println("Warning: " + title + "\nWarning: " + warning);
1235 JvOptionPane.showInternalMessageDialog(this, warning, title,
1236 JvOptionPane.WARNING_MESSAGE);
1248 protected void outputText_actionPerformed(ActionEvent e)
1250 FileFormatI fileFormat = FileFormats.getInstance().forName(
1251 e.getActionCommand());
1252 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1254 if (exportData.getSettings().isCancelled())
1258 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1259 cap.setForInput(null);
1262 FileFormatI format = fileFormat;
1263 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1264 .formatSequences(format, exportData.getAlignment(),
1265 exportData.getOmitHidden(),
1267 .getStartEndPostions(), viewport
1268 .getAlignment().getHiddenColumns()));
1269 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1270 "label.alignment_output_command",
1271 new Object[] { e.getActionCommand() }), 600, 500);
1272 } catch (OutOfMemoryError oom)
1274 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1280 public static AlignmentExportData getAlignmentForExport(
1281 FileFormatI format, AlignViewportI viewport,
1282 AlignExportSettingI exportSettings)
1284 AlignmentI alignmentToExport = null;
1285 AlignExportSettingI settings = exportSettings;
1286 String[] omitHidden = null;
1288 HiddenSequences hiddenSeqs = viewport.getAlignment()
1289 .getHiddenSequences();
1291 alignmentToExport = viewport.getAlignment();
1293 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1294 if (settings == null)
1296 settings = new AlignExportSettings(hasHiddenSeqs,
1297 viewport.hasHiddenColumns(), format);
1299 // settings.isExportAnnotations();
1301 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1303 omitHidden = viewport.getViewAsString(false,
1304 settings.isExportHiddenSequences());
1307 int[] alignmentStartEnd = new int[2];
1308 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1310 alignmentToExport = hiddenSeqs.getFullAlignment();
1314 alignmentToExport = viewport.getAlignment();
1316 alignmentStartEnd = alignmentToExport
1317 .getVisibleStartAndEndIndex(viewport.getAlignment()
1320 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1321 omitHidden, alignmentStartEnd, settings);
1332 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1334 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1335 htmlSVG.exportHTML(null);
1339 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1341 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1342 bjs.exportHTML(null);
1345 public void createImageMap(File file, String image)
1347 alignPanel.makePNGImageMap(file, image);
1357 public void createPNG(File f)
1359 alignPanel.makePNG(f);
1369 public void createEPS(File f)
1371 alignPanel.makeEPS(f);
1375 public void createSVG(File f)
1377 alignPanel.makeSVG(f);
1381 public void pageSetup_actionPerformed(ActionEvent e)
1383 PrinterJob printJob = PrinterJob.getPrinterJob();
1384 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1394 public void printMenuItem_actionPerformed(ActionEvent e)
1396 // Putting in a thread avoids Swing painting problems
1397 PrintThread thread = new PrintThread(alignPanel);
1402 public void exportFeatures_actionPerformed(ActionEvent e)
1404 new AnnotationExporter().exportFeatures(alignPanel);
1408 public void exportAnnotations_actionPerformed(ActionEvent e)
1410 new AnnotationExporter().exportAnnotations(alignPanel);
1414 public void associatedData_actionPerformed(ActionEvent e)
1416 // Pick the tree file
1417 JalviewFileChooser chooser = new JalviewFileChooser(
1418 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1419 chooser.setFileView(new JalviewFileView());
1420 chooser.setDialogTitle(MessageManager
1421 .getString("label.load_jalview_annotations"));
1422 chooser.setToolTipText(MessageManager
1423 .getString("label.load_jalview_annotations"));
1425 int value = chooser.showOpenDialog(null);
1427 if (value == JalviewFileChooser.APPROVE_OPTION)
1429 String choice = chooser.getSelectedFile().getPath();
1430 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1431 loadJalviewDataFile(choice, null, null, null);
1437 * Close the current view or all views in the alignment frame. If the frame
1438 * only contains one view then the alignment will be removed from memory.
1440 * @param closeAllTabs
1443 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1445 if (alignPanels != null && alignPanels.size() < 2)
1447 closeAllTabs = true;
1452 if (alignPanels != null)
1456 if (this.isClosed())
1458 // really close all the windows - otherwise wait till
1459 // setClosed(true) is called
1460 for (int i = 0; i < alignPanels.size(); i++)
1462 AlignmentPanel ap = alignPanels.get(i);
1469 closeView(alignPanel);
1476 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1477 * be called recursively, with the frame now in 'closed' state
1479 this.setClosed(true);
1481 } catch (Exception ex)
1483 ex.printStackTrace();
1488 * Close the specified panel and close up tabs appropriately.
1490 * @param panelToClose
1492 public void closeView(AlignmentPanel panelToClose)
1494 int index = tabbedPane.getSelectedIndex();
1495 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1496 alignPanels.remove(panelToClose);
1497 panelToClose.closePanel();
1498 panelToClose = null;
1500 tabbedPane.removeTabAt(closedindex);
1501 tabbedPane.validate();
1503 if (index > closedindex || index == tabbedPane.getTabCount())
1505 // modify currently selected tab index if necessary.
1509 this.tabSelectionChanged(index);
1515 void updateEditMenuBar()
1518 if (viewport.getHistoryList().size() > 0)
1520 undoMenuItem.setEnabled(true);
1521 CommandI command = viewport.getHistoryList().peek();
1522 undoMenuItem.setText(MessageManager.formatMessage(
1523 "label.undo_command",
1524 new Object[] { command.getDescription() }));
1528 undoMenuItem.setEnabled(false);
1529 undoMenuItem.setText(MessageManager.getString("action.undo"));
1532 if (viewport.getRedoList().size() > 0)
1534 redoMenuItem.setEnabled(true);
1536 CommandI command = viewport.getRedoList().peek();
1537 redoMenuItem.setText(MessageManager.formatMessage(
1538 "label.redo_command",
1539 new Object[] { command.getDescription() }));
1543 redoMenuItem.setEnabled(false);
1544 redoMenuItem.setText(MessageManager.getString("action.redo"));
1549 public void addHistoryItem(CommandI command)
1551 if (command.getSize() > 0)
1553 viewport.addToHistoryList(command);
1554 viewport.clearRedoList();
1555 updateEditMenuBar();
1556 viewport.updateHiddenColumns();
1557 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1558 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1559 // viewport.getColumnSelection()
1560 // .getHiddenColumns().size() > 0);
1566 * @return alignment objects for all views
1568 AlignmentI[] getViewAlignments()
1570 if (alignPanels != null)
1572 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1574 for (AlignmentPanel ap : alignPanels)
1576 als[i++] = ap.av.getAlignment();
1580 if (viewport != null)
1582 return new AlignmentI[] { viewport.getAlignment() };
1594 protected void undoMenuItem_actionPerformed(ActionEvent e)
1596 if (viewport.getHistoryList().isEmpty())
1600 CommandI command = viewport.getHistoryList().pop();
1601 viewport.addToRedoList(command);
1602 command.undoCommand(getViewAlignments());
1604 AlignmentViewport originalSource = getOriginatingSource(command);
1605 updateEditMenuBar();
1607 if (originalSource != null)
1609 if (originalSource != viewport)
1612 .warn("Implementation worry: mismatch of viewport origin for undo");
1614 originalSource.updateHiddenColumns();
1615 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1617 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1618 // viewport.getColumnSelection()
1619 // .getHiddenColumns().size() > 0);
1620 originalSource.firePropertyChange("alignment", null, originalSource
1621 .getAlignment().getSequences());
1632 protected void redoMenuItem_actionPerformed(ActionEvent e)
1634 if (viewport.getRedoList().size() < 1)
1639 CommandI command = viewport.getRedoList().pop();
1640 viewport.addToHistoryList(command);
1641 command.doCommand(getViewAlignments());
1643 AlignmentViewport originalSource = getOriginatingSource(command);
1644 updateEditMenuBar();
1646 if (originalSource != null)
1649 if (originalSource != viewport)
1652 .warn("Implementation worry: mismatch of viewport origin for redo");
1654 originalSource.updateHiddenColumns();
1655 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1657 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1658 // viewport.getColumnSelection()
1659 // .getHiddenColumns().size() > 0);
1660 originalSource.firePropertyChange("alignment", null, originalSource
1661 .getAlignment().getSequences());
1665 AlignmentViewport getOriginatingSource(CommandI command)
1667 AlignmentViewport originalSource = null;
1668 // For sequence removal and addition, we need to fire
1669 // the property change event FROM the viewport where the
1670 // original alignment was altered
1671 AlignmentI al = null;
1672 if (command instanceof EditCommand)
1674 EditCommand editCommand = (EditCommand) command;
1675 al = editCommand.getAlignment();
1676 List<Component> comps = PaintRefresher.components.get(viewport
1677 .getSequenceSetId());
1679 for (Component comp : comps)
1681 if (comp instanceof AlignmentPanel)
1683 if (al == ((AlignmentPanel) comp).av.getAlignment())
1685 originalSource = ((AlignmentPanel) comp).av;
1692 if (originalSource == null)
1694 // The original view is closed, we must validate
1695 // the current view against the closed view first
1698 PaintRefresher.validateSequences(al, viewport.getAlignment());
1701 originalSource = viewport;
1704 return originalSource;
1713 public void moveSelectedSequences(boolean up)
1715 SequenceGroup sg = viewport.getSelectionGroup();
1721 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1722 viewport.getHiddenRepSequences(), up);
1723 alignPanel.paintAlignment(true);
1726 synchronized void slideSequences(boolean right, int size)
1728 List<SequenceI> sg = new ArrayList<SequenceI>();
1729 if (viewport.cursorMode)
1731 sg.add(viewport.getAlignment().getSequenceAt(
1732 alignPanel.getSeqPanel().seqCanvas.cursorY));
1734 else if (viewport.getSelectionGroup() != null
1735 && viewport.getSelectionGroup().getSize() != viewport
1736 .getAlignment().getHeight())
1738 sg = viewport.getSelectionGroup().getSequences(
1739 viewport.getHiddenRepSequences());
1747 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1749 for (SequenceI seq : viewport.getAlignment().getSequences())
1751 if (!sg.contains(seq))
1753 invertGroup.add(seq);
1757 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1759 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1760 for (int i = 0; i < invertGroup.size(); i++)
1762 seqs2[i] = invertGroup.get(i);
1765 SlideSequencesCommand ssc;
1768 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1769 size, viewport.getGapCharacter());
1773 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1774 size, viewport.getGapCharacter());
1777 int groupAdjustment = 0;
1778 if (ssc.getGapsInsertedBegin() && right)
1780 if (viewport.cursorMode)
1782 alignPanel.getSeqPanel().moveCursor(size, 0);
1786 groupAdjustment = size;
1789 else if (!ssc.getGapsInsertedBegin() && !right)
1791 if (viewport.cursorMode)
1793 alignPanel.getSeqPanel().moveCursor(-size, 0);
1797 groupAdjustment = -size;
1801 if (groupAdjustment != 0)
1803 viewport.getSelectionGroup().setStartRes(
1804 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1805 viewport.getSelectionGroup().setEndRes(
1806 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1810 * just extend the last slide command if compatible; but not if in
1811 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1813 boolean appendHistoryItem = false;
1814 Deque<CommandI> historyList = viewport.getHistoryList();
1815 boolean inSplitFrame = getSplitViewContainer() != null;
1816 if (!inSplitFrame && historyList != null && historyList.size() > 0
1817 && historyList.peek() instanceof SlideSequencesCommand)
1819 appendHistoryItem = ssc
1820 .appendSlideCommand((SlideSequencesCommand) historyList
1824 if (!appendHistoryItem)
1826 addHistoryItem(ssc);
1839 protected void copy_actionPerformed(ActionEvent e)
1842 if (viewport.getSelectionGroup() == null)
1846 // TODO: preserve the ordering of displayed alignment annotation in any
1847 // internal paste (particularly sequence associated annotation)
1848 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1849 String[] omitHidden = null;
1851 if (viewport.hasHiddenColumns())
1853 omitHidden = viewport.getViewAsString(true);
1856 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1857 seqs, omitHidden, null);
1859 StringSelection ss = new StringSelection(output);
1863 jalview.gui.Desktop.internalCopy = true;
1864 // Its really worth setting the clipboard contents
1865 // to empty before setting the large StringSelection!!
1866 Toolkit.getDefaultToolkit().getSystemClipboard()
1867 .setContents(new StringSelection(""), null);
1869 Toolkit.getDefaultToolkit().getSystemClipboard()
1870 .setContents(ss, Desktop.instance);
1871 } catch (OutOfMemoryError er)
1873 new OOMWarning("copying region", er);
1877 ArrayList<int[]> hiddenColumns = null;
1878 if (viewport.hasHiddenColumns())
1880 hiddenColumns = new ArrayList<int[]>();
1881 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1882 .getSelectionGroup().getEndRes();
1883 for (int[] region : viewport.getAlignment().getHiddenColumns()
1886 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1888 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1889 region[1] - hiddenOffset });
1894 Desktop.jalviewClipboard = new Object[] { seqs,
1895 viewport.getAlignment().getDataset(), hiddenColumns };
1896 statusBar.setText(MessageManager.formatMessage(
1897 "label.copied_sequences_to_clipboard", new Object[] { Integer
1898 .valueOf(seqs.length).toString() }));
1908 protected void pasteNew_actionPerformed(ActionEvent e)
1920 protected void pasteThis_actionPerformed(ActionEvent e)
1926 * Paste contents of Jalview clipboard
1928 * @param newAlignment
1929 * true to paste to a new alignment, otherwise add to this.
1931 void paste(boolean newAlignment)
1933 boolean externalPaste = true;
1936 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1937 Transferable contents = c.getContents(this);
1939 if (contents == null)
1948 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1949 if (str.length() < 1)
1954 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1956 } catch (OutOfMemoryError er)
1958 new OOMWarning("Out of memory pasting sequences!!", er);
1962 SequenceI[] sequences;
1963 boolean annotationAdded = false;
1964 AlignmentI alignment = null;
1966 if (Desktop.jalviewClipboard != null)
1968 // The clipboard was filled from within Jalview, we must use the
1970 // And dataset from the copied alignment
1971 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1972 // be doubly sure that we create *new* sequence objects.
1973 sequences = new SequenceI[newseq.length];
1974 for (int i = 0; i < newseq.length; i++)
1976 sequences[i] = new Sequence(newseq[i]);
1978 alignment = new Alignment(sequences);
1979 externalPaste = false;
1983 // parse the clipboard as an alignment.
1984 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1986 sequences = alignment.getSequencesArray();
1990 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1996 if (Desktop.jalviewClipboard != null)
1998 // dataset is inherited
1999 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2003 // new dataset is constructed
2004 alignment.setDataset(null);
2006 alwidth = alignment.getWidth() + 1;
2010 AlignmentI pastedal = alignment; // preserve pasted alignment object
2011 // Add pasted sequences and dataset into existing alignment.
2012 alignment = viewport.getAlignment();
2013 alwidth = alignment.getWidth() + 1;
2014 // decide if we need to import sequences from an existing dataset
2015 boolean importDs = Desktop.jalviewClipboard != null
2016 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2017 // importDs==true instructs us to copy over new dataset sequences from
2018 // an existing alignment
2019 Vector newDs = (importDs) ? new Vector() : null; // used to create
2020 // minimum dataset set
2022 for (int i = 0; i < sequences.length; i++)
2026 newDs.addElement(null);
2028 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2030 if (importDs && ds != null)
2032 if (!newDs.contains(ds))
2034 newDs.setElementAt(ds, i);
2035 ds = new Sequence(ds);
2036 // update with new dataset sequence
2037 sequences[i].setDatasetSequence(ds);
2041 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2046 // copy and derive new dataset sequence
2047 sequences[i] = sequences[i].deriveSequence();
2048 alignment.getDataset().addSequence(
2049 sequences[i].getDatasetSequence());
2050 // TODO: avoid creation of duplicate dataset sequences with a
2051 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2053 alignment.addSequence(sequences[i]); // merges dataset
2057 newDs.clear(); // tidy up
2059 if (alignment.getAlignmentAnnotation() != null)
2061 for (AlignmentAnnotation alan : alignment
2062 .getAlignmentAnnotation())
2064 if (alan.graphGroup > fgroup)
2066 fgroup = alan.graphGroup;
2070 if (pastedal.getAlignmentAnnotation() != null)
2072 // Add any annotation attached to alignment.
2073 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2074 for (int i = 0; i < alann.length; i++)
2076 annotationAdded = true;
2077 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2079 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2080 if (newann.graphGroup > -1)
2082 if (newGraphGroups.size() <= newann.graphGroup
2083 || newGraphGroups.get(newann.graphGroup) == null)
2085 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2087 newGraphGroups.add(q, null);
2089 newGraphGroups.set(newann.graphGroup, new Integer(
2092 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2096 newann.padAnnotation(alwidth);
2097 alignment.addAnnotation(newann);
2107 addHistoryItem(new EditCommand(
2108 MessageManager.getString("label.add_sequences"),
2109 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2111 // Add any annotations attached to sequences
2112 for (int i = 0; i < sequences.length; i++)
2114 if (sequences[i].getAnnotation() != null)
2116 AlignmentAnnotation newann;
2117 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2119 annotationAdded = true;
2120 newann = sequences[i].getAnnotation()[a];
2121 newann.adjustForAlignment();
2122 newann.padAnnotation(alwidth);
2123 if (newann.graphGroup > -1)
2125 if (newann.graphGroup > -1)
2127 if (newGraphGroups.size() <= newann.graphGroup
2128 || newGraphGroups.get(newann.graphGroup) == null)
2130 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2132 newGraphGroups.add(q, null);
2134 newGraphGroups.set(newann.graphGroup, new Integer(
2137 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2141 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2146 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2153 // propagate alignment changed.
2154 vpRanges.setEndSeq(alignment.getHeight());
2155 if (annotationAdded)
2157 // Duplicate sequence annotation in all views.
2158 AlignmentI[] alview = this.getViewAlignments();
2159 for (int i = 0; i < sequences.length; i++)
2161 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2166 for (int avnum = 0; avnum < alview.length; avnum++)
2168 if (alview[avnum] != alignment)
2170 // duplicate in a view other than the one with input focus
2171 int avwidth = alview[avnum].getWidth() + 1;
2172 // this relies on sann being preserved after we
2173 // modify the sequence's annotation array for each duplication
2174 for (int a = 0; a < sann.length; a++)
2176 AlignmentAnnotation newann = new AlignmentAnnotation(
2178 sequences[i].addAlignmentAnnotation(newann);
2179 newann.padAnnotation(avwidth);
2180 alview[avnum].addAnnotation(newann); // annotation was
2181 // duplicated earlier
2182 // TODO JAL-1145 graphGroups are not updated for sequence
2183 // annotation added to several views. This may cause
2185 alview[avnum].setAnnotationIndex(newann, a);
2190 buildSortByAnnotationScoresMenu();
2192 viewport.firePropertyChange("alignment", null,
2193 alignment.getSequences());
2194 if (alignPanels != null)
2196 for (AlignmentPanel ap : alignPanels)
2198 ap.validateAnnotationDimensions(false);
2203 alignPanel.validateAnnotationDimensions(false);
2209 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2211 String newtitle = new String("Copied sequences");
2213 if (Desktop.jalviewClipboard != null
2214 && Desktop.jalviewClipboard[2] != null)
2216 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2217 for (int[] region : hc)
2219 af.viewport.hideColumns(region[0], region[1]);
2223 // >>>This is a fix for the moment, until a better solution is
2225 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2227 alignPanel.getSeqPanel().seqCanvas
2228 .getFeatureRenderer());
2230 // TODO: maintain provenance of an alignment, rather than just make the
2231 // title a concatenation of operations.
2234 if (title.startsWith("Copied sequences"))
2240 newtitle = newtitle.concat("- from " + title);
2245 newtitle = new String("Pasted sequences");
2248 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2253 } catch (Exception ex)
2255 ex.printStackTrace();
2256 System.out.println("Exception whilst pasting: " + ex);
2257 // could be anything being pasted in here
2263 protected void expand_newalign(ActionEvent e)
2267 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2268 .getAlignment(), -1);
2269 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2271 String newtitle = new String("Flanking alignment");
2273 if (Desktop.jalviewClipboard != null
2274 && Desktop.jalviewClipboard[2] != null)
2276 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2277 for (int region[] : hc)
2279 af.viewport.hideColumns(region[0], region[1]);
2283 // >>>This is a fix for the moment, until a better solution is
2285 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2287 alignPanel.getSeqPanel().seqCanvas
2288 .getFeatureRenderer());
2290 // TODO: maintain provenance of an alignment, rather than just make the
2291 // title a concatenation of operations.
2293 if (title.startsWith("Copied sequences"))
2299 newtitle = newtitle.concat("- from " + title);
2303 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2305 } catch (Exception ex)
2307 ex.printStackTrace();
2308 System.out.println("Exception whilst pasting: " + ex);
2309 // could be anything being pasted in here
2310 } catch (OutOfMemoryError oom)
2312 new OOMWarning("Viewing flanking region of alignment", oom);
2323 protected void cut_actionPerformed(ActionEvent e)
2325 copy_actionPerformed(null);
2326 delete_actionPerformed(null);
2336 protected void delete_actionPerformed(ActionEvent evt)
2339 SequenceGroup sg = viewport.getSelectionGroup();
2346 * If the cut affects all sequences, warn, remove highlighted columns
2348 if (sg.getSize() == viewport.getAlignment().getHeight())
2350 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2351 .getAlignment().getWidth()) ? true : false;
2352 if (isEntireAlignWidth)
2354 int confirm = JvOptionPane.showConfirmDialog(this,
2355 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2356 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2357 JvOptionPane.OK_CANCEL_OPTION);
2359 if (confirm == JvOptionPane.CANCEL_OPTION
2360 || confirm == JvOptionPane.CLOSED_OPTION)
2365 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2366 sg.getEndRes() + 1);
2368 SequenceI[] cut = sg.getSequences()
2369 .toArray(new SequenceI[sg.getSize()]);
2371 addHistoryItem(new EditCommand(
2372 MessageManager.getString("label.cut_sequences"), Action.CUT,
2373 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2374 viewport.getAlignment()));
2376 viewport.setSelectionGroup(null);
2377 viewport.sendSelection();
2378 viewport.getAlignment().deleteGroup(sg);
2380 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2382 if (viewport.getAlignment().getHeight() < 1)
2386 this.setClosed(true);
2387 } catch (Exception ex)
2400 protected void deleteGroups_actionPerformed(ActionEvent e)
2402 if (avc.deleteGroups())
2404 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2405 alignPanel.updateAnnotation();
2406 alignPanel.paintAlignment(true);
2417 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2419 SequenceGroup sg = new SequenceGroup();
2421 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2423 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2426 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2427 viewport.setSelectionGroup(sg);
2428 viewport.sendSelection();
2429 // JAL-2034 - should delegate to
2430 // alignPanel to decide if overview needs
2432 alignPanel.paintAlignment(false);
2433 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2443 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2445 if (viewport.cursorMode)
2447 alignPanel.getSeqPanel().keyboardNo1 = null;
2448 alignPanel.getSeqPanel().keyboardNo2 = null;
2450 viewport.setSelectionGroup(null);
2451 viewport.getColumnSelection().clear();
2452 viewport.setSelectionGroup(null);
2453 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2454 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2455 // JAL-2034 - should delegate to
2456 // alignPanel to decide if overview needs
2458 alignPanel.paintAlignment(false);
2459 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2460 viewport.sendSelection();
2470 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2472 SequenceGroup sg = viewport.getSelectionGroup();
2476 selectAllSequenceMenuItem_actionPerformed(null);
2481 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2483 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2485 // JAL-2034 - should delegate to
2486 // alignPanel to decide if overview needs
2489 alignPanel.paintAlignment(true);
2490 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2491 viewport.sendSelection();
2495 public void invertColSel_actionPerformed(ActionEvent e)
2497 viewport.invertColumnSelection();
2498 alignPanel.paintAlignment(true);
2499 viewport.sendSelection();
2509 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2511 trimAlignment(true);
2521 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2523 trimAlignment(false);
2526 void trimAlignment(boolean trimLeft)
2528 ColumnSelection colSel = viewport.getColumnSelection();
2531 if (!colSel.isEmpty())
2535 column = colSel.getMin();
2539 column = colSel.getMax();
2543 if (viewport.getSelectionGroup() != null)
2545 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2546 viewport.getHiddenRepSequences());
2550 seqs = viewport.getAlignment().getSequencesArray();
2553 TrimRegionCommand trimRegion;
2556 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2557 column, viewport.getAlignment());
2558 vpRanges.setStartRes(0);
2562 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2563 column, viewport.getAlignment());
2566 statusBar.setText(MessageManager.formatMessage(
2567 "label.removed_columns",
2568 new String[] { Integer.valueOf(trimRegion.getSize())
2571 addHistoryItem(trimRegion);
2573 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2575 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2576 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2578 viewport.getAlignment().deleteGroup(sg);
2582 viewport.firePropertyChange("alignment", null, viewport
2583 .getAlignment().getSequences());
2594 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2596 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2599 if (viewport.getSelectionGroup() != null)
2601 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2602 viewport.getHiddenRepSequences());
2603 start = viewport.getSelectionGroup().getStartRes();
2604 end = viewport.getSelectionGroup().getEndRes();
2608 seqs = viewport.getAlignment().getSequencesArray();
2611 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2612 "Remove Gapped Columns", seqs, start, end,
2613 viewport.getAlignment());
2615 addHistoryItem(removeGapCols);
2617 statusBar.setText(MessageManager.formatMessage(
2618 "label.removed_empty_columns",
2619 new Object[] { Integer.valueOf(removeGapCols.getSize())
2622 // This is to maintain viewport position on first residue
2623 // of first sequence
2624 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2625 int startRes = seq.findPosition(vpRanges.getStartRes());
2626 // ShiftList shifts;
2627 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2628 // edit.alColumnChanges=shifts.getInverse();
2629 // if (viewport.hasHiddenColumns)
2630 // viewport.getColumnSelection().compensateForEdits(shifts);
2631 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2632 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2644 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2646 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2649 if (viewport.getSelectionGroup() != null)
2651 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2652 viewport.getHiddenRepSequences());
2653 start = viewport.getSelectionGroup().getStartRes();
2654 end = viewport.getSelectionGroup().getEndRes();
2658 seqs = viewport.getAlignment().getSequencesArray();
2661 // This is to maintain viewport position on first residue
2662 // of first sequence
2663 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2664 int startRes = seq.findPosition(vpRanges.getStartRes());
2666 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2667 viewport.getAlignment()));
2669 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2671 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2683 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2685 viewport.setPadGaps(padGapsMenuitem.isSelected());
2686 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2697 public void findMenuItem_actionPerformed(ActionEvent e)
2703 * Create a new view of the current alignment.
2706 public void newView_actionPerformed(ActionEvent e)
2708 newView(null, true);
2712 * Creates and shows a new view of the current alignment.
2715 * title of newly created view; if null, one will be generated
2716 * @param copyAnnotation
2717 * if true then duplicate all annnotation, groups and settings
2718 * @return new alignment panel, already displayed.
2720 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2723 * Create a new AlignmentPanel (with its own, new Viewport)
2725 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2727 if (!copyAnnotation)
2730 * remove all groups and annotation except for the automatic stuff
2732 newap.av.getAlignment().deleteAllGroups();
2733 newap.av.getAlignment().deleteAllAnnotations(false);
2736 newap.av.setGatherViewsHere(false);
2738 if (viewport.viewName == null)
2740 viewport.viewName = MessageManager
2741 .getString("label.view_name_original");
2745 * Views share the same edits undo and redo stacks
2747 newap.av.setHistoryList(viewport.getHistoryList());
2748 newap.av.setRedoList(viewport.getRedoList());
2751 * Views share the same mappings; need to deregister any new mappings
2752 * created by copyAlignPanel, and register the new reference to the shared
2755 newap.av.replaceMappings(viewport.getAlignment());
2758 * start up cDNA consensus (if applicable) now mappings are in place
2760 if (newap.av.initComplementConsensus())
2762 newap.refresh(true); // adjust layout of annotations
2765 newap.av.viewName = getNewViewName(viewTitle);
2767 addAlignmentPanel(newap, true);
2768 newap.alignmentChanged();
2770 if (alignPanels.size() == 2)
2772 viewport.setGatherViewsHere(true);
2774 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2779 * Make a new name for the view, ensuring it is unique within the current
2780 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2781 * these now use viewId. Unique view names are still desirable for usability.)
2786 protected String getNewViewName(String viewTitle)
2788 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2789 boolean addFirstIndex = false;
2790 if (viewTitle == null || viewTitle.trim().length() == 0)
2792 viewTitle = MessageManager.getString("action.view");
2793 addFirstIndex = true;
2797 index = 1;// we count from 1 if given a specific name
2799 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2801 List<Component> comps = PaintRefresher.components.get(viewport
2802 .getSequenceSetId());
2804 List<String> existingNames = getExistingViewNames(comps);
2806 while (existingNames.contains(newViewName))
2808 newViewName = viewTitle + " " + (++index);
2814 * Returns a list of distinct view names found in the given list of
2815 * components. View names are held on the viewport of an AlignmentPanel.
2820 protected List<String> getExistingViewNames(List<Component> comps)
2822 List<String> existingNames = new ArrayList<String>();
2823 for (Component comp : comps)
2825 if (comp instanceof AlignmentPanel)
2827 AlignmentPanel ap = (AlignmentPanel) comp;
2828 if (!existingNames.contains(ap.av.viewName))
2830 existingNames.add(ap.av.viewName);
2834 return existingNames;
2838 * Explode tabbed views into separate windows.
2841 public void expandViews_actionPerformed(ActionEvent e)
2843 Desktop.explodeViews(this);
2847 * Gather views in separate windows back into a tabbed presentation.
2850 public void gatherViews_actionPerformed(ActionEvent e)
2852 Desktop.instance.gatherViews(this);
2862 public void font_actionPerformed(ActionEvent e)
2864 new FontChooser(alignPanel);
2874 protected void seqLimit_actionPerformed(ActionEvent e)
2876 viewport.setShowJVSuffix(seqLimits.isSelected());
2878 alignPanel.getIdPanel().getIdCanvas()
2879 .setPreferredSize(alignPanel.calculateIdWidth());
2880 alignPanel.paintAlignment(true);
2884 public void idRightAlign_actionPerformed(ActionEvent e)
2886 viewport.setRightAlignIds(idRightAlign.isSelected());
2887 alignPanel.paintAlignment(true);
2891 public void centreColumnLabels_actionPerformed(ActionEvent e)
2893 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2894 alignPanel.paintAlignment(true);
2900 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2903 protected void followHighlight_actionPerformed()
2906 * Set the 'follow' flag on the Viewport (and scroll to position if now
2909 final boolean state = this.followHighlightMenuItem.getState();
2910 viewport.setFollowHighlight(state);
2913 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2924 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2926 viewport.setColourText(colourTextMenuItem.isSelected());
2927 alignPanel.paintAlignment(true);
2937 public void wrapMenuItem_actionPerformed(ActionEvent e)
2939 scaleAbove.setVisible(wrapMenuItem.isSelected());
2940 scaleLeft.setVisible(wrapMenuItem.isSelected());
2941 scaleRight.setVisible(wrapMenuItem.isSelected());
2942 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2943 alignPanel.updateLayout();
2947 public void showAllSeqs_actionPerformed(ActionEvent e)
2949 viewport.showAllHiddenSeqs();
2953 public void showAllColumns_actionPerformed(ActionEvent e)
2955 viewport.showAllHiddenColumns();
2957 viewport.sendSelection();
2961 public void hideSelSequences_actionPerformed(ActionEvent e)
2963 viewport.hideAllSelectedSeqs();
2964 // alignPanel.paintAlignment(true);
2968 * called by key handler and the hide all/show all menu items
2973 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2976 boolean hide = false;
2977 SequenceGroup sg = viewport.getSelectionGroup();
2978 if (!toggleSeqs && !toggleCols)
2980 // Hide everything by the current selection - this is a hack - we do the
2981 // invert and then hide
2982 // first check that there will be visible columns after the invert.
2983 if (viewport.hasSelectedColumns()
2984 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2987 // now invert the sequence set, if required - empty selection implies
2988 // that no hiding is required.
2991 invertSequenceMenuItem_actionPerformed(null);
2992 sg = viewport.getSelectionGroup();
2996 viewport.expandColSelection(sg, true);
2997 // finally invert the column selection and get the new sequence
2999 invertColSel_actionPerformed(null);
3006 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3008 hideSelSequences_actionPerformed(null);
3011 else if (!(toggleCols && viewport.hasSelectedColumns()))
3013 showAllSeqs_actionPerformed(null);
3019 if (viewport.hasSelectedColumns())
3021 hideSelColumns_actionPerformed(null);
3024 viewport.setSelectionGroup(sg);
3029 showAllColumns_actionPerformed(null);
3038 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3039 * event.ActionEvent)
3042 public void hideAllButSelection_actionPerformed(ActionEvent e)
3044 toggleHiddenRegions(false, false);
3045 viewport.sendSelection();
3052 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3056 public void hideAllSelection_actionPerformed(ActionEvent e)
3058 SequenceGroup sg = viewport.getSelectionGroup();
3059 viewport.expandColSelection(sg, false);
3060 viewport.hideAllSelectedSeqs();
3061 viewport.hideSelectedColumns();
3062 alignPanel.paintAlignment(true);
3063 viewport.sendSelection();
3070 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3074 public void showAllhidden_actionPerformed(ActionEvent e)
3076 viewport.showAllHiddenColumns();
3077 viewport.showAllHiddenSeqs();
3078 alignPanel.paintAlignment(true);
3079 viewport.sendSelection();
3083 public void hideSelColumns_actionPerformed(ActionEvent e)
3085 viewport.hideSelectedColumns();
3086 alignPanel.paintAlignment(true);
3087 viewport.sendSelection();
3091 public void hiddenMarkers_actionPerformed(ActionEvent e)
3093 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3104 protected void scaleAbove_actionPerformed(ActionEvent e)
3106 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3107 alignPanel.paintAlignment(true);
3117 protected void scaleLeft_actionPerformed(ActionEvent e)
3119 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3120 alignPanel.paintAlignment(true);
3130 protected void scaleRight_actionPerformed(ActionEvent e)
3132 viewport.setScaleRightWrapped(scaleRight.isSelected());
3133 alignPanel.paintAlignment(true);
3143 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3145 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3146 alignPanel.paintAlignment(true);
3156 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3158 viewport.setShowText(viewTextMenuItem.isSelected());
3159 alignPanel.paintAlignment(true);
3169 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3171 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3172 alignPanel.paintAlignment(true);
3175 public FeatureSettings featureSettings;
3178 public FeatureSettingsControllerI getFeatureSettingsUI()
3180 return featureSettings;
3184 public void featureSettings_actionPerformed(ActionEvent e)
3186 if (featureSettings != null)
3188 featureSettings.close();
3189 featureSettings = null;
3191 if (!showSeqFeatures.isSelected())
3193 // make sure features are actually displayed
3194 showSeqFeatures.setSelected(true);
3195 showSeqFeatures_actionPerformed(null);
3197 featureSettings = new FeatureSettings(this);
3201 * Set or clear 'Show Sequence Features'
3207 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3209 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3210 alignPanel.paintAlignment(true);
3211 if (alignPanel.getOverviewPanel() != null)
3213 alignPanel.getOverviewPanel().updateOverviewImage();
3218 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3219 * the annotations panel as a whole.
3221 * The options to show/hide all annotations should be enabled when the panel
3222 * is shown, and disabled when the panel is hidden.
3227 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3229 final boolean setVisible = annotationPanelMenuItem.isSelected();
3230 viewport.setShowAnnotation(setVisible);
3231 this.showAllSeqAnnotations.setEnabled(setVisible);
3232 this.hideAllSeqAnnotations.setEnabled(setVisible);
3233 this.showAllAlAnnotations.setEnabled(setVisible);
3234 this.hideAllAlAnnotations.setEnabled(setVisible);
3235 alignPanel.updateLayout();
3239 public void alignmentProperties()
3241 JEditorPane editPane = new JEditorPane("text/html", "");
3242 editPane.setEditable(false);
3243 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3245 editPane.setText(MessageManager.formatMessage("label.html_content",
3246 new Object[] { contents.toString() }));
3247 JInternalFrame frame = new JInternalFrame();
3248 frame.getContentPane().add(new JScrollPane(editPane));
3250 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3251 "label.alignment_properties", new Object[] { getTitle() }),
3262 public void overviewMenuItem_actionPerformed(ActionEvent e)
3264 if (alignPanel.overviewPanel != null)
3269 JInternalFrame frame = new JInternalFrame();
3270 OverviewPanel overview = new OverviewPanel(alignPanel);
3271 frame.setContentPane(overview);
3272 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3273 "label.overview_params", new Object[] { this.getTitle() }),
3274 frame.getWidth(), frame.getHeight());
3276 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3277 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3280 public void internalFrameClosed(
3281 javax.swing.event.InternalFrameEvent evt)
3283 alignPanel.setOverviewPanel(null);
3287 alignPanel.setOverviewPanel(overview);
3291 public void textColour_actionPerformed()
3293 new TextColourChooser().chooseColour(alignPanel, null);
3297 * public void covariationColour_actionPerformed() {
3299 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3303 public void annotationColour_actionPerformed()
3305 new AnnotationColourChooser(viewport, alignPanel);
3309 public void annotationColumn_actionPerformed(ActionEvent e)
3311 new AnnotationColumnChooser(viewport, alignPanel);
3315 * Action on the user checking or unchecking the option to apply the selected
3316 * colour scheme to all groups. If unchecked, groups may have their own
3317 * independent colour schemes.
3322 public void applyToAllGroups_actionPerformed(boolean selected)
3324 viewport.setColourAppliesToAllGroups(selected);
3328 * Action on user selecting a colour from the colour menu
3331 * the name (not the menu item label!) of the colour scheme
3334 public void changeColour_actionPerformed(String name)
3337 * 'User Defined' opens a panel to configure or load a
3338 * user-defined colour scheme
3340 if (ResidueColourScheme.USER_DEFINED.equals(name))
3342 new UserDefinedColours(alignPanel);
3347 * otherwise set the chosen colour scheme (or null for 'None')
3349 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3350 viewport.getAlignment(), viewport.getHiddenRepSequences());
3355 * Actions on setting or changing the alignment colour scheme
3360 public void changeColour(ColourSchemeI cs)
3362 // TODO: pull up to controller method
3363 ColourMenuHelper.setColourSelected(colourMenu, cs);
3365 viewport.setGlobalColourScheme(cs);
3367 alignPanel.paintAlignment(true);
3371 * Show the PID threshold slider panel
3374 protected void modifyPID_actionPerformed()
3376 SliderPanel.setPIDSliderSource(alignPanel,
3377 viewport.getResidueShading(), alignPanel.getViewName());
3378 SliderPanel.showPIDSlider();
3382 * Show the Conservation slider panel
3385 protected void modifyConservation_actionPerformed()
3387 SliderPanel.setConservationSlider(alignPanel,
3388 viewport.getResidueShading(), alignPanel.getViewName());
3389 SliderPanel.showConservationSlider();
3393 * Action on selecting or deselecting (Colour) By Conservation
3396 public void conservationMenuItem_actionPerformed(boolean selected)
3398 modifyConservation.setEnabled(selected);
3399 viewport.setConservationSelected(selected);
3400 viewport.getResidueShading().setConservationApplied(selected);
3402 changeColour(viewport.getGlobalColourScheme());
3405 modifyConservation_actionPerformed();
3409 SliderPanel.hideConservationSlider();
3414 * Action on selecting or deselecting (Colour) Above PID Threshold
3417 public void abovePIDThreshold_actionPerformed(boolean selected)
3419 modifyPID.setEnabled(selected);
3420 viewport.setAbovePIDThreshold(selected);
3423 viewport.getResidueShading().setThreshold(0,
3424 viewport.isIgnoreGapsConsensus());
3427 changeColour(viewport.getGlobalColourScheme());
3430 modifyPID_actionPerformed();
3434 SliderPanel.hidePIDSlider();
3445 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3447 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3448 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3449 .getAlignment().getSequenceAt(0), null);
3450 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3451 viewport.getAlignment()));
3452 alignPanel.paintAlignment(true);
3462 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3464 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3465 AlignmentSorter.sortByID(viewport.getAlignment());
3466 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3467 viewport.getAlignment()));
3468 alignPanel.paintAlignment(true);
3478 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3480 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3481 AlignmentSorter.sortByLength(viewport.getAlignment());
3482 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3483 viewport.getAlignment()));
3484 alignPanel.paintAlignment(true);
3494 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3496 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3497 AlignmentSorter.sortByGroup(viewport.getAlignment());
3498 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3499 viewport.getAlignment()));
3501 alignPanel.paintAlignment(true);
3511 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3513 new RedundancyPanel(alignPanel, this);
3523 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3525 if ((viewport.getSelectionGroup() == null)
3526 || (viewport.getSelectionGroup().getSize() < 2))
3528 JvOptionPane.showInternalMessageDialog(this, MessageManager
3529 .getString("label.you_must_select_least_two_sequences"),
3530 MessageManager.getString("label.invalid_selection"),
3531 JvOptionPane.WARNING_MESSAGE);
3535 JInternalFrame frame = new JInternalFrame();
3536 frame.setContentPane(new PairwiseAlignPanel(viewport));
3537 Desktop.addInternalFrame(frame,
3538 MessageManager.getString("action.pairwise_alignment"), 600,
3550 public void PCAMenuItem_actionPerformed(ActionEvent e)
3552 if (((viewport.getSelectionGroup() != null)
3553 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3554 .getSelectionGroup().getSize() > 0))
3555 || (viewport.getAlignment().getHeight() < 4))
3558 .showInternalMessageDialog(
3561 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3563 .getString("label.sequence_selection_insufficient"),
3564 JvOptionPane.WARNING_MESSAGE);
3569 new PCAPanel(alignPanel);
3573 public void autoCalculate_actionPerformed(ActionEvent e)
3575 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3576 if (viewport.autoCalculateConsensus)
3578 viewport.firePropertyChange("alignment", null, viewport
3579 .getAlignment().getSequences());
3584 public void sortByTreeOption_actionPerformed(ActionEvent e)
3586 viewport.sortByTree = sortByTree.isSelected();
3590 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3592 viewport.followSelection = listenToViewSelections.isSelected();
3602 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3604 newTreePanel("AV", "PID", "Average distance tree using PID");
3614 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3616 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3626 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3628 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3638 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3640 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3653 void newTreePanel(String type, String pwType, String title)
3657 if (viewport.getSelectionGroup() != null
3658 && viewport.getSelectionGroup().getSize() > 0)
3660 if (viewport.getSelectionGroup().getSize() < 3)
3666 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3668 .getString("label.not_enough_sequences"),
3669 JvOptionPane.WARNING_MESSAGE);
3673 SequenceGroup sg = viewport.getSelectionGroup();
3675 /* Decide if the selection is a column region */
3676 for (SequenceI _s : sg.getSequences())
3678 if (_s.getLength() < sg.getEndRes())
3684 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3686 .getString("label.sequences_selection_not_aligned"),
3687 JvOptionPane.WARNING_MESSAGE);
3693 title = title + " on region";
3694 tp = new TreePanel(alignPanel, type, pwType);
3698 // are the visible sequences aligned?
3699 if (!viewport.getAlignment().isAligned(false))
3705 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3707 .getString("label.sequences_not_aligned"),
3708 JvOptionPane.WARNING_MESSAGE);
3713 if (viewport.getAlignment().getHeight() < 2)
3718 tp = new TreePanel(alignPanel, type, pwType);
3723 if (viewport.viewName != null)
3725 title += viewport.viewName + " of ";
3728 title += this.title;
3730 Desktop.addInternalFrame(tp, title, 600, 500);
3741 public void addSortByOrderMenuItem(String title,
3742 final AlignmentOrder order)
3744 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3745 "action.by_title_param", new Object[] { title }));
3747 item.addActionListener(new java.awt.event.ActionListener()
3750 public void actionPerformed(ActionEvent e)
3752 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3754 // TODO: JBPNote - have to map order entries to curent SequenceI
3756 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3758 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3761 alignPanel.paintAlignment(true);
3767 * Add a new sort by annotation score menu item
3770 * the menu to add the option to
3772 * the label used to retrieve scores for each sequence on the
3775 public void addSortByAnnotScoreMenuItem(JMenu sort,
3776 final String scoreLabel)
3778 final JMenuItem item = new JMenuItem(scoreLabel);
3780 item.addActionListener(new java.awt.event.ActionListener()
3783 public void actionPerformed(ActionEvent e)
3785 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3786 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3787 viewport.getAlignment());// ,viewport.getSelectionGroup());
3788 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3789 viewport.getAlignment()));
3790 alignPanel.paintAlignment(true);
3796 * last hash for alignment's annotation array - used to minimise cost of
3799 protected int _annotationScoreVectorHash;
3802 * search the alignment and rebuild the sort by annotation score submenu the
3803 * last alignment annotation vector hash is stored to minimize cost of
3804 * rebuilding in subsequence calls.
3808 public void buildSortByAnnotationScoresMenu()
3810 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3815 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3817 sortByAnnotScore.removeAll();
3818 // almost certainly a quicker way to do this - but we keep it simple
3819 Hashtable scoreSorts = new Hashtable();
3820 AlignmentAnnotation aann[];
3821 for (SequenceI sqa : viewport.getAlignment().getSequences())
3823 aann = sqa.getAnnotation();
3824 for (int i = 0; aann != null && i < aann.length; i++)
3826 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3828 scoreSorts.put(aann[i].label, aann[i].label);
3832 Enumeration labels = scoreSorts.keys();
3833 while (labels.hasMoreElements())
3835 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3836 (String) labels.nextElement());
3838 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3841 _annotationScoreVectorHash = viewport.getAlignment()
3842 .getAlignmentAnnotation().hashCode();
3847 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3848 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3849 * call. Listeners are added to remove the menu item when the treePanel is
3850 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3854 * Displayed tree window.
3856 * SortBy menu item title.
3859 public void buildTreeMenu()
3861 calculateTree.removeAll();
3862 // build the calculate menu
3864 for (final String type : new String[] { "NJ", "AV" })
3866 String treecalcnm = MessageManager.getString("label.tree_calc_"
3867 + type.toLowerCase());
3868 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
3870 JMenuItem tm = new JMenuItem();
3871 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
3872 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
3873 || sm.isProtein() == !viewport.getAlignment()
3876 String smn = MessageManager.getStringOrReturn(
3877 "label.score_model_", sm.getName());
3878 final String title = MessageManager.formatMessage(
3879 "label.treecalc_title", treecalcnm, smn);
3880 tm.setText(title);//
3881 tm.addActionListener(new java.awt.event.ActionListener()
3884 public void actionPerformed(ActionEvent e)
3886 newTreePanel(type, pwtype, title);
3889 calculateTree.add(tm);
3894 sortByTreeMenu.removeAll();
3896 List<Component> comps = PaintRefresher.components.get(viewport
3897 .getSequenceSetId());
3898 List<TreePanel> treePanels = new ArrayList<TreePanel>();
3899 for (Component comp : comps)
3901 if (comp instanceof TreePanel)
3903 treePanels.add((TreePanel) comp);
3907 if (treePanels.size() < 1)
3909 sortByTreeMenu.setVisible(false);
3913 sortByTreeMenu.setVisible(true);
3915 for (final TreePanel tp : treePanels)
3917 final JMenuItem item = new JMenuItem(tp.getTitle());
3918 item.addActionListener(new java.awt.event.ActionListener()
3921 public void actionPerformed(ActionEvent e)
3923 tp.sortByTree_actionPerformed();
3924 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3929 sortByTreeMenu.add(item);
3933 public boolean sortBy(AlignmentOrder alorder, String undoname)
3935 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3936 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3937 if (undoname != null)
3939 addHistoryItem(new OrderCommand(undoname, oldOrder,
3940 viewport.getAlignment()));
3942 alignPanel.paintAlignment(true);
3947 * Work out whether the whole set of sequences or just the selected set will
3948 * be submitted for multiple alignment.
3951 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3953 // Now, check we have enough sequences
3954 AlignmentView msa = null;
3956 if ((viewport.getSelectionGroup() != null)
3957 && (viewport.getSelectionGroup().getSize() > 1))
3959 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3960 // some common interface!
3962 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3963 * SequenceI[sz = seqs.getSize(false)];
3965 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3966 * seqs.getSequenceAt(i); }
3968 msa = viewport.getAlignmentView(true);
3970 else if (viewport.getSelectionGroup() != null
3971 && viewport.getSelectionGroup().getSize() == 1)
3973 int option = JvOptionPane.showConfirmDialog(this,
3974 MessageManager.getString("warn.oneseq_msainput_selection"),
3975 MessageManager.getString("label.invalid_selection"),
3976 JvOptionPane.OK_CANCEL_OPTION);
3977 if (option == JvOptionPane.OK_OPTION)
3979 msa = viewport.getAlignmentView(false);
3984 msa = viewport.getAlignmentView(false);
3990 * Decides what is submitted to a secondary structure prediction service: the
3991 * first sequence in the alignment, or in the current selection, or, if the
3992 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3993 * region or the whole alignment. (where the first sequence in the set is the
3994 * one that the prediction will be for).
3996 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3998 AlignmentView seqs = null;
4000 if ((viewport.getSelectionGroup() != null)
4001 && (viewport.getSelectionGroup().getSize() > 0))
4003 seqs = viewport.getAlignmentView(true);
4007 seqs = viewport.getAlignmentView(false);
4009 // limit sequences - JBPNote in future - could spawn multiple prediction
4011 // TODO: viewport.getAlignment().isAligned is a global state - the local
4012 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4013 if (!viewport.getAlignment().isAligned(false))
4015 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4016 // TODO: if seqs.getSequences().length>1 then should really have warned
4030 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4032 // Pick the tree file
4033 JalviewFileChooser chooser = new JalviewFileChooser(
4034 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4035 chooser.setFileView(new JalviewFileView());
4036 chooser.setDialogTitle(MessageManager
4037 .getString("label.select_newick_like_tree_file"));
4038 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4040 int value = chooser.showOpenDialog(null);
4042 if (value == JalviewFileChooser.APPROVE_OPTION)
4044 String choice = chooser.getSelectedFile().getPath();
4045 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4046 jalview.io.NewickFile fin = null;
4049 fin = new NewickFile(choice, DataSourceType.FILE);
4050 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4051 } catch (Exception ex)
4058 .getString("label.problem_reading_tree_file"),
4059 JvOptionPane.WARNING_MESSAGE);
4060 ex.printStackTrace();
4062 if (fin != null && fin.hasWarningMessage())
4064 JvOptionPane.showMessageDialog(Desktop.desktop, fin
4065 .getWarningMessage(), MessageManager
4066 .getString("label.possible_problem_with_tree_file"),
4067 JvOptionPane.WARNING_MESSAGE);
4072 public TreePanel ShowNewickTree(NewickFile nf, String title)
4074 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4077 public TreePanel ShowNewickTree(NewickFile nf, String title,
4078 AlignmentView input)
4080 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4083 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4084 int h, int x, int y)
4086 return ShowNewickTree(nf, title, null, w, h, x, y);
4090 * Add a treeviewer for the tree extracted from a newick file object to the
4091 * current alignment view
4098 * Associated alignment input data (or null)
4107 * @return TreePanel handle
4109 public TreePanel ShowNewickTree(NewickFile nf, String title,
4110 AlignmentView input, int w, int h, int x, int y)
4112 TreePanel tp = null;
4118 if (nf.getTree() != null)
4120 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4126 tp.setLocation(x, y);
4129 Desktop.addInternalFrame(tp, title, w, h);
4131 } catch (Exception ex)
4133 ex.printStackTrace();
4139 private boolean buildingMenu = false;
4142 * Generates menu items and listener event actions for web service clients
4145 public void BuildWebServiceMenu()
4147 while (buildingMenu)
4151 System.err.println("Waiting for building menu to finish.");
4153 } catch (Exception e)
4157 final AlignFrame me = this;
4158 buildingMenu = true;
4159 new Thread(new Runnable()
4164 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4167 // System.err.println("Building ws menu again "
4168 // + Thread.currentThread());
4169 // TODO: add support for context dependent disabling of services based
4171 // alignment and current selection
4172 // TODO: add additional serviceHandle parameter to specify abstract
4174 // class independently of AbstractName
4175 // TODO: add in rediscovery GUI function to restart discoverer
4176 // TODO: group services by location as well as function and/or
4178 // object broker mechanism.
4179 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4180 final IProgressIndicator af = me;
4183 * do not i18n these strings - they are hard-coded in class
4184 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4185 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4187 final JMenu msawsmenu = new JMenu("Alignment");
4188 final JMenu secstrmenu = new JMenu(
4189 "Secondary Structure Prediction");
4190 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4191 final JMenu analymenu = new JMenu("Analysis");
4192 final JMenu dismenu = new JMenu("Protein Disorder");
4193 // JAL-940 - only show secondary structure prediction services from
4194 // the legacy server
4195 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4197 Discoverer.services != null && (Discoverer.services.size() > 0))
4199 // TODO: refactor to allow list of AbstractName/Handler bindings to
4201 // stored or retrieved from elsewhere
4202 // No MSAWS used any more:
4203 // Vector msaws = null; // (Vector)
4204 // Discoverer.services.get("MsaWS");
4205 Vector secstrpr = (Vector) Discoverer.services
4207 if (secstrpr != null)
4209 // Add any secondary structure prediction services
4210 for (int i = 0, j = secstrpr.size(); i < j; i++)
4212 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4214 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4215 .getServiceClient(sh);
4216 int p = secstrmenu.getItemCount();
4217 impl.attachWSMenuEntry(secstrmenu, me);
4218 int q = secstrmenu.getItemCount();
4219 for (int litm = p; litm < q; litm++)
4221 legacyItems.add(secstrmenu.getItem(litm));
4227 // Add all submenus in the order they should appear on the web
4229 wsmenu.add(msawsmenu);
4230 wsmenu.add(secstrmenu);
4231 wsmenu.add(dismenu);
4232 wsmenu.add(analymenu);
4233 // No search services yet
4234 // wsmenu.add(seqsrchmenu);
4236 javax.swing.SwingUtilities.invokeLater(new Runnable()
4243 webService.removeAll();
4244 // first, add discovered services onto the webservices menu
4245 if (wsmenu.size() > 0)
4247 for (int i = 0, j = wsmenu.size(); i < j; i++)
4249 webService.add(wsmenu.get(i));
4254 webService.add(me.webServiceNoServices);
4256 // TODO: move into separate menu builder class.
4257 boolean new_sspred = false;
4258 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4260 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4261 if (jws2servs != null)
4263 if (jws2servs.hasServices())
4265 jws2servs.attachWSMenuEntry(webService, me);
4266 for (Jws2Instance sv : jws2servs.getServices())
4268 if (sv.description.toLowerCase().contains("jpred"))
4270 for (JMenuItem jmi : legacyItems)
4272 jmi.setVisible(false);
4278 if (jws2servs.isRunning())
4280 JMenuItem tm = new JMenuItem(
4281 "Still discovering JABA Services");
4282 tm.setEnabled(false);
4287 build_urlServiceMenu(me.webService);
4288 build_fetchdbmenu(webService);
4289 for (JMenu item : wsmenu)
4291 if (item.getItemCount() == 0)
4293 item.setEnabled(false);
4297 item.setEnabled(true);
4300 } catch (Exception e)
4303 .debug("Exception during web service menu building process.",
4308 } catch (Exception e)
4311 buildingMenu = false;
4318 * construct any groupURL type service menu entries.
4322 private void build_urlServiceMenu(JMenu webService)
4324 // TODO: remove this code when 2.7 is released
4325 // DEBUG - alignmentView
4327 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4328 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4330 * @Override public void actionPerformed(ActionEvent e) {
4331 * jalview.datamodel.AlignmentView
4332 * .testSelectionViews(af.viewport.getAlignment(),
4333 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4335 * }); webService.add(testAlView);
4337 // TODO: refactor to RestClient discoverer and merge menu entries for
4338 // rest-style services with other types of analysis/calculation service
4339 // SHmmr test client - still being implemented.
4340 // DEBUG - alignmentView
4342 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4345 client.attachWSMenuEntry(
4346 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4352 * Searches the alignment sequences for xRefs and builds the Show
4353 * Cross-References menu (formerly called Show Products), with database
4354 * sources for which cross-references are found (protein sources for a
4355 * nucleotide alignment and vice versa)
4357 * @return true if Show Cross-references menu should be enabled
4359 public boolean canShowProducts()
4361 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4362 AlignmentI dataset = viewport.getAlignment().getDataset();
4364 showProducts.removeAll();
4365 final boolean dna = viewport.getAlignment().isNucleotide();
4367 if (seqs == null || seqs.length == 0)
4369 // nothing to see here.
4373 boolean showp = false;
4376 List<String> ptypes = new CrossRef(seqs, dataset)
4377 .findXrefSourcesForSequences(dna);
4379 for (final String source : ptypes)
4382 final AlignFrame af = this;
4383 JMenuItem xtype = new JMenuItem(source);
4384 xtype.addActionListener(new ActionListener()
4387 public void actionPerformed(ActionEvent e)
4389 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4392 showProducts.add(xtype);
4394 showProducts.setVisible(showp);
4395 showProducts.setEnabled(showp);
4396 } catch (Exception e)
4399 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4407 * Finds and displays cross-references for the selected sequences (protein
4408 * products for nucleotide sequences, dna coding sequences for peptides).
4411 * the sequences to show cross-references for
4413 * true if from a nucleotide alignment (so showing proteins)
4415 * the database to show cross-references for
4417 protected void showProductsFor(final SequenceI[] sel,
4418 final boolean _odna, final String source)
4420 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4425 * Construct and display a new frame containing the translation of this
4426 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4429 public void showTranslation_actionPerformed(ActionEvent e)
4431 AlignmentI al = null;
4434 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4436 al = dna.translateCdna();
4437 } catch (Exception ex)
4439 jalview.bin.Cache.log.error(
4440 "Exception during translation. Please report this !", ex);
4441 final String msg = MessageManager
4442 .getString("label.error_when_translating_sequences_submit_bug_report");
4443 final String errorTitle = MessageManager
4444 .getString("label.implementation_error")
4445 + MessageManager.getString("label.translation_failed");
4446 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4447 JvOptionPane.ERROR_MESSAGE);
4450 if (al == null || al.getHeight() == 0)
4452 final String msg = MessageManager
4453 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4454 final String errorTitle = MessageManager
4455 .getString("label.translation_failed");
4456 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4457 JvOptionPane.WARNING_MESSAGE);
4461 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4462 af.setFileFormat(this.currentFileFormat);
4463 final String newTitle = MessageManager.formatMessage(
4464 "label.translation_of_params",
4465 new Object[] { this.getTitle() });
4466 af.setTitle(newTitle);
4467 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4469 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4470 viewport.openSplitFrame(af, new Alignment(seqs));
4474 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4481 * Set the file format
4485 public void setFileFormat(FileFormatI format)
4487 this.currentFileFormat = format;
4491 * Try to load a features file onto the alignment.
4494 * contents or path to retrieve file
4496 * access mode of file (see jalview.io.AlignFile)
4497 * @return true if features file was parsed correctly.
4499 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4501 return avc.parseFeaturesFile(file, sourceType,
4502 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4507 public void refreshFeatureUI(boolean enableIfNecessary)
4509 // note - currently this is only still here rather than in the controller
4510 // because of the featureSettings hard reference that is yet to be
4512 if (enableIfNecessary)
4514 viewport.setShowSequenceFeatures(true);
4515 showSeqFeatures.setSelected(true);
4521 public void dragEnter(DropTargetDragEvent evt)
4526 public void dragExit(DropTargetEvent evt)
4531 public void dragOver(DropTargetDragEvent evt)
4536 public void dropActionChanged(DropTargetDragEvent evt)
4541 public void drop(DropTargetDropEvent evt)
4543 // JAL-1552 - acceptDrop required before getTransferable call for
4544 // Java's Transferable for native dnd
4545 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4546 Transferable t = evt.getTransferable();
4547 List<String> files = new ArrayList<String>();
4548 List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4552 Desktop.transferFromDropTarget(files, protocols, evt, t);
4553 } catch (Exception e)
4555 e.printStackTrace();
4561 // check to see if any of these files have names matching sequences in
4563 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4564 .getAlignment().getSequencesArray());
4566 * Object[] { String,SequenceI}
4568 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4569 ArrayList<String> filesnotmatched = new ArrayList<String>();
4570 for (int i = 0; i < files.size(); i++)
4572 String file = files.get(i).toString();
4574 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4575 if (protocol == DataSourceType.FILE)
4577 File fl = new File(file);
4578 pdbfn = fl.getName();
4580 else if (protocol == DataSourceType.URL)
4582 URL url = new URL(file);
4583 pdbfn = url.getFile();
4585 if (pdbfn.length() > 0)
4587 // attempt to find a match in the alignment
4588 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4589 int l = 0, c = pdbfn.indexOf(".");
4590 while (mtch == null && c != -1)
4595 } while ((c = pdbfn.indexOf(".", l)) > l);
4598 pdbfn = pdbfn.substring(0, l);
4600 mtch = idm.findAllIdMatches(pdbfn);
4604 FileFormatI type = null;
4607 type = new IdentifyFile().identify(file, protocol);
4608 } catch (Exception ex)
4612 if (type != null && type.isStructureFile())
4614 filesmatched.add(new Object[] { file, protocol, mtch });
4618 // File wasn't named like one of the sequences or wasn't a PDB file.
4619 filesnotmatched.add(file);
4623 if (filesmatched.size() > 0)
4625 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4631 "label.automatically_associate_structure_files_with_sequences_same_name",
4632 new Object[] { Integer
4638 .getString("label.automatically_associate_structure_files_by_name"),
4639 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4642 for (Object[] fm : filesmatched)
4644 // try and associate
4645 // TODO: may want to set a standard ID naming formalism for
4646 // associating PDB files which have no IDs.
4647 for (SequenceI toassoc : (SequenceI[]) fm[2])
4649 PDBEntry pe = new AssociatePdbFileWithSeq()
4650 .associatePdbWithSeq((String) fm[0],
4651 (DataSourceType) fm[1], toassoc, false,
4655 System.err.println("Associated file : "
4656 + ((String) fm[0]) + " with "
4657 + toassoc.getDisplayId(true));
4661 alignPanel.paintAlignment(true);
4665 if (filesnotmatched.size() > 0)
4668 && (Cache.getDefault(
4669 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4675 "label.ignore_unmatched_dropped_files_info",
4676 new Object[] { Integer
4683 .getString("label.ignore_unmatched_dropped_files"),
4684 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4688 for (String fn : filesnotmatched)
4690 loadJalviewDataFile(fn, null, null, null);
4694 } catch (Exception ex)
4696 ex.printStackTrace();
4702 * Attempt to load a "dropped" file or URL string: First by testing whether
4703 * it's an Annotation file, then a JNet file, and finally a features file. If
4704 * all are false then the user may have dropped an alignment file onto this
4708 * either a filename or a URL string.
4710 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4711 FileFormatI format, SequenceI assocSeq)
4715 if (sourceType == null)
4717 sourceType = FormatAdapter.checkProtocol(file);
4719 // if the file isn't identified, or not positively identified as some
4720 // other filetype (PFAM is default unidentified alignment file type) then
4721 // try to parse as annotation.
4722 boolean isAnnotation = (format == null || FileFormat.Pfam
4723 .equals(format)) ? new AnnotationFile()
4724 .annotateAlignmentView(viewport, file, sourceType) : false;
4728 // first see if its a T-COFFEE score file
4729 TCoffeeScoreFile tcf = null;
4732 tcf = new TCoffeeScoreFile(file, sourceType);
4735 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4738 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4739 isAnnotation = true;
4741 .setText(MessageManager
4742 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4746 // some problem - if no warning its probable that the ID matching
4747 // process didn't work
4751 tcf.getWarningMessage() == null ? MessageManager
4752 .getString("label.check_file_matches_sequence_ids_alignment")
4753 : tcf.getWarningMessage(),
4755 .getString("label.problem_reading_tcoffee_score_file"),
4756 JvOptionPane.WARNING_MESSAGE);
4763 } catch (Exception x)
4766 .debug("Exception when processing data source as T-COFFEE score file",
4772 // try to see if its a JNet 'concise' style annotation file *before*
4774 // try to parse it as a features file
4777 format = new IdentifyFile().identify(file, sourceType);
4779 if (FileFormat.Jnet.equals(format))
4781 JPredFile predictions = new JPredFile(file, sourceType);
4782 new JnetAnnotationMaker();
4783 JnetAnnotationMaker.add_annotation(predictions,
4784 viewport.getAlignment(), 0, false);
4785 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4786 viewport.getAlignment().setSeqrep(repseq);
4787 HiddenColumns cs = new HiddenColumns();
4788 cs.hideInsertionsFor(repseq);
4789 viewport.getAlignment().setHiddenColumns(cs);
4790 isAnnotation = true;
4792 // else if (IdentifyFile.FeaturesFile.equals(format))
4793 else if (FileFormat.Features.equals(format))
4795 if (parseFeaturesFile(file, sourceType))
4797 alignPanel.paintAlignment(true);
4802 new FileLoader().LoadFile(viewport, file, sourceType, format);
4809 alignPanel.adjustAnnotationHeight();
4810 viewport.updateSequenceIdColours();
4811 buildSortByAnnotationScoresMenu();
4812 alignPanel.paintAlignment(true);
4814 } catch (Exception ex)
4816 ex.printStackTrace();
4817 } catch (OutOfMemoryError oom)
4822 } catch (Exception x)
4827 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4828 : "using " + sourceType + " from " + file)
4830 + (format != null ? "(parsing as '" + format
4831 + "' file)" : ""), oom, Desktop.desktop);
4836 * Method invoked by the ChangeListener on the tabbed pane, in other words
4837 * when a different tabbed pane is selected by the user or programmatically.
4840 public void tabSelectionChanged(int index)
4844 alignPanel = alignPanels.get(index);
4845 viewport = alignPanel.av;
4846 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4847 setMenusFromViewport(viewport);
4851 * 'focus' any colour slider that is open to the selected viewport
4853 if (viewport.getConservationSelected())
4855 SliderPanel.setConservationSlider(alignPanel,
4856 viewport.getResidueShading(), alignPanel.getViewName());
4860 SliderPanel.hideConservationSlider();
4862 if (viewport.getAbovePIDThreshold())
4864 SliderPanel.setPIDSliderSource(alignPanel,
4865 viewport.getResidueShading(), alignPanel.getViewName());
4869 SliderPanel.hidePIDSlider();
4873 * If there is a frame linked to this one in a SplitPane, switch it to the
4874 * same view tab index. No infinite recursion of calls should happen, since
4875 * tabSelectionChanged() should not get invoked on setting the selected
4876 * index to an unchanged value. Guard against setting an invalid index
4877 * before the new view peer tab has been created.
4879 final AlignViewportI peer = viewport.getCodingComplement();
4882 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4883 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4885 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4891 * On right mouse click on view tab, prompt for and set new view name.
4894 public void tabbedPane_mousePressed(MouseEvent e)
4896 if (e.isPopupTrigger())
4898 String msg = MessageManager.getString("label.enter_view_name");
4899 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4900 JvOptionPane.QUESTION_MESSAGE);
4904 viewport.viewName = reply;
4905 // TODO warn if reply is in getExistingViewNames()?
4906 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4911 public AlignViewport getCurrentView()
4917 * Open the dialog for regex description parsing.
4920 protected void extractScores_actionPerformed(ActionEvent e)
4922 ParseProperties pp = new jalview.analysis.ParseProperties(
4923 viewport.getAlignment());
4924 // TODO: verify regex and introduce GUI dialog for version 2.5
4925 // if (pp.getScoresFromDescription("col", "score column ",
4926 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4928 if (pp.getScoresFromDescription("description column",
4929 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4931 buildSortByAnnotationScoresMenu();
4939 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4943 protected void showDbRefs_actionPerformed(ActionEvent e)
4945 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4951 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4955 protected void showNpFeats_actionPerformed(ActionEvent e)
4957 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4961 * find the viewport amongst the tabs in this alignment frame and close that
4966 public boolean closeView(AlignViewportI av)
4970 this.closeMenuItem_actionPerformed(false);
4973 Component[] comp = tabbedPane.getComponents();
4974 for (int i = 0; comp != null && i < comp.length; i++)
4976 if (comp[i] instanceof AlignmentPanel)
4978 if (((AlignmentPanel) comp[i]).av == av)
4981 closeView((AlignmentPanel) comp[i]);
4989 protected void build_fetchdbmenu(JMenu webService)
4991 // Temporary hack - DBRef Fetcher always top level ws entry.
4992 // TODO We probably want to store a sequence database checklist in
4993 // preferences and have checkboxes.. rather than individual sources selected
4995 final JMenu rfetch = new JMenu(
4996 MessageManager.getString("action.fetch_db_references"));
4997 rfetch.setToolTipText(MessageManager
4998 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4999 webService.add(rfetch);
5001 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5002 MessageManager.getString("option.trim_retrieved_seqs"));
5003 trimrs.setToolTipText(MessageManager
5004 .getString("label.trim_retrieved_sequences"));
5005 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5006 trimrs.addActionListener(new ActionListener()
5009 public void actionPerformed(ActionEvent e)
5011 trimrs.setSelected(trimrs.isSelected());
5012 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5013 Boolean.valueOf(trimrs.isSelected()).toString());
5017 JMenuItem fetchr = new JMenuItem(
5018 MessageManager.getString("label.standard_databases"));
5019 fetchr.setToolTipText(MessageManager
5020 .getString("label.fetch_embl_uniprot"));
5021 fetchr.addActionListener(new ActionListener()
5025 public void actionPerformed(ActionEvent e)
5027 new Thread(new Runnable()
5032 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5033 .getAlignment().isNucleotide();
5034 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5035 .getSequenceSelection(), alignPanel.alignFrame, null,
5036 alignPanel.alignFrame.featureSettings, isNucleotide);
5037 dbRefFetcher.addListener(new FetchFinishedListenerI()
5040 public void finished()
5042 AlignFrame.this.setMenusForViewport();
5045 dbRefFetcher.fetchDBRefs(false);
5053 final AlignFrame me = this;
5054 new Thread(new Runnable()
5059 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5060 .getSequenceFetcherSingleton(me);
5061 javax.swing.SwingUtilities.invokeLater(new Runnable()
5066 String[] dbclasses = sf.getOrderedSupportedSources();
5067 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5068 // jalview.util.QuickSort.sort(otherdb, otherdb);
5069 List<DbSourceProxy> otherdb;
5070 JMenu dfetch = new JMenu();
5071 JMenu ifetch = new JMenu();
5072 JMenuItem fetchr = null;
5073 int comp = 0, icomp = 0, mcomp = 15;
5074 String mname = null;
5076 for (String dbclass : dbclasses)
5078 otherdb = sf.getSourceProxy(dbclass);
5079 // add a single entry for this class, or submenu allowing 'fetch
5081 if (otherdb == null || otherdb.size() < 1)
5085 // List<DbSourceProxy> dbs=otherdb;
5086 // otherdb=new ArrayList<DbSourceProxy>();
5087 // for (DbSourceProxy db:dbs)
5089 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5093 mname = "From " + dbclass;
5095 if (otherdb.size() == 1)
5097 final DbSourceProxy[] dassource = otherdb
5098 .toArray(new DbSourceProxy[0]);
5099 DbSourceProxy src = otherdb.get(0);
5100 fetchr = new JMenuItem(src.getDbSource());
5101 fetchr.addActionListener(new ActionListener()
5105 public void actionPerformed(ActionEvent e)
5107 new Thread(new Runnable()
5113 boolean isNucleotide = alignPanel.alignFrame
5114 .getViewport().getAlignment()
5116 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5117 alignPanel.av.getSequenceSelection(),
5118 alignPanel.alignFrame, dassource,
5119 alignPanel.alignFrame.featureSettings,
5122 .addListener(new FetchFinishedListenerI()
5125 public void finished()
5127 AlignFrame.this.setMenusForViewport();
5130 dbRefFetcher.fetchDBRefs(false);
5136 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5137 MessageManager.formatMessage(
5138 "label.fetch_retrieve_from",
5139 new Object[] { src.getDbName() })));
5145 final DbSourceProxy[] dassource = otherdb
5146 .toArray(new DbSourceProxy[0]);
5148 DbSourceProxy src = otherdb.get(0);
5149 fetchr = new JMenuItem(MessageManager.formatMessage(
5150 "label.fetch_all_param",
5151 new Object[] { src.getDbSource() }));
5152 fetchr.addActionListener(new ActionListener()
5155 public void actionPerformed(ActionEvent e)
5157 new Thread(new Runnable()
5163 boolean isNucleotide = alignPanel.alignFrame
5164 .getViewport().getAlignment()
5166 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5167 alignPanel.av.getSequenceSelection(),
5168 alignPanel.alignFrame, dassource,
5169 alignPanel.alignFrame.featureSettings,
5172 .addListener(new FetchFinishedListenerI()
5175 public void finished()
5177 AlignFrame.this.setMenusForViewport();
5180 dbRefFetcher.fetchDBRefs(false);
5186 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5187 MessageManager.formatMessage(
5188 "label.fetch_retrieve_from_all_sources",
5190 Integer.valueOf(otherdb.size())
5191 .toString(), src.getDbSource(),
5192 src.getDbName() })));
5195 // and then build the rest of the individual menus
5196 ifetch = new JMenu(MessageManager.formatMessage(
5197 "label.source_from_db_source",
5198 new Object[] { src.getDbSource() }));
5200 String imname = null;
5202 for (DbSourceProxy sproxy : otherdb)
5204 String dbname = sproxy.getDbName();
5205 String sname = dbname.length() > 5 ? dbname.substring(0,
5206 5) + "..." : dbname;
5207 String msname = dbname.length() > 10 ? dbname.substring(
5208 0, 10) + "..." : dbname;
5211 imname = MessageManager.formatMessage(
5212 "label.from_msname", new Object[] { sname });
5214 fetchr = new JMenuItem(msname);
5215 final DbSourceProxy[] dassrc = { sproxy };
5216 fetchr.addActionListener(new ActionListener()
5220 public void actionPerformed(ActionEvent e)
5222 new Thread(new Runnable()
5228 boolean isNucleotide = alignPanel.alignFrame
5229 .getViewport().getAlignment()
5231 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5232 alignPanel.av.getSequenceSelection(),
5233 alignPanel.alignFrame, dassrc,
5234 alignPanel.alignFrame.featureSettings,
5237 .addListener(new FetchFinishedListenerI()
5240 public void finished()
5242 AlignFrame.this.setMenusForViewport();
5245 dbRefFetcher.fetchDBRefs(false);
5251 fetchr.setToolTipText("<html>"
5252 + MessageManager.formatMessage(
5253 "label.fetch_retrieve_from", new Object[]
5257 if (++icomp >= mcomp || i == (otherdb.size()))
5259 ifetch.setText(MessageManager.formatMessage(
5260 "label.source_to_target", imname, sname));
5262 ifetch = new JMenu();
5270 if (comp >= mcomp || dbi >= (dbclasses.length))
5272 dfetch.setText(MessageManager.formatMessage(
5273 "label.source_to_target", mname, dbclass));
5275 dfetch = new JMenu();
5288 * Left justify the whole alignment.
5291 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5293 AlignmentI al = viewport.getAlignment();
5295 viewport.firePropertyChange("alignment", null, al);
5299 * Right justify the whole alignment.
5302 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5304 AlignmentI al = viewport.getAlignment();
5306 viewport.firePropertyChange("alignment", null, al);
5310 public void setShowSeqFeatures(boolean b)
5312 showSeqFeatures.setSelected(b);
5313 viewport.setShowSequenceFeatures(b);
5320 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5321 * awt.event.ActionEvent)
5324 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5326 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5327 alignPanel.paintAlignment(true);
5334 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5338 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5340 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5341 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5349 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5350 * .event.ActionEvent)
5353 protected void showGroupConservation_actionPerformed(ActionEvent e)
5355 viewport.setShowGroupConservation(showGroupConservation.getState());
5356 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5363 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5364 * .event.ActionEvent)
5367 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5369 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5370 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5377 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5378 * .event.ActionEvent)
5381 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5383 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5384 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5388 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5390 showSequenceLogo.setState(true);
5391 viewport.setShowSequenceLogo(true);
5392 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5393 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5397 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5399 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5406 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5407 * .event.ActionEvent)
5410 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5412 if (avc.makeGroupsFromSelection())
5414 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5415 alignPanel.updateAnnotation();
5416 alignPanel.paintAlignment(true);
5420 public void clearAlignmentSeqRep()
5422 // TODO refactor alignmentseqrep to controller
5423 if (viewport.getAlignment().hasSeqrep())
5425 viewport.getAlignment().setSeqrep(null);
5426 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5427 alignPanel.updateAnnotation();
5428 alignPanel.paintAlignment(true);
5433 protected void createGroup_actionPerformed(ActionEvent e)
5435 if (avc.createGroup())
5437 alignPanel.alignmentChanged();
5442 protected void unGroup_actionPerformed(ActionEvent e)
5446 alignPanel.alignmentChanged();
5451 * make the given alignmentPanel the currently selected tab
5453 * @param alignmentPanel
5455 public void setDisplayedView(AlignmentPanel alignmentPanel)
5457 if (!viewport.getSequenceSetId().equals(
5458 alignmentPanel.av.getSequenceSetId()))
5462 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5464 if (tabbedPane != null
5465 && tabbedPane.getTabCount() > 0
5466 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5467 .getSelectedIndex())
5469 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5474 * Action on selection of menu options to Show or Hide annotations.
5477 * @param forSequences
5478 * update sequence-related annotations
5479 * @param forAlignment
5480 * update non-sequence-related annotations
5483 protected void setAnnotationsVisibility(boolean visible,
5484 boolean forSequences, boolean forAlignment)
5486 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5487 .getAlignmentAnnotation();
5492 for (AlignmentAnnotation aa : anns)
5495 * don't display non-positional annotations on an alignment
5497 if (aa.annotations == null)
5501 boolean apply = (aa.sequenceRef == null && forAlignment)
5502 || (aa.sequenceRef != null && forSequences);
5505 aa.visible = visible;
5508 alignPanel.validateAnnotationDimensions(true);
5509 alignPanel.alignmentChanged();
5513 * Store selected annotation sort order for the view and repaint.
5516 protected void sortAnnotations_actionPerformed()
5518 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5520 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5521 alignPanel.paintAlignment(true);
5526 * @return alignment panels in this alignment frame
5528 public List<? extends AlignmentViewPanel> getAlignPanels()
5530 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5534 * Open a new alignment window, with the cDNA associated with this (protein)
5535 * alignment, aligned as is the protein.
5537 protected void viewAsCdna_actionPerformed()
5539 // TODO no longer a menu action - refactor as required
5540 final AlignmentI alignment = getViewport().getAlignment();
5541 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5542 if (mappings == null)
5546 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5547 for (SequenceI aaSeq : alignment.getSequences())
5549 for (AlignedCodonFrame acf : mappings)
5551 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5555 * There is a cDNA mapping for this protein sequence - add to new
5556 * alignment. It will share the same dataset sequence as other mapped
5557 * cDNA (no new mappings need to be created).
5559 final Sequence newSeq = new Sequence(dnaSeq);
5560 newSeq.setDatasetSequence(dnaSeq);
5561 cdnaSeqs.add(newSeq);
5565 if (cdnaSeqs.size() == 0)
5567 // show a warning dialog no mapped cDNA
5570 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5572 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5573 AlignFrame.DEFAULT_HEIGHT);
5574 cdna.alignAs(alignment);
5575 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5577 Desktop.addInternalFrame(alignFrame, newtitle,
5578 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5582 * Set visibility of dna/protein complement view (available when shown in a
5588 protected void showComplement_actionPerformed(boolean show)
5590 SplitContainerI sf = getSplitViewContainer();
5593 sf.setComplementVisible(this, show);
5598 * Generate the reverse (optionally complemented) of the selected sequences,
5599 * and add them to the alignment
5602 protected void showReverse_actionPerformed(boolean complement)
5604 AlignmentI al = null;
5607 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5608 al = dna.reverseCdna(complement);
5609 viewport.addAlignment(al, "");
5610 addHistoryItem(new EditCommand(
5611 MessageManager.getString("label.add_sequences"),
5612 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5613 viewport.getAlignment()));
5614 } catch (Exception ex)
5616 System.err.println(ex.getMessage());
5622 * Try to run a script in the Groovy console, having first ensured that this
5623 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5624 * be targeted at this alignment.
5627 protected void runGroovy_actionPerformed()
5629 Jalview.setCurrentAlignFrame(this);
5630 groovy.ui.Console console = Desktop.getGroovyConsole();
5631 if (console != null)
5635 console.runScript();
5636 } catch (Exception ex)
5638 System.err.println((ex.toString()));
5640 .showInternalMessageDialog(Desktop.desktop, MessageManager
5641 .getString("label.couldnt_run_groovy_script"),
5643 .getString("label.groovy_support_failed"),
5644 JvOptionPane.ERROR_MESSAGE);
5649 System.err.println("Can't run Groovy script as console not found");
5654 * Hides columns containing (or not containing) a specified feature, provided
5655 * that would not leave all columns hidden
5657 * @param featureType
5658 * @param columnsContaining
5661 public boolean hideFeatureColumns(String featureType,
5662 boolean columnsContaining)
5664 boolean notForHiding = avc.markColumnsContainingFeatures(
5665 columnsContaining, false, false, featureType);
5668 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5669 false, featureType))
5671 getViewport().hideSelectedColumns();
5679 protected void selectHighlightedColumns_actionPerformed(
5680 ActionEvent actionEvent)
5682 // include key modifier check in case user selects from menu
5683 avc.markHighlightedColumns(
5684 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5686 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5690 * Rebuilds the Colour menu, including any user-defined colours which have
5691 * been loaded either on startup or during the session
5693 public void buildColourMenu()
5695 colourMenu.removeAll();
5697 colourMenu.add(applyToAllGroups);
5698 colourMenu.add(textColour);
5699 colourMenu.addSeparator();
5701 ColourMenuHelper.addMenuItems(colourMenu, this,
5702 viewport.getAlignment(), false);
5704 colourMenu.addSeparator();
5705 colourMenu.add(conservationMenuItem);
5706 colourMenu.add(modifyConservation);
5707 colourMenu.add(abovePIDThreshold);
5708 colourMenu.add(modifyPID);
5709 colourMenu.add(annotationColour);
5711 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5712 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5716 class PrintThread extends Thread
5720 public PrintThread(AlignmentPanel ap)
5725 static PageFormat pf;
5730 PrinterJob printJob = PrinterJob.getPrinterJob();
5734 printJob.setPrintable(ap, pf);
5738 printJob.setPrintable(ap);
5741 if (printJob.printDialog())
5746 } catch (Exception PrintException)
5748 PrintException.printStackTrace();