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.SimilarityParamsI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenSequences;
57 import jalview.datamodel.PDBEntry;
58 import jalview.datamodel.SeqCigar;
59 import jalview.datamodel.Sequence;
60 import jalview.datamodel.SequenceGroup;
61 import jalview.datamodel.SequenceI;
62 import jalview.gui.ColourMenuHelper.ColourChangeListener;
63 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
64 import jalview.io.AlignmentProperties;
65 import jalview.io.AnnotationFile;
66 import jalview.io.BioJsHTMLOutput;
67 import jalview.io.DataSourceType;
68 import jalview.io.FileFormat;
69 import jalview.io.FileFormatI;
70 import jalview.io.FileFormats;
71 import jalview.io.FileLoader;
72 import jalview.io.FileParse;
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.ScoreMatrixFile;
82 import jalview.io.TCoffeeScoreFile;
83 import jalview.jbgui.GAlignFrame;
84 import jalview.schemes.ColourSchemeI;
85 import jalview.schemes.ColourSchemes;
86 import jalview.schemes.ResidueColourScheme;
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, ColumnSelection 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, ColumnSelection 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, ColumnSelection 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 ColumnSelection 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();
368 calculateTree.addActionListener(new ActionListener()
372 public void actionPerformed(ActionEvent e)
379 if (Desktop.desktop != null)
381 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
382 addServiceListeners();
386 if (viewport.getWrapAlignment())
388 wrapMenuItem_actionPerformed(null);
391 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
393 this.overviewMenuItem_actionPerformed(null);
398 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
399 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
400 final String menuLabel = MessageManager
401 .getString("label.copy_format_from");
402 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
403 new ViewSetProvider()
407 public AlignmentPanel[] getAllAlignmentPanels()
410 origview.add(alignPanel);
411 // make an array of all alignment panels except for this one
412 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
413 Arrays.asList(Desktop.getAlignmentPanels(null)));
414 aps.remove(AlignFrame.this.alignPanel);
415 return aps.toArray(new AlignmentPanel[aps.size()]);
417 }, selviews, new ItemListener()
421 public void itemStateChanged(ItemEvent e)
423 if (origview.size() > 0)
425 final AlignmentPanel ap = origview.get(0);
428 * Copy the ViewStyle of the selected panel to 'this one'.
429 * Don't change value of 'scaleProteinAsCdna' unless copying
432 ViewStyleI vs = selviews.get(0).getAlignViewport()
434 boolean fromSplitFrame = selviews.get(0)
435 .getAlignViewport().getCodingComplement() != null;
438 vs.setScaleProteinAsCdna(ap.getAlignViewport()
439 .getViewStyle().isScaleProteinAsCdna());
441 ap.getAlignViewport().setViewStyle(vs);
444 * Also rescale ViewStyle of SplitFrame complement if there is
445 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
446 * the whole ViewStyle (allow cDNA protein to have different
449 AlignViewportI complement = ap.getAlignViewport()
450 .getCodingComplement();
451 if (complement != null && vs.isScaleProteinAsCdna())
453 AlignFrame af = Desktop.getAlignFrameFor(complement);
454 ((SplitFrame) af.getSplitViewContainer())
456 af.setMenusForViewport();
460 ap.setSelected(true);
461 ap.alignFrame.setMenusForViewport();
466 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
467 .indexOf("devel") > -1
468 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
469 .indexOf("test") > -1)
471 formatMenu.add(vsel);
473 addFocusListener(new FocusAdapter()
476 public void focusGained(FocusEvent e)
478 Jalview.setCurrentAlignFrame(AlignFrame.this);
485 * Change the filename and format for the alignment, and enable the 'reload'
486 * button functionality.
493 public void setFileName(String file, FileFormatI format)
496 setFileFormat(format);
497 reload.setEnabled(true);
501 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
504 void addKeyListener()
506 addKeyListener(new KeyAdapter()
509 public void keyPressed(KeyEvent evt)
511 if (viewport.cursorMode
512 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
513 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
514 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
515 && Character.isDigit(evt.getKeyChar()))
517 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
520 switch (evt.getKeyCode())
523 case 27: // escape key
524 deselectAllSequenceMenuItem_actionPerformed(null);
528 case KeyEvent.VK_DOWN:
529 if (evt.isAltDown() || !viewport.cursorMode)
531 moveSelectedSequences(false);
533 if (viewport.cursorMode)
535 alignPanel.getSeqPanel().moveCursor(0, 1);
540 if (evt.isAltDown() || !viewport.cursorMode)
542 moveSelectedSequences(true);
544 if (viewport.cursorMode)
546 alignPanel.getSeqPanel().moveCursor(0, -1);
551 case KeyEvent.VK_LEFT:
552 if (evt.isAltDown() || !viewport.cursorMode)
554 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
558 alignPanel.getSeqPanel().moveCursor(-1, 0);
563 case KeyEvent.VK_RIGHT:
564 if (evt.isAltDown() || !viewport.cursorMode)
566 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
570 alignPanel.getSeqPanel().moveCursor(1, 0);
574 case KeyEvent.VK_SPACE:
575 if (viewport.cursorMode)
577 alignPanel.getSeqPanel().insertGapAtCursor(
578 evt.isControlDown() || evt.isShiftDown()
583 // case KeyEvent.VK_A:
584 // if (viewport.cursorMode)
586 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
587 // //System.out.println("A");
591 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
592 * System.out.println("closing bracket"); } break;
594 case KeyEvent.VK_DELETE:
595 case KeyEvent.VK_BACK_SPACE:
596 if (!viewport.cursorMode)
598 cut_actionPerformed(null);
602 alignPanel.getSeqPanel().deleteGapAtCursor(
603 evt.isControlDown() || evt.isShiftDown()
610 if (viewport.cursorMode)
612 alignPanel.getSeqPanel().setCursorRow();
616 if (viewport.cursorMode && !evt.isControlDown())
618 alignPanel.getSeqPanel().setCursorColumn();
622 if (viewport.cursorMode)
624 alignPanel.getSeqPanel().setCursorPosition();
628 case KeyEvent.VK_ENTER:
629 case KeyEvent.VK_COMMA:
630 if (viewport.cursorMode)
632 alignPanel.getSeqPanel().setCursorRowAndColumn();
637 if (viewport.cursorMode)
639 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
643 if (viewport.cursorMode)
645 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
650 viewport.cursorMode = !viewport.cursorMode;
651 statusBar.setText(MessageManager.formatMessage(
652 "label.keyboard_editing_mode",
653 new String[] { (viewport.cursorMode ? "on" : "off") }));
654 if (viewport.cursorMode)
656 alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
658 alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
661 alignPanel.getSeqPanel().seqCanvas.repaint();
667 Help.showHelpWindow();
668 } catch (Exception ex)
670 ex.printStackTrace();
675 boolean toggleSeqs = !evt.isControlDown();
676 boolean toggleCols = !evt.isShiftDown();
677 toggleHiddenRegions(toggleSeqs, toggleCols);
682 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
683 boolean modifyExisting = true; // always modify, don't clear
684 // evt.isShiftDown();
685 boolean invertHighlighted = evt.isAltDown();
686 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
690 case KeyEvent.VK_PAGE_UP:
691 if (viewport.getWrapAlignment())
693 alignPanel.scrollUp(true);
697 alignPanel.setScrollValues(vpRanges.getStartRes(),
698 2 * vpRanges.getStartSeq() - vpRanges.getEndSeq());
701 case KeyEvent.VK_PAGE_DOWN:
702 if (viewport.getWrapAlignment())
704 alignPanel.scrollUp(false);
708 alignPanel.setScrollValues(vpRanges.getStartRes(),
709 vpRanges.getEndSeq());
716 public void keyReleased(KeyEvent evt)
718 switch (evt.getKeyCode())
720 case KeyEvent.VK_LEFT:
721 if (evt.isAltDown() || !viewport.cursorMode)
723 viewport.firePropertyChange("alignment", null, viewport
724 .getAlignment().getSequences());
728 case KeyEvent.VK_RIGHT:
729 if (evt.isAltDown() || !viewport.cursorMode)
731 viewport.firePropertyChange("alignment", null, viewport
732 .getAlignment().getSequences());
740 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
742 ap.alignFrame = this;
743 avc = new jalview.controller.AlignViewController(this, viewport,
748 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
750 int aSize = alignPanels.size();
752 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
754 if (aSize == 1 && ap.av.viewName == null)
756 this.getContentPane().add(ap, BorderLayout.CENTER);
762 setInitialTabVisible();
765 expandViews.setEnabled(true);
766 gatherViews.setEnabled(true);
767 tabbedPane.addTab(ap.av.viewName, ap);
769 ap.setVisible(false);
774 if (ap.av.isPadGaps())
776 ap.av.getAlignment().padGaps();
778 ap.av.updateConservation(ap);
779 ap.av.updateConsensus(ap);
780 ap.av.updateStrucConsensus(ap);
784 public void setInitialTabVisible()
786 expandViews.setEnabled(true);
787 gatherViews.setEnabled(true);
788 tabbedPane.setVisible(true);
789 AlignmentPanel first = alignPanels.get(0);
790 tabbedPane.addTab(first.av.viewName, first);
791 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
794 public AlignViewport getViewport()
799 /* Set up intrinsic listeners for dynamically generated GUI bits. */
800 private void addServiceListeners()
802 final java.beans.PropertyChangeListener thisListener;
803 Desktop.instance.addJalviewPropertyChangeListener("services",
804 thisListener = new java.beans.PropertyChangeListener()
807 public void propertyChange(PropertyChangeEvent evt)
809 // // System.out.println("Discoverer property change.");
810 // if (evt.getPropertyName().equals("services"))
812 SwingUtilities.invokeLater(new Runnable()
819 .println("Rebuild WS Menu for service change");
820 BuildWebServiceMenu();
827 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
830 public void internalFrameClosed(
831 javax.swing.event.InternalFrameEvent evt)
833 // System.out.println("deregistering discoverer listener");
834 Desktop.instance.removeJalviewPropertyChangeListener("services",
836 closeMenuItem_actionPerformed(true);
839 // Finally, build the menu once to get current service state
840 new Thread(new Runnable()
845 BuildWebServiceMenu();
851 * Configure menu items that vary according to whether the alignment is
852 * nucleotide or protein
854 public void setGUINucleotide()
856 AlignmentI al = getViewport().getAlignment();
857 boolean nucleotide = al.isNucleotide();
859 showTranslation.setVisible(nucleotide);
860 showReverse.setVisible(nucleotide);
861 showReverseComplement.setVisible(nucleotide);
862 conservationMenuItem.setEnabled(!nucleotide);
863 modifyConservation.setEnabled(!nucleotide
864 && conservationMenuItem.isSelected());
865 showGroupConservation.setEnabled(!nucleotide);
867 showComplementMenuItem.setText(nucleotide ? MessageManager
868 .getString("label.protein") : MessageManager
869 .getString("label.nucleotide"));
873 * set up menus for the current viewport. This may be called after any
874 * operation that affects the data in the current view (selection changed,
875 * etc) to update the menus to reflect the new state.
878 public void setMenusForViewport()
880 setMenusFromViewport(viewport);
884 * Need to call this method when tabs are selected for multiple views, or when
885 * loading from Jalview2XML.java
890 void setMenusFromViewport(AlignViewport av)
892 padGapsMenuitem.setSelected(av.isPadGaps());
893 colourTextMenuItem.setSelected(av.isShowColourText());
894 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
895 modifyPID.setEnabled(abovePIDThreshold.isSelected());
896 conservationMenuItem.setSelected(av.getConservationSelected());
897 modifyConservation.setEnabled(conservationMenuItem.isSelected());
898 seqLimits.setSelected(av.getShowJVSuffix());
899 idRightAlign.setSelected(av.isRightAlignIds());
900 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
901 renderGapsMenuItem.setSelected(av.isRenderGaps());
902 wrapMenuItem.setSelected(av.getWrapAlignment());
903 scaleAbove.setVisible(av.getWrapAlignment());
904 scaleLeft.setVisible(av.getWrapAlignment());
905 scaleRight.setVisible(av.getWrapAlignment());
906 annotationPanelMenuItem.setState(av.isShowAnnotation());
908 * Show/hide annotations only enabled if annotation panel is shown
910 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
911 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
912 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
913 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
914 viewBoxesMenuItem.setSelected(av.getShowBoxes());
915 viewTextMenuItem.setSelected(av.getShowText());
916 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
917 showGroupConsensus.setSelected(av.isShowGroupConsensus());
918 showGroupConservation.setSelected(av.isShowGroupConservation());
919 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
920 showSequenceLogo.setSelected(av.isShowSequenceLogo());
921 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
923 ColourMenuHelper.setColourSelected(colourMenu,
924 av.getGlobalColourScheme());
926 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
927 hiddenMarkers.setState(av.getShowHiddenMarkers());
928 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
929 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
930 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
931 autoCalculate.setSelected(av.autoCalculateConsensus);
932 sortByTree.setSelected(av.sortByTree);
933 listenToViewSelections.setSelected(av.followSelection);
935 showProducts.setEnabled(canShowProducts());
936 setGroovyEnabled(Desktop.getGroovyConsole() != null);
942 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
946 public void setGroovyEnabled(boolean b)
948 runGroovy.setEnabled(b);
951 private IProgressIndicator progressBar;
956 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
959 public void setProgressBar(String message, long id)
961 progressBar.setProgressBar(message, id);
965 public void registerHandler(final long id,
966 final IProgressIndicatorHandler handler)
968 progressBar.registerHandler(id, handler);
973 * @return true if any progress bars are still active
976 public boolean operationInProgress()
978 return progressBar.operationInProgress();
982 public void setStatus(String text)
984 statusBar.setText(text);
988 * Added so Castor Mapping file can obtain Jalview Version
990 public String getVersion()
992 return jalview.bin.Cache.getProperty("VERSION");
995 public FeatureRenderer getFeatureRenderer()
997 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1001 public void fetchSequence_actionPerformed(ActionEvent e)
1003 new jalview.gui.SequenceFetcher(this);
1007 public void addFromFile_actionPerformed(ActionEvent e)
1009 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1013 public void reload_actionPerformed(ActionEvent e)
1015 if (fileName != null)
1017 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1018 // originating file's format
1019 // TODO: work out how to recover feature settings for correct view(s) when
1020 // file is reloaded.
1021 if (FileFormat.Jalview.equals(currentFileFormat))
1023 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1024 for (int i = 0; i < frames.length; i++)
1026 if (frames[i] instanceof AlignFrame && frames[i] != this
1027 && ((AlignFrame) frames[i]).fileName != null
1028 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1032 frames[i].setSelected(true);
1033 Desktop.instance.closeAssociatedWindows();
1034 } catch (java.beans.PropertyVetoException ex)
1040 Desktop.instance.closeAssociatedWindows();
1042 FileLoader loader = new FileLoader();
1043 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1044 : DataSourceType.FILE;
1045 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1049 Rectangle bounds = this.getBounds();
1051 FileLoader loader = new FileLoader();
1052 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1053 : DataSourceType.FILE;
1054 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1055 protocol, currentFileFormat);
1057 newframe.setBounds(bounds);
1058 if (featureSettings != null && featureSettings.isShowing())
1060 final Rectangle fspos = featureSettings.frame.getBounds();
1061 // TODO: need a 'show feature settings' function that takes bounds -
1062 // need to refactor Desktop.addFrame
1063 newframe.featureSettings_actionPerformed(null);
1064 final FeatureSettings nfs = newframe.featureSettings;
1065 SwingUtilities.invokeLater(new Runnable()
1070 nfs.frame.setBounds(fspos);
1073 this.featureSettings.close();
1074 this.featureSettings = null;
1076 this.closeMenuItem_actionPerformed(true);
1082 public void addFromText_actionPerformed(ActionEvent e)
1084 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1089 public void addFromURL_actionPerformed(ActionEvent e)
1091 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1095 public void save_actionPerformed(ActionEvent e)
1097 if (fileName == null || (currentFileFormat == null)
1098 || fileName.startsWith("http"))
1100 saveAs_actionPerformed(null);
1104 saveAlignment(fileName, currentFileFormat);
1115 public void saveAs_actionPerformed(ActionEvent e)
1117 String format = currentFileFormat == null ? null : currentFileFormat
1119 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1120 Cache.getProperty("LAST_DIRECTORY"), format);
1122 chooser.setFileView(new JalviewFileView());
1123 chooser.setDialogTitle(MessageManager
1124 .getString("label.save_alignment_to_file"));
1125 chooser.setToolTipText(MessageManager.getString("action.save"));
1127 int value = chooser.showSaveDialog(this);
1129 if (value == JalviewFileChooser.APPROVE_OPTION)
1131 currentFileFormat = chooser.getSelectedFormat();
1132 while (currentFileFormat == null)
1135 .showInternalMessageDialog(
1138 .getString("label.select_file_format_before_saving"),
1140 .getString("label.file_format_not_specified"),
1141 JvOptionPane.WARNING_MESSAGE);
1142 currentFileFormat = chooser.getSelectedFormat();
1143 value = chooser.showSaveDialog(this);
1144 if (value != JalviewFileChooser.APPROVE_OPTION)
1150 fileName = chooser.getSelectedFile().getPath();
1152 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1154 Cache.setProperty("LAST_DIRECTORY", fileName);
1155 saveAlignment(fileName, currentFileFormat);
1159 public boolean saveAlignment(String file, FileFormatI format)
1161 boolean success = true;
1163 if (FileFormat.Jalview.equals(format))
1165 String shortName = title;
1167 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1169 shortName = shortName.substring(shortName
1170 .lastIndexOf(java.io.File.separatorChar) + 1);
1173 success = new Jalview2XML().saveAlignment(this, file, shortName);
1175 statusBar.setText(MessageManager.formatMessage(
1176 "label.successfully_saved_to_file_in_format", new Object[] {
1177 fileName, format }));
1182 AlignmentExportData exportData = getAlignmentForExport(format,
1184 if (exportData.getSettings().isCancelled())
1188 FormatAdapter f = new FormatAdapter(alignPanel,
1189 exportData.getSettings());
1190 String output = f.formatSequences(
1192 exportData.getAlignment(), // class cast exceptions will
1193 // occur in the distant future
1194 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1195 f.getCacheSuffixDefault(format),
1196 viewport.getColumnSelection());
1206 PrintWriter out = new PrintWriter(new FileWriter(file));
1210 this.setTitle(file);
1211 statusBar.setText(MessageManager.formatMessage(
1212 "label.successfully_saved_to_file_in_format",
1213 new Object[] { fileName, format.getName() }));
1214 } catch (Exception ex)
1217 ex.printStackTrace();
1224 JvOptionPane.showInternalMessageDialog(this, MessageManager
1225 .formatMessage("label.couldnt_save_file",
1226 new Object[] { fileName }), MessageManager
1227 .getString("label.error_saving_file"),
1228 JvOptionPane.WARNING_MESSAGE);
1234 private void warningMessage(String warning, String title)
1236 if (new jalview.util.Platform().isHeadless())
1238 System.err.println("Warning: " + title + "\nWarning: " + warning);
1243 JvOptionPane.showInternalMessageDialog(this, warning, title,
1244 JvOptionPane.WARNING_MESSAGE);
1256 protected void outputText_actionPerformed(ActionEvent e)
1258 FileFormatI fileFormat = FileFormats.getInstance().forName(
1259 e.getActionCommand());
1260 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1262 if (exportData.getSettings().isCancelled())
1266 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1267 cap.setForInput(null);
1270 FileFormatI format = fileFormat;
1271 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1272 .formatSequences(format, exportData.getAlignment(),
1273 exportData.getOmitHidden(),
1274 exportData.getStartEndPostions(),
1275 viewport.getColumnSelection()));
1276 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1277 "label.alignment_output_command",
1278 new Object[] { e.getActionCommand() }), 600, 500);
1279 } catch (OutOfMemoryError oom)
1281 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1287 public static AlignmentExportData getAlignmentForExport(
1288 FileFormatI format, AlignViewportI viewport,
1289 AlignExportSettingI exportSettings)
1291 AlignmentI alignmentToExport = null;
1292 AlignExportSettingI settings = exportSettings;
1293 String[] omitHidden = null;
1295 HiddenSequences hiddenSeqs = viewport.getAlignment()
1296 .getHiddenSequences();
1298 alignmentToExport = viewport.getAlignment();
1300 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1301 if (settings == null)
1303 settings = new AlignExportSettings(hasHiddenSeqs,
1304 viewport.hasHiddenColumns(), format);
1306 // settings.isExportAnnotations();
1308 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1310 omitHidden = viewport.getViewAsString(false,
1311 settings.isExportHiddenSequences());
1314 int[] alignmentStartEnd = new int[2];
1315 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1317 alignmentToExport = hiddenSeqs.getFullAlignment();
1321 alignmentToExport = viewport.getAlignment();
1323 alignmentStartEnd = alignmentToExport
1324 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1325 .getHiddenColumns());
1326 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1327 omitHidden, alignmentStartEnd, settings);
1338 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1340 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1341 htmlSVG.exportHTML(null);
1345 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1347 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1348 bjs.exportHTML(null);
1351 public void createImageMap(File file, String image)
1353 alignPanel.makePNGImageMap(file, image);
1363 public void createPNG(File f)
1365 alignPanel.makePNG(f);
1375 public void createEPS(File f)
1377 alignPanel.makeEPS(f);
1381 public void createSVG(File f)
1383 alignPanel.makeSVG(f);
1387 public void pageSetup_actionPerformed(ActionEvent e)
1389 PrinterJob printJob = PrinterJob.getPrinterJob();
1390 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1400 public void printMenuItem_actionPerformed(ActionEvent e)
1402 // Putting in a thread avoids Swing painting problems
1403 PrintThread thread = new PrintThread(alignPanel);
1408 public void exportFeatures_actionPerformed(ActionEvent e)
1410 new AnnotationExporter().exportFeatures(alignPanel);
1414 public void exportAnnotations_actionPerformed(ActionEvent e)
1416 new AnnotationExporter().exportAnnotations(alignPanel);
1420 public void associatedData_actionPerformed(ActionEvent e)
1422 // Pick the tree file
1423 JalviewFileChooser chooser = new JalviewFileChooser(
1424 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1425 chooser.setFileView(new JalviewFileView());
1426 chooser.setDialogTitle(MessageManager
1427 .getString("label.load_jalview_annotations"));
1428 chooser.setToolTipText(MessageManager
1429 .getString("label.load_jalview_annotations"));
1431 int value = chooser.showOpenDialog(null);
1433 if (value == JalviewFileChooser.APPROVE_OPTION)
1435 String choice = chooser.getSelectedFile().getPath();
1436 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1437 loadJalviewDataFile(choice, null, null, null);
1443 * Close the current view or all views in the alignment frame. If the frame
1444 * only contains one view then the alignment will be removed from memory.
1446 * @param closeAllTabs
1449 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1451 if (alignPanels != null && alignPanels.size() < 2)
1453 closeAllTabs = true;
1458 if (alignPanels != null)
1462 if (this.isClosed())
1464 // really close all the windows - otherwise wait till
1465 // setClosed(true) is called
1466 for (int i = 0; i < alignPanels.size(); i++)
1468 AlignmentPanel ap = alignPanels.get(i);
1475 closeView(alignPanel);
1482 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1483 * be called recursively, with the frame now in 'closed' state
1485 this.setClosed(true);
1487 } catch (Exception ex)
1489 ex.printStackTrace();
1494 * Close the specified panel and close up tabs appropriately.
1496 * @param panelToClose
1498 public void closeView(AlignmentPanel panelToClose)
1500 int index = tabbedPane.getSelectedIndex();
1501 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1502 alignPanels.remove(panelToClose);
1503 panelToClose.closePanel();
1504 panelToClose = null;
1506 tabbedPane.removeTabAt(closedindex);
1507 tabbedPane.validate();
1509 if (index > closedindex || index == tabbedPane.getTabCount())
1511 // modify currently selected tab index if necessary.
1515 this.tabSelectionChanged(index);
1521 void updateEditMenuBar()
1524 if (viewport.getHistoryList().size() > 0)
1526 undoMenuItem.setEnabled(true);
1527 CommandI command = viewport.getHistoryList().peek();
1528 undoMenuItem.setText(MessageManager.formatMessage(
1529 "label.undo_command",
1530 new Object[] { command.getDescription() }));
1534 undoMenuItem.setEnabled(false);
1535 undoMenuItem.setText(MessageManager.getString("action.undo"));
1538 if (viewport.getRedoList().size() > 0)
1540 redoMenuItem.setEnabled(true);
1542 CommandI command = viewport.getRedoList().peek();
1543 redoMenuItem.setText(MessageManager.formatMessage(
1544 "label.redo_command",
1545 new Object[] { command.getDescription() }));
1549 redoMenuItem.setEnabled(false);
1550 redoMenuItem.setText(MessageManager.getString("action.redo"));
1555 public void addHistoryItem(CommandI command)
1557 if (command.getSize() > 0)
1559 viewport.addToHistoryList(command);
1560 viewport.clearRedoList();
1561 updateEditMenuBar();
1562 viewport.updateHiddenColumns();
1563 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1564 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1565 // viewport.getColumnSelection()
1566 // .getHiddenColumns().size() > 0);
1572 * @return alignment objects for all views
1574 AlignmentI[] getViewAlignments()
1576 if (alignPanels != null)
1578 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1580 for (AlignmentPanel ap : alignPanels)
1582 als[i++] = ap.av.getAlignment();
1586 if (viewport != null)
1588 return new AlignmentI[] { viewport.getAlignment() };
1600 protected void undoMenuItem_actionPerformed(ActionEvent e)
1602 if (viewport.getHistoryList().isEmpty())
1606 CommandI command = viewport.getHistoryList().pop();
1607 viewport.addToRedoList(command);
1608 command.undoCommand(getViewAlignments());
1610 AlignmentViewport originalSource = getOriginatingSource(command);
1611 updateEditMenuBar();
1613 if (originalSource != null)
1615 if (originalSource != viewport)
1618 .warn("Implementation worry: mismatch of viewport origin for undo");
1620 originalSource.updateHiddenColumns();
1621 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1623 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1624 // viewport.getColumnSelection()
1625 // .getHiddenColumns().size() > 0);
1626 originalSource.firePropertyChange("alignment", null, originalSource
1627 .getAlignment().getSequences());
1638 protected void redoMenuItem_actionPerformed(ActionEvent e)
1640 if (viewport.getRedoList().size() < 1)
1645 CommandI command = viewport.getRedoList().pop();
1646 viewport.addToHistoryList(command);
1647 command.doCommand(getViewAlignments());
1649 AlignmentViewport originalSource = getOriginatingSource(command);
1650 updateEditMenuBar();
1652 if (originalSource != null)
1655 if (originalSource != viewport)
1658 .warn("Implementation worry: mismatch of viewport origin for redo");
1660 originalSource.updateHiddenColumns();
1661 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1663 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1664 // viewport.getColumnSelection()
1665 // .getHiddenColumns().size() > 0);
1666 originalSource.firePropertyChange("alignment", null, originalSource
1667 .getAlignment().getSequences());
1671 AlignmentViewport getOriginatingSource(CommandI command)
1673 AlignmentViewport originalSource = null;
1674 // For sequence removal and addition, we need to fire
1675 // the property change event FROM the viewport where the
1676 // original alignment was altered
1677 AlignmentI al = null;
1678 if (command instanceof EditCommand)
1680 EditCommand editCommand = (EditCommand) command;
1681 al = editCommand.getAlignment();
1682 List<Component> comps = PaintRefresher.components.get(viewport
1683 .getSequenceSetId());
1685 for (Component comp : comps)
1687 if (comp instanceof AlignmentPanel)
1689 if (al == ((AlignmentPanel) comp).av.getAlignment())
1691 originalSource = ((AlignmentPanel) comp).av;
1698 if (originalSource == null)
1700 // The original view is closed, we must validate
1701 // the current view against the closed view first
1704 PaintRefresher.validateSequences(al, viewport.getAlignment());
1707 originalSource = viewport;
1710 return originalSource;
1719 public void moveSelectedSequences(boolean up)
1721 SequenceGroup sg = viewport.getSelectionGroup();
1727 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1728 viewport.getHiddenRepSequences(), up);
1729 alignPanel.paintAlignment(true);
1732 synchronized void slideSequences(boolean right, int size)
1734 List<SequenceI> sg = new ArrayList<SequenceI>();
1735 if (viewport.cursorMode)
1737 sg.add(viewport.getAlignment().getSequenceAt(
1738 alignPanel.getSeqPanel().seqCanvas.cursorY));
1740 else if (viewport.getSelectionGroup() != null
1741 && viewport.getSelectionGroup().getSize() != viewport
1742 .getAlignment().getHeight())
1744 sg = viewport.getSelectionGroup().getSequences(
1745 viewport.getHiddenRepSequences());
1753 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1755 for (SequenceI seq : viewport.getAlignment().getSequences())
1757 if (!sg.contains(seq))
1759 invertGroup.add(seq);
1763 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1765 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1766 for (int i = 0; i < invertGroup.size(); i++)
1768 seqs2[i] = invertGroup.get(i);
1771 SlideSequencesCommand ssc;
1774 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1775 size, viewport.getGapCharacter());
1779 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1780 size, viewport.getGapCharacter());
1783 int groupAdjustment = 0;
1784 if (ssc.getGapsInsertedBegin() && right)
1786 if (viewport.cursorMode)
1788 alignPanel.getSeqPanel().moveCursor(size, 0);
1792 groupAdjustment = size;
1795 else if (!ssc.getGapsInsertedBegin() && !right)
1797 if (viewport.cursorMode)
1799 alignPanel.getSeqPanel().moveCursor(-size, 0);
1803 groupAdjustment = -size;
1807 if (groupAdjustment != 0)
1809 viewport.getSelectionGroup().setStartRes(
1810 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1811 viewport.getSelectionGroup().setEndRes(
1812 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1816 * just extend the last slide command if compatible; but not if in
1817 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1819 boolean appendHistoryItem = false;
1820 Deque<CommandI> historyList = viewport.getHistoryList();
1821 boolean inSplitFrame = getSplitViewContainer() != null;
1822 if (!inSplitFrame && historyList != null && historyList.size() > 0
1823 && historyList.peek() instanceof SlideSequencesCommand)
1825 appendHistoryItem = ssc
1826 .appendSlideCommand((SlideSequencesCommand) historyList
1830 if (!appendHistoryItem)
1832 addHistoryItem(ssc);
1845 protected void copy_actionPerformed(ActionEvent e)
1848 if (viewport.getSelectionGroup() == null)
1852 // TODO: preserve the ordering of displayed alignment annotation in any
1853 // internal paste (particularly sequence associated annotation)
1854 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1855 String[] omitHidden = null;
1857 if (viewport.hasHiddenColumns())
1859 omitHidden = viewport.getViewAsString(true);
1862 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1863 seqs, omitHidden, null);
1865 StringSelection ss = new StringSelection(output);
1869 jalview.gui.Desktop.internalCopy = true;
1870 // Its really worth setting the clipboard contents
1871 // to empty before setting the large StringSelection!!
1872 Toolkit.getDefaultToolkit().getSystemClipboard()
1873 .setContents(new StringSelection(""), null);
1875 Toolkit.getDefaultToolkit().getSystemClipboard()
1876 .setContents(ss, Desktop.instance);
1877 } catch (OutOfMemoryError er)
1879 new OOMWarning("copying region", er);
1883 ArrayList<int[]> hiddenColumns = null;
1884 if (viewport.hasHiddenColumns())
1886 hiddenColumns = new ArrayList<int[]>();
1887 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1888 .getSelectionGroup().getEndRes();
1889 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1891 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1893 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1894 region[1] - hiddenOffset });
1899 Desktop.jalviewClipboard = new Object[] { seqs,
1900 viewport.getAlignment().getDataset(), hiddenColumns };
1901 statusBar.setText(MessageManager.formatMessage(
1902 "label.copied_sequences_to_clipboard", new Object[] { Integer
1903 .valueOf(seqs.length).toString() }));
1913 protected void pasteNew_actionPerformed(ActionEvent e)
1925 protected void pasteThis_actionPerformed(ActionEvent e)
1931 * Paste contents of Jalview clipboard
1933 * @param newAlignment
1934 * true to paste to a new alignment, otherwise add to this.
1936 void paste(boolean newAlignment)
1938 boolean externalPaste = true;
1941 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1942 Transferable contents = c.getContents(this);
1944 if (contents == null)
1953 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1954 if (str.length() < 1)
1959 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1961 } catch (OutOfMemoryError er)
1963 new OOMWarning("Out of memory pasting sequences!!", er);
1967 SequenceI[] sequences;
1968 boolean annotationAdded = false;
1969 AlignmentI alignment = null;
1971 if (Desktop.jalviewClipboard != null)
1973 // The clipboard was filled from within Jalview, we must use the
1975 // And dataset from the copied alignment
1976 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1977 // be doubly sure that we create *new* sequence objects.
1978 sequences = new SequenceI[newseq.length];
1979 for (int i = 0; i < newseq.length; i++)
1981 sequences[i] = new Sequence(newseq[i]);
1983 alignment = new Alignment(sequences);
1984 externalPaste = false;
1988 // parse the clipboard as an alignment.
1989 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1991 sequences = alignment.getSequencesArray();
1995 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2001 if (Desktop.jalviewClipboard != null)
2003 // dataset is inherited
2004 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2008 // new dataset is constructed
2009 alignment.setDataset(null);
2011 alwidth = alignment.getWidth() + 1;
2015 AlignmentI pastedal = alignment; // preserve pasted alignment object
2016 // Add pasted sequences and dataset into existing alignment.
2017 alignment = viewport.getAlignment();
2018 alwidth = alignment.getWidth() + 1;
2019 // decide if we need to import sequences from an existing dataset
2020 boolean importDs = Desktop.jalviewClipboard != null
2021 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2022 // importDs==true instructs us to copy over new dataset sequences from
2023 // an existing alignment
2024 Vector newDs = (importDs) ? new Vector() : null; // used to create
2025 // minimum dataset set
2027 for (int i = 0; i < sequences.length; i++)
2031 newDs.addElement(null);
2033 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2035 if (importDs && ds != null)
2037 if (!newDs.contains(ds))
2039 newDs.setElementAt(ds, i);
2040 ds = new Sequence(ds);
2041 // update with new dataset sequence
2042 sequences[i].setDatasetSequence(ds);
2046 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2051 // copy and derive new dataset sequence
2052 sequences[i] = sequences[i].deriveSequence();
2053 alignment.getDataset().addSequence(
2054 sequences[i].getDatasetSequence());
2055 // TODO: avoid creation of duplicate dataset sequences with a
2056 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2058 alignment.addSequence(sequences[i]); // merges dataset
2062 newDs.clear(); // tidy up
2064 if (alignment.getAlignmentAnnotation() != null)
2066 for (AlignmentAnnotation alan : alignment
2067 .getAlignmentAnnotation())
2069 if (alan.graphGroup > fgroup)
2071 fgroup = alan.graphGroup;
2075 if (pastedal.getAlignmentAnnotation() != null)
2077 // Add any annotation attached to alignment.
2078 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2079 for (int i = 0; i < alann.length; i++)
2081 annotationAdded = true;
2082 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2084 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2085 if (newann.graphGroup > -1)
2087 if (newGraphGroups.size() <= newann.graphGroup
2088 || newGraphGroups.get(newann.graphGroup) == null)
2090 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2092 newGraphGroups.add(q, null);
2094 newGraphGroups.set(newann.graphGroup, new Integer(
2097 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2101 newann.padAnnotation(alwidth);
2102 alignment.addAnnotation(newann);
2112 addHistoryItem(new EditCommand(
2113 MessageManager.getString("label.add_sequences"),
2114 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2116 // Add any annotations attached to sequences
2117 for (int i = 0; i < sequences.length; i++)
2119 if (sequences[i].getAnnotation() != null)
2121 AlignmentAnnotation newann;
2122 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2124 annotationAdded = true;
2125 newann = sequences[i].getAnnotation()[a];
2126 newann.adjustForAlignment();
2127 newann.padAnnotation(alwidth);
2128 if (newann.graphGroup > -1)
2130 if (newann.graphGroup > -1)
2132 if (newGraphGroups.size() <= newann.graphGroup
2133 || newGraphGroups.get(newann.graphGroup) == null)
2135 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2137 newGraphGroups.add(q, null);
2139 newGraphGroups.set(newann.graphGroup, new Integer(
2142 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2146 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2151 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2158 // propagate alignment changed.
2159 vpRanges.setEndSeq(alignment.getHeight());
2160 if (annotationAdded)
2162 // Duplicate sequence annotation in all views.
2163 AlignmentI[] alview = this.getViewAlignments();
2164 for (int i = 0; i < sequences.length; i++)
2166 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2171 for (int avnum = 0; avnum < alview.length; avnum++)
2173 if (alview[avnum] != alignment)
2175 // duplicate in a view other than the one with input focus
2176 int avwidth = alview[avnum].getWidth() + 1;
2177 // this relies on sann being preserved after we
2178 // modify the sequence's annotation array for each duplication
2179 for (int a = 0; a < sann.length; a++)
2181 AlignmentAnnotation newann = new AlignmentAnnotation(
2183 sequences[i].addAlignmentAnnotation(newann);
2184 newann.padAnnotation(avwidth);
2185 alview[avnum].addAnnotation(newann); // annotation was
2186 // duplicated earlier
2187 // TODO JAL-1145 graphGroups are not updated for sequence
2188 // annotation added to several views. This may cause
2190 alview[avnum].setAnnotationIndex(newann, a);
2195 buildSortByAnnotationScoresMenu();
2197 viewport.firePropertyChange("alignment", null,
2198 alignment.getSequences());
2199 if (alignPanels != null)
2201 for (AlignmentPanel ap : alignPanels)
2203 ap.validateAnnotationDimensions(false);
2208 alignPanel.validateAnnotationDimensions(false);
2214 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2216 String newtitle = new String("Copied sequences");
2218 if (Desktop.jalviewClipboard != null
2219 && Desktop.jalviewClipboard[2] != null)
2221 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2222 for (int[] region : hc)
2224 af.viewport.hideColumns(region[0], region[1]);
2228 // >>>This is a fix for the moment, until a better solution is
2230 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2232 alignPanel.getSeqPanel().seqCanvas
2233 .getFeatureRenderer());
2235 // TODO: maintain provenance of an alignment, rather than just make the
2236 // title a concatenation of operations.
2239 if (title.startsWith("Copied sequences"))
2245 newtitle = newtitle.concat("- from " + title);
2250 newtitle = new String("Pasted sequences");
2253 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2258 } catch (Exception ex)
2260 ex.printStackTrace();
2261 System.out.println("Exception whilst pasting: " + ex);
2262 // could be anything being pasted in here
2268 protected void expand_newalign(ActionEvent e)
2272 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2273 .getAlignment(), -1);
2274 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2276 String newtitle = new String("Flanking alignment");
2278 if (Desktop.jalviewClipboard != null
2279 && Desktop.jalviewClipboard[2] != null)
2281 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2282 for (int region[] : hc)
2284 af.viewport.hideColumns(region[0], region[1]);
2288 // >>>This is a fix for the moment, until a better solution is
2290 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2292 alignPanel.getSeqPanel().seqCanvas
2293 .getFeatureRenderer());
2295 // TODO: maintain provenance of an alignment, rather than just make the
2296 // title a concatenation of operations.
2298 if (title.startsWith("Copied sequences"))
2304 newtitle = newtitle.concat("- from " + title);
2308 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2310 } catch (Exception ex)
2312 ex.printStackTrace();
2313 System.out.println("Exception whilst pasting: " + ex);
2314 // could be anything being pasted in here
2315 } catch (OutOfMemoryError oom)
2317 new OOMWarning("Viewing flanking region of alignment", oom);
2328 protected void cut_actionPerformed(ActionEvent e)
2330 copy_actionPerformed(null);
2331 delete_actionPerformed(null);
2341 protected void delete_actionPerformed(ActionEvent evt)
2344 SequenceGroup sg = viewport.getSelectionGroup();
2351 * If the cut affects all sequences, warn, remove highlighted columns
2353 if (sg.getSize() == viewport.getAlignment().getHeight())
2355 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2356 .getAlignment().getWidth()) ? true : false;
2357 if (isEntireAlignWidth)
2359 int confirm = JvOptionPane.showConfirmDialog(this,
2360 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2361 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2362 JvOptionPane.OK_CANCEL_OPTION);
2364 if (confirm == JvOptionPane.CANCEL_OPTION
2365 || confirm == JvOptionPane.CLOSED_OPTION)
2370 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2371 sg.getEndRes() + 1);
2373 SequenceI[] cut = sg.getSequences()
2374 .toArray(new SequenceI[sg.getSize()]);
2376 addHistoryItem(new EditCommand(
2377 MessageManager.getString("label.cut_sequences"), Action.CUT,
2378 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2379 viewport.getAlignment()));
2381 viewport.setSelectionGroup(null);
2382 viewport.sendSelection();
2383 viewport.getAlignment().deleteGroup(sg);
2385 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2387 if (viewport.getAlignment().getHeight() < 1)
2391 this.setClosed(true);
2392 } catch (Exception ex)
2405 protected void deleteGroups_actionPerformed(ActionEvent e)
2407 if (avc.deleteGroups())
2409 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2410 alignPanel.updateAnnotation();
2411 alignPanel.paintAlignment(true);
2422 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2424 SequenceGroup sg = new SequenceGroup();
2426 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2428 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2431 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2432 viewport.setSelectionGroup(sg);
2433 viewport.sendSelection();
2434 // JAL-2034 - should delegate to
2435 // alignPanel to decide if overview needs
2437 alignPanel.paintAlignment(false);
2438 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2448 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2450 if (viewport.cursorMode)
2452 alignPanel.getSeqPanel().keyboardNo1 = null;
2453 alignPanel.getSeqPanel().keyboardNo2 = null;
2455 viewport.setSelectionGroup(null);
2456 viewport.getColumnSelection().clear();
2457 viewport.setSelectionGroup(null);
2458 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2459 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2460 // JAL-2034 - should delegate to
2461 // alignPanel to decide if overview needs
2463 alignPanel.paintAlignment(false);
2464 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2465 viewport.sendSelection();
2475 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2477 SequenceGroup sg = viewport.getSelectionGroup();
2481 selectAllSequenceMenuItem_actionPerformed(null);
2486 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2488 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2490 // JAL-2034 - should delegate to
2491 // alignPanel to decide if overview needs
2494 alignPanel.paintAlignment(true);
2495 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2496 viewport.sendSelection();
2500 public void invertColSel_actionPerformed(ActionEvent e)
2502 viewport.invertColumnSelection();
2503 alignPanel.paintAlignment(true);
2504 viewport.sendSelection();
2514 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2516 trimAlignment(true);
2526 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2528 trimAlignment(false);
2531 void trimAlignment(boolean trimLeft)
2533 ColumnSelection colSel = viewport.getColumnSelection();
2536 if (!colSel.isEmpty())
2540 column = colSel.getMin();
2544 column = colSel.getMax();
2548 if (viewport.getSelectionGroup() != null)
2550 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2551 viewport.getHiddenRepSequences());
2555 seqs = viewport.getAlignment().getSequencesArray();
2558 TrimRegionCommand trimRegion;
2561 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2562 column, viewport.getAlignment());
2563 vpRanges.setStartRes(0);
2567 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2568 column, viewport.getAlignment());
2571 statusBar.setText(MessageManager.formatMessage(
2572 "label.removed_columns",
2573 new String[] { Integer.valueOf(trimRegion.getSize())
2576 addHistoryItem(trimRegion);
2578 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2580 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2581 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2583 viewport.getAlignment().deleteGroup(sg);
2587 viewport.firePropertyChange("alignment", null, viewport
2588 .getAlignment().getSequences());
2599 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2601 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2604 if (viewport.getSelectionGroup() != null)
2606 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2607 viewport.getHiddenRepSequences());
2608 start = viewport.getSelectionGroup().getStartRes();
2609 end = viewport.getSelectionGroup().getEndRes();
2613 seqs = viewport.getAlignment().getSequencesArray();
2616 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2617 "Remove Gapped Columns", seqs, start, end,
2618 viewport.getAlignment());
2620 addHistoryItem(removeGapCols);
2622 statusBar.setText(MessageManager.formatMessage(
2623 "label.removed_empty_columns",
2624 new Object[] { Integer.valueOf(removeGapCols.getSize())
2627 // This is to maintain viewport position on first residue
2628 // of first sequence
2629 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2630 int startRes = seq.findPosition(vpRanges.getStartRes());
2631 // ShiftList shifts;
2632 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2633 // edit.alColumnChanges=shifts.getInverse();
2634 // if (viewport.hasHiddenColumns)
2635 // viewport.getColumnSelection().compensateForEdits(shifts);
2636 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2637 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2649 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2651 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2654 if (viewport.getSelectionGroup() != null)
2656 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2657 viewport.getHiddenRepSequences());
2658 start = viewport.getSelectionGroup().getStartRes();
2659 end = viewport.getSelectionGroup().getEndRes();
2663 seqs = viewport.getAlignment().getSequencesArray();
2666 // This is to maintain viewport position on first residue
2667 // of first sequence
2668 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2669 int startRes = seq.findPosition(vpRanges.getStartRes());
2671 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2672 viewport.getAlignment()));
2674 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2676 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2688 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2690 viewport.setPadGaps(padGapsMenuitem.isSelected());
2691 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2702 public void findMenuItem_actionPerformed(ActionEvent e)
2708 * Create a new view of the current alignment.
2711 public void newView_actionPerformed(ActionEvent e)
2713 newView(null, true);
2717 * Creates and shows a new view of the current alignment.
2720 * title of newly created view; if null, one will be generated
2721 * @param copyAnnotation
2722 * if true then duplicate all annnotation, groups and settings
2723 * @return new alignment panel, already displayed.
2725 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2728 * Create a new AlignmentPanel (with its own, new Viewport)
2730 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2732 if (!copyAnnotation)
2735 * remove all groups and annotation except for the automatic stuff
2737 newap.av.getAlignment().deleteAllGroups();
2738 newap.av.getAlignment().deleteAllAnnotations(false);
2741 newap.av.setGatherViewsHere(false);
2743 if (viewport.viewName == null)
2745 viewport.viewName = MessageManager
2746 .getString("label.view_name_original");
2750 * Views share the same edits undo and redo stacks
2752 newap.av.setHistoryList(viewport.getHistoryList());
2753 newap.av.setRedoList(viewport.getRedoList());
2756 * Views share the same mappings; need to deregister any new mappings
2757 * created by copyAlignPanel, and register the new reference to the shared
2760 newap.av.replaceMappings(viewport.getAlignment());
2763 * start up cDNA consensus (if applicable) now mappings are in place
2765 if (newap.av.initComplementConsensus())
2767 newap.refresh(true); // adjust layout of annotations
2770 newap.av.viewName = getNewViewName(viewTitle);
2772 addAlignmentPanel(newap, true);
2773 newap.alignmentChanged();
2775 if (alignPanels.size() == 2)
2777 viewport.setGatherViewsHere(true);
2779 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2784 * Make a new name for the view, ensuring it is unique within the current
2785 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2786 * these now use viewId. Unique view names are still desirable for usability.)
2791 protected String getNewViewName(String viewTitle)
2793 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2794 boolean addFirstIndex = false;
2795 if (viewTitle == null || viewTitle.trim().length() == 0)
2797 viewTitle = MessageManager.getString("action.view");
2798 addFirstIndex = true;
2802 index = 1;// we count from 1 if given a specific name
2804 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2806 List<Component> comps = PaintRefresher.components.get(viewport
2807 .getSequenceSetId());
2809 List<String> existingNames = getExistingViewNames(comps);
2811 while (existingNames.contains(newViewName))
2813 newViewName = viewTitle + " " + (++index);
2819 * Returns a list of distinct view names found in the given list of
2820 * components. View names are held on the viewport of an AlignmentPanel.
2825 protected List<String> getExistingViewNames(List<Component> comps)
2827 List<String> existingNames = new ArrayList<String>();
2828 for (Component comp : comps)
2830 if (comp instanceof AlignmentPanel)
2832 AlignmentPanel ap = (AlignmentPanel) comp;
2833 if (!existingNames.contains(ap.av.viewName))
2835 existingNames.add(ap.av.viewName);
2839 return existingNames;
2843 * Explode tabbed views into separate windows.
2846 public void expandViews_actionPerformed(ActionEvent e)
2848 Desktop.explodeViews(this);
2852 * Gather views in separate windows back into a tabbed presentation.
2855 public void gatherViews_actionPerformed(ActionEvent e)
2857 Desktop.instance.gatherViews(this);
2867 public void font_actionPerformed(ActionEvent e)
2869 new FontChooser(alignPanel);
2879 protected void seqLimit_actionPerformed(ActionEvent e)
2881 viewport.setShowJVSuffix(seqLimits.isSelected());
2883 alignPanel.getIdPanel().getIdCanvas()
2884 .setPreferredSize(alignPanel.calculateIdWidth());
2885 alignPanel.paintAlignment(true);
2889 public void idRightAlign_actionPerformed(ActionEvent e)
2891 viewport.setRightAlignIds(idRightAlign.isSelected());
2892 alignPanel.paintAlignment(true);
2896 public void centreColumnLabels_actionPerformed(ActionEvent e)
2898 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2899 alignPanel.paintAlignment(true);
2905 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2908 protected void followHighlight_actionPerformed()
2911 * Set the 'follow' flag on the Viewport (and scroll to position if now
2914 final boolean state = this.followHighlightMenuItem.getState();
2915 viewport.setFollowHighlight(state);
2918 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2929 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2931 viewport.setColourText(colourTextMenuItem.isSelected());
2932 alignPanel.paintAlignment(true);
2942 public void wrapMenuItem_actionPerformed(ActionEvent e)
2944 scaleAbove.setVisible(wrapMenuItem.isSelected());
2945 scaleLeft.setVisible(wrapMenuItem.isSelected());
2946 scaleRight.setVisible(wrapMenuItem.isSelected());
2947 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2948 alignPanel.updateLayout();
2952 public void showAllSeqs_actionPerformed(ActionEvent e)
2954 viewport.showAllHiddenSeqs();
2958 public void showAllColumns_actionPerformed(ActionEvent e)
2960 viewport.showAllHiddenColumns();
2962 viewport.sendSelection();
2966 public void hideSelSequences_actionPerformed(ActionEvent e)
2968 viewport.hideAllSelectedSeqs();
2969 // alignPanel.paintAlignment(true);
2973 * called by key handler and the hide all/show all menu items
2978 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2981 boolean hide = false;
2982 SequenceGroup sg = viewport.getSelectionGroup();
2983 if (!toggleSeqs && !toggleCols)
2985 // Hide everything by the current selection - this is a hack - we do the
2986 // invert and then hide
2987 // first check that there will be visible columns after the invert.
2988 if (viewport.hasSelectedColumns()
2989 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2992 // now invert the sequence set, if required - empty selection implies
2993 // that no hiding is required.
2996 invertSequenceMenuItem_actionPerformed(null);
2997 sg = viewport.getSelectionGroup();
3001 viewport.expandColSelection(sg, true);
3002 // finally invert the column selection and get the new sequence
3004 invertColSel_actionPerformed(null);
3011 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3013 hideSelSequences_actionPerformed(null);
3016 else if (!(toggleCols && viewport.hasSelectedColumns()))
3018 showAllSeqs_actionPerformed(null);
3024 if (viewport.hasSelectedColumns())
3026 hideSelColumns_actionPerformed(null);
3029 viewport.setSelectionGroup(sg);
3034 showAllColumns_actionPerformed(null);
3043 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3044 * event.ActionEvent)
3047 public void hideAllButSelection_actionPerformed(ActionEvent e)
3049 toggleHiddenRegions(false, false);
3050 viewport.sendSelection();
3057 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3061 public void hideAllSelection_actionPerformed(ActionEvent e)
3063 SequenceGroup sg = viewport.getSelectionGroup();
3064 viewport.expandColSelection(sg, false);
3065 viewport.hideAllSelectedSeqs();
3066 viewport.hideSelectedColumns();
3067 alignPanel.paintAlignment(true);
3068 viewport.sendSelection();
3075 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3079 public void showAllhidden_actionPerformed(ActionEvent e)
3081 viewport.showAllHiddenColumns();
3082 viewport.showAllHiddenSeqs();
3083 alignPanel.paintAlignment(true);
3084 viewport.sendSelection();
3088 public void hideSelColumns_actionPerformed(ActionEvent e)
3090 viewport.hideSelectedColumns();
3091 alignPanel.paintAlignment(true);
3092 viewport.sendSelection();
3096 public void hiddenMarkers_actionPerformed(ActionEvent e)
3098 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3109 protected void scaleAbove_actionPerformed(ActionEvent e)
3111 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3112 alignPanel.paintAlignment(true);
3122 protected void scaleLeft_actionPerformed(ActionEvent e)
3124 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3125 alignPanel.paintAlignment(true);
3135 protected void scaleRight_actionPerformed(ActionEvent e)
3137 viewport.setScaleRightWrapped(scaleRight.isSelected());
3138 alignPanel.paintAlignment(true);
3148 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3150 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3151 alignPanel.paintAlignment(true);
3161 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3163 viewport.setShowText(viewTextMenuItem.isSelected());
3164 alignPanel.paintAlignment(true);
3174 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3176 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3177 alignPanel.paintAlignment(true);
3180 public FeatureSettings featureSettings;
3183 public FeatureSettingsControllerI getFeatureSettingsUI()
3185 return featureSettings;
3189 public void featureSettings_actionPerformed(ActionEvent e)
3191 if (featureSettings != null)
3193 featureSettings.close();
3194 featureSettings = null;
3196 if (!showSeqFeatures.isSelected())
3198 // make sure features are actually displayed
3199 showSeqFeatures.setSelected(true);
3200 showSeqFeatures_actionPerformed(null);
3202 featureSettings = new FeatureSettings(this);
3206 * Set or clear 'Show Sequence Features'
3212 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3214 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3215 alignPanel.paintAlignment(true);
3216 if (alignPanel.getOverviewPanel() != null)
3218 alignPanel.getOverviewPanel().updateOverviewImage();
3223 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3224 * the annotations panel as a whole.
3226 * The options to show/hide all annotations should be enabled when the panel
3227 * is shown, and disabled when the panel is hidden.
3232 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3234 final boolean setVisible = annotationPanelMenuItem.isSelected();
3235 viewport.setShowAnnotation(setVisible);
3236 this.showAllSeqAnnotations.setEnabled(setVisible);
3237 this.hideAllSeqAnnotations.setEnabled(setVisible);
3238 this.showAllAlAnnotations.setEnabled(setVisible);
3239 this.hideAllAlAnnotations.setEnabled(setVisible);
3240 alignPanel.updateLayout();
3244 public void alignmentProperties()
3246 JEditorPane editPane = new JEditorPane("text/html", "");
3247 editPane.setEditable(false);
3248 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3250 editPane.setText(MessageManager.formatMessage("label.html_content",
3251 new Object[] { contents.toString() }));
3252 JInternalFrame frame = new JInternalFrame();
3253 frame.getContentPane().add(new JScrollPane(editPane));
3255 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3256 "label.alignment_properties", new Object[] { getTitle() }),
3267 public void overviewMenuItem_actionPerformed(ActionEvent e)
3269 if (alignPanel.overviewPanel != null)
3274 JInternalFrame frame = new JInternalFrame();
3275 OverviewPanel overview = new OverviewPanel(alignPanel);
3276 frame.setContentPane(overview);
3277 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3278 "label.overview_params", new Object[] { this.getTitle() }),
3279 frame.getWidth(), frame.getHeight());
3281 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3282 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3285 public void internalFrameClosed(
3286 javax.swing.event.InternalFrameEvent evt)
3288 alignPanel.setOverviewPanel(null);
3292 alignPanel.setOverviewPanel(overview);
3296 public void textColour_actionPerformed()
3298 new TextColourChooser().chooseColour(alignPanel, null);
3302 * public void covariationColour_actionPerformed() {
3304 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3308 public void annotationColour_actionPerformed()
3310 new AnnotationColourChooser(viewport, alignPanel);
3314 public void annotationColumn_actionPerformed(ActionEvent e)
3316 new AnnotationColumnChooser(viewport, alignPanel);
3320 * Action on the user checking or unchecking the option to apply the selected
3321 * colour scheme to all groups. If unchecked, groups may have their own
3322 * independent colour schemes.
3327 public void applyToAllGroups_actionPerformed(boolean selected)
3329 viewport.setColourAppliesToAllGroups(selected);
3333 * Action on user selecting a colour from the colour menu
3336 * the name (not the menu item label!) of the colour scheme
3339 public void changeColour_actionPerformed(String name)
3342 * 'User Defined' opens a panel to configure or load a
3343 * user-defined colour scheme
3345 if (ResidueColourScheme.USER_DEFINED.equals(name))
3347 new UserDefinedColours(alignPanel);
3352 * otherwise set the chosen colour scheme (or null for 'None')
3354 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3355 viewport.getAlignment(), viewport.getHiddenRepSequences());
3360 * Actions on setting or changing the alignment colour scheme
3365 public void changeColour(ColourSchemeI cs)
3367 // TODO: pull up to controller method
3368 ColourMenuHelper.setColourSelected(colourMenu, cs);
3370 viewport.setGlobalColourScheme(cs);
3372 alignPanel.paintAlignment(true);
3376 * Show the PID threshold slider panel
3379 protected void modifyPID_actionPerformed()
3381 SliderPanel.setPIDSliderSource(alignPanel,
3382 viewport.getResidueShading(), alignPanel.getViewName());
3383 SliderPanel.showPIDSlider();
3387 * Show the Conservation slider panel
3390 protected void modifyConservation_actionPerformed()
3392 SliderPanel.setConservationSlider(alignPanel,
3393 viewport.getResidueShading(), alignPanel.getViewName());
3394 SliderPanel.showConservationSlider();
3398 * Action on selecting or deselecting (Colour) By Conservation
3401 public void conservationMenuItem_actionPerformed(boolean selected)
3403 modifyConservation.setEnabled(selected);
3404 viewport.setConservationSelected(selected);
3405 viewport.getResidueShading().setConservationApplied(selected);
3407 changeColour(viewport.getGlobalColourScheme());
3410 modifyConservation_actionPerformed();
3414 SliderPanel.hideConservationSlider();
3419 * Action on selecting or deselecting (Colour) Above PID Threshold
3422 public void abovePIDThreshold_actionPerformed(boolean selected)
3424 modifyPID.setEnabled(selected);
3425 viewport.setAbovePIDThreshold(selected);
3428 viewport.getResidueShading().setThreshold(0,
3429 viewport.isIgnoreGapsConsensus());
3432 changeColour(viewport.getGlobalColourScheme());
3435 modifyPID_actionPerformed();
3439 SliderPanel.hidePIDSlider();
3450 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3452 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3453 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3454 .getAlignment().getSequenceAt(0));
3455 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3456 viewport.getAlignment()));
3457 alignPanel.paintAlignment(true);
3467 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3469 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3470 AlignmentSorter.sortByID(viewport.getAlignment());
3471 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3472 viewport.getAlignment()));
3473 alignPanel.paintAlignment(true);
3483 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3485 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3486 AlignmentSorter.sortByLength(viewport.getAlignment());
3487 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3488 viewport.getAlignment()));
3489 alignPanel.paintAlignment(true);
3499 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3501 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3502 AlignmentSorter.sortByGroup(viewport.getAlignment());
3503 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3504 viewport.getAlignment()));
3506 alignPanel.paintAlignment(true);
3516 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3518 new RedundancyPanel(alignPanel, this);
3528 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3530 if ((viewport.getSelectionGroup() == null)
3531 || (viewport.getSelectionGroup().getSize() < 2))
3533 JvOptionPane.showInternalMessageDialog(this, MessageManager
3534 .getString("label.you_must_select_least_two_sequences"),
3535 MessageManager.getString("label.invalid_selection"),
3536 JvOptionPane.WARNING_MESSAGE);
3540 JInternalFrame frame = new JInternalFrame();
3541 frame.setContentPane(new PairwiseAlignPanel(viewport));
3542 Desktop.addInternalFrame(frame,
3543 MessageManager.getString("action.pairwise_alignment"), 600,
3549 public void autoCalculate_actionPerformed(ActionEvent e)
3551 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3552 if (viewport.autoCalculateConsensus)
3554 viewport.firePropertyChange("alignment", null, viewport
3555 .getAlignment().getSequences());
3560 public void sortByTreeOption_actionPerformed(ActionEvent e)
3562 viewport.sortByTree = sortByTree.isSelected();
3566 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3568 viewport.followSelection = listenToViewSelections.isSelected();
3572 * Constructs a tree panel and adds it to the desktop
3575 * tree type (NJ or AV)
3577 * name of score model used to compute the tree
3579 * parameters for the distance or similarity calculation
3581 void newTreePanel(String type, String modelName, SimilarityParamsI options)
3583 String frameTitle = "";
3586 boolean onSelection = false;
3587 if (viewport.getSelectionGroup() != null
3588 && viewport.getSelectionGroup().getSize() > 0)
3590 if (viewport.getSelectionGroup().getSize() < 3)
3596 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3598 .getString("label.not_enough_sequences"),
3599 JvOptionPane.WARNING_MESSAGE);
3603 SequenceGroup sg = viewport.getSelectionGroup();
3605 /* Decide if the selection is a column region */
3606 for (SequenceI _s : sg.getSequences())
3608 if (_s.getLength() < sg.getEndRes())
3614 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3616 .getString("label.sequences_selection_not_aligned"),
3617 JvOptionPane.WARNING_MESSAGE);
3626 if (viewport.getAlignment().getHeight() < 2)
3632 tp = new TreePanel(alignPanel, type, modelName, options);
3633 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3635 frameTitle += " from ";
3637 if (viewport.viewName != null)
3639 frameTitle += viewport.viewName + " of ";
3642 frameTitle += this.title;
3644 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3655 public void addSortByOrderMenuItem(String title,
3656 final AlignmentOrder order)
3658 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3659 "action.by_title_param", new Object[] { title }));
3661 item.addActionListener(new java.awt.event.ActionListener()
3664 public void actionPerformed(ActionEvent e)
3666 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3668 // TODO: JBPNote - have to map order entries to curent SequenceI
3670 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3672 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3675 alignPanel.paintAlignment(true);
3681 * Add a new sort by annotation score menu item
3684 * the menu to add the option to
3686 * the label used to retrieve scores for each sequence on the
3689 public void addSortByAnnotScoreMenuItem(JMenu sort,
3690 final String scoreLabel)
3692 final JMenuItem item = new JMenuItem(scoreLabel);
3694 item.addActionListener(new java.awt.event.ActionListener()
3697 public void actionPerformed(ActionEvent e)
3699 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3700 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3701 viewport.getAlignment());// ,viewport.getSelectionGroup());
3702 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3703 viewport.getAlignment()));
3704 alignPanel.paintAlignment(true);
3710 * last hash for alignment's annotation array - used to minimise cost of
3713 protected int _annotationScoreVectorHash;
3716 * search the alignment and rebuild the sort by annotation score submenu the
3717 * last alignment annotation vector hash is stored to minimize cost of
3718 * rebuilding in subsequence calls.
3722 public void buildSortByAnnotationScoresMenu()
3724 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3729 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3731 sortByAnnotScore.removeAll();
3732 // almost certainly a quicker way to do this - but we keep it simple
3733 Hashtable scoreSorts = new Hashtable();
3734 AlignmentAnnotation aann[];
3735 for (SequenceI sqa : viewport.getAlignment().getSequences())
3737 aann = sqa.getAnnotation();
3738 for (int i = 0; aann != null && i < aann.length; i++)
3740 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3742 scoreSorts.put(aann[i].label, aann[i].label);
3746 Enumeration labels = scoreSorts.keys();
3747 while (labels.hasMoreElements())
3749 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3750 (String) labels.nextElement());
3752 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3755 _annotationScoreVectorHash = viewport.getAlignment()
3756 .getAlignmentAnnotation().hashCode();
3761 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3762 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3763 * call. Listeners are added to remove the menu item when the treePanel is
3764 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3768 public void buildTreeSortMenu()
3770 sortByTreeMenu.removeAll();
3772 List<Component> comps = PaintRefresher.components.get(viewport
3773 .getSequenceSetId());
3774 List<TreePanel> treePanels = new ArrayList<TreePanel>();
3775 for (Component comp : comps)
3777 if (comp instanceof TreePanel)
3779 treePanels.add((TreePanel) comp);
3783 if (treePanels.size() < 1)
3785 sortByTreeMenu.setVisible(false);
3789 sortByTreeMenu.setVisible(true);
3791 for (final TreePanel tp : treePanels)
3793 final JMenuItem item = new JMenuItem(tp.getTitle());
3794 item.addActionListener(new java.awt.event.ActionListener()
3797 public void actionPerformed(ActionEvent e)
3799 tp.sortByTree_actionPerformed();
3800 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3805 sortByTreeMenu.add(item);
3809 public boolean sortBy(AlignmentOrder alorder, String undoname)
3811 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3812 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3813 if (undoname != null)
3815 addHistoryItem(new OrderCommand(undoname, oldOrder,
3816 viewport.getAlignment()));
3818 alignPanel.paintAlignment(true);
3823 * Work out whether the whole set of sequences or just the selected set will
3824 * be submitted for multiple alignment.
3827 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3829 // Now, check we have enough sequences
3830 AlignmentView msa = null;
3832 if ((viewport.getSelectionGroup() != null)
3833 && (viewport.getSelectionGroup().getSize() > 1))
3835 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3836 // some common interface!
3838 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3839 * SequenceI[sz = seqs.getSize(false)];
3841 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3842 * seqs.getSequenceAt(i); }
3844 msa = viewport.getAlignmentView(true);
3846 else if (viewport.getSelectionGroup() != null
3847 && viewport.getSelectionGroup().getSize() == 1)
3849 int option = JvOptionPane.showConfirmDialog(this,
3850 MessageManager.getString("warn.oneseq_msainput_selection"),
3851 MessageManager.getString("label.invalid_selection"),
3852 JvOptionPane.OK_CANCEL_OPTION);
3853 if (option == JvOptionPane.OK_OPTION)
3855 msa = viewport.getAlignmentView(false);
3860 msa = viewport.getAlignmentView(false);
3866 * Decides what is submitted to a secondary structure prediction service: the
3867 * first sequence in the alignment, or in the current selection, or, if the
3868 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3869 * region or the whole alignment. (where the first sequence in the set is the
3870 * one that the prediction will be for).
3872 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3874 AlignmentView seqs = null;
3876 if ((viewport.getSelectionGroup() != null)
3877 && (viewport.getSelectionGroup().getSize() > 0))
3879 seqs = viewport.getAlignmentView(true);
3883 seqs = viewport.getAlignmentView(false);
3885 // limit sequences - JBPNote in future - could spawn multiple prediction
3887 // TODO: viewport.getAlignment().isAligned is a global state - the local
3888 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3889 if (!viewport.getAlignment().isAligned(false))
3891 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3892 // TODO: if seqs.getSequences().length>1 then should really have warned
3906 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3908 // Pick the tree file
3909 JalviewFileChooser chooser = new JalviewFileChooser(
3910 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3911 chooser.setFileView(new JalviewFileView());
3912 chooser.setDialogTitle(MessageManager
3913 .getString("label.select_newick_like_tree_file"));
3914 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3916 int value = chooser.showOpenDialog(null);
3918 if (value == JalviewFileChooser.APPROVE_OPTION)
3920 String filePath = chooser.getSelectedFile().getPath();
3921 Cache.setProperty("LAST_DIRECTORY", filePath);
3922 NewickFile fin = null;
3925 fin = new NewickFile(filePath, DataSourceType.FILE);
3926 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3927 } catch (Exception ex)
3934 .getString("label.problem_reading_tree_file"),
3935 JvOptionPane.WARNING_MESSAGE);
3936 ex.printStackTrace();
3938 if (fin != null && fin.hasWarningMessage())
3940 JvOptionPane.showMessageDialog(Desktop.desktop, fin
3941 .getWarningMessage(), MessageManager
3942 .getString("label.possible_problem_with_tree_file"),
3943 JvOptionPane.WARNING_MESSAGE);
3948 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3950 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3953 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3954 int h, int x, int y)
3956 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3960 * Add a treeviewer for the tree extracted from a Newick file object to the
3961 * current alignment view
3968 * Associated alignment input data (or null)
3977 * @return TreePanel handle
3979 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3980 AlignmentView input, int w, int h, int x, int y)
3982 TreePanel tp = null;
3988 if (nf.getTree() != null)
3990 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3996 tp.setLocation(x, y);
3999 Desktop.addInternalFrame(tp, treeTitle, w, h);
4001 } catch (Exception ex)
4003 ex.printStackTrace();
4009 private boolean buildingMenu = false;
4012 * Generates menu items and listener event actions for web service clients
4015 public void BuildWebServiceMenu()
4017 while (buildingMenu)
4021 System.err.println("Waiting for building menu to finish.");
4023 } catch (Exception e)
4027 final AlignFrame me = this;
4028 buildingMenu = true;
4029 new Thread(new Runnable()
4034 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4037 // System.err.println("Building ws menu again "
4038 // + Thread.currentThread());
4039 // TODO: add support for context dependent disabling of services based
4041 // alignment and current selection
4042 // TODO: add additional serviceHandle parameter to specify abstract
4044 // class independently of AbstractName
4045 // TODO: add in rediscovery GUI function to restart discoverer
4046 // TODO: group services by location as well as function and/or
4048 // object broker mechanism.
4049 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4050 final IProgressIndicator af = me;
4053 * do not i18n these strings - they are hard-coded in class
4054 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4055 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4057 final JMenu msawsmenu = new JMenu("Alignment");
4058 final JMenu secstrmenu = new JMenu(
4059 "Secondary Structure Prediction");
4060 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4061 final JMenu analymenu = new JMenu("Analysis");
4062 final JMenu dismenu = new JMenu("Protein Disorder");
4063 // JAL-940 - only show secondary structure prediction services from
4064 // the legacy server
4065 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4067 Discoverer.services != null && (Discoverer.services.size() > 0))
4069 // TODO: refactor to allow list of AbstractName/Handler bindings to
4071 // stored or retrieved from elsewhere
4072 // No MSAWS used any more:
4073 // Vector msaws = null; // (Vector)
4074 // Discoverer.services.get("MsaWS");
4075 Vector secstrpr = (Vector) Discoverer.services
4077 if (secstrpr != null)
4079 // Add any secondary structure prediction services
4080 for (int i = 0, j = secstrpr.size(); i < j; i++)
4082 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4084 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4085 .getServiceClient(sh);
4086 int p = secstrmenu.getItemCount();
4087 impl.attachWSMenuEntry(secstrmenu, me);
4088 int q = secstrmenu.getItemCount();
4089 for (int litm = p; litm < q; litm++)
4091 legacyItems.add(secstrmenu.getItem(litm));
4097 // Add all submenus in the order they should appear on the web
4099 wsmenu.add(msawsmenu);
4100 wsmenu.add(secstrmenu);
4101 wsmenu.add(dismenu);
4102 wsmenu.add(analymenu);
4103 // No search services yet
4104 // wsmenu.add(seqsrchmenu);
4106 javax.swing.SwingUtilities.invokeLater(new Runnable()
4113 webService.removeAll();
4114 // first, add discovered services onto the webservices menu
4115 if (wsmenu.size() > 0)
4117 for (int i = 0, j = wsmenu.size(); i < j; i++)
4119 webService.add(wsmenu.get(i));
4124 webService.add(me.webServiceNoServices);
4126 // TODO: move into separate menu builder class.
4127 boolean new_sspred = false;
4128 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4130 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4131 if (jws2servs != null)
4133 if (jws2servs.hasServices())
4135 jws2servs.attachWSMenuEntry(webService, me);
4136 for (Jws2Instance sv : jws2servs.getServices())
4138 if (sv.description.toLowerCase().contains("jpred"))
4140 for (JMenuItem jmi : legacyItems)
4142 jmi.setVisible(false);
4148 if (jws2servs.isRunning())
4150 JMenuItem tm = new JMenuItem(
4151 "Still discovering JABA Services");
4152 tm.setEnabled(false);
4157 build_urlServiceMenu(me.webService);
4158 build_fetchdbmenu(webService);
4159 for (JMenu item : wsmenu)
4161 if (item.getItemCount() == 0)
4163 item.setEnabled(false);
4167 item.setEnabled(true);
4170 } catch (Exception e)
4173 .debug("Exception during web service menu building process.",
4178 } catch (Exception e)
4181 buildingMenu = false;
4188 * construct any groupURL type service menu entries.
4192 private void build_urlServiceMenu(JMenu webService)
4194 // TODO: remove this code when 2.7 is released
4195 // DEBUG - alignmentView
4197 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4198 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4200 * @Override public void actionPerformed(ActionEvent e) {
4201 * jalview.datamodel.AlignmentView
4202 * .testSelectionViews(af.viewport.getAlignment(),
4203 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4205 * }); webService.add(testAlView);
4207 // TODO: refactor to RestClient discoverer and merge menu entries for
4208 // rest-style services with other types of analysis/calculation service
4209 // SHmmr test client - still being implemented.
4210 // DEBUG - alignmentView
4212 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4215 client.attachWSMenuEntry(
4216 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4222 * Searches the alignment sequences for xRefs and builds the Show
4223 * Cross-References menu (formerly called Show Products), with database
4224 * sources for which cross-references are found (protein sources for a
4225 * nucleotide alignment and vice versa)
4227 * @return true if Show Cross-references menu should be enabled
4229 public boolean canShowProducts()
4231 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4232 AlignmentI dataset = viewport.getAlignment().getDataset();
4234 showProducts.removeAll();
4235 final boolean dna = viewport.getAlignment().isNucleotide();
4237 if (seqs == null || seqs.length == 0)
4239 // nothing to see here.
4243 boolean showp = false;
4246 List<String> ptypes = new CrossRef(seqs, dataset)
4247 .findXrefSourcesForSequences(dna);
4249 for (final String source : ptypes)
4252 final AlignFrame af = this;
4253 JMenuItem xtype = new JMenuItem(source);
4254 xtype.addActionListener(new ActionListener()
4257 public void actionPerformed(ActionEvent e)
4259 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4262 showProducts.add(xtype);
4264 showProducts.setVisible(showp);
4265 showProducts.setEnabled(showp);
4266 } catch (Exception e)
4269 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4277 * Finds and displays cross-references for the selected sequences (protein
4278 * products for nucleotide sequences, dna coding sequences for peptides).
4281 * the sequences to show cross-references for
4283 * true if from a nucleotide alignment (so showing proteins)
4285 * the database to show cross-references for
4287 protected void showProductsFor(final SequenceI[] sel,
4288 final boolean _odna, final String source)
4290 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4295 * Construct and display a new frame containing the translation of this
4296 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4299 public void showTranslation_actionPerformed(ActionEvent e)
4301 AlignmentI al = null;
4304 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4306 al = dna.translateCdna();
4307 } catch (Exception ex)
4309 jalview.bin.Cache.log.error(
4310 "Exception during translation. Please report this !", ex);
4311 final String msg = MessageManager
4312 .getString("label.error_when_translating_sequences_submit_bug_report");
4313 final String errorTitle = MessageManager
4314 .getString("label.implementation_error")
4315 + MessageManager.getString("label.translation_failed");
4316 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4317 JvOptionPane.ERROR_MESSAGE);
4320 if (al == null || al.getHeight() == 0)
4322 final String msg = MessageManager
4323 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4324 final String errorTitle = MessageManager
4325 .getString("label.translation_failed");
4326 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4327 JvOptionPane.WARNING_MESSAGE);
4331 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4332 af.setFileFormat(this.currentFileFormat);
4333 final String newTitle = MessageManager.formatMessage(
4334 "label.translation_of_params",
4335 new Object[] { this.getTitle() });
4336 af.setTitle(newTitle);
4337 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4339 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4340 viewport.openSplitFrame(af, new Alignment(seqs));
4344 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4351 * Set the file format
4355 public void setFileFormat(FileFormatI format)
4357 this.currentFileFormat = format;
4361 * Try to load a features file onto the alignment.
4364 * contents or path to retrieve file
4366 * access mode of file (see jalview.io.AlignFile)
4367 * @return true if features file was parsed correctly.
4369 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4371 return avc.parseFeaturesFile(file, sourceType,
4372 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4377 public void refreshFeatureUI(boolean enableIfNecessary)
4379 // note - currently this is only still here rather than in the controller
4380 // because of the featureSettings hard reference that is yet to be
4382 if (enableIfNecessary)
4384 viewport.setShowSequenceFeatures(true);
4385 showSeqFeatures.setSelected(true);
4391 public void dragEnter(DropTargetDragEvent evt)
4396 public void dragExit(DropTargetEvent evt)
4401 public void dragOver(DropTargetDragEvent evt)
4406 public void dropActionChanged(DropTargetDragEvent evt)
4411 public void drop(DropTargetDropEvent evt)
4413 // JAL-1552 - acceptDrop required before getTransferable call for
4414 // Java's Transferable for native dnd
4415 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4416 Transferable t = evt.getTransferable();
4417 List<String> files = new ArrayList<String>();
4418 List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4422 Desktop.transferFromDropTarget(files, protocols, evt, t);
4423 } catch (Exception e)
4425 e.printStackTrace();
4431 // check to see if any of these files have names matching sequences in
4433 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4434 .getAlignment().getSequencesArray());
4436 * Object[] { String,SequenceI}
4438 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4439 ArrayList<String> filesnotmatched = new ArrayList<String>();
4440 for (int i = 0; i < files.size(); i++)
4442 String file = files.get(i).toString();
4444 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4445 if (protocol == DataSourceType.FILE)
4447 File fl = new File(file);
4448 pdbfn = fl.getName();
4450 else if (protocol == DataSourceType.URL)
4452 URL url = new URL(file);
4453 pdbfn = url.getFile();
4455 if (pdbfn.length() > 0)
4457 // attempt to find a match in the alignment
4458 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4459 int l = 0, c = pdbfn.indexOf(".");
4460 while (mtch == null && c != -1)
4465 } while ((c = pdbfn.indexOf(".", l)) > l);
4468 pdbfn = pdbfn.substring(0, l);
4470 mtch = idm.findAllIdMatches(pdbfn);
4474 FileFormatI type = null;
4477 type = new IdentifyFile().identify(file, protocol);
4478 } catch (Exception ex)
4482 if (type != null && type.isStructureFile())
4484 filesmatched.add(new Object[] { file, protocol, mtch });
4488 // File wasn't named like one of the sequences or wasn't a PDB file.
4489 filesnotmatched.add(file);
4493 if (filesmatched.size() > 0)
4495 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4501 "label.automatically_associate_structure_files_with_sequences_same_name",
4502 new Object[] { Integer
4508 .getString("label.automatically_associate_structure_files_by_name"),
4509 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4512 for (Object[] fm : filesmatched)
4514 // try and associate
4515 // TODO: may want to set a standard ID naming formalism for
4516 // associating PDB files which have no IDs.
4517 for (SequenceI toassoc : (SequenceI[]) fm[2])
4519 PDBEntry pe = new AssociatePdbFileWithSeq()
4520 .associatePdbWithSeq((String) fm[0],
4521 (DataSourceType) fm[1], toassoc, false,
4525 System.err.println("Associated file : "
4526 + ((String) fm[0]) + " with "
4527 + toassoc.getDisplayId(true));
4531 alignPanel.paintAlignment(true);
4535 if (filesnotmatched.size() > 0)
4538 && (Cache.getDefault(
4539 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4545 "label.ignore_unmatched_dropped_files_info",
4546 new Object[] { Integer
4553 .getString("label.ignore_unmatched_dropped_files"),
4554 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4558 for (String fn : filesnotmatched)
4560 loadJalviewDataFile(fn, null, null, null);
4564 } catch (Exception ex)
4566 ex.printStackTrace();
4572 * Attempt to load a "dropped" file or URL string, by testing in turn for
4574 * <li>an Annotation file</li>
4575 * <li>a JNet file</li>
4576 * <li>a features file</li>
4577 * <li>else try to interpret as an alignment file</li>
4581 * either a filename or a URL string.
4583 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4584 FileFormatI format, SequenceI assocSeq)
4588 if (sourceType == null)
4590 sourceType = FormatAdapter.checkProtocol(file);
4592 // if the file isn't identified, or not positively identified as some
4593 // other filetype (PFAM is default unidentified alignment file type) then
4594 // try to parse as annotation.
4595 boolean isAnnotation = (format == null || FileFormat.Pfam
4596 .equals(format)) ? new AnnotationFile()
4597 .annotateAlignmentView(viewport, file, sourceType) : false;
4601 // first see if its a T-COFFEE score file
4602 TCoffeeScoreFile tcf = null;
4605 tcf = new TCoffeeScoreFile(file, sourceType);
4608 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4611 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4612 isAnnotation = true;
4614 .setText(MessageManager
4615 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4619 // some problem - if no warning its probable that the ID matching
4620 // process didn't work
4624 tcf.getWarningMessage() == null ? MessageManager
4625 .getString("label.check_file_matches_sequence_ids_alignment")
4626 : tcf.getWarningMessage(),
4628 .getString("label.problem_reading_tcoffee_score_file"),
4629 JvOptionPane.WARNING_MESSAGE);
4636 } catch (Exception x)
4639 .debug("Exception when processing data source as T-COFFEE score file",
4645 // try to see if its a JNet 'concise' style annotation file *before*
4647 // try to parse it as a features file
4650 format = new IdentifyFile().identify(file, sourceType);
4652 if (FileFormat.ScoreMatrix == format)
4654 ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4657 // todo: i18n this message
4659 .setText(MessageManager.formatMessage(
4660 "label.successfully_loaded_matrix",
4661 sm.getMatrixName()));
4663 else if (FileFormat.Jnet.equals(format))
4665 JPredFile predictions = new JPredFile(file, sourceType);
4666 new JnetAnnotationMaker();
4667 JnetAnnotationMaker.add_annotation(predictions,
4668 viewport.getAlignment(), 0, false);
4669 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4670 viewport.getAlignment().setSeqrep(repseq);
4671 ColumnSelection cs = new ColumnSelection();
4672 cs.hideInsertionsFor(repseq);
4673 viewport.setColumnSelection(cs);
4674 isAnnotation = true;
4676 // else if (IdentifyFile.FeaturesFile.equals(format))
4677 else if (FileFormat.Features.equals(format))
4679 if (parseFeaturesFile(file, sourceType))
4681 alignPanel.paintAlignment(true);
4686 new FileLoader().LoadFile(viewport, file, sourceType, format);
4693 alignPanel.adjustAnnotationHeight();
4694 viewport.updateSequenceIdColours();
4695 buildSortByAnnotationScoresMenu();
4696 alignPanel.paintAlignment(true);
4698 } catch (Exception ex)
4700 ex.printStackTrace();
4701 } catch (OutOfMemoryError oom)
4706 } catch (Exception x)
4711 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4712 : "using " + sourceType + " from " + file)
4714 + (format != null ? "(parsing as '" + format
4715 + "' file)" : ""), oom, Desktop.desktop);
4720 * Method invoked by the ChangeListener on the tabbed pane, in other words
4721 * when a different tabbed pane is selected by the user or programmatically.
4724 public void tabSelectionChanged(int index)
4728 alignPanel = alignPanels.get(index);
4729 viewport = alignPanel.av;
4730 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4731 setMenusFromViewport(viewport);
4735 * 'focus' any colour slider that is open to the selected viewport
4737 if (viewport.getConservationSelected())
4739 SliderPanel.setConservationSlider(alignPanel,
4740 viewport.getResidueShading(), alignPanel.getViewName());
4744 SliderPanel.hideConservationSlider();
4746 if (viewport.getAbovePIDThreshold())
4748 SliderPanel.setPIDSliderSource(alignPanel,
4749 viewport.getResidueShading(), alignPanel.getViewName());
4753 SliderPanel.hidePIDSlider();
4757 * If there is a frame linked to this one in a SplitPane, switch it to the
4758 * same view tab index. No infinite recursion of calls should happen, since
4759 * tabSelectionChanged() should not get invoked on setting the selected
4760 * index to an unchanged value. Guard against setting an invalid index
4761 * before the new view peer tab has been created.
4763 final AlignViewportI peer = viewport.getCodingComplement();
4766 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4767 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4769 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4775 * On right mouse click on view tab, prompt for and set new view name.
4778 public void tabbedPane_mousePressed(MouseEvent e)
4780 if (e.isPopupTrigger())
4782 String msg = MessageManager.getString("label.enter_view_name");
4783 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4784 JvOptionPane.QUESTION_MESSAGE);
4788 viewport.viewName = reply;
4789 // TODO warn if reply is in getExistingViewNames()?
4790 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4795 public AlignViewport getCurrentView()
4801 * Open the dialog for regex description parsing.
4804 protected void extractScores_actionPerformed(ActionEvent e)
4806 ParseProperties pp = new jalview.analysis.ParseProperties(
4807 viewport.getAlignment());
4808 // TODO: verify regex and introduce GUI dialog for version 2.5
4809 // if (pp.getScoresFromDescription("col", "score column ",
4810 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4812 if (pp.getScoresFromDescription("description column",
4813 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4815 buildSortByAnnotationScoresMenu();
4823 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4827 protected void showDbRefs_actionPerformed(ActionEvent e)
4829 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4835 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4839 protected void showNpFeats_actionPerformed(ActionEvent e)
4841 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4845 * find the viewport amongst the tabs in this alignment frame and close that
4850 public boolean closeView(AlignViewportI av)
4854 this.closeMenuItem_actionPerformed(false);
4857 Component[] comp = tabbedPane.getComponents();
4858 for (int i = 0; comp != null && i < comp.length; i++)
4860 if (comp[i] instanceof AlignmentPanel)
4862 if (((AlignmentPanel) comp[i]).av == av)
4865 closeView((AlignmentPanel) comp[i]);
4873 protected void build_fetchdbmenu(JMenu webService)
4875 // Temporary hack - DBRef Fetcher always top level ws entry.
4876 // TODO We probably want to store a sequence database checklist in
4877 // preferences and have checkboxes.. rather than individual sources selected
4879 final JMenu rfetch = new JMenu(
4880 MessageManager.getString("action.fetch_db_references"));
4881 rfetch.setToolTipText(MessageManager
4882 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4883 webService.add(rfetch);
4885 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4886 MessageManager.getString("option.trim_retrieved_seqs"));
4887 trimrs.setToolTipText(MessageManager
4888 .getString("label.trim_retrieved_sequences"));
4889 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4890 trimrs.addActionListener(new ActionListener()
4893 public void actionPerformed(ActionEvent e)
4895 trimrs.setSelected(trimrs.isSelected());
4896 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4897 Boolean.valueOf(trimrs.isSelected()).toString());
4901 JMenuItem fetchr = new JMenuItem(
4902 MessageManager.getString("label.standard_databases"));
4903 fetchr.setToolTipText(MessageManager
4904 .getString("label.fetch_embl_uniprot"));
4905 fetchr.addActionListener(new ActionListener()
4909 public void actionPerformed(ActionEvent e)
4911 new Thread(new Runnable()
4916 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4917 .getAlignment().isNucleotide();
4918 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
4919 .getSequenceSelection(), alignPanel.alignFrame, null,
4920 alignPanel.alignFrame.featureSettings, isNucleotide);
4921 dbRefFetcher.addListener(new FetchFinishedListenerI()
4924 public void finished()
4926 AlignFrame.this.setMenusForViewport();
4929 dbRefFetcher.fetchDBRefs(false);
4937 final AlignFrame me = this;
4938 new Thread(new Runnable()
4943 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4944 .getSequenceFetcherSingleton(me);
4945 javax.swing.SwingUtilities.invokeLater(new Runnable()
4950 String[] dbclasses = sf.getOrderedSupportedSources();
4951 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4952 // jalview.util.QuickSort.sort(otherdb, otherdb);
4953 List<DbSourceProxy> otherdb;
4954 JMenu dfetch = new JMenu();
4955 JMenu ifetch = new JMenu();
4956 JMenuItem fetchr = null;
4957 int comp = 0, icomp = 0, mcomp = 15;
4958 String mname = null;
4960 for (String dbclass : dbclasses)
4962 otherdb = sf.getSourceProxy(dbclass);
4963 // add a single entry for this class, or submenu allowing 'fetch
4965 if (otherdb == null || otherdb.size() < 1)
4969 // List<DbSourceProxy> dbs=otherdb;
4970 // otherdb=new ArrayList<DbSourceProxy>();
4971 // for (DbSourceProxy db:dbs)
4973 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4977 mname = "From " + dbclass;
4979 if (otherdb.size() == 1)
4981 final DbSourceProxy[] dassource = otherdb
4982 .toArray(new DbSourceProxy[0]);
4983 DbSourceProxy src = otherdb.get(0);
4984 fetchr = new JMenuItem(src.getDbSource());
4985 fetchr.addActionListener(new ActionListener()
4989 public void actionPerformed(ActionEvent e)
4991 new Thread(new Runnable()
4997 boolean isNucleotide = alignPanel.alignFrame
4998 .getViewport().getAlignment()
5000 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5001 alignPanel.av.getSequenceSelection(),
5002 alignPanel.alignFrame, dassource,
5003 alignPanel.alignFrame.featureSettings,
5006 .addListener(new FetchFinishedListenerI()
5009 public void finished()
5011 AlignFrame.this.setMenusForViewport();
5014 dbRefFetcher.fetchDBRefs(false);
5020 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5021 MessageManager.formatMessage(
5022 "label.fetch_retrieve_from",
5023 new Object[] { src.getDbName() })));
5029 final DbSourceProxy[] dassource = otherdb
5030 .toArray(new DbSourceProxy[0]);
5032 DbSourceProxy src = otherdb.get(0);
5033 fetchr = new JMenuItem(MessageManager.formatMessage(
5034 "label.fetch_all_param",
5035 new Object[] { src.getDbSource() }));
5036 fetchr.addActionListener(new ActionListener()
5039 public void actionPerformed(ActionEvent e)
5041 new Thread(new Runnable()
5047 boolean isNucleotide = alignPanel.alignFrame
5048 .getViewport().getAlignment()
5050 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5051 alignPanel.av.getSequenceSelection(),
5052 alignPanel.alignFrame, dassource,
5053 alignPanel.alignFrame.featureSettings,
5056 .addListener(new FetchFinishedListenerI()
5059 public void finished()
5061 AlignFrame.this.setMenusForViewport();
5064 dbRefFetcher.fetchDBRefs(false);
5070 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5071 MessageManager.formatMessage(
5072 "label.fetch_retrieve_from_all_sources",
5074 Integer.valueOf(otherdb.size())
5075 .toString(), src.getDbSource(),
5076 src.getDbName() })));
5079 // and then build the rest of the individual menus
5080 ifetch = new JMenu(MessageManager.formatMessage(
5081 "label.source_from_db_source",
5082 new Object[] { src.getDbSource() }));
5084 String imname = null;
5086 for (DbSourceProxy sproxy : otherdb)
5088 String dbname = sproxy.getDbName();
5089 String sname = dbname.length() > 5 ? dbname.substring(0,
5090 5) + "..." : dbname;
5091 String msname = dbname.length() > 10 ? dbname.substring(
5092 0, 10) + "..." : dbname;
5095 imname = MessageManager.formatMessage(
5096 "label.from_msname", new Object[] { sname });
5098 fetchr = new JMenuItem(msname);
5099 final DbSourceProxy[] dassrc = { sproxy };
5100 fetchr.addActionListener(new ActionListener()
5104 public void actionPerformed(ActionEvent e)
5106 new Thread(new Runnable()
5112 boolean isNucleotide = alignPanel.alignFrame
5113 .getViewport().getAlignment()
5115 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5116 alignPanel.av.getSequenceSelection(),
5117 alignPanel.alignFrame, dassrc,
5118 alignPanel.alignFrame.featureSettings,
5121 .addListener(new FetchFinishedListenerI()
5124 public void finished()
5126 AlignFrame.this.setMenusForViewport();
5129 dbRefFetcher.fetchDBRefs(false);
5135 fetchr.setToolTipText("<html>"
5136 + MessageManager.formatMessage(
5137 "label.fetch_retrieve_from", new Object[]
5141 if (++icomp >= mcomp || i == (otherdb.size()))
5143 ifetch.setText(MessageManager.formatMessage(
5144 "label.source_to_target", imname, sname));
5146 ifetch = new JMenu();
5154 if (comp >= mcomp || dbi >= (dbclasses.length))
5156 dfetch.setText(MessageManager.formatMessage(
5157 "label.source_to_target", mname, dbclass));
5159 dfetch = new JMenu();
5172 * Left justify the whole alignment.
5175 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5177 AlignmentI al = viewport.getAlignment();
5179 viewport.firePropertyChange("alignment", null, al);
5183 * Right justify the whole alignment.
5186 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5188 AlignmentI al = viewport.getAlignment();
5190 viewport.firePropertyChange("alignment", null, al);
5194 public void setShowSeqFeatures(boolean b)
5196 showSeqFeatures.setSelected(b);
5197 viewport.setShowSequenceFeatures(b);
5204 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5205 * awt.event.ActionEvent)
5208 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5210 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5211 alignPanel.paintAlignment(true);
5218 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5222 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5224 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5225 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5233 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5234 * .event.ActionEvent)
5237 protected void showGroupConservation_actionPerformed(ActionEvent e)
5239 viewport.setShowGroupConservation(showGroupConservation.getState());
5240 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5247 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5248 * .event.ActionEvent)
5251 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5253 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5254 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5261 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5262 * .event.ActionEvent)
5265 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5267 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5268 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5272 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5274 showSequenceLogo.setState(true);
5275 viewport.setShowSequenceLogo(true);
5276 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5277 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5281 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5283 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5290 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5291 * .event.ActionEvent)
5294 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5296 if (avc.makeGroupsFromSelection())
5298 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5299 alignPanel.updateAnnotation();
5300 alignPanel.paintAlignment(true);
5304 public void clearAlignmentSeqRep()
5306 // TODO refactor alignmentseqrep to controller
5307 if (viewport.getAlignment().hasSeqrep())
5309 viewport.getAlignment().setSeqrep(null);
5310 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5311 alignPanel.updateAnnotation();
5312 alignPanel.paintAlignment(true);
5317 protected void createGroup_actionPerformed(ActionEvent e)
5319 if (avc.createGroup())
5321 alignPanel.alignmentChanged();
5326 protected void unGroup_actionPerformed(ActionEvent e)
5330 alignPanel.alignmentChanged();
5335 * make the given alignmentPanel the currently selected tab
5337 * @param alignmentPanel
5339 public void setDisplayedView(AlignmentPanel alignmentPanel)
5341 if (!viewport.getSequenceSetId().equals(
5342 alignmentPanel.av.getSequenceSetId()))
5346 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5348 if (tabbedPane != null
5349 && tabbedPane.getTabCount() > 0
5350 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5351 .getSelectedIndex())
5353 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5358 * Action on selection of menu options to Show or Hide annotations.
5361 * @param forSequences
5362 * update sequence-related annotations
5363 * @param forAlignment
5364 * update non-sequence-related annotations
5367 protected void setAnnotationsVisibility(boolean visible,
5368 boolean forSequences, boolean forAlignment)
5370 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5371 .getAlignmentAnnotation();
5376 for (AlignmentAnnotation aa : anns)
5379 * don't display non-positional annotations on an alignment
5381 if (aa.annotations == null)
5385 boolean apply = (aa.sequenceRef == null && forAlignment)
5386 || (aa.sequenceRef != null && forSequences);
5389 aa.visible = visible;
5392 alignPanel.validateAnnotationDimensions(true);
5393 alignPanel.alignmentChanged();
5397 * Store selected annotation sort order for the view and repaint.
5400 protected void sortAnnotations_actionPerformed()
5402 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5404 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5405 alignPanel.paintAlignment(true);
5410 * @return alignment panels in this alignment frame
5412 public List<? extends AlignmentViewPanel> getAlignPanels()
5414 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5418 * Open a new alignment window, with the cDNA associated with this (protein)
5419 * alignment, aligned as is the protein.
5421 protected void viewAsCdna_actionPerformed()
5423 // TODO no longer a menu action - refactor as required
5424 final AlignmentI alignment = getViewport().getAlignment();
5425 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5426 if (mappings == null)
5430 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5431 for (SequenceI aaSeq : alignment.getSequences())
5433 for (AlignedCodonFrame acf : mappings)
5435 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5439 * There is a cDNA mapping for this protein sequence - add to new
5440 * alignment. It will share the same dataset sequence as other mapped
5441 * cDNA (no new mappings need to be created).
5443 final Sequence newSeq = new Sequence(dnaSeq);
5444 newSeq.setDatasetSequence(dnaSeq);
5445 cdnaSeqs.add(newSeq);
5449 if (cdnaSeqs.size() == 0)
5451 // show a warning dialog no mapped cDNA
5454 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5456 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5457 AlignFrame.DEFAULT_HEIGHT);
5458 cdna.alignAs(alignment);
5459 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5461 Desktop.addInternalFrame(alignFrame, newtitle,
5462 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5466 * Set visibility of dna/protein complement view (available when shown in a
5472 protected void showComplement_actionPerformed(boolean show)
5474 SplitContainerI sf = getSplitViewContainer();
5477 sf.setComplementVisible(this, show);
5482 * Generate the reverse (optionally complemented) of the selected sequences,
5483 * and add them to the alignment
5486 protected void showReverse_actionPerformed(boolean complement)
5488 AlignmentI al = null;
5491 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5492 al = dna.reverseCdna(complement);
5493 viewport.addAlignment(al, "");
5494 addHistoryItem(new EditCommand(
5495 MessageManager.getString("label.add_sequences"),
5496 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5497 viewport.getAlignment()));
5498 } catch (Exception ex)
5500 System.err.println(ex.getMessage());
5506 * Try to run a script in the Groovy console, having first ensured that this
5507 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5508 * be targeted at this alignment.
5511 protected void runGroovy_actionPerformed()
5513 Jalview.setCurrentAlignFrame(this);
5514 groovy.ui.Console console = Desktop.getGroovyConsole();
5515 if (console != null)
5519 console.runScript();
5520 } catch (Exception ex)
5522 System.err.println((ex.toString()));
5524 .showInternalMessageDialog(Desktop.desktop, MessageManager
5525 .getString("label.couldnt_run_groovy_script"),
5527 .getString("label.groovy_support_failed"),
5528 JvOptionPane.ERROR_MESSAGE);
5533 System.err.println("Can't run Groovy script as console not found");
5538 * Hides columns containing (or not containing) a specified feature, provided
5539 * that would not leave all columns hidden
5541 * @param featureType
5542 * @param columnsContaining
5545 public boolean hideFeatureColumns(String featureType,
5546 boolean columnsContaining)
5548 boolean notForHiding = avc.markColumnsContainingFeatures(
5549 columnsContaining, false, false, featureType);
5552 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5553 false, featureType))
5555 getViewport().hideSelectedColumns();
5563 protected void selectHighlightedColumns_actionPerformed(
5564 ActionEvent actionEvent)
5566 // include key modifier check in case user selects from menu
5567 avc.markHighlightedColumns(
5568 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5570 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5574 * Rebuilds the Colour menu, including any user-defined colours which have
5575 * been loaded either on startup or during the session
5577 public void buildColourMenu()
5579 colourMenu.removeAll();
5581 colourMenu.add(applyToAllGroups);
5582 colourMenu.add(textColour);
5583 colourMenu.addSeparator();
5585 ColourMenuHelper.addMenuItems(colourMenu, this,
5586 viewport.getAlignment(), false);
5588 colourMenu.addSeparator();
5589 colourMenu.add(conservationMenuItem);
5590 colourMenu.add(modifyConservation);
5591 colourMenu.add(abovePIDThreshold);
5592 colourMenu.add(modifyPID);
5593 colourMenu.add(annotationColour);
5595 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5596 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5600 * Open a dialog (if not already open) that allows the user to select and
5601 * calculate PCA or Tree analysis
5603 protected void openTreePcaDialog()
5605 if (alignPanel.getCalculationDialog() == null)
5607 new CalculationChooser(AlignFrame.this);
5612 class PrintThread extends Thread
5616 public PrintThread(AlignmentPanel ap)
5621 static PageFormat pf;
5626 PrinterJob printJob = PrinterJob.getPrinterJob();
5630 printJob.setPrintable(ap, pf);
5634 printJob.setPrintable(ap);
5637 if (printJob.printDialog())
5642 } catch (Exception PrintException)
5644 PrintException.printStackTrace();