2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.ScoreModelI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenSequences;
57 import jalview.datamodel.PDBEntry;
58 import jalview.datamodel.SeqCigar;
59 import jalview.datamodel.Sequence;
60 import jalview.datamodel.SequenceGroup;
61 import jalview.datamodel.SequenceI;
62 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
63 import jalview.io.AlignmentProperties;
64 import jalview.io.AnnotationFile;
65 import jalview.io.BioJsHTMLOutput;
66 import jalview.io.DataSourceType;
67 import jalview.io.FileFormat;
68 import jalview.io.FileFormatI;
69 import jalview.io.FileLoader;
70 import jalview.io.FormatAdapter;
71 import jalview.io.HtmlSvgOutput;
72 import jalview.io.IdentifyFile;
73 import jalview.io.JPredFile;
74 import jalview.io.JalviewFileChooser;
75 import jalview.io.JalviewFileView;
76 import jalview.io.JnetAnnotationMaker;
77 import jalview.io.NewickFile;
78 import jalview.io.TCoffeeScoreFile;
79 import jalview.jbgui.GAlignFrame;
80 import jalview.schemes.ColourSchemeI;
81 import jalview.schemes.ColourSchemeProperty;
82 import jalview.schemes.ColourSchemes;
83 import jalview.schemes.ResidueColourScheme;
84 import jalview.schemes.ResidueProperties;
85 import jalview.schemes.TCoffeeColourScheme;
86 import jalview.schemes.UserColourScheme;
87 import jalview.util.MessageManager;
88 import jalview.viewmodel.AlignmentViewport;
89 import jalview.ws.DBRefFetcher;
90 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
91 import jalview.ws.jws1.Discoverer;
92 import jalview.ws.jws2.Jws2Discoverer;
93 import jalview.ws.jws2.jabaws2.Jws2Instance;
94 import jalview.ws.seqfetcher.DbSourceProxy;
96 import java.awt.BorderLayout;
97 import java.awt.Component;
98 import java.awt.Rectangle;
99 import java.awt.Toolkit;
100 import java.awt.datatransfer.Clipboard;
101 import java.awt.datatransfer.DataFlavor;
102 import java.awt.datatransfer.StringSelection;
103 import java.awt.datatransfer.Transferable;
104 import java.awt.dnd.DnDConstants;
105 import java.awt.dnd.DropTargetDragEvent;
106 import java.awt.dnd.DropTargetDropEvent;
107 import java.awt.dnd.DropTargetEvent;
108 import java.awt.dnd.DropTargetListener;
109 import java.awt.event.ActionEvent;
110 import java.awt.event.ActionListener;
111 import java.awt.event.FocusAdapter;
112 import java.awt.event.FocusEvent;
113 import java.awt.event.ItemEvent;
114 import java.awt.event.ItemListener;
115 import java.awt.event.KeyAdapter;
116 import java.awt.event.KeyEvent;
117 import java.awt.event.MouseAdapter;
118 import java.awt.event.MouseEvent;
119 import java.awt.print.PageFormat;
120 import java.awt.print.PrinterJob;
121 import java.beans.PropertyChangeEvent;
124 import java.util.ArrayList;
125 import java.util.Arrays;
126 import java.util.Deque;
127 import java.util.Enumeration;
128 import java.util.Hashtable;
129 import java.util.List;
130 import java.util.Vector;
132 import javax.swing.ButtonGroup;
133 import javax.swing.JCheckBoxMenuItem;
134 import javax.swing.JEditorPane;
135 import javax.swing.JInternalFrame;
136 import javax.swing.JLayeredPane;
137 import javax.swing.JMenu;
138 import javax.swing.JMenuItem;
139 import javax.swing.JRadioButtonMenuItem;
140 import javax.swing.JScrollPane;
141 import javax.swing.SwingUtilities;
147 * @version $Revision$
149 public class AlignFrame extends GAlignFrame implements DropTargetListener,
150 IProgressIndicator, AlignViewControllerGuiI
153 public static final int DEFAULT_WIDTH = 700;
155 public static final int DEFAULT_HEIGHT = 500;
158 * The currently displayed panel (selected tabbed view if more than one)
160 public AlignmentPanel alignPanel;
162 AlignViewport viewport;
164 public AlignViewControllerI avc;
166 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
169 * Last format used to load or save alignments in this window
171 FileFormatI currentFileFormat = null;
174 * Current filename for this alignment
176 String fileName = null;
179 * Creates a new AlignFrame object with specific width and height.
185 public AlignFrame(AlignmentI al, int width, int height)
187 this(al, null, width, height);
191 * Creates a new AlignFrame object with specific width, height and
197 * @param sequenceSetId
199 public AlignFrame(AlignmentI al, int width, int height,
200 String sequenceSetId)
202 this(al, null, width, height, sequenceSetId);
206 * Creates a new AlignFrame object with specific width, height and
212 * @param sequenceSetId
215 public AlignFrame(AlignmentI al, int width, int height,
216 String sequenceSetId, String viewId)
218 this(al, null, width, height, sequenceSetId, viewId);
222 * new alignment window with hidden columns
226 * @param hiddenColumns
227 * ColumnSelection or null
229 * Width of alignment frame
233 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
234 int width, int height)
236 this(al, hiddenColumns, width, height, null);
240 * Create alignment frame for al with hiddenColumns, a specific width and
241 * height, and specific sequenceId
244 * @param hiddenColumns
247 * @param sequenceSetId
250 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
251 int width, int height, String sequenceSetId)
253 this(al, hiddenColumns, width, height, sequenceSetId, null);
257 * Create alignment frame for al with hiddenColumns, a specific width and
258 * height, and specific sequenceId
261 * @param hiddenColumns
264 * @param sequenceSetId
269 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
270 int width, int height, String sequenceSetId, String viewId)
272 setSize(width, height);
274 if (al.getDataset() == null)
279 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
281 alignPanel = new AlignmentPanel(this, viewport);
283 addAlignmentPanel(alignPanel, true);
287 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
288 ColumnSelection hiddenColumns, int width, int height)
290 setSize(width, height);
292 if (al.getDataset() == null)
297 viewport = new AlignViewport(al, hiddenColumns);
299 if (hiddenSeqs != null && hiddenSeqs.length > 0)
301 viewport.hideSequence(hiddenSeqs);
303 alignPanel = new AlignmentPanel(this, viewport);
304 addAlignmentPanel(alignPanel, true);
309 * Make a new AlignFrame from existing alignmentPanels
316 public AlignFrame(AlignmentPanel ap)
320 addAlignmentPanel(ap, false);
325 * initalise the alignframe from the underlying viewport data and the
330 if (!Jalview.isHeadlessMode())
332 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
335 avc = new jalview.controller.AlignViewController(this, viewport,
337 if (viewport.getAlignmentConservationAnnotation() == null)
339 // BLOSUM62Colour.setEnabled(false);
340 conservationMenuItem.setEnabled(false);
341 modifyConservation.setEnabled(false);
342 // PIDColour.setEnabled(false);
343 // abovePIDThreshold.setEnabled(false);
344 // modifyPID.setEnabled(false);
347 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
350 if (sortby.equals("Id"))
352 sortIDMenuItem_actionPerformed(null);
354 else if (sortby.equals("Pairwise Identity"))
356 sortPairwiseMenuItem_actionPerformed(null);
360 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
362 setMenusFromViewport(viewport);
363 buildSortByAnnotationScoresMenu();
367 if (Desktop.desktop != null)
369 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
370 addServiceListeners();
374 if (viewport.getWrapAlignment())
376 wrapMenuItem_actionPerformed(null);
379 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
381 this.overviewMenuItem_actionPerformed(null);
386 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
387 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
388 final String menuLabel = MessageManager
389 .getString("label.copy_format_from");
390 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
391 new ViewSetProvider()
395 public AlignmentPanel[] getAllAlignmentPanels()
398 origview.add(alignPanel);
399 // make an array of all alignment panels except for this one
400 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
401 Arrays.asList(Desktop.getAlignmentPanels(null)));
402 aps.remove(AlignFrame.this.alignPanel);
403 return aps.toArray(new AlignmentPanel[aps.size()]);
405 }, selviews, new ItemListener()
409 public void itemStateChanged(ItemEvent e)
411 if (origview.size() > 0)
413 final AlignmentPanel ap = origview.get(0);
416 * Copy the ViewStyle of the selected panel to 'this one'.
417 * Don't change value of 'scaleProteinAsCdna' unless copying
420 ViewStyleI vs = selviews.get(0).getAlignViewport()
422 boolean fromSplitFrame = selviews.get(0)
423 .getAlignViewport().getCodingComplement() != null;
426 vs.setScaleProteinAsCdna(ap.getAlignViewport()
427 .getViewStyle().isScaleProteinAsCdna());
429 ap.getAlignViewport().setViewStyle(vs);
432 * Also rescale ViewStyle of SplitFrame complement if there is
433 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
434 * the whole ViewStyle (allow cDNA protein to have different
437 AlignViewportI complement = ap.getAlignViewport()
438 .getCodingComplement();
439 if (complement != null && vs.isScaleProteinAsCdna())
441 AlignFrame af = Desktop.getAlignFrameFor(complement);
442 ((SplitFrame) af.getSplitViewContainer())
444 af.setMenusForViewport();
448 ap.setSelected(true);
449 ap.alignFrame.setMenusForViewport();
454 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
455 .indexOf("devel") > -1
456 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
457 .indexOf("test") > -1)
459 formatMenu.add(vsel);
461 addFocusListener(new FocusAdapter()
464 public void focusGained(FocusEvent e)
466 Jalview.setCurrentAlignFrame(AlignFrame.this);
473 * Change the filename and format for the alignment, and enable the 'reload'
474 * button functionality.
481 public void setFileName(String file, FileFormatI format)
484 setFileFormat(format);
485 reload.setEnabled(true);
489 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
492 void addKeyListener()
494 addKeyListener(new KeyAdapter()
497 public void keyPressed(KeyEvent evt)
499 if (viewport.cursorMode
500 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
501 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
502 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
503 && Character.isDigit(evt.getKeyChar()))
505 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
508 switch (evt.getKeyCode())
511 case 27: // escape key
512 deselectAllSequenceMenuItem_actionPerformed(null);
516 case KeyEvent.VK_DOWN:
517 if (evt.isAltDown() || !viewport.cursorMode)
519 moveSelectedSequences(false);
521 if (viewport.cursorMode)
523 alignPanel.getSeqPanel().moveCursor(0, 1);
528 if (evt.isAltDown() || !viewport.cursorMode)
530 moveSelectedSequences(true);
532 if (viewport.cursorMode)
534 alignPanel.getSeqPanel().moveCursor(0, -1);
539 case KeyEvent.VK_LEFT:
540 if (evt.isAltDown() || !viewport.cursorMode)
542 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
546 alignPanel.getSeqPanel().moveCursor(-1, 0);
551 case KeyEvent.VK_RIGHT:
552 if (evt.isAltDown() || !viewport.cursorMode)
554 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
558 alignPanel.getSeqPanel().moveCursor(1, 0);
562 case KeyEvent.VK_SPACE:
563 if (viewport.cursorMode)
565 alignPanel.getSeqPanel().insertGapAtCursor(
566 evt.isControlDown() || evt.isShiftDown()
571 // case KeyEvent.VK_A:
572 // if (viewport.cursorMode)
574 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
575 // //System.out.println("A");
579 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
580 * System.out.println("closing bracket"); } break;
582 case KeyEvent.VK_DELETE:
583 case KeyEvent.VK_BACK_SPACE:
584 if (!viewport.cursorMode)
586 cut_actionPerformed(null);
590 alignPanel.getSeqPanel().deleteGapAtCursor(
591 evt.isControlDown() || evt.isShiftDown()
598 if (viewport.cursorMode)
600 alignPanel.getSeqPanel().setCursorRow();
604 if (viewport.cursorMode && !evt.isControlDown())
606 alignPanel.getSeqPanel().setCursorColumn();
610 if (viewport.cursorMode)
612 alignPanel.getSeqPanel().setCursorPosition();
616 case KeyEvent.VK_ENTER:
617 case KeyEvent.VK_COMMA:
618 if (viewport.cursorMode)
620 alignPanel.getSeqPanel().setCursorRowAndColumn();
625 if (viewport.cursorMode)
627 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
631 if (viewport.cursorMode)
633 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
638 viewport.cursorMode = !viewport.cursorMode;
639 statusBar.setText(MessageManager.formatMessage(
640 "label.keyboard_editing_mode",
641 new String[] { (viewport.cursorMode ? "on" : "off") }));
642 if (viewport.cursorMode)
644 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
645 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
647 alignPanel.getSeqPanel().seqCanvas.repaint();
653 Help.showHelpWindow();
654 } catch (Exception ex)
656 ex.printStackTrace();
661 boolean toggleSeqs = !evt.isControlDown();
662 boolean toggleCols = !evt.isShiftDown();
663 toggleHiddenRegions(toggleSeqs, toggleCols);
668 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
669 boolean modifyExisting = true; // always modify, don't clear
670 // evt.isShiftDown();
671 boolean invertHighlighted = evt.isAltDown();
672 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
676 case KeyEvent.VK_PAGE_UP:
677 if (viewport.getWrapAlignment())
679 alignPanel.scrollUp(true);
683 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
684 - viewport.endSeq + viewport.startSeq);
687 case KeyEvent.VK_PAGE_DOWN:
688 if (viewport.getWrapAlignment())
690 alignPanel.scrollUp(false);
694 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
695 + viewport.endSeq - viewport.startSeq);
702 public void keyReleased(KeyEvent evt)
704 switch (evt.getKeyCode())
706 case KeyEvent.VK_LEFT:
707 if (evt.isAltDown() || !viewport.cursorMode)
709 viewport.firePropertyChange("alignment", null, viewport
710 .getAlignment().getSequences());
714 case KeyEvent.VK_RIGHT:
715 if (evt.isAltDown() || !viewport.cursorMode)
717 viewport.firePropertyChange("alignment", null, viewport
718 .getAlignment().getSequences());
726 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
728 ap.alignFrame = this;
729 avc = new jalview.controller.AlignViewController(this, viewport,
734 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
736 int aSize = alignPanels.size();
738 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
740 if (aSize == 1 && ap.av.viewName == null)
742 this.getContentPane().add(ap, BorderLayout.CENTER);
748 setInitialTabVisible();
751 expandViews.setEnabled(true);
752 gatherViews.setEnabled(true);
753 tabbedPane.addTab(ap.av.viewName, ap);
755 ap.setVisible(false);
760 if (ap.av.isPadGaps())
762 ap.av.getAlignment().padGaps();
764 ap.av.updateConservation(ap);
765 ap.av.updateConsensus(ap);
766 ap.av.updateStrucConsensus(ap);
770 public void setInitialTabVisible()
772 expandViews.setEnabled(true);
773 gatherViews.setEnabled(true);
774 tabbedPane.setVisible(true);
775 AlignmentPanel first = alignPanels.get(0);
776 tabbedPane.addTab(first.av.viewName, first);
777 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
780 public AlignViewport getViewport()
785 /* Set up intrinsic listeners for dynamically generated GUI bits. */
786 private void addServiceListeners()
788 final java.beans.PropertyChangeListener thisListener;
789 Desktop.instance.addJalviewPropertyChangeListener("services",
790 thisListener = new java.beans.PropertyChangeListener()
793 public void propertyChange(PropertyChangeEvent evt)
795 // // System.out.println("Discoverer property change.");
796 // if (evt.getPropertyName().equals("services"))
798 SwingUtilities.invokeLater(new Runnable()
805 .println("Rebuild WS Menu for service change");
806 BuildWebServiceMenu();
813 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
816 public void internalFrameClosed(
817 javax.swing.event.InternalFrameEvent evt)
819 // System.out.println("deregistering discoverer listener");
820 Desktop.instance.removeJalviewPropertyChangeListener("services",
822 closeMenuItem_actionPerformed(true);
825 // Finally, build the menu once to get current service state
826 new Thread(new Runnable()
831 BuildWebServiceMenu();
837 * Configure menu items that vary according to whether the alignment is
838 * nucleotide or protein
840 public void setGUINucleotide()
842 boolean nucleotide = viewport.getAlignment().isNucleotide();
844 showTranslation.setVisible(nucleotide);
845 showReverse.setVisible(nucleotide);
846 showReverseComplement.setVisible(nucleotide);
847 conservationMenuItem.setEnabled(!nucleotide);
848 modifyConservation.setEnabled(!nucleotide);
849 showGroupConservation.setEnabled(!nucleotide);
851 AlignmentI al = getViewport().getAlignment();
854 * enable / disable colour schemes by querying whether they
855 * are applicable to the alignment data (for example, peptide or
856 * nucleotide specific, or require certain annotation present)
858 for (Component menuItem : colourMenu.getMenuComponents())
860 if (menuItem instanceof JRadioButtonMenuItem)
862 String colourName = ((JRadioButtonMenuItem) menuItem).getName();
863 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(
864 colourName, viewport);
867 ((JRadioButtonMenuItem) menuItem).setEnabled(cs
868 .isApplicableTo(al));
873 showComplementMenuItem.setText(nucleotide ? MessageManager
874 .getString("label.protein") : MessageManager
875 .getString("label.nucleotide"));
877 String selectedColourScheme = Cache.getDefault(
878 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
879 : Preferences.DEFAULT_COLOUR_PROT,
880 ResidueColourScheme.NONE);
881 setColourSelected(selectedColourScheme);
885 * set up menus for the current viewport. This may be called after any
886 * operation that affects the data in the current view (selection changed,
887 * etc) to update the menus to reflect the new state.
890 public void setMenusForViewport()
892 setMenusFromViewport(viewport);
896 * Need to call this method when tabs are selected for multiple views, or when
897 * loading from Jalview2XML.java
902 void setMenusFromViewport(AlignViewport av)
904 padGapsMenuitem.setSelected(av.isPadGaps());
905 colourTextMenuItem.setSelected(av.isShowColourText());
906 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
907 conservationMenuItem.setSelected(av.getConservationSelected());
908 seqLimits.setSelected(av.getShowJVSuffix());
909 idRightAlign.setSelected(av.isRightAlignIds());
910 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
911 renderGapsMenuItem.setSelected(av.isRenderGaps());
912 wrapMenuItem.setSelected(av.getWrapAlignment());
913 scaleAbove.setVisible(av.getWrapAlignment());
914 scaleLeft.setVisible(av.getWrapAlignment());
915 scaleRight.setVisible(av.getWrapAlignment());
916 annotationPanelMenuItem.setState(av.isShowAnnotation());
918 * Show/hide annotations only enabled if annotation panel is shown
920 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
921 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
922 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
923 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
924 viewBoxesMenuItem.setSelected(av.getShowBoxes());
925 viewTextMenuItem.setSelected(av.getShowText());
926 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
927 showGroupConsensus.setSelected(av.isShowGroupConsensus());
928 showGroupConservation.setSelected(av.isShowGroupConservation());
929 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
930 showSequenceLogo.setSelected(av.isShowSequenceLogo());
931 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
933 setColourSelected(ColourSchemeProperty.getColourName(av
934 .getGlobalColourScheme()));
936 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
937 hiddenMarkers.setState(av.getShowHiddenMarkers());
938 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
939 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
940 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
941 autoCalculate.setSelected(av.autoCalculateConsensus);
942 sortByTree.setSelected(av.sortByTree);
943 listenToViewSelections.setSelected(av.followSelection);
945 showProducts.setEnabled(canShowProducts());
946 setGroovyEnabled(Desktop.getGroovyConsole() != null);
952 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
956 public void setGroovyEnabled(boolean b)
958 runGroovy.setEnabled(b);
961 private IProgressIndicator progressBar;
966 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
969 public void setProgressBar(String message, long id)
971 progressBar.setProgressBar(message, id);
975 public void registerHandler(final long id,
976 final IProgressIndicatorHandler handler)
978 progressBar.registerHandler(id, handler);
983 * @return true if any progress bars are still active
986 public boolean operationInProgress()
988 return progressBar.operationInProgress();
992 public void setStatus(String text)
994 statusBar.setText(text);
998 * Added so Castor Mapping file can obtain Jalview Version
1000 public String getVersion()
1002 return jalview.bin.Cache.getProperty("VERSION");
1005 public FeatureRenderer getFeatureRenderer()
1007 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1011 public void fetchSequence_actionPerformed(ActionEvent e)
1013 new jalview.gui.SequenceFetcher(this);
1017 public void addFromFile_actionPerformed(ActionEvent e)
1019 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1023 public void reload_actionPerformed(ActionEvent e)
1025 if (fileName != null)
1027 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1028 // originating file's format
1029 // TODO: work out how to recover feature settings for correct view(s) when
1030 // file is reloaded.
1031 if (FileFormat.Jalview.equals(currentFileFormat))
1033 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1034 for (int i = 0; i < frames.length; i++)
1036 if (frames[i] instanceof AlignFrame && frames[i] != this
1037 && ((AlignFrame) frames[i]).fileName != null
1038 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1042 frames[i].setSelected(true);
1043 Desktop.instance.closeAssociatedWindows();
1044 } catch (java.beans.PropertyVetoException ex)
1050 Desktop.instance.closeAssociatedWindows();
1052 FileLoader loader = new FileLoader();
1053 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1054 : DataSourceType.FILE;
1055 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1059 Rectangle bounds = this.getBounds();
1061 FileLoader loader = new FileLoader();
1062 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1063 : DataSourceType.FILE;
1064 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1065 protocol, currentFileFormat);
1067 newframe.setBounds(bounds);
1068 if (featureSettings != null && featureSettings.isShowing())
1070 final Rectangle fspos = featureSettings.frame.getBounds();
1071 // TODO: need a 'show feature settings' function that takes bounds -
1072 // need to refactor Desktop.addFrame
1073 newframe.featureSettings_actionPerformed(null);
1074 final FeatureSettings nfs = newframe.featureSettings;
1075 SwingUtilities.invokeLater(new Runnable()
1080 nfs.frame.setBounds(fspos);
1083 this.featureSettings.close();
1084 this.featureSettings = null;
1086 this.closeMenuItem_actionPerformed(true);
1092 public void addFromText_actionPerformed(ActionEvent e)
1094 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1099 public void addFromURL_actionPerformed(ActionEvent e)
1101 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1105 public void save_actionPerformed(ActionEvent e)
1107 if (fileName == null || (currentFileFormat == null)
1108 || fileName.startsWith("http"))
1110 saveAs_actionPerformed(null);
1114 saveAlignment(fileName, currentFileFormat);
1125 public void saveAs_actionPerformed(ActionEvent e)
1127 String format = currentFileFormat == null ? null : currentFileFormat
1129 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1130 Cache.getProperty("LAST_DIRECTORY"), format);
1132 chooser.setFileView(new JalviewFileView());
1133 chooser.setDialogTitle(MessageManager
1134 .getString("label.save_alignment_to_file"));
1135 chooser.setToolTipText(MessageManager.getString("action.save"));
1137 int value = chooser.showSaveDialog(this);
1139 if (value == JalviewFileChooser.APPROVE_OPTION)
1141 currentFileFormat = chooser.getSelectedFormat();
1142 while (currentFileFormat == null)
1145 .showInternalMessageDialog(
1148 .getString("label.select_file_format_before_saving"),
1150 .getString("label.file_format_not_specified"),
1151 JvOptionPane.WARNING_MESSAGE);
1152 currentFileFormat = chooser.getSelectedFormat();
1153 value = chooser.showSaveDialog(this);
1154 if (value != JalviewFileChooser.APPROVE_OPTION)
1160 fileName = chooser.getSelectedFile().getPath();
1162 Cache.setProperty("DEFAULT_FILE_FORMAT",
1163 currentFileFormat.toString());
1165 Cache.setProperty("LAST_DIRECTORY", fileName);
1166 saveAlignment(fileName, currentFileFormat);
1170 public boolean saveAlignment(String file, FileFormatI format)
1172 boolean success = true;
1174 if (FileFormat.Jalview.equals(format))
1176 String shortName = title;
1178 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1180 shortName = shortName.substring(shortName
1181 .lastIndexOf(java.io.File.separatorChar) + 1);
1184 success = new Jalview2XML().saveAlignment(this, file, shortName);
1186 statusBar.setText(MessageManager.formatMessage(
1187 "label.successfully_saved_to_file_in_format", new Object[] {
1188 fileName, format }));
1193 // if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1195 // warningMessage("Cannot save file " + fileName + " using format "
1196 // + format, "Alignment output format not supported");
1197 // if (!Jalview.isHeadlessMode())
1199 // saveAs_actionPerformed(null);
1204 AlignmentExportData exportData = getAlignmentForExport(format,
1206 if (exportData.getSettings().isCancelled())
1210 FormatAdapter f = new FormatAdapter(alignPanel,
1211 exportData.getSettings());
1212 String output = f.formatSequences(
1214 exportData.getAlignment(), // class cast exceptions will
1215 // occur in the distant future
1216 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1217 f.getCacheSuffixDefault(format),
1218 viewport.getColumnSelection());
1228 java.io.PrintWriter out = new java.io.PrintWriter(
1229 new java.io.FileWriter(file));
1233 this.setTitle(file);
1234 statusBar.setText(MessageManager.formatMessage(
1235 "label.successfully_saved_to_file_in_format",
1236 new Object[] { fileName, format }));
1237 } catch (Exception ex)
1240 ex.printStackTrace();
1247 JvOptionPane.showInternalMessageDialog(this, MessageManager
1248 .formatMessage("label.couldnt_save_file",
1249 new Object[] { fileName }), MessageManager
1250 .getString("label.error_saving_file"),
1251 JvOptionPane.WARNING_MESSAGE);
1257 private void warningMessage(String warning, String title)
1259 if (new jalview.util.Platform().isHeadless())
1261 System.err.println("Warning: " + title + "\nWarning: " + warning);
1266 JvOptionPane.showInternalMessageDialog(this, warning, title,
1267 JvOptionPane.WARNING_MESSAGE);
1279 protected void outputText_actionPerformed(ActionEvent e)
1282 FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
1283 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1285 if (exportData.getSettings().isCancelled())
1289 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1290 cap.setForInput(null);
1293 FileFormatI format = fileFormat;
1294 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1295 .formatSequences(format,
1296 exportData.getAlignment(),
1297 exportData.getOmitHidden(),
1298 exportData.getStartEndPostions(),
1299 viewport.getColumnSelection()));
1300 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1301 "label.alignment_output_command",
1302 new Object[] { e.getActionCommand() }), 600, 500);
1303 } catch (OutOfMemoryError oom)
1305 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1311 public static AlignmentExportData getAlignmentForExport(
1312 FileFormatI format, AlignViewportI viewport,
1313 AlignExportSettingI exportSettings)
1315 AlignmentI alignmentToExport = null;
1316 AlignExportSettingI settings = exportSettings;
1317 String[] omitHidden = null;
1319 HiddenSequences hiddenSeqs = viewport.getAlignment()
1320 .getHiddenSequences();
1322 alignmentToExport = viewport.getAlignment();
1324 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1325 if (settings == null)
1327 settings = new AlignExportSettings(hasHiddenSeqs,
1328 viewport.hasHiddenColumns(), format);
1330 // settings.isExportAnnotations();
1332 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1334 omitHidden = viewport.getViewAsString(false,
1335 settings.isExportHiddenSequences());
1338 int[] alignmentStartEnd = new int[2];
1339 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1341 alignmentToExport = hiddenSeqs.getFullAlignment();
1345 alignmentToExport = viewport.getAlignment();
1347 alignmentStartEnd = alignmentToExport
1348 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1349 .getHiddenColumns());
1350 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1351 omitHidden, alignmentStartEnd, settings);
1362 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1364 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1365 htmlSVG.exportHTML(null);
1369 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1371 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1372 bjs.exportHTML(null);
1375 public void createImageMap(File file, String image)
1377 alignPanel.makePNGImageMap(file, image);
1387 public void createPNG(File f)
1389 alignPanel.makePNG(f);
1399 public void createEPS(File f)
1401 alignPanel.makeEPS(f);
1405 public void createSVG(File f)
1407 alignPanel.makeSVG(f);
1411 public void pageSetup_actionPerformed(ActionEvent e)
1413 PrinterJob printJob = PrinterJob.getPrinterJob();
1414 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1424 public void printMenuItem_actionPerformed(ActionEvent e)
1426 // Putting in a thread avoids Swing painting problems
1427 PrintThread thread = new PrintThread(alignPanel);
1432 public void exportFeatures_actionPerformed(ActionEvent e)
1434 new AnnotationExporter().exportFeatures(alignPanel);
1438 public void exportAnnotations_actionPerformed(ActionEvent e)
1440 new AnnotationExporter().exportAnnotations(alignPanel);
1444 public void associatedData_actionPerformed(ActionEvent e)
1446 // Pick the tree file
1447 JalviewFileChooser chooser = new JalviewFileChooser(
1448 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1449 chooser.setFileView(new JalviewFileView());
1450 chooser.setDialogTitle(MessageManager
1451 .getString("label.load_jalview_annotations"));
1452 chooser.setToolTipText(MessageManager
1453 .getString("label.load_jalview_annotations"));
1455 int value = chooser.showOpenDialog(null);
1457 if (value == JalviewFileChooser.APPROVE_OPTION)
1459 String choice = chooser.getSelectedFile().getPath();
1460 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1461 loadJalviewDataFile(choice, null, null, null);
1467 * Close the current view or all views in the alignment frame. If the frame
1468 * only contains one view then the alignment will be removed from memory.
1470 * @param closeAllTabs
1473 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1475 if (alignPanels != null && alignPanels.size() < 2)
1477 closeAllTabs = true;
1482 if (alignPanels != null)
1486 if (this.isClosed())
1488 // really close all the windows - otherwise wait till
1489 // setClosed(true) is called
1490 for (int i = 0; i < alignPanels.size(); i++)
1492 AlignmentPanel ap = alignPanels.get(i);
1499 closeView(alignPanel);
1506 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1507 * be called recursively, with the frame now in 'closed' state
1509 this.setClosed(true);
1511 } catch (Exception ex)
1513 ex.printStackTrace();
1518 * Close the specified panel and close up tabs appropriately.
1520 * @param panelToClose
1522 public void closeView(AlignmentPanel panelToClose)
1524 int index = tabbedPane.getSelectedIndex();
1525 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1526 alignPanels.remove(panelToClose);
1527 panelToClose.closePanel();
1528 panelToClose = null;
1530 tabbedPane.removeTabAt(closedindex);
1531 tabbedPane.validate();
1533 if (index > closedindex || index == tabbedPane.getTabCount())
1535 // modify currently selected tab index if necessary.
1539 this.tabSelectionChanged(index);
1545 void updateEditMenuBar()
1548 if (viewport.getHistoryList().size() > 0)
1550 undoMenuItem.setEnabled(true);
1551 CommandI command = viewport.getHistoryList().peek();
1552 undoMenuItem.setText(MessageManager.formatMessage(
1553 "label.undo_command",
1554 new Object[] { command.getDescription() }));
1558 undoMenuItem.setEnabled(false);
1559 undoMenuItem.setText(MessageManager.getString("action.undo"));
1562 if (viewport.getRedoList().size() > 0)
1564 redoMenuItem.setEnabled(true);
1566 CommandI command = viewport.getRedoList().peek();
1567 redoMenuItem.setText(MessageManager.formatMessage(
1568 "label.redo_command",
1569 new Object[] { command.getDescription() }));
1573 redoMenuItem.setEnabled(false);
1574 redoMenuItem.setText(MessageManager.getString("action.redo"));
1579 public void addHistoryItem(CommandI command)
1581 if (command.getSize() > 0)
1583 viewport.addToHistoryList(command);
1584 viewport.clearRedoList();
1585 updateEditMenuBar();
1586 viewport.updateHiddenColumns();
1587 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1588 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1589 // viewport.getColumnSelection()
1590 // .getHiddenColumns().size() > 0);
1596 * @return alignment objects for all views
1598 AlignmentI[] getViewAlignments()
1600 if (alignPanels != null)
1602 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1604 for (AlignmentPanel ap : alignPanels)
1606 als[i++] = ap.av.getAlignment();
1610 if (viewport != null)
1612 return new AlignmentI[] { viewport.getAlignment() };
1624 protected void undoMenuItem_actionPerformed(ActionEvent e)
1626 if (viewport.getHistoryList().isEmpty())
1630 CommandI command = viewport.getHistoryList().pop();
1631 viewport.addToRedoList(command);
1632 command.undoCommand(getViewAlignments());
1634 AlignmentViewport originalSource = getOriginatingSource(command);
1635 updateEditMenuBar();
1637 if (originalSource != null)
1639 if (originalSource != viewport)
1642 .warn("Implementation worry: mismatch of viewport origin for undo");
1644 originalSource.updateHiddenColumns();
1645 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1647 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1648 // viewport.getColumnSelection()
1649 // .getHiddenColumns().size() > 0);
1650 originalSource.firePropertyChange("alignment", null, originalSource
1651 .getAlignment().getSequences());
1662 protected void redoMenuItem_actionPerformed(ActionEvent e)
1664 if (viewport.getRedoList().size() < 1)
1669 CommandI command = viewport.getRedoList().pop();
1670 viewport.addToHistoryList(command);
1671 command.doCommand(getViewAlignments());
1673 AlignmentViewport originalSource = getOriginatingSource(command);
1674 updateEditMenuBar();
1676 if (originalSource != null)
1679 if (originalSource != viewport)
1682 .warn("Implementation worry: mismatch of viewport origin for redo");
1684 originalSource.updateHiddenColumns();
1685 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1687 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1688 // viewport.getColumnSelection()
1689 // .getHiddenColumns().size() > 0);
1690 originalSource.firePropertyChange("alignment", null, originalSource
1691 .getAlignment().getSequences());
1695 AlignmentViewport getOriginatingSource(CommandI command)
1697 AlignmentViewport originalSource = null;
1698 // For sequence removal and addition, we need to fire
1699 // the property change event FROM the viewport where the
1700 // original alignment was altered
1701 AlignmentI al = null;
1702 if (command instanceof EditCommand)
1704 EditCommand editCommand = (EditCommand) command;
1705 al = editCommand.getAlignment();
1706 List<Component> comps = PaintRefresher.components.get(viewport
1707 .getSequenceSetId());
1709 for (Component comp : comps)
1711 if (comp instanceof AlignmentPanel)
1713 if (al == ((AlignmentPanel) comp).av.getAlignment())
1715 originalSource = ((AlignmentPanel) comp).av;
1722 if (originalSource == null)
1724 // The original view is closed, we must validate
1725 // the current view against the closed view first
1728 PaintRefresher.validateSequences(al, viewport.getAlignment());
1731 originalSource = viewport;
1734 return originalSource;
1743 public void moveSelectedSequences(boolean up)
1745 SequenceGroup sg = viewport.getSelectionGroup();
1751 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1752 viewport.getHiddenRepSequences(), up);
1753 alignPanel.paintAlignment(true);
1756 synchronized void slideSequences(boolean right, int size)
1758 List<SequenceI> sg = new ArrayList<SequenceI>();
1759 if (viewport.cursorMode)
1761 sg.add(viewport.getAlignment().getSequenceAt(
1762 alignPanel.getSeqPanel().seqCanvas.cursorY));
1764 else if (viewport.getSelectionGroup() != null
1765 && viewport.getSelectionGroup().getSize() != viewport
1766 .getAlignment().getHeight())
1768 sg = viewport.getSelectionGroup().getSequences(
1769 viewport.getHiddenRepSequences());
1777 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1779 for (SequenceI seq : viewport.getAlignment().getSequences())
1781 if (!sg.contains(seq))
1783 invertGroup.add(seq);
1787 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1789 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1790 for (int i = 0; i < invertGroup.size(); i++)
1792 seqs2[i] = invertGroup.get(i);
1795 SlideSequencesCommand ssc;
1798 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1799 size, viewport.getGapCharacter());
1803 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1804 size, viewport.getGapCharacter());
1807 int groupAdjustment = 0;
1808 if (ssc.getGapsInsertedBegin() && right)
1810 if (viewport.cursorMode)
1812 alignPanel.getSeqPanel().moveCursor(size, 0);
1816 groupAdjustment = size;
1819 else if (!ssc.getGapsInsertedBegin() && !right)
1821 if (viewport.cursorMode)
1823 alignPanel.getSeqPanel().moveCursor(-size, 0);
1827 groupAdjustment = -size;
1831 if (groupAdjustment != 0)
1833 viewport.getSelectionGroup().setStartRes(
1834 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1835 viewport.getSelectionGroup().setEndRes(
1836 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1840 * just extend the last slide command if compatible; but not if in
1841 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1843 boolean appendHistoryItem = false;
1844 Deque<CommandI> historyList = viewport.getHistoryList();
1845 boolean inSplitFrame = getSplitViewContainer() != null;
1846 if (!inSplitFrame && historyList != null && historyList.size() > 0
1847 && historyList.peek() instanceof SlideSequencesCommand)
1849 appendHistoryItem = ssc
1850 .appendSlideCommand((SlideSequencesCommand) historyList
1854 if (!appendHistoryItem)
1856 addHistoryItem(ssc);
1869 protected void copy_actionPerformed(ActionEvent e)
1872 if (viewport.getSelectionGroup() == null)
1876 // TODO: preserve the ordering of displayed alignment annotation in any
1877 // internal paste (particularly sequence associated annotation)
1878 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1879 String[] omitHidden = null;
1881 if (viewport.hasHiddenColumns())
1883 omitHidden = viewport.getViewAsString(true);
1886 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1890 StringSelection ss = new StringSelection(output);
1894 jalview.gui.Desktop.internalCopy = true;
1895 // Its really worth setting the clipboard contents
1896 // to empty before setting the large StringSelection!!
1897 Toolkit.getDefaultToolkit().getSystemClipboard()
1898 .setContents(new StringSelection(""), null);
1900 Toolkit.getDefaultToolkit().getSystemClipboard()
1901 .setContents(ss, Desktop.instance);
1902 } catch (OutOfMemoryError er)
1904 new OOMWarning("copying region", er);
1908 ArrayList<int[]> hiddenColumns = null;
1909 if (viewport.hasHiddenColumns())
1911 hiddenColumns = new ArrayList<int[]>();
1912 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1913 .getSelectionGroup().getEndRes();
1914 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1916 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1918 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1919 region[1] - hiddenOffset });
1924 Desktop.jalviewClipboard = new Object[] { seqs,
1925 viewport.getAlignment().getDataset(), hiddenColumns };
1926 statusBar.setText(MessageManager.formatMessage(
1927 "label.copied_sequences_to_clipboard", new Object[] { Integer
1928 .valueOf(seqs.length).toString() }));
1938 protected void pasteNew_actionPerformed(ActionEvent e)
1950 protected void pasteThis_actionPerformed(ActionEvent e)
1956 * Paste contents of Jalview clipboard
1958 * @param newAlignment
1959 * true to paste to a new alignment, otherwise add to this.
1961 void paste(boolean newAlignment)
1963 boolean externalPaste = true;
1966 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1967 Transferable contents = c.getContents(this);
1969 if (contents == null)
1978 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1979 if (str.length() < 1)
1984 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1986 } catch (OutOfMemoryError er)
1988 new OOMWarning("Out of memory pasting sequences!!", er);
1992 SequenceI[] sequences;
1993 boolean annotationAdded = false;
1994 AlignmentI alignment = null;
1996 if (Desktop.jalviewClipboard != null)
1998 // The clipboard was filled from within Jalview, we must use the
2000 // And dataset from the copied alignment
2001 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2002 // be doubly sure that we create *new* sequence objects.
2003 sequences = new SequenceI[newseq.length];
2004 for (int i = 0; i < newseq.length; i++)
2006 sequences[i] = new Sequence(newseq[i]);
2008 alignment = new Alignment(sequences);
2009 externalPaste = false;
2013 // parse the clipboard as an alignment.
2014 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2016 sequences = alignment.getSequencesArray();
2020 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2026 if (Desktop.jalviewClipboard != null)
2028 // dataset is inherited
2029 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2033 // new dataset is constructed
2034 alignment.setDataset(null);
2036 alwidth = alignment.getWidth() + 1;
2040 AlignmentI pastedal = alignment; // preserve pasted alignment object
2041 // Add pasted sequences and dataset into existing alignment.
2042 alignment = viewport.getAlignment();
2043 alwidth = alignment.getWidth() + 1;
2044 // decide if we need to import sequences from an existing dataset
2045 boolean importDs = Desktop.jalviewClipboard != null
2046 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2047 // importDs==true instructs us to copy over new dataset sequences from
2048 // an existing alignment
2049 Vector newDs = (importDs) ? new Vector() : null; // used to create
2050 // minimum dataset set
2052 for (int i = 0; i < sequences.length; i++)
2056 newDs.addElement(null);
2058 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2060 if (importDs && ds != null)
2062 if (!newDs.contains(ds))
2064 newDs.setElementAt(ds, i);
2065 ds = new Sequence(ds);
2066 // update with new dataset sequence
2067 sequences[i].setDatasetSequence(ds);
2071 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2076 // copy and derive new dataset sequence
2077 sequences[i] = sequences[i].deriveSequence();
2078 alignment.getDataset().addSequence(
2079 sequences[i].getDatasetSequence());
2080 // TODO: avoid creation of duplicate dataset sequences with a
2081 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2083 alignment.addSequence(sequences[i]); // merges dataset
2087 newDs.clear(); // tidy up
2089 if (alignment.getAlignmentAnnotation() != null)
2091 for (AlignmentAnnotation alan : alignment
2092 .getAlignmentAnnotation())
2094 if (alan.graphGroup > fgroup)
2096 fgroup = alan.graphGroup;
2100 if (pastedal.getAlignmentAnnotation() != null)
2102 // Add any annotation attached to alignment.
2103 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2104 for (int i = 0; i < alann.length; i++)
2106 annotationAdded = true;
2107 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2109 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2110 if (newann.graphGroup > -1)
2112 if (newGraphGroups.size() <= newann.graphGroup
2113 || newGraphGroups.get(newann.graphGroup) == null)
2115 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2117 newGraphGroups.add(q, null);
2119 newGraphGroups.set(newann.graphGroup, new Integer(
2122 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2126 newann.padAnnotation(alwidth);
2127 alignment.addAnnotation(newann);
2137 addHistoryItem(new EditCommand(
2138 MessageManager.getString("label.add_sequences"),
2139 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2141 // Add any annotations attached to sequences
2142 for (int i = 0; i < sequences.length; i++)
2144 if (sequences[i].getAnnotation() != null)
2146 AlignmentAnnotation newann;
2147 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2149 annotationAdded = true;
2150 newann = sequences[i].getAnnotation()[a];
2151 newann.adjustForAlignment();
2152 newann.padAnnotation(alwidth);
2153 if (newann.graphGroup > -1)
2155 if (newann.graphGroup > -1)
2157 if (newGraphGroups.size() <= newann.graphGroup
2158 || newGraphGroups.get(newann.graphGroup) == null)
2160 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2162 newGraphGroups.add(q, null);
2164 newGraphGroups.set(newann.graphGroup, new Integer(
2167 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2171 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2176 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2183 // propagate alignment changed.
2184 viewport.setEndSeq(alignment.getHeight());
2185 if (annotationAdded)
2187 // Duplicate sequence annotation in all views.
2188 AlignmentI[] alview = this.getViewAlignments();
2189 for (int i = 0; i < sequences.length; i++)
2191 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2196 for (int avnum = 0; avnum < alview.length; avnum++)
2198 if (alview[avnum] != alignment)
2200 // duplicate in a view other than the one with input focus
2201 int avwidth = alview[avnum].getWidth() + 1;
2202 // this relies on sann being preserved after we
2203 // modify the sequence's annotation array for each duplication
2204 for (int a = 0; a < sann.length; a++)
2206 AlignmentAnnotation newann = new AlignmentAnnotation(
2208 sequences[i].addAlignmentAnnotation(newann);
2209 newann.padAnnotation(avwidth);
2210 alview[avnum].addAnnotation(newann); // annotation was
2211 // duplicated earlier
2212 // TODO JAL-1145 graphGroups are not updated for sequence
2213 // annotation added to several views. This may cause
2215 alview[avnum].setAnnotationIndex(newann, a);
2220 buildSortByAnnotationScoresMenu();
2222 viewport.firePropertyChange("alignment", null,
2223 alignment.getSequences());
2224 if (alignPanels != null)
2226 for (AlignmentPanel ap : alignPanels)
2228 ap.validateAnnotationDimensions(false);
2233 alignPanel.validateAnnotationDimensions(false);
2239 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2241 String newtitle = new String("Copied sequences");
2243 if (Desktop.jalviewClipboard != null
2244 && Desktop.jalviewClipboard[2] != null)
2246 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2247 for (int[] region : hc)
2249 af.viewport.hideColumns(region[0], region[1]);
2253 // >>>This is a fix for the moment, until a better solution is
2255 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2257 alignPanel.getSeqPanel().seqCanvas
2258 .getFeatureRenderer());
2260 // TODO: maintain provenance of an alignment, rather than just make the
2261 // title a concatenation of operations.
2264 if (title.startsWith("Copied sequences"))
2270 newtitle = newtitle.concat("- from " + title);
2275 newtitle = new String("Pasted sequences");
2278 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2283 } catch (Exception ex)
2285 ex.printStackTrace();
2286 System.out.println("Exception whilst pasting: " + ex);
2287 // could be anything being pasted in here
2293 protected void expand_newalign(ActionEvent e)
2297 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2298 .getAlignment(), -1);
2299 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2301 String newtitle = new String("Flanking alignment");
2303 if (Desktop.jalviewClipboard != null
2304 && Desktop.jalviewClipboard[2] != null)
2306 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2307 for (int region[] : hc)
2309 af.viewport.hideColumns(region[0], region[1]);
2313 // >>>This is a fix for the moment, until a better solution is
2315 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2317 alignPanel.getSeqPanel().seqCanvas
2318 .getFeatureRenderer());
2320 // TODO: maintain provenance of an alignment, rather than just make the
2321 // title a concatenation of operations.
2323 if (title.startsWith("Copied sequences"))
2329 newtitle = newtitle.concat("- from " + title);
2333 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2335 } catch (Exception ex)
2337 ex.printStackTrace();
2338 System.out.println("Exception whilst pasting: " + ex);
2339 // could be anything being pasted in here
2340 } catch (OutOfMemoryError oom)
2342 new OOMWarning("Viewing flanking region of alignment", oom);
2353 protected void cut_actionPerformed(ActionEvent e)
2355 copy_actionPerformed(null);
2356 delete_actionPerformed(null);
2366 protected void delete_actionPerformed(ActionEvent evt)
2369 SequenceGroup sg = viewport.getSelectionGroup();
2376 * If the cut affects all sequences, warn, remove highlighted columns
2378 if (sg.getSize() == viewport.getAlignment().getHeight())
2380 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2381 .getAlignment().getWidth()) ? true : false;
2382 if (isEntireAlignWidth)
2384 int confirm = JvOptionPane.showConfirmDialog(this,
2385 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2386 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2387 JvOptionPane.OK_CANCEL_OPTION);
2389 if (confirm == JvOptionPane.CANCEL_OPTION
2390 || confirm == JvOptionPane.CLOSED_OPTION)
2395 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2396 sg.getEndRes() + 1);
2398 SequenceI[] cut = sg.getSequences()
2399 .toArray(new SequenceI[sg.getSize()]);
2401 addHistoryItem(new EditCommand(
2402 MessageManager.getString("label.cut_sequences"), Action.CUT,
2403 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2404 viewport.getAlignment()));
2406 viewport.setSelectionGroup(null);
2407 viewport.sendSelection();
2408 viewport.getAlignment().deleteGroup(sg);
2410 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2412 if (viewport.getAlignment().getHeight() < 1)
2416 this.setClosed(true);
2417 } catch (Exception ex)
2430 protected void deleteGroups_actionPerformed(ActionEvent e)
2432 if (avc.deleteGroups())
2434 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2435 alignPanel.updateAnnotation();
2436 alignPanel.paintAlignment(true);
2447 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2449 SequenceGroup sg = new SequenceGroup();
2451 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2453 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2456 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2457 viewport.setSelectionGroup(sg);
2458 viewport.sendSelection();
2459 // JAL-2034 - should delegate to
2460 // alignPanel to decide if overview needs
2462 alignPanel.paintAlignment(false);
2463 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2473 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2475 if (viewport.cursorMode)
2477 alignPanel.getSeqPanel().keyboardNo1 = null;
2478 alignPanel.getSeqPanel().keyboardNo2 = null;
2480 viewport.setSelectionGroup(null);
2481 viewport.getColumnSelection().clear();
2482 viewport.setSelectionGroup(null);
2483 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2484 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2485 // JAL-2034 - should delegate to
2486 // alignPanel to decide if overview needs
2488 alignPanel.paintAlignment(false);
2489 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2490 viewport.sendSelection();
2500 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2502 SequenceGroup sg = viewport.getSelectionGroup();
2506 selectAllSequenceMenuItem_actionPerformed(null);
2511 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2513 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2515 // JAL-2034 - should delegate to
2516 // alignPanel to decide if overview needs
2519 alignPanel.paintAlignment(true);
2520 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2521 viewport.sendSelection();
2525 public void invertColSel_actionPerformed(ActionEvent e)
2527 viewport.invertColumnSelection();
2528 alignPanel.paintAlignment(true);
2529 viewport.sendSelection();
2539 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2541 trimAlignment(true);
2551 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2553 trimAlignment(false);
2556 void trimAlignment(boolean trimLeft)
2558 ColumnSelection colSel = viewport.getColumnSelection();
2561 if (!colSel.isEmpty())
2565 column = colSel.getMin();
2569 column = colSel.getMax();
2573 if (viewport.getSelectionGroup() != null)
2575 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2576 viewport.getHiddenRepSequences());
2580 seqs = viewport.getAlignment().getSequencesArray();
2583 TrimRegionCommand trimRegion;
2586 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2587 column, viewport.getAlignment());
2588 viewport.setStartRes(0);
2592 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2593 column, viewport.getAlignment());
2596 statusBar.setText(MessageManager.formatMessage(
2597 "label.removed_columns",
2598 new String[] { Integer.valueOf(trimRegion.getSize())
2601 addHistoryItem(trimRegion);
2603 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2605 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2606 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2608 viewport.getAlignment().deleteGroup(sg);
2612 viewport.firePropertyChange("alignment", null, viewport
2613 .getAlignment().getSequences());
2624 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2626 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2629 if (viewport.getSelectionGroup() != null)
2631 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2632 viewport.getHiddenRepSequences());
2633 start = viewport.getSelectionGroup().getStartRes();
2634 end = viewport.getSelectionGroup().getEndRes();
2638 seqs = viewport.getAlignment().getSequencesArray();
2641 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2642 "Remove Gapped Columns", seqs, start, end,
2643 viewport.getAlignment());
2645 addHistoryItem(removeGapCols);
2647 statusBar.setText(MessageManager.formatMessage(
2648 "label.removed_empty_columns",
2649 new Object[] { Integer.valueOf(removeGapCols.getSize())
2652 // This is to maintain viewport position on first residue
2653 // of first sequence
2654 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2655 int startRes = seq.findPosition(viewport.startRes);
2656 // ShiftList shifts;
2657 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2658 // edit.alColumnChanges=shifts.getInverse();
2659 // if (viewport.hasHiddenColumns)
2660 // viewport.getColumnSelection().compensateForEdits(shifts);
2661 viewport.setStartRes(seq.findIndex(startRes) - 1);
2662 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2674 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2676 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2679 if (viewport.getSelectionGroup() != null)
2681 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2682 viewport.getHiddenRepSequences());
2683 start = viewport.getSelectionGroup().getStartRes();
2684 end = viewport.getSelectionGroup().getEndRes();
2688 seqs = viewport.getAlignment().getSequencesArray();
2691 // This is to maintain viewport position on first residue
2692 // of first sequence
2693 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2694 int startRes = seq.findPosition(viewport.startRes);
2696 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2697 viewport.getAlignment()));
2699 viewport.setStartRes(seq.findIndex(startRes) - 1);
2701 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2713 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2715 viewport.setPadGaps(padGapsMenuitem.isSelected());
2716 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2727 public void findMenuItem_actionPerformed(ActionEvent e)
2733 * Create a new view of the current alignment.
2736 public void newView_actionPerformed(ActionEvent e)
2738 newView(null, true);
2742 * Creates and shows a new view of the current alignment.
2745 * title of newly created view; if null, one will be generated
2746 * @param copyAnnotation
2747 * if true then duplicate all annnotation, groups and settings
2748 * @return new alignment panel, already displayed.
2750 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2753 * Create a new AlignmentPanel (with its own, new Viewport)
2755 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2757 if (!copyAnnotation)
2760 * remove all groups and annotation except for the automatic stuff
2762 newap.av.getAlignment().deleteAllGroups();
2763 newap.av.getAlignment().deleteAllAnnotations(false);
2766 newap.av.setGatherViewsHere(false);
2768 if (viewport.viewName == null)
2770 viewport.viewName = MessageManager
2771 .getString("label.view_name_original");
2775 * Views share the same edits undo and redo stacks
2777 newap.av.setHistoryList(viewport.getHistoryList());
2778 newap.av.setRedoList(viewport.getRedoList());
2781 * Views share the same mappings; need to deregister any new mappings
2782 * created by copyAlignPanel, and register the new reference to the shared
2785 newap.av.replaceMappings(viewport.getAlignment());
2787 newap.av.viewName = getNewViewName(viewTitle);
2789 addAlignmentPanel(newap, true);
2790 newap.alignmentChanged();
2792 if (alignPanels.size() == 2)
2794 viewport.setGatherViewsHere(true);
2796 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2801 * Make a new name for the view, ensuring it is unique within the current
2802 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2803 * these now use viewId. Unique view names are still desirable for usability.)
2808 protected String getNewViewName(String viewTitle)
2810 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2811 boolean addFirstIndex = false;
2812 if (viewTitle == null || viewTitle.trim().length() == 0)
2814 viewTitle = MessageManager.getString("action.view");
2815 addFirstIndex = true;
2819 index = 1;// we count from 1 if given a specific name
2821 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2823 List<Component> comps = PaintRefresher.components.get(viewport
2824 .getSequenceSetId());
2826 List<String> existingNames = getExistingViewNames(comps);
2828 while (existingNames.contains(newViewName))
2830 newViewName = viewTitle + " " + (++index);
2836 * Returns a list of distinct view names found in the given list of
2837 * components. View names are held on the viewport of an AlignmentPanel.
2842 protected List<String> getExistingViewNames(List<Component> comps)
2844 List<String> existingNames = new ArrayList<String>();
2845 for (Component comp : comps)
2847 if (comp instanceof AlignmentPanel)
2849 AlignmentPanel ap = (AlignmentPanel) comp;
2850 if (!existingNames.contains(ap.av.viewName))
2852 existingNames.add(ap.av.viewName);
2856 return existingNames;
2860 * Explode tabbed views into separate windows.
2863 public void expandViews_actionPerformed(ActionEvent e)
2865 Desktop.explodeViews(this);
2869 * Gather views in separate windows back into a tabbed presentation.
2872 public void gatherViews_actionPerformed(ActionEvent e)
2874 Desktop.instance.gatherViews(this);
2884 public void font_actionPerformed(ActionEvent e)
2886 new FontChooser(alignPanel);
2896 protected void seqLimit_actionPerformed(ActionEvent e)
2898 viewport.setShowJVSuffix(seqLimits.isSelected());
2900 alignPanel.getIdPanel().getIdCanvas()
2901 .setPreferredSize(alignPanel.calculateIdWidth());
2902 alignPanel.paintAlignment(true);
2906 public void idRightAlign_actionPerformed(ActionEvent e)
2908 viewport.setRightAlignIds(idRightAlign.isSelected());
2909 alignPanel.paintAlignment(true);
2913 public void centreColumnLabels_actionPerformed(ActionEvent e)
2915 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2916 alignPanel.paintAlignment(true);
2922 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2925 protected void followHighlight_actionPerformed()
2928 * Set the 'follow' flag on the Viewport (and scroll to position if now
2931 final boolean state = this.followHighlightMenuItem.getState();
2932 viewport.setFollowHighlight(state);
2935 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2946 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2948 viewport.setColourText(colourTextMenuItem.isSelected());
2949 alignPanel.paintAlignment(true);
2959 public void wrapMenuItem_actionPerformed(ActionEvent e)
2961 scaleAbove.setVisible(wrapMenuItem.isSelected());
2962 scaleLeft.setVisible(wrapMenuItem.isSelected());
2963 scaleRight.setVisible(wrapMenuItem.isSelected());
2964 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2965 alignPanel.updateLayout();
2969 public void showAllSeqs_actionPerformed(ActionEvent e)
2971 viewport.showAllHiddenSeqs();
2975 public void showAllColumns_actionPerformed(ActionEvent e)
2977 viewport.showAllHiddenColumns();
2979 viewport.sendSelection();
2983 public void hideSelSequences_actionPerformed(ActionEvent e)
2985 viewport.hideAllSelectedSeqs();
2986 // alignPanel.paintAlignment(true);
2990 * called by key handler and the hide all/show all menu items
2995 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2998 boolean hide = false;
2999 SequenceGroup sg = viewport.getSelectionGroup();
3000 if (!toggleSeqs && !toggleCols)
3002 // Hide everything by the current selection - this is a hack - we do the
3003 // invert and then hide
3004 // first check that there will be visible columns after the invert.
3005 if (viewport.hasSelectedColumns()
3006 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3009 // now invert the sequence set, if required - empty selection implies
3010 // that no hiding is required.
3013 invertSequenceMenuItem_actionPerformed(null);
3014 sg = viewport.getSelectionGroup();
3018 viewport.expandColSelection(sg, true);
3019 // finally invert the column selection and get the new sequence
3021 invertColSel_actionPerformed(null);
3028 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3030 hideSelSequences_actionPerformed(null);
3033 else if (!(toggleCols && viewport.hasSelectedColumns()))
3035 showAllSeqs_actionPerformed(null);
3041 if (viewport.hasSelectedColumns())
3043 hideSelColumns_actionPerformed(null);
3046 viewport.setSelectionGroup(sg);
3051 showAllColumns_actionPerformed(null);
3060 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3061 * event.ActionEvent)
3064 public void hideAllButSelection_actionPerformed(ActionEvent e)
3066 toggleHiddenRegions(false, false);
3067 viewport.sendSelection();
3074 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3078 public void hideAllSelection_actionPerformed(ActionEvent e)
3080 SequenceGroup sg = viewport.getSelectionGroup();
3081 viewport.expandColSelection(sg, false);
3082 viewport.hideAllSelectedSeqs();
3083 viewport.hideSelectedColumns();
3084 alignPanel.paintAlignment(true);
3085 viewport.sendSelection();
3092 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3096 public void showAllhidden_actionPerformed(ActionEvent e)
3098 viewport.showAllHiddenColumns();
3099 viewport.showAllHiddenSeqs();
3100 alignPanel.paintAlignment(true);
3101 viewport.sendSelection();
3105 public void hideSelColumns_actionPerformed(ActionEvent e)
3107 viewport.hideSelectedColumns();
3108 alignPanel.paintAlignment(true);
3109 viewport.sendSelection();
3113 public void hiddenMarkers_actionPerformed(ActionEvent e)
3115 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3126 protected void scaleAbove_actionPerformed(ActionEvent e)
3128 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3129 alignPanel.paintAlignment(true);
3139 protected void scaleLeft_actionPerformed(ActionEvent e)
3141 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3142 alignPanel.paintAlignment(true);
3152 protected void scaleRight_actionPerformed(ActionEvent e)
3154 viewport.setScaleRightWrapped(scaleRight.isSelected());
3155 alignPanel.paintAlignment(true);
3165 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3167 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3168 alignPanel.paintAlignment(true);
3178 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3180 viewport.setShowText(viewTextMenuItem.isSelected());
3181 alignPanel.paintAlignment(true);
3191 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3193 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3194 alignPanel.paintAlignment(true);
3197 public FeatureSettings featureSettings;
3200 public FeatureSettingsControllerI getFeatureSettingsUI()
3202 return featureSettings;
3206 public void featureSettings_actionPerformed(ActionEvent e)
3208 if (featureSettings != null)
3210 featureSettings.close();
3211 featureSettings = null;
3213 if (!showSeqFeatures.isSelected())
3215 // make sure features are actually displayed
3216 showSeqFeatures.setSelected(true);
3217 showSeqFeatures_actionPerformed(null);
3219 featureSettings = new FeatureSettings(this);
3223 * Set or clear 'Show Sequence Features'
3229 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3231 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3232 alignPanel.paintAlignment(true);
3233 if (alignPanel.getOverviewPanel() != null)
3235 alignPanel.getOverviewPanel().updateOverviewImage();
3240 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3241 * the annotations panel as a whole.
3243 * The options to show/hide all annotations should be enabled when the panel
3244 * is shown, and disabled when the panel is hidden.
3249 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3251 final boolean setVisible = annotationPanelMenuItem.isSelected();
3252 viewport.setShowAnnotation(setVisible);
3253 this.showAllSeqAnnotations.setEnabled(setVisible);
3254 this.hideAllSeqAnnotations.setEnabled(setVisible);
3255 this.showAllAlAnnotations.setEnabled(setVisible);
3256 this.hideAllAlAnnotations.setEnabled(setVisible);
3257 alignPanel.updateLayout();
3261 public void alignmentProperties()
3263 JEditorPane editPane = new JEditorPane("text/html", "");
3264 editPane.setEditable(false);
3265 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3267 editPane.setText(MessageManager.formatMessage("label.html_content",
3268 new Object[] { contents.toString() }));
3269 JInternalFrame frame = new JInternalFrame();
3270 frame.getContentPane().add(new JScrollPane(editPane));
3272 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3273 "label.alignment_properties", new Object[] { getTitle() }),
3284 public void overviewMenuItem_actionPerformed(ActionEvent e)
3286 if (alignPanel.overviewPanel != null)
3291 JInternalFrame frame = new JInternalFrame();
3292 OverviewPanel overview = new OverviewPanel(alignPanel);
3293 frame.setContentPane(overview);
3294 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3295 "label.overview_params", new Object[] { this.getTitle() }),
3296 frame.getWidth(), frame.getHeight());
3298 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3299 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3302 public void internalFrameClosed(
3303 javax.swing.event.InternalFrameEvent evt)
3305 alignPanel.setOverviewPanel(null);
3309 alignPanel.setOverviewPanel(overview);
3313 public void textColour_actionPerformed()
3315 new TextColourChooser().chooseColour(alignPanel, null);
3325 protected void noColourmenuItem_actionPerformed()
3331 * public void covariationColour_actionPerformed() {
3333 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3337 public void annotationColour_actionPerformed()
3339 new AnnotationColourChooser(viewport, alignPanel);
3343 public void annotationColumn_actionPerformed(ActionEvent e)
3345 new AnnotationColumnChooser(viewport, alignPanel);
3349 * Action on the user checking or unchecking the option to apply the selected
3350 * colour scheme to all groups. If unchecked, groups may have their own
3351 * independent colour schemes.
3355 protected void applyToAllGroups_actionPerformed()
3357 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3361 * Action on user selecting a colour from the colour menu
3364 * the name (not the menu item label!) of the colour scheme
3366 public void changeColour_actionPerformed(String name)
3368 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3374 * Actions on setting or changing the alignment colour scheme
3379 public void changeColour(ColourSchemeI cs)
3381 // TODO: pull up to controller method
3384 setColourSelected(cs.getSchemeName());
3385 // Make sure viewport is up to date w.r.t. any sliders
3386 if (viewport.getAbovePIDThreshold())
3388 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3390 viewport.setThreshold(threshold);
3393 if (viewport.getConservationSelected())
3395 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3400 viewport.setGlobalColourScheme(cs);
3402 alignPanel.paintAlignment(true);
3412 protected void modifyPID_actionPerformed()
3414 if (viewport.getAbovePIDThreshold()
3415 && viewport.getGlobalColourScheme() != null)
3417 SliderPanel.setPIDSliderSource(alignPanel,
3418 viewport.getGlobalColourScheme(), "Background");
3419 SliderPanel.showPIDSlider();
3430 protected void modifyConservation_actionPerformed()
3432 if (viewport.getConservationSelected()
3433 && viewport.getGlobalColourScheme() != null)
3435 SliderPanel.setConservationSlider(alignPanel,
3436 viewport.getGlobalColourScheme(), "Background");
3437 SliderPanel.showConservationSlider();
3448 protected void conservationMenuItem_actionPerformed()
3450 viewport.setConservationSelected(conservationMenuItem.isSelected());
3452 viewport.setAbovePIDThreshold(false);
3453 abovePIDThreshold.setSelected(false);
3455 changeColour(viewport.getGlobalColourScheme());
3457 modifyConservation_actionPerformed();
3467 public void abovePIDThreshold_actionPerformed()
3469 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3471 conservationMenuItem.setSelected(false);
3472 viewport.setConservationSelected(false);
3474 changeColour(viewport.getGlobalColourScheme());
3476 modifyPID_actionPerformed();
3480 * Action on the user selecting the option "User Defined" to create or load a
3486 public void userDefinedColour_actionPerformed(ActionEvent e)
3488 new UserDefinedColours(alignPanel, null);
3498 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3500 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3501 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3502 .getAlignment().getSequenceAt(0), null);
3503 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3504 viewport.getAlignment()));
3505 alignPanel.paintAlignment(true);
3515 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3517 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3518 AlignmentSorter.sortByID(viewport.getAlignment());
3519 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3520 viewport.getAlignment()));
3521 alignPanel.paintAlignment(true);
3531 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3533 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3534 AlignmentSorter.sortByLength(viewport.getAlignment());
3535 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3536 viewport.getAlignment()));
3537 alignPanel.paintAlignment(true);
3547 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3549 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3550 AlignmentSorter.sortByGroup(viewport.getAlignment());
3551 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3552 viewport.getAlignment()));
3554 alignPanel.paintAlignment(true);
3564 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3566 new RedundancyPanel(alignPanel, this);
3576 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3578 if ((viewport.getSelectionGroup() == null)
3579 || (viewport.getSelectionGroup().getSize() < 2))
3581 JvOptionPane.showInternalMessageDialog(this, MessageManager
3582 .getString("label.you_must_select_least_two_sequences"),
3583 MessageManager.getString("label.invalid_selection"),
3584 JvOptionPane.WARNING_MESSAGE);
3588 JInternalFrame frame = new JInternalFrame();
3589 frame.setContentPane(new PairwiseAlignPanel(viewport));
3590 Desktop.addInternalFrame(frame,
3591 MessageManager.getString("action.pairwise_alignment"), 600,
3603 public void PCAMenuItem_actionPerformed(ActionEvent e)
3605 if (((viewport.getSelectionGroup() != null)
3606 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3607 .getSelectionGroup().getSize() > 0))
3608 || (viewport.getAlignment().getHeight() < 4))
3611 .showInternalMessageDialog(
3614 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3616 .getString("label.sequence_selection_insufficient"),
3617 JvOptionPane.WARNING_MESSAGE);
3622 new PCAPanel(alignPanel);
3626 public void autoCalculate_actionPerformed(ActionEvent e)
3628 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3629 if (viewport.autoCalculateConsensus)
3631 viewport.firePropertyChange("alignment", null, viewport
3632 .getAlignment().getSequences());
3637 public void sortByTreeOption_actionPerformed(ActionEvent e)
3639 viewport.sortByTree = sortByTree.isSelected();
3643 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3645 viewport.followSelection = listenToViewSelections.isSelected();
3655 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3657 newTreePanel("AV", "PID", "Average distance tree using PID");
3667 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3669 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3679 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3681 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3691 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3693 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3706 void newTreePanel(String type, String pwType, String title)
3710 if (viewport.getSelectionGroup() != null
3711 && viewport.getSelectionGroup().getSize() > 0)
3713 if (viewport.getSelectionGroup().getSize() < 3)
3719 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3721 .getString("label.not_enough_sequences"),
3722 JvOptionPane.WARNING_MESSAGE);
3726 SequenceGroup sg = viewport.getSelectionGroup();
3728 /* Decide if the selection is a column region */
3729 for (SequenceI _s : sg.getSequences())
3731 if (_s.getLength() < sg.getEndRes())
3737 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3739 .getString("label.sequences_selection_not_aligned"),
3740 JvOptionPane.WARNING_MESSAGE);
3746 title = title + " on region";
3747 tp = new TreePanel(alignPanel, type, pwType);
3751 // are the visible sequences aligned?
3752 if (!viewport.getAlignment().isAligned(false))
3758 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3760 .getString("label.sequences_not_aligned"),
3761 JvOptionPane.WARNING_MESSAGE);
3766 if (viewport.getAlignment().getHeight() < 2)
3771 tp = new TreePanel(alignPanel, type, pwType);
3776 if (viewport.viewName != null)
3778 title += viewport.viewName + " of ";
3781 title += this.title;
3783 Desktop.addInternalFrame(tp, title, 600, 500);
3794 public void addSortByOrderMenuItem(String title,
3795 final AlignmentOrder order)
3797 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3798 "action.by_title_param", new Object[] { title }));
3800 item.addActionListener(new java.awt.event.ActionListener()
3803 public void actionPerformed(ActionEvent e)
3805 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3807 // TODO: JBPNote - have to map order entries to curent SequenceI
3809 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3811 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3814 alignPanel.paintAlignment(true);
3820 * Add a new sort by annotation score menu item
3823 * the menu to add the option to
3825 * the label used to retrieve scores for each sequence on the
3828 public void addSortByAnnotScoreMenuItem(JMenu sort,
3829 final String scoreLabel)
3831 final JMenuItem item = new JMenuItem(scoreLabel);
3833 item.addActionListener(new java.awt.event.ActionListener()
3836 public void actionPerformed(ActionEvent e)
3838 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3839 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3840 viewport.getAlignment());// ,viewport.getSelectionGroup());
3841 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3842 viewport.getAlignment()));
3843 alignPanel.paintAlignment(true);
3849 * last hash for alignment's annotation array - used to minimise cost of
3852 protected int _annotationScoreVectorHash;
3855 * search the alignment and rebuild the sort by annotation score submenu the
3856 * last alignment annotation vector hash is stored to minimize cost of
3857 * rebuilding in subsequence calls.
3861 public void buildSortByAnnotationScoresMenu()
3863 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3868 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3870 sortByAnnotScore.removeAll();
3871 // almost certainly a quicker way to do this - but we keep it simple
3872 Hashtable scoreSorts = new Hashtable();
3873 AlignmentAnnotation aann[];
3874 for (SequenceI sqa : viewport.getAlignment().getSequences())
3876 aann = sqa.getAnnotation();
3877 for (int i = 0; aann != null && i < aann.length; i++)
3879 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3881 scoreSorts.put(aann[i].label, aann[i].label);
3885 Enumeration labels = scoreSorts.keys();
3886 while (labels.hasMoreElements())
3888 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3889 (String) labels.nextElement());
3891 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3894 _annotationScoreVectorHash = viewport.getAlignment()
3895 .getAlignmentAnnotation().hashCode();
3900 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3901 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3902 * call. Listeners are added to remove the menu item when the treePanel is
3903 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3907 * Displayed tree window.
3909 * SortBy menu item title.
3912 public void buildTreeMenu()
3914 calculateTree.removeAll();
3915 // build the calculate menu
3917 for (final String type : new String[] { "NJ", "AV" })
3919 String treecalcnm = MessageManager.getString("label.tree_calc_"
3920 + type.toLowerCase());
3921 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
3923 JMenuItem tm = new JMenuItem();
3924 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
3925 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
3926 || sm.isProtein() == !viewport.getAlignment()
3929 String smn = MessageManager.getStringOrReturn(
3930 "label.score_model_", sm.getName());
3931 final String title = MessageManager.formatMessage(
3932 "label.treecalc_title", treecalcnm, smn);
3933 tm.setText(title);//
3934 tm.addActionListener(new java.awt.event.ActionListener()
3937 public void actionPerformed(ActionEvent e)
3939 newTreePanel(type, pwtype, title);
3942 calculateTree.add(tm);
3947 sortByTreeMenu.removeAll();
3949 List<Component> comps = PaintRefresher.components.get(viewport
3950 .getSequenceSetId());
3951 List<TreePanel> treePanels = new ArrayList<TreePanel>();
3952 for (Component comp : comps)
3954 if (comp instanceof TreePanel)
3956 treePanels.add((TreePanel) comp);
3960 if (treePanels.size() < 1)
3962 sortByTreeMenu.setVisible(false);
3966 sortByTreeMenu.setVisible(true);
3968 for (final TreePanel tp : treePanels)
3970 final JMenuItem item = new JMenuItem(tp.getTitle());
3971 item.addActionListener(new java.awt.event.ActionListener()
3974 public void actionPerformed(ActionEvent e)
3976 tp.sortByTree_actionPerformed();
3977 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3982 sortByTreeMenu.add(item);
3986 public boolean sortBy(AlignmentOrder alorder, String undoname)
3988 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3989 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3990 if (undoname != null)
3992 addHistoryItem(new OrderCommand(undoname, oldOrder,
3993 viewport.getAlignment()));
3995 alignPanel.paintAlignment(true);
4000 * Work out whether the whole set of sequences or just the selected set will
4001 * be submitted for multiple alignment.
4004 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4006 // Now, check we have enough sequences
4007 AlignmentView msa = null;
4009 if ((viewport.getSelectionGroup() != null)
4010 && (viewport.getSelectionGroup().getSize() > 1))
4012 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4013 // some common interface!
4015 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4016 * SequenceI[sz = seqs.getSize(false)];
4018 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4019 * seqs.getSequenceAt(i); }
4021 msa = viewport.getAlignmentView(true);
4023 else if (viewport.getSelectionGroup() != null
4024 && viewport.getSelectionGroup().getSize() == 1)
4026 int option = JvOptionPane.showConfirmDialog(this,
4027 MessageManager.getString("warn.oneseq_msainput_selection"),
4028 MessageManager.getString("label.invalid_selection"),
4029 JvOptionPane.OK_CANCEL_OPTION);
4030 if (option == JvOptionPane.OK_OPTION)
4032 msa = viewport.getAlignmentView(false);
4037 msa = viewport.getAlignmentView(false);
4043 * Decides what is submitted to a secondary structure prediction service: the
4044 * first sequence in the alignment, or in the current selection, or, if the
4045 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4046 * region or the whole alignment. (where the first sequence in the set is the
4047 * one that the prediction will be for).
4049 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4051 AlignmentView seqs = null;
4053 if ((viewport.getSelectionGroup() != null)
4054 && (viewport.getSelectionGroup().getSize() > 0))
4056 seqs = viewport.getAlignmentView(true);
4060 seqs = viewport.getAlignmentView(false);
4062 // limit sequences - JBPNote in future - could spawn multiple prediction
4064 // TODO: viewport.getAlignment().isAligned is a global state - the local
4065 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4066 if (!viewport.getAlignment().isAligned(false))
4068 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4069 // TODO: if seqs.getSequences().length>1 then should really have warned
4083 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4085 // Pick the tree file
4086 JalviewFileChooser chooser = new JalviewFileChooser(
4087 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4088 chooser.setFileView(new JalviewFileView());
4089 chooser.setDialogTitle(MessageManager
4090 .getString("label.select_newick_like_tree_file"));
4091 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4093 int value = chooser.showOpenDialog(null);
4095 if (value == JalviewFileChooser.APPROVE_OPTION)
4097 String choice = chooser.getSelectedFile().getPath();
4098 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4099 jalview.io.NewickFile fin = null;
4102 fin = new NewickFile(choice, DataSourceType.FILE);
4103 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4104 } catch (Exception ex)
4111 .getString("label.problem_reading_tree_file"),
4112 JvOptionPane.WARNING_MESSAGE);
4113 ex.printStackTrace();
4115 if (fin != null && fin.hasWarningMessage())
4117 JvOptionPane.showMessageDialog(Desktop.desktop, fin
4118 .getWarningMessage(), MessageManager
4119 .getString("label.possible_problem_with_tree_file"),
4120 JvOptionPane.WARNING_MESSAGE);
4125 public TreePanel ShowNewickTree(NewickFile nf, String title)
4127 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4130 public TreePanel ShowNewickTree(NewickFile nf, String title,
4131 AlignmentView input)
4133 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4136 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4137 int h, int x, int y)
4139 return ShowNewickTree(nf, title, null, w, h, x, y);
4143 * Add a treeviewer for the tree extracted from a newick file object to the
4144 * current alignment view
4151 * Associated alignment input data (or null)
4160 * @return TreePanel handle
4162 public TreePanel ShowNewickTree(NewickFile nf, String title,
4163 AlignmentView input, int w, int h, int x, int y)
4165 TreePanel tp = null;
4171 if (nf.getTree() != null)
4173 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4179 tp.setLocation(x, y);
4182 Desktop.addInternalFrame(tp, title, w, h);
4184 } catch (Exception ex)
4186 ex.printStackTrace();
4192 private boolean buildingMenu = false;
4195 * Generates menu items and listener event actions for web service clients
4198 public void BuildWebServiceMenu()
4200 while (buildingMenu)
4204 System.err.println("Waiting for building menu to finish.");
4206 } catch (Exception e)
4210 final AlignFrame me = this;
4211 buildingMenu = true;
4212 new Thread(new Runnable()
4217 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4220 // System.err.println("Building ws menu again "
4221 // + Thread.currentThread());
4222 // TODO: add support for context dependent disabling of services based
4224 // alignment and current selection
4225 // TODO: add additional serviceHandle parameter to specify abstract
4227 // class independently of AbstractName
4228 // TODO: add in rediscovery GUI function to restart discoverer
4229 // TODO: group services by location as well as function and/or
4231 // object broker mechanism.
4232 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4233 final IProgressIndicator af = me;
4236 * do not i18n these strings - they are hard-coded in class
4237 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4238 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4240 final JMenu msawsmenu = new JMenu("Alignment");
4241 final JMenu secstrmenu = new JMenu(
4242 "Secondary Structure Prediction");
4243 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4244 final JMenu analymenu = new JMenu("Analysis");
4245 final JMenu dismenu = new JMenu("Protein Disorder");
4246 // JAL-940 - only show secondary structure prediction services from
4247 // the legacy server
4248 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4250 Discoverer.services != null && (Discoverer.services.size() > 0))
4252 // TODO: refactor to allow list of AbstractName/Handler bindings to
4254 // stored or retrieved from elsewhere
4255 // No MSAWS used any more:
4256 // Vector msaws = null; // (Vector)
4257 // Discoverer.services.get("MsaWS");
4258 Vector secstrpr = (Vector) Discoverer.services
4260 if (secstrpr != null)
4262 // Add any secondary structure prediction services
4263 for (int i = 0, j = secstrpr.size(); i < j; i++)
4265 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4267 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4268 .getServiceClient(sh);
4269 int p = secstrmenu.getItemCount();
4270 impl.attachWSMenuEntry(secstrmenu, me);
4271 int q = secstrmenu.getItemCount();
4272 for (int litm = p; litm < q; litm++)
4274 legacyItems.add(secstrmenu.getItem(litm));
4280 // Add all submenus in the order they should appear on the web
4282 wsmenu.add(msawsmenu);
4283 wsmenu.add(secstrmenu);
4284 wsmenu.add(dismenu);
4285 wsmenu.add(analymenu);
4286 // No search services yet
4287 // wsmenu.add(seqsrchmenu);
4289 javax.swing.SwingUtilities.invokeLater(new Runnable()
4296 webService.removeAll();
4297 // first, add discovered services onto the webservices menu
4298 if (wsmenu.size() > 0)
4300 for (int i = 0, j = wsmenu.size(); i < j; i++)
4302 webService.add(wsmenu.get(i));
4307 webService.add(me.webServiceNoServices);
4309 // TODO: move into separate menu builder class.
4310 boolean new_sspred = false;
4311 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4313 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4314 if (jws2servs != null)
4316 if (jws2servs.hasServices())
4318 jws2servs.attachWSMenuEntry(webService, me);
4319 for (Jws2Instance sv : jws2servs.getServices())
4321 if (sv.description.toLowerCase().contains("jpred"))
4323 for (JMenuItem jmi : legacyItems)
4325 jmi.setVisible(false);
4331 if (jws2servs.isRunning())
4333 JMenuItem tm = new JMenuItem(
4334 "Still discovering JABA Services");
4335 tm.setEnabled(false);
4340 build_urlServiceMenu(me.webService);
4341 build_fetchdbmenu(webService);
4342 for (JMenu item : wsmenu)
4344 if (item.getItemCount() == 0)
4346 item.setEnabled(false);
4350 item.setEnabled(true);
4353 } catch (Exception e)
4356 .debug("Exception during web service menu building process.",
4361 } catch (Exception e)
4364 buildingMenu = false;
4371 * construct any groupURL type service menu entries.
4375 private void build_urlServiceMenu(JMenu webService)
4377 // TODO: remove this code when 2.7 is released
4378 // DEBUG - alignmentView
4380 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4381 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4383 * @Override public void actionPerformed(ActionEvent e) {
4384 * jalview.datamodel.AlignmentView
4385 * .testSelectionViews(af.viewport.getAlignment(),
4386 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4388 * }); webService.add(testAlView);
4390 // TODO: refactor to RestClient discoverer and merge menu entries for
4391 // rest-style services with other types of analysis/calculation service
4392 // SHmmr test client - still being implemented.
4393 // DEBUG - alignmentView
4395 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4398 client.attachWSMenuEntry(
4399 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4405 * Searches the alignment sequences for xRefs and builds the Show
4406 * Cross-References menu (formerly called Show Products), with database
4407 * sources for which cross-references are found (protein sources for a
4408 * nucleotide alignment and vice versa)
4410 * @return true if Show Cross-references menu should be enabled
4412 public boolean canShowProducts()
4414 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4415 AlignmentI dataset = viewport.getAlignment().getDataset();
4417 showProducts.removeAll();
4418 final boolean dna = viewport.getAlignment().isNucleotide();
4420 if (seqs == null || seqs.length == 0)
4422 // nothing to see here.
4426 boolean showp = false;
4429 List<String> ptypes = new CrossRef(seqs, dataset)
4430 .findXrefSourcesForSequences(dna);
4432 for (final String source : ptypes)
4435 final AlignFrame af = this;
4436 JMenuItem xtype = new JMenuItem(source);
4437 xtype.addActionListener(new ActionListener()
4440 public void actionPerformed(ActionEvent e)
4442 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4445 showProducts.add(xtype);
4447 showProducts.setVisible(showp);
4448 showProducts.setEnabled(showp);
4449 } catch (Exception e)
4452 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4460 * Finds and displays cross-references for the selected sequences (protein
4461 * products for nucleotide sequences, dna coding sequences for peptides).
4464 * the sequences to show cross-references for
4466 * true if from a nucleotide alignment (so showing proteins)
4468 * the database to show cross-references for
4470 protected void showProductsFor(final SequenceI[] sel,
4471 final boolean _odna, final String source)
4473 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4478 * Construct and display a new frame containing the translation of this
4479 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4482 public void showTranslation_actionPerformed(ActionEvent e)
4484 AlignmentI al = null;
4487 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4489 al = dna.translateCdna();
4490 } catch (Exception ex)
4492 jalview.bin.Cache.log.error(
4493 "Exception during translation. Please report this !", ex);
4494 final String msg = MessageManager
4495 .getString("label.error_when_translating_sequences_submit_bug_report");
4496 final String errorTitle = MessageManager
4497 .getString("label.implementation_error")
4498 + MessageManager.getString("label.translation_failed");
4499 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4500 JvOptionPane.ERROR_MESSAGE);
4503 if (al == null || al.getHeight() == 0)
4505 final String msg = MessageManager
4506 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4507 final String errorTitle = MessageManager
4508 .getString("label.translation_failed");
4509 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4510 JvOptionPane.WARNING_MESSAGE);
4514 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4515 af.setFileFormat(this.currentFileFormat);
4516 final String newTitle = MessageManager.formatMessage(
4517 "label.translation_of_params",
4518 new Object[] { this.getTitle() });
4519 af.setTitle(newTitle);
4520 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4522 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4523 viewport.openSplitFrame(af, new Alignment(seqs));
4527 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4534 * Set the file format
4538 public void setFileFormat(FileFormatI format)
4540 this.currentFileFormat = format;
4544 * Try to load a features file onto the alignment.
4547 * contents or path to retrieve file
4549 * access mode of file (see jalview.io.AlignFile)
4550 * @return true if features file was parsed correctly.
4552 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4554 return avc.parseFeaturesFile(file, sourceType,
4555 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4560 public void refreshFeatureUI(boolean enableIfNecessary)
4562 // note - currently this is only still here rather than in the controller
4563 // because of the featureSettings hard reference that is yet to be
4565 if (enableIfNecessary)
4567 viewport.setShowSequenceFeatures(true);
4568 showSeqFeatures.setSelected(true);
4574 public void dragEnter(DropTargetDragEvent evt)
4579 public void dragExit(DropTargetEvent evt)
4584 public void dragOver(DropTargetDragEvent evt)
4589 public void dropActionChanged(DropTargetDragEvent evt)
4594 public void drop(DropTargetDropEvent evt)
4596 // JAL-1552 - acceptDrop required before getTransferable call for
4597 // Java's Transferable for native dnd
4598 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4599 Transferable t = evt.getTransferable();
4600 List<String> files = new ArrayList<String>();
4601 List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4605 Desktop.transferFromDropTarget(files, protocols, evt, t);
4606 } catch (Exception e)
4608 e.printStackTrace();
4614 // check to see if any of these files have names matching sequences in
4616 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4617 .getAlignment().getSequencesArray());
4619 * Object[] { String,SequenceI}
4621 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4622 ArrayList<String> filesnotmatched = new ArrayList<String>();
4623 for (int i = 0; i < files.size(); i++)
4625 String file = files.get(i).toString();
4627 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4628 if (protocol == DataSourceType.FILE)
4630 File fl = new File(file);
4631 pdbfn = fl.getName();
4633 else if (protocol == DataSourceType.URL)
4635 URL url = new URL(file);
4636 pdbfn = url.getFile();
4638 if (pdbfn.length() > 0)
4640 // attempt to find a match in the alignment
4641 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4642 int l = 0, c = pdbfn.indexOf(".");
4643 while (mtch == null && c != -1)
4648 } while ((c = pdbfn.indexOf(".", l)) > l);
4651 pdbfn = pdbfn.substring(0, l);
4653 mtch = idm.findAllIdMatches(pdbfn);
4657 FileFormatI type = null;
4660 type = new IdentifyFile().identify(file, protocol);
4661 } catch (Exception ex)
4665 if (type != null && type.isStructureFile())
4667 filesmatched.add(new Object[] { file, protocol, mtch });
4671 // File wasn't named like one of the sequences or wasn't a PDB file.
4672 filesnotmatched.add(file);
4676 if (filesmatched.size() > 0)
4678 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4684 "label.automatically_associate_structure_files_with_sequences_same_name",
4685 new Object[] { Integer
4691 .getString("label.automatically_associate_structure_files_by_name"),
4692 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4695 for (Object[] fm : filesmatched)
4697 // try and associate
4698 // TODO: may want to set a standard ID naming formalism for
4699 // associating PDB files which have no IDs.
4700 for (SequenceI toassoc : (SequenceI[]) fm[2])
4702 PDBEntry pe = new AssociatePdbFileWithSeq()
4703 .associatePdbWithSeq((String) fm[0],
4704 (DataSourceType) fm[1], toassoc, false,
4708 System.err.println("Associated file : "
4709 + ((String) fm[0]) + " with "
4710 + toassoc.getDisplayId(true));
4714 alignPanel.paintAlignment(true);
4718 if (filesnotmatched.size() > 0)
4721 && (Cache.getDefault(
4722 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4728 "label.ignore_unmatched_dropped_files_info",
4729 new Object[] { Integer
4736 .getString("label.ignore_unmatched_dropped_files"),
4737 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4741 for (String fn : filesnotmatched)
4743 loadJalviewDataFile(fn, null, null, null);
4747 } catch (Exception ex)
4749 ex.printStackTrace();
4755 * Attempt to load a "dropped" file or URL string: First by testing whether
4756 * it's an Annotation file, then a JNet file, and finally a features file. If
4757 * all are false then the user may have dropped an alignment file onto this
4761 * either a filename or a URL string.
4763 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4764 FileFormatI format, SequenceI assocSeq)
4768 if (sourceType == null)
4770 sourceType = FormatAdapter.checkProtocol(file);
4772 // if the file isn't identified, or not positively identified as some
4773 // other filetype (PFAM is default unidentified alignment file type) then
4774 // try to parse as annotation.
4775 boolean isAnnotation = (format == null || FileFormat.Pfam
4776 .equals(format)) ? new AnnotationFile()
4777 .annotateAlignmentView(viewport, file, sourceType) : false;
4781 // first see if its a T-COFFEE score file
4782 TCoffeeScoreFile tcf = null;
4785 tcf = new TCoffeeScoreFile(file, sourceType);
4788 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4790 // tcoffeeColour.setEnabled(true);
4791 // tcoffeeColour.setSelected(true);
4792 for (Component menuItem : colourMenu.getMenuComponents())
4794 if (menuItem instanceof JRadioButtonMenuItem
4795 && ((JRadioButtonMenuItem) menuItem).getText()
4796 .equals("T-Coffee Scores"))
4798 ((JRadioButtonMenuItem) menuItem).setSelected(true);
4802 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4803 isAnnotation = true;
4805 .setText(MessageManager
4806 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4810 // some problem - if no warning its probable that the ID matching
4811 // process didn't work
4815 tcf.getWarningMessage() == null ? MessageManager
4816 .getString("label.check_file_matches_sequence_ids_alignment")
4817 : tcf.getWarningMessage(),
4819 .getString("label.problem_reading_tcoffee_score_file"),
4820 JvOptionPane.WARNING_MESSAGE);
4827 } catch (Exception x)
4830 .debug("Exception when processing data source as T-COFFEE score file",
4836 // try to see if its a JNet 'concise' style annotation file *before*
4838 // try to parse it as a features file
4841 format = new IdentifyFile().identify(file, sourceType);
4843 if (FileFormat.Jnet.equals(format))
4845 JPredFile predictions = new JPredFile(
4847 new JnetAnnotationMaker();
4848 JnetAnnotationMaker.add_annotation(predictions,
4849 viewport.getAlignment(), 0, false);
4850 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4851 viewport.getAlignment().setSeqrep(repseq);
4852 ColumnSelection cs = new ColumnSelection();
4853 cs.hideInsertionsFor(repseq);
4854 viewport.setColumnSelection(cs);
4855 isAnnotation = true;
4857 // else if (IdentifyFile.FeaturesFile.equals(format))
4858 else if (FileFormat.Features.equals(format))
4860 if (parseFeaturesFile(file, sourceType))
4862 alignPanel.paintAlignment(true);
4867 new FileLoader().LoadFile(viewport, file, sourceType, format);
4874 alignPanel.adjustAnnotationHeight();
4875 viewport.updateSequenceIdColours();
4876 buildSortByAnnotationScoresMenu();
4877 alignPanel.paintAlignment(true);
4879 } catch (Exception ex)
4881 ex.printStackTrace();
4882 } catch (OutOfMemoryError oom)
4887 } catch (Exception x)
4892 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4893 : "using " + sourceType + " from " + file)
4895 + (format != null ? "(parsing as '" + format
4896 + "' file)" : ""), oom, Desktop.desktop);
4901 * Method invoked by the ChangeListener on the tabbed pane, in other words
4902 * when a different tabbed pane is selected by the user or programmatically.
4905 public void tabSelectionChanged(int index)
4909 alignPanel = alignPanels.get(index);
4910 viewport = alignPanel.av;
4911 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4912 setMenusFromViewport(viewport);
4916 * If there is a frame linked to this one in a SplitPane, switch it to the
4917 * same view tab index. No infinite recursion of calls should happen, since
4918 * tabSelectionChanged() should not get invoked on setting the selected
4919 * index to an unchanged value. Guard against setting an invalid index
4920 * before the new view peer tab has been created.
4922 final AlignViewportI peer = viewport.getCodingComplement();
4925 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4926 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4928 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4934 * On right mouse click on view tab, prompt for and set new view name.
4937 public void tabbedPane_mousePressed(MouseEvent e)
4939 if (e.isPopupTrigger())
4941 String msg = MessageManager.getString("label.enter_view_name");
4942 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4943 JvOptionPane.QUESTION_MESSAGE);
4947 viewport.viewName = reply;
4948 // TODO warn if reply is in getExistingViewNames()?
4949 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4954 public AlignViewport getCurrentView()
4960 * Open the dialog for regex description parsing.
4963 protected void extractScores_actionPerformed(ActionEvent e)
4965 ParseProperties pp = new jalview.analysis.ParseProperties(
4966 viewport.getAlignment());
4967 // TODO: verify regex and introduce GUI dialog for version 2.5
4968 // if (pp.getScoresFromDescription("col", "score column ",
4969 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4971 if (pp.getScoresFromDescription("description column",
4972 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4974 buildSortByAnnotationScoresMenu();
4982 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4986 protected void showDbRefs_actionPerformed(ActionEvent e)
4988 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4994 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4998 protected void showNpFeats_actionPerformed(ActionEvent e)
5000 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5004 * find the viewport amongst the tabs in this alignment frame and close that
5009 public boolean closeView(AlignViewportI av)
5013 this.closeMenuItem_actionPerformed(false);
5016 Component[] comp = tabbedPane.getComponents();
5017 for (int i = 0; comp != null && i < comp.length; i++)
5019 if (comp[i] instanceof AlignmentPanel)
5021 if (((AlignmentPanel) comp[i]).av == av)
5024 closeView((AlignmentPanel) comp[i]);
5032 protected void build_fetchdbmenu(JMenu webService)
5034 // Temporary hack - DBRef Fetcher always top level ws entry.
5035 // TODO We probably want to store a sequence database checklist in
5036 // preferences and have checkboxes.. rather than individual sources selected
5038 final JMenu rfetch = new JMenu(
5039 MessageManager.getString("action.fetch_db_references"));
5040 rfetch.setToolTipText(MessageManager
5041 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5042 webService.add(rfetch);
5044 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5045 MessageManager.getString("option.trim_retrieved_seqs"));
5046 trimrs.setToolTipText(MessageManager
5047 .getString("label.trim_retrieved_sequences"));
5048 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5049 trimrs.addActionListener(new ActionListener()
5052 public void actionPerformed(ActionEvent e)
5054 trimrs.setSelected(trimrs.isSelected());
5055 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5056 Boolean.valueOf(trimrs.isSelected()).toString());
5060 JMenuItem fetchr = new JMenuItem(
5061 MessageManager.getString("label.standard_databases"));
5062 fetchr.setToolTipText(MessageManager
5063 .getString("label.fetch_embl_uniprot"));
5064 fetchr.addActionListener(new ActionListener()
5068 public void actionPerformed(ActionEvent e)
5070 new Thread(new Runnable()
5075 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5076 .getAlignment().isNucleotide();
5077 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5078 .getSequenceSelection(), alignPanel.alignFrame, null,
5079 alignPanel.alignFrame.featureSettings, isNucleotide);
5080 dbRefFetcher.addListener(new FetchFinishedListenerI()
5083 public void finished()
5085 AlignFrame.this.setMenusForViewport();
5088 dbRefFetcher.fetchDBRefs(false);
5096 final AlignFrame me = this;
5097 new Thread(new Runnable()
5102 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5103 .getSequenceFetcherSingleton(me);
5104 javax.swing.SwingUtilities.invokeLater(new Runnable()
5109 String[] dbclasses = sf.getOrderedSupportedSources();
5110 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5111 // jalview.util.QuickSort.sort(otherdb, otherdb);
5112 List<DbSourceProxy> otherdb;
5113 JMenu dfetch = new JMenu();
5114 JMenu ifetch = new JMenu();
5115 JMenuItem fetchr = null;
5116 int comp = 0, icomp = 0, mcomp = 15;
5117 String mname = null;
5119 for (String dbclass : dbclasses)
5121 otherdb = sf.getSourceProxy(dbclass);
5122 // add a single entry for this class, or submenu allowing 'fetch
5124 if (otherdb == null || otherdb.size() < 1)
5128 // List<DbSourceProxy> dbs=otherdb;
5129 // otherdb=new ArrayList<DbSourceProxy>();
5130 // for (DbSourceProxy db:dbs)
5132 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5136 mname = "From " + dbclass;
5138 if (otherdb.size() == 1)
5140 final DbSourceProxy[] dassource = otherdb
5141 .toArray(new DbSourceProxy[0]);
5142 DbSourceProxy src = otherdb.get(0);
5143 fetchr = new JMenuItem(src.getDbSource());
5144 fetchr.addActionListener(new ActionListener()
5148 public void actionPerformed(ActionEvent e)
5150 new Thread(new Runnable()
5156 boolean isNucleotide = alignPanel.alignFrame
5157 .getViewport().getAlignment()
5159 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5160 alignPanel.av.getSequenceSelection(),
5161 alignPanel.alignFrame, dassource,
5162 alignPanel.alignFrame.featureSettings,
5165 .addListener(new FetchFinishedListenerI()
5168 public void finished()
5170 AlignFrame.this.setMenusForViewport();
5173 dbRefFetcher.fetchDBRefs(false);
5179 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5180 MessageManager.formatMessage(
5181 "label.fetch_retrieve_from",
5182 new Object[] { src.getDbName() })));
5188 final DbSourceProxy[] dassource = otherdb
5189 .toArray(new DbSourceProxy[0]);
5191 DbSourceProxy src = otherdb.get(0);
5192 fetchr = new JMenuItem(MessageManager.formatMessage(
5193 "label.fetch_all_param",
5194 new Object[] { src.getDbSource() }));
5195 fetchr.addActionListener(new ActionListener()
5198 public void actionPerformed(ActionEvent e)
5200 new Thread(new Runnable()
5206 boolean isNucleotide = alignPanel.alignFrame
5207 .getViewport().getAlignment()
5209 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5210 alignPanel.av.getSequenceSelection(),
5211 alignPanel.alignFrame, dassource,
5212 alignPanel.alignFrame.featureSettings,
5215 .addListener(new FetchFinishedListenerI()
5218 public void finished()
5220 AlignFrame.this.setMenusForViewport();
5223 dbRefFetcher.fetchDBRefs(false);
5229 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5230 MessageManager.formatMessage(
5231 "label.fetch_retrieve_from_all_sources",
5233 Integer.valueOf(otherdb.size())
5234 .toString(), src.getDbSource(),
5235 src.getDbName() })));
5238 // and then build the rest of the individual menus
5239 ifetch = new JMenu(MessageManager.formatMessage(
5240 "label.source_from_db_source",
5241 new Object[] { src.getDbSource() }));
5243 String imname = null;
5245 for (DbSourceProxy sproxy : otherdb)
5247 String dbname = sproxy.getDbName();
5248 String sname = dbname.length() > 5 ? dbname.substring(0,
5249 5) + "..." : dbname;
5250 String msname = dbname.length() > 10 ? dbname.substring(
5251 0, 10) + "..." : dbname;
5254 imname = MessageManager.formatMessage(
5255 "label.from_msname", new Object[] { sname });
5257 fetchr = new JMenuItem(msname);
5258 final DbSourceProxy[] dassrc = { sproxy };
5259 fetchr.addActionListener(new ActionListener()
5263 public void actionPerformed(ActionEvent e)
5265 new Thread(new Runnable()
5271 boolean isNucleotide = alignPanel.alignFrame
5272 .getViewport().getAlignment()
5274 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5275 alignPanel.av.getSequenceSelection(),
5276 alignPanel.alignFrame, dassrc,
5277 alignPanel.alignFrame.featureSettings,
5280 .addListener(new FetchFinishedListenerI()
5283 public void finished()
5285 AlignFrame.this.setMenusForViewport();
5288 dbRefFetcher.fetchDBRefs(false);
5294 fetchr.setToolTipText("<html>"
5295 + MessageManager.formatMessage(
5296 "label.fetch_retrieve_from", new Object[]
5300 if (++icomp >= mcomp || i == (otherdb.size()))
5302 ifetch.setText(MessageManager.formatMessage(
5303 "label.source_to_target", imname, sname));
5305 ifetch = new JMenu();
5313 if (comp >= mcomp || dbi >= (dbclasses.length))
5315 dfetch.setText(MessageManager.formatMessage(
5316 "label.source_to_target", mname, dbclass));
5318 dfetch = new JMenu();
5331 * Left justify the whole alignment.
5334 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5336 AlignmentI al = viewport.getAlignment();
5338 viewport.firePropertyChange("alignment", null, al);
5342 * Right justify the whole alignment.
5345 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5347 AlignmentI al = viewport.getAlignment();
5349 viewport.firePropertyChange("alignment", null, al);
5353 public void setShowSeqFeatures(boolean b)
5355 showSeqFeatures.setSelected(b);
5356 viewport.setShowSequenceFeatures(b);
5363 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5364 * awt.event.ActionEvent)
5367 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5369 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5370 alignPanel.paintAlignment(true);
5377 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5381 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5383 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5384 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5392 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5393 * .event.ActionEvent)
5396 protected void showGroupConservation_actionPerformed(ActionEvent e)
5398 viewport.setShowGroupConservation(showGroupConservation.getState());
5399 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5406 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5407 * .event.ActionEvent)
5410 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5412 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5413 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5420 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5421 * .event.ActionEvent)
5424 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5426 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5427 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5431 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5433 showSequenceLogo.setState(true);
5434 viewport.setShowSequenceLogo(true);
5435 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5436 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5440 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5442 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5449 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5450 * .event.ActionEvent)
5453 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5455 if (avc.makeGroupsFromSelection())
5457 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5458 alignPanel.updateAnnotation();
5459 alignPanel.paintAlignment(true);
5463 public void clearAlignmentSeqRep()
5465 // TODO refactor alignmentseqrep to controller
5466 if (viewport.getAlignment().hasSeqrep())
5468 viewport.getAlignment().setSeqrep(null);
5469 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5470 alignPanel.updateAnnotation();
5471 alignPanel.paintAlignment(true);
5476 protected void createGroup_actionPerformed(ActionEvent e)
5478 if (avc.createGroup())
5480 alignPanel.alignmentChanged();
5485 protected void unGroup_actionPerformed(ActionEvent e)
5489 alignPanel.alignmentChanged();
5494 * make the given alignmentPanel the currently selected tab
5496 * @param alignmentPanel
5498 public void setDisplayedView(AlignmentPanel alignmentPanel)
5500 if (!viewport.getSequenceSetId().equals(
5501 alignmentPanel.av.getSequenceSetId()))
5505 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5507 if (tabbedPane != null
5508 && tabbedPane.getTabCount() > 0
5509 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5510 .getSelectedIndex())
5512 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5517 * Action on selection of menu options to Show or Hide annotations.
5520 * @param forSequences
5521 * update sequence-related annotations
5522 * @param forAlignment
5523 * update non-sequence-related annotations
5526 protected void setAnnotationsVisibility(boolean visible,
5527 boolean forSequences, boolean forAlignment)
5529 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5530 .getAlignmentAnnotation();
5535 for (AlignmentAnnotation aa : anns)
5538 * don't display non-positional annotations on an alignment
5540 if (aa.annotations == null)
5544 boolean apply = (aa.sequenceRef == null && forAlignment)
5545 || (aa.sequenceRef != null && forSequences);
5548 aa.visible = visible;
5551 alignPanel.validateAnnotationDimensions(true);
5552 alignPanel.alignmentChanged();
5556 * Store selected annotation sort order for the view and repaint.
5559 protected void sortAnnotations_actionPerformed()
5561 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5563 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5564 alignPanel.paintAlignment(true);
5569 * @return alignment panels in this alignment frame
5571 public List<? extends AlignmentViewPanel> getAlignPanels()
5573 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5577 * Open a new alignment window, with the cDNA associated with this (protein)
5578 * alignment, aligned as is the protein.
5580 protected void viewAsCdna_actionPerformed()
5582 // TODO no longer a menu action - refactor as required
5583 final AlignmentI alignment = getViewport().getAlignment();
5584 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5585 if (mappings == null)
5589 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5590 for (SequenceI aaSeq : alignment.getSequences())
5592 for (AlignedCodonFrame acf : mappings)
5594 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5598 * There is a cDNA mapping for this protein sequence - add to new
5599 * alignment. It will share the same dataset sequence as other mapped
5600 * cDNA (no new mappings need to be created).
5602 final Sequence newSeq = new Sequence(dnaSeq);
5603 newSeq.setDatasetSequence(dnaSeq);
5604 cdnaSeqs.add(newSeq);
5608 if (cdnaSeqs.size() == 0)
5610 // show a warning dialog no mapped cDNA
5613 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5615 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5616 AlignFrame.DEFAULT_HEIGHT);
5617 cdna.alignAs(alignment);
5618 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5620 Desktop.addInternalFrame(alignFrame, newtitle,
5621 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5625 * Set visibility of dna/protein complement view (available when shown in a
5631 protected void showComplement_actionPerformed(boolean show)
5633 SplitContainerI sf = getSplitViewContainer();
5636 sf.setComplementVisible(this, show);
5641 * Generate the reverse (optionally complemented) of the selected sequences,
5642 * and add them to the alignment
5645 protected void showReverse_actionPerformed(boolean complement)
5647 AlignmentI al = null;
5650 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5651 al = dna.reverseCdna(complement);
5652 viewport.addAlignment(al, "");
5653 addHistoryItem(new EditCommand(
5654 MessageManager.getString("label.add_sequences"),
5655 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5656 viewport.getAlignment()));
5657 } catch (Exception ex)
5659 System.err.println(ex.getMessage());
5665 * Try to run a script in the Groovy console, having first ensured that this
5666 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5667 * be targeted at this alignment.
5670 protected void runGroovy_actionPerformed()
5672 Jalview.setCurrentAlignFrame(this);
5673 groovy.ui.Console console = Desktop.getGroovyConsole();
5674 if (console != null)
5678 console.runScript();
5679 } catch (Exception ex)
5681 System.err.println((ex.toString()));
5683 .showInternalMessageDialog(Desktop.desktop, MessageManager
5684 .getString("label.couldnt_run_groovy_script"),
5686 .getString("label.groovy_support_failed"),
5687 JvOptionPane.ERROR_MESSAGE);
5692 System.err.println("Can't run Groovy script as console not found");
5697 * Hides columns containing (or not containing) a specified feature, provided
5698 * that would not leave all columns hidden
5700 * @param featureType
5701 * @param columnsContaining
5704 public boolean hideFeatureColumns(String featureType,
5705 boolean columnsContaining)
5707 boolean notForHiding = avc.markColumnsContainingFeatures(
5708 columnsContaining, false, false, featureType);
5711 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5712 false, featureType))
5714 getViewport().hideSelectedColumns();
5722 protected void selectHighlightedColumns_actionPerformed(
5723 ActionEvent actionEvent)
5725 // include key modifier check in case user selects from menu
5726 avc.markHighlightedColumns(
5727 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5729 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5733 * Rebuilds the Colour menu, including any user-defined colours which have
5734 * been loaded either on startup or during the session
5736 public void buildColourMenu()
5738 colourMenu.removeAll();
5741 * ButtonGroup groups those items whose
5742 * selection is mutually exclusive
5744 ButtonGroup colours = new ButtonGroup();
5746 colourMenu.add(applyToAllGroups);
5747 colourMenu.add(textColour);
5748 colourMenu.addSeparator();
5749 colourMenu.add(noColourmenuItem);
5750 colours.add(noColourmenuItem);
5753 * scan registered colour schemes (built-in or user-defined
5754 * and add them to the menu (in the order they were added)
5756 Iterable<ColourSchemeI> colourSchemes = ColourSchemes.getInstance()
5757 .getColourSchemes();
5758 for (ColourSchemeI scheme : colourSchemes)
5761 * button text is i18n'd but the name is the canonical name of
5762 * the colour scheme (inspected in changeColour_actionPerformed)
5764 final String name = scheme.getSchemeName();
5765 String label = MessageManager.getString("label.colourScheme_"
5766 + name.toLowerCase().replace(" ", "_"));
5767 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(label);
5768 radioItem.setName(name);
5769 if (scheme instanceof UserColourScheme)
5772 * user-defined colour scheme loaded on startup or during the
5773 * Jalview session; right-click on this offers the option to
5774 * remove it as a colour choice
5776 radioItem.setText(((UserColourScheme) scheme).getName());
5777 radioItem.addMouseListener(new MouseAdapter()
5780 public void mousePressed(MouseEvent evt)
5782 if (evt.isPopupTrigger()) // Mac
5789 public void mouseReleased(MouseEvent evt)
5791 if (evt.isPopupTrigger()) // Windows
5799 ActionListener al = radioItem.getActionListeners()[0];
5800 radioItem.removeActionListener(al);
5801 int option = JvOptionPane.showInternalConfirmDialog(
5802 Desktop.desktop, MessageManager
5803 .getString("label.remove_from_default_list"),
5805 .getString("label.remove_user_defined_colour"),
5806 JvOptionPane.YES_NO_OPTION);
5807 if (option == JvOptionPane.YES_OPTION)
5809 UserDefinedColours.removeColourFromDefaults(radioItem
5811 ColourSchemes.getInstance().removeColourScheme(
5812 radioItem.getName());
5813 colourMenu.remove(radioItem);
5817 radioItem.addActionListener(al);
5822 radioItem.addActionListener(new ActionListener()
5825 public void actionPerformed(ActionEvent evt)
5827 changeColour_actionPerformed(name);
5830 colourMenu.add(radioItem);
5831 colours.add(radioItem);
5834 colourMenu.add(userDefinedColour);
5835 colours.add(userDefinedColour);
5837 colourMenu.addSeparator();
5838 colourMenu.add(conservationMenuItem);
5839 colourMenu.add(modifyConservation);
5840 colourMenu.add(abovePIDThreshold);
5841 colourMenu.add(modifyPID);
5842 colourMenu.add(annotationColour);
5844 setColourSelected(Cache.getDefault(Preferences.DEFAULT_COLOUR,
5845 ResidueColourScheme.NONE));
5851 class PrintThread extends Thread
5855 public PrintThread(AlignmentPanel ap)
5860 static PageFormat pf;
5865 PrinterJob printJob = PrinterJob.getPrinterJob();
5869 printJob.setPrintable(ap, pf);
5873 printJob.setPrintable(ap);
5876 if (printJob.printDialog())
5881 } catch (Exception PrintException)
5883 PrintException.printStackTrace();