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.FileLoader;
67 import jalview.io.FormatAdapter;
68 import jalview.io.HtmlSvgOutput;
69 import jalview.io.IdentifyFile;
70 import jalview.io.JalviewFileChooser;
71 import jalview.io.JalviewFileView;
72 import jalview.io.JnetAnnotationMaker;
73 import jalview.io.NewickFile;
74 import jalview.io.TCoffeeScoreFile;
75 import jalview.jbgui.GAlignFrame;
76 import jalview.schemes.Blosum62ColourScheme;
77 import jalview.schemes.BuriedColourScheme;
78 import jalview.schemes.ClustalxColourScheme;
79 import jalview.schemes.ColourSchemeI;
80 import jalview.schemes.ColourSchemeProperty;
81 import jalview.schemes.HelixColourScheme;
82 import jalview.schemes.HydrophobicColourScheme;
83 import jalview.schemes.NucleotideColourScheme;
84 import jalview.schemes.PIDColourScheme;
85 import jalview.schemes.PurinePyrimidineColourScheme;
86 import jalview.schemes.RNAHelicesColourChooser;
87 import jalview.schemes.ResidueProperties;
88 import jalview.schemes.StrandColourScheme;
89 import jalview.schemes.TCoffeeColourScheme;
90 import jalview.schemes.TaylorColourScheme;
91 import jalview.schemes.TurnColourScheme;
92 import jalview.schemes.UserColourScheme;
93 import jalview.schemes.ZappoColourScheme;
94 import jalview.util.MessageManager;
95 import jalview.viewmodel.AlignmentViewport;
96 import jalview.ws.DBRefFetcher;
97 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
98 import jalview.ws.jws1.Discoverer;
99 import jalview.ws.jws2.Jws2Discoverer;
100 import jalview.ws.jws2.jabaws2.Jws2Instance;
101 import jalview.ws.seqfetcher.DbSourceProxy;
103 import java.awt.BorderLayout;
104 import java.awt.Component;
105 import java.awt.Rectangle;
106 import java.awt.Toolkit;
107 import java.awt.datatransfer.Clipboard;
108 import java.awt.datatransfer.DataFlavor;
109 import java.awt.datatransfer.StringSelection;
110 import java.awt.datatransfer.Transferable;
111 import java.awt.dnd.DnDConstants;
112 import java.awt.dnd.DropTargetDragEvent;
113 import java.awt.dnd.DropTargetDropEvent;
114 import java.awt.dnd.DropTargetEvent;
115 import java.awt.dnd.DropTargetListener;
116 import java.awt.event.ActionEvent;
117 import java.awt.event.ActionListener;
118 import java.awt.event.FocusAdapter;
119 import java.awt.event.FocusEvent;
120 import java.awt.event.ItemEvent;
121 import java.awt.event.ItemListener;
122 import java.awt.event.KeyAdapter;
123 import java.awt.event.KeyEvent;
124 import java.awt.event.MouseAdapter;
125 import java.awt.event.MouseEvent;
126 import java.awt.print.PageFormat;
127 import java.awt.print.PrinterJob;
128 import java.beans.PropertyChangeEvent;
131 import java.util.ArrayList;
132 import java.util.Arrays;
133 import java.util.Deque;
134 import java.util.Enumeration;
135 import java.util.Hashtable;
136 import java.util.List;
137 import java.util.Vector;
139 import javax.swing.JCheckBoxMenuItem;
140 import javax.swing.JEditorPane;
141 import javax.swing.JInternalFrame;
142 import javax.swing.JLayeredPane;
143 import javax.swing.JMenu;
144 import javax.swing.JMenuItem;
145 import javax.swing.JOptionPane;
146 import javax.swing.JRadioButtonMenuItem;
147 import javax.swing.JScrollPane;
148 import javax.swing.SwingUtilities;
154 * @version $Revision$
156 public class AlignFrame extends GAlignFrame implements DropTargetListener,
157 IProgressIndicator, AlignViewControllerGuiI
160 public static final int DEFAULT_WIDTH = 700;
162 public static final int DEFAULT_HEIGHT = 500;
165 * The currently displayed panel (selected tabbed view if more than one)
167 public AlignmentPanel alignPanel;
169 AlignViewport viewport;
171 public AlignViewControllerI avc;
173 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
176 * Last format used to load or save alignments in this window
178 String currentFileFormat = null;
181 * Current filename for this alignment
183 String fileName = null;
186 * Creates a new AlignFrame object with specific width and height.
192 public AlignFrame(AlignmentI al, int width, int height)
194 this(al, null, width, height);
198 * Creates a new AlignFrame object with specific width, height and
204 * @param sequenceSetId
206 public AlignFrame(AlignmentI al, int width, int height,
207 String sequenceSetId)
209 this(al, null, width, height, sequenceSetId);
213 * Creates a new AlignFrame object with specific width, height and
219 * @param sequenceSetId
222 public AlignFrame(AlignmentI al, int width, int height,
223 String sequenceSetId, String viewId)
225 this(al, null, width, height, sequenceSetId, viewId);
229 * new alignment window with hidden columns
233 * @param hiddenColumns
234 * ColumnSelection or null
236 * Width of alignment frame
240 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
241 int width, int height)
243 this(al, hiddenColumns, width, height, null);
247 * Create alignment frame for al with hiddenColumns, a specific width and
248 * height, and specific sequenceId
251 * @param hiddenColumns
254 * @param sequenceSetId
257 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
258 int width, int height, String sequenceSetId)
260 this(al, hiddenColumns, width, height, sequenceSetId, null);
264 * Create alignment frame for al with hiddenColumns, a specific width and
265 * height, and specific sequenceId
268 * @param hiddenColumns
271 * @param sequenceSetId
276 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
277 int width, int height, String sequenceSetId, String viewId)
279 setSize(width, height);
281 if (al.getDataset() == null)
286 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
288 alignPanel = new AlignmentPanel(this, viewport);
290 addAlignmentPanel(alignPanel, true);
294 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
295 ColumnSelection hiddenColumns, int width, int height)
297 setSize(width, height);
299 if (al.getDataset() == null)
304 viewport = new AlignViewport(al, hiddenColumns);
306 if (hiddenSeqs != null && hiddenSeqs.length > 0)
308 viewport.hideSequence(hiddenSeqs);
310 alignPanel = new AlignmentPanel(this, viewport);
311 addAlignmentPanel(alignPanel, true);
316 * Make a new AlignFrame from existing alignmentPanels
323 public AlignFrame(AlignmentPanel ap)
327 addAlignmentPanel(ap, false);
332 * initalise the alignframe from the underlying viewport data and the
337 if (!Jalview.isHeadlessMode())
339 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
342 avc = new jalview.controller.AlignViewController(this, viewport,
344 if (viewport.getAlignmentConservationAnnotation() == null)
346 BLOSUM62Colour.setEnabled(false);
347 conservationMenuItem.setEnabled(false);
348 modifyConservation.setEnabled(false);
349 // PIDColour.setEnabled(false);
350 // abovePIDThreshold.setEnabled(false);
351 // modifyPID.setEnabled(false);
354 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
357 if (sortby.equals("Id"))
359 sortIDMenuItem_actionPerformed(null);
361 else if (sortby.equals("Pairwise Identity"))
363 sortPairwiseMenuItem_actionPerformed(null);
366 if (Desktop.desktop != null)
368 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
369 addServiceListeners();
370 setGUINucleotide(viewport.getAlignment().isNucleotide());
374 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
376 setMenusFromViewport(viewport);
377 buildSortByAnnotationScoresMenu();
380 if (viewport.getWrapAlignment())
382 wrapMenuItem_actionPerformed(null);
385 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
387 this.overviewMenuItem_actionPerformed(null);
392 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
393 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
394 final String menuLabel = MessageManager
395 .getString("label.copy_format_from");
396 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
397 new ViewSetProvider()
401 public AlignmentPanel[] getAllAlignmentPanels()
404 origview.add(alignPanel);
405 // make an array of all alignment panels except for this one
406 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
407 Arrays.asList(Desktop.getAlignmentPanels(null)));
408 aps.remove(AlignFrame.this.alignPanel);
409 return aps.toArray(new AlignmentPanel[aps.size()]);
411 }, selviews, new ItemListener()
415 public void itemStateChanged(ItemEvent e)
417 if (origview.size() > 0)
419 final AlignmentPanel ap = origview.get(0);
422 * Copy the ViewStyle of the selected panel to 'this one'.
423 * Don't change value of 'scaleProteinAsCdna' unless copying
426 ViewStyleI vs = selviews.get(0).getAlignViewport()
428 boolean fromSplitFrame = selviews.get(0)
429 .getAlignViewport().getCodingComplement() != null;
432 vs.setScaleProteinAsCdna(ap.getAlignViewport()
433 .getViewStyle().isScaleProteinAsCdna());
435 ap.getAlignViewport().setViewStyle(vs);
438 * Also rescale ViewStyle of SplitFrame complement if there is
439 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
440 * the whole ViewStyle (allow cDNA protein to have different
443 AlignViewportI complement = ap.getAlignViewport()
444 .getCodingComplement();
445 if (complement != null && vs.isScaleProteinAsCdna())
447 AlignFrame af = Desktop.getAlignFrameFor(complement);
448 ((SplitFrame) af.getSplitViewContainer())
450 af.setMenusForViewport();
454 ap.setSelected(true);
455 ap.alignFrame.setMenusForViewport();
460 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
461 .indexOf("devel") > -1
462 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
463 .indexOf("test") > -1)
465 formatMenu.add(vsel);
467 addFocusListener(new FocusAdapter()
470 public void focusGained(FocusEvent e)
472 Jalview.setCurrentAlignFrame(AlignFrame.this);
479 * Change the filename and format for the alignment, and enable the 'reload'
480 * button functionality.
487 public void setFileName(String file, String format)
490 setFileFormat(format);
491 reload.setEnabled(true);
495 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
498 void addKeyListener()
500 addKeyListener(new KeyAdapter()
503 public void keyPressed(KeyEvent evt)
505 if (viewport.cursorMode
506 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
507 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
508 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
509 && Character.isDigit(evt.getKeyChar()))
511 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
514 switch (evt.getKeyCode())
517 case 27: // escape key
518 deselectAllSequenceMenuItem_actionPerformed(null);
522 case KeyEvent.VK_DOWN:
523 if (evt.isAltDown() || !viewport.cursorMode)
525 moveSelectedSequences(false);
527 if (viewport.cursorMode)
529 alignPanel.getSeqPanel().moveCursor(0, 1);
534 if (evt.isAltDown() || !viewport.cursorMode)
536 moveSelectedSequences(true);
538 if (viewport.cursorMode)
540 alignPanel.getSeqPanel().moveCursor(0, -1);
545 case KeyEvent.VK_LEFT:
546 if (evt.isAltDown() || !viewport.cursorMode)
548 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
552 alignPanel.getSeqPanel().moveCursor(-1, 0);
557 case KeyEvent.VK_RIGHT:
558 if (evt.isAltDown() || !viewport.cursorMode)
560 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
564 alignPanel.getSeqPanel().moveCursor(1, 0);
568 case KeyEvent.VK_SPACE:
569 if (viewport.cursorMode)
571 alignPanel.getSeqPanel().insertGapAtCursor(
572 evt.isControlDown() || evt.isShiftDown()
577 // case KeyEvent.VK_A:
578 // if (viewport.cursorMode)
580 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
581 // //System.out.println("A");
585 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
586 * System.out.println("closing bracket"); } break;
588 case KeyEvent.VK_DELETE:
589 case KeyEvent.VK_BACK_SPACE:
590 if (!viewport.cursorMode)
592 cut_actionPerformed(null);
596 alignPanel.getSeqPanel().deleteGapAtCursor(
597 evt.isControlDown() || evt.isShiftDown()
604 if (viewport.cursorMode)
606 alignPanel.getSeqPanel().setCursorRow();
610 if (viewport.cursorMode && !evt.isControlDown())
612 alignPanel.getSeqPanel().setCursorColumn();
616 if (viewport.cursorMode)
618 alignPanel.getSeqPanel().setCursorPosition();
622 case KeyEvent.VK_ENTER:
623 case KeyEvent.VK_COMMA:
624 if (viewport.cursorMode)
626 alignPanel.getSeqPanel().setCursorRowAndColumn();
631 if (viewport.cursorMode)
633 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
637 if (viewport.cursorMode)
639 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
644 viewport.cursorMode = !viewport.cursorMode;
645 statusBar.setText(MessageManager.formatMessage(
646 "label.keyboard_editing_mode",
647 new String[] { (viewport.cursorMode ? "on" : "off") }));
648 if (viewport.cursorMode)
650 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
651 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
653 alignPanel.getSeqPanel().seqCanvas.repaint();
659 Help.showHelpWindow();
660 } catch (Exception ex)
662 ex.printStackTrace();
667 boolean toggleSeqs = !evt.isControlDown();
668 boolean toggleCols = !evt.isShiftDown();
669 toggleHiddenRegions(toggleSeqs, toggleCols);
672 case KeyEvent.VK_PAGE_UP:
673 if (viewport.getWrapAlignment())
675 alignPanel.scrollUp(true);
679 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
680 - viewport.endSeq + viewport.startSeq);
683 case KeyEvent.VK_PAGE_DOWN:
684 if (viewport.getWrapAlignment())
686 alignPanel.scrollUp(false);
690 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
691 + viewport.endSeq - viewport.startSeq);
698 public void keyReleased(KeyEvent evt)
700 switch (evt.getKeyCode())
702 case KeyEvent.VK_LEFT:
703 if (evt.isAltDown() || !viewport.cursorMode)
705 viewport.firePropertyChange("alignment", null, viewport
706 .getAlignment().getSequences());
710 case KeyEvent.VK_RIGHT:
711 if (evt.isAltDown() || !viewport.cursorMode)
713 viewport.firePropertyChange("alignment", null, viewport
714 .getAlignment().getSequences());
722 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
724 ap.alignFrame = this;
725 avc = new jalview.controller.AlignViewController(this, viewport,
730 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
732 int aSize = alignPanels.size();
734 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
736 if (aSize == 1 && ap.av.viewName == null)
738 this.getContentPane().add(ap, BorderLayout.CENTER);
744 setInitialTabVisible();
747 expandViews.setEnabled(true);
748 gatherViews.setEnabled(true);
749 tabbedPane.addTab(ap.av.viewName, ap);
751 ap.setVisible(false);
756 if (ap.av.isPadGaps())
758 ap.av.getAlignment().padGaps();
760 ap.av.updateConservation(ap);
761 ap.av.updateConsensus(ap);
762 ap.av.updateStrucConsensus(ap);
766 public void setInitialTabVisible()
768 expandViews.setEnabled(true);
769 gatherViews.setEnabled(true);
770 tabbedPane.setVisible(true);
771 AlignmentPanel first = alignPanels.get(0);
772 tabbedPane.addTab(first.av.viewName, first);
773 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
776 public AlignViewport getViewport()
781 /* Set up intrinsic listeners for dynamically generated GUI bits. */
782 private void addServiceListeners()
784 final java.beans.PropertyChangeListener thisListener;
785 Desktop.instance.addJalviewPropertyChangeListener("services",
786 thisListener = new java.beans.PropertyChangeListener()
789 public void propertyChange(PropertyChangeEvent evt)
791 // // System.out.println("Discoverer property change.");
792 // if (evt.getPropertyName().equals("services"))
794 SwingUtilities.invokeLater(new Runnable()
801 .println("Rebuild WS Menu for service change");
802 BuildWebServiceMenu();
809 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
812 public void internalFrameClosed(
813 javax.swing.event.InternalFrameEvent evt)
815 // System.out.println("deregistering discoverer listener");
816 Desktop.instance.removeJalviewPropertyChangeListener("services",
818 closeMenuItem_actionPerformed(true);
821 // Finally, build the menu once to get current service state
822 new Thread(new Runnable()
827 BuildWebServiceMenu();
833 * Configure menu items that vary according to whether the alignment is
834 * nucleotide or protein
838 public void setGUINucleotide(boolean nucleotide)
840 showTranslation.setVisible(nucleotide);
841 showReverse.setVisible(nucleotide);
842 showReverseComplement.setVisible(nucleotide);
843 conservationMenuItem.setEnabled(!nucleotide);
844 modifyConservation.setEnabled(!nucleotide);
845 showGroupConservation.setEnabled(!nucleotide);
846 rnahelicesColour.setEnabled(nucleotide);
847 purinePyrimidineColour.setEnabled(nucleotide);
848 showComplementMenuItem.setText(nucleotide ? MessageManager
849 .getString("label.protein") : MessageManager
850 .getString("label.nucleotide"));
851 setColourSelected(jalview.bin.Cache.getDefault(
852 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
853 : Preferences.DEFAULT_COLOUR_PROT, "None"));
857 * set up menus for the current viewport. This may be called after any
858 * operation that affects the data in the current view (selection changed,
859 * etc) to update the menus to reflect the new state.
862 public void setMenusForViewport()
864 setMenusFromViewport(viewport);
868 * Need to call this method when tabs are selected for multiple views, or when
869 * loading from Jalview2XML.java
874 void setMenusFromViewport(AlignViewport av)
876 padGapsMenuitem.setSelected(av.isPadGaps());
877 colourTextMenuItem.setSelected(av.isShowColourText());
878 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
879 conservationMenuItem.setSelected(av.getConservationSelected());
880 seqLimits.setSelected(av.getShowJVSuffix());
881 idRightAlign.setSelected(av.isRightAlignIds());
882 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
883 renderGapsMenuItem.setSelected(av.isRenderGaps());
884 wrapMenuItem.setSelected(av.getWrapAlignment());
885 scaleAbove.setVisible(av.getWrapAlignment());
886 scaleLeft.setVisible(av.getWrapAlignment());
887 scaleRight.setVisible(av.getWrapAlignment());
888 annotationPanelMenuItem.setState(av.isShowAnnotation());
890 * Show/hide annotations only enabled if annotation panel is shown
892 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
893 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
894 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
895 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
896 viewBoxesMenuItem.setSelected(av.getShowBoxes());
897 viewTextMenuItem.setSelected(av.getShowText());
898 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
899 showGroupConsensus.setSelected(av.isShowGroupConsensus());
900 showGroupConservation.setSelected(av.isShowGroupConservation());
901 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
902 showSequenceLogo.setSelected(av.isShowSequenceLogo());
903 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
905 setColourSelected(ColourSchemeProperty.getColourName(av
906 .getGlobalColourScheme()));
908 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
909 hiddenMarkers.setState(av.getShowHiddenMarkers());
910 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
911 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
912 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
913 autoCalculate.setSelected(av.autoCalculateConsensus);
914 sortByTree.setSelected(av.sortByTree);
915 listenToViewSelections.setSelected(av.followSelection);
916 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
918 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
920 showProducts.setEnabled(canShowProducts());
921 setGroovyEnabled(Desktop.getGroovyConsole() != null);
927 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
931 public void setGroovyEnabled(boolean b)
933 runGroovy.setEnabled(b);
936 private IProgressIndicator progressBar;
941 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
944 public void setProgressBar(String message, long id)
946 progressBar.setProgressBar(message, id);
950 public void registerHandler(final long id,
951 final IProgressIndicatorHandler handler)
953 progressBar.registerHandler(id, handler);
958 * @return true if any progress bars are still active
961 public boolean operationInProgress()
963 return progressBar.operationInProgress();
967 public void setStatus(String text)
969 statusBar.setText(text);
973 * Added so Castor Mapping file can obtain Jalview Version
975 public String getVersion()
977 return jalview.bin.Cache.getProperty("VERSION");
980 public FeatureRenderer getFeatureRenderer()
982 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
986 public void fetchSequence_actionPerformed(ActionEvent e)
988 new jalview.gui.SequenceFetcher(this);
992 public void addFromFile_actionPerformed(ActionEvent e)
994 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
998 public void reload_actionPerformed(ActionEvent e)
1000 if (fileName != null)
1002 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1003 // originating file's format
1004 // TODO: work out how to recover feature settings for correct view(s) when
1005 // file is reloaded.
1006 if (currentFileFormat.equals("Jalview"))
1008 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1009 for (int i = 0; i < frames.length; i++)
1011 if (frames[i] instanceof AlignFrame && frames[i] != this
1012 && ((AlignFrame) frames[i]).fileName != null
1013 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1017 frames[i].setSelected(true);
1018 Desktop.instance.closeAssociatedWindows();
1019 } catch (java.beans.PropertyVetoException ex)
1025 Desktop.instance.closeAssociatedWindows();
1027 FileLoader loader = new FileLoader();
1028 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1029 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1033 Rectangle bounds = this.getBounds();
1035 FileLoader loader = new FileLoader();
1036 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1037 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1038 protocol, currentFileFormat);
1040 newframe.setBounds(bounds);
1041 if (featureSettings != null && featureSettings.isShowing())
1043 final Rectangle fspos = featureSettings.frame.getBounds();
1044 // TODO: need a 'show feature settings' function that takes bounds -
1045 // need to refactor Desktop.addFrame
1046 newframe.featureSettings_actionPerformed(null);
1047 final FeatureSettings nfs = newframe.featureSettings;
1048 SwingUtilities.invokeLater(new Runnable()
1053 nfs.frame.setBounds(fspos);
1056 this.featureSettings.close();
1057 this.featureSettings = null;
1059 this.closeMenuItem_actionPerformed(true);
1065 public void addFromText_actionPerformed(ActionEvent e)
1067 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1072 public void addFromURL_actionPerformed(ActionEvent e)
1074 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1078 public void save_actionPerformed(ActionEvent e)
1080 if (fileName == null
1081 || (currentFileFormat == null || !jalview.io.FormatAdapter
1082 .isValidIOFormat(currentFileFormat, true))
1083 || fileName.startsWith("http"))
1085 saveAs_actionPerformed(null);
1089 saveAlignment(fileName, currentFileFormat);
1100 public void saveAs_actionPerformed(ActionEvent e)
1102 JalviewFileChooser chooser = new JalviewFileChooser(
1103 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1104 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1105 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1106 currentFileFormat, false);
1108 chooser.setFileView(new JalviewFileView());
1109 chooser.setDialogTitle(MessageManager
1110 .getString("label.save_alignment_to_file"));
1111 chooser.setToolTipText(MessageManager.getString("action.save"));
1113 int value = chooser.showSaveDialog(this);
1115 if (value == JalviewFileChooser.APPROVE_OPTION)
1117 currentFileFormat = chooser.getSelectedFormat();
1118 while (currentFileFormat == null)
1121 .showInternalMessageDialog(
1124 .getString("label.select_file_format_before_saving"),
1126 .getString("label.file_format_not_specified"),
1127 JOptionPane.WARNING_MESSAGE);
1128 currentFileFormat = chooser.getSelectedFormat();
1129 value = chooser.showSaveDialog(this);
1130 if (value != JalviewFileChooser.APPROVE_OPTION)
1136 fileName = chooser.getSelectedFile().getPath();
1138 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1141 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1142 if (currentFileFormat.indexOf(" ") > -1)
1144 currentFileFormat = currentFileFormat.substring(0,
1145 currentFileFormat.indexOf(" "));
1147 saveAlignment(fileName, currentFileFormat);
1151 public boolean saveAlignment(String file, String format)
1153 boolean success = true;
1155 if (format.equalsIgnoreCase("Jalview"))
1157 String shortName = title;
1159 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1161 shortName = shortName.substring(shortName
1162 .lastIndexOf(java.io.File.separatorChar) + 1);
1165 success = new Jalview2XML().saveAlignment(this, file, shortName);
1167 statusBar.setText(MessageManager.formatMessage(
1168 "label.successfully_saved_to_file_in_format", new Object[] {
1169 fileName, format }));
1174 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1176 warningMessage("Cannot save file " + fileName + " using format "
1177 + format, "Alignment output format not supported");
1178 if (!Jalview.isHeadlessMode())
1180 saveAs_actionPerformed(null);
1185 AlignmentExportData exportData = getAlignmentForExport(format,
1187 if (exportData.getSettings().isCancelled())
1191 FormatAdapter f = new FormatAdapter(alignPanel,
1192 exportData.getSettings());
1193 String output = f.formatSequences(
1195 exportData.getAlignment(), // class cast exceptions will
1196 // occur in the distant future
1197 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1198 f.getCacheSuffixDefault(format),
1199 viewport.getColumnSelection());
1209 java.io.PrintWriter out = new java.io.PrintWriter(
1210 new java.io.FileWriter(file));
1214 this.setTitle(file);
1215 statusBar.setText(MessageManager.formatMessage(
1216 "label.successfully_saved_to_file_in_format",
1217 new Object[] { fileName, format }));
1218 } catch (Exception ex)
1221 ex.printStackTrace();
1228 JOptionPane.showInternalMessageDialog(this, MessageManager
1229 .formatMessage("label.couldnt_save_file",
1230 new Object[] { fileName }), MessageManager
1231 .getString("label.error_saving_file"),
1232 JOptionPane.WARNING_MESSAGE);
1238 private void warningMessage(String warning, String title)
1240 if (new jalview.util.Platform().isHeadless())
1242 System.err.println("Warning: " + title + "\nWarning: " + warning);
1247 JOptionPane.showInternalMessageDialog(this, warning, title,
1248 JOptionPane.WARNING_MESSAGE);
1260 protected void outputText_actionPerformed(ActionEvent e)
1263 AlignmentExportData exportData = getAlignmentForExport(
1264 e.getActionCommand(), viewport, null);
1265 if (exportData.getSettings().isCancelled())
1269 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1270 cap.setForInput(null);
1273 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1274 .formatSequences(e.getActionCommand(),
1275 exportData.getAlignment(),
1276 exportData.getOmitHidden(),
1277 exportData.getStartEndPostions(),
1278 viewport.getColumnSelection()));
1279 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1280 "label.alignment_output_command",
1281 new Object[] { e.getActionCommand() }), 600, 500);
1282 } catch (OutOfMemoryError oom)
1284 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1290 public static AlignmentExportData getAlignmentForExport(
1291 String exportFormat, AlignViewportI viewport,
1292 AlignExportSettingI exportSettings)
1294 AlignmentI alignmentToExport = null;
1295 AlignExportSettingI settings = exportSettings;
1296 String[] omitHidden = null;
1298 HiddenSequences hiddenSeqs = viewport.getAlignment()
1299 .getHiddenSequences();
1301 alignmentToExport = viewport.getAlignment();
1303 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1304 if (settings == null)
1306 settings = new AlignExportSettings(hasHiddenSeqs,
1307 viewport.hasHiddenColumns(), exportFormat);
1309 // settings.isExportAnnotations();
1311 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1313 omitHidden = viewport.getViewAsString(false,
1314 settings.isExportHiddenSequences());
1317 int[] alignmentStartEnd = new int[2];
1318 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1320 alignmentToExport = hiddenSeqs.getFullAlignment();
1324 alignmentToExport = viewport.getAlignment();
1326 alignmentStartEnd = alignmentToExport
1327 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1328 .getHiddenColumns());
1329 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1330 omitHidden, alignmentStartEnd, settings);
1341 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1343 new HtmlSvgOutput(null, alignPanel);
1347 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1349 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1350 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1353 public void createImageMap(File file, String image)
1355 alignPanel.makePNGImageMap(file, image);
1365 public void createPNG(File f)
1367 alignPanel.makePNG(f);
1377 public void createEPS(File f)
1379 alignPanel.makeEPS(f);
1383 public void createSVG(File f)
1385 alignPanel.makeSVG(f);
1389 public void pageSetup_actionPerformed(ActionEvent e)
1391 PrinterJob printJob = PrinterJob.getPrinterJob();
1392 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1402 public void printMenuItem_actionPerformed(ActionEvent e)
1404 // Putting in a thread avoids Swing painting problems
1405 PrintThread thread = new PrintThread(alignPanel);
1410 public void exportFeatures_actionPerformed(ActionEvent e)
1412 new AnnotationExporter().exportFeatures(alignPanel);
1416 public void exportAnnotations_actionPerformed(ActionEvent e)
1418 new AnnotationExporter().exportAnnotations(alignPanel);
1422 public void associatedData_actionPerformed(ActionEvent e)
1424 // Pick the tree file
1425 JalviewFileChooser chooser = new JalviewFileChooser(
1426 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1427 chooser.setFileView(new JalviewFileView());
1428 chooser.setDialogTitle(MessageManager
1429 .getString("label.load_jalview_annotations"));
1430 chooser.setToolTipText(MessageManager
1431 .getString("label.load_jalview_annotations"));
1433 int value = chooser.showOpenDialog(null);
1435 if (value == JalviewFileChooser.APPROVE_OPTION)
1437 String choice = chooser.getSelectedFile().getPath();
1438 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1439 loadJalviewDataFile(choice, null, null, null);
1445 * Close the current view or all views in the alignment frame. If the frame
1446 * only contains one view then the alignment will be removed from memory.
1448 * @param closeAllTabs
1451 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1453 if (alignPanels != null && alignPanels.size() < 2)
1455 closeAllTabs = true;
1460 if (alignPanels != null)
1464 if (this.isClosed())
1466 // really close all the windows - otherwise wait till
1467 // setClosed(true) is called
1468 for (int i = 0; i < alignPanels.size(); i++)
1470 AlignmentPanel ap = alignPanels.get(i);
1477 closeView(alignPanel);
1484 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1485 * be called recursively, with the frame now in 'closed' state
1487 this.setClosed(true);
1489 } catch (Exception ex)
1491 ex.printStackTrace();
1496 * Close the specified panel and close up tabs appropriately.
1498 * @param panelToClose
1500 public void closeView(AlignmentPanel panelToClose)
1502 int index = tabbedPane.getSelectedIndex();
1503 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1504 alignPanels.remove(panelToClose);
1505 panelToClose.closePanel();
1506 panelToClose = null;
1508 tabbedPane.removeTabAt(closedindex);
1509 tabbedPane.validate();
1511 if (index > closedindex || index == tabbedPane.getTabCount())
1513 // modify currently selected tab index if necessary.
1517 this.tabSelectionChanged(index);
1523 void updateEditMenuBar()
1526 if (viewport.getHistoryList().size() > 0)
1528 undoMenuItem.setEnabled(true);
1529 CommandI command = viewport.getHistoryList().peek();
1530 undoMenuItem.setText(MessageManager.formatMessage(
1531 "label.undo_command",
1532 new Object[] { command.getDescription() }));
1536 undoMenuItem.setEnabled(false);
1537 undoMenuItem.setText(MessageManager.getString("action.undo"));
1540 if (viewport.getRedoList().size() > 0)
1542 redoMenuItem.setEnabled(true);
1544 CommandI command = viewport.getRedoList().peek();
1545 redoMenuItem.setText(MessageManager.formatMessage(
1546 "label.redo_command",
1547 new Object[] { command.getDescription() }));
1551 redoMenuItem.setEnabled(false);
1552 redoMenuItem.setText(MessageManager.getString("action.redo"));
1557 public void addHistoryItem(CommandI command)
1559 if (command.getSize() > 0)
1561 viewport.addToHistoryList(command);
1562 viewport.clearRedoList();
1563 updateEditMenuBar();
1564 viewport.updateHiddenColumns();
1565 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1566 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1567 // viewport.getColumnSelection()
1568 // .getHiddenColumns().size() > 0);
1574 * @return alignment objects for all views
1576 AlignmentI[] getViewAlignments()
1578 if (alignPanels != null)
1580 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1582 for (AlignmentPanel ap : alignPanels)
1584 als[i++] = ap.av.getAlignment();
1588 if (viewport != null)
1590 return new AlignmentI[] { viewport.getAlignment() };
1602 protected void undoMenuItem_actionPerformed(ActionEvent e)
1604 if (viewport.getHistoryList().isEmpty())
1608 CommandI command = viewport.getHistoryList().pop();
1609 viewport.addToRedoList(command);
1610 command.undoCommand(getViewAlignments());
1612 AlignmentViewport originalSource = getOriginatingSource(command);
1613 updateEditMenuBar();
1615 if (originalSource != null)
1617 if (originalSource != viewport)
1620 .warn("Implementation worry: mismatch of viewport origin for undo");
1622 originalSource.updateHiddenColumns();
1623 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1625 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1626 // viewport.getColumnSelection()
1627 // .getHiddenColumns().size() > 0);
1628 originalSource.firePropertyChange("alignment", null, originalSource
1629 .getAlignment().getSequences());
1640 protected void redoMenuItem_actionPerformed(ActionEvent e)
1642 if (viewport.getRedoList().size() < 1)
1647 CommandI command = viewport.getRedoList().pop();
1648 viewport.addToHistoryList(command);
1649 command.doCommand(getViewAlignments());
1651 AlignmentViewport originalSource = getOriginatingSource(command);
1652 updateEditMenuBar();
1654 if (originalSource != null)
1657 if (originalSource != viewport)
1660 .warn("Implementation worry: mismatch of viewport origin for redo");
1662 originalSource.updateHiddenColumns();
1663 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1665 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1666 // viewport.getColumnSelection()
1667 // .getHiddenColumns().size() > 0);
1668 originalSource.firePropertyChange("alignment", null, originalSource
1669 .getAlignment().getSequences());
1673 AlignmentViewport getOriginatingSource(CommandI command)
1675 AlignmentViewport originalSource = null;
1676 // For sequence removal and addition, we need to fire
1677 // the property change event FROM the viewport where the
1678 // original alignment was altered
1679 AlignmentI al = null;
1680 if (command instanceof EditCommand)
1682 EditCommand editCommand = (EditCommand) command;
1683 al = editCommand.getAlignment();
1684 List<Component> comps = PaintRefresher.components.get(viewport
1685 .getSequenceSetId());
1687 for (Component comp : comps)
1689 if (comp instanceof AlignmentPanel)
1691 if (al == ((AlignmentPanel) comp).av.getAlignment())
1693 originalSource = ((AlignmentPanel) comp).av;
1700 if (originalSource == null)
1702 // The original view is closed, we must validate
1703 // the current view against the closed view first
1706 PaintRefresher.validateSequences(al, viewport.getAlignment());
1709 originalSource = viewport;
1712 return originalSource;
1721 public void moveSelectedSequences(boolean up)
1723 SequenceGroup sg = viewport.getSelectionGroup();
1729 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1730 viewport.getHiddenRepSequences(), up);
1731 alignPanel.paintAlignment(true);
1734 synchronized void slideSequences(boolean right, int size)
1736 List<SequenceI> sg = new ArrayList<SequenceI>();
1737 if (viewport.cursorMode)
1739 sg.add(viewport.getAlignment().getSequenceAt(
1740 alignPanel.getSeqPanel().seqCanvas.cursorY));
1742 else if (viewport.getSelectionGroup() != null
1743 && viewport.getSelectionGroup().getSize() != viewport
1744 .getAlignment().getHeight())
1746 sg = viewport.getSelectionGroup().getSequences(
1747 viewport.getHiddenRepSequences());
1755 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1757 for (SequenceI seq : viewport.getAlignment().getSequences())
1759 if (!sg.contains(seq))
1761 invertGroup.add(seq);
1765 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1767 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1768 for (int i = 0; i < invertGroup.size(); i++)
1770 seqs2[i] = invertGroup.get(i);
1773 SlideSequencesCommand ssc;
1776 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1777 size, viewport.getGapCharacter());
1781 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1782 size, viewport.getGapCharacter());
1785 int groupAdjustment = 0;
1786 if (ssc.getGapsInsertedBegin() && right)
1788 if (viewport.cursorMode)
1790 alignPanel.getSeqPanel().moveCursor(size, 0);
1794 groupAdjustment = size;
1797 else if (!ssc.getGapsInsertedBegin() && !right)
1799 if (viewport.cursorMode)
1801 alignPanel.getSeqPanel().moveCursor(-size, 0);
1805 groupAdjustment = -size;
1809 if (groupAdjustment != 0)
1811 viewport.getSelectionGroup().setStartRes(
1812 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1813 viewport.getSelectionGroup().setEndRes(
1814 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1818 * just extend the last slide command if compatible; but not if in
1819 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1821 boolean appendHistoryItem = false;
1822 Deque<CommandI> historyList = viewport.getHistoryList();
1823 boolean inSplitFrame = getSplitViewContainer() != null;
1824 if (!inSplitFrame && historyList != null && historyList.size() > 0
1825 && historyList.peek() instanceof SlideSequencesCommand)
1827 appendHistoryItem = ssc
1828 .appendSlideCommand((SlideSequencesCommand) historyList
1832 if (!appendHistoryItem)
1834 addHistoryItem(ssc);
1847 protected void copy_actionPerformed(ActionEvent e)
1850 if (viewport.getSelectionGroup() == null)
1854 // TODO: preserve the ordering of displayed alignment annotation in any
1855 // internal paste (particularly sequence associated annotation)
1856 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1857 String[] omitHidden = null;
1859 if (viewport.hasHiddenColumns())
1861 omitHidden = viewport.getViewAsString(true);
1864 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1867 StringSelection ss = new StringSelection(output);
1871 jalview.gui.Desktop.internalCopy = true;
1872 // Its really worth setting the clipboard contents
1873 // to empty before setting the large StringSelection!!
1874 Toolkit.getDefaultToolkit().getSystemClipboard()
1875 .setContents(new StringSelection(""), null);
1877 Toolkit.getDefaultToolkit().getSystemClipboard()
1878 .setContents(ss, Desktop.instance);
1879 } catch (OutOfMemoryError er)
1881 new OOMWarning("copying region", er);
1885 ArrayList<int[]> hiddenColumns = null;
1886 if (viewport.hasHiddenColumns())
1888 hiddenColumns = new ArrayList<int[]>();
1889 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1890 .getSelectionGroup().getEndRes();
1891 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1893 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1895 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1896 region[1] - hiddenOffset });
1901 Desktop.jalviewClipboard = new Object[] { seqs,
1902 viewport.getAlignment().getDataset(), hiddenColumns };
1903 statusBar.setText(MessageManager.formatMessage(
1904 "label.copied_sequences_to_clipboard", new Object[] { Integer
1905 .valueOf(seqs.length).toString() }));
1915 protected void pasteNew_actionPerformed(ActionEvent e)
1927 protected void pasteThis_actionPerformed(ActionEvent e)
1933 * Paste contents of Jalview clipboard
1935 * @param newAlignment
1936 * true to paste to a new alignment, otherwise add to this.
1938 void paste(boolean newAlignment)
1940 boolean externalPaste = true;
1943 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1944 Transferable contents = c.getContents(this);
1946 if (contents == null)
1954 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1955 if (str.length() < 1)
1960 format = new IdentifyFile().identify(str, "Paste");
1962 } catch (OutOfMemoryError er)
1964 new OOMWarning("Out of memory pasting sequences!!", er);
1968 SequenceI[] sequences;
1969 boolean annotationAdded = false;
1970 AlignmentI alignment = null;
1972 if (Desktop.jalviewClipboard != null)
1974 // The clipboard was filled from within Jalview, we must use the
1976 // And dataset from the copied alignment
1977 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1978 // be doubly sure that we create *new* sequence objects.
1979 sequences = new SequenceI[newseq.length];
1980 for (int i = 0; i < newseq.length; i++)
1982 sequences[i] = new Sequence(newseq[i]);
1984 alignment = new Alignment(sequences);
1985 externalPaste = false;
1989 // parse the clipboard as an alignment.
1990 alignment = new FormatAdapter().readFile(str, "Paste", format);
1991 sequences = alignment.getSequencesArray();
1995 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2001 if (Desktop.jalviewClipboard != null)
2003 // dataset is inherited
2004 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2008 // new dataset is constructed
2009 alignment.setDataset(null);
2011 alwidth = alignment.getWidth() + 1;
2015 AlignmentI pastedal = alignment; // preserve pasted alignment object
2016 // Add pasted sequences and dataset into existing alignment.
2017 alignment = viewport.getAlignment();
2018 alwidth = alignment.getWidth() + 1;
2019 // decide if we need to import sequences from an existing dataset
2020 boolean importDs = Desktop.jalviewClipboard != null
2021 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2022 // importDs==true instructs us to copy over new dataset sequences from
2023 // an existing alignment
2024 Vector newDs = (importDs) ? new Vector() : null; // used to create
2025 // minimum dataset set
2027 for (int i = 0; i < sequences.length; i++)
2031 newDs.addElement(null);
2033 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2035 if (importDs && ds != null)
2037 if (!newDs.contains(ds))
2039 newDs.setElementAt(ds, i);
2040 ds = new Sequence(ds);
2041 // update with new dataset sequence
2042 sequences[i].setDatasetSequence(ds);
2046 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2051 // copy and derive new dataset sequence
2052 sequences[i] = sequences[i].deriveSequence();
2053 alignment.getDataset().addSequence(
2054 sequences[i].getDatasetSequence());
2055 // TODO: avoid creation of duplicate dataset sequences with a
2056 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2058 alignment.addSequence(sequences[i]); // merges dataset
2062 newDs.clear(); // tidy up
2064 if (alignment.getAlignmentAnnotation() != null)
2066 for (AlignmentAnnotation alan : alignment
2067 .getAlignmentAnnotation())
2069 if (alan.graphGroup > fgroup)
2071 fgroup = alan.graphGroup;
2075 if (pastedal.getAlignmentAnnotation() != null)
2077 // Add any annotation attached to alignment.
2078 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2079 for (int i = 0; i < alann.length; i++)
2081 annotationAdded = true;
2082 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2084 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2085 if (newann.graphGroup > -1)
2087 if (newGraphGroups.size() <= newann.graphGroup
2088 || newGraphGroups.get(newann.graphGroup) == null)
2090 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2092 newGraphGroups.add(q, null);
2094 newGraphGroups.set(newann.graphGroup, new Integer(
2097 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2101 newann.padAnnotation(alwidth);
2102 alignment.addAnnotation(newann);
2112 addHistoryItem(new EditCommand(
2113 MessageManager.getString("label.add_sequences"),
2114 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2116 // Add any annotations attached to sequences
2117 for (int i = 0; i < sequences.length; i++)
2119 if (sequences[i].getAnnotation() != null)
2121 AlignmentAnnotation newann;
2122 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2124 annotationAdded = true;
2125 newann = sequences[i].getAnnotation()[a];
2126 newann.adjustForAlignment();
2127 newann.padAnnotation(alwidth);
2128 if (newann.graphGroup > -1)
2130 if (newann.graphGroup > -1)
2132 if (newGraphGroups.size() <= newann.graphGroup
2133 || newGraphGroups.get(newann.graphGroup) == null)
2135 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2137 newGraphGroups.add(q, null);
2139 newGraphGroups.set(newann.graphGroup, new Integer(
2142 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2146 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2151 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2158 // propagate alignment changed.
2159 viewport.setEndSeq(alignment.getHeight());
2160 if (annotationAdded)
2162 // Duplicate sequence annotation in all views.
2163 AlignmentI[] alview = this.getViewAlignments();
2164 for (int i = 0; i < sequences.length; i++)
2166 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2171 for (int avnum = 0; avnum < alview.length; avnum++)
2173 if (alview[avnum] != alignment)
2175 // duplicate in a view other than the one with input focus
2176 int avwidth = alview[avnum].getWidth() + 1;
2177 // this relies on sann being preserved after we
2178 // modify the sequence's annotation array for each duplication
2179 for (int a = 0; a < sann.length; a++)
2181 AlignmentAnnotation newann = new AlignmentAnnotation(
2183 sequences[i].addAlignmentAnnotation(newann);
2184 newann.padAnnotation(avwidth);
2185 alview[avnum].addAnnotation(newann); // annotation was
2186 // duplicated earlier
2187 // TODO JAL-1145 graphGroups are not updated for sequence
2188 // annotation added to several views. This may cause
2190 alview[avnum].setAnnotationIndex(newann, a);
2195 buildSortByAnnotationScoresMenu();
2197 viewport.firePropertyChange("alignment", null,
2198 alignment.getSequences());
2199 if (alignPanels != null)
2201 for (AlignmentPanel ap : alignPanels)
2203 ap.validateAnnotationDimensions(false);
2208 alignPanel.validateAnnotationDimensions(false);
2214 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2216 String newtitle = new String("Copied sequences");
2218 if (Desktop.jalviewClipboard != null
2219 && Desktop.jalviewClipboard[2] != null)
2221 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2222 for (int[] region : hc)
2224 af.viewport.hideColumns(region[0], region[1]);
2228 // >>>This is a fix for the moment, until a better solution is
2230 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2232 alignPanel.getSeqPanel().seqCanvas
2233 .getFeatureRenderer());
2235 // TODO: maintain provenance of an alignment, rather than just make the
2236 // title a concatenation of operations.
2239 if (title.startsWith("Copied sequences"))
2245 newtitle = newtitle.concat("- from " + title);
2250 newtitle = new String("Pasted sequences");
2253 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2258 } catch (Exception ex)
2260 ex.printStackTrace();
2261 System.out.println("Exception whilst pasting: " + ex);
2262 // could be anything being pasted in here
2268 protected void expand_newalign(ActionEvent e)
2272 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2273 .getAlignment(), -1);
2274 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2276 String newtitle = new String("Flanking alignment");
2278 if (Desktop.jalviewClipboard != null
2279 && Desktop.jalviewClipboard[2] != null)
2281 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2282 for (int region[] : hc)
2284 af.viewport.hideColumns(region[0], region[1]);
2288 // >>>This is a fix for the moment, until a better solution is
2290 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2292 alignPanel.getSeqPanel().seqCanvas
2293 .getFeatureRenderer());
2295 // TODO: maintain provenance of an alignment, rather than just make the
2296 // title a concatenation of operations.
2298 if (title.startsWith("Copied sequences"))
2304 newtitle = newtitle.concat("- from " + title);
2308 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2310 } catch (Exception ex)
2312 ex.printStackTrace();
2313 System.out.println("Exception whilst pasting: " + ex);
2314 // could be anything being pasted in here
2315 } catch (OutOfMemoryError oom)
2317 new OOMWarning("Viewing flanking region of alignment", oom);
2328 protected void cut_actionPerformed(ActionEvent e)
2330 copy_actionPerformed(null);
2331 delete_actionPerformed(null);
2341 protected void delete_actionPerformed(ActionEvent evt)
2344 SequenceGroup sg = viewport.getSelectionGroup();
2351 * If the cut affects all sequences, warn, remove highlighted columns
2353 if (sg.getSize() == viewport.getAlignment().getHeight())
2355 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2356 .getAlignment().getWidth()) ? true : false;
2357 if (isEntireAlignWidth)
2359 int confirm = JOptionPane.showConfirmDialog(this,
2360 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2361 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2362 JOptionPane.OK_CANCEL_OPTION);
2364 if (confirm == JOptionPane.CANCEL_OPTION
2365 || confirm == JOptionPane.CLOSED_OPTION)
2370 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2371 sg.getEndRes() + 1);
2373 SequenceI[] cut = sg.getSequences()
2374 .toArray(new SequenceI[sg.getSize()]);
2376 addHistoryItem(new EditCommand(
2377 MessageManager.getString("label.cut_sequences"), Action.CUT,
2378 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2379 viewport.getAlignment()));
2381 viewport.setSelectionGroup(null);
2382 viewport.sendSelection();
2383 viewport.getAlignment().deleteGroup(sg);
2385 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2387 if (viewport.getAlignment().getHeight() < 1)
2391 this.setClosed(true);
2392 } catch (Exception ex)
2405 protected void deleteGroups_actionPerformed(ActionEvent e)
2407 if (avc.deleteGroups())
2409 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2410 alignPanel.updateAnnotation();
2411 alignPanel.paintAlignment(true);
2422 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2424 SequenceGroup sg = new SequenceGroup();
2426 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2428 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2431 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2432 viewport.setSelectionGroup(sg);
2433 viewport.sendSelection();
2434 // JAL-2034 - should delegate to
2435 // alignPanel to decide if overview needs
2437 alignPanel.paintAlignment(false);
2438 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2448 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2450 if (viewport.cursorMode)
2452 alignPanel.getSeqPanel().keyboardNo1 = null;
2453 alignPanel.getSeqPanel().keyboardNo2 = null;
2455 viewport.setSelectionGroup(null);
2456 viewport.getColumnSelection().clear();
2457 viewport.setSelectionGroup(null);
2458 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2459 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2460 // JAL-2034 - should delegate to
2461 // alignPanel to decide if overview needs
2463 alignPanel.paintAlignment(false);
2464 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2465 viewport.sendSelection();
2475 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2477 SequenceGroup sg = viewport.getSelectionGroup();
2481 selectAllSequenceMenuItem_actionPerformed(null);
2486 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2488 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2490 // JAL-2034 - should delegate to
2491 // alignPanel to decide if overview needs
2494 alignPanel.paintAlignment(true);
2495 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2496 viewport.sendSelection();
2500 public void invertColSel_actionPerformed(ActionEvent e)
2502 viewport.invertColumnSelection();
2503 alignPanel.paintAlignment(true);
2504 viewport.sendSelection();
2514 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2516 trimAlignment(true);
2526 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2528 trimAlignment(false);
2531 void trimAlignment(boolean trimLeft)
2533 ColumnSelection colSel = viewport.getColumnSelection();
2536 if (!colSel.isEmpty())
2540 column = colSel.getMin();
2544 column = colSel.getMax();
2548 if (viewport.getSelectionGroup() != null)
2550 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2551 viewport.getHiddenRepSequences());
2555 seqs = viewport.getAlignment().getSequencesArray();
2558 TrimRegionCommand trimRegion;
2561 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2562 column, viewport.getAlignment());
2563 viewport.setStartRes(0);
2567 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2568 column, viewport.getAlignment());
2571 statusBar.setText(MessageManager.formatMessage(
2572 "label.removed_columns",
2573 new String[] { Integer.valueOf(trimRegion.getSize())
2576 addHistoryItem(trimRegion);
2578 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2580 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2581 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2583 viewport.getAlignment().deleteGroup(sg);
2587 viewport.firePropertyChange("alignment", null, viewport
2588 .getAlignment().getSequences());
2599 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2601 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2604 if (viewport.getSelectionGroup() != null)
2606 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2607 viewport.getHiddenRepSequences());
2608 start = viewport.getSelectionGroup().getStartRes();
2609 end = viewport.getSelectionGroup().getEndRes();
2613 seqs = viewport.getAlignment().getSequencesArray();
2616 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2617 "Remove Gapped Columns", seqs, start, end,
2618 viewport.getAlignment());
2620 addHistoryItem(removeGapCols);
2622 statusBar.setText(MessageManager.formatMessage(
2623 "label.removed_empty_columns",
2624 new Object[] { Integer.valueOf(removeGapCols.getSize())
2627 // This is to maintain viewport position on first residue
2628 // of first sequence
2629 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2630 int startRes = seq.findPosition(viewport.startRes);
2631 // ShiftList shifts;
2632 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2633 // edit.alColumnChanges=shifts.getInverse();
2634 // if (viewport.hasHiddenColumns)
2635 // viewport.getColumnSelection().compensateForEdits(shifts);
2636 viewport.setStartRes(seq.findIndex(startRes) - 1);
2637 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2649 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2651 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2654 if (viewport.getSelectionGroup() != null)
2656 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2657 viewport.getHiddenRepSequences());
2658 start = viewport.getSelectionGroup().getStartRes();
2659 end = viewport.getSelectionGroup().getEndRes();
2663 seqs = viewport.getAlignment().getSequencesArray();
2666 // This is to maintain viewport position on first residue
2667 // of first sequence
2668 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2669 int startRes = seq.findPosition(viewport.startRes);
2671 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2672 viewport.getAlignment()));
2674 viewport.setStartRes(seq.findIndex(startRes) - 1);
2676 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2688 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2690 viewport.setPadGaps(padGapsMenuitem.isSelected());
2691 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2702 public void findMenuItem_actionPerformed(ActionEvent e)
2708 * Create a new view of the current alignment.
2711 public void newView_actionPerformed(ActionEvent e)
2713 newView(null, true);
2717 * Creates and shows a new view of the current alignment.
2720 * title of newly created view; if null, one will be generated
2721 * @param copyAnnotation
2722 * if true then duplicate all annnotation, groups and settings
2723 * @return new alignment panel, already displayed.
2725 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2728 * Create a new AlignmentPanel (with its own, new Viewport)
2730 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2732 if (!copyAnnotation)
2735 * remove all groups and annotation except for the automatic stuff
2737 newap.av.getAlignment().deleteAllGroups();
2738 newap.av.getAlignment().deleteAllAnnotations(false);
2741 newap.av.setGatherViewsHere(false);
2743 if (viewport.viewName == null)
2745 viewport.viewName = MessageManager
2746 .getString("label.view_name_original");
2750 * Views share the same edits undo and redo stacks
2752 newap.av.setHistoryList(viewport.getHistoryList());
2753 newap.av.setRedoList(viewport.getRedoList());
2756 * Views share the same mappings; need to deregister any new mappings
2757 * created by copyAlignPanel, and register the new reference to the shared
2760 newap.av.replaceMappings(viewport.getAlignment());
2762 newap.av.viewName = getNewViewName(viewTitle);
2764 addAlignmentPanel(newap, true);
2765 newap.alignmentChanged();
2767 if (alignPanels.size() == 2)
2769 viewport.setGatherViewsHere(true);
2771 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2776 * Make a new name for the view, ensuring it is unique within the current
2777 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2778 * these now use viewId. Unique view names are still desirable for usability.)
2783 protected String getNewViewName(String viewTitle)
2785 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2786 boolean addFirstIndex = false;
2787 if (viewTitle == null || viewTitle.trim().length() == 0)
2789 viewTitle = MessageManager.getString("action.view");
2790 addFirstIndex = true;
2794 index = 1;// we count from 1 if given a specific name
2796 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2798 List<Component> comps = PaintRefresher.components.get(viewport
2799 .getSequenceSetId());
2801 List<String> existingNames = getExistingViewNames(comps);
2803 while (existingNames.contains(newViewName))
2805 newViewName = viewTitle + " " + (++index);
2811 * Returns a list of distinct view names found in the given list of
2812 * components. View names are held on the viewport of an AlignmentPanel.
2817 protected List<String> getExistingViewNames(List<Component> comps)
2819 List<String> existingNames = new ArrayList<String>();
2820 for (Component comp : comps)
2822 if (comp instanceof AlignmentPanel)
2824 AlignmentPanel ap = (AlignmentPanel) comp;
2825 if (!existingNames.contains(ap.av.viewName))
2827 existingNames.add(ap.av.viewName);
2831 return existingNames;
2835 * Explode tabbed views into separate windows.
2838 public void expandViews_actionPerformed(ActionEvent e)
2840 Desktop.explodeViews(this);
2844 * Gather views in separate windows back into a tabbed presentation.
2847 public void gatherViews_actionPerformed(ActionEvent e)
2849 Desktop.instance.gatherViews(this);
2859 public void font_actionPerformed(ActionEvent e)
2861 new FontChooser(alignPanel);
2871 protected void seqLimit_actionPerformed(ActionEvent e)
2873 viewport.setShowJVSuffix(seqLimits.isSelected());
2875 alignPanel.getIdPanel().getIdCanvas()
2876 .setPreferredSize(alignPanel.calculateIdWidth());
2877 alignPanel.paintAlignment(true);
2881 public void idRightAlign_actionPerformed(ActionEvent e)
2883 viewport.setRightAlignIds(idRightAlign.isSelected());
2884 alignPanel.paintAlignment(true);
2888 public void centreColumnLabels_actionPerformed(ActionEvent e)
2890 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2891 alignPanel.paintAlignment(true);
2897 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2900 protected void followHighlight_actionPerformed()
2903 * Set the 'follow' flag on the Viewport (and scroll to position if now
2906 final boolean state = this.followHighlightMenuItem.getState();
2907 viewport.setFollowHighlight(state);
2910 alignPanel.scrollToPosition(
2911 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2922 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2924 viewport.setColourText(colourTextMenuItem.isSelected());
2925 alignPanel.paintAlignment(true);
2935 public void wrapMenuItem_actionPerformed(ActionEvent e)
2937 scaleAbove.setVisible(wrapMenuItem.isSelected());
2938 scaleLeft.setVisible(wrapMenuItem.isSelected());
2939 scaleRight.setVisible(wrapMenuItem.isSelected());
2940 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2941 alignPanel.updateLayout();
2945 public void showAllSeqs_actionPerformed(ActionEvent e)
2947 viewport.showAllHiddenSeqs();
2951 public void showAllColumns_actionPerformed(ActionEvent e)
2953 viewport.showAllHiddenColumns();
2955 viewport.sendSelection();
2959 public void hideSelSequences_actionPerformed(ActionEvent e)
2961 viewport.hideAllSelectedSeqs();
2962 // alignPanel.paintAlignment(true);
2966 * called by key handler and the hide all/show all menu items
2971 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2974 boolean hide = false;
2975 SequenceGroup sg = viewport.getSelectionGroup();
2976 if (!toggleSeqs && !toggleCols)
2978 // Hide everything by the current selection - this is a hack - we do the
2979 // invert and then hide
2980 // first check that there will be visible columns after the invert.
2981 if (viewport.hasSelectedColumns()
2982 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2985 // now invert the sequence set, if required - empty selection implies
2986 // that no hiding is required.
2989 invertSequenceMenuItem_actionPerformed(null);
2990 sg = viewport.getSelectionGroup();
2994 viewport.expandColSelection(sg, true);
2995 // finally invert the column selection and get the new sequence
2997 invertColSel_actionPerformed(null);
3004 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3006 hideSelSequences_actionPerformed(null);
3009 else if (!(toggleCols && viewport.hasSelectedColumns()))
3011 showAllSeqs_actionPerformed(null);
3017 if (viewport.hasSelectedColumns())
3019 hideSelColumns_actionPerformed(null);
3022 viewport.setSelectionGroup(sg);
3027 showAllColumns_actionPerformed(null);
3036 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3037 * event.ActionEvent)
3040 public void hideAllButSelection_actionPerformed(ActionEvent e)
3042 toggleHiddenRegions(false, false);
3043 viewport.sendSelection();
3050 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3054 public void hideAllSelection_actionPerformed(ActionEvent e)
3056 SequenceGroup sg = viewport.getSelectionGroup();
3057 viewport.expandColSelection(sg, false);
3058 viewport.hideAllSelectedSeqs();
3059 viewport.hideSelectedColumns();
3060 alignPanel.paintAlignment(true);
3061 viewport.sendSelection();
3068 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3072 public void showAllhidden_actionPerformed(ActionEvent e)
3074 viewport.showAllHiddenColumns();
3075 viewport.showAllHiddenSeqs();
3076 alignPanel.paintAlignment(true);
3077 viewport.sendSelection();
3081 public void hideSelColumns_actionPerformed(ActionEvent e)
3083 viewport.hideSelectedColumns();
3084 alignPanel.paintAlignment(true);
3085 viewport.sendSelection();
3089 public void hiddenMarkers_actionPerformed(ActionEvent e)
3091 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3102 protected void scaleAbove_actionPerformed(ActionEvent e)
3104 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3105 alignPanel.paintAlignment(true);
3115 protected void scaleLeft_actionPerformed(ActionEvent e)
3117 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3118 alignPanel.paintAlignment(true);
3128 protected void scaleRight_actionPerformed(ActionEvent e)
3130 viewport.setScaleRightWrapped(scaleRight.isSelected());
3131 alignPanel.paintAlignment(true);
3141 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3143 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3144 alignPanel.paintAlignment(true);
3154 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3156 viewport.setShowText(viewTextMenuItem.isSelected());
3157 alignPanel.paintAlignment(true);
3167 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3169 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3170 alignPanel.paintAlignment(true);
3173 public FeatureSettings featureSettings;
3176 public FeatureSettingsControllerI getFeatureSettingsUI()
3178 return featureSettings;
3182 public void featureSettings_actionPerformed(ActionEvent e)
3184 if (featureSettings != null)
3186 featureSettings.close();
3187 featureSettings = null;
3189 if (!showSeqFeatures.isSelected())
3191 // make sure features are actually displayed
3192 showSeqFeatures.setSelected(true);
3193 showSeqFeatures_actionPerformed(null);
3195 featureSettings = new FeatureSettings(this);
3199 * Set or clear 'Show Sequence Features'
3205 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3207 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3208 alignPanel.paintAlignment(true);
3209 if (alignPanel.getOverviewPanel() != null)
3211 alignPanel.getOverviewPanel().updateOverviewImage();
3216 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3217 * the annotations panel as a whole.
3219 * The options to show/hide all annotations should be enabled when the panel
3220 * is shown, and disabled when the panel is hidden.
3225 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3227 final boolean setVisible = annotationPanelMenuItem.isSelected();
3228 viewport.setShowAnnotation(setVisible);
3229 this.showAllSeqAnnotations.setEnabled(setVisible);
3230 this.hideAllSeqAnnotations.setEnabled(setVisible);
3231 this.showAllAlAnnotations.setEnabled(setVisible);
3232 this.hideAllAlAnnotations.setEnabled(setVisible);
3233 alignPanel.updateLayout();
3237 public void alignmentProperties()
3239 JEditorPane editPane = new JEditorPane("text/html", "");
3240 editPane.setEditable(false);
3241 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3243 editPane.setText(MessageManager.formatMessage("label.html_content",
3244 new Object[] { contents.toString() }));
3245 JInternalFrame frame = new JInternalFrame();
3246 frame.getContentPane().add(new JScrollPane(editPane));
3248 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3249 "label.alignment_properties", new Object[] { getTitle() }),
3260 public void overviewMenuItem_actionPerformed(ActionEvent e)
3262 if (alignPanel.overviewPanel != null)
3267 JInternalFrame frame = new JInternalFrame();
3268 OverviewPanel overview = new OverviewPanel(alignPanel);
3269 frame.setContentPane(overview);
3270 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3271 "label.overview_params", new Object[] { this.getTitle() }),
3272 frame.getWidth(), frame.getHeight());
3274 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3275 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3278 public void internalFrameClosed(
3279 javax.swing.event.InternalFrameEvent evt)
3281 alignPanel.setOverviewPanel(null);
3285 alignPanel.setOverviewPanel(overview);
3289 public void textColour_actionPerformed(ActionEvent e)
3291 new TextColourChooser().chooseColour(alignPanel, null);
3301 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3313 public void clustalColour_actionPerformed(ActionEvent e)
3315 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3316 viewport.getHiddenRepSequences()));
3326 public void zappoColour_actionPerformed(ActionEvent e)
3328 changeColour(new ZappoColourScheme());
3338 public void taylorColour_actionPerformed(ActionEvent e)
3340 changeColour(new TaylorColourScheme());
3350 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3352 changeColour(new HydrophobicColourScheme());
3362 public void helixColour_actionPerformed(ActionEvent e)
3364 changeColour(new HelixColourScheme());
3374 public void strandColour_actionPerformed(ActionEvent e)
3376 changeColour(new StrandColourScheme());
3386 public void turnColour_actionPerformed(ActionEvent e)
3388 changeColour(new TurnColourScheme());
3398 public void buriedColour_actionPerformed(ActionEvent e)
3400 changeColour(new BuriedColourScheme());
3410 public void nucleotideColour_actionPerformed(ActionEvent e)
3412 changeColour(new NucleotideColourScheme());
3416 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3418 changeColour(new PurinePyrimidineColourScheme());
3422 * public void covariationColour_actionPerformed(ActionEvent e) {
3424 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3428 public void annotationColour_actionPerformed(ActionEvent e)
3430 new AnnotationColourChooser(viewport, alignPanel);
3434 public void annotationColumn_actionPerformed(ActionEvent e)
3436 new AnnotationColumnChooser(viewport, alignPanel);
3440 public void rnahelicesColour_actionPerformed(ActionEvent e)
3442 new RNAHelicesColourChooser(viewport, alignPanel);
3452 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3454 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3464 public void changeColour(ColourSchemeI cs)
3466 // TODO: pull up to controller method
3470 // Make sure viewport is up to date w.r.t. any sliders
3471 if (viewport.getAbovePIDThreshold())
3473 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3475 viewport.setThreshold(threshold);
3478 if (viewport.getConservationSelected())
3480 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3483 if (cs instanceof TCoffeeColourScheme)
3485 tcoffeeColour.setEnabled(true);
3486 tcoffeeColour.setSelected(true);
3490 viewport.setGlobalColourScheme(cs);
3492 alignPanel.paintAlignment(true);
3502 protected void modifyPID_actionPerformed(ActionEvent e)
3504 if (viewport.getAbovePIDThreshold()
3505 && viewport.getGlobalColourScheme() != null)
3507 SliderPanel.setPIDSliderSource(alignPanel,
3508 viewport.getGlobalColourScheme(), "Background");
3509 SliderPanel.showPIDSlider();
3520 protected void modifyConservation_actionPerformed(ActionEvent e)
3522 if (viewport.getConservationSelected()
3523 && viewport.getGlobalColourScheme() != null)
3525 SliderPanel.setConservationSlider(alignPanel,
3526 viewport.getGlobalColourScheme(), "Background");
3527 SliderPanel.showConservationSlider();
3538 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3540 viewport.setConservationSelected(conservationMenuItem.isSelected());
3542 viewport.setAbovePIDThreshold(false);
3543 abovePIDThreshold.setSelected(false);
3545 changeColour(viewport.getGlobalColourScheme());
3547 modifyConservation_actionPerformed(null);
3557 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3559 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3561 conservationMenuItem.setSelected(false);
3562 viewport.setConservationSelected(false);
3564 changeColour(viewport.getGlobalColourScheme());
3566 modifyPID_actionPerformed(null);
3576 public void userDefinedColour_actionPerformed(ActionEvent e)
3578 if (e.getActionCommand().equals(
3579 MessageManager.getString("action.user_defined")))
3581 new UserDefinedColours(alignPanel, null);
3585 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3586 .getUserColourSchemes().get(e.getActionCommand());
3592 public void updateUserColourMenu()
3595 Component[] menuItems = colourMenu.getMenuComponents();
3596 int iSize = menuItems.length;
3597 for (int i = 0; i < iSize; i++)
3599 if (menuItems[i].getName() != null
3600 && menuItems[i].getName().equals("USER_DEFINED"))
3602 colourMenu.remove(menuItems[i]);
3606 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3608 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3609 .getUserColourSchemes().keys();
3611 while (userColours.hasMoreElements())
3613 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3614 userColours.nextElement().toString());
3615 radioItem.setName("USER_DEFINED");
3616 radioItem.addMouseListener(new MouseAdapter()
3619 public void mousePressed(MouseEvent evt)
3621 if (evt.isPopupTrigger()) // Mac
3623 offerRemoval(radioItem);
3628 public void mouseReleased(MouseEvent evt)
3630 if (evt.isPopupTrigger()) // Windows
3632 offerRemoval(radioItem);
3639 void offerRemoval(final JRadioButtonMenuItem radioItem)
3641 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3643 int option = JOptionPane.showInternalConfirmDialog(
3644 jalview.gui.Desktop.desktop, MessageManager
3645 .getString("label.remove_from_default_list"),
3647 .getString("label.remove_user_defined_colour"),
3648 JOptionPane.YES_NO_OPTION);
3649 if (option == JOptionPane.YES_OPTION)
3651 jalview.gui.UserDefinedColours
3652 .removeColourFromDefaults(radioItem.getText());
3653 colourMenu.remove(radioItem);
3657 radioItem.addActionListener(new ActionListener()
3660 public void actionPerformed(ActionEvent evt)
3662 userDefinedColour_actionPerformed(evt);
3668 radioItem.addActionListener(new ActionListener()
3671 public void actionPerformed(ActionEvent evt)
3673 userDefinedColour_actionPerformed(evt);
3677 colourMenu.insert(radioItem, 15);
3678 colours.add(radioItem);
3690 public void PIDColour_actionPerformed(ActionEvent e)
3692 changeColour(new PIDColourScheme());
3702 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3704 changeColour(new Blosum62ColourScheme());
3714 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3716 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3717 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3718 .getAlignment().getSequenceAt(0), null);
3719 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3720 viewport.getAlignment()));
3721 alignPanel.paintAlignment(true);
3731 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3733 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3734 AlignmentSorter.sortByID(viewport.getAlignment());
3735 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3736 viewport.getAlignment()));
3737 alignPanel.paintAlignment(true);
3747 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3749 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3750 AlignmentSorter.sortByLength(viewport.getAlignment());
3751 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3752 viewport.getAlignment()));
3753 alignPanel.paintAlignment(true);
3763 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3765 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3766 AlignmentSorter.sortByGroup(viewport.getAlignment());
3767 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3768 viewport.getAlignment()));
3770 alignPanel.paintAlignment(true);
3780 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3782 new RedundancyPanel(alignPanel, this);
3792 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3794 if ((viewport.getSelectionGroup() == null)
3795 || (viewport.getSelectionGroup().getSize() < 2))
3797 JOptionPane.showInternalMessageDialog(this, MessageManager
3798 .getString("label.you_must_select_least_two_sequences"),
3799 MessageManager.getString("label.invalid_selection"),
3800 JOptionPane.WARNING_MESSAGE);
3804 JInternalFrame frame = new JInternalFrame();
3805 frame.setContentPane(new PairwiseAlignPanel(viewport));
3806 Desktop.addInternalFrame(frame,
3807 MessageManager.getString("action.pairwise_alignment"), 600,
3819 public void PCAMenuItem_actionPerformed(ActionEvent e)
3821 if (((viewport.getSelectionGroup() != null)
3822 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3823 .getSelectionGroup().getSize() > 0))
3824 || (viewport.getAlignment().getHeight() < 4))
3827 .showInternalMessageDialog(
3830 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3832 .getString("label.sequence_selection_insufficient"),
3833 JOptionPane.WARNING_MESSAGE);
3838 new PCAPanel(alignPanel);
3842 public void autoCalculate_actionPerformed(ActionEvent e)
3844 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3845 if (viewport.autoCalculateConsensus)
3847 viewport.firePropertyChange("alignment", null, viewport
3848 .getAlignment().getSequences());
3853 public void sortByTreeOption_actionPerformed(ActionEvent e)
3855 viewport.sortByTree = sortByTree.isSelected();
3859 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3861 viewport.followSelection = listenToViewSelections.isSelected();
3871 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3873 newTreePanel("AV", "PID", "Average distance tree using PID");
3883 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3885 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3895 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3897 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3907 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3909 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3922 void newTreePanel(String type, String pwType, String title)
3926 if (viewport.getSelectionGroup() != null
3927 && viewport.getSelectionGroup().getSize() > 0)
3929 if (viewport.getSelectionGroup().getSize() < 3)
3935 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3937 .getString("label.not_enough_sequences"),
3938 JOptionPane.WARNING_MESSAGE);
3942 SequenceGroup sg = viewport.getSelectionGroup();
3944 /* Decide if the selection is a column region */
3945 for (SequenceI _s : sg.getSequences())
3947 if (_s.getLength() < sg.getEndRes())
3953 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3955 .getString("label.sequences_selection_not_aligned"),
3956 JOptionPane.WARNING_MESSAGE);
3962 title = title + " on region";
3963 tp = new TreePanel(alignPanel, type, pwType);
3967 // are the visible sequences aligned?
3968 if (!viewport.getAlignment().isAligned(false))
3974 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3976 .getString("label.sequences_not_aligned"),
3977 JOptionPane.WARNING_MESSAGE);
3982 if (viewport.getAlignment().getHeight() < 2)
3987 tp = new TreePanel(alignPanel, type, pwType);
3992 if (viewport.viewName != null)
3994 title += viewport.viewName + " of ";
3997 title += this.title;
3999 Desktop.addInternalFrame(tp, title, 600, 500);
4010 public void addSortByOrderMenuItem(String title,
4011 final AlignmentOrder order)
4013 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4014 "action.by_title_param", new Object[] { title }));
4016 item.addActionListener(new java.awt.event.ActionListener()
4019 public void actionPerformed(ActionEvent e)
4021 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4023 // TODO: JBPNote - have to map order entries to curent SequenceI
4025 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4027 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4030 alignPanel.paintAlignment(true);
4036 * Add a new sort by annotation score menu item
4039 * the menu to add the option to
4041 * the label used to retrieve scores for each sequence on the
4044 public void addSortByAnnotScoreMenuItem(JMenu sort,
4045 final String scoreLabel)
4047 final JMenuItem item = new JMenuItem(scoreLabel);
4049 item.addActionListener(new java.awt.event.ActionListener()
4052 public void actionPerformed(ActionEvent e)
4054 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4055 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4056 viewport.getAlignment());// ,viewport.getSelectionGroup());
4057 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4058 viewport.getAlignment()));
4059 alignPanel.paintAlignment(true);
4065 * last hash for alignment's annotation array - used to minimise cost of
4068 protected int _annotationScoreVectorHash;
4071 * search the alignment and rebuild the sort by annotation score submenu the
4072 * last alignment annotation vector hash is stored to minimize cost of
4073 * rebuilding in subsequence calls.
4077 public void buildSortByAnnotationScoresMenu()
4079 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4084 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4086 sortByAnnotScore.removeAll();
4087 // almost certainly a quicker way to do this - but we keep it simple
4088 Hashtable scoreSorts = new Hashtable();
4089 AlignmentAnnotation aann[];
4090 for (SequenceI sqa : viewport.getAlignment().getSequences())
4092 aann = sqa.getAnnotation();
4093 for (int i = 0; aann != null && i < aann.length; i++)
4095 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4097 scoreSorts.put(aann[i].label, aann[i].label);
4101 Enumeration labels = scoreSorts.keys();
4102 while (labels.hasMoreElements())
4104 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4105 (String) labels.nextElement());
4107 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4110 _annotationScoreVectorHash = viewport.getAlignment()
4111 .getAlignmentAnnotation().hashCode();
4116 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4117 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4118 * call. Listeners are added to remove the menu item when the treePanel is
4119 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4123 * Displayed tree window.
4125 * SortBy menu item title.
4128 public void buildTreeMenu()
4130 calculateTree.removeAll();
4131 // build the calculate menu
4133 for (final String type : new String[] { "NJ", "AV" })
4135 String treecalcnm = MessageManager.getString("label.tree_calc_"
4136 + type.toLowerCase());
4137 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4139 JMenuItem tm = new JMenuItem();
4140 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4141 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4142 || sm.isProtein() == !viewport.getAlignment()
4145 String smn = MessageManager.getStringOrReturn(
4146 "label.score_model_", sm.getName());
4147 final String title = MessageManager.formatMessage(
4148 "label.treecalc_title", treecalcnm, smn);
4149 tm.setText(title);//
4150 tm.addActionListener(new java.awt.event.ActionListener()
4153 public void actionPerformed(ActionEvent e)
4155 newTreePanel(type, pwtype, title);
4158 calculateTree.add(tm);
4163 sortByTreeMenu.removeAll();
4165 List<Component> comps = PaintRefresher.components.get(viewport
4166 .getSequenceSetId());
4167 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4168 for (Component comp : comps)
4170 if (comp instanceof TreePanel)
4172 treePanels.add((TreePanel) comp);
4176 if (treePanels.size() < 1)
4178 sortByTreeMenu.setVisible(false);
4182 sortByTreeMenu.setVisible(true);
4184 for (final TreePanel tp : treePanels)
4186 final JMenuItem item = new JMenuItem(tp.getTitle());
4187 item.addActionListener(new java.awt.event.ActionListener()
4190 public void actionPerformed(ActionEvent e)
4192 tp.sortByTree_actionPerformed();
4193 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4198 sortByTreeMenu.add(item);
4202 public boolean sortBy(AlignmentOrder alorder, String undoname)
4204 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4205 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4206 if (undoname != null)
4208 addHistoryItem(new OrderCommand(undoname, oldOrder,
4209 viewport.getAlignment()));
4211 alignPanel.paintAlignment(true);
4216 * Work out whether the whole set of sequences or just the selected set will
4217 * be submitted for multiple alignment.
4220 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4222 // Now, check we have enough sequences
4223 AlignmentView msa = null;
4225 if ((viewport.getSelectionGroup() != null)
4226 && (viewport.getSelectionGroup().getSize() > 1))
4228 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4229 // some common interface!
4231 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4232 * SequenceI[sz = seqs.getSize(false)];
4234 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4235 * seqs.getSequenceAt(i); }
4237 msa = viewport.getAlignmentView(true);
4239 else if (viewport.getSelectionGroup() != null
4240 && viewport.getSelectionGroup().getSize() == 1)
4242 int option = JOptionPane.showConfirmDialog(this,
4243 MessageManager.getString("warn.oneseq_msainput_selection"),
4244 MessageManager.getString("label.invalid_selection"),
4245 JOptionPane.OK_CANCEL_OPTION);
4246 if (option == JOptionPane.OK_OPTION)
4248 msa = viewport.getAlignmentView(false);
4253 msa = viewport.getAlignmentView(false);
4259 * Decides what is submitted to a secondary structure prediction service: the
4260 * first sequence in the alignment, or in the current selection, or, if the
4261 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4262 * region or the whole alignment. (where the first sequence in the set is the
4263 * one that the prediction will be for).
4265 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4267 AlignmentView seqs = null;
4269 if ((viewport.getSelectionGroup() != null)
4270 && (viewport.getSelectionGroup().getSize() > 0))
4272 seqs = viewport.getAlignmentView(true);
4276 seqs = viewport.getAlignmentView(false);
4278 // limit sequences - JBPNote in future - could spawn multiple prediction
4280 // TODO: viewport.getAlignment().isAligned is a global state - the local
4281 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4282 if (!viewport.getAlignment().isAligned(false))
4284 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4285 // TODO: if seqs.getSequences().length>1 then should really have warned
4299 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4301 // Pick the tree file
4302 JalviewFileChooser chooser = new JalviewFileChooser(
4303 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4304 chooser.setFileView(new JalviewFileView());
4305 chooser.setDialogTitle(MessageManager
4306 .getString("label.select_newick_like_tree_file"));
4307 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4309 int value = chooser.showOpenDialog(null);
4311 if (value == JalviewFileChooser.APPROVE_OPTION)
4313 String choice = chooser.getSelectedFile().getPath();
4314 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4315 jalview.io.NewickFile fin = null;
4318 fin = new jalview.io.NewickFile(choice, "File");
4319 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4320 } catch (Exception ex)
4327 .getString("label.problem_reading_tree_file"),
4328 JOptionPane.WARNING_MESSAGE);
4329 ex.printStackTrace();
4331 if (fin != null && fin.hasWarningMessage())
4333 JOptionPane.showMessageDialog(Desktop.desktop, fin
4334 .getWarningMessage(), MessageManager
4335 .getString("label.possible_problem_with_tree_file"),
4336 JOptionPane.WARNING_MESSAGE);
4342 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4344 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4347 public TreePanel ShowNewickTree(NewickFile nf, String title)
4349 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4352 public TreePanel ShowNewickTree(NewickFile nf, String title,
4353 AlignmentView input)
4355 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4358 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4359 int h, int x, int y)
4361 return ShowNewickTree(nf, title, null, w, h, x, y);
4365 * Add a treeviewer for the tree extracted from a newick file object to the
4366 * current alignment view
4373 * Associated alignment input data (or null)
4382 * @return TreePanel handle
4384 public TreePanel ShowNewickTree(NewickFile nf, String title,
4385 AlignmentView input, int w, int h, int x, int y)
4387 TreePanel tp = null;
4393 if (nf.getTree() != null)
4395 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4401 tp.setLocation(x, y);
4404 Desktop.addInternalFrame(tp, title, w, h);
4406 } catch (Exception ex)
4408 ex.printStackTrace();
4414 private boolean buildingMenu = false;
4417 * Generates menu items and listener event actions for web service clients
4420 public void BuildWebServiceMenu()
4422 while (buildingMenu)
4426 System.err.println("Waiting for building menu to finish.");
4428 } catch (Exception e)
4432 final AlignFrame me = this;
4433 buildingMenu = true;
4434 new Thread(new Runnable()
4439 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4442 // System.err.println("Building ws menu again "
4443 // + Thread.currentThread());
4444 // TODO: add support for context dependent disabling of services based
4446 // alignment and current selection
4447 // TODO: add additional serviceHandle parameter to specify abstract
4449 // class independently of AbstractName
4450 // TODO: add in rediscovery GUI function to restart discoverer
4451 // TODO: group services by location as well as function and/or
4453 // object broker mechanism.
4454 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4455 final IProgressIndicator af = me;
4458 * do not i18n these strings - they are hard-coded in class
4459 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4460 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4462 final JMenu msawsmenu = new JMenu("Alignment");
4463 final JMenu secstrmenu = new JMenu(
4464 "Secondary Structure Prediction");
4465 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4466 final JMenu analymenu = new JMenu("Analysis");
4467 final JMenu dismenu = new JMenu("Protein Disorder");
4468 // JAL-940 - only show secondary structure prediction services from
4469 // the legacy server
4470 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4472 Discoverer.services != null && (Discoverer.services.size() > 0))
4474 // TODO: refactor to allow list of AbstractName/Handler bindings to
4476 // stored or retrieved from elsewhere
4477 // No MSAWS used any more:
4478 // Vector msaws = null; // (Vector)
4479 // Discoverer.services.get("MsaWS");
4480 Vector secstrpr = (Vector) Discoverer.services
4482 if (secstrpr != null)
4484 // Add any secondary structure prediction services
4485 for (int i = 0, j = secstrpr.size(); i < j; i++)
4487 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4489 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4490 .getServiceClient(sh);
4491 int p = secstrmenu.getItemCount();
4492 impl.attachWSMenuEntry(secstrmenu, me);
4493 int q = secstrmenu.getItemCount();
4494 for (int litm = p; litm < q; litm++)
4496 legacyItems.add(secstrmenu.getItem(litm));
4502 // Add all submenus in the order they should appear on the web
4504 wsmenu.add(msawsmenu);
4505 wsmenu.add(secstrmenu);
4506 wsmenu.add(dismenu);
4507 wsmenu.add(analymenu);
4508 // No search services yet
4509 // wsmenu.add(seqsrchmenu);
4511 javax.swing.SwingUtilities.invokeLater(new Runnable()
4518 webService.removeAll();
4519 // first, add discovered services onto the webservices menu
4520 if (wsmenu.size() > 0)
4522 for (int i = 0, j = wsmenu.size(); i < j; i++)
4524 webService.add(wsmenu.get(i));
4529 webService.add(me.webServiceNoServices);
4531 // TODO: move into separate menu builder class.
4532 boolean new_sspred = false;
4533 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4535 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4536 if (jws2servs != null)
4538 if (jws2servs.hasServices())
4540 jws2servs.attachWSMenuEntry(webService, me);
4541 for (Jws2Instance sv : jws2servs.getServices())
4543 if (sv.description.toLowerCase().contains("jpred"))
4545 for (JMenuItem jmi : legacyItems)
4547 jmi.setVisible(false);
4553 if (jws2servs.isRunning())
4555 JMenuItem tm = new JMenuItem(
4556 "Still discovering JABA Services");
4557 tm.setEnabled(false);
4562 build_urlServiceMenu(me.webService);
4563 build_fetchdbmenu(webService);
4564 for (JMenu item : wsmenu)
4566 if (item.getItemCount() == 0)
4568 item.setEnabled(false);
4572 item.setEnabled(true);
4575 } catch (Exception e)
4578 .debug("Exception during web service menu building process.",
4583 } catch (Exception e)
4586 buildingMenu = false;
4593 * construct any groupURL type service menu entries.
4597 private void build_urlServiceMenu(JMenu webService)
4599 // TODO: remove this code when 2.7 is released
4600 // DEBUG - alignmentView
4602 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4603 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4605 * @Override public void actionPerformed(ActionEvent e) {
4606 * jalview.datamodel.AlignmentView
4607 * .testSelectionViews(af.viewport.getAlignment(),
4608 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4610 * }); webService.add(testAlView);
4612 // TODO: refactor to RestClient discoverer and merge menu entries for
4613 // rest-style services with other types of analysis/calculation service
4614 // SHmmr test client - still being implemented.
4615 // DEBUG - alignmentView
4617 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4620 client.attachWSMenuEntry(
4621 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4627 * Searches the alignment sequences for xRefs and builds the Show
4628 * Cross-References menu (formerly called Show Products), with database
4629 * sources for which cross-references are found (protein sources for a
4630 * nucleotide alignment and vice versa)
4632 * @return true if Show Cross-references menu should be enabled
4634 public boolean canShowProducts()
4636 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4637 AlignmentI dataset = viewport.getAlignment().getDataset();
4639 showProducts.removeAll();
4640 final boolean dna = viewport.getAlignment().isNucleotide();
4642 if (seqs == null || seqs.length == 0)
4644 // nothing to see here.
4648 boolean showp = false;
4651 List<String> ptypes = new CrossRef(seqs, dataset)
4652 .findXrefSourcesForSequences(dna);
4654 for (final String source : ptypes)
4657 final AlignFrame af = this;
4658 JMenuItem xtype = new JMenuItem(source);
4659 xtype.addActionListener(new ActionListener()
4662 public void actionPerformed(ActionEvent e)
4664 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4667 showProducts.add(xtype);
4669 showProducts.setVisible(showp);
4670 showProducts.setEnabled(showp);
4671 } catch (Exception e)
4674 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4682 * Finds and displays cross-references for the selected sequences (protein
4683 * products for nucleotide sequences, dna coding sequences for peptides).
4686 * the sequences to show cross-references for
4688 * true if from a nucleotide alignment (so showing proteins)
4690 * the database to show cross-references for
4692 protected void showProductsFor(final SequenceI[] sel,
4693 final boolean _odna, final String source)
4695 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4700 * Construct and display a new frame containing the translation of this
4701 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4704 public void showTranslation_actionPerformed(ActionEvent e)
4706 AlignmentI al = null;
4709 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4711 al = dna.translateCdna();
4712 } catch (Exception ex)
4714 jalview.bin.Cache.log.error(
4715 "Exception during translation. Please report this !", ex);
4716 final String msg = MessageManager
4717 .getString("label.error_when_translating_sequences_submit_bug_report");
4718 final String errorTitle = MessageManager
4719 .getString("label.implementation_error")
4720 + MessageManager.getString("label.translation_failed");
4721 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4722 JOptionPane.ERROR_MESSAGE);
4725 if (al == null || al.getHeight() == 0)
4727 final String msg = MessageManager
4728 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4729 final String errorTitle = MessageManager
4730 .getString("label.translation_failed");
4731 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4732 JOptionPane.WARNING_MESSAGE);
4736 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4737 af.setFileFormat(this.currentFileFormat);
4738 final String newTitle = MessageManager.formatMessage(
4739 "label.translation_of_params",
4740 new Object[] { this.getTitle() });
4741 af.setTitle(newTitle);
4742 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4744 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4745 viewport.openSplitFrame(af, new Alignment(seqs));
4749 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4756 * Set the file format
4760 public void setFileFormat(String fileFormat)
4762 this.currentFileFormat = fileFormat;
4766 * Try to load a features file onto the alignment.
4769 * contents or path to retrieve file
4771 * access mode of file (see jalview.io.AlignFile)
4772 * @return true if features file was parsed correctly.
4774 public boolean parseFeaturesFile(String file, String type)
4776 return avc.parseFeaturesFile(file, type,
4777 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4782 public void refreshFeatureUI(boolean enableIfNecessary)
4784 // note - currently this is only still here rather than in the controller
4785 // because of the featureSettings hard reference that is yet to be
4787 if (enableIfNecessary)
4789 viewport.setShowSequenceFeatures(true);
4790 showSeqFeatures.setSelected(true);
4796 public void dragEnter(DropTargetDragEvent evt)
4801 public void dragExit(DropTargetEvent evt)
4806 public void dragOver(DropTargetDragEvent evt)
4811 public void dropActionChanged(DropTargetDragEvent evt)
4816 public void drop(DropTargetDropEvent evt)
4818 // JAL-1552 - acceptDrop required before getTransferable call for
4819 // Java's Transferable for native dnd
4820 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4821 Transferable t = evt.getTransferable();
4822 java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
4826 Desktop.transferFromDropTarget(files, protocols, evt, t);
4827 } catch (Exception e)
4829 e.printStackTrace();
4835 // check to see if any of these files have names matching sequences in
4837 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4838 .getAlignment().getSequencesArray());
4840 * Object[] { String,SequenceI}
4842 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4843 ArrayList<String> filesnotmatched = new ArrayList<String>();
4844 for (int i = 0; i < files.size(); i++)
4846 String file = files.get(i).toString();
4848 String protocol = FormatAdapter.checkProtocol(file);
4849 if (protocol == jalview.io.FormatAdapter.FILE)
4851 File fl = new File(file);
4852 pdbfn = fl.getName();
4854 else if (protocol == jalview.io.FormatAdapter.URL)
4856 URL url = new URL(file);
4857 pdbfn = url.getFile();
4859 if (pdbfn.length() > 0)
4861 // attempt to find a match in the alignment
4862 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4863 int l = 0, c = pdbfn.indexOf(".");
4864 while (mtch == null && c != -1)
4869 } while ((c = pdbfn.indexOf(".", l)) > l);
4872 pdbfn = pdbfn.substring(0, l);
4874 mtch = idm.findAllIdMatches(pdbfn);
4881 type = new IdentifyFile().identify(file, protocol);
4882 } catch (Exception ex)
4888 if (type.equalsIgnoreCase("PDB"))
4890 filesmatched.add(new Object[] { file, protocol, mtch });
4895 // File wasn't named like one of the sequences or wasn't a PDB file.
4896 filesnotmatched.add(file);
4900 if (filesmatched.size() > 0)
4902 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4908 "label.automatically_associate_pdb_files_with_sequences_same_name",
4909 new Object[] { Integer
4915 .getString("label.automatically_associate_pdb_files_by_name"),
4916 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4919 for (Object[] fm : filesmatched)
4921 // try and associate
4922 // TODO: may want to set a standard ID naming formalism for
4923 // associating PDB files which have no IDs.
4924 for (SequenceI toassoc : (SequenceI[]) fm[2])
4926 PDBEntry pe = new AssociatePdbFileWithSeq()
4927 .associatePdbWithSeq((String) fm[0],
4928 (String) fm[1], toassoc, false,
4932 System.err.println("Associated file : "
4933 + ((String) fm[0]) + " with "
4934 + toassoc.getDisplayId(true));
4938 alignPanel.paintAlignment(true);
4942 if (filesnotmatched.size() > 0)
4945 && (Cache.getDefault(
4946 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4952 "label.ignore_unmatched_dropped_files_info",
4953 new Object[] { Integer
4960 .getString("label.ignore_unmatched_dropped_files"),
4961 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4965 for (String fn : filesnotmatched)
4967 loadJalviewDataFile(fn, null, null, null);
4971 } catch (Exception ex)
4973 ex.printStackTrace();
4979 * Attempt to load a "dropped" file or URL string: First by testing whether
4980 * it's an Annotation file, then a JNet file, and finally a features file. If
4981 * all are false then the user may have dropped an alignment file onto this
4985 * either a filename or a URL string.
4987 public void loadJalviewDataFile(String file, String protocol,
4988 String format, SequenceI assocSeq)
4992 if (protocol == null)
4994 protocol = FormatAdapter.checkProtocol(file);
4996 // if the file isn't identified, or not positively identified as some
4997 // other filetype (PFAM is default unidentified alignment file type) then
4998 // try to parse as annotation.
4999 boolean isAnnotation = (format == null || format
5000 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5001 .annotateAlignmentView(viewport, file, protocol) : false;
5005 // first see if its a T-COFFEE score file
5006 TCoffeeScoreFile tcf = null;
5009 tcf = new TCoffeeScoreFile(file, protocol);
5012 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5014 tcoffeeColour.setEnabled(true);
5015 tcoffeeColour.setSelected(true);
5016 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5017 isAnnotation = true;
5019 .setText(MessageManager
5020 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5024 // some problem - if no warning its probable that the ID matching
5025 // process didn't work
5029 tcf.getWarningMessage() == null ? MessageManager
5030 .getString("label.check_file_matches_sequence_ids_alignment")
5031 : tcf.getWarningMessage(),
5033 .getString("label.problem_reading_tcoffee_score_file"),
5034 JOptionPane.WARNING_MESSAGE);
5041 } catch (Exception x)
5044 .debug("Exception when processing data source as T-COFFEE score file",
5050 // try to see if its a JNet 'concise' style annotation file *before*
5052 // try to parse it as a features file
5055 format = new IdentifyFile().identify(file, protocol);
5057 if (format.equalsIgnoreCase("JnetFile"))
5059 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5061 new JnetAnnotationMaker();
5062 JnetAnnotationMaker.add_annotation(predictions,
5063 viewport.getAlignment(), 0, false);
5064 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5065 viewport.getAlignment().setSeqrep(repseq);
5066 ColumnSelection cs = new ColumnSelection();
5067 cs.hideInsertionsFor(repseq);
5068 viewport.setColumnSelection(cs);
5069 isAnnotation = true;
5071 else if (IdentifyFile.FeaturesFile.equals(format))
5073 if (parseFeaturesFile(file, protocol))
5075 alignPanel.paintAlignment(true);
5080 new FileLoader().LoadFile(viewport, file, protocol, format);
5087 alignPanel.adjustAnnotationHeight();
5088 viewport.updateSequenceIdColours();
5089 buildSortByAnnotationScoresMenu();
5090 alignPanel.paintAlignment(true);
5092 } catch (Exception ex)
5094 ex.printStackTrace();
5095 } catch (OutOfMemoryError oom)
5100 } catch (Exception x)
5105 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5106 : "using " + protocol + " from " + file)
5108 + (format != null ? "(parsing as '" + format
5109 + "' file)" : ""), oom, Desktop.desktop);
5114 * Method invoked by the ChangeListener on the tabbed pane, in other words
5115 * when a different tabbed pane is selected by the user or programmatically.
5118 public void tabSelectionChanged(int index)
5122 alignPanel = alignPanels.get(index);
5123 viewport = alignPanel.av;
5124 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5125 setMenusFromViewport(viewport);
5129 * If there is a frame linked to this one in a SplitPane, switch it to the
5130 * same view tab index. No infinite recursion of calls should happen, since
5131 * tabSelectionChanged() should not get invoked on setting the selected
5132 * index to an unchanged value. Guard against setting an invalid index
5133 * before the new view peer tab has been created.
5135 final AlignViewportI peer = viewport.getCodingComplement();
5138 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5139 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5141 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5147 * On right mouse click on view tab, prompt for and set new view name.
5150 public void tabbedPane_mousePressed(MouseEvent e)
5152 if (e.isPopupTrigger())
5154 String msg = MessageManager.getString("label.enter_view_name");
5155 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5156 JOptionPane.QUESTION_MESSAGE);
5160 viewport.viewName = reply;
5161 // TODO warn if reply is in getExistingViewNames()?
5162 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5167 public AlignViewport getCurrentView()
5173 * Open the dialog for regex description parsing.
5176 protected void extractScores_actionPerformed(ActionEvent e)
5178 ParseProperties pp = new jalview.analysis.ParseProperties(
5179 viewport.getAlignment());
5180 // TODO: verify regex and introduce GUI dialog for version 2.5
5181 // if (pp.getScoresFromDescription("col", "score column ",
5182 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5184 if (pp.getScoresFromDescription("description column",
5185 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5187 buildSortByAnnotationScoresMenu();
5195 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5199 protected void showDbRefs_actionPerformed(ActionEvent e)
5201 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5207 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5211 protected void showNpFeats_actionPerformed(ActionEvent e)
5213 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5217 * find the viewport amongst the tabs in this alignment frame and close that
5222 public boolean closeView(AlignViewportI av)
5226 this.closeMenuItem_actionPerformed(false);
5229 Component[] comp = tabbedPane.getComponents();
5230 for (int i = 0; comp != null && i < comp.length; i++)
5232 if (comp[i] instanceof AlignmentPanel)
5234 if (((AlignmentPanel) comp[i]).av == av)
5237 closeView((AlignmentPanel) comp[i]);
5245 protected void build_fetchdbmenu(JMenu webService)
5247 // Temporary hack - DBRef Fetcher always top level ws entry.
5248 // TODO We probably want to store a sequence database checklist in
5249 // preferences and have checkboxes.. rather than individual sources selected
5251 final JMenu rfetch = new JMenu(
5252 MessageManager.getString("action.fetch_db_references"));
5253 rfetch.setToolTipText(MessageManager
5254 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5255 webService.add(rfetch);
5257 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5258 MessageManager.getString("option.trim_retrieved_seqs"));
5259 trimrs.setToolTipText(MessageManager
5260 .getString("label.trim_retrieved_sequences"));
5261 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5262 trimrs.addActionListener(new ActionListener()
5265 public void actionPerformed(ActionEvent e)
5267 trimrs.setSelected(trimrs.isSelected());
5268 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5269 Boolean.valueOf(trimrs.isSelected()).toString());
5273 JMenuItem fetchr = new JMenuItem(
5274 MessageManager.getString("label.standard_databases"));
5275 fetchr.setToolTipText(MessageManager
5276 .getString("label.fetch_embl_uniprot"));
5277 fetchr.addActionListener(new ActionListener()
5281 public void actionPerformed(ActionEvent e)
5283 new Thread(new Runnable()
5288 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5289 .getAlignment().isNucleotide();
5290 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5291 .getSequenceSelection(), alignPanel.alignFrame, null,
5292 alignPanel.alignFrame.featureSettings, isNucleotide);
5293 dbRefFetcher.addListener(new FetchFinishedListenerI()
5296 public void finished()
5298 AlignFrame.this.setMenusForViewport();
5301 dbRefFetcher.fetchDBRefs(false);
5309 final AlignFrame me = this;
5310 new Thread(new Runnable()
5315 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5316 .getSequenceFetcherSingleton(me);
5317 javax.swing.SwingUtilities.invokeLater(new Runnable()
5322 String[] dbclasses = sf.getOrderedSupportedSources();
5323 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5324 // jalview.util.QuickSort.sort(otherdb, otherdb);
5325 List<DbSourceProxy> otherdb;
5326 JMenu dfetch = new JMenu();
5327 JMenu ifetch = new JMenu();
5328 JMenuItem fetchr = null;
5329 int comp = 0, icomp = 0, mcomp = 15;
5330 String mname = null;
5332 for (String dbclass : dbclasses)
5334 otherdb = sf.getSourceProxy(dbclass);
5335 // add a single entry for this class, or submenu allowing 'fetch
5337 if (otherdb == null || otherdb.size() < 1)
5341 // List<DbSourceProxy> dbs=otherdb;
5342 // otherdb=new ArrayList<DbSourceProxy>();
5343 // for (DbSourceProxy db:dbs)
5345 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5349 mname = "From " + dbclass;
5351 if (otherdb.size() == 1)
5353 final DbSourceProxy[] dassource = otherdb
5354 .toArray(new DbSourceProxy[0]);
5355 DbSourceProxy src = otherdb.get(0);
5356 fetchr = new JMenuItem(src.getDbSource());
5357 fetchr.addActionListener(new ActionListener()
5361 public void actionPerformed(ActionEvent e)
5363 new Thread(new Runnable()
5369 boolean isNucleotide = alignPanel.alignFrame
5370 .getViewport().getAlignment()
5372 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5373 alignPanel.av.getSequenceSelection(),
5374 alignPanel.alignFrame, dassource,
5375 alignPanel.alignFrame.featureSettings,
5378 .addListener(new FetchFinishedListenerI()
5381 public void finished()
5383 AlignFrame.this.setMenusForViewport();
5386 dbRefFetcher.fetchDBRefs(false);
5392 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5393 MessageManager.formatMessage(
5394 "label.fetch_retrieve_from",
5395 new Object[] { src.getDbName() })));
5401 final DbSourceProxy[] dassource = otherdb
5402 .toArray(new DbSourceProxy[0]);
5404 DbSourceProxy src = otherdb.get(0);
5405 fetchr = new JMenuItem(MessageManager.formatMessage(
5406 "label.fetch_all_param",
5407 new Object[] { src.getDbSource() }));
5408 fetchr.addActionListener(new ActionListener()
5411 public void actionPerformed(ActionEvent e)
5413 new Thread(new Runnable()
5419 boolean isNucleotide = alignPanel.alignFrame
5420 .getViewport().getAlignment()
5422 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5423 alignPanel.av.getSequenceSelection(),
5424 alignPanel.alignFrame, dassource,
5425 alignPanel.alignFrame.featureSettings,
5428 .addListener(new FetchFinishedListenerI()
5431 public void finished()
5433 AlignFrame.this.setMenusForViewport();
5436 dbRefFetcher.fetchDBRefs(false);
5442 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5443 MessageManager.formatMessage(
5444 "label.fetch_retrieve_from_all_sources",
5446 Integer.valueOf(otherdb.size())
5447 .toString(), src.getDbSource(),
5448 src.getDbName() })));
5451 // and then build the rest of the individual menus
5452 ifetch = new JMenu(MessageManager.formatMessage(
5453 "label.source_from_db_source",
5454 new Object[] { src.getDbSource() }));
5456 String imname = null;
5458 for (DbSourceProxy sproxy : otherdb)
5460 String dbname = sproxy.getDbName();
5461 String sname = dbname.length() > 5 ? dbname.substring(0,
5462 5) + "..." : dbname;
5463 String msname = dbname.length() > 10 ? dbname.substring(
5464 0, 10) + "..." : dbname;
5467 imname = MessageManager.formatMessage(
5468 "label.from_msname", new Object[] { sname });
5470 fetchr = new JMenuItem(msname);
5471 final DbSourceProxy[] dassrc = { sproxy };
5472 fetchr.addActionListener(new ActionListener()
5476 public void actionPerformed(ActionEvent e)
5478 new Thread(new Runnable()
5484 boolean isNucleotide = alignPanel.alignFrame
5485 .getViewport().getAlignment()
5487 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5488 alignPanel.av.getSequenceSelection(),
5489 alignPanel.alignFrame, dassrc,
5490 alignPanel.alignFrame.featureSettings,
5493 .addListener(new FetchFinishedListenerI()
5496 public void finished()
5498 AlignFrame.this.setMenusForViewport();
5501 dbRefFetcher.fetchDBRefs(false);
5507 fetchr.setToolTipText("<html>"
5508 + MessageManager.formatMessage(
5509 "label.fetch_retrieve_from", new Object[]
5513 if (++icomp >= mcomp || i == (otherdb.size()))
5515 ifetch.setText(MessageManager.formatMessage(
5516 "label.source_to_target", imname, sname));
5518 ifetch = new JMenu();
5526 if (comp >= mcomp || dbi >= (dbclasses.length))
5528 dfetch.setText(MessageManager.formatMessage(
5529 "label.source_to_target", mname, dbclass));
5531 dfetch = new JMenu();
5544 * Left justify the whole alignment.
5547 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5549 AlignmentI al = viewport.getAlignment();
5551 viewport.firePropertyChange("alignment", null, al);
5555 * Right justify the whole alignment.
5558 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5560 AlignmentI al = viewport.getAlignment();
5562 viewport.firePropertyChange("alignment", null, al);
5566 public void setShowSeqFeatures(boolean b)
5568 showSeqFeatures.setSelected(b);
5569 viewport.setShowSequenceFeatures(b);
5576 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5577 * awt.event.ActionEvent)
5580 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5582 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5583 alignPanel.paintAlignment(true);
5590 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5594 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5596 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5597 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5605 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5606 * .event.ActionEvent)
5609 protected void showGroupConservation_actionPerformed(ActionEvent e)
5611 viewport.setShowGroupConservation(showGroupConservation.getState());
5612 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5619 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5620 * .event.ActionEvent)
5623 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5625 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5626 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5633 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5634 * .event.ActionEvent)
5637 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5639 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5640 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5644 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5646 showSequenceLogo.setState(true);
5647 viewport.setShowSequenceLogo(true);
5648 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5649 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5653 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5655 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5662 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5663 * .event.ActionEvent)
5666 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5668 if (avc.makeGroupsFromSelection())
5670 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5671 alignPanel.updateAnnotation();
5672 alignPanel.paintAlignment(true);
5676 public void clearAlignmentSeqRep()
5678 // TODO refactor alignmentseqrep to controller
5679 if (viewport.getAlignment().hasSeqrep())
5681 viewport.getAlignment().setSeqrep(null);
5682 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5683 alignPanel.updateAnnotation();
5684 alignPanel.paintAlignment(true);
5689 protected void createGroup_actionPerformed(ActionEvent e)
5691 if (avc.createGroup())
5693 alignPanel.alignmentChanged();
5698 protected void unGroup_actionPerformed(ActionEvent e)
5702 alignPanel.alignmentChanged();
5707 * make the given alignmentPanel the currently selected tab
5709 * @param alignmentPanel
5711 public void setDisplayedView(AlignmentPanel alignmentPanel)
5713 if (!viewport.getSequenceSetId().equals(
5714 alignmentPanel.av.getSequenceSetId()))
5718 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5720 if (tabbedPane != null
5721 && tabbedPane.getTabCount() > 0
5722 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5723 .getSelectedIndex())
5725 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5730 * Action on selection of menu options to Show or Hide annotations.
5733 * @param forSequences
5734 * update sequence-related annotations
5735 * @param forAlignment
5736 * update non-sequence-related annotations
5739 protected void setAnnotationsVisibility(boolean visible,
5740 boolean forSequences, boolean forAlignment)
5742 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5743 .getAlignmentAnnotation();
5748 for (AlignmentAnnotation aa : anns)
5751 * don't display non-positional annotations on an alignment
5753 if (aa.annotations == null)
5757 boolean apply = (aa.sequenceRef == null && forAlignment)
5758 || (aa.sequenceRef != null && forSequences);
5761 aa.visible = visible;
5764 alignPanel.validateAnnotationDimensions(true);
5765 alignPanel.alignmentChanged();
5769 * Store selected annotation sort order for the view and repaint.
5772 protected void sortAnnotations_actionPerformed()
5774 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5776 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5777 alignPanel.paintAlignment(true);
5782 * @return alignment panels in this alignment frame
5784 public List<? extends AlignmentViewPanel> getAlignPanels()
5786 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5790 * Open a new alignment window, with the cDNA associated with this (protein)
5791 * alignment, aligned as is the protein.
5793 protected void viewAsCdna_actionPerformed()
5795 // TODO no longer a menu action - refactor as required
5796 final AlignmentI alignment = getViewport().getAlignment();
5797 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5798 if (mappings == null)
5802 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5803 for (SequenceI aaSeq : alignment.getSequences())
5805 for (AlignedCodonFrame acf : mappings)
5807 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5811 * There is a cDNA mapping for this protein sequence - add to new
5812 * alignment. It will share the same dataset sequence as other mapped
5813 * cDNA (no new mappings need to be created).
5815 final Sequence newSeq = new Sequence(dnaSeq);
5816 newSeq.setDatasetSequence(dnaSeq);
5817 cdnaSeqs.add(newSeq);
5821 if (cdnaSeqs.size() == 0)
5823 // show a warning dialog no mapped cDNA
5826 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5828 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5829 AlignFrame.DEFAULT_HEIGHT);
5830 cdna.alignAs(alignment);
5831 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5833 Desktop.addInternalFrame(alignFrame, newtitle,
5834 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5838 * Set visibility of dna/protein complement view (available when shown in a
5844 protected void showComplement_actionPerformed(boolean show)
5846 SplitContainerI sf = getSplitViewContainer();
5849 sf.setComplementVisible(this, show);
5854 * Generate the reverse (optionally complemented) of the selected sequences,
5855 * and add them to the alignment
5858 protected void showReverse_actionPerformed(boolean complement)
5860 AlignmentI al = null;
5863 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5864 al = dna.reverseCdna(complement);
5865 viewport.addAlignment(al, "");
5866 addHistoryItem(new EditCommand(
5867 MessageManager.getString("label.add_sequences"),
5868 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5869 viewport.getAlignment()));
5870 } catch (Exception ex)
5872 System.err.println(ex.getMessage());
5878 * Try to run a script in the Groovy console, having first ensured that this
5879 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5880 * be targeted at this alignment.
5883 protected void runGroovy_actionPerformed()
5885 Jalview.setCurrentAlignFrame(this);
5886 groovy.ui.Console console = Desktop.getGroovyConsole();
5887 if (console != null)
5891 console.runScript();
5892 } catch (Exception ex)
5894 System.err.println((ex.toString()));
5896 .showInternalMessageDialog(Desktop.desktop, MessageManager
5897 .getString("label.couldnt_run_groovy_script"),
5899 .getString("label.groovy_support_failed"),
5900 JOptionPane.ERROR_MESSAGE);
5905 System.err.println("Can't run Groovy script as console not found");
5910 * Hides columns containing (or not containing) a specified feature, provided
5911 * that would not leave all columns hidden
5913 * @param featureType
5914 * @param columnsContaining
5917 public boolean hideFeatureColumns(String featureType,
5918 boolean columnsContaining)
5920 boolean notForHiding = avc.markColumnsContainingFeatures(
5921 columnsContaining, false, false, featureType);
5924 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5925 false, featureType))
5927 getViewport().hideSelectedColumns();
5935 class PrintThread extends Thread
5939 public PrintThread(AlignmentPanel ap)
5944 static PageFormat pf;
5949 PrinterJob printJob = PrinterJob.getPrinterJob();
5953 printJob.setPrintable(ap, pf);
5957 printJob.setPrintable(ap);
5960 if (printJob.printDialog())
5965 } catch (Exception PrintException)
5967 PrintException.printStackTrace();