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.StructureFile;
75 import jalview.io.TCoffeeScoreFile;
76 import jalview.jbgui.GAlignFrame;
77 import jalview.schemes.Blosum62ColourScheme;
78 import jalview.schemes.BuriedColourScheme;
79 import jalview.schemes.ClustalxColourScheme;
80 import jalview.schemes.ColourSchemeI;
81 import jalview.schemes.ColourSchemeProperty;
82 import jalview.schemes.HelixColourScheme;
83 import jalview.schemes.HydrophobicColourScheme;
84 import jalview.schemes.NucleotideColourScheme;
85 import jalview.schemes.PIDColourScheme;
86 import jalview.schemes.PurinePyrimidineColourScheme;
87 import jalview.schemes.RNAHelicesColourChooser;
88 import jalview.schemes.ResidueProperties;
89 import jalview.schemes.StrandColourScheme;
90 import jalview.schemes.TCoffeeColourScheme;
91 import jalview.schemes.TaylorColourScheme;
92 import jalview.schemes.TurnColourScheme;
93 import jalview.schemes.UserColourScheme;
94 import jalview.schemes.ZappoColourScheme;
95 import jalview.util.MessageManager;
96 import jalview.viewmodel.AlignmentViewport;
97 import jalview.ws.DBRefFetcher;
98 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
99 import jalview.ws.jws1.Discoverer;
100 import jalview.ws.jws2.Jws2Discoverer;
101 import jalview.ws.jws2.jabaws2.Jws2Instance;
102 import jalview.ws.seqfetcher.DbSourceProxy;
104 import java.awt.BorderLayout;
105 import java.awt.Component;
106 import java.awt.Rectangle;
107 import java.awt.Toolkit;
108 import java.awt.datatransfer.Clipboard;
109 import java.awt.datatransfer.DataFlavor;
110 import java.awt.datatransfer.StringSelection;
111 import java.awt.datatransfer.Transferable;
112 import java.awt.dnd.DnDConstants;
113 import java.awt.dnd.DropTargetDragEvent;
114 import java.awt.dnd.DropTargetDropEvent;
115 import java.awt.dnd.DropTargetEvent;
116 import java.awt.dnd.DropTargetListener;
117 import java.awt.event.ActionEvent;
118 import java.awt.event.ActionListener;
119 import java.awt.event.FocusAdapter;
120 import java.awt.event.FocusEvent;
121 import java.awt.event.ItemEvent;
122 import java.awt.event.ItemListener;
123 import java.awt.event.KeyAdapter;
124 import java.awt.event.KeyEvent;
125 import java.awt.event.MouseAdapter;
126 import java.awt.event.MouseEvent;
127 import java.awt.print.PageFormat;
128 import java.awt.print.PrinterJob;
129 import java.beans.PropertyChangeEvent;
132 import java.util.ArrayList;
133 import java.util.Arrays;
134 import java.util.Deque;
135 import java.util.Enumeration;
136 import java.util.Hashtable;
137 import java.util.List;
138 import java.util.Vector;
140 import javax.swing.JCheckBoxMenuItem;
141 import javax.swing.JEditorPane;
142 import javax.swing.JInternalFrame;
143 import javax.swing.JLayeredPane;
144 import javax.swing.JMenu;
145 import javax.swing.JMenuItem;
146 import javax.swing.JOptionPane;
147 import javax.swing.JRadioButtonMenuItem;
148 import javax.swing.JScrollPane;
149 import javax.swing.SwingUtilities;
155 * @version $Revision$
157 public class AlignFrame extends GAlignFrame implements DropTargetListener,
158 IProgressIndicator, AlignViewControllerGuiI
161 public static final int DEFAULT_WIDTH = 700;
163 public static final int DEFAULT_HEIGHT = 500;
166 * The currently displayed panel (selected tabbed view if more than one)
168 public AlignmentPanel alignPanel;
170 AlignViewport viewport;
172 public AlignViewControllerI avc;
174 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
177 * Last format used to load or save alignments in this window
179 String currentFileFormat = null;
182 * Current filename for this alignment
184 String fileName = null;
187 * Creates a new AlignFrame object with specific width and height.
193 public AlignFrame(AlignmentI al, int width, int height)
195 this(al, null, width, height);
199 * Creates a new AlignFrame object with specific width, height and
205 * @param sequenceSetId
207 public AlignFrame(AlignmentI al, int width, int height,
208 String sequenceSetId)
210 this(al, null, width, height, sequenceSetId);
214 * Creates a new AlignFrame object with specific width, height and
220 * @param sequenceSetId
223 public AlignFrame(AlignmentI al, int width, int height,
224 String sequenceSetId, String viewId)
226 this(al, null, width, height, sequenceSetId, viewId);
230 * new alignment window with hidden columns
234 * @param hiddenColumns
235 * ColumnSelection or null
237 * Width of alignment frame
241 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
242 int width, int height)
244 this(al, hiddenColumns, width, height, null);
248 * Create alignment frame for al with hiddenColumns, a specific width and
249 * height, and specific sequenceId
252 * @param hiddenColumns
255 * @param sequenceSetId
258 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
259 int width, int height, String sequenceSetId)
261 this(al, hiddenColumns, width, height, sequenceSetId, null);
265 * Create alignment frame for al with hiddenColumns, a specific width and
266 * height, and specific sequenceId
269 * @param hiddenColumns
272 * @param sequenceSetId
277 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
278 int width, int height, String sequenceSetId, String viewId)
280 setSize(width, height);
282 if (al.getDataset() == null)
287 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
289 alignPanel = new AlignmentPanel(this, viewport);
291 addAlignmentPanel(alignPanel, true);
295 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
296 ColumnSelection hiddenColumns, int width, int height)
298 setSize(width, height);
300 if (al.getDataset() == null)
305 viewport = new AlignViewport(al, hiddenColumns);
307 if (hiddenSeqs != null && hiddenSeqs.length > 0)
309 viewport.hideSequence(hiddenSeqs);
311 alignPanel = new AlignmentPanel(this, viewport);
312 addAlignmentPanel(alignPanel, true);
317 * Make a new AlignFrame from existing alignmentPanels
324 public AlignFrame(AlignmentPanel ap)
328 addAlignmentPanel(ap, false);
333 * initalise the alignframe from the underlying viewport data and the
338 if (!Jalview.isHeadlessMode())
340 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
343 avc = new jalview.controller.AlignViewController(this, viewport,
345 if (viewport.getAlignmentConservationAnnotation() == null)
347 BLOSUM62Colour.setEnabled(false);
348 conservationMenuItem.setEnabled(false);
349 modifyConservation.setEnabled(false);
350 // PIDColour.setEnabled(false);
351 // abovePIDThreshold.setEnabled(false);
352 // modifyPID.setEnabled(false);
355 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
358 if (sortby.equals("Id"))
360 sortIDMenuItem_actionPerformed(null);
362 else if (sortby.equals("Pairwise Identity"))
364 sortPairwiseMenuItem_actionPerformed(null);
367 if (Desktop.desktop != null)
369 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
370 addServiceListeners();
371 setGUINucleotide(viewport.getAlignment().isNucleotide());
375 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
377 setMenusFromViewport(viewport);
378 buildSortByAnnotationScoresMenu();
381 if (viewport.getWrapAlignment())
383 wrapMenuItem_actionPerformed(null);
386 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
388 this.overviewMenuItem_actionPerformed(null);
393 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
394 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
395 final String menuLabel = MessageManager
396 .getString("label.copy_format_from");
397 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
398 new ViewSetProvider()
402 public AlignmentPanel[] getAllAlignmentPanels()
405 origview.add(alignPanel);
406 // make an array of all alignment panels except for this one
407 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
408 Arrays.asList(Desktop.getAlignmentPanels(null)));
409 aps.remove(AlignFrame.this.alignPanel);
410 return aps.toArray(new AlignmentPanel[aps.size()]);
412 }, selviews, new ItemListener()
416 public void itemStateChanged(ItemEvent e)
418 if (origview.size() > 0)
420 final AlignmentPanel ap = origview.get(0);
423 * Copy the ViewStyle of the selected panel to 'this one'.
424 * Don't change value of 'scaleProteinAsCdna' unless copying
427 ViewStyleI vs = selviews.get(0).getAlignViewport()
429 boolean fromSplitFrame = selviews.get(0)
430 .getAlignViewport().getCodingComplement() != null;
433 vs.setScaleProteinAsCdna(ap.getAlignViewport()
434 .getViewStyle().isScaleProteinAsCdna());
436 ap.getAlignViewport().setViewStyle(vs);
439 * Also rescale ViewStyle of SplitFrame complement if there is
440 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
441 * the whole ViewStyle (allow cDNA protein to have different
444 AlignViewportI complement = ap.getAlignViewport()
445 .getCodingComplement();
446 if (complement != null && vs.isScaleProteinAsCdna())
448 AlignFrame af = Desktop.getAlignFrameFor(complement);
449 ((SplitFrame) af.getSplitViewContainer())
451 af.setMenusForViewport();
455 ap.setSelected(true);
456 ap.alignFrame.setMenusForViewport();
461 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
462 .indexOf("devel") > -1
463 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
464 .indexOf("test") > -1)
466 formatMenu.add(vsel);
468 addFocusListener(new FocusAdapter()
471 public void focusGained(FocusEvent e)
473 Jalview.setCurrentAlignFrame(AlignFrame.this);
480 * Change the filename and format for the alignment, and enable the 'reload'
481 * button functionality.
488 public void setFileName(String file, String format)
491 setFileFormat(format);
492 reload.setEnabled(true);
496 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
499 void addKeyListener()
501 addKeyListener(new KeyAdapter()
504 public void keyPressed(KeyEvent evt)
506 if (viewport.cursorMode
507 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
508 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
509 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
510 && Character.isDigit(evt.getKeyChar()))
512 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
515 switch (evt.getKeyCode())
518 case 27: // escape key
519 deselectAllSequenceMenuItem_actionPerformed(null);
523 case KeyEvent.VK_DOWN:
524 if (evt.isAltDown() || !viewport.cursorMode)
526 moveSelectedSequences(false);
528 if (viewport.cursorMode)
530 alignPanel.getSeqPanel().moveCursor(0, 1);
535 if (evt.isAltDown() || !viewport.cursorMode)
537 moveSelectedSequences(true);
539 if (viewport.cursorMode)
541 alignPanel.getSeqPanel().moveCursor(0, -1);
546 case KeyEvent.VK_LEFT:
547 if (evt.isAltDown() || !viewport.cursorMode)
549 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
553 alignPanel.getSeqPanel().moveCursor(-1, 0);
558 case KeyEvent.VK_RIGHT:
559 if (evt.isAltDown() || !viewport.cursorMode)
561 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
565 alignPanel.getSeqPanel().moveCursor(1, 0);
569 case KeyEvent.VK_SPACE:
570 if (viewport.cursorMode)
572 alignPanel.getSeqPanel().insertGapAtCursor(
573 evt.isControlDown() || evt.isShiftDown()
578 // case KeyEvent.VK_A:
579 // if (viewport.cursorMode)
581 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
582 // //System.out.println("A");
586 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
587 * System.out.println("closing bracket"); } break;
589 case KeyEvent.VK_DELETE:
590 case KeyEvent.VK_BACK_SPACE:
591 if (!viewport.cursorMode)
593 cut_actionPerformed(null);
597 alignPanel.getSeqPanel().deleteGapAtCursor(
598 evt.isControlDown() || evt.isShiftDown()
605 if (viewport.cursorMode)
607 alignPanel.getSeqPanel().setCursorRow();
611 if (viewport.cursorMode && !evt.isControlDown())
613 alignPanel.getSeqPanel().setCursorColumn();
617 if (viewport.cursorMode)
619 alignPanel.getSeqPanel().setCursorPosition();
623 case KeyEvent.VK_ENTER:
624 case KeyEvent.VK_COMMA:
625 if (viewport.cursorMode)
627 alignPanel.getSeqPanel().setCursorRowAndColumn();
632 if (viewport.cursorMode)
634 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
638 if (viewport.cursorMode)
640 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
645 viewport.cursorMode = !viewport.cursorMode;
646 statusBar.setText(MessageManager.formatMessage(
647 "label.keyboard_editing_mode",
648 new String[] { (viewport.cursorMode ? "on" : "off") }));
649 if (viewport.cursorMode)
651 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
652 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
654 alignPanel.getSeqPanel().seqCanvas.repaint();
660 Help.showHelpWindow();
661 } catch (Exception ex)
663 ex.printStackTrace();
668 boolean toggleSeqs = !evt.isControlDown();
669 boolean toggleCols = !evt.isShiftDown();
670 toggleHiddenRegions(toggleSeqs, toggleCols);
673 case KeyEvent.VK_PAGE_UP:
674 if (viewport.getWrapAlignment())
676 alignPanel.scrollUp(true);
680 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
681 - viewport.endSeq + viewport.startSeq);
684 case KeyEvent.VK_PAGE_DOWN:
685 if (viewport.getWrapAlignment())
687 alignPanel.scrollUp(false);
691 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
692 + viewport.endSeq - viewport.startSeq);
699 public void keyReleased(KeyEvent evt)
701 switch (evt.getKeyCode())
703 case KeyEvent.VK_LEFT:
704 if (evt.isAltDown() || !viewport.cursorMode)
706 viewport.firePropertyChange("alignment", null, viewport
707 .getAlignment().getSequences());
711 case KeyEvent.VK_RIGHT:
712 if (evt.isAltDown() || !viewport.cursorMode)
714 viewport.firePropertyChange("alignment", null, viewport
715 .getAlignment().getSequences());
723 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
725 ap.alignFrame = this;
726 avc = new jalview.controller.AlignViewController(this, viewport,
731 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
733 int aSize = alignPanels.size();
735 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
737 if (aSize == 1 && ap.av.viewName == null)
739 this.getContentPane().add(ap, BorderLayout.CENTER);
745 setInitialTabVisible();
748 expandViews.setEnabled(true);
749 gatherViews.setEnabled(true);
750 tabbedPane.addTab(ap.av.viewName, ap);
752 ap.setVisible(false);
757 if (ap.av.isPadGaps())
759 ap.av.getAlignment().padGaps();
761 ap.av.updateConservation(ap);
762 ap.av.updateConsensus(ap);
763 ap.av.updateStrucConsensus(ap);
767 public void setInitialTabVisible()
769 expandViews.setEnabled(true);
770 gatherViews.setEnabled(true);
771 tabbedPane.setVisible(true);
772 AlignmentPanel first = alignPanels.get(0);
773 tabbedPane.addTab(first.av.viewName, first);
774 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
777 public AlignViewport getViewport()
782 /* Set up intrinsic listeners for dynamically generated GUI bits. */
783 private void addServiceListeners()
785 final java.beans.PropertyChangeListener thisListener;
786 Desktop.instance.addJalviewPropertyChangeListener("services",
787 thisListener = new java.beans.PropertyChangeListener()
790 public void propertyChange(PropertyChangeEvent evt)
792 // // System.out.println("Discoverer property change.");
793 // if (evt.getPropertyName().equals("services"))
795 SwingUtilities.invokeLater(new Runnable()
802 .println("Rebuild WS Menu for service change");
803 BuildWebServiceMenu();
810 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
813 public void internalFrameClosed(
814 javax.swing.event.InternalFrameEvent evt)
816 // System.out.println("deregistering discoverer listener");
817 Desktop.instance.removeJalviewPropertyChangeListener("services",
819 closeMenuItem_actionPerformed(true);
822 // Finally, build the menu once to get current service state
823 new Thread(new Runnable()
828 BuildWebServiceMenu();
834 * Configure menu items that vary according to whether the alignment is
835 * nucleotide or protein
839 public void setGUINucleotide(boolean nucleotide)
841 showTranslation.setVisible(nucleotide);
842 showReverse.setVisible(nucleotide);
843 showReverseComplement.setVisible(nucleotide);
844 conservationMenuItem.setEnabled(!nucleotide);
845 modifyConservation.setEnabled(!nucleotide);
846 showGroupConservation.setEnabled(!nucleotide);
847 rnahelicesColour.setEnabled(nucleotide);
848 purinePyrimidineColour.setEnabled(nucleotide);
849 showComplementMenuItem.setText(nucleotide ? MessageManager
850 .getString("label.protein") : MessageManager
851 .getString("label.nucleotide"));
852 setColourSelected(jalview.bin.Cache.getDefault(
853 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
854 : Preferences.DEFAULT_COLOUR_PROT, "None"));
858 * set up menus for the current viewport. This may be called after any
859 * operation that affects the data in the current view (selection changed,
860 * etc) to update the menus to reflect the new state.
863 public void setMenusForViewport()
865 setMenusFromViewport(viewport);
869 * Need to call this method when tabs are selected for multiple views, or when
870 * loading from Jalview2XML.java
875 void setMenusFromViewport(AlignViewport av)
877 padGapsMenuitem.setSelected(av.isPadGaps());
878 colourTextMenuItem.setSelected(av.isShowColourText());
879 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
880 conservationMenuItem.setSelected(av.getConservationSelected());
881 seqLimits.setSelected(av.getShowJVSuffix());
882 idRightAlign.setSelected(av.isRightAlignIds());
883 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
884 renderGapsMenuItem.setSelected(av.isRenderGaps());
885 wrapMenuItem.setSelected(av.getWrapAlignment());
886 scaleAbove.setVisible(av.getWrapAlignment());
887 scaleLeft.setVisible(av.getWrapAlignment());
888 scaleRight.setVisible(av.getWrapAlignment());
889 annotationPanelMenuItem.setState(av.isShowAnnotation());
891 * Show/hide annotations only enabled if annotation panel is shown
893 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
894 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
895 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
896 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
897 viewBoxesMenuItem.setSelected(av.getShowBoxes());
898 viewTextMenuItem.setSelected(av.getShowText());
899 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
900 showGroupConsensus.setSelected(av.isShowGroupConsensus());
901 showGroupConservation.setSelected(av.isShowGroupConservation());
902 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
903 showSequenceLogo.setSelected(av.isShowSequenceLogo());
904 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
906 setColourSelected(ColourSchemeProperty.getColourName(av
907 .getGlobalColourScheme()));
909 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
910 hiddenMarkers.setState(av.getShowHiddenMarkers());
911 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
912 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
913 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
914 autoCalculate.setSelected(av.autoCalculateConsensus);
915 sortByTree.setSelected(av.sortByTree);
916 listenToViewSelections.setSelected(av.followSelection);
917 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
919 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
921 showProducts.setEnabled(canShowProducts());
922 setGroovyEnabled(Desktop.getGroovyConsole() != null);
928 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
932 public void setGroovyEnabled(boolean b)
934 runGroovy.setEnabled(b);
937 private IProgressIndicator progressBar;
942 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
945 public void setProgressBar(String message, long id)
947 progressBar.setProgressBar(message, id);
951 public void registerHandler(final long id,
952 final IProgressIndicatorHandler handler)
954 progressBar.registerHandler(id, handler);
959 * @return true if any progress bars are still active
962 public boolean operationInProgress()
964 return progressBar.operationInProgress();
968 public void setStatus(String text)
970 statusBar.setText(text);
974 * Added so Castor Mapping file can obtain Jalview Version
976 public String getVersion()
978 return jalview.bin.Cache.getProperty("VERSION");
981 public FeatureRenderer getFeatureRenderer()
983 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
987 public void fetchSequence_actionPerformed(ActionEvent e)
989 new jalview.gui.SequenceFetcher(this);
993 public void addFromFile_actionPerformed(ActionEvent e)
995 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
999 public void reload_actionPerformed(ActionEvent e)
1001 if (fileName != null)
1003 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1004 // originating file's format
1005 // TODO: work out how to recover feature settings for correct view(s) when
1006 // file is reloaded.
1007 if (currentFileFormat.equals("Jalview"))
1009 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1010 for (int i = 0; i < frames.length; i++)
1012 if (frames[i] instanceof AlignFrame && frames[i] != this
1013 && ((AlignFrame) frames[i]).fileName != null
1014 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1018 frames[i].setSelected(true);
1019 Desktop.instance.closeAssociatedWindows();
1020 } catch (java.beans.PropertyVetoException ex)
1026 Desktop.instance.closeAssociatedWindows();
1028 FileLoader loader = new FileLoader();
1029 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1030 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1034 Rectangle bounds = this.getBounds();
1036 FileLoader loader = new FileLoader();
1037 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1038 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1039 protocol, currentFileFormat);
1041 newframe.setBounds(bounds);
1042 if (featureSettings != null && featureSettings.isShowing())
1044 final Rectangle fspos = featureSettings.frame.getBounds();
1045 // TODO: need a 'show feature settings' function that takes bounds -
1046 // need to refactor Desktop.addFrame
1047 newframe.featureSettings_actionPerformed(null);
1048 final FeatureSettings nfs = newframe.featureSettings;
1049 SwingUtilities.invokeLater(new Runnable()
1054 nfs.frame.setBounds(fspos);
1057 this.featureSettings.close();
1058 this.featureSettings = null;
1060 this.closeMenuItem_actionPerformed(true);
1066 public void addFromText_actionPerformed(ActionEvent e)
1068 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1073 public void addFromURL_actionPerformed(ActionEvent e)
1075 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1079 public void save_actionPerformed(ActionEvent e)
1081 if (fileName == null
1082 || (currentFileFormat == null || !jalview.io.FormatAdapter
1083 .isValidIOFormat(currentFileFormat, true))
1084 || fileName.startsWith("http"))
1086 saveAs_actionPerformed(null);
1090 saveAlignment(fileName, currentFileFormat);
1101 public void saveAs_actionPerformed(ActionEvent e)
1103 JalviewFileChooser chooser = new JalviewFileChooser(
1104 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1105 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1106 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1107 currentFileFormat, false);
1109 chooser.setFileView(new JalviewFileView());
1110 chooser.setDialogTitle(MessageManager
1111 .getString("label.save_alignment_to_file"));
1112 chooser.setToolTipText(MessageManager.getString("action.save"));
1114 int value = chooser.showSaveDialog(this);
1116 if (value == JalviewFileChooser.APPROVE_OPTION)
1118 currentFileFormat = chooser.getSelectedFormat();
1119 while (currentFileFormat == null)
1122 .showInternalMessageDialog(
1125 .getString("label.select_file_format_before_saving"),
1127 .getString("label.file_format_not_specified"),
1128 JOptionPane.WARNING_MESSAGE);
1129 currentFileFormat = chooser.getSelectedFormat();
1130 value = chooser.showSaveDialog(this);
1131 if (value != JalviewFileChooser.APPROVE_OPTION)
1137 fileName = chooser.getSelectedFile().getPath();
1139 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1142 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1143 if (currentFileFormat.indexOf(" ") > -1)
1145 currentFileFormat = currentFileFormat.substring(0,
1146 currentFileFormat.indexOf(" "));
1148 saveAlignment(fileName, currentFileFormat);
1152 public boolean saveAlignment(String file, String format)
1154 boolean success = true;
1156 if (format.equalsIgnoreCase("Jalview"))
1158 String shortName = title;
1160 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1162 shortName = shortName.substring(shortName
1163 .lastIndexOf(java.io.File.separatorChar) + 1);
1166 success = new Jalview2XML().saveAlignment(this, file, shortName);
1168 statusBar.setText(MessageManager.formatMessage(
1169 "label.successfully_saved_to_file_in_format", new Object[] {
1170 fileName, format }));
1175 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1177 warningMessage("Cannot save file " + fileName + " using format "
1178 + format, "Alignment output format not supported");
1179 if (!Jalview.isHeadlessMode())
1181 saveAs_actionPerformed(null);
1186 AlignmentExportData exportData = getAlignmentForExport(format,
1188 if (exportData.getSettings().isCancelled())
1192 FormatAdapter f = new FormatAdapter(alignPanel,
1193 exportData.getSettings());
1194 String output = f.formatSequences(
1196 exportData.getAlignment(), // class cast exceptions will
1197 // occur in the distant future
1198 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1199 f.getCacheSuffixDefault(format),
1200 viewport.getColumnSelection());
1210 java.io.PrintWriter out = new java.io.PrintWriter(
1211 new java.io.FileWriter(file));
1215 this.setTitle(file);
1216 statusBar.setText(MessageManager.formatMessage(
1217 "label.successfully_saved_to_file_in_format",
1218 new Object[] { fileName, format }));
1219 } catch (Exception ex)
1222 ex.printStackTrace();
1229 JOptionPane.showInternalMessageDialog(this, MessageManager
1230 .formatMessage("label.couldnt_save_file",
1231 new Object[] { fileName }), MessageManager
1232 .getString("label.error_saving_file"),
1233 JOptionPane.WARNING_MESSAGE);
1239 private void warningMessage(String warning, String title)
1241 if (new jalview.util.Platform().isHeadless())
1243 System.err.println("Warning: " + title + "\nWarning: " + warning);
1248 JOptionPane.showInternalMessageDialog(this, warning, title,
1249 JOptionPane.WARNING_MESSAGE);
1261 protected void outputText_actionPerformed(ActionEvent e)
1264 AlignmentExportData exportData = getAlignmentForExport(
1265 e.getActionCommand(), viewport, null);
1266 if (exportData.getSettings().isCancelled())
1270 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1271 cap.setForInput(null);
1274 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1275 .formatSequences(e.getActionCommand(),
1276 exportData.getAlignment(),
1277 exportData.getOmitHidden(),
1278 exportData.getStartEndPostions(),
1279 viewport.getColumnSelection()));
1280 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1281 "label.alignment_output_command",
1282 new Object[] { e.getActionCommand() }), 600, 500);
1283 } catch (OutOfMemoryError oom)
1285 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1291 public static AlignmentExportData getAlignmentForExport(
1292 String exportFormat, AlignViewportI viewport,
1293 AlignExportSettingI exportSettings)
1295 AlignmentI alignmentToExport = null;
1296 AlignExportSettingI settings = exportSettings;
1297 String[] omitHidden = null;
1299 HiddenSequences hiddenSeqs = viewport.getAlignment()
1300 .getHiddenSequences();
1302 alignmentToExport = viewport.getAlignment();
1304 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1305 if (settings == null)
1307 settings = new AlignExportSettings(hasHiddenSeqs,
1308 viewport.hasHiddenColumns(), exportFormat);
1310 // settings.isExportAnnotations();
1312 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1314 omitHidden = viewport.getViewAsString(false,
1315 settings.isExportHiddenSequences());
1318 int[] alignmentStartEnd = new int[2];
1319 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1321 alignmentToExport = hiddenSeqs.getFullAlignment();
1325 alignmentToExport = viewport.getAlignment();
1327 alignmentStartEnd = alignmentToExport
1328 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1329 .getHiddenColumns());
1330 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1331 omitHidden, alignmentStartEnd, settings);
1342 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1344 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1345 htmlSVG.generateHtmlSvgOutput(null);
1349 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1351 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1352 bjs.exportJalviewAlignmentAsBioJsHtmlFile(null);
1355 public void createImageMap(File file, String image)
1357 alignPanel.makePNGImageMap(file, image);
1367 public void createPNG(File f)
1369 alignPanel.makePNG(f);
1379 public void createEPS(File f)
1381 alignPanel.makeEPS(f);
1385 public void createSVG(File f)
1387 alignPanel.makeSVG(f);
1391 public void pageSetup_actionPerformed(ActionEvent e)
1393 PrinterJob printJob = PrinterJob.getPrinterJob();
1394 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1404 public void printMenuItem_actionPerformed(ActionEvent e)
1406 // Putting in a thread avoids Swing painting problems
1407 PrintThread thread = new PrintThread(alignPanel);
1412 public void exportFeatures_actionPerformed(ActionEvent e)
1414 new AnnotationExporter().exportFeatures(alignPanel);
1418 public void exportAnnotations_actionPerformed(ActionEvent e)
1420 new AnnotationExporter().exportAnnotations(alignPanel);
1424 public void associatedData_actionPerformed(ActionEvent e)
1426 // Pick the tree file
1427 JalviewFileChooser chooser = new JalviewFileChooser(
1428 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1429 chooser.setFileView(new JalviewFileView());
1430 chooser.setDialogTitle(MessageManager
1431 .getString("label.load_jalview_annotations"));
1432 chooser.setToolTipText(MessageManager
1433 .getString("label.load_jalview_annotations"));
1435 int value = chooser.showOpenDialog(null);
1437 if (value == JalviewFileChooser.APPROVE_OPTION)
1439 String choice = chooser.getSelectedFile().getPath();
1440 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1441 loadJalviewDataFile(choice, null, null, null);
1447 * Close the current view or all views in the alignment frame. If the frame
1448 * only contains one view then the alignment will be removed from memory.
1450 * @param closeAllTabs
1453 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1455 if (alignPanels != null && alignPanels.size() < 2)
1457 closeAllTabs = true;
1462 if (alignPanels != null)
1466 if (this.isClosed())
1468 // really close all the windows - otherwise wait till
1469 // setClosed(true) is called
1470 for (int i = 0; i < alignPanels.size(); i++)
1472 AlignmentPanel ap = alignPanels.get(i);
1479 closeView(alignPanel);
1486 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1487 * be called recursively, with the frame now in 'closed' state
1489 this.setClosed(true);
1491 } catch (Exception ex)
1493 ex.printStackTrace();
1498 * Close the specified panel and close up tabs appropriately.
1500 * @param panelToClose
1502 public void closeView(AlignmentPanel panelToClose)
1504 int index = tabbedPane.getSelectedIndex();
1505 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1506 alignPanels.remove(panelToClose);
1507 panelToClose.closePanel();
1508 panelToClose = null;
1510 tabbedPane.removeTabAt(closedindex);
1511 tabbedPane.validate();
1513 if (index > closedindex || index == tabbedPane.getTabCount())
1515 // modify currently selected tab index if necessary.
1519 this.tabSelectionChanged(index);
1525 void updateEditMenuBar()
1528 if (viewport.getHistoryList().size() > 0)
1530 undoMenuItem.setEnabled(true);
1531 CommandI command = viewport.getHistoryList().peek();
1532 undoMenuItem.setText(MessageManager.formatMessage(
1533 "label.undo_command",
1534 new Object[] { command.getDescription() }));
1538 undoMenuItem.setEnabled(false);
1539 undoMenuItem.setText(MessageManager.getString("action.undo"));
1542 if (viewport.getRedoList().size() > 0)
1544 redoMenuItem.setEnabled(true);
1546 CommandI command = viewport.getRedoList().peek();
1547 redoMenuItem.setText(MessageManager.formatMessage(
1548 "label.redo_command",
1549 new Object[] { command.getDescription() }));
1553 redoMenuItem.setEnabled(false);
1554 redoMenuItem.setText(MessageManager.getString("action.redo"));
1559 public void addHistoryItem(CommandI command)
1561 if (command.getSize() > 0)
1563 viewport.addToHistoryList(command);
1564 viewport.clearRedoList();
1565 updateEditMenuBar();
1566 viewport.updateHiddenColumns();
1567 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1568 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1569 // viewport.getColumnSelection()
1570 // .getHiddenColumns().size() > 0);
1576 * @return alignment objects for all views
1578 AlignmentI[] getViewAlignments()
1580 if (alignPanels != null)
1582 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1584 for (AlignmentPanel ap : alignPanels)
1586 als[i++] = ap.av.getAlignment();
1590 if (viewport != null)
1592 return new AlignmentI[] { viewport.getAlignment() };
1604 protected void undoMenuItem_actionPerformed(ActionEvent e)
1606 if (viewport.getHistoryList().isEmpty())
1610 CommandI command = viewport.getHistoryList().pop();
1611 viewport.addToRedoList(command);
1612 command.undoCommand(getViewAlignments());
1614 AlignmentViewport originalSource = getOriginatingSource(command);
1615 updateEditMenuBar();
1617 if (originalSource != null)
1619 if (originalSource != viewport)
1622 .warn("Implementation worry: mismatch of viewport origin for undo");
1624 originalSource.updateHiddenColumns();
1625 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1627 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1628 // viewport.getColumnSelection()
1629 // .getHiddenColumns().size() > 0);
1630 originalSource.firePropertyChange("alignment", null, originalSource
1631 .getAlignment().getSequences());
1642 protected void redoMenuItem_actionPerformed(ActionEvent e)
1644 if (viewport.getRedoList().size() < 1)
1649 CommandI command = viewport.getRedoList().pop();
1650 viewport.addToHistoryList(command);
1651 command.doCommand(getViewAlignments());
1653 AlignmentViewport originalSource = getOriginatingSource(command);
1654 updateEditMenuBar();
1656 if (originalSource != null)
1659 if (originalSource != viewport)
1662 .warn("Implementation worry: mismatch of viewport origin for redo");
1664 originalSource.updateHiddenColumns();
1665 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1667 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1668 // viewport.getColumnSelection()
1669 // .getHiddenColumns().size() > 0);
1670 originalSource.firePropertyChange("alignment", null, originalSource
1671 .getAlignment().getSequences());
1675 AlignmentViewport getOriginatingSource(CommandI command)
1677 AlignmentViewport originalSource = null;
1678 // For sequence removal and addition, we need to fire
1679 // the property change event FROM the viewport where the
1680 // original alignment was altered
1681 AlignmentI al = null;
1682 if (command instanceof EditCommand)
1684 EditCommand editCommand = (EditCommand) command;
1685 al = editCommand.getAlignment();
1686 List<Component> comps = PaintRefresher.components.get(viewport
1687 .getSequenceSetId());
1689 for (Component comp : comps)
1691 if (comp instanceof AlignmentPanel)
1693 if (al == ((AlignmentPanel) comp).av.getAlignment())
1695 originalSource = ((AlignmentPanel) comp).av;
1702 if (originalSource == null)
1704 // The original view is closed, we must validate
1705 // the current view against the closed view first
1708 PaintRefresher.validateSequences(al, viewport.getAlignment());
1711 originalSource = viewport;
1714 return originalSource;
1723 public void moveSelectedSequences(boolean up)
1725 SequenceGroup sg = viewport.getSelectionGroup();
1731 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1732 viewport.getHiddenRepSequences(), up);
1733 alignPanel.paintAlignment(true);
1736 synchronized void slideSequences(boolean right, int size)
1738 List<SequenceI> sg = new ArrayList<SequenceI>();
1739 if (viewport.cursorMode)
1741 sg.add(viewport.getAlignment().getSequenceAt(
1742 alignPanel.getSeqPanel().seqCanvas.cursorY));
1744 else if (viewport.getSelectionGroup() != null
1745 && viewport.getSelectionGroup().getSize() != viewport
1746 .getAlignment().getHeight())
1748 sg = viewport.getSelectionGroup().getSequences(
1749 viewport.getHiddenRepSequences());
1757 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1759 for (SequenceI seq : viewport.getAlignment().getSequences())
1761 if (!sg.contains(seq))
1763 invertGroup.add(seq);
1767 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1769 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1770 for (int i = 0; i < invertGroup.size(); i++)
1772 seqs2[i] = invertGroup.get(i);
1775 SlideSequencesCommand ssc;
1778 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1779 size, viewport.getGapCharacter());
1783 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1784 size, viewport.getGapCharacter());
1787 int groupAdjustment = 0;
1788 if (ssc.getGapsInsertedBegin() && right)
1790 if (viewport.cursorMode)
1792 alignPanel.getSeqPanel().moveCursor(size, 0);
1796 groupAdjustment = size;
1799 else if (!ssc.getGapsInsertedBegin() && !right)
1801 if (viewport.cursorMode)
1803 alignPanel.getSeqPanel().moveCursor(-size, 0);
1807 groupAdjustment = -size;
1811 if (groupAdjustment != 0)
1813 viewport.getSelectionGroup().setStartRes(
1814 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1815 viewport.getSelectionGroup().setEndRes(
1816 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1820 * just extend the last slide command if compatible; but not if in
1821 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1823 boolean appendHistoryItem = false;
1824 Deque<CommandI> historyList = viewport.getHistoryList();
1825 boolean inSplitFrame = getSplitViewContainer() != null;
1826 if (!inSplitFrame && historyList != null && historyList.size() > 0
1827 && historyList.peek() instanceof SlideSequencesCommand)
1829 appendHistoryItem = ssc
1830 .appendSlideCommand((SlideSequencesCommand) historyList
1834 if (!appendHistoryItem)
1836 addHistoryItem(ssc);
1849 protected void copy_actionPerformed(ActionEvent e)
1852 if (viewport.getSelectionGroup() == null)
1856 // TODO: preserve the ordering of displayed alignment annotation in any
1857 // internal paste (particularly sequence associated annotation)
1858 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1859 String[] omitHidden = null;
1861 if (viewport.hasHiddenColumns())
1863 omitHidden = viewport.getViewAsString(true);
1866 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1869 StringSelection ss = new StringSelection(output);
1873 jalview.gui.Desktop.internalCopy = true;
1874 // Its really worth setting the clipboard contents
1875 // to empty before setting the large StringSelection!!
1876 Toolkit.getDefaultToolkit().getSystemClipboard()
1877 .setContents(new StringSelection(""), null);
1879 Toolkit.getDefaultToolkit().getSystemClipboard()
1880 .setContents(ss, Desktop.instance);
1881 } catch (OutOfMemoryError er)
1883 new OOMWarning("copying region", er);
1887 ArrayList<int[]> hiddenColumns = null;
1888 if (viewport.hasHiddenColumns())
1890 hiddenColumns = new ArrayList<int[]>();
1891 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1892 .getSelectionGroup().getEndRes();
1893 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1895 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1897 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1898 region[1] - hiddenOffset });
1903 Desktop.jalviewClipboard = new Object[] { seqs,
1904 viewport.getAlignment().getDataset(), hiddenColumns };
1905 statusBar.setText(MessageManager.formatMessage(
1906 "label.copied_sequences_to_clipboard", new Object[] { Integer
1907 .valueOf(seqs.length).toString() }));
1917 protected void pasteNew_actionPerformed(ActionEvent e)
1929 protected void pasteThis_actionPerformed(ActionEvent e)
1935 * Paste contents of Jalview clipboard
1937 * @param newAlignment
1938 * true to paste to a new alignment, otherwise add to this.
1940 void paste(boolean newAlignment)
1942 boolean externalPaste = true;
1945 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1946 Transferable contents = c.getContents(this);
1948 if (contents == null)
1956 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1957 if (str.length() < 1)
1962 format = new IdentifyFile().identify(str, "Paste");
1964 } catch (OutOfMemoryError er)
1966 new OOMWarning("Out of memory pasting sequences!!", er);
1970 SequenceI[] sequences;
1971 boolean annotationAdded = false;
1972 AlignmentI alignment = null;
1974 if (Desktop.jalviewClipboard != null)
1976 // The clipboard was filled from within Jalview, we must use the
1978 // And dataset from the copied alignment
1979 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1980 // be doubly sure that we create *new* sequence objects.
1981 sequences = new SequenceI[newseq.length];
1982 for (int i = 0; i < newseq.length; i++)
1984 sequences[i] = new Sequence(newseq[i]);
1986 alignment = new Alignment(sequences);
1987 externalPaste = false;
1991 // parse the clipboard as an alignment.
1992 alignment = new FormatAdapter().readFile(str, "Paste", format);
1993 sequences = alignment.getSequencesArray();
1997 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2003 if (Desktop.jalviewClipboard != null)
2005 // dataset is inherited
2006 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2010 // new dataset is constructed
2011 alignment.setDataset(null);
2013 alwidth = alignment.getWidth() + 1;
2017 AlignmentI pastedal = alignment; // preserve pasted alignment object
2018 // Add pasted sequences and dataset into existing alignment.
2019 alignment = viewport.getAlignment();
2020 alwidth = alignment.getWidth() + 1;
2021 // decide if we need to import sequences from an existing dataset
2022 boolean importDs = Desktop.jalviewClipboard != null
2023 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2024 // importDs==true instructs us to copy over new dataset sequences from
2025 // an existing alignment
2026 Vector newDs = (importDs) ? new Vector() : null; // used to create
2027 // minimum dataset set
2029 for (int i = 0; i < sequences.length; i++)
2033 newDs.addElement(null);
2035 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2037 if (importDs && ds != null)
2039 if (!newDs.contains(ds))
2041 newDs.setElementAt(ds, i);
2042 ds = new Sequence(ds);
2043 // update with new dataset sequence
2044 sequences[i].setDatasetSequence(ds);
2048 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2053 // copy and derive new dataset sequence
2054 sequences[i] = sequences[i].deriveSequence();
2055 alignment.getDataset().addSequence(
2056 sequences[i].getDatasetSequence());
2057 // TODO: avoid creation of duplicate dataset sequences with a
2058 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2060 alignment.addSequence(sequences[i]); // merges dataset
2064 newDs.clear(); // tidy up
2066 if (alignment.getAlignmentAnnotation() != null)
2068 for (AlignmentAnnotation alan : alignment
2069 .getAlignmentAnnotation())
2071 if (alan.graphGroup > fgroup)
2073 fgroup = alan.graphGroup;
2077 if (pastedal.getAlignmentAnnotation() != null)
2079 // Add any annotation attached to alignment.
2080 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2081 for (int i = 0; i < alann.length; i++)
2083 annotationAdded = true;
2084 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2086 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2087 if (newann.graphGroup > -1)
2089 if (newGraphGroups.size() <= newann.graphGroup
2090 || newGraphGroups.get(newann.graphGroup) == null)
2092 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2094 newGraphGroups.add(q, null);
2096 newGraphGroups.set(newann.graphGroup, new Integer(
2099 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2103 newann.padAnnotation(alwidth);
2104 alignment.addAnnotation(newann);
2114 addHistoryItem(new EditCommand(
2115 MessageManager.getString("label.add_sequences"),
2116 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2118 // Add any annotations attached to sequences
2119 for (int i = 0; i < sequences.length; i++)
2121 if (sequences[i].getAnnotation() != null)
2123 AlignmentAnnotation newann;
2124 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2126 annotationAdded = true;
2127 newann = sequences[i].getAnnotation()[a];
2128 newann.adjustForAlignment();
2129 newann.padAnnotation(alwidth);
2130 if (newann.graphGroup > -1)
2132 if (newann.graphGroup > -1)
2134 if (newGraphGroups.size() <= newann.graphGroup
2135 || newGraphGroups.get(newann.graphGroup) == null)
2137 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2139 newGraphGroups.add(q, null);
2141 newGraphGroups.set(newann.graphGroup, new Integer(
2144 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2148 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2153 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2160 // propagate alignment changed.
2161 viewport.setEndSeq(alignment.getHeight());
2162 if (annotationAdded)
2164 // Duplicate sequence annotation in all views.
2165 AlignmentI[] alview = this.getViewAlignments();
2166 for (int i = 0; i < sequences.length; i++)
2168 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2173 for (int avnum = 0; avnum < alview.length; avnum++)
2175 if (alview[avnum] != alignment)
2177 // duplicate in a view other than the one with input focus
2178 int avwidth = alview[avnum].getWidth() + 1;
2179 // this relies on sann being preserved after we
2180 // modify the sequence's annotation array for each duplication
2181 for (int a = 0; a < sann.length; a++)
2183 AlignmentAnnotation newann = new AlignmentAnnotation(
2185 sequences[i].addAlignmentAnnotation(newann);
2186 newann.padAnnotation(avwidth);
2187 alview[avnum].addAnnotation(newann); // annotation was
2188 // duplicated earlier
2189 // TODO JAL-1145 graphGroups are not updated for sequence
2190 // annotation added to several views. This may cause
2192 alview[avnum].setAnnotationIndex(newann, a);
2197 buildSortByAnnotationScoresMenu();
2199 viewport.firePropertyChange("alignment", null,
2200 alignment.getSequences());
2201 if (alignPanels != null)
2203 for (AlignmentPanel ap : alignPanels)
2205 ap.validateAnnotationDimensions(false);
2210 alignPanel.validateAnnotationDimensions(false);
2216 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2218 String newtitle = new String("Copied sequences");
2220 if (Desktop.jalviewClipboard != null
2221 && Desktop.jalviewClipboard[2] != null)
2223 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2224 for (int[] region : hc)
2226 af.viewport.hideColumns(region[0], region[1]);
2230 // >>>This is a fix for the moment, until a better solution is
2232 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2234 alignPanel.getSeqPanel().seqCanvas
2235 .getFeatureRenderer());
2237 // TODO: maintain provenance of an alignment, rather than just make the
2238 // title a concatenation of operations.
2241 if (title.startsWith("Copied sequences"))
2247 newtitle = newtitle.concat("- from " + title);
2252 newtitle = new String("Pasted sequences");
2255 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2260 } catch (Exception ex)
2262 ex.printStackTrace();
2263 System.out.println("Exception whilst pasting: " + ex);
2264 // could be anything being pasted in here
2270 protected void expand_newalign(ActionEvent e)
2274 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2275 .getAlignment(), -1);
2276 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2278 String newtitle = new String("Flanking alignment");
2280 if (Desktop.jalviewClipboard != null
2281 && Desktop.jalviewClipboard[2] != null)
2283 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2284 for (int region[] : hc)
2286 af.viewport.hideColumns(region[0], region[1]);
2290 // >>>This is a fix for the moment, until a better solution is
2292 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2294 alignPanel.getSeqPanel().seqCanvas
2295 .getFeatureRenderer());
2297 // TODO: maintain provenance of an alignment, rather than just make the
2298 // title a concatenation of operations.
2300 if (title.startsWith("Copied sequences"))
2306 newtitle = newtitle.concat("- from " + title);
2310 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2312 } catch (Exception ex)
2314 ex.printStackTrace();
2315 System.out.println("Exception whilst pasting: " + ex);
2316 // could be anything being pasted in here
2317 } catch (OutOfMemoryError oom)
2319 new OOMWarning("Viewing flanking region of alignment", oom);
2330 protected void cut_actionPerformed(ActionEvent e)
2332 copy_actionPerformed(null);
2333 delete_actionPerformed(null);
2343 protected void delete_actionPerformed(ActionEvent evt)
2346 SequenceGroup sg = viewport.getSelectionGroup();
2353 * If the cut affects all sequences, warn, remove highlighted columns
2355 if (sg.getSize() == viewport.getAlignment().getHeight())
2357 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2358 .getAlignment().getWidth()) ? true : false;
2359 if (isEntireAlignWidth)
2361 int confirm = JOptionPane.showConfirmDialog(this,
2362 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2363 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2364 JOptionPane.OK_CANCEL_OPTION);
2366 if (confirm == JOptionPane.CANCEL_OPTION
2367 || confirm == JOptionPane.CLOSED_OPTION)
2372 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2373 sg.getEndRes() + 1);
2375 SequenceI[] cut = sg.getSequences()
2376 .toArray(new SequenceI[sg.getSize()]);
2378 addHistoryItem(new EditCommand(
2379 MessageManager.getString("label.cut_sequences"), Action.CUT,
2380 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2381 viewport.getAlignment()));
2383 viewport.setSelectionGroup(null);
2384 viewport.sendSelection();
2385 viewport.getAlignment().deleteGroup(sg);
2387 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2389 if (viewport.getAlignment().getHeight() < 1)
2393 this.setClosed(true);
2394 } catch (Exception ex)
2407 protected void deleteGroups_actionPerformed(ActionEvent e)
2409 if (avc.deleteGroups())
2411 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2412 alignPanel.updateAnnotation();
2413 alignPanel.paintAlignment(true);
2424 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2426 SequenceGroup sg = new SequenceGroup();
2428 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2430 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2433 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2434 viewport.setSelectionGroup(sg);
2435 viewport.sendSelection();
2436 // JAL-2034 - should delegate to
2437 // alignPanel to decide if overview needs
2439 alignPanel.paintAlignment(false);
2440 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2450 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2452 if (viewport.cursorMode)
2454 alignPanel.getSeqPanel().keyboardNo1 = null;
2455 alignPanel.getSeqPanel().keyboardNo2 = null;
2457 viewport.setSelectionGroup(null);
2458 viewport.getColumnSelection().clear();
2459 viewport.setSelectionGroup(null);
2460 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2461 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2462 // JAL-2034 - should delegate to
2463 // alignPanel to decide if overview needs
2465 alignPanel.paintAlignment(false);
2466 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2467 viewport.sendSelection();
2477 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2479 SequenceGroup sg = viewport.getSelectionGroup();
2483 selectAllSequenceMenuItem_actionPerformed(null);
2488 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2490 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2492 // JAL-2034 - should delegate to
2493 // alignPanel to decide if overview needs
2496 alignPanel.paintAlignment(true);
2497 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2498 viewport.sendSelection();
2502 public void invertColSel_actionPerformed(ActionEvent e)
2504 viewport.invertColumnSelection();
2505 alignPanel.paintAlignment(true);
2506 viewport.sendSelection();
2516 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2518 trimAlignment(true);
2528 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2530 trimAlignment(false);
2533 void trimAlignment(boolean trimLeft)
2535 ColumnSelection colSel = viewport.getColumnSelection();
2538 if (!colSel.isEmpty())
2542 column = colSel.getMin();
2546 column = colSel.getMax();
2550 if (viewport.getSelectionGroup() != null)
2552 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2553 viewport.getHiddenRepSequences());
2557 seqs = viewport.getAlignment().getSequencesArray();
2560 TrimRegionCommand trimRegion;
2563 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2564 column, viewport.getAlignment());
2565 viewport.setStartRes(0);
2569 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2570 column, viewport.getAlignment());
2573 statusBar.setText(MessageManager.formatMessage(
2574 "label.removed_columns",
2575 new String[] { Integer.valueOf(trimRegion.getSize())
2578 addHistoryItem(trimRegion);
2580 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2582 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2583 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2585 viewport.getAlignment().deleteGroup(sg);
2589 viewport.firePropertyChange("alignment", null, viewport
2590 .getAlignment().getSequences());
2601 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2603 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2606 if (viewport.getSelectionGroup() != null)
2608 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2609 viewport.getHiddenRepSequences());
2610 start = viewport.getSelectionGroup().getStartRes();
2611 end = viewport.getSelectionGroup().getEndRes();
2615 seqs = viewport.getAlignment().getSequencesArray();
2618 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2619 "Remove Gapped Columns", seqs, start, end,
2620 viewport.getAlignment());
2622 addHistoryItem(removeGapCols);
2624 statusBar.setText(MessageManager.formatMessage(
2625 "label.removed_empty_columns",
2626 new Object[] { Integer.valueOf(removeGapCols.getSize())
2629 // This is to maintain viewport position on first residue
2630 // of first sequence
2631 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2632 int startRes = seq.findPosition(viewport.startRes);
2633 // ShiftList shifts;
2634 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2635 // edit.alColumnChanges=shifts.getInverse();
2636 // if (viewport.hasHiddenColumns)
2637 // viewport.getColumnSelection().compensateForEdits(shifts);
2638 viewport.setStartRes(seq.findIndex(startRes) - 1);
2639 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2651 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2653 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2656 if (viewport.getSelectionGroup() != null)
2658 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2659 viewport.getHiddenRepSequences());
2660 start = viewport.getSelectionGroup().getStartRes();
2661 end = viewport.getSelectionGroup().getEndRes();
2665 seqs = viewport.getAlignment().getSequencesArray();
2668 // This is to maintain viewport position on first residue
2669 // of first sequence
2670 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2671 int startRes = seq.findPosition(viewport.startRes);
2673 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2674 viewport.getAlignment()));
2676 viewport.setStartRes(seq.findIndex(startRes) - 1);
2678 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2690 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2692 viewport.setPadGaps(padGapsMenuitem.isSelected());
2693 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2704 public void findMenuItem_actionPerformed(ActionEvent e)
2710 * Create a new view of the current alignment.
2713 public void newView_actionPerformed(ActionEvent e)
2715 newView(null, true);
2719 * Creates and shows a new view of the current alignment.
2722 * title of newly created view; if null, one will be generated
2723 * @param copyAnnotation
2724 * if true then duplicate all annnotation, groups and settings
2725 * @return new alignment panel, already displayed.
2727 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2730 * Create a new AlignmentPanel (with its own, new Viewport)
2732 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2734 if (!copyAnnotation)
2737 * remove all groups and annotation except for the automatic stuff
2739 newap.av.getAlignment().deleteAllGroups();
2740 newap.av.getAlignment().deleteAllAnnotations(false);
2743 newap.av.setGatherViewsHere(false);
2745 if (viewport.viewName == null)
2747 viewport.viewName = MessageManager
2748 .getString("label.view_name_original");
2752 * Views share the same edits undo and redo stacks
2754 newap.av.setHistoryList(viewport.getHistoryList());
2755 newap.av.setRedoList(viewport.getRedoList());
2758 * Views share the same mappings; need to deregister any new mappings
2759 * created by copyAlignPanel, and register the new reference to the shared
2762 newap.av.replaceMappings(viewport.getAlignment());
2764 newap.av.viewName = getNewViewName(viewTitle);
2766 addAlignmentPanel(newap, true);
2767 newap.alignmentChanged();
2769 if (alignPanels.size() == 2)
2771 viewport.setGatherViewsHere(true);
2773 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2778 * Make a new name for the view, ensuring it is unique within the current
2779 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2780 * these now use viewId. Unique view names are still desirable for usability.)
2785 protected String getNewViewName(String viewTitle)
2787 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2788 boolean addFirstIndex = false;
2789 if (viewTitle == null || viewTitle.trim().length() == 0)
2791 viewTitle = MessageManager.getString("action.view");
2792 addFirstIndex = true;
2796 index = 1;// we count from 1 if given a specific name
2798 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2800 List<Component> comps = PaintRefresher.components.get(viewport
2801 .getSequenceSetId());
2803 List<String> existingNames = getExistingViewNames(comps);
2805 while (existingNames.contains(newViewName))
2807 newViewName = viewTitle + " " + (++index);
2813 * Returns a list of distinct view names found in the given list of
2814 * components. View names are held on the viewport of an AlignmentPanel.
2819 protected List<String> getExistingViewNames(List<Component> comps)
2821 List<String> existingNames = new ArrayList<String>();
2822 for (Component comp : comps)
2824 if (comp instanceof AlignmentPanel)
2826 AlignmentPanel ap = (AlignmentPanel) comp;
2827 if (!existingNames.contains(ap.av.viewName))
2829 existingNames.add(ap.av.viewName);
2833 return existingNames;
2837 * Explode tabbed views into separate windows.
2840 public void expandViews_actionPerformed(ActionEvent e)
2842 Desktop.explodeViews(this);
2846 * Gather views in separate windows back into a tabbed presentation.
2849 public void gatherViews_actionPerformed(ActionEvent e)
2851 Desktop.instance.gatherViews(this);
2861 public void font_actionPerformed(ActionEvent e)
2863 new FontChooser(alignPanel);
2873 protected void seqLimit_actionPerformed(ActionEvent e)
2875 viewport.setShowJVSuffix(seqLimits.isSelected());
2877 alignPanel.getIdPanel().getIdCanvas()
2878 .setPreferredSize(alignPanel.calculateIdWidth());
2879 alignPanel.paintAlignment(true);
2883 public void idRightAlign_actionPerformed(ActionEvent e)
2885 viewport.setRightAlignIds(idRightAlign.isSelected());
2886 alignPanel.paintAlignment(true);
2890 public void centreColumnLabels_actionPerformed(ActionEvent e)
2892 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2893 alignPanel.paintAlignment(true);
2899 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2902 protected void followHighlight_actionPerformed()
2905 * Set the 'follow' flag on the Viewport (and scroll to position if now
2908 final boolean state = this.followHighlightMenuItem.getState();
2909 viewport.setFollowHighlight(state);
2912 alignPanel.scrollToPosition(
2913 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2924 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2926 viewport.setColourText(colourTextMenuItem.isSelected());
2927 alignPanel.paintAlignment(true);
2937 public void wrapMenuItem_actionPerformed(ActionEvent e)
2939 scaleAbove.setVisible(wrapMenuItem.isSelected());
2940 scaleLeft.setVisible(wrapMenuItem.isSelected());
2941 scaleRight.setVisible(wrapMenuItem.isSelected());
2942 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2943 alignPanel.updateLayout();
2947 public void showAllSeqs_actionPerformed(ActionEvent e)
2949 viewport.showAllHiddenSeqs();
2953 public void showAllColumns_actionPerformed(ActionEvent e)
2955 viewport.showAllHiddenColumns();
2957 viewport.sendSelection();
2961 public void hideSelSequences_actionPerformed(ActionEvent e)
2963 viewport.hideAllSelectedSeqs();
2964 // alignPanel.paintAlignment(true);
2968 * called by key handler and the hide all/show all menu items
2973 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2976 boolean hide = false;
2977 SequenceGroup sg = viewport.getSelectionGroup();
2978 if (!toggleSeqs && !toggleCols)
2980 // Hide everything by the current selection - this is a hack - we do the
2981 // invert and then hide
2982 // first check that there will be visible columns after the invert.
2983 if (viewport.hasSelectedColumns()
2984 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2987 // now invert the sequence set, if required - empty selection implies
2988 // that no hiding is required.
2991 invertSequenceMenuItem_actionPerformed(null);
2992 sg = viewport.getSelectionGroup();
2996 viewport.expandColSelection(sg, true);
2997 // finally invert the column selection and get the new sequence
2999 invertColSel_actionPerformed(null);
3006 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3008 hideSelSequences_actionPerformed(null);
3011 else if (!(toggleCols && viewport.hasSelectedColumns()))
3013 showAllSeqs_actionPerformed(null);
3019 if (viewport.hasSelectedColumns())
3021 hideSelColumns_actionPerformed(null);
3024 viewport.setSelectionGroup(sg);
3029 showAllColumns_actionPerformed(null);
3038 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3039 * event.ActionEvent)
3042 public void hideAllButSelection_actionPerformed(ActionEvent e)
3044 toggleHiddenRegions(false, false);
3045 viewport.sendSelection();
3052 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3056 public void hideAllSelection_actionPerformed(ActionEvent e)
3058 SequenceGroup sg = viewport.getSelectionGroup();
3059 viewport.expandColSelection(sg, false);
3060 viewport.hideAllSelectedSeqs();
3061 viewport.hideSelectedColumns();
3062 alignPanel.paintAlignment(true);
3063 viewport.sendSelection();
3070 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3074 public void showAllhidden_actionPerformed(ActionEvent e)
3076 viewport.showAllHiddenColumns();
3077 viewport.showAllHiddenSeqs();
3078 alignPanel.paintAlignment(true);
3079 viewport.sendSelection();
3083 public void hideSelColumns_actionPerformed(ActionEvent e)
3085 viewport.hideSelectedColumns();
3086 alignPanel.paintAlignment(true);
3087 viewport.sendSelection();
3091 public void hiddenMarkers_actionPerformed(ActionEvent e)
3093 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3104 protected void scaleAbove_actionPerformed(ActionEvent e)
3106 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3107 alignPanel.paintAlignment(true);
3117 protected void scaleLeft_actionPerformed(ActionEvent e)
3119 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3120 alignPanel.paintAlignment(true);
3130 protected void scaleRight_actionPerformed(ActionEvent e)
3132 viewport.setScaleRightWrapped(scaleRight.isSelected());
3133 alignPanel.paintAlignment(true);
3143 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3145 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3146 alignPanel.paintAlignment(true);
3156 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3158 viewport.setShowText(viewTextMenuItem.isSelected());
3159 alignPanel.paintAlignment(true);
3169 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3171 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3172 alignPanel.paintAlignment(true);
3175 public FeatureSettings featureSettings;
3178 public FeatureSettingsControllerI getFeatureSettingsUI()
3180 return featureSettings;
3184 public void featureSettings_actionPerformed(ActionEvent e)
3186 if (featureSettings != null)
3188 featureSettings.close();
3189 featureSettings = null;
3191 if (!showSeqFeatures.isSelected())
3193 // make sure features are actually displayed
3194 showSeqFeatures.setSelected(true);
3195 showSeqFeatures_actionPerformed(null);
3197 featureSettings = new FeatureSettings(this);
3201 * Set or clear 'Show Sequence Features'
3207 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3209 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3210 alignPanel.paintAlignment(true);
3211 if (alignPanel.getOverviewPanel() != null)
3213 alignPanel.getOverviewPanel().updateOverviewImage();
3218 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3219 * the annotations panel as a whole.
3221 * The options to show/hide all annotations should be enabled when the panel
3222 * is shown, and disabled when the panel is hidden.
3227 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3229 final boolean setVisible = annotationPanelMenuItem.isSelected();
3230 viewport.setShowAnnotation(setVisible);
3231 this.showAllSeqAnnotations.setEnabled(setVisible);
3232 this.hideAllSeqAnnotations.setEnabled(setVisible);
3233 this.showAllAlAnnotations.setEnabled(setVisible);
3234 this.hideAllAlAnnotations.setEnabled(setVisible);
3235 alignPanel.updateLayout();
3239 public void alignmentProperties()
3241 JEditorPane editPane = new JEditorPane("text/html", "");
3242 editPane.setEditable(false);
3243 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3245 editPane.setText(MessageManager.formatMessage("label.html_content",
3246 new Object[] { contents.toString() }));
3247 JInternalFrame frame = new JInternalFrame();
3248 frame.getContentPane().add(new JScrollPane(editPane));
3250 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3251 "label.alignment_properties", new Object[] { getTitle() }),
3262 public void overviewMenuItem_actionPerformed(ActionEvent e)
3264 if (alignPanel.overviewPanel != null)
3269 JInternalFrame frame = new JInternalFrame();
3270 OverviewPanel overview = new OverviewPanel(alignPanel);
3271 frame.setContentPane(overview);
3272 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3273 "label.overview_params", new Object[] { this.getTitle() }),
3274 frame.getWidth(), frame.getHeight());
3276 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3277 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3280 public void internalFrameClosed(
3281 javax.swing.event.InternalFrameEvent evt)
3283 alignPanel.setOverviewPanel(null);
3287 alignPanel.setOverviewPanel(overview);
3291 public void textColour_actionPerformed(ActionEvent e)
3293 new TextColourChooser().chooseColour(alignPanel, null);
3303 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3315 public void clustalColour_actionPerformed(ActionEvent e)
3317 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3318 viewport.getHiddenRepSequences()));
3328 public void zappoColour_actionPerformed(ActionEvent e)
3330 changeColour(new ZappoColourScheme());
3340 public void taylorColour_actionPerformed(ActionEvent e)
3342 changeColour(new TaylorColourScheme());
3352 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3354 changeColour(new HydrophobicColourScheme());
3364 public void helixColour_actionPerformed(ActionEvent e)
3366 changeColour(new HelixColourScheme());
3376 public void strandColour_actionPerformed(ActionEvent e)
3378 changeColour(new StrandColourScheme());
3388 public void turnColour_actionPerformed(ActionEvent e)
3390 changeColour(new TurnColourScheme());
3400 public void buriedColour_actionPerformed(ActionEvent e)
3402 changeColour(new BuriedColourScheme());
3412 public void nucleotideColour_actionPerformed(ActionEvent e)
3414 changeColour(new NucleotideColourScheme());
3418 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3420 changeColour(new PurinePyrimidineColourScheme());
3424 * public void covariationColour_actionPerformed(ActionEvent e) {
3426 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3430 public void annotationColour_actionPerformed(ActionEvent e)
3432 new AnnotationColourChooser(viewport, alignPanel);
3436 public void annotationColumn_actionPerformed(ActionEvent e)
3438 new AnnotationColumnChooser(viewport, alignPanel);
3442 public void rnahelicesColour_actionPerformed(ActionEvent e)
3444 new RNAHelicesColourChooser(viewport, alignPanel);
3454 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3456 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3466 public void changeColour(ColourSchemeI cs)
3468 // TODO: pull up to controller method
3472 // Make sure viewport is up to date w.r.t. any sliders
3473 if (viewport.getAbovePIDThreshold())
3475 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3477 viewport.setThreshold(threshold);
3480 if (viewport.getConservationSelected())
3482 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3485 if (cs instanceof TCoffeeColourScheme)
3487 tcoffeeColour.setEnabled(true);
3488 tcoffeeColour.setSelected(true);
3492 viewport.setGlobalColourScheme(cs);
3494 alignPanel.paintAlignment(true);
3504 protected void modifyPID_actionPerformed(ActionEvent e)
3506 if (viewport.getAbovePIDThreshold()
3507 && viewport.getGlobalColourScheme() != null)
3509 SliderPanel.setPIDSliderSource(alignPanel,
3510 viewport.getGlobalColourScheme(), "Background");
3511 SliderPanel.showPIDSlider();
3522 protected void modifyConservation_actionPerformed(ActionEvent e)
3524 if (viewport.getConservationSelected()
3525 && viewport.getGlobalColourScheme() != null)
3527 SliderPanel.setConservationSlider(alignPanel,
3528 viewport.getGlobalColourScheme(), "Background");
3529 SliderPanel.showConservationSlider();
3540 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3542 viewport.setConservationSelected(conservationMenuItem.isSelected());
3544 viewport.setAbovePIDThreshold(false);
3545 abovePIDThreshold.setSelected(false);
3547 changeColour(viewport.getGlobalColourScheme());
3549 modifyConservation_actionPerformed(null);
3559 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3561 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3563 conservationMenuItem.setSelected(false);
3564 viewport.setConservationSelected(false);
3566 changeColour(viewport.getGlobalColourScheme());
3568 modifyPID_actionPerformed(null);
3578 public void userDefinedColour_actionPerformed(ActionEvent e)
3580 if (e.getActionCommand().equals(
3581 MessageManager.getString("action.user_defined")))
3583 new UserDefinedColours(alignPanel, null);
3587 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3588 .getUserColourSchemes().get(e.getActionCommand());
3594 public void updateUserColourMenu()
3597 Component[] menuItems = colourMenu.getMenuComponents();
3598 int iSize = menuItems.length;
3599 for (int i = 0; i < iSize; i++)
3601 if (menuItems[i].getName() != null
3602 && menuItems[i].getName().equals("USER_DEFINED"))
3604 colourMenu.remove(menuItems[i]);
3608 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3610 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3611 .getUserColourSchemes().keys();
3613 while (userColours.hasMoreElements())
3615 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3616 userColours.nextElement().toString());
3617 radioItem.setName("USER_DEFINED");
3618 radioItem.addMouseListener(new MouseAdapter()
3621 public void mousePressed(MouseEvent evt)
3623 if (evt.isPopupTrigger()) // Mac
3625 offerRemoval(radioItem);
3630 public void mouseReleased(MouseEvent evt)
3632 if (evt.isPopupTrigger()) // Windows
3634 offerRemoval(radioItem);
3641 void offerRemoval(final JRadioButtonMenuItem radioItem)
3643 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3645 int option = JOptionPane.showInternalConfirmDialog(
3646 jalview.gui.Desktop.desktop, MessageManager
3647 .getString("label.remove_from_default_list"),
3649 .getString("label.remove_user_defined_colour"),
3650 JOptionPane.YES_NO_OPTION);
3651 if (option == JOptionPane.YES_OPTION)
3653 jalview.gui.UserDefinedColours
3654 .removeColourFromDefaults(radioItem.getText());
3655 colourMenu.remove(radioItem);
3659 radioItem.addActionListener(new ActionListener()
3662 public void actionPerformed(ActionEvent evt)
3664 userDefinedColour_actionPerformed(evt);
3670 radioItem.addActionListener(new ActionListener()
3673 public void actionPerformed(ActionEvent evt)
3675 userDefinedColour_actionPerformed(evt);
3679 colourMenu.insert(radioItem, 15);
3680 colours.add(radioItem);
3692 public void PIDColour_actionPerformed(ActionEvent e)
3694 changeColour(new PIDColourScheme());
3704 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3706 changeColour(new Blosum62ColourScheme());
3716 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3718 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3719 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3720 .getAlignment().getSequenceAt(0), null);
3721 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3722 viewport.getAlignment()));
3723 alignPanel.paintAlignment(true);
3733 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3735 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3736 AlignmentSorter.sortByID(viewport.getAlignment());
3737 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3738 viewport.getAlignment()));
3739 alignPanel.paintAlignment(true);
3749 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3751 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3752 AlignmentSorter.sortByLength(viewport.getAlignment());
3753 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3754 viewport.getAlignment()));
3755 alignPanel.paintAlignment(true);
3765 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3767 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3768 AlignmentSorter.sortByGroup(viewport.getAlignment());
3769 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3770 viewport.getAlignment()));
3772 alignPanel.paintAlignment(true);
3782 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3784 new RedundancyPanel(alignPanel, this);
3794 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3796 if ((viewport.getSelectionGroup() == null)
3797 || (viewport.getSelectionGroup().getSize() < 2))
3799 JOptionPane.showInternalMessageDialog(this, MessageManager
3800 .getString("label.you_must_select_least_two_sequences"),
3801 MessageManager.getString("label.invalid_selection"),
3802 JOptionPane.WARNING_MESSAGE);
3806 JInternalFrame frame = new JInternalFrame();
3807 frame.setContentPane(new PairwiseAlignPanel(viewport));
3808 Desktop.addInternalFrame(frame,
3809 MessageManager.getString("action.pairwise_alignment"), 600,
3821 public void PCAMenuItem_actionPerformed(ActionEvent e)
3823 if (((viewport.getSelectionGroup() != null)
3824 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3825 .getSelectionGroup().getSize() > 0))
3826 || (viewport.getAlignment().getHeight() < 4))
3829 .showInternalMessageDialog(
3832 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3834 .getString("label.sequence_selection_insufficient"),
3835 JOptionPane.WARNING_MESSAGE);
3840 new PCAPanel(alignPanel);
3844 public void autoCalculate_actionPerformed(ActionEvent e)
3846 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3847 if (viewport.autoCalculateConsensus)
3849 viewport.firePropertyChange("alignment", null, viewport
3850 .getAlignment().getSequences());
3855 public void sortByTreeOption_actionPerformed(ActionEvent e)
3857 viewport.sortByTree = sortByTree.isSelected();
3861 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3863 viewport.followSelection = listenToViewSelections.isSelected();
3873 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3875 newTreePanel("AV", "PID", "Average distance tree using PID");
3885 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3887 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3897 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3899 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3909 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3911 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3924 void newTreePanel(String type, String pwType, String title)
3928 if (viewport.getSelectionGroup() != null
3929 && viewport.getSelectionGroup().getSize() > 0)
3931 if (viewport.getSelectionGroup().getSize() < 3)
3937 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3939 .getString("label.not_enough_sequences"),
3940 JOptionPane.WARNING_MESSAGE);
3944 SequenceGroup sg = viewport.getSelectionGroup();
3946 /* Decide if the selection is a column region */
3947 for (SequenceI _s : sg.getSequences())
3949 if (_s.getLength() < sg.getEndRes())
3955 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3957 .getString("label.sequences_selection_not_aligned"),
3958 JOptionPane.WARNING_MESSAGE);
3964 title = title + " on region";
3965 tp = new TreePanel(alignPanel, type, pwType);
3969 // are the visible sequences aligned?
3970 if (!viewport.getAlignment().isAligned(false))
3976 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3978 .getString("label.sequences_not_aligned"),
3979 JOptionPane.WARNING_MESSAGE);
3984 if (viewport.getAlignment().getHeight() < 2)
3989 tp = new TreePanel(alignPanel, type, pwType);
3994 if (viewport.viewName != null)
3996 title += viewport.viewName + " of ";
3999 title += this.title;
4001 Desktop.addInternalFrame(tp, title, 600, 500);
4012 public void addSortByOrderMenuItem(String title,
4013 final AlignmentOrder order)
4015 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4016 "action.by_title_param", new Object[] { title }));
4018 item.addActionListener(new java.awt.event.ActionListener()
4021 public void actionPerformed(ActionEvent e)
4023 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4025 // TODO: JBPNote - have to map order entries to curent SequenceI
4027 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4029 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4032 alignPanel.paintAlignment(true);
4038 * Add a new sort by annotation score menu item
4041 * the menu to add the option to
4043 * the label used to retrieve scores for each sequence on the
4046 public void addSortByAnnotScoreMenuItem(JMenu sort,
4047 final String scoreLabel)
4049 final JMenuItem item = new JMenuItem(scoreLabel);
4051 item.addActionListener(new java.awt.event.ActionListener()
4054 public void actionPerformed(ActionEvent e)
4056 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4057 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4058 viewport.getAlignment());// ,viewport.getSelectionGroup());
4059 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4060 viewport.getAlignment()));
4061 alignPanel.paintAlignment(true);
4067 * last hash for alignment's annotation array - used to minimise cost of
4070 protected int _annotationScoreVectorHash;
4073 * search the alignment and rebuild the sort by annotation score submenu the
4074 * last alignment annotation vector hash is stored to minimize cost of
4075 * rebuilding in subsequence calls.
4079 public void buildSortByAnnotationScoresMenu()
4081 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4086 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4088 sortByAnnotScore.removeAll();
4089 // almost certainly a quicker way to do this - but we keep it simple
4090 Hashtable scoreSorts = new Hashtable();
4091 AlignmentAnnotation aann[];
4092 for (SequenceI sqa : viewport.getAlignment().getSequences())
4094 aann = sqa.getAnnotation();
4095 for (int i = 0; aann != null && i < aann.length; i++)
4097 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4099 scoreSorts.put(aann[i].label, aann[i].label);
4103 Enumeration labels = scoreSorts.keys();
4104 while (labels.hasMoreElements())
4106 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4107 (String) labels.nextElement());
4109 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4112 _annotationScoreVectorHash = viewport.getAlignment()
4113 .getAlignmentAnnotation().hashCode();
4118 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4119 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4120 * call. Listeners are added to remove the menu item when the treePanel is
4121 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4125 * Displayed tree window.
4127 * SortBy menu item title.
4130 public void buildTreeMenu()
4132 calculateTree.removeAll();
4133 // build the calculate menu
4135 for (final String type : new String[] { "NJ", "AV" })
4137 String treecalcnm = MessageManager.getString("label.tree_calc_"
4138 + type.toLowerCase());
4139 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4141 JMenuItem tm = new JMenuItem();
4142 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4143 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4144 || sm.isProtein() == !viewport.getAlignment()
4147 String smn = MessageManager.getStringOrReturn(
4148 "label.score_model_", sm.getName());
4149 final String title = MessageManager.formatMessage(
4150 "label.treecalc_title", treecalcnm, smn);
4151 tm.setText(title);//
4152 tm.addActionListener(new java.awt.event.ActionListener()
4155 public void actionPerformed(ActionEvent e)
4157 newTreePanel(type, pwtype, title);
4160 calculateTree.add(tm);
4165 sortByTreeMenu.removeAll();
4167 List<Component> comps = PaintRefresher.components.get(viewport
4168 .getSequenceSetId());
4169 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4170 for (Component comp : comps)
4172 if (comp instanceof TreePanel)
4174 treePanels.add((TreePanel) comp);
4178 if (treePanels.size() < 1)
4180 sortByTreeMenu.setVisible(false);
4184 sortByTreeMenu.setVisible(true);
4186 for (final TreePanel tp : treePanels)
4188 final JMenuItem item = new JMenuItem(tp.getTitle());
4189 item.addActionListener(new java.awt.event.ActionListener()
4192 public void actionPerformed(ActionEvent e)
4194 tp.sortByTree_actionPerformed();
4195 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4200 sortByTreeMenu.add(item);
4204 public boolean sortBy(AlignmentOrder alorder, String undoname)
4206 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4207 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4208 if (undoname != null)
4210 addHistoryItem(new OrderCommand(undoname, oldOrder,
4211 viewport.getAlignment()));
4213 alignPanel.paintAlignment(true);
4218 * Work out whether the whole set of sequences or just the selected set will
4219 * be submitted for multiple alignment.
4222 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4224 // Now, check we have enough sequences
4225 AlignmentView msa = null;
4227 if ((viewport.getSelectionGroup() != null)
4228 && (viewport.getSelectionGroup().getSize() > 1))
4230 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4231 // some common interface!
4233 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4234 * SequenceI[sz = seqs.getSize(false)];
4236 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4237 * seqs.getSequenceAt(i); }
4239 msa = viewport.getAlignmentView(true);
4241 else if (viewport.getSelectionGroup() != null
4242 && viewport.getSelectionGroup().getSize() == 1)
4244 int option = JOptionPane.showConfirmDialog(this,
4245 MessageManager.getString("warn.oneseq_msainput_selection"),
4246 MessageManager.getString("label.invalid_selection"),
4247 JOptionPane.OK_CANCEL_OPTION);
4248 if (option == JOptionPane.OK_OPTION)
4250 msa = viewport.getAlignmentView(false);
4255 msa = viewport.getAlignmentView(false);
4261 * Decides what is submitted to a secondary structure prediction service: the
4262 * first sequence in the alignment, or in the current selection, or, if the
4263 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4264 * region or the whole alignment. (where the first sequence in the set is the
4265 * one that the prediction will be for).
4267 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4269 AlignmentView seqs = null;
4271 if ((viewport.getSelectionGroup() != null)
4272 && (viewport.getSelectionGroup().getSize() > 0))
4274 seqs = viewport.getAlignmentView(true);
4278 seqs = viewport.getAlignmentView(false);
4280 // limit sequences - JBPNote in future - could spawn multiple prediction
4282 // TODO: viewport.getAlignment().isAligned is a global state - the local
4283 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4284 if (!viewport.getAlignment().isAligned(false))
4286 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4287 // TODO: if seqs.getSequences().length>1 then should really have warned
4301 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4303 // Pick the tree file
4304 JalviewFileChooser chooser = new JalviewFileChooser(
4305 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4306 chooser.setFileView(new JalviewFileView());
4307 chooser.setDialogTitle(MessageManager
4308 .getString("label.select_newick_like_tree_file"));
4309 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4311 int value = chooser.showOpenDialog(null);
4313 if (value == JalviewFileChooser.APPROVE_OPTION)
4315 String choice = chooser.getSelectedFile().getPath();
4316 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4317 jalview.io.NewickFile fin = null;
4320 fin = new jalview.io.NewickFile(choice, "File");
4321 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4322 } catch (Exception ex)
4329 .getString("label.problem_reading_tree_file"),
4330 JOptionPane.WARNING_MESSAGE);
4331 ex.printStackTrace();
4333 if (fin != null && fin.hasWarningMessage())
4335 JOptionPane.showMessageDialog(Desktop.desktop, fin
4336 .getWarningMessage(), MessageManager
4337 .getString("label.possible_problem_with_tree_file"),
4338 JOptionPane.WARNING_MESSAGE);
4344 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4346 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4349 public TreePanel ShowNewickTree(NewickFile nf, String title)
4351 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4354 public TreePanel ShowNewickTree(NewickFile nf, String title,
4355 AlignmentView input)
4357 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4360 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4361 int h, int x, int y)
4363 return ShowNewickTree(nf, title, null, w, h, x, y);
4367 * Add a treeviewer for the tree extracted from a newick file object to the
4368 * current alignment view
4375 * Associated alignment input data (or null)
4384 * @return TreePanel handle
4386 public TreePanel ShowNewickTree(NewickFile nf, String title,
4387 AlignmentView input, int w, int h, int x, int y)
4389 TreePanel tp = null;
4395 if (nf.getTree() != null)
4397 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4403 tp.setLocation(x, y);
4406 Desktop.addInternalFrame(tp, title, w, h);
4408 } catch (Exception ex)
4410 ex.printStackTrace();
4416 private boolean buildingMenu = false;
4419 * Generates menu items and listener event actions for web service clients
4422 public void BuildWebServiceMenu()
4424 while (buildingMenu)
4428 System.err.println("Waiting for building menu to finish.");
4430 } catch (Exception e)
4434 final AlignFrame me = this;
4435 buildingMenu = true;
4436 new Thread(new Runnable()
4441 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4444 // System.err.println("Building ws menu again "
4445 // + Thread.currentThread());
4446 // TODO: add support for context dependent disabling of services based
4448 // alignment and current selection
4449 // TODO: add additional serviceHandle parameter to specify abstract
4451 // class independently of AbstractName
4452 // TODO: add in rediscovery GUI function to restart discoverer
4453 // TODO: group services by location as well as function and/or
4455 // object broker mechanism.
4456 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4457 final IProgressIndicator af = me;
4460 * do not i18n these strings - they are hard-coded in class
4461 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4462 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4464 final JMenu msawsmenu = new JMenu("Alignment");
4465 final JMenu secstrmenu = new JMenu(
4466 "Secondary Structure Prediction");
4467 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4468 final JMenu analymenu = new JMenu("Analysis");
4469 final JMenu dismenu = new JMenu("Protein Disorder");
4470 // JAL-940 - only show secondary structure prediction services from
4471 // the legacy server
4472 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4474 Discoverer.services != null && (Discoverer.services.size() > 0))
4476 // TODO: refactor to allow list of AbstractName/Handler bindings to
4478 // stored or retrieved from elsewhere
4479 // No MSAWS used any more:
4480 // Vector msaws = null; // (Vector)
4481 // Discoverer.services.get("MsaWS");
4482 Vector secstrpr = (Vector) Discoverer.services
4484 if (secstrpr != null)
4486 // Add any secondary structure prediction services
4487 for (int i = 0, j = secstrpr.size(); i < j; i++)
4489 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4491 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4492 .getServiceClient(sh);
4493 int p = secstrmenu.getItemCount();
4494 impl.attachWSMenuEntry(secstrmenu, me);
4495 int q = secstrmenu.getItemCount();
4496 for (int litm = p; litm < q; litm++)
4498 legacyItems.add(secstrmenu.getItem(litm));
4504 // Add all submenus in the order they should appear on the web
4506 wsmenu.add(msawsmenu);
4507 wsmenu.add(secstrmenu);
4508 wsmenu.add(dismenu);
4509 wsmenu.add(analymenu);
4510 // No search services yet
4511 // wsmenu.add(seqsrchmenu);
4513 javax.swing.SwingUtilities.invokeLater(new Runnable()
4520 webService.removeAll();
4521 // first, add discovered services onto the webservices menu
4522 if (wsmenu.size() > 0)
4524 for (int i = 0, j = wsmenu.size(); i < j; i++)
4526 webService.add(wsmenu.get(i));
4531 webService.add(me.webServiceNoServices);
4533 // TODO: move into separate menu builder class.
4534 boolean new_sspred = false;
4535 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4537 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4538 if (jws2servs != null)
4540 if (jws2servs.hasServices())
4542 jws2servs.attachWSMenuEntry(webService, me);
4543 for (Jws2Instance sv : jws2servs.getServices())
4545 if (sv.description.toLowerCase().contains("jpred"))
4547 for (JMenuItem jmi : legacyItems)
4549 jmi.setVisible(false);
4555 if (jws2servs.isRunning())
4557 JMenuItem tm = new JMenuItem(
4558 "Still discovering JABA Services");
4559 tm.setEnabled(false);
4564 build_urlServiceMenu(me.webService);
4565 build_fetchdbmenu(webService);
4566 for (JMenu item : wsmenu)
4568 if (item.getItemCount() == 0)
4570 item.setEnabled(false);
4574 item.setEnabled(true);
4577 } catch (Exception e)
4580 .debug("Exception during web service menu building process.",
4585 } catch (Exception e)
4588 buildingMenu = false;
4595 * construct any groupURL type service menu entries.
4599 private void build_urlServiceMenu(JMenu webService)
4601 // TODO: remove this code when 2.7 is released
4602 // DEBUG - alignmentView
4604 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4605 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4607 * @Override public void actionPerformed(ActionEvent e) {
4608 * jalview.datamodel.AlignmentView
4609 * .testSelectionViews(af.viewport.getAlignment(),
4610 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4612 * }); webService.add(testAlView);
4614 // TODO: refactor to RestClient discoverer and merge menu entries for
4615 // rest-style services with other types of analysis/calculation service
4616 // SHmmr test client - still being implemented.
4617 // DEBUG - alignmentView
4619 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4622 client.attachWSMenuEntry(
4623 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4629 * Searches the alignment sequences for xRefs and builds the Show
4630 * Cross-References menu (formerly called Show Products), with database
4631 * sources for which cross-references are found (protein sources for a
4632 * nucleotide alignment and vice versa)
4634 * @return true if Show Cross-references menu should be enabled
4636 public boolean canShowProducts()
4638 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4639 AlignmentI dataset = viewport.getAlignment().getDataset();
4641 showProducts.removeAll();
4642 final boolean dna = viewport.getAlignment().isNucleotide();
4644 if (seqs == null || seqs.length == 0)
4646 // nothing to see here.
4650 boolean showp = false;
4653 List<String> ptypes = new CrossRef(seqs, dataset)
4654 .findXrefSourcesForSequences(dna);
4656 for (final String source : ptypes)
4659 final AlignFrame af = this;
4660 JMenuItem xtype = new JMenuItem(source);
4661 xtype.addActionListener(new ActionListener()
4664 public void actionPerformed(ActionEvent e)
4666 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4669 showProducts.add(xtype);
4671 showProducts.setVisible(showp);
4672 showProducts.setEnabled(showp);
4673 } catch (Exception e)
4676 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4684 * Finds and displays cross-references for the selected sequences (protein
4685 * products for nucleotide sequences, dna coding sequences for peptides).
4688 * the sequences to show cross-references for
4690 * true if from a nucleotide alignment (so showing proteins)
4692 * the database to show cross-references for
4694 protected void showProductsFor(final SequenceI[] sel,
4695 final boolean _odna, final String source)
4697 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4702 * Construct and display a new frame containing the translation of this
4703 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4706 public void showTranslation_actionPerformed(ActionEvent e)
4708 AlignmentI al = null;
4711 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4713 al = dna.translateCdna();
4714 } catch (Exception ex)
4716 jalview.bin.Cache.log.error(
4717 "Exception during translation. Please report this !", ex);
4718 final String msg = MessageManager
4719 .getString("label.error_when_translating_sequences_submit_bug_report");
4720 final String errorTitle = MessageManager
4721 .getString("label.implementation_error")
4722 + MessageManager.getString("label.translation_failed");
4723 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4724 JOptionPane.ERROR_MESSAGE);
4727 if (al == null || al.getHeight() == 0)
4729 final String msg = MessageManager
4730 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4731 final String errorTitle = MessageManager
4732 .getString("label.translation_failed");
4733 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4734 JOptionPane.WARNING_MESSAGE);
4738 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4739 af.setFileFormat(this.currentFileFormat);
4740 final String newTitle = MessageManager.formatMessage(
4741 "label.translation_of_params",
4742 new Object[] { this.getTitle() });
4743 af.setTitle(newTitle);
4744 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4746 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4747 viewport.openSplitFrame(af, new Alignment(seqs));
4751 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4758 * Set the file format
4762 public void setFileFormat(String fileFormat)
4764 this.currentFileFormat = fileFormat;
4768 * Try to load a features file onto the alignment.
4771 * contents or path to retrieve file
4773 * access mode of file (see jalview.io.AlignFile)
4774 * @return true if features file was parsed correctly.
4776 public boolean parseFeaturesFile(String file, String type)
4778 return avc.parseFeaturesFile(file, type,
4779 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4784 public void refreshFeatureUI(boolean enableIfNecessary)
4786 // note - currently this is only still here rather than in the controller
4787 // because of the featureSettings hard reference that is yet to be
4789 if (enableIfNecessary)
4791 viewport.setShowSequenceFeatures(true);
4792 showSeqFeatures.setSelected(true);
4798 public void dragEnter(DropTargetDragEvent evt)
4803 public void dragExit(DropTargetEvent evt)
4808 public void dragOver(DropTargetDragEvent evt)
4813 public void dropActionChanged(DropTargetDragEvent evt)
4818 public void drop(DropTargetDropEvent evt)
4820 // JAL-1552 - acceptDrop required before getTransferable call for
4821 // Java's Transferable for native dnd
4822 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4823 Transferable t = evt.getTransferable();
4824 java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
4828 Desktop.transferFromDropTarget(files, protocols, evt, t);
4829 } catch (Exception e)
4831 e.printStackTrace();
4837 // check to see if any of these files have names matching sequences in
4839 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4840 .getAlignment().getSequencesArray());
4842 * Object[] { String,SequenceI}
4844 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4845 ArrayList<String> filesnotmatched = new ArrayList<String>();
4846 for (int i = 0; i < files.size(); i++)
4848 String file = files.get(i).toString();
4850 String protocol = FormatAdapter.checkProtocol(file);
4851 if (protocol == jalview.io.FormatAdapter.FILE)
4853 File fl = new File(file);
4854 pdbfn = fl.getName();
4856 else if (protocol == jalview.io.FormatAdapter.URL)
4858 URL url = new URL(file);
4859 pdbfn = url.getFile();
4861 if (pdbfn.length() > 0)
4863 // attempt to find a match in the alignment
4864 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4865 int l = 0, c = pdbfn.indexOf(".");
4866 while (mtch == null && c != -1)
4871 } while ((c = pdbfn.indexOf(".", l)) > l);
4874 pdbfn = pdbfn.substring(0, l);
4876 mtch = idm.findAllIdMatches(pdbfn);
4883 type = new IdentifyFile().identify(file, protocol);
4884 } catch (Exception ex)
4890 if (StructureFile.isStructureFile(type))
4892 filesmatched.add(new Object[] { file, protocol, mtch });
4897 // File wasn't named like one of the sequences or wasn't a PDB file.
4898 filesnotmatched.add(file);
4902 if (filesmatched.size() > 0)
4904 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4910 "label.automatically_associate_structure_files_with_sequences_same_name",
4911 new Object[] { Integer
4917 .getString("label.automatically_associate_structure_files_by_name"),
4918 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4921 for (Object[] fm : filesmatched)
4923 // try and associate
4924 // TODO: may want to set a standard ID naming formalism for
4925 // associating PDB files which have no IDs.
4926 for (SequenceI toassoc : (SequenceI[]) fm[2])
4928 PDBEntry pe = new AssociatePdbFileWithSeq()
4929 .associatePdbWithSeq((String) fm[0],
4930 (String) fm[1], toassoc, false,
4934 System.err.println("Associated file : "
4935 + ((String) fm[0]) + " with "
4936 + toassoc.getDisplayId(true));
4940 alignPanel.paintAlignment(true);
4944 if (filesnotmatched.size() > 0)
4947 && (Cache.getDefault(
4948 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4954 "label.ignore_unmatched_dropped_files_info",
4955 new Object[] { Integer
4962 .getString("label.ignore_unmatched_dropped_files"),
4963 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4967 for (String fn : filesnotmatched)
4969 loadJalviewDataFile(fn, null, null, null);
4973 } catch (Exception ex)
4975 ex.printStackTrace();
4981 * Attempt to load a "dropped" file or URL string: First by testing whether
4982 * it's an Annotation file, then a JNet file, and finally a features file. If
4983 * all are false then the user may have dropped an alignment file onto this
4987 * either a filename or a URL string.
4989 public void loadJalviewDataFile(String file, String protocol,
4990 String format, SequenceI assocSeq)
4994 if (protocol == null)
4996 protocol = FormatAdapter.checkProtocol(file);
4998 // if the file isn't identified, or not positively identified as some
4999 // other filetype (PFAM is default unidentified alignment file type) then
5000 // try to parse as annotation.
5001 boolean isAnnotation = (format == null || format
5002 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5003 .annotateAlignmentView(viewport, file, protocol) : false;
5007 // first see if its a T-COFFEE score file
5008 TCoffeeScoreFile tcf = null;
5011 tcf = new TCoffeeScoreFile(file, protocol);
5014 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5016 tcoffeeColour.setEnabled(true);
5017 tcoffeeColour.setSelected(true);
5018 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5019 isAnnotation = true;
5021 .setText(MessageManager
5022 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5026 // some problem - if no warning its probable that the ID matching
5027 // process didn't work
5031 tcf.getWarningMessage() == null ? MessageManager
5032 .getString("label.check_file_matches_sequence_ids_alignment")
5033 : tcf.getWarningMessage(),
5035 .getString("label.problem_reading_tcoffee_score_file"),
5036 JOptionPane.WARNING_MESSAGE);
5043 } catch (Exception x)
5046 .debug("Exception when processing data source as T-COFFEE score file",
5052 // try to see if its a JNet 'concise' style annotation file *before*
5054 // try to parse it as a features file
5057 format = new IdentifyFile().identify(file, protocol);
5059 if (format.equalsIgnoreCase("JnetFile"))
5061 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5063 new JnetAnnotationMaker();
5064 JnetAnnotationMaker.add_annotation(predictions,
5065 viewport.getAlignment(), 0, false);
5066 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5067 viewport.getAlignment().setSeqrep(repseq);
5068 ColumnSelection cs = new ColumnSelection();
5069 cs.hideInsertionsFor(repseq);
5070 viewport.setColumnSelection(cs);
5071 isAnnotation = true;
5073 else if (IdentifyFile.FeaturesFile.equals(format))
5075 if (parseFeaturesFile(file, protocol))
5077 alignPanel.paintAlignment(true);
5082 new FileLoader().LoadFile(viewport, file, protocol, format);
5089 alignPanel.adjustAnnotationHeight();
5090 viewport.updateSequenceIdColours();
5091 buildSortByAnnotationScoresMenu();
5092 alignPanel.paintAlignment(true);
5094 } catch (Exception ex)
5096 ex.printStackTrace();
5097 } catch (OutOfMemoryError oom)
5102 } catch (Exception x)
5107 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5108 : "using " + protocol + " from " + file)
5110 + (format != null ? "(parsing as '" + format
5111 + "' file)" : ""), oom, Desktop.desktop);
5116 * Method invoked by the ChangeListener on the tabbed pane, in other words
5117 * when a different tabbed pane is selected by the user or programmatically.
5120 public void tabSelectionChanged(int index)
5124 alignPanel = alignPanels.get(index);
5125 viewport = alignPanel.av;
5126 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5127 setMenusFromViewport(viewport);
5131 * If there is a frame linked to this one in a SplitPane, switch it to the
5132 * same view tab index. No infinite recursion of calls should happen, since
5133 * tabSelectionChanged() should not get invoked on setting the selected
5134 * index to an unchanged value. Guard against setting an invalid index
5135 * before the new view peer tab has been created.
5137 final AlignViewportI peer = viewport.getCodingComplement();
5140 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5141 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5143 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5149 * On right mouse click on view tab, prompt for and set new view name.
5152 public void tabbedPane_mousePressed(MouseEvent e)
5154 if (e.isPopupTrigger())
5156 String msg = MessageManager.getString("label.enter_view_name");
5157 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5158 JOptionPane.QUESTION_MESSAGE);
5162 viewport.viewName = reply;
5163 // TODO warn if reply is in getExistingViewNames()?
5164 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5169 public AlignViewport getCurrentView()
5175 * Open the dialog for regex description parsing.
5178 protected void extractScores_actionPerformed(ActionEvent e)
5180 ParseProperties pp = new jalview.analysis.ParseProperties(
5181 viewport.getAlignment());
5182 // TODO: verify regex and introduce GUI dialog for version 2.5
5183 // if (pp.getScoresFromDescription("col", "score column ",
5184 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5186 if (pp.getScoresFromDescription("description column",
5187 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5189 buildSortByAnnotationScoresMenu();
5197 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5201 protected void showDbRefs_actionPerformed(ActionEvent e)
5203 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5209 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5213 protected void showNpFeats_actionPerformed(ActionEvent e)
5215 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5219 * find the viewport amongst the tabs in this alignment frame and close that
5224 public boolean closeView(AlignViewportI av)
5228 this.closeMenuItem_actionPerformed(false);
5231 Component[] comp = tabbedPane.getComponents();
5232 for (int i = 0; comp != null && i < comp.length; i++)
5234 if (comp[i] instanceof AlignmentPanel)
5236 if (((AlignmentPanel) comp[i]).av == av)
5239 closeView((AlignmentPanel) comp[i]);
5247 protected void build_fetchdbmenu(JMenu webService)
5249 // Temporary hack - DBRef Fetcher always top level ws entry.
5250 // TODO We probably want to store a sequence database checklist in
5251 // preferences and have checkboxes.. rather than individual sources selected
5253 final JMenu rfetch = new JMenu(
5254 MessageManager.getString("action.fetch_db_references"));
5255 rfetch.setToolTipText(MessageManager
5256 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5257 webService.add(rfetch);
5259 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5260 MessageManager.getString("option.trim_retrieved_seqs"));
5261 trimrs.setToolTipText(MessageManager
5262 .getString("label.trim_retrieved_sequences"));
5263 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5264 trimrs.addActionListener(new ActionListener()
5267 public void actionPerformed(ActionEvent e)
5269 trimrs.setSelected(trimrs.isSelected());
5270 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5271 Boolean.valueOf(trimrs.isSelected()).toString());
5275 JMenuItem fetchr = new JMenuItem(
5276 MessageManager.getString("label.standard_databases"));
5277 fetchr.setToolTipText(MessageManager
5278 .getString("label.fetch_embl_uniprot"));
5279 fetchr.addActionListener(new ActionListener()
5283 public void actionPerformed(ActionEvent e)
5285 new Thread(new Runnable()
5290 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5291 .getAlignment().isNucleotide();
5292 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5293 .getSequenceSelection(), alignPanel.alignFrame, null,
5294 alignPanel.alignFrame.featureSettings, isNucleotide);
5295 dbRefFetcher.addListener(new FetchFinishedListenerI()
5298 public void finished()
5300 AlignFrame.this.setMenusForViewport();
5303 dbRefFetcher.fetchDBRefs(false);
5311 final AlignFrame me = this;
5312 new Thread(new Runnable()
5317 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5318 .getSequenceFetcherSingleton(me);
5319 javax.swing.SwingUtilities.invokeLater(new Runnable()
5324 String[] dbclasses = sf.getOrderedSupportedSources();
5325 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5326 // jalview.util.QuickSort.sort(otherdb, otherdb);
5327 List<DbSourceProxy> otherdb;
5328 JMenu dfetch = new JMenu();
5329 JMenu ifetch = new JMenu();
5330 JMenuItem fetchr = null;
5331 int comp = 0, icomp = 0, mcomp = 15;
5332 String mname = null;
5334 for (String dbclass : dbclasses)
5336 otherdb = sf.getSourceProxy(dbclass);
5337 // add a single entry for this class, or submenu allowing 'fetch
5339 if (otherdb == null || otherdb.size() < 1)
5343 // List<DbSourceProxy> dbs=otherdb;
5344 // otherdb=new ArrayList<DbSourceProxy>();
5345 // for (DbSourceProxy db:dbs)
5347 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5351 mname = "From " + dbclass;
5353 if (otherdb.size() == 1)
5355 final DbSourceProxy[] dassource = otherdb
5356 .toArray(new DbSourceProxy[0]);
5357 DbSourceProxy src = otherdb.get(0);
5358 fetchr = new JMenuItem(src.getDbSource());
5359 fetchr.addActionListener(new ActionListener()
5363 public void actionPerformed(ActionEvent e)
5365 new Thread(new Runnable()
5371 boolean isNucleotide = alignPanel.alignFrame
5372 .getViewport().getAlignment()
5374 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5375 alignPanel.av.getSequenceSelection(),
5376 alignPanel.alignFrame, dassource,
5377 alignPanel.alignFrame.featureSettings,
5380 .addListener(new FetchFinishedListenerI()
5383 public void finished()
5385 AlignFrame.this.setMenusForViewport();
5388 dbRefFetcher.fetchDBRefs(false);
5394 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5395 MessageManager.formatMessage(
5396 "label.fetch_retrieve_from",
5397 new Object[] { src.getDbName() })));
5403 final DbSourceProxy[] dassource = otherdb
5404 .toArray(new DbSourceProxy[0]);
5406 DbSourceProxy src = otherdb.get(0);
5407 fetchr = new JMenuItem(MessageManager.formatMessage(
5408 "label.fetch_all_param",
5409 new Object[] { src.getDbSource() }));
5410 fetchr.addActionListener(new ActionListener()
5413 public void actionPerformed(ActionEvent e)
5415 new Thread(new Runnable()
5421 boolean isNucleotide = alignPanel.alignFrame
5422 .getViewport().getAlignment()
5424 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5425 alignPanel.av.getSequenceSelection(),
5426 alignPanel.alignFrame, dassource,
5427 alignPanel.alignFrame.featureSettings,
5430 .addListener(new FetchFinishedListenerI()
5433 public void finished()
5435 AlignFrame.this.setMenusForViewport();
5438 dbRefFetcher.fetchDBRefs(false);
5444 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5445 MessageManager.formatMessage(
5446 "label.fetch_retrieve_from_all_sources",
5448 Integer.valueOf(otherdb.size())
5449 .toString(), src.getDbSource(),
5450 src.getDbName() })));
5453 // and then build the rest of the individual menus
5454 ifetch = new JMenu(MessageManager.formatMessage(
5455 "label.source_from_db_source",
5456 new Object[] { src.getDbSource() }));
5458 String imname = null;
5460 for (DbSourceProxy sproxy : otherdb)
5462 String dbname = sproxy.getDbName();
5463 String sname = dbname.length() > 5 ? dbname.substring(0,
5464 5) + "..." : dbname;
5465 String msname = dbname.length() > 10 ? dbname.substring(
5466 0, 10) + "..." : dbname;
5469 imname = MessageManager.formatMessage(
5470 "label.from_msname", new Object[] { sname });
5472 fetchr = new JMenuItem(msname);
5473 final DbSourceProxy[] dassrc = { sproxy };
5474 fetchr.addActionListener(new ActionListener()
5478 public void actionPerformed(ActionEvent e)
5480 new Thread(new Runnable()
5486 boolean isNucleotide = alignPanel.alignFrame
5487 .getViewport().getAlignment()
5489 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5490 alignPanel.av.getSequenceSelection(),
5491 alignPanel.alignFrame, dassrc,
5492 alignPanel.alignFrame.featureSettings,
5495 .addListener(new FetchFinishedListenerI()
5498 public void finished()
5500 AlignFrame.this.setMenusForViewport();
5503 dbRefFetcher.fetchDBRefs(false);
5509 fetchr.setToolTipText("<html>"
5510 + MessageManager.formatMessage(
5511 "label.fetch_retrieve_from", new Object[]
5515 if (++icomp >= mcomp || i == (otherdb.size()))
5517 ifetch.setText(MessageManager.formatMessage(
5518 "label.source_to_target", imname, sname));
5520 ifetch = new JMenu();
5528 if (comp >= mcomp || dbi >= (dbclasses.length))
5530 dfetch.setText(MessageManager.formatMessage(
5531 "label.source_to_target", mname, dbclass));
5533 dfetch = new JMenu();
5546 * Left justify the whole alignment.
5549 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5551 AlignmentI al = viewport.getAlignment();
5553 viewport.firePropertyChange("alignment", null, al);
5557 * Right justify the whole alignment.
5560 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5562 AlignmentI al = viewport.getAlignment();
5564 viewport.firePropertyChange("alignment", null, al);
5568 public void setShowSeqFeatures(boolean b)
5570 showSeqFeatures.setSelected(b);
5571 viewport.setShowSequenceFeatures(b);
5578 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5579 * awt.event.ActionEvent)
5582 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5584 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5585 alignPanel.paintAlignment(true);
5592 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5596 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5598 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5599 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5607 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5608 * .event.ActionEvent)
5611 protected void showGroupConservation_actionPerformed(ActionEvent e)
5613 viewport.setShowGroupConservation(showGroupConservation.getState());
5614 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5621 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5622 * .event.ActionEvent)
5625 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5627 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5628 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5635 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5636 * .event.ActionEvent)
5639 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5641 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5642 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5646 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5648 showSequenceLogo.setState(true);
5649 viewport.setShowSequenceLogo(true);
5650 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5651 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5655 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5657 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5664 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5665 * .event.ActionEvent)
5668 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5670 if (avc.makeGroupsFromSelection())
5672 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5673 alignPanel.updateAnnotation();
5674 alignPanel.paintAlignment(true);
5678 public void clearAlignmentSeqRep()
5680 // TODO refactor alignmentseqrep to controller
5681 if (viewport.getAlignment().hasSeqrep())
5683 viewport.getAlignment().setSeqrep(null);
5684 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5685 alignPanel.updateAnnotation();
5686 alignPanel.paintAlignment(true);
5691 protected void createGroup_actionPerformed(ActionEvent e)
5693 if (avc.createGroup())
5695 alignPanel.alignmentChanged();
5700 protected void unGroup_actionPerformed(ActionEvent e)
5704 alignPanel.alignmentChanged();
5709 * make the given alignmentPanel the currently selected tab
5711 * @param alignmentPanel
5713 public void setDisplayedView(AlignmentPanel alignmentPanel)
5715 if (!viewport.getSequenceSetId().equals(
5716 alignmentPanel.av.getSequenceSetId()))
5720 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5722 if (tabbedPane != null
5723 && tabbedPane.getTabCount() > 0
5724 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5725 .getSelectedIndex())
5727 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5732 * Action on selection of menu options to Show or Hide annotations.
5735 * @param forSequences
5736 * update sequence-related annotations
5737 * @param forAlignment
5738 * update non-sequence-related annotations
5741 protected void setAnnotationsVisibility(boolean visible,
5742 boolean forSequences, boolean forAlignment)
5744 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5745 .getAlignmentAnnotation();
5750 for (AlignmentAnnotation aa : anns)
5753 * don't display non-positional annotations on an alignment
5755 if (aa.annotations == null)
5759 boolean apply = (aa.sequenceRef == null && forAlignment)
5760 || (aa.sequenceRef != null && forSequences);
5763 aa.visible = visible;
5766 alignPanel.validateAnnotationDimensions(true);
5767 alignPanel.alignmentChanged();
5771 * Store selected annotation sort order for the view and repaint.
5774 protected void sortAnnotations_actionPerformed()
5776 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5778 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5779 alignPanel.paintAlignment(true);
5784 * @return alignment panels in this alignment frame
5786 public List<? extends AlignmentViewPanel> getAlignPanels()
5788 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5792 * Open a new alignment window, with the cDNA associated with this (protein)
5793 * alignment, aligned as is the protein.
5795 protected void viewAsCdna_actionPerformed()
5797 // TODO no longer a menu action - refactor as required
5798 final AlignmentI alignment = getViewport().getAlignment();
5799 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5800 if (mappings == null)
5804 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5805 for (SequenceI aaSeq : alignment.getSequences())
5807 for (AlignedCodonFrame acf : mappings)
5809 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5813 * There is a cDNA mapping for this protein sequence - add to new
5814 * alignment. It will share the same dataset sequence as other mapped
5815 * cDNA (no new mappings need to be created).
5817 final Sequence newSeq = new Sequence(dnaSeq);
5818 newSeq.setDatasetSequence(dnaSeq);
5819 cdnaSeqs.add(newSeq);
5823 if (cdnaSeqs.size() == 0)
5825 // show a warning dialog no mapped cDNA
5828 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5830 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5831 AlignFrame.DEFAULT_HEIGHT);
5832 cdna.alignAs(alignment);
5833 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5835 Desktop.addInternalFrame(alignFrame, newtitle,
5836 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5840 * Set visibility of dna/protein complement view (available when shown in a
5846 protected void showComplement_actionPerformed(boolean show)
5848 SplitContainerI sf = getSplitViewContainer();
5851 sf.setComplementVisible(this, show);
5856 * Generate the reverse (optionally complemented) of the selected sequences,
5857 * and add them to the alignment
5860 protected void showReverse_actionPerformed(boolean complement)
5862 AlignmentI al = null;
5865 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5866 al = dna.reverseCdna(complement);
5867 viewport.addAlignment(al, "");
5868 addHistoryItem(new EditCommand(
5869 MessageManager.getString("label.add_sequences"),
5870 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5871 viewport.getAlignment()));
5872 } catch (Exception ex)
5874 System.err.println(ex.getMessage());
5880 * Try to run a script in the Groovy console, having first ensured that this
5881 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5882 * be targeted at this alignment.
5885 protected void runGroovy_actionPerformed()
5887 Jalview.setCurrentAlignFrame(this);
5888 groovy.ui.Console console = Desktop.getGroovyConsole();
5889 if (console != null)
5893 console.runScript();
5894 } catch (Exception ex)
5896 System.err.println((ex.toString()));
5898 .showInternalMessageDialog(Desktop.desktop, MessageManager
5899 .getString("label.couldnt_run_groovy_script"),
5901 .getString("label.groovy_support_failed"),
5902 JOptionPane.ERROR_MESSAGE);
5907 System.err.println("Can't run Groovy script as console not found");
5912 * Hides columns containing (or not containing) a specified feature, provided
5913 * that would not leave all columns hidden
5915 * @param featureType
5916 * @param columnsContaining
5919 public boolean hideFeatureColumns(String featureType,
5920 boolean columnsContaining)
5922 boolean notForHiding = avc.markColumnsContainingFeatures(
5923 columnsContaining, false, false, featureType);
5926 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5927 false, featureType))
5929 getViewport().hideSelectedColumns();
5937 class PrintThread extends Thread
5941 public PrintThread(AlignmentPanel ap)
5946 static PageFormat pf;
5951 PrinterJob printJob = PrinterJob.getPrinterJob();
5955 printJob.setPrintable(ap, pf);
5959 printJob.setPrintable(ap);
5962 if (printJob.printDialog())
5967 } catch (Exception PrintException)
5969 PrintException.printStackTrace();