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 new HtmlSvgOutput(null, alignPanel);
1348 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1350 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1351 bjs.exportJalviewAlignmentAsBioJsHtmlFile(null);
1354 public void createImageMap(File file, String image)
1356 alignPanel.makePNGImageMap(file, image);
1366 public void createPNG(File f)
1368 alignPanel.makePNG(f);
1378 public void createEPS(File f)
1380 alignPanel.makeEPS(f);
1384 public void createSVG(File f)
1386 alignPanel.makeSVG(f);
1390 public void pageSetup_actionPerformed(ActionEvent e)
1392 PrinterJob printJob = PrinterJob.getPrinterJob();
1393 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1403 public void printMenuItem_actionPerformed(ActionEvent e)
1405 // Putting in a thread avoids Swing painting problems
1406 PrintThread thread = new PrintThread(alignPanel);
1411 public void exportFeatures_actionPerformed(ActionEvent e)
1413 new AnnotationExporter().exportFeatures(alignPanel);
1417 public void exportAnnotations_actionPerformed(ActionEvent e)
1419 new AnnotationExporter().exportAnnotations(alignPanel);
1423 public void associatedData_actionPerformed(ActionEvent e)
1425 // Pick the tree file
1426 JalviewFileChooser chooser = new JalviewFileChooser(
1427 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1428 chooser.setFileView(new JalviewFileView());
1429 chooser.setDialogTitle(MessageManager
1430 .getString("label.load_jalview_annotations"));
1431 chooser.setToolTipText(MessageManager
1432 .getString("label.load_jalview_annotations"));
1434 int value = chooser.showOpenDialog(null);
1436 if (value == JalviewFileChooser.APPROVE_OPTION)
1438 String choice = chooser.getSelectedFile().getPath();
1439 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1440 loadJalviewDataFile(choice, null, null, null);
1446 * Close the current view or all views in the alignment frame. If the frame
1447 * only contains one view then the alignment will be removed from memory.
1449 * @param closeAllTabs
1452 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1454 if (alignPanels != null && alignPanels.size() < 2)
1456 closeAllTabs = true;
1461 if (alignPanels != null)
1465 if (this.isClosed())
1467 // really close all the windows - otherwise wait till
1468 // setClosed(true) is called
1469 for (int i = 0; i < alignPanels.size(); i++)
1471 AlignmentPanel ap = alignPanels.get(i);
1478 closeView(alignPanel);
1485 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1486 * be called recursively, with the frame now in 'closed' state
1488 this.setClosed(true);
1490 } catch (Exception ex)
1492 ex.printStackTrace();
1497 * Close the specified panel and close up tabs appropriately.
1499 * @param panelToClose
1501 public void closeView(AlignmentPanel panelToClose)
1503 int index = tabbedPane.getSelectedIndex();
1504 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1505 alignPanels.remove(panelToClose);
1506 panelToClose.closePanel();
1507 panelToClose = null;
1509 tabbedPane.removeTabAt(closedindex);
1510 tabbedPane.validate();
1512 if (index > closedindex || index == tabbedPane.getTabCount())
1514 // modify currently selected tab index if necessary.
1518 this.tabSelectionChanged(index);
1524 void updateEditMenuBar()
1527 if (viewport.getHistoryList().size() > 0)
1529 undoMenuItem.setEnabled(true);
1530 CommandI command = viewport.getHistoryList().peek();
1531 undoMenuItem.setText(MessageManager.formatMessage(
1532 "label.undo_command",
1533 new Object[] { command.getDescription() }));
1537 undoMenuItem.setEnabled(false);
1538 undoMenuItem.setText(MessageManager.getString("action.undo"));
1541 if (viewport.getRedoList().size() > 0)
1543 redoMenuItem.setEnabled(true);
1545 CommandI command = viewport.getRedoList().peek();
1546 redoMenuItem.setText(MessageManager.formatMessage(
1547 "label.redo_command",
1548 new Object[] { command.getDescription() }));
1552 redoMenuItem.setEnabled(false);
1553 redoMenuItem.setText(MessageManager.getString("action.redo"));
1558 public void addHistoryItem(CommandI command)
1560 if (command.getSize() > 0)
1562 viewport.addToHistoryList(command);
1563 viewport.clearRedoList();
1564 updateEditMenuBar();
1565 viewport.updateHiddenColumns();
1566 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1567 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1568 // viewport.getColumnSelection()
1569 // .getHiddenColumns().size() > 0);
1575 * @return alignment objects for all views
1577 AlignmentI[] getViewAlignments()
1579 if (alignPanels != null)
1581 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1583 for (AlignmentPanel ap : alignPanels)
1585 als[i++] = ap.av.getAlignment();
1589 if (viewport != null)
1591 return new AlignmentI[] { viewport.getAlignment() };
1603 protected void undoMenuItem_actionPerformed(ActionEvent e)
1605 if (viewport.getHistoryList().isEmpty())
1609 CommandI command = viewport.getHistoryList().pop();
1610 viewport.addToRedoList(command);
1611 command.undoCommand(getViewAlignments());
1613 AlignmentViewport originalSource = getOriginatingSource(command);
1614 updateEditMenuBar();
1616 if (originalSource != null)
1618 if (originalSource != viewport)
1621 .warn("Implementation worry: mismatch of viewport origin for undo");
1623 originalSource.updateHiddenColumns();
1624 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1626 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1627 // viewport.getColumnSelection()
1628 // .getHiddenColumns().size() > 0);
1629 originalSource.firePropertyChange("alignment", null, originalSource
1630 .getAlignment().getSequences());
1641 protected void redoMenuItem_actionPerformed(ActionEvent e)
1643 if (viewport.getRedoList().size() < 1)
1648 CommandI command = viewport.getRedoList().pop();
1649 viewport.addToHistoryList(command);
1650 command.doCommand(getViewAlignments());
1652 AlignmentViewport originalSource = getOriginatingSource(command);
1653 updateEditMenuBar();
1655 if (originalSource != null)
1658 if (originalSource != viewport)
1661 .warn("Implementation worry: mismatch of viewport origin for redo");
1663 originalSource.updateHiddenColumns();
1664 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1666 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1667 // viewport.getColumnSelection()
1668 // .getHiddenColumns().size() > 0);
1669 originalSource.firePropertyChange("alignment", null, originalSource
1670 .getAlignment().getSequences());
1674 AlignmentViewport getOriginatingSource(CommandI command)
1676 AlignmentViewport originalSource = null;
1677 // For sequence removal and addition, we need to fire
1678 // the property change event FROM the viewport where the
1679 // original alignment was altered
1680 AlignmentI al = null;
1681 if (command instanceof EditCommand)
1683 EditCommand editCommand = (EditCommand) command;
1684 al = editCommand.getAlignment();
1685 List<Component> comps = PaintRefresher.components.get(viewport
1686 .getSequenceSetId());
1688 for (Component comp : comps)
1690 if (comp instanceof AlignmentPanel)
1692 if (al == ((AlignmentPanel) comp).av.getAlignment())
1694 originalSource = ((AlignmentPanel) comp).av;
1701 if (originalSource == null)
1703 // The original view is closed, we must validate
1704 // the current view against the closed view first
1707 PaintRefresher.validateSequences(al, viewport.getAlignment());
1710 originalSource = viewport;
1713 return originalSource;
1722 public void moveSelectedSequences(boolean up)
1724 SequenceGroup sg = viewport.getSelectionGroup();
1730 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1731 viewport.getHiddenRepSequences(), up);
1732 alignPanel.paintAlignment(true);
1735 synchronized void slideSequences(boolean right, int size)
1737 List<SequenceI> sg = new ArrayList<SequenceI>();
1738 if (viewport.cursorMode)
1740 sg.add(viewport.getAlignment().getSequenceAt(
1741 alignPanel.getSeqPanel().seqCanvas.cursorY));
1743 else if (viewport.getSelectionGroup() != null
1744 && viewport.getSelectionGroup().getSize() != viewport
1745 .getAlignment().getHeight())
1747 sg = viewport.getSelectionGroup().getSequences(
1748 viewport.getHiddenRepSequences());
1756 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1758 for (SequenceI seq : viewport.getAlignment().getSequences())
1760 if (!sg.contains(seq))
1762 invertGroup.add(seq);
1766 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1768 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1769 for (int i = 0; i < invertGroup.size(); i++)
1771 seqs2[i] = invertGroup.get(i);
1774 SlideSequencesCommand ssc;
1777 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1778 size, viewport.getGapCharacter());
1782 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1783 size, viewport.getGapCharacter());
1786 int groupAdjustment = 0;
1787 if (ssc.getGapsInsertedBegin() && right)
1789 if (viewport.cursorMode)
1791 alignPanel.getSeqPanel().moveCursor(size, 0);
1795 groupAdjustment = size;
1798 else if (!ssc.getGapsInsertedBegin() && !right)
1800 if (viewport.cursorMode)
1802 alignPanel.getSeqPanel().moveCursor(-size, 0);
1806 groupAdjustment = -size;
1810 if (groupAdjustment != 0)
1812 viewport.getSelectionGroup().setStartRes(
1813 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1814 viewport.getSelectionGroup().setEndRes(
1815 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1819 * just extend the last slide command if compatible; but not if in
1820 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1822 boolean appendHistoryItem = false;
1823 Deque<CommandI> historyList = viewport.getHistoryList();
1824 boolean inSplitFrame = getSplitViewContainer() != null;
1825 if (!inSplitFrame && historyList != null && historyList.size() > 0
1826 && historyList.peek() instanceof SlideSequencesCommand)
1828 appendHistoryItem = ssc
1829 .appendSlideCommand((SlideSequencesCommand) historyList
1833 if (!appendHistoryItem)
1835 addHistoryItem(ssc);
1848 protected void copy_actionPerformed(ActionEvent e)
1851 if (viewport.getSelectionGroup() == null)
1855 // TODO: preserve the ordering of displayed alignment annotation in any
1856 // internal paste (particularly sequence associated annotation)
1857 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1858 String[] omitHidden = null;
1860 if (viewport.hasHiddenColumns())
1862 omitHidden = viewport.getViewAsString(true);
1865 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1868 StringSelection ss = new StringSelection(output);
1872 jalview.gui.Desktop.internalCopy = true;
1873 // Its really worth setting the clipboard contents
1874 // to empty before setting the large StringSelection!!
1875 Toolkit.getDefaultToolkit().getSystemClipboard()
1876 .setContents(new StringSelection(""), null);
1878 Toolkit.getDefaultToolkit().getSystemClipboard()
1879 .setContents(ss, Desktop.instance);
1880 } catch (OutOfMemoryError er)
1882 new OOMWarning("copying region", er);
1886 ArrayList<int[]> hiddenColumns = null;
1887 if (viewport.hasHiddenColumns())
1889 hiddenColumns = new ArrayList<int[]>();
1890 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1891 .getSelectionGroup().getEndRes();
1892 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1894 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1896 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1897 region[1] - hiddenOffset });
1902 Desktop.jalviewClipboard = new Object[] { seqs,
1903 viewport.getAlignment().getDataset(), hiddenColumns };
1904 statusBar.setText(MessageManager.formatMessage(
1905 "label.copied_sequences_to_clipboard", new Object[] { Integer
1906 .valueOf(seqs.length).toString() }));
1916 protected void pasteNew_actionPerformed(ActionEvent e)
1928 protected void pasteThis_actionPerformed(ActionEvent e)
1934 * Paste contents of Jalview clipboard
1936 * @param newAlignment
1937 * true to paste to a new alignment, otherwise add to this.
1939 void paste(boolean newAlignment)
1941 boolean externalPaste = true;
1944 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1945 Transferable contents = c.getContents(this);
1947 if (contents == null)
1955 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1956 if (str.length() < 1)
1961 format = new IdentifyFile().identify(str, "Paste");
1963 } catch (OutOfMemoryError er)
1965 new OOMWarning("Out of memory pasting sequences!!", er);
1969 SequenceI[] sequences;
1970 boolean annotationAdded = false;
1971 AlignmentI alignment = null;
1973 if (Desktop.jalviewClipboard != null)
1975 // The clipboard was filled from within Jalview, we must use the
1977 // And dataset from the copied alignment
1978 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1979 // be doubly sure that we create *new* sequence objects.
1980 sequences = new SequenceI[newseq.length];
1981 for (int i = 0; i < newseq.length; i++)
1983 sequences[i] = new Sequence(newseq[i]);
1985 alignment = new Alignment(sequences);
1986 externalPaste = false;
1990 // parse the clipboard as an alignment.
1991 alignment = new FormatAdapter().readFile(str, "Paste", format);
1992 sequences = alignment.getSequencesArray();
1996 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2002 if (Desktop.jalviewClipboard != null)
2004 // dataset is inherited
2005 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2009 // new dataset is constructed
2010 alignment.setDataset(null);
2012 alwidth = alignment.getWidth() + 1;
2016 AlignmentI pastedal = alignment; // preserve pasted alignment object
2017 // Add pasted sequences and dataset into existing alignment.
2018 alignment = viewport.getAlignment();
2019 alwidth = alignment.getWidth() + 1;
2020 // decide if we need to import sequences from an existing dataset
2021 boolean importDs = Desktop.jalviewClipboard != null
2022 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2023 // importDs==true instructs us to copy over new dataset sequences from
2024 // an existing alignment
2025 Vector newDs = (importDs) ? new Vector() : null; // used to create
2026 // minimum dataset set
2028 for (int i = 0; i < sequences.length; i++)
2032 newDs.addElement(null);
2034 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2036 if (importDs && ds != null)
2038 if (!newDs.contains(ds))
2040 newDs.setElementAt(ds, i);
2041 ds = new Sequence(ds);
2042 // update with new dataset sequence
2043 sequences[i].setDatasetSequence(ds);
2047 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2052 // copy and derive new dataset sequence
2053 sequences[i] = sequences[i].deriveSequence();
2054 alignment.getDataset().addSequence(
2055 sequences[i].getDatasetSequence());
2056 // TODO: avoid creation of duplicate dataset sequences with a
2057 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2059 alignment.addSequence(sequences[i]); // merges dataset
2063 newDs.clear(); // tidy up
2065 if (alignment.getAlignmentAnnotation() != null)
2067 for (AlignmentAnnotation alan : alignment
2068 .getAlignmentAnnotation())
2070 if (alan.graphGroup > fgroup)
2072 fgroup = alan.graphGroup;
2076 if (pastedal.getAlignmentAnnotation() != null)
2078 // Add any annotation attached to alignment.
2079 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2080 for (int i = 0; i < alann.length; i++)
2082 annotationAdded = true;
2083 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2085 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2086 if (newann.graphGroup > -1)
2088 if (newGraphGroups.size() <= newann.graphGroup
2089 || newGraphGroups.get(newann.graphGroup) == null)
2091 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2093 newGraphGroups.add(q, null);
2095 newGraphGroups.set(newann.graphGroup, new Integer(
2098 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2102 newann.padAnnotation(alwidth);
2103 alignment.addAnnotation(newann);
2113 addHistoryItem(new EditCommand(
2114 MessageManager.getString("label.add_sequences"),
2115 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2117 // Add any annotations attached to sequences
2118 for (int i = 0; i < sequences.length; i++)
2120 if (sequences[i].getAnnotation() != null)
2122 AlignmentAnnotation newann;
2123 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2125 annotationAdded = true;
2126 newann = sequences[i].getAnnotation()[a];
2127 newann.adjustForAlignment();
2128 newann.padAnnotation(alwidth);
2129 if (newann.graphGroup > -1)
2131 if (newann.graphGroup > -1)
2133 if (newGraphGroups.size() <= newann.graphGroup
2134 || newGraphGroups.get(newann.graphGroup) == null)
2136 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2138 newGraphGroups.add(q, null);
2140 newGraphGroups.set(newann.graphGroup, new Integer(
2143 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2147 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2152 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2159 // propagate alignment changed.
2160 viewport.setEndSeq(alignment.getHeight());
2161 if (annotationAdded)
2163 // Duplicate sequence annotation in all views.
2164 AlignmentI[] alview = this.getViewAlignments();
2165 for (int i = 0; i < sequences.length; i++)
2167 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2172 for (int avnum = 0; avnum < alview.length; avnum++)
2174 if (alview[avnum] != alignment)
2176 // duplicate in a view other than the one with input focus
2177 int avwidth = alview[avnum].getWidth() + 1;
2178 // this relies on sann being preserved after we
2179 // modify the sequence's annotation array for each duplication
2180 for (int a = 0; a < sann.length; a++)
2182 AlignmentAnnotation newann = new AlignmentAnnotation(
2184 sequences[i].addAlignmentAnnotation(newann);
2185 newann.padAnnotation(avwidth);
2186 alview[avnum].addAnnotation(newann); // annotation was
2187 // duplicated earlier
2188 // TODO JAL-1145 graphGroups are not updated for sequence
2189 // annotation added to several views. This may cause
2191 alview[avnum].setAnnotationIndex(newann, a);
2196 buildSortByAnnotationScoresMenu();
2198 viewport.firePropertyChange("alignment", null,
2199 alignment.getSequences());
2200 if (alignPanels != null)
2202 for (AlignmentPanel ap : alignPanels)
2204 ap.validateAnnotationDimensions(false);
2209 alignPanel.validateAnnotationDimensions(false);
2215 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2217 String newtitle = new String("Copied sequences");
2219 if (Desktop.jalviewClipboard != null
2220 && Desktop.jalviewClipboard[2] != null)
2222 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2223 for (int[] region : hc)
2225 af.viewport.hideColumns(region[0], region[1]);
2229 // >>>This is a fix for the moment, until a better solution is
2231 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2233 alignPanel.getSeqPanel().seqCanvas
2234 .getFeatureRenderer());
2236 // TODO: maintain provenance of an alignment, rather than just make the
2237 // title a concatenation of operations.
2240 if (title.startsWith("Copied sequences"))
2246 newtitle = newtitle.concat("- from " + title);
2251 newtitle = new String("Pasted sequences");
2254 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2259 } catch (Exception ex)
2261 ex.printStackTrace();
2262 System.out.println("Exception whilst pasting: " + ex);
2263 // could be anything being pasted in here
2269 protected void expand_newalign(ActionEvent e)
2273 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2274 .getAlignment(), -1);
2275 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2277 String newtitle = new String("Flanking alignment");
2279 if (Desktop.jalviewClipboard != null
2280 && Desktop.jalviewClipboard[2] != null)
2282 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2283 for (int region[] : hc)
2285 af.viewport.hideColumns(region[0], region[1]);
2289 // >>>This is a fix for the moment, until a better solution is
2291 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2293 alignPanel.getSeqPanel().seqCanvas
2294 .getFeatureRenderer());
2296 // TODO: maintain provenance of an alignment, rather than just make the
2297 // title a concatenation of operations.
2299 if (title.startsWith("Copied sequences"))
2305 newtitle = newtitle.concat("- from " + title);
2309 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2311 } catch (Exception ex)
2313 ex.printStackTrace();
2314 System.out.println("Exception whilst pasting: " + ex);
2315 // could be anything being pasted in here
2316 } catch (OutOfMemoryError oom)
2318 new OOMWarning("Viewing flanking region of alignment", oom);
2329 protected void cut_actionPerformed(ActionEvent e)
2331 copy_actionPerformed(null);
2332 delete_actionPerformed(null);
2342 protected void delete_actionPerformed(ActionEvent evt)
2345 SequenceGroup sg = viewport.getSelectionGroup();
2352 * If the cut affects all sequences, warn, remove highlighted columns
2354 if (sg.getSize() == viewport.getAlignment().getHeight())
2356 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2357 .getAlignment().getWidth()) ? true : false;
2358 if (isEntireAlignWidth)
2360 int confirm = JOptionPane.showConfirmDialog(this,
2361 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2362 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2363 JOptionPane.OK_CANCEL_OPTION);
2365 if (confirm == JOptionPane.CANCEL_OPTION
2366 || confirm == JOptionPane.CLOSED_OPTION)
2371 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2372 sg.getEndRes() + 1);
2374 SequenceI[] cut = sg.getSequences()
2375 .toArray(new SequenceI[sg.getSize()]);
2377 addHistoryItem(new EditCommand(
2378 MessageManager.getString("label.cut_sequences"), Action.CUT,
2379 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2380 viewport.getAlignment()));
2382 viewport.setSelectionGroup(null);
2383 viewport.sendSelection();
2384 viewport.getAlignment().deleteGroup(sg);
2386 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2388 if (viewport.getAlignment().getHeight() < 1)
2392 this.setClosed(true);
2393 } catch (Exception ex)
2406 protected void deleteGroups_actionPerformed(ActionEvent e)
2408 if (avc.deleteGroups())
2410 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2411 alignPanel.updateAnnotation();
2412 alignPanel.paintAlignment(true);
2423 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2425 SequenceGroup sg = new SequenceGroup();
2427 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2429 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2432 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2433 viewport.setSelectionGroup(sg);
2434 viewport.sendSelection();
2435 // JAL-2034 - should delegate to
2436 // alignPanel to decide if overview needs
2438 alignPanel.paintAlignment(false);
2439 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2449 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2451 if (viewport.cursorMode)
2453 alignPanel.getSeqPanel().keyboardNo1 = null;
2454 alignPanel.getSeqPanel().keyboardNo2 = null;
2456 viewport.setSelectionGroup(null);
2457 viewport.getColumnSelection().clear();
2458 viewport.setSelectionGroup(null);
2459 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2460 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2461 // JAL-2034 - should delegate to
2462 // alignPanel to decide if overview needs
2464 alignPanel.paintAlignment(false);
2465 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2466 viewport.sendSelection();
2476 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2478 SequenceGroup sg = viewport.getSelectionGroup();
2482 selectAllSequenceMenuItem_actionPerformed(null);
2487 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2489 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2491 // JAL-2034 - should delegate to
2492 // alignPanel to decide if overview needs
2495 alignPanel.paintAlignment(true);
2496 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2497 viewport.sendSelection();
2501 public void invertColSel_actionPerformed(ActionEvent e)
2503 viewport.invertColumnSelection();
2504 alignPanel.paintAlignment(true);
2505 viewport.sendSelection();
2515 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2517 trimAlignment(true);
2527 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2529 trimAlignment(false);
2532 void trimAlignment(boolean trimLeft)
2534 ColumnSelection colSel = viewport.getColumnSelection();
2537 if (!colSel.isEmpty())
2541 column = colSel.getMin();
2545 column = colSel.getMax();
2549 if (viewport.getSelectionGroup() != null)
2551 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2552 viewport.getHiddenRepSequences());
2556 seqs = viewport.getAlignment().getSequencesArray();
2559 TrimRegionCommand trimRegion;
2562 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2563 column, viewport.getAlignment());
2564 viewport.setStartRes(0);
2568 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2569 column, viewport.getAlignment());
2572 statusBar.setText(MessageManager.formatMessage(
2573 "label.removed_columns",
2574 new String[] { Integer.valueOf(trimRegion.getSize())
2577 addHistoryItem(trimRegion);
2579 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2581 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2582 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2584 viewport.getAlignment().deleteGroup(sg);
2588 viewport.firePropertyChange("alignment", null, viewport
2589 .getAlignment().getSequences());
2600 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2602 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2605 if (viewport.getSelectionGroup() != null)
2607 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2608 viewport.getHiddenRepSequences());
2609 start = viewport.getSelectionGroup().getStartRes();
2610 end = viewport.getSelectionGroup().getEndRes();
2614 seqs = viewport.getAlignment().getSequencesArray();
2617 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2618 "Remove Gapped Columns", seqs, start, end,
2619 viewport.getAlignment());
2621 addHistoryItem(removeGapCols);
2623 statusBar.setText(MessageManager.formatMessage(
2624 "label.removed_empty_columns",
2625 new Object[] { Integer.valueOf(removeGapCols.getSize())
2628 // This is to maintain viewport position on first residue
2629 // of first sequence
2630 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2631 int startRes = seq.findPosition(viewport.startRes);
2632 // ShiftList shifts;
2633 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2634 // edit.alColumnChanges=shifts.getInverse();
2635 // if (viewport.hasHiddenColumns)
2636 // viewport.getColumnSelection().compensateForEdits(shifts);
2637 viewport.setStartRes(seq.findIndex(startRes) - 1);
2638 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2650 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2652 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2655 if (viewport.getSelectionGroup() != null)
2657 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2658 viewport.getHiddenRepSequences());
2659 start = viewport.getSelectionGroup().getStartRes();
2660 end = viewport.getSelectionGroup().getEndRes();
2664 seqs = viewport.getAlignment().getSequencesArray();
2667 // This is to maintain viewport position on first residue
2668 // of first sequence
2669 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2670 int startRes = seq.findPosition(viewport.startRes);
2672 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2673 viewport.getAlignment()));
2675 viewport.setStartRes(seq.findIndex(startRes) - 1);
2677 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2689 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2691 viewport.setPadGaps(padGapsMenuitem.isSelected());
2692 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2703 public void findMenuItem_actionPerformed(ActionEvent e)
2709 * Create a new view of the current alignment.
2712 public void newView_actionPerformed(ActionEvent e)
2714 newView(null, true);
2718 * Creates and shows a new view of the current alignment.
2721 * title of newly created view; if null, one will be generated
2722 * @param copyAnnotation
2723 * if true then duplicate all annnotation, groups and settings
2724 * @return new alignment panel, already displayed.
2726 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2729 * Create a new AlignmentPanel (with its own, new Viewport)
2731 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2733 if (!copyAnnotation)
2736 * remove all groups and annotation except for the automatic stuff
2738 newap.av.getAlignment().deleteAllGroups();
2739 newap.av.getAlignment().deleteAllAnnotations(false);
2742 newap.av.setGatherViewsHere(false);
2744 if (viewport.viewName == null)
2746 viewport.viewName = MessageManager
2747 .getString("label.view_name_original");
2751 * Views share the same edits undo and redo stacks
2753 newap.av.setHistoryList(viewport.getHistoryList());
2754 newap.av.setRedoList(viewport.getRedoList());
2757 * Views share the same mappings; need to deregister any new mappings
2758 * created by copyAlignPanel, and register the new reference to the shared
2761 newap.av.replaceMappings(viewport.getAlignment());
2763 newap.av.viewName = getNewViewName(viewTitle);
2765 addAlignmentPanel(newap, true);
2766 newap.alignmentChanged();
2768 if (alignPanels.size() == 2)
2770 viewport.setGatherViewsHere(true);
2772 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2777 * Make a new name for the view, ensuring it is unique within the current
2778 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2779 * these now use viewId. Unique view names are still desirable for usability.)
2784 protected String getNewViewName(String viewTitle)
2786 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2787 boolean addFirstIndex = false;
2788 if (viewTitle == null || viewTitle.trim().length() == 0)
2790 viewTitle = MessageManager.getString("action.view");
2791 addFirstIndex = true;
2795 index = 1;// we count from 1 if given a specific name
2797 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2799 List<Component> comps = PaintRefresher.components.get(viewport
2800 .getSequenceSetId());
2802 List<String> existingNames = getExistingViewNames(comps);
2804 while (existingNames.contains(newViewName))
2806 newViewName = viewTitle + " " + (++index);
2812 * Returns a list of distinct view names found in the given list of
2813 * components. View names are held on the viewport of an AlignmentPanel.
2818 protected List<String> getExistingViewNames(List<Component> comps)
2820 List<String> existingNames = new ArrayList<String>();
2821 for (Component comp : comps)
2823 if (comp instanceof AlignmentPanel)
2825 AlignmentPanel ap = (AlignmentPanel) comp;
2826 if (!existingNames.contains(ap.av.viewName))
2828 existingNames.add(ap.av.viewName);
2832 return existingNames;
2836 * Explode tabbed views into separate windows.
2839 public void expandViews_actionPerformed(ActionEvent e)
2841 Desktop.explodeViews(this);
2845 * Gather views in separate windows back into a tabbed presentation.
2848 public void gatherViews_actionPerformed(ActionEvent e)
2850 Desktop.instance.gatherViews(this);
2860 public void font_actionPerformed(ActionEvent e)
2862 new FontChooser(alignPanel);
2872 protected void seqLimit_actionPerformed(ActionEvent e)
2874 viewport.setShowJVSuffix(seqLimits.isSelected());
2876 alignPanel.getIdPanel().getIdCanvas()
2877 .setPreferredSize(alignPanel.calculateIdWidth());
2878 alignPanel.paintAlignment(true);
2882 public void idRightAlign_actionPerformed(ActionEvent e)
2884 viewport.setRightAlignIds(idRightAlign.isSelected());
2885 alignPanel.paintAlignment(true);
2889 public void centreColumnLabels_actionPerformed(ActionEvent e)
2891 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2892 alignPanel.paintAlignment(true);
2898 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2901 protected void followHighlight_actionPerformed()
2904 * Set the 'follow' flag on the Viewport (and scroll to position if now
2907 final boolean state = this.followHighlightMenuItem.getState();
2908 viewport.setFollowHighlight(state);
2911 alignPanel.scrollToPosition(
2912 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2923 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2925 viewport.setColourText(colourTextMenuItem.isSelected());
2926 alignPanel.paintAlignment(true);
2936 public void wrapMenuItem_actionPerformed(ActionEvent e)
2938 scaleAbove.setVisible(wrapMenuItem.isSelected());
2939 scaleLeft.setVisible(wrapMenuItem.isSelected());
2940 scaleRight.setVisible(wrapMenuItem.isSelected());
2941 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2942 alignPanel.updateLayout();
2946 public void showAllSeqs_actionPerformed(ActionEvent e)
2948 viewport.showAllHiddenSeqs();
2952 public void showAllColumns_actionPerformed(ActionEvent e)
2954 viewport.showAllHiddenColumns();
2956 viewport.sendSelection();
2960 public void hideSelSequences_actionPerformed(ActionEvent e)
2962 viewport.hideAllSelectedSeqs();
2963 // alignPanel.paintAlignment(true);
2967 * called by key handler and the hide all/show all menu items
2972 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2975 boolean hide = false;
2976 SequenceGroup sg = viewport.getSelectionGroup();
2977 if (!toggleSeqs && !toggleCols)
2979 // Hide everything by the current selection - this is a hack - we do the
2980 // invert and then hide
2981 // first check that there will be visible columns after the invert.
2982 if (viewport.hasSelectedColumns()
2983 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2986 // now invert the sequence set, if required - empty selection implies
2987 // that no hiding is required.
2990 invertSequenceMenuItem_actionPerformed(null);
2991 sg = viewport.getSelectionGroup();
2995 viewport.expandColSelection(sg, true);
2996 // finally invert the column selection and get the new sequence
2998 invertColSel_actionPerformed(null);
3005 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3007 hideSelSequences_actionPerformed(null);
3010 else if (!(toggleCols && viewport.hasSelectedColumns()))
3012 showAllSeqs_actionPerformed(null);
3018 if (viewport.hasSelectedColumns())
3020 hideSelColumns_actionPerformed(null);
3023 viewport.setSelectionGroup(sg);
3028 showAllColumns_actionPerformed(null);
3037 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3038 * event.ActionEvent)
3041 public void hideAllButSelection_actionPerformed(ActionEvent e)
3043 toggleHiddenRegions(false, false);
3044 viewport.sendSelection();
3051 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3055 public void hideAllSelection_actionPerformed(ActionEvent e)
3057 SequenceGroup sg = viewport.getSelectionGroup();
3058 viewport.expandColSelection(sg, false);
3059 viewport.hideAllSelectedSeqs();
3060 viewport.hideSelectedColumns();
3061 alignPanel.paintAlignment(true);
3062 viewport.sendSelection();
3069 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3073 public void showAllhidden_actionPerformed(ActionEvent e)
3075 viewport.showAllHiddenColumns();
3076 viewport.showAllHiddenSeqs();
3077 alignPanel.paintAlignment(true);
3078 viewport.sendSelection();
3082 public void hideSelColumns_actionPerformed(ActionEvent e)
3084 viewport.hideSelectedColumns();
3085 alignPanel.paintAlignment(true);
3086 viewport.sendSelection();
3090 public void hiddenMarkers_actionPerformed(ActionEvent e)
3092 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3103 protected void scaleAbove_actionPerformed(ActionEvent e)
3105 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3106 alignPanel.paintAlignment(true);
3116 protected void scaleLeft_actionPerformed(ActionEvent e)
3118 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3119 alignPanel.paintAlignment(true);
3129 protected void scaleRight_actionPerformed(ActionEvent e)
3131 viewport.setScaleRightWrapped(scaleRight.isSelected());
3132 alignPanel.paintAlignment(true);
3142 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3144 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3145 alignPanel.paintAlignment(true);
3155 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3157 viewport.setShowText(viewTextMenuItem.isSelected());
3158 alignPanel.paintAlignment(true);
3168 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3170 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3171 alignPanel.paintAlignment(true);
3174 public FeatureSettings featureSettings;
3177 public FeatureSettingsControllerI getFeatureSettingsUI()
3179 return featureSettings;
3183 public void featureSettings_actionPerformed(ActionEvent e)
3185 if (featureSettings != null)
3187 featureSettings.close();
3188 featureSettings = null;
3190 if (!showSeqFeatures.isSelected())
3192 // make sure features are actually displayed
3193 showSeqFeatures.setSelected(true);
3194 showSeqFeatures_actionPerformed(null);
3196 featureSettings = new FeatureSettings(this);
3200 * Set or clear 'Show Sequence Features'
3206 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3208 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3209 alignPanel.paintAlignment(true);
3210 if (alignPanel.getOverviewPanel() != null)
3212 alignPanel.getOverviewPanel().updateOverviewImage();
3217 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3218 * the annotations panel as a whole.
3220 * The options to show/hide all annotations should be enabled when the panel
3221 * is shown, and disabled when the panel is hidden.
3226 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3228 final boolean setVisible = annotationPanelMenuItem.isSelected();
3229 viewport.setShowAnnotation(setVisible);
3230 this.showAllSeqAnnotations.setEnabled(setVisible);
3231 this.hideAllSeqAnnotations.setEnabled(setVisible);
3232 this.showAllAlAnnotations.setEnabled(setVisible);
3233 this.hideAllAlAnnotations.setEnabled(setVisible);
3234 alignPanel.updateLayout();
3238 public void alignmentProperties()
3240 JEditorPane editPane = new JEditorPane("text/html", "");
3241 editPane.setEditable(false);
3242 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3244 editPane.setText(MessageManager.formatMessage("label.html_content",
3245 new Object[] { contents.toString() }));
3246 JInternalFrame frame = new JInternalFrame();
3247 frame.getContentPane().add(new JScrollPane(editPane));
3249 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3250 "label.alignment_properties", new Object[] { getTitle() }),
3261 public void overviewMenuItem_actionPerformed(ActionEvent e)
3263 if (alignPanel.overviewPanel != null)
3268 JInternalFrame frame = new JInternalFrame();
3269 OverviewPanel overview = new OverviewPanel(alignPanel);
3270 frame.setContentPane(overview);
3271 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3272 "label.overview_params", new Object[] { this.getTitle() }),
3273 frame.getWidth(), frame.getHeight());
3275 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3276 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3279 public void internalFrameClosed(
3280 javax.swing.event.InternalFrameEvent evt)
3282 alignPanel.setOverviewPanel(null);
3286 alignPanel.setOverviewPanel(overview);
3290 public void textColour_actionPerformed(ActionEvent e)
3292 new TextColourChooser().chooseColour(alignPanel, null);
3302 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3314 public void clustalColour_actionPerformed(ActionEvent e)
3316 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3317 viewport.getHiddenRepSequences()));
3327 public void zappoColour_actionPerformed(ActionEvent e)
3329 changeColour(new ZappoColourScheme());
3339 public void taylorColour_actionPerformed(ActionEvent e)
3341 changeColour(new TaylorColourScheme());
3351 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3353 changeColour(new HydrophobicColourScheme());
3363 public void helixColour_actionPerformed(ActionEvent e)
3365 changeColour(new HelixColourScheme());
3375 public void strandColour_actionPerformed(ActionEvent e)
3377 changeColour(new StrandColourScheme());
3387 public void turnColour_actionPerformed(ActionEvent e)
3389 changeColour(new TurnColourScheme());
3399 public void buriedColour_actionPerformed(ActionEvent e)
3401 changeColour(new BuriedColourScheme());
3411 public void nucleotideColour_actionPerformed(ActionEvent e)
3413 changeColour(new NucleotideColourScheme());
3417 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3419 changeColour(new PurinePyrimidineColourScheme());
3423 * public void covariationColour_actionPerformed(ActionEvent e) {
3425 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3429 public void annotationColour_actionPerformed(ActionEvent e)
3431 new AnnotationColourChooser(viewport, alignPanel);
3435 public void annotationColumn_actionPerformed(ActionEvent e)
3437 new AnnotationColumnChooser(viewport, alignPanel);
3441 public void rnahelicesColour_actionPerformed(ActionEvent e)
3443 new RNAHelicesColourChooser(viewport, alignPanel);
3453 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3455 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3465 public void changeColour(ColourSchemeI cs)
3467 // TODO: pull up to controller method
3471 // Make sure viewport is up to date w.r.t. any sliders
3472 if (viewport.getAbovePIDThreshold())
3474 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3476 viewport.setThreshold(threshold);
3479 if (viewport.getConservationSelected())
3481 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3484 if (cs instanceof TCoffeeColourScheme)
3486 tcoffeeColour.setEnabled(true);
3487 tcoffeeColour.setSelected(true);
3491 viewport.setGlobalColourScheme(cs);
3493 alignPanel.paintAlignment(true);
3503 protected void modifyPID_actionPerformed(ActionEvent e)
3505 if (viewport.getAbovePIDThreshold()
3506 && viewport.getGlobalColourScheme() != null)
3508 SliderPanel.setPIDSliderSource(alignPanel,
3509 viewport.getGlobalColourScheme(), "Background");
3510 SliderPanel.showPIDSlider();
3521 protected void modifyConservation_actionPerformed(ActionEvent e)
3523 if (viewport.getConservationSelected()
3524 && viewport.getGlobalColourScheme() != null)
3526 SliderPanel.setConservationSlider(alignPanel,
3527 viewport.getGlobalColourScheme(), "Background");
3528 SliderPanel.showConservationSlider();
3539 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3541 viewport.setConservationSelected(conservationMenuItem.isSelected());
3543 viewport.setAbovePIDThreshold(false);
3544 abovePIDThreshold.setSelected(false);
3546 changeColour(viewport.getGlobalColourScheme());
3548 modifyConservation_actionPerformed(null);
3558 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3560 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3562 conservationMenuItem.setSelected(false);
3563 viewport.setConservationSelected(false);
3565 changeColour(viewport.getGlobalColourScheme());
3567 modifyPID_actionPerformed(null);
3577 public void userDefinedColour_actionPerformed(ActionEvent e)
3579 if (e.getActionCommand().equals(
3580 MessageManager.getString("action.user_defined")))
3582 new UserDefinedColours(alignPanel, null);
3586 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3587 .getUserColourSchemes().get(e.getActionCommand());
3593 public void updateUserColourMenu()
3596 Component[] menuItems = colourMenu.getMenuComponents();
3597 int iSize = menuItems.length;
3598 for (int i = 0; i < iSize; i++)
3600 if (menuItems[i].getName() != null
3601 && menuItems[i].getName().equals("USER_DEFINED"))
3603 colourMenu.remove(menuItems[i]);
3607 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3609 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3610 .getUserColourSchemes().keys();
3612 while (userColours.hasMoreElements())
3614 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3615 userColours.nextElement().toString());
3616 radioItem.setName("USER_DEFINED");
3617 radioItem.addMouseListener(new MouseAdapter()
3620 public void mousePressed(MouseEvent evt)
3622 if (evt.isPopupTrigger()) // Mac
3624 offerRemoval(radioItem);
3629 public void mouseReleased(MouseEvent evt)
3631 if (evt.isPopupTrigger()) // Windows
3633 offerRemoval(radioItem);
3640 void offerRemoval(final JRadioButtonMenuItem radioItem)
3642 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3644 int option = JOptionPane.showInternalConfirmDialog(
3645 jalview.gui.Desktop.desktop, MessageManager
3646 .getString("label.remove_from_default_list"),
3648 .getString("label.remove_user_defined_colour"),
3649 JOptionPane.YES_NO_OPTION);
3650 if (option == JOptionPane.YES_OPTION)
3652 jalview.gui.UserDefinedColours
3653 .removeColourFromDefaults(radioItem.getText());
3654 colourMenu.remove(radioItem);
3658 radioItem.addActionListener(new ActionListener()
3661 public void actionPerformed(ActionEvent evt)
3663 userDefinedColour_actionPerformed(evt);
3669 radioItem.addActionListener(new ActionListener()
3672 public void actionPerformed(ActionEvent evt)
3674 userDefinedColour_actionPerformed(evt);
3678 colourMenu.insert(radioItem, 15);
3679 colours.add(radioItem);
3691 public void PIDColour_actionPerformed(ActionEvent e)
3693 changeColour(new PIDColourScheme());
3703 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3705 changeColour(new Blosum62ColourScheme());
3715 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3717 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3718 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3719 .getAlignment().getSequenceAt(0), null);
3720 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3721 viewport.getAlignment()));
3722 alignPanel.paintAlignment(true);
3732 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3734 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3735 AlignmentSorter.sortByID(viewport.getAlignment());
3736 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3737 viewport.getAlignment()));
3738 alignPanel.paintAlignment(true);
3748 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3750 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3751 AlignmentSorter.sortByLength(viewport.getAlignment());
3752 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3753 viewport.getAlignment()));
3754 alignPanel.paintAlignment(true);
3764 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3766 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3767 AlignmentSorter.sortByGroup(viewport.getAlignment());
3768 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3769 viewport.getAlignment()));
3771 alignPanel.paintAlignment(true);
3781 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3783 new RedundancyPanel(alignPanel, this);
3793 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3795 if ((viewport.getSelectionGroup() == null)
3796 || (viewport.getSelectionGroup().getSize() < 2))
3798 JOptionPane.showInternalMessageDialog(this, MessageManager
3799 .getString("label.you_must_select_least_two_sequences"),
3800 MessageManager.getString("label.invalid_selection"),
3801 JOptionPane.WARNING_MESSAGE);
3805 JInternalFrame frame = new JInternalFrame();
3806 frame.setContentPane(new PairwiseAlignPanel(viewport));
3807 Desktop.addInternalFrame(frame,
3808 MessageManager.getString("action.pairwise_alignment"), 600,
3820 public void PCAMenuItem_actionPerformed(ActionEvent e)
3822 if (((viewport.getSelectionGroup() != null)
3823 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3824 .getSelectionGroup().getSize() > 0))
3825 || (viewport.getAlignment().getHeight() < 4))
3828 .showInternalMessageDialog(
3831 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3833 .getString("label.sequence_selection_insufficient"),
3834 JOptionPane.WARNING_MESSAGE);
3839 new PCAPanel(alignPanel);
3843 public void autoCalculate_actionPerformed(ActionEvent e)
3845 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3846 if (viewport.autoCalculateConsensus)
3848 viewport.firePropertyChange("alignment", null, viewport
3849 .getAlignment().getSequences());
3854 public void sortByTreeOption_actionPerformed(ActionEvent e)
3856 viewport.sortByTree = sortByTree.isSelected();
3860 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3862 viewport.followSelection = listenToViewSelections.isSelected();
3872 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3874 newTreePanel("AV", "PID", "Average distance tree using PID");
3884 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3886 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3896 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3898 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3908 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3910 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3923 void newTreePanel(String type, String pwType, String title)
3927 if (viewport.getSelectionGroup() != null
3928 && viewport.getSelectionGroup().getSize() > 0)
3930 if (viewport.getSelectionGroup().getSize() < 3)
3936 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3938 .getString("label.not_enough_sequences"),
3939 JOptionPane.WARNING_MESSAGE);
3943 SequenceGroup sg = viewport.getSelectionGroup();
3945 /* Decide if the selection is a column region */
3946 for (SequenceI _s : sg.getSequences())
3948 if (_s.getLength() < sg.getEndRes())
3954 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3956 .getString("label.sequences_selection_not_aligned"),
3957 JOptionPane.WARNING_MESSAGE);
3963 title = title + " on region";
3964 tp = new TreePanel(alignPanel, type, pwType);
3968 // are the visible sequences aligned?
3969 if (!viewport.getAlignment().isAligned(false))
3975 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3977 .getString("label.sequences_not_aligned"),
3978 JOptionPane.WARNING_MESSAGE);
3983 if (viewport.getAlignment().getHeight() < 2)
3988 tp = new TreePanel(alignPanel, type, pwType);
3993 if (viewport.viewName != null)
3995 title += viewport.viewName + " of ";
3998 title += this.title;
4000 Desktop.addInternalFrame(tp, title, 600, 500);
4011 public void addSortByOrderMenuItem(String title,
4012 final AlignmentOrder order)
4014 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4015 "action.by_title_param", new Object[] { title }));
4017 item.addActionListener(new java.awt.event.ActionListener()
4020 public void actionPerformed(ActionEvent e)
4022 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4024 // TODO: JBPNote - have to map order entries to curent SequenceI
4026 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4028 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4031 alignPanel.paintAlignment(true);
4037 * Add a new sort by annotation score menu item
4040 * the menu to add the option to
4042 * the label used to retrieve scores for each sequence on the
4045 public void addSortByAnnotScoreMenuItem(JMenu sort,
4046 final String scoreLabel)
4048 final JMenuItem item = new JMenuItem(scoreLabel);
4050 item.addActionListener(new java.awt.event.ActionListener()
4053 public void actionPerformed(ActionEvent e)
4055 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4056 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4057 viewport.getAlignment());// ,viewport.getSelectionGroup());
4058 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4059 viewport.getAlignment()));
4060 alignPanel.paintAlignment(true);
4066 * last hash for alignment's annotation array - used to minimise cost of
4069 protected int _annotationScoreVectorHash;
4072 * search the alignment and rebuild the sort by annotation score submenu the
4073 * last alignment annotation vector hash is stored to minimize cost of
4074 * rebuilding in subsequence calls.
4078 public void buildSortByAnnotationScoresMenu()
4080 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4085 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4087 sortByAnnotScore.removeAll();
4088 // almost certainly a quicker way to do this - but we keep it simple
4089 Hashtable scoreSorts = new Hashtable();
4090 AlignmentAnnotation aann[];
4091 for (SequenceI sqa : viewport.getAlignment().getSequences())
4093 aann = sqa.getAnnotation();
4094 for (int i = 0; aann != null && i < aann.length; i++)
4096 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4098 scoreSorts.put(aann[i].label, aann[i].label);
4102 Enumeration labels = scoreSorts.keys();
4103 while (labels.hasMoreElements())
4105 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4106 (String) labels.nextElement());
4108 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4111 _annotationScoreVectorHash = viewport.getAlignment()
4112 .getAlignmentAnnotation().hashCode();
4117 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4118 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4119 * call. Listeners are added to remove the menu item when the treePanel is
4120 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4124 * Displayed tree window.
4126 * SortBy menu item title.
4129 public void buildTreeMenu()
4131 calculateTree.removeAll();
4132 // build the calculate menu
4134 for (final String type : new String[] { "NJ", "AV" })
4136 String treecalcnm = MessageManager.getString("label.tree_calc_"
4137 + type.toLowerCase());
4138 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4140 JMenuItem tm = new JMenuItem();
4141 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4142 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4143 || sm.isProtein() == !viewport.getAlignment()
4146 String smn = MessageManager.getStringOrReturn(
4147 "label.score_model_", sm.getName());
4148 final String title = MessageManager.formatMessage(
4149 "label.treecalc_title", treecalcnm, smn);
4150 tm.setText(title);//
4151 tm.addActionListener(new java.awt.event.ActionListener()
4154 public void actionPerformed(ActionEvent e)
4156 newTreePanel(type, pwtype, title);
4159 calculateTree.add(tm);
4164 sortByTreeMenu.removeAll();
4166 List<Component> comps = PaintRefresher.components.get(viewport
4167 .getSequenceSetId());
4168 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4169 for (Component comp : comps)
4171 if (comp instanceof TreePanel)
4173 treePanels.add((TreePanel) comp);
4177 if (treePanels.size() < 1)
4179 sortByTreeMenu.setVisible(false);
4183 sortByTreeMenu.setVisible(true);
4185 for (final TreePanel tp : treePanels)
4187 final JMenuItem item = new JMenuItem(tp.getTitle());
4188 item.addActionListener(new java.awt.event.ActionListener()
4191 public void actionPerformed(ActionEvent e)
4193 tp.sortByTree_actionPerformed();
4194 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4199 sortByTreeMenu.add(item);
4203 public boolean sortBy(AlignmentOrder alorder, String undoname)
4205 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4206 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4207 if (undoname != null)
4209 addHistoryItem(new OrderCommand(undoname, oldOrder,
4210 viewport.getAlignment()));
4212 alignPanel.paintAlignment(true);
4217 * Work out whether the whole set of sequences or just the selected set will
4218 * be submitted for multiple alignment.
4221 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4223 // Now, check we have enough sequences
4224 AlignmentView msa = null;
4226 if ((viewport.getSelectionGroup() != null)
4227 && (viewport.getSelectionGroup().getSize() > 1))
4229 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4230 // some common interface!
4232 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4233 * SequenceI[sz = seqs.getSize(false)];
4235 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4236 * seqs.getSequenceAt(i); }
4238 msa = viewport.getAlignmentView(true);
4240 else if (viewport.getSelectionGroup() != null
4241 && viewport.getSelectionGroup().getSize() == 1)
4243 int option = JOptionPane.showConfirmDialog(this,
4244 MessageManager.getString("warn.oneseq_msainput_selection"),
4245 MessageManager.getString("label.invalid_selection"),
4246 JOptionPane.OK_CANCEL_OPTION);
4247 if (option == JOptionPane.OK_OPTION)
4249 msa = viewport.getAlignmentView(false);
4254 msa = viewport.getAlignmentView(false);
4260 * Decides what is submitted to a secondary structure prediction service: the
4261 * first sequence in the alignment, or in the current selection, or, if the
4262 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4263 * region or the whole alignment. (where the first sequence in the set is the
4264 * one that the prediction will be for).
4266 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4268 AlignmentView seqs = null;
4270 if ((viewport.getSelectionGroup() != null)
4271 && (viewport.getSelectionGroup().getSize() > 0))
4273 seqs = viewport.getAlignmentView(true);
4277 seqs = viewport.getAlignmentView(false);
4279 // limit sequences - JBPNote in future - could spawn multiple prediction
4281 // TODO: viewport.getAlignment().isAligned is a global state - the local
4282 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4283 if (!viewport.getAlignment().isAligned(false))
4285 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4286 // TODO: if seqs.getSequences().length>1 then should really have warned
4300 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4302 // Pick the tree file
4303 JalviewFileChooser chooser = new JalviewFileChooser(
4304 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4305 chooser.setFileView(new JalviewFileView());
4306 chooser.setDialogTitle(MessageManager
4307 .getString("label.select_newick_like_tree_file"));
4308 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4310 int value = chooser.showOpenDialog(null);
4312 if (value == JalviewFileChooser.APPROVE_OPTION)
4314 String choice = chooser.getSelectedFile().getPath();
4315 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4316 jalview.io.NewickFile fin = null;
4319 fin = new jalview.io.NewickFile(choice, "File");
4320 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4321 } catch (Exception ex)
4328 .getString("label.problem_reading_tree_file"),
4329 JOptionPane.WARNING_MESSAGE);
4330 ex.printStackTrace();
4332 if (fin != null && fin.hasWarningMessage())
4334 JOptionPane.showMessageDialog(Desktop.desktop, fin
4335 .getWarningMessage(), MessageManager
4336 .getString("label.possible_problem_with_tree_file"),
4337 JOptionPane.WARNING_MESSAGE);
4343 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4345 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4348 public TreePanel ShowNewickTree(NewickFile nf, String title)
4350 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4353 public TreePanel ShowNewickTree(NewickFile nf, String title,
4354 AlignmentView input)
4356 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4359 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4360 int h, int x, int y)
4362 return ShowNewickTree(nf, title, null, w, h, x, y);
4366 * Add a treeviewer for the tree extracted from a newick file object to the
4367 * current alignment view
4374 * Associated alignment input data (or null)
4383 * @return TreePanel handle
4385 public TreePanel ShowNewickTree(NewickFile nf, String title,
4386 AlignmentView input, int w, int h, int x, int y)
4388 TreePanel tp = null;
4394 if (nf.getTree() != null)
4396 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4402 tp.setLocation(x, y);
4405 Desktop.addInternalFrame(tp, title, w, h);
4407 } catch (Exception ex)
4409 ex.printStackTrace();
4415 private boolean buildingMenu = false;
4418 * Generates menu items and listener event actions for web service clients
4421 public void BuildWebServiceMenu()
4423 while (buildingMenu)
4427 System.err.println("Waiting for building menu to finish.");
4429 } catch (Exception e)
4433 final AlignFrame me = this;
4434 buildingMenu = true;
4435 new Thread(new Runnable()
4440 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4443 // System.err.println("Building ws menu again "
4444 // + Thread.currentThread());
4445 // TODO: add support for context dependent disabling of services based
4447 // alignment and current selection
4448 // TODO: add additional serviceHandle parameter to specify abstract
4450 // class independently of AbstractName
4451 // TODO: add in rediscovery GUI function to restart discoverer
4452 // TODO: group services by location as well as function and/or
4454 // object broker mechanism.
4455 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4456 final IProgressIndicator af = me;
4459 * do not i18n these strings - they are hard-coded in class
4460 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4461 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4463 final JMenu msawsmenu = new JMenu("Alignment");
4464 final JMenu secstrmenu = new JMenu(
4465 "Secondary Structure Prediction");
4466 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4467 final JMenu analymenu = new JMenu("Analysis");
4468 final JMenu dismenu = new JMenu("Protein Disorder");
4469 // JAL-940 - only show secondary structure prediction services from
4470 // the legacy server
4471 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4473 Discoverer.services != null && (Discoverer.services.size() > 0))
4475 // TODO: refactor to allow list of AbstractName/Handler bindings to
4477 // stored or retrieved from elsewhere
4478 // No MSAWS used any more:
4479 // Vector msaws = null; // (Vector)
4480 // Discoverer.services.get("MsaWS");
4481 Vector secstrpr = (Vector) Discoverer.services
4483 if (secstrpr != null)
4485 // Add any secondary structure prediction services
4486 for (int i = 0, j = secstrpr.size(); i < j; i++)
4488 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4490 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4491 .getServiceClient(sh);
4492 int p = secstrmenu.getItemCount();
4493 impl.attachWSMenuEntry(secstrmenu, me);
4494 int q = secstrmenu.getItemCount();
4495 for (int litm = p; litm < q; litm++)
4497 legacyItems.add(secstrmenu.getItem(litm));
4503 // Add all submenus in the order they should appear on the web
4505 wsmenu.add(msawsmenu);
4506 wsmenu.add(secstrmenu);
4507 wsmenu.add(dismenu);
4508 wsmenu.add(analymenu);
4509 // No search services yet
4510 // wsmenu.add(seqsrchmenu);
4512 javax.swing.SwingUtilities.invokeLater(new Runnable()
4519 webService.removeAll();
4520 // first, add discovered services onto the webservices menu
4521 if (wsmenu.size() > 0)
4523 for (int i = 0, j = wsmenu.size(); i < j; i++)
4525 webService.add(wsmenu.get(i));
4530 webService.add(me.webServiceNoServices);
4532 // TODO: move into separate menu builder class.
4533 boolean new_sspred = false;
4534 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4536 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4537 if (jws2servs != null)
4539 if (jws2servs.hasServices())
4541 jws2servs.attachWSMenuEntry(webService, me);
4542 for (Jws2Instance sv : jws2servs.getServices())
4544 if (sv.description.toLowerCase().contains("jpred"))
4546 for (JMenuItem jmi : legacyItems)
4548 jmi.setVisible(false);
4554 if (jws2servs.isRunning())
4556 JMenuItem tm = new JMenuItem(
4557 "Still discovering JABA Services");
4558 tm.setEnabled(false);
4563 build_urlServiceMenu(me.webService);
4564 build_fetchdbmenu(webService);
4565 for (JMenu item : wsmenu)
4567 if (item.getItemCount() == 0)
4569 item.setEnabled(false);
4573 item.setEnabled(true);
4576 } catch (Exception e)
4579 .debug("Exception during web service menu building process.",
4584 } catch (Exception e)
4587 buildingMenu = false;
4594 * construct any groupURL type service menu entries.
4598 private void build_urlServiceMenu(JMenu webService)
4600 // TODO: remove this code when 2.7 is released
4601 // DEBUG - alignmentView
4603 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4604 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4606 * @Override public void actionPerformed(ActionEvent e) {
4607 * jalview.datamodel.AlignmentView
4608 * .testSelectionViews(af.viewport.getAlignment(),
4609 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4611 * }); webService.add(testAlView);
4613 // TODO: refactor to RestClient discoverer and merge menu entries for
4614 // rest-style services with other types of analysis/calculation service
4615 // SHmmr test client - still being implemented.
4616 // DEBUG - alignmentView
4618 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4621 client.attachWSMenuEntry(
4622 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4628 * Searches the alignment sequences for xRefs and builds the Show
4629 * Cross-References menu (formerly called Show Products), with database
4630 * sources for which cross-references are found (protein sources for a
4631 * nucleotide alignment and vice versa)
4633 * @return true if Show Cross-references menu should be enabled
4635 public boolean canShowProducts()
4637 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4638 AlignmentI dataset = viewport.getAlignment().getDataset();
4640 showProducts.removeAll();
4641 final boolean dna = viewport.getAlignment().isNucleotide();
4643 if (seqs == null || seqs.length == 0)
4645 // nothing to see here.
4649 boolean showp = false;
4652 List<String> ptypes = new CrossRef(seqs, dataset)
4653 .findXrefSourcesForSequences(dna);
4655 for (final String source : ptypes)
4658 final AlignFrame af = this;
4659 JMenuItem xtype = new JMenuItem(source);
4660 xtype.addActionListener(new ActionListener()
4663 public void actionPerformed(ActionEvent e)
4665 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4668 showProducts.add(xtype);
4670 showProducts.setVisible(showp);
4671 showProducts.setEnabled(showp);
4672 } catch (Exception e)
4675 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4683 * Finds and displays cross-references for the selected sequences (protein
4684 * products for nucleotide sequences, dna coding sequences for peptides).
4687 * the sequences to show cross-references for
4689 * true if from a nucleotide alignment (so showing proteins)
4691 * the database to show cross-references for
4693 protected void showProductsFor(final SequenceI[] sel,
4694 final boolean _odna, final String source)
4696 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4701 * Construct and display a new frame containing the translation of this
4702 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4705 public void showTranslation_actionPerformed(ActionEvent e)
4707 AlignmentI al = null;
4710 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4712 al = dna.translateCdna();
4713 } catch (Exception ex)
4715 jalview.bin.Cache.log.error(
4716 "Exception during translation. Please report this !", ex);
4717 final String msg = MessageManager
4718 .getString("label.error_when_translating_sequences_submit_bug_report");
4719 final String errorTitle = MessageManager
4720 .getString("label.implementation_error")
4721 + MessageManager.getString("label.translation_failed");
4722 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4723 JOptionPane.ERROR_MESSAGE);
4726 if (al == null || al.getHeight() == 0)
4728 final String msg = MessageManager
4729 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4730 final String errorTitle = MessageManager
4731 .getString("label.translation_failed");
4732 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4733 JOptionPane.WARNING_MESSAGE);
4737 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4738 af.setFileFormat(this.currentFileFormat);
4739 final String newTitle = MessageManager.formatMessage(
4740 "label.translation_of_params",
4741 new Object[] { this.getTitle() });
4742 af.setTitle(newTitle);
4743 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4745 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4746 viewport.openSplitFrame(af, new Alignment(seqs));
4750 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4757 * Set the file format
4761 public void setFileFormat(String fileFormat)
4763 this.currentFileFormat = fileFormat;
4767 * Try to load a features file onto the alignment.
4770 * contents or path to retrieve file
4772 * access mode of file (see jalview.io.AlignFile)
4773 * @return true if features file was parsed correctly.
4775 public boolean parseFeaturesFile(String file, String type)
4777 return avc.parseFeaturesFile(file, type,
4778 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4783 public void refreshFeatureUI(boolean enableIfNecessary)
4785 // note - currently this is only still here rather than in the controller
4786 // because of the featureSettings hard reference that is yet to be
4788 if (enableIfNecessary)
4790 viewport.setShowSequenceFeatures(true);
4791 showSeqFeatures.setSelected(true);
4797 public void dragEnter(DropTargetDragEvent evt)
4802 public void dragExit(DropTargetEvent evt)
4807 public void dragOver(DropTargetDragEvent evt)
4812 public void dropActionChanged(DropTargetDragEvent evt)
4817 public void drop(DropTargetDropEvent evt)
4819 // JAL-1552 - acceptDrop required before getTransferable call for
4820 // Java's Transferable for native dnd
4821 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4822 Transferable t = evt.getTransferable();
4823 java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
4827 Desktop.transferFromDropTarget(files, protocols, evt, t);
4828 } catch (Exception e)
4830 e.printStackTrace();
4836 // check to see if any of these files have names matching sequences in
4838 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4839 .getAlignment().getSequencesArray());
4841 * Object[] { String,SequenceI}
4843 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4844 ArrayList<String> filesnotmatched = new ArrayList<String>();
4845 for (int i = 0; i < files.size(); i++)
4847 String file = files.get(i).toString();
4849 String protocol = FormatAdapter.checkProtocol(file);
4850 if (protocol == jalview.io.FormatAdapter.FILE)
4852 File fl = new File(file);
4853 pdbfn = fl.getName();
4855 else if (protocol == jalview.io.FormatAdapter.URL)
4857 URL url = new URL(file);
4858 pdbfn = url.getFile();
4860 if (pdbfn.length() > 0)
4862 // attempt to find a match in the alignment
4863 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4864 int l = 0, c = pdbfn.indexOf(".");
4865 while (mtch == null && c != -1)
4870 } while ((c = pdbfn.indexOf(".", l)) > l);
4873 pdbfn = pdbfn.substring(0, l);
4875 mtch = idm.findAllIdMatches(pdbfn);
4882 type = new IdentifyFile().identify(file, protocol);
4883 } catch (Exception ex)
4889 if (StructureFile.isStructureFile(type))
4891 filesmatched.add(new Object[] { file, protocol, mtch });
4896 // File wasn't named like one of the sequences or wasn't a PDB file.
4897 filesnotmatched.add(file);
4901 if (filesmatched.size() > 0)
4903 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4909 "label.automatically_associate_structure_files_with_sequences_same_name",
4910 new Object[] { Integer
4916 .getString("label.automatically_associate_structure_files_by_name"),
4917 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4920 for (Object[] fm : filesmatched)
4922 // try and associate
4923 // TODO: may want to set a standard ID naming formalism for
4924 // associating PDB files which have no IDs.
4925 for (SequenceI toassoc : (SequenceI[]) fm[2])
4927 PDBEntry pe = new AssociatePdbFileWithSeq()
4928 .associatePdbWithSeq((String) fm[0],
4929 (String) fm[1], toassoc, false,
4933 System.err.println("Associated file : "
4934 + ((String) fm[0]) + " with "
4935 + toassoc.getDisplayId(true));
4939 alignPanel.paintAlignment(true);
4943 if (filesnotmatched.size() > 0)
4946 && (Cache.getDefault(
4947 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4953 "label.ignore_unmatched_dropped_files_info",
4954 new Object[] { Integer
4961 .getString("label.ignore_unmatched_dropped_files"),
4962 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4966 for (String fn : filesnotmatched)
4968 loadJalviewDataFile(fn, null, null, null);
4972 } catch (Exception ex)
4974 ex.printStackTrace();
4980 * Attempt to load a "dropped" file or URL string: First by testing whether
4981 * it's an Annotation file, then a JNet file, and finally a features file. If
4982 * all are false then the user may have dropped an alignment file onto this
4986 * either a filename or a URL string.
4988 public void loadJalviewDataFile(String file, String protocol,
4989 String format, SequenceI assocSeq)
4993 if (protocol == null)
4995 protocol = FormatAdapter.checkProtocol(file);
4997 // if the file isn't identified, or not positively identified as some
4998 // other filetype (PFAM is default unidentified alignment file type) then
4999 // try to parse as annotation.
5000 boolean isAnnotation = (format == null || format
5001 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5002 .annotateAlignmentView(viewport, file, protocol) : false;
5006 // first see if its a T-COFFEE score file
5007 TCoffeeScoreFile tcf = null;
5010 tcf = new TCoffeeScoreFile(file, protocol);
5013 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5015 tcoffeeColour.setEnabled(true);
5016 tcoffeeColour.setSelected(true);
5017 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5018 isAnnotation = true;
5020 .setText(MessageManager
5021 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5025 // some problem - if no warning its probable that the ID matching
5026 // process didn't work
5030 tcf.getWarningMessage() == null ? MessageManager
5031 .getString("label.check_file_matches_sequence_ids_alignment")
5032 : tcf.getWarningMessage(),
5034 .getString("label.problem_reading_tcoffee_score_file"),
5035 JOptionPane.WARNING_MESSAGE);
5042 } catch (Exception x)
5045 .debug("Exception when processing data source as T-COFFEE score file",
5051 // try to see if its a JNet 'concise' style annotation file *before*
5053 // try to parse it as a features file
5056 format = new IdentifyFile().identify(file, protocol);
5058 if (format.equalsIgnoreCase("JnetFile"))
5060 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5062 new JnetAnnotationMaker();
5063 JnetAnnotationMaker.add_annotation(predictions,
5064 viewport.getAlignment(), 0, false);
5065 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5066 viewport.getAlignment().setSeqrep(repseq);
5067 ColumnSelection cs = new ColumnSelection();
5068 cs.hideInsertionsFor(repseq);
5069 viewport.setColumnSelection(cs);
5070 isAnnotation = true;
5072 else if (IdentifyFile.FeaturesFile.equals(format))
5074 if (parseFeaturesFile(file, protocol))
5076 alignPanel.paintAlignment(true);
5081 new FileLoader().LoadFile(viewport, file, protocol, format);
5088 alignPanel.adjustAnnotationHeight();
5089 viewport.updateSequenceIdColours();
5090 buildSortByAnnotationScoresMenu();
5091 alignPanel.paintAlignment(true);
5093 } catch (Exception ex)
5095 ex.printStackTrace();
5096 } catch (OutOfMemoryError oom)
5101 } catch (Exception x)
5106 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5107 : "using " + protocol + " from " + file)
5109 + (format != null ? "(parsing as '" + format
5110 + "' file)" : ""), oom, Desktop.desktop);
5115 * Method invoked by the ChangeListener on the tabbed pane, in other words
5116 * when a different tabbed pane is selected by the user or programmatically.
5119 public void tabSelectionChanged(int index)
5123 alignPanel = alignPanels.get(index);
5124 viewport = alignPanel.av;
5125 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5126 setMenusFromViewport(viewport);
5130 * If there is a frame linked to this one in a SplitPane, switch it to the
5131 * same view tab index. No infinite recursion of calls should happen, since
5132 * tabSelectionChanged() should not get invoked on setting the selected
5133 * index to an unchanged value. Guard against setting an invalid index
5134 * before the new view peer tab has been created.
5136 final AlignViewportI peer = viewport.getCodingComplement();
5139 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5140 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5142 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5148 * On right mouse click on view tab, prompt for and set new view name.
5151 public void tabbedPane_mousePressed(MouseEvent e)
5153 if (e.isPopupTrigger())
5155 String msg = MessageManager.getString("label.enter_view_name");
5156 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5157 JOptionPane.QUESTION_MESSAGE);
5161 viewport.viewName = reply;
5162 // TODO warn if reply is in getExistingViewNames()?
5163 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5168 public AlignViewport getCurrentView()
5174 * Open the dialog for regex description parsing.
5177 protected void extractScores_actionPerformed(ActionEvent e)
5179 ParseProperties pp = new jalview.analysis.ParseProperties(
5180 viewport.getAlignment());
5181 // TODO: verify regex and introduce GUI dialog for version 2.5
5182 // if (pp.getScoresFromDescription("col", "score column ",
5183 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5185 if (pp.getScoresFromDescription("description column",
5186 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5188 buildSortByAnnotationScoresMenu();
5196 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5200 protected void showDbRefs_actionPerformed(ActionEvent e)
5202 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5208 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5212 protected void showNpFeats_actionPerformed(ActionEvent e)
5214 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5218 * find the viewport amongst the tabs in this alignment frame and close that
5223 public boolean closeView(AlignViewportI av)
5227 this.closeMenuItem_actionPerformed(false);
5230 Component[] comp = tabbedPane.getComponents();
5231 for (int i = 0; comp != null && i < comp.length; i++)
5233 if (comp[i] instanceof AlignmentPanel)
5235 if (((AlignmentPanel) comp[i]).av == av)
5238 closeView((AlignmentPanel) comp[i]);
5246 protected void build_fetchdbmenu(JMenu webService)
5248 // Temporary hack - DBRef Fetcher always top level ws entry.
5249 // TODO We probably want to store a sequence database checklist in
5250 // preferences and have checkboxes.. rather than individual sources selected
5252 final JMenu rfetch = new JMenu(
5253 MessageManager.getString("action.fetch_db_references"));
5254 rfetch.setToolTipText(MessageManager
5255 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5256 webService.add(rfetch);
5258 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5259 MessageManager.getString("option.trim_retrieved_seqs"));
5260 trimrs.setToolTipText(MessageManager
5261 .getString("label.trim_retrieved_sequences"));
5262 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5263 trimrs.addActionListener(new ActionListener()
5266 public void actionPerformed(ActionEvent e)
5268 trimrs.setSelected(trimrs.isSelected());
5269 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5270 Boolean.valueOf(trimrs.isSelected()).toString());
5274 JMenuItem fetchr = new JMenuItem(
5275 MessageManager.getString("label.standard_databases"));
5276 fetchr.setToolTipText(MessageManager
5277 .getString("label.fetch_embl_uniprot"));
5278 fetchr.addActionListener(new ActionListener()
5282 public void actionPerformed(ActionEvent e)
5284 new Thread(new Runnable()
5289 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5290 .getAlignment().isNucleotide();
5291 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5292 .getSequenceSelection(), alignPanel.alignFrame, null,
5293 alignPanel.alignFrame.featureSettings, isNucleotide);
5294 dbRefFetcher.addListener(new FetchFinishedListenerI()
5297 public void finished()
5299 AlignFrame.this.setMenusForViewport();
5302 dbRefFetcher.fetchDBRefs(false);
5310 final AlignFrame me = this;
5311 new Thread(new Runnable()
5316 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5317 .getSequenceFetcherSingleton(me);
5318 javax.swing.SwingUtilities.invokeLater(new Runnable()
5323 String[] dbclasses = sf.getOrderedSupportedSources();
5324 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5325 // jalview.util.QuickSort.sort(otherdb, otherdb);
5326 List<DbSourceProxy> otherdb;
5327 JMenu dfetch = new JMenu();
5328 JMenu ifetch = new JMenu();
5329 JMenuItem fetchr = null;
5330 int comp = 0, icomp = 0, mcomp = 15;
5331 String mname = null;
5333 for (String dbclass : dbclasses)
5335 otherdb = sf.getSourceProxy(dbclass);
5336 // add a single entry for this class, or submenu allowing 'fetch
5338 if (otherdb == null || otherdb.size() < 1)
5342 // List<DbSourceProxy> dbs=otherdb;
5343 // otherdb=new ArrayList<DbSourceProxy>();
5344 // for (DbSourceProxy db:dbs)
5346 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5350 mname = "From " + dbclass;
5352 if (otherdb.size() == 1)
5354 final DbSourceProxy[] dassource = otherdb
5355 .toArray(new DbSourceProxy[0]);
5356 DbSourceProxy src = otherdb.get(0);
5357 fetchr = new JMenuItem(src.getDbSource());
5358 fetchr.addActionListener(new ActionListener()
5362 public void actionPerformed(ActionEvent e)
5364 new Thread(new Runnable()
5370 boolean isNucleotide = alignPanel.alignFrame
5371 .getViewport().getAlignment()
5373 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5374 alignPanel.av.getSequenceSelection(),
5375 alignPanel.alignFrame, dassource,
5376 alignPanel.alignFrame.featureSettings,
5379 .addListener(new FetchFinishedListenerI()
5382 public void finished()
5384 AlignFrame.this.setMenusForViewport();
5387 dbRefFetcher.fetchDBRefs(false);
5393 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5394 MessageManager.formatMessage(
5395 "label.fetch_retrieve_from",
5396 new Object[] { src.getDbName() })));
5402 final DbSourceProxy[] dassource = otherdb
5403 .toArray(new DbSourceProxy[0]);
5405 DbSourceProxy src = otherdb.get(0);
5406 fetchr = new JMenuItem(MessageManager.formatMessage(
5407 "label.fetch_all_param",
5408 new Object[] { src.getDbSource() }));
5409 fetchr.addActionListener(new ActionListener()
5412 public void actionPerformed(ActionEvent e)
5414 new Thread(new Runnable()
5420 boolean isNucleotide = alignPanel.alignFrame
5421 .getViewport().getAlignment()
5423 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5424 alignPanel.av.getSequenceSelection(),
5425 alignPanel.alignFrame, dassource,
5426 alignPanel.alignFrame.featureSettings,
5429 .addListener(new FetchFinishedListenerI()
5432 public void finished()
5434 AlignFrame.this.setMenusForViewport();
5437 dbRefFetcher.fetchDBRefs(false);
5443 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5444 MessageManager.formatMessage(
5445 "label.fetch_retrieve_from_all_sources",
5447 Integer.valueOf(otherdb.size())
5448 .toString(), src.getDbSource(),
5449 src.getDbName() })));
5452 // and then build the rest of the individual menus
5453 ifetch = new JMenu(MessageManager.formatMessage(
5454 "label.source_from_db_source",
5455 new Object[] { src.getDbSource() }));
5457 String imname = null;
5459 for (DbSourceProxy sproxy : otherdb)
5461 String dbname = sproxy.getDbName();
5462 String sname = dbname.length() > 5 ? dbname.substring(0,
5463 5) + "..." : dbname;
5464 String msname = dbname.length() > 10 ? dbname.substring(
5465 0, 10) + "..." : dbname;
5468 imname = MessageManager.formatMessage(
5469 "label.from_msname", new Object[] { sname });
5471 fetchr = new JMenuItem(msname);
5472 final DbSourceProxy[] dassrc = { sproxy };
5473 fetchr.addActionListener(new ActionListener()
5477 public void actionPerformed(ActionEvent e)
5479 new Thread(new Runnable()
5485 boolean isNucleotide = alignPanel.alignFrame
5486 .getViewport().getAlignment()
5488 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5489 alignPanel.av.getSequenceSelection(),
5490 alignPanel.alignFrame, dassrc,
5491 alignPanel.alignFrame.featureSettings,
5494 .addListener(new FetchFinishedListenerI()
5497 public void finished()
5499 AlignFrame.this.setMenusForViewport();
5502 dbRefFetcher.fetchDBRefs(false);
5508 fetchr.setToolTipText("<html>"
5509 + MessageManager.formatMessage(
5510 "label.fetch_retrieve_from", new Object[]
5514 if (++icomp >= mcomp || i == (otherdb.size()))
5516 ifetch.setText(MessageManager.formatMessage(
5517 "label.source_to_target", imname, sname));
5519 ifetch = new JMenu();
5527 if (comp >= mcomp || dbi >= (dbclasses.length))
5529 dfetch.setText(MessageManager.formatMessage(
5530 "label.source_to_target", mname, dbclass));
5532 dfetch = new JMenu();
5545 * Left justify the whole alignment.
5548 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5550 AlignmentI al = viewport.getAlignment();
5552 viewport.firePropertyChange("alignment", null, al);
5556 * Right justify the whole alignment.
5559 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5561 AlignmentI al = viewport.getAlignment();
5563 viewport.firePropertyChange("alignment", null, al);
5567 public void setShowSeqFeatures(boolean b)
5569 showSeqFeatures.setSelected(b);
5570 viewport.setShowSequenceFeatures(b);
5577 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5578 * awt.event.ActionEvent)
5581 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5583 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5584 alignPanel.paintAlignment(true);
5591 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5595 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5597 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5598 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5606 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5607 * .event.ActionEvent)
5610 protected void showGroupConservation_actionPerformed(ActionEvent e)
5612 viewport.setShowGroupConservation(showGroupConservation.getState());
5613 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5620 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5621 * .event.ActionEvent)
5624 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5626 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5627 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5634 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5635 * .event.ActionEvent)
5638 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5640 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5641 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5645 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5647 showSequenceLogo.setState(true);
5648 viewport.setShowSequenceLogo(true);
5649 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5650 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5654 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5656 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5663 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5664 * .event.ActionEvent)
5667 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5669 if (avc.makeGroupsFromSelection())
5671 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5672 alignPanel.updateAnnotation();
5673 alignPanel.paintAlignment(true);
5677 public void clearAlignmentSeqRep()
5679 // TODO refactor alignmentseqrep to controller
5680 if (viewport.getAlignment().hasSeqrep())
5682 viewport.getAlignment().setSeqrep(null);
5683 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5684 alignPanel.updateAnnotation();
5685 alignPanel.paintAlignment(true);
5690 protected void createGroup_actionPerformed(ActionEvent e)
5692 if (avc.createGroup())
5694 alignPanel.alignmentChanged();
5699 protected void unGroup_actionPerformed(ActionEvent e)
5703 alignPanel.alignmentChanged();
5708 * make the given alignmentPanel the currently selected tab
5710 * @param alignmentPanel
5712 public void setDisplayedView(AlignmentPanel alignmentPanel)
5714 if (!viewport.getSequenceSetId().equals(
5715 alignmentPanel.av.getSequenceSetId()))
5719 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5721 if (tabbedPane != null
5722 && tabbedPane.getTabCount() > 0
5723 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5724 .getSelectedIndex())
5726 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5731 * Action on selection of menu options to Show or Hide annotations.
5734 * @param forSequences
5735 * update sequence-related annotations
5736 * @param forAlignment
5737 * update non-sequence-related annotations
5740 protected void setAnnotationsVisibility(boolean visible,
5741 boolean forSequences, boolean forAlignment)
5743 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5744 .getAlignmentAnnotation();
5749 for (AlignmentAnnotation aa : anns)
5752 * don't display non-positional annotations on an alignment
5754 if (aa.annotations == null)
5758 boolean apply = (aa.sequenceRef == null && forAlignment)
5759 || (aa.sequenceRef != null && forSequences);
5762 aa.visible = visible;
5765 alignPanel.validateAnnotationDimensions(true);
5766 alignPanel.alignmentChanged();
5770 * Store selected annotation sort order for the view and repaint.
5773 protected void sortAnnotations_actionPerformed()
5775 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5777 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5778 alignPanel.paintAlignment(true);
5783 * @return alignment panels in this alignment frame
5785 public List<? extends AlignmentViewPanel> getAlignPanels()
5787 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5791 * Open a new alignment window, with the cDNA associated with this (protein)
5792 * alignment, aligned as is the protein.
5794 protected void viewAsCdna_actionPerformed()
5796 // TODO no longer a menu action - refactor as required
5797 final AlignmentI alignment = getViewport().getAlignment();
5798 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5799 if (mappings == null)
5803 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5804 for (SequenceI aaSeq : alignment.getSequences())
5806 for (AlignedCodonFrame acf : mappings)
5808 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5812 * There is a cDNA mapping for this protein sequence - add to new
5813 * alignment. It will share the same dataset sequence as other mapped
5814 * cDNA (no new mappings need to be created).
5816 final Sequence newSeq = new Sequence(dnaSeq);
5817 newSeq.setDatasetSequence(dnaSeq);
5818 cdnaSeqs.add(newSeq);
5822 if (cdnaSeqs.size() == 0)
5824 // show a warning dialog no mapped cDNA
5827 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5829 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5830 AlignFrame.DEFAULT_HEIGHT);
5831 cdna.alignAs(alignment);
5832 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5834 Desktop.addInternalFrame(alignFrame, newtitle,
5835 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5839 * Set visibility of dna/protein complement view (available when shown in a
5845 protected void showComplement_actionPerformed(boolean show)
5847 SplitContainerI sf = getSplitViewContainer();
5850 sf.setComplementVisible(this, show);
5855 * Generate the reverse (optionally complemented) of the selected sequences,
5856 * and add them to the alignment
5859 protected void showReverse_actionPerformed(boolean complement)
5861 AlignmentI al = null;
5864 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5865 al = dna.reverseCdna(complement);
5866 viewport.addAlignment(al, "");
5867 addHistoryItem(new EditCommand(
5868 MessageManager.getString("label.add_sequences"),
5869 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5870 viewport.getAlignment()));
5871 } catch (Exception ex)
5873 System.err.println(ex.getMessage());
5879 * Try to run a script in the Groovy console, having first ensured that this
5880 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5881 * be targeted at this alignment.
5884 protected void runGroovy_actionPerformed()
5886 Jalview.setCurrentAlignFrame(this);
5887 groovy.ui.Console console = Desktop.getGroovyConsole();
5888 if (console != null)
5892 console.runScript();
5893 } catch (Exception ex)
5895 System.err.println((ex.toString()));
5897 .showInternalMessageDialog(Desktop.desktop, MessageManager
5898 .getString("label.couldnt_run_groovy_script"),
5900 .getString("label.groovy_support_failed"),
5901 JOptionPane.ERROR_MESSAGE);
5906 System.err.println("Can't run Groovy script as console not found");
5911 * Hides columns containing (or not containing) a specified feature, provided
5912 * that would not leave all columns hidden
5914 * @param featureType
5915 * @param columnsContaining
5918 public boolean hideFeatureColumns(String featureType,
5919 boolean columnsContaining)
5921 boolean notForHiding = avc.markColumnsContainingFeatures(
5922 columnsContaining, false, false, featureType);
5925 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5926 false, featureType))
5928 getViewport().hideSelectedColumns();
5936 class PrintThread extends Thread
5940 public PrintThread(AlignmentPanel ap)
5945 static PageFormat pf;
5950 PrinterJob printJob = PrinterJob.getPrinterJob();
5954 printJob.setPrintable(ap, pf);
5958 printJob.setPrintable(ap);
5961 if (printJob.printDialog())
5966 } catch (Exception PrintException)
5968 PrintException.printStackTrace();