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.ColourMenuHelper.ColourChangeListener;
63 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
64 import jalview.io.AlignmentProperties;
65 import jalview.io.AnnotationFile;
66 import jalview.io.BioJsHTMLOutput;
67 import jalview.io.DataSourceType;
68 import jalview.io.FileFormat;
69 import jalview.io.FileFormatI;
70 import jalview.io.FileFormats;
71 import jalview.io.FileLoader;
72 import jalview.io.FormatAdapter;
73 import jalview.io.HtmlSvgOutput;
74 import jalview.io.IdentifyFile;
75 import jalview.io.JPredFile;
76 import jalview.io.JalviewFileChooser;
77 import jalview.io.JalviewFileView;
78 import jalview.io.JnetAnnotationMaker;
79 import jalview.io.NewickFile;
80 import jalview.io.TCoffeeScoreFile;
81 import jalview.jbgui.GAlignFrame;
82 import jalview.schemes.ColourSchemeI;
83 import jalview.schemes.ColourSchemes;
84 import jalview.schemes.ResidueColourScheme;
85 import jalview.schemes.ResidueProperties;
86 import jalview.schemes.TCoffeeColourScheme;
87 import jalview.util.MessageManager;
88 import jalview.viewmodel.AlignmentViewport;
89 import jalview.ws.DBRefFetcher;
90 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
91 import jalview.ws.jws1.Discoverer;
92 import jalview.ws.jws2.Jws2Discoverer;
93 import jalview.ws.jws2.jabaws2.Jws2Instance;
94 import jalview.ws.seqfetcher.DbSourceProxy;
96 import java.awt.BorderLayout;
97 import java.awt.Component;
98 import java.awt.Rectangle;
99 import java.awt.Toolkit;
100 import java.awt.datatransfer.Clipboard;
101 import java.awt.datatransfer.DataFlavor;
102 import java.awt.datatransfer.StringSelection;
103 import java.awt.datatransfer.Transferable;
104 import java.awt.dnd.DnDConstants;
105 import java.awt.dnd.DropTargetDragEvent;
106 import java.awt.dnd.DropTargetDropEvent;
107 import java.awt.dnd.DropTargetEvent;
108 import java.awt.dnd.DropTargetListener;
109 import java.awt.event.ActionEvent;
110 import java.awt.event.ActionListener;
111 import java.awt.event.FocusAdapter;
112 import java.awt.event.FocusEvent;
113 import java.awt.event.ItemEvent;
114 import java.awt.event.ItemListener;
115 import java.awt.event.KeyAdapter;
116 import java.awt.event.KeyEvent;
117 import java.awt.event.MouseEvent;
118 import java.awt.print.PageFormat;
119 import java.awt.print.PrinterJob;
120 import java.beans.PropertyChangeEvent;
122 import java.io.FileWriter;
123 import java.io.PrintWriter;
125 import java.util.ArrayList;
126 import java.util.Arrays;
127 import java.util.Deque;
128 import java.util.Enumeration;
129 import java.util.Hashtable;
130 import java.util.List;
131 import java.util.Vector;
133 import javax.swing.JCheckBoxMenuItem;
134 import javax.swing.JEditorPane;
135 import javax.swing.JInternalFrame;
136 import javax.swing.JLayeredPane;
137 import javax.swing.JMenu;
138 import javax.swing.JMenuItem;
139 import javax.swing.JScrollPane;
140 import javax.swing.SwingUtilities;
146 * @version $Revision$
148 public class AlignFrame extends GAlignFrame implements DropTargetListener,
149 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
152 public static final int DEFAULT_WIDTH = 700;
154 public static final int DEFAULT_HEIGHT = 500;
157 * The currently displayed panel (selected tabbed view if more than one)
159 public AlignmentPanel alignPanel;
161 AlignViewport viewport;
163 public AlignViewControllerI avc;
165 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
168 * Last format used to load or save alignments in this window
170 FileFormatI currentFileFormat = null;
173 * Current filename for this alignment
175 String fileName = null;
178 * Creates a new AlignFrame object with specific width and height.
184 public AlignFrame(AlignmentI al, int width, int height)
186 this(al, null, width, height);
190 * Creates a new AlignFrame object with specific width, height and
196 * @param sequenceSetId
198 public AlignFrame(AlignmentI al, int width, int height,
199 String sequenceSetId)
201 this(al, null, width, height, sequenceSetId);
205 * Creates a new AlignFrame object with specific width, height and
211 * @param sequenceSetId
214 public AlignFrame(AlignmentI al, int width, int height,
215 String sequenceSetId, String viewId)
217 this(al, null, width, height, sequenceSetId, viewId);
221 * new alignment window with hidden columns
225 * @param hiddenColumns
226 * ColumnSelection or null
228 * Width of alignment frame
232 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
233 int width, int height)
235 this(al, hiddenColumns, width, height, null);
239 * Create alignment frame for al with hiddenColumns, a specific width and
240 * height, and specific sequenceId
243 * @param hiddenColumns
246 * @param sequenceSetId
249 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
250 int width, int height, String sequenceSetId)
252 this(al, hiddenColumns, width, height, sequenceSetId, null);
256 * Create alignment frame for al with hiddenColumns, a specific width and
257 * height, and specific sequenceId
260 * @param hiddenColumns
263 * @param sequenceSetId
268 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
269 int width, int height, String sequenceSetId, String viewId)
271 setSize(width, height);
273 if (al.getDataset() == null)
278 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
280 alignPanel = new AlignmentPanel(this, viewport);
282 addAlignmentPanel(alignPanel, true);
286 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
287 ColumnSelection hiddenColumns, int width, int height)
289 setSize(width, height);
291 if (al.getDataset() == null)
296 viewport = new AlignViewport(al, hiddenColumns);
298 if (hiddenSeqs != null && hiddenSeqs.length > 0)
300 viewport.hideSequence(hiddenSeqs);
302 alignPanel = new AlignmentPanel(this, viewport);
303 addAlignmentPanel(alignPanel, true);
308 * Make a new AlignFrame from existing alignmentPanels
315 public AlignFrame(AlignmentPanel ap)
319 addAlignmentPanel(ap, false);
324 * initalise the alignframe from the underlying viewport data and the
329 if (!Jalview.isHeadlessMode())
331 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
334 avc = new jalview.controller.AlignViewController(this, viewport,
336 if (viewport.getAlignmentConservationAnnotation() == null)
338 // BLOSUM62Colour.setEnabled(false);
339 conservationMenuItem.setEnabled(false);
340 modifyConservation.setEnabled(false);
341 // PIDColour.setEnabled(false);
342 // abovePIDThreshold.setEnabled(false);
343 // modifyPID.setEnabled(false);
346 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
349 if (sortby.equals("Id"))
351 sortIDMenuItem_actionPerformed(null);
353 else if (sortby.equals("Pairwise Identity"))
355 sortPairwiseMenuItem_actionPerformed(null);
359 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
361 setMenusFromViewport(viewport);
362 buildSortByAnnotationScoresMenu();
366 if (Desktop.desktop != null)
368 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
369 addServiceListeners();
373 if (viewport.getWrapAlignment())
375 wrapMenuItem_actionPerformed(null);
378 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
380 this.overviewMenuItem_actionPerformed(null);
385 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
386 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
387 final String menuLabel = MessageManager
388 .getString("label.copy_format_from");
389 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
390 new ViewSetProvider()
394 public AlignmentPanel[] getAllAlignmentPanels()
397 origview.add(alignPanel);
398 // make an array of all alignment panels except for this one
399 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
400 Arrays.asList(Desktop.getAlignmentPanels(null)));
401 aps.remove(AlignFrame.this.alignPanel);
402 return aps.toArray(new AlignmentPanel[aps.size()]);
404 }, selviews, new ItemListener()
408 public void itemStateChanged(ItemEvent e)
410 if (origview.size() > 0)
412 final AlignmentPanel ap = origview.get(0);
415 * Copy the ViewStyle of the selected panel to 'this one'.
416 * Don't change value of 'scaleProteinAsCdna' unless copying
419 ViewStyleI vs = selviews.get(0).getAlignViewport()
421 boolean fromSplitFrame = selviews.get(0)
422 .getAlignViewport().getCodingComplement() != null;
425 vs.setScaleProteinAsCdna(ap.getAlignViewport()
426 .getViewStyle().isScaleProteinAsCdna());
428 ap.getAlignViewport().setViewStyle(vs);
431 * Also rescale ViewStyle of SplitFrame complement if there is
432 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
433 * the whole ViewStyle (allow cDNA protein to have different
436 AlignViewportI complement = ap.getAlignViewport()
437 .getCodingComplement();
438 if (complement != null && vs.isScaleProteinAsCdna())
440 AlignFrame af = Desktop.getAlignFrameFor(complement);
441 ((SplitFrame) af.getSplitViewContainer())
443 af.setMenusForViewport();
447 ap.setSelected(true);
448 ap.alignFrame.setMenusForViewport();
453 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
454 .indexOf("devel") > -1
455 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
456 .indexOf("test") > -1)
458 formatMenu.add(vsel);
460 addFocusListener(new FocusAdapter()
463 public void focusGained(FocusEvent e)
465 Jalview.setCurrentAlignFrame(AlignFrame.this);
472 * Change the filename and format for the alignment, and enable the 'reload'
473 * button functionality.
480 public void setFileName(String file, FileFormatI format)
483 setFileFormat(format);
484 reload.setEnabled(true);
488 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
491 void addKeyListener()
493 addKeyListener(new KeyAdapter()
496 public void keyPressed(KeyEvent evt)
498 if (viewport.cursorMode
499 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
500 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
501 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
502 && Character.isDigit(evt.getKeyChar()))
504 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
507 switch (evt.getKeyCode())
510 case 27: // escape key
511 deselectAllSequenceMenuItem_actionPerformed(null);
515 case KeyEvent.VK_DOWN:
516 if (evt.isAltDown() || !viewport.cursorMode)
518 moveSelectedSequences(false);
520 if (viewport.cursorMode)
522 alignPanel.getSeqPanel().moveCursor(0, 1);
527 if (evt.isAltDown() || !viewport.cursorMode)
529 moveSelectedSequences(true);
531 if (viewport.cursorMode)
533 alignPanel.getSeqPanel().moveCursor(0, -1);
538 case KeyEvent.VK_LEFT:
539 if (evt.isAltDown() || !viewport.cursorMode)
541 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
545 alignPanel.getSeqPanel().moveCursor(-1, 0);
550 case KeyEvent.VK_RIGHT:
551 if (evt.isAltDown() || !viewport.cursorMode)
553 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
557 alignPanel.getSeqPanel().moveCursor(1, 0);
561 case KeyEvent.VK_SPACE:
562 if (viewport.cursorMode)
564 alignPanel.getSeqPanel().insertGapAtCursor(
565 evt.isControlDown() || evt.isShiftDown()
570 // case KeyEvent.VK_A:
571 // if (viewport.cursorMode)
573 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
574 // //System.out.println("A");
578 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
579 * System.out.println("closing bracket"); } break;
581 case KeyEvent.VK_DELETE:
582 case KeyEvent.VK_BACK_SPACE:
583 if (!viewport.cursorMode)
585 cut_actionPerformed(null);
589 alignPanel.getSeqPanel().deleteGapAtCursor(
590 evt.isControlDown() || evt.isShiftDown()
597 if (viewport.cursorMode)
599 alignPanel.getSeqPanel().setCursorRow();
603 if (viewport.cursorMode && !evt.isControlDown())
605 alignPanel.getSeqPanel().setCursorColumn();
609 if (viewport.cursorMode)
611 alignPanel.getSeqPanel().setCursorPosition();
615 case KeyEvent.VK_ENTER:
616 case KeyEvent.VK_COMMA:
617 if (viewport.cursorMode)
619 alignPanel.getSeqPanel().setCursorRowAndColumn();
624 if (viewport.cursorMode)
626 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
630 if (viewport.cursorMode)
632 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
637 viewport.cursorMode = !viewport.cursorMode;
638 statusBar.setText(MessageManager.formatMessage(
639 "label.keyboard_editing_mode",
640 new String[] { (viewport.cursorMode ? "on" : "off") }));
641 if (viewport.cursorMode)
643 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
644 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
646 alignPanel.getSeqPanel().seqCanvas.repaint();
652 Help.showHelpWindow();
653 } catch (Exception ex)
655 ex.printStackTrace();
660 boolean toggleSeqs = !evt.isControlDown();
661 boolean toggleCols = !evt.isShiftDown();
662 toggleHiddenRegions(toggleSeqs, toggleCols);
667 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
668 boolean modifyExisting = true; // always modify, don't clear
669 // evt.isShiftDown();
670 boolean invertHighlighted = evt.isAltDown();
671 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
675 case KeyEvent.VK_PAGE_UP:
676 if (viewport.getWrapAlignment())
678 alignPanel.scrollUp(true);
682 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
683 - viewport.endSeq + viewport.startSeq);
686 case KeyEvent.VK_PAGE_DOWN:
687 if (viewport.getWrapAlignment())
689 alignPanel.scrollUp(false);
693 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
694 + viewport.endSeq - viewport.startSeq);
701 public void keyReleased(KeyEvent evt)
703 switch (evt.getKeyCode())
705 case KeyEvent.VK_LEFT:
706 if (evt.isAltDown() || !viewport.cursorMode)
708 viewport.firePropertyChange("alignment", null, viewport
709 .getAlignment().getSequences());
713 case KeyEvent.VK_RIGHT:
714 if (evt.isAltDown() || !viewport.cursorMode)
716 viewport.firePropertyChange("alignment", null, viewport
717 .getAlignment().getSequences());
725 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
727 ap.alignFrame = this;
728 avc = new jalview.controller.AlignViewController(this, viewport,
733 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
735 int aSize = alignPanels.size();
737 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
739 if (aSize == 1 && ap.av.viewName == null)
741 this.getContentPane().add(ap, BorderLayout.CENTER);
747 setInitialTabVisible();
750 expandViews.setEnabled(true);
751 gatherViews.setEnabled(true);
752 tabbedPane.addTab(ap.av.viewName, ap);
754 ap.setVisible(false);
759 if (ap.av.isPadGaps())
761 ap.av.getAlignment().padGaps();
763 ap.av.updateConservation(ap);
764 ap.av.updateConsensus(ap);
765 ap.av.updateStrucConsensus(ap);
769 public void setInitialTabVisible()
771 expandViews.setEnabled(true);
772 gatherViews.setEnabled(true);
773 tabbedPane.setVisible(true);
774 AlignmentPanel first = alignPanels.get(0);
775 tabbedPane.addTab(first.av.viewName, first);
776 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
779 public AlignViewport getViewport()
784 /* Set up intrinsic listeners for dynamically generated GUI bits. */
785 private void addServiceListeners()
787 final java.beans.PropertyChangeListener thisListener;
788 Desktop.instance.addJalviewPropertyChangeListener("services",
789 thisListener = new java.beans.PropertyChangeListener()
792 public void propertyChange(PropertyChangeEvent evt)
794 // // System.out.println("Discoverer property change.");
795 // if (evt.getPropertyName().equals("services"))
797 SwingUtilities.invokeLater(new Runnable()
804 .println("Rebuild WS Menu for service change");
805 BuildWebServiceMenu();
812 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
815 public void internalFrameClosed(
816 javax.swing.event.InternalFrameEvent evt)
818 // System.out.println("deregistering discoverer listener");
819 Desktop.instance.removeJalviewPropertyChangeListener("services",
821 closeMenuItem_actionPerformed(true);
824 // Finally, build the menu once to get current service state
825 new Thread(new Runnable()
830 BuildWebServiceMenu();
836 * Configure menu items that vary according to whether the alignment is
837 * nucleotide or protein
839 public void setGUINucleotide()
841 AlignmentI al = getViewport().getAlignment();
842 boolean nucleotide = al.isNucleotide();
844 showTranslation.setVisible(nucleotide);
845 showReverse.setVisible(nucleotide);
846 showReverseComplement.setVisible(nucleotide);
847 conservationMenuItem.setEnabled(!nucleotide);
848 modifyConservation.setEnabled(!nucleotide);
849 showGroupConservation.setEnabled(!nucleotide);
851 showComplementMenuItem.setText(nucleotide ? MessageManager
852 .getString("label.protein") : MessageManager
853 .getString("label.nucleotide"));
857 * set up menus for the current viewport. This may be called after any
858 * operation that affects the data in the current view (selection changed,
859 * etc) to update the menus to reflect the new state.
862 public void setMenusForViewport()
864 setMenusFromViewport(viewport);
868 * Need to call this method when tabs are selected for multiple views, or when
869 * loading from Jalview2XML.java
874 void setMenusFromViewport(AlignViewport av)
876 padGapsMenuitem.setSelected(av.isPadGaps());
877 colourTextMenuItem.setSelected(av.isShowColourText());
878 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
879 conservationMenuItem.setSelected(av.getConservationSelected());
880 seqLimits.setSelected(av.getShowJVSuffix());
881 idRightAlign.setSelected(av.isRightAlignIds());
882 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
883 renderGapsMenuItem.setSelected(av.isRenderGaps());
884 wrapMenuItem.setSelected(av.getWrapAlignment());
885 scaleAbove.setVisible(av.getWrapAlignment());
886 scaleLeft.setVisible(av.getWrapAlignment());
887 scaleRight.setVisible(av.getWrapAlignment());
888 annotationPanelMenuItem.setState(av.isShowAnnotation());
890 * Show/hide annotations only enabled if annotation panel is shown
892 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
893 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
894 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
895 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
896 viewBoxesMenuItem.setSelected(av.getShowBoxes());
897 viewTextMenuItem.setSelected(av.getShowText());
898 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
899 showGroupConsensus.setSelected(av.isShowGroupConsensus());
900 showGroupConservation.setSelected(av.isShowGroupConservation());
901 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
902 showSequenceLogo.setSelected(av.isShowSequenceLogo());
903 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
905 ColourMenuHelper.setColourSelected(colourMenu,
906 av.getGlobalColourScheme());
908 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
909 hiddenMarkers.setState(av.getShowHiddenMarkers());
910 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
911 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
912 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
913 autoCalculate.setSelected(av.autoCalculateConsensus);
914 sortByTree.setSelected(av.sortByTree);
915 listenToViewSelections.setSelected(av.followSelection);
917 showProducts.setEnabled(canShowProducts());
918 setGroovyEnabled(Desktop.getGroovyConsole() != null);
924 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
928 public void setGroovyEnabled(boolean b)
930 runGroovy.setEnabled(b);
933 private IProgressIndicator progressBar;
938 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
941 public void setProgressBar(String message, long id)
943 progressBar.setProgressBar(message, id);
947 public void registerHandler(final long id,
948 final IProgressIndicatorHandler handler)
950 progressBar.registerHandler(id, handler);
955 * @return true if any progress bars are still active
958 public boolean operationInProgress()
960 return progressBar.operationInProgress();
964 public void setStatus(String text)
966 statusBar.setText(text);
970 * Added so Castor Mapping file can obtain Jalview Version
972 public String getVersion()
974 return jalview.bin.Cache.getProperty("VERSION");
977 public FeatureRenderer getFeatureRenderer()
979 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
983 public void fetchSequence_actionPerformed(ActionEvent e)
985 new jalview.gui.SequenceFetcher(this);
989 public void addFromFile_actionPerformed(ActionEvent e)
991 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
995 public void reload_actionPerformed(ActionEvent e)
997 if (fileName != null)
999 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1000 // originating file's format
1001 // TODO: work out how to recover feature settings for correct view(s) when
1002 // file is reloaded.
1003 if (FileFormat.Jalview.equals(currentFileFormat))
1005 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1006 for (int i = 0; i < frames.length; i++)
1008 if (frames[i] instanceof AlignFrame && frames[i] != this
1009 && ((AlignFrame) frames[i]).fileName != null
1010 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1014 frames[i].setSelected(true);
1015 Desktop.instance.closeAssociatedWindows();
1016 } catch (java.beans.PropertyVetoException ex)
1022 Desktop.instance.closeAssociatedWindows();
1024 FileLoader loader = new FileLoader();
1025 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1026 : DataSourceType.FILE;
1027 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1031 Rectangle bounds = this.getBounds();
1033 FileLoader loader = new FileLoader();
1034 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1035 : DataSourceType.FILE;
1036 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1037 protocol, currentFileFormat);
1039 newframe.setBounds(bounds);
1040 if (featureSettings != null && featureSettings.isShowing())
1042 final Rectangle fspos = featureSettings.frame.getBounds();
1043 // TODO: need a 'show feature settings' function that takes bounds -
1044 // need to refactor Desktop.addFrame
1045 newframe.featureSettings_actionPerformed(null);
1046 final FeatureSettings nfs = newframe.featureSettings;
1047 SwingUtilities.invokeLater(new Runnable()
1052 nfs.frame.setBounds(fspos);
1055 this.featureSettings.close();
1056 this.featureSettings = null;
1058 this.closeMenuItem_actionPerformed(true);
1064 public void addFromText_actionPerformed(ActionEvent e)
1066 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1071 public void addFromURL_actionPerformed(ActionEvent e)
1073 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1077 public void save_actionPerformed(ActionEvent e)
1079 if (fileName == null || (currentFileFormat == null)
1080 || fileName.startsWith("http"))
1082 saveAs_actionPerformed(null);
1086 saveAlignment(fileName, currentFileFormat);
1097 public void saveAs_actionPerformed(ActionEvent e)
1099 String format = currentFileFormat == null ? null : currentFileFormat
1101 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1102 Cache.getProperty("LAST_DIRECTORY"), format);
1104 chooser.setFileView(new JalviewFileView());
1105 chooser.setDialogTitle(MessageManager
1106 .getString("label.save_alignment_to_file"));
1107 chooser.setToolTipText(MessageManager.getString("action.save"));
1109 int value = chooser.showSaveDialog(this);
1111 if (value == JalviewFileChooser.APPROVE_OPTION)
1113 currentFileFormat = chooser.getSelectedFormat();
1114 while (currentFileFormat == null)
1117 .showInternalMessageDialog(
1120 .getString("label.select_file_format_before_saving"),
1122 .getString("label.file_format_not_specified"),
1123 JvOptionPane.WARNING_MESSAGE);
1124 currentFileFormat = chooser.getSelectedFormat();
1125 value = chooser.showSaveDialog(this);
1126 if (value != JalviewFileChooser.APPROVE_OPTION)
1132 fileName = chooser.getSelectedFile().getPath();
1134 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1136 Cache.setProperty("LAST_DIRECTORY", fileName);
1137 saveAlignment(fileName, currentFileFormat);
1141 public boolean saveAlignment(String file, FileFormatI format)
1143 boolean success = true;
1145 if (FileFormat.Jalview.equals(format))
1147 String shortName = title;
1149 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1151 shortName = shortName.substring(shortName
1152 .lastIndexOf(java.io.File.separatorChar) + 1);
1155 success = new Jalview2XML().saveAlignment(this, file, shortName);
1157 statusBar.setText(MessageManager.formatMessage(
1158 "label.successfully_saved_to_file_in_format", new Object[] {
1159 fileName, format }));
1164 AlignmentExportData exportData = getAlignmentForExport(format,
1166 if (exportData.getSettings().isCancelled())
1170 FormatAdapter f = new FormatAdapter(alignPanel,
1171 exportData.getSettings());
1172 String output = f.formatSequences(
1174 exportData.getAlignment(), // class cast exceptions will
1175 // occur in the distant future
1176 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1177 f.getCacheSuffixDefault(format),
1178 viewport.getColumnSelection());
1188 PrintWriter out = new PrintWriter(new FileWriter(file));
1192 this.setTitle(file);
1193 statusBar.setText(MessageManager.formatMessage(
1194 "label.successfully_saved_to_file_in_format",
1195 new Object[] { fileName, format.getName() }));
1196 } catch (Exception ex)
1199 ex.printStackTrace();
1206 JvOptionPane.showInternalMessageDialog(this, MessageManager
1207 .formatMessage("label.couldnt_save_file",
1208 new Object[] { fileName }), MessageManager
1209 .getString("label.error_saving_file"),
1210 JvOptionPane.WARNING_MESSAGE);
1216 private void warningMessage(String warning, String title)
1218 if (new jalview.util.Platform().isHeadless())
1220 System.err.println("Warning: " + title + "\nWarning: " + warning);
1225 JvOptionPane.showInternalMessageDialog(this, warning, title,
1226 JvOptionPane.WARNING_MESSAGE);
1238 protected void outputText_actionPerformed(ActionEvent e)
1240 FileFormatI fileFormat = FileFormats.getInstance().forName(
1241 e.getActionCommand());
1242 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1244 if (exportData.getSettings().isCancelled())
1248 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1249 cap.setForInput(null);
1252 FileFormatI format = fileFormat;
1253 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1254 .formatSequences(format,
1255 exportData.getAlignment(),
1256 exportData.getOmitHidden(),
1257 exportData.getStartEndPostions(),
1258 viewport.getColumnSelection()));
1259 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1260 "label.alignment_output_command",
1261 new Object[] { e.getActionCommand() }), 600, 500);
1262 } catch (OutOfMemoryError oom)
1264 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1270 public static AlignmentExportData getAlignmentForExport(
1271 FileFormatI format, AlignViewportI viewport,
1272 AlignExportSettingI exportSettings)
1274 AlignmentI alignmentToExport = null;
1275 AlignExportSettingI settings = exportSettings;
1276 String[] omitHidden = null;
1278 HiddenSequences hiddenSeqs = viewport.getAlignment()
1279 .getHiddenSequences();
1281 alignmentToExport = viewport.getAlignment();
1283 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1284 if (settings == null)
1286 settings = new AlignExportSettings(hasHiddenSeqs,
1287 viewport.hasHiddenColumns(), format);
1289 // settings.isExportAnnotations();
1291 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1293 omitHidden = viewport.getViewAsString(false,
1294 settings.isExportHiddenSequences());
1297 int[] alignmentStartEnd = new int[2];
1298 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1300 alignmentToExport = hiddenSeqs.getFullAlignment();
1304 alignmentToExport = viewport.getAlignment();
1306 alignmentStartEnd = alignmentToExport
1307 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1308 .getHiddenColumns());
1309 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1310 omitHidden, alignmentStartEnd, settings);
1321 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1323 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1324 htmlSVG.exportHTML(null);
1328 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1330 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1331 bjs.exportHTML(null);
1334 public void createImageMap(File file, String image)
1336 alignPanel.makePNGImageMap(file, image);
1346 public void createPNG(File f)
1348 alignPanel.makePNG(f);
1358 public void createEPS(File f)
1360 alignPanel.makeEPS(f);
1364 public void createSVG(File f)
1366 alignPanel.makeSVG(f);
1370 public void pageSetup_actionPerformed(ActionEvent e)
1372 PrinterJob printJob = PrinterJob.getPrinterJob();
1373 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1383 public void printMenuItem_actionPerformed(ActionEvent e)
1385 // Putting in a thread avoids Swing painting problems
1386 PrintThread thread = new PrintThread(alignPanel);
1391 public void exportFeatures_actionPerformed(ActionEvent e)
1393 new AnnotationExporter().exportFeatures(alignPanel);
1397 public void exportAnnotations_actionPerformed(ActionEvent e)
1399 new AnnotationExporter().exportAnnotations(alignPanel);
1403 public void associatedData_actionPerformed(ActionEvent e)
1405 // Pick the tree file
1406 JalviewFileChooser chooser = new JalviewFileChooser(
1407 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1408 chooser.setFileView(new JalviewFileView());
1409 chooser.setDialogTitle(MessageManager
1410 .getString("label.load_jalview_annotations"));
1411 chooser.setToolTipText(MessageManager
1412 .getString("label.load_jalview_annotations"));
1414 int value = chooser.showOpenDialog(null);
1416 if (value == JalviewFileChooser.APPROVE_OPTION)
1418 String choice = chooser.getSelectedFile().getPath();
1419 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1420 loadJalviewDataFile(choice, null, null, null);
1426 * Close the current view or all views in the alignment frame. If the frame
1427 * only contains one view then the alignment will be removed from memory.
1429 * @param closeAllTabs
1432 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1434 if (alignPanels != null && alignPanels.size() < 2)
1436 closeAllTabs = true;
1441 if (alignPanels != null)
1445 if (this.isClosed())
1447 // really close all the windows - otherwise wait till
1448 // setClosed(true) is called
1449 for (int i = 0; i < alignPanels.size(); i++)
1451 AlignmentPanel ap = alignPanels.get(i);
1458 closeView(alignPanel);
1465 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1466 * be called recursively, with the frame now in 'closed' state
1468 this.setClosed(true);
1470 } catch (Exception ex)
1472 ex.printStackTrace();
1477 * Close the specified panel and close up tabs appropriately.
1479 * @param panelToClose
1481 public void closeView(AlignmentPanel panelToClose)
1483 int index = tabbedPane.getSelectedIndex();
1484 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1485 alignPanels.remove(panelToClose);
1486 panelToClose.closePanel();
1487 panelToClose = null;
1489 tabbedPane.removeTabAt(closedindex);
1490 tabbedPane.validate();
1492 if (index > closedindex || index == tabbedPane.getTabCount())
1494 // modify currently selected tab index if necessary.
1498 this.tabSelectionChanged(index);
1504 void updateEditMenuBar()
1507 if (viewport.getHistoryList().size() > 0)
1509 undoMenuItem.setEnabled(true);
1510 CommandI command = viewport.getHistoryList().peek();
1511 undoMenuItem.setText(MessageManager.formatMessage(
1512 "label.undo_command",
1513 new Object[] { command.getDescription() }));
1517 undoMenuItem.setEnabled(false);
1518 undoMenuItem.setText(MessageManager.getString("action.undo"));
1521 if (viewport.getRedoList().size() > 0)
1523 redoMenuItem.setEnabled(true);
1525 CommandI command = viewport.getRedoList().peek();
1526 redoMenuItem.setText(MessageManager.formatMessage(
1527 "label.redo_command",
1528 new Object[] { command.getDescription() }));
1532 redoMenuItem.setEnabled(false);
1533 redoMenuItem.setText(MessageManager.getString("action.redo"));
1538 public void addHistoryItem(CommandI command)
1540 if (command.getSize() > 0)
1542 viewport.addToHistoryList(command);
1543 viewport.clearRedoList();
1544 updateEditMenuBar();
1545 viewport.updateHiddenColumns();
1546 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1547 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1548 // viewport.getColumnSelection()
1549 // .getHiddenColumns().size() > 0);
1555 * @return alignment objects for all views
1557 AlignmentI[] getViewAlignments()
1559 if (alignPanels != null)
1561 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1563 for (AlignmentPanel ap : alignPanels)
1565 als[i++] = ap.av.getAlignment();
1569 if (viewport != null)
1571 return new AlignmentI[] { viewport.getAlignment() };
1583 protected void undoMenuItem_actionPerformed(ActionEvent e)
1585 if (viewport.getHistoryList().isEmpty())
1589 CommandI command = viewport.getHistoryList().pop();
1590 viewport.addToRedoList(command);
1591 command.undoCommand(getViewAlignments());
1593 AlignmentViewport originalSource = getOriginatingSource(command);
1594 updateEditMenuBar();
1596 if (originalSource != null)
1598 if (originalSource != viewport)
1601 .warn("Implementation worry: mismatch of viewport origin for undo");
1603 originalSource.updateHiddenColumns();
1604 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1606 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1607 // viewport.getColumnSelection()
1608 // .getHiddenColumns().size() > 0);
1609 originalSource.firePropertyChange("alignment", null, originalSource
1610 .getAlignment().getSequences());
1621 protected void redoMenuItem_actionPerformed(ActionEvent e)
1623 if (viewport.getRedoList().size() < 1)
1628 CommandI command = viewport.getRedoList().pop();
1629 viewport.addToHistoryList(command);
1630 command.doCommand(getViewAlignments());
1632 AlignmentViewport originalSource = getOriginatingSource(command);
1633 updateEditMenuBar();
1635 if (originalSource != null)
1638 if (originalSource != viewport)
1641 .warn("Implementation worry: mismatch of viewport origin for redo");
1643 originalSource.updateHiddenColumns();
1644 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1646 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1647 // viewport.getColumnSelection()
1648 // .getHiddenColumns().size() > 0);
1649 originalSource.firePropertyChange("alignment", null, originalSource
1650 .getAlignment().getSequences());
1654 AlignmentViewport getOriginatingSource(CommandI command)
1656 AlignmentViewport originalSource = null;
1657 // For sequence removal and addition, we need to fire
1658 // the property change event FROM the viewport where the
1659 // original alignment was altered
1660 AlignmentI al = null;
1661 if (command instanceof EditCommand)
1663 EditCommand editCommand = (EditCommand) command;
1664 al = editCommand.getAlignment();
1665 List<Component> comps = PaintRefresher.components.get(viewport
1666 .getSequenceSetId());
1668 for (Component comp : comps)
1670 if (comp instanceof AlignmentPanel)
1672 if (al == ((AlignmentPanel) comp).av.getAlignment())
1674 originalSource = ((AlignmentPanel) comp).av;
1681 if (originalSource == null)
1683 // The original view is closed, we must validate
1684 // the current view against the closed view first
1687 PaintRefresher.validateSequences(al, viewport.getAlignment());
1690 originalSource = viewport;
1693 return originalSource;
1702 public void moveSelectedSequences(boolean up)
1704 SequenceGroup sg = viewport.getSelectionGroup();
1710 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1711 viewport.getHiddenRepSequences(), up);
1712 alignPanel.paintAlignment(true);
1715 synchronized void slideSequences(boolean right, int size)
1717 List<SequenceI> sg = new ArrayList<SequenceI>();
1718 if (viewport.cursorMode)
1720 sg.add(viewport.getAlignment().getSequenceAt(
1721 alignPanel.getSeqPanel().seqCanvas.cursorY));
1723 else if (viewport.getSelectionGroup() != null
1724 && viewport.getSelectionGroup().getSize() != viewport
1725 .getAlignment().getHeight())
1727 sg = viewport.getSelectionGroup().getSequences(
1728 viewport.getHiddenRepSequences());
1736 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1738 for (SequenceI seq : viewport.getAlignment().getSequences())
1740 if (!sg.contains(seq))
1742 invertGroup.add(seq);
1746 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1748 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1749 for (int i = 0; i < invertGroup.size(); i++)
1751 seqs2[i] = invertGroup.get(i);
1754 SlideSequencesCommand ssc;
1757 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1758 size, viewport.getGapCharacter());
1762 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1763 size, viewport.getGapCharacter());
1766 int groupAdjustment = 0;
1767 if (ssc.getGapsInsertedBegin() && right)
1769 if (viewport.cursorMode)
1771 alignPanel.getSeqPanel().moveCursor(size, 0);
1775 groupAdjustment = size;
1778 else if (!ssc.getGapsInsertedBegin() && !right)
1780 if (viewport.cursorMode)
1782 alignPanel.getSeqPanel().moveCursor(-size, 0);
1786 groupAdjustment = -size;
1790 if (groupAdjustment != 0)
1792 viewport.getSelectionGroup().setStartRes(
1793 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1794 viewport.getSelectionGroup().setEndRes(
1795 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1799 * just extend the last slide command if compatible; but not if in
1800 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1802 boolean appendHistoryItem = false;
1803 Deque<CommandI> historyList = viewport.getHistoryList();
1804 boolean inSplitFrame = getSplitViewContainer() != null;
1805 if (!inSplitFrame && historyList != null && historyList.size() > 0
1806 && historyList.peek() instanceof SlideSequencesCommand)
1808 appendHistoryItem = ssc
1809 .appendSlideCommand((SlideSequencesCommand) historyList
1813 if (!appendHistoryItem)
1815 addHistoryItem(ssc);
1828 protected void copy_actionPerformed(ActionEvent e)
1831 if (viewport.getSelectionGroup() == null)
1835 // TODO: preserve the ordering of displayed alignment annotation in any
1836 // internal paste (particularly sequence associated annotation)
1837 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1838 String[] omitHidden = null;
1840 if (viewport.hasHiddenColumns())
1842 omitHidden = viewport.getViewAsString(true);
1845 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1849 StringSelection ss = new StringSelection(output);
1853 jalview.gui.Desktop.internalCopy = true;
1854 // Its really worth setting the clipboard contents
1855 // to empty before setting the large StringSelection!!
1856 Toolkit.getDefaultToolkit().getSystemClipboard()
1857 .setContents(new StringSelection(""), null);
1859 Toolkit.getDefaultToolkit().getSystemClipboard()
1860 .setContents(ss, Desktop.instance);
1861 } catch (OutOfMemoryError er)
1863 new OOMWarning("copying region", er);
1867 ArrayList<int[]> hiddenColumns = null;
1868 if (viewport.hasHiddenColumns())
1870 hiddenColumns = new ArrayList<int[]>();
1871 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1872 .getSelectionGroup().getEndRes();
1873 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1875 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1877 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1878 region[1] - hiddenOffset });
1883 Desktop.jalviewClipboard = new Object[] { seqs,
1884 viewport.getAlignment().getDataset(), hiddenColumns };
1885 statusBar.setText(MessageManager.formatMessage(
1886 "label.copied_sequences_to_clipboard", new Object[] { Integer
1887 .valueOf(seqs.length).toString() }));
1897 protected void pasteNew_actionPerformed(ActionEvent e)
1909 protected void pasteThis_actionPerformed(ActionEvent e)
1915 * Paste contents of Jalview clipboard
1917 * @param newAlignment
1918 * true to paste to a new alignment, otherwise add to this.
1920 void paste(boolean newAlignment)
1922 boolean externalPaste = true;
1925 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1926 Transferable contents = c.getContents(this);
1928 if (contents == null)
1937 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1938 if (str.length() < 1)
1943 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1945 } catch (OutOfMemoryError er)
1947 new OOMWarning("Out of memory pasting sequences!!", er);
1951 SequenceI[] sequences;
1952 boolean annotationAdded = false;
1953 AlignmentI alignment = null;
1955 if (Desktop.jalviewClipboard != null)
1957 // The clipboard was filled from within Jalview, we must use the
1959 // And dataset from the copied alignment
1960 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1961 // be doubly sure that we create *new* sequence objects.
1962 sequences = new SequenceI[newseq.length];
1963 for (int i = 0; i < newseq.length; i++)
1965 sequences[i] = new Sequence(newseq[i]);
1967 alignment = new Alignment(sequences);
1968 externalPaste = false;
1972 // parse the clipboard as an alignment.
1973 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1975 sequences = alignment.getSequencesArray();
1979 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1985 if (Desktop.jalviewClipboard != null)
1987 // dataset is inherited
1988 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1992 // new dataset is constructed
1993 alignment.setDataset(null);
1995 alwidth = alignment.getWidth() + 1;
1999 AlignmentI pastedal = alignment; // preserve pasted alignment object
2000 // Add pasted sequences and dataset into existing alignment.
2001 alignment = viewport.getAlignment();
2002 alwidth = alignment.getWidth() + 1;
2003 // decide if we need to import sequences from an existing dataset
2004 boolean importDs = Desktop.jalviewClipboard != null
2005 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2006 // importDs==true instructs us to copy over new dataset sequences from
2007 // an existing alignment
2008 Vector newDs = (importDs) ? new Vector() : null; // used to create
2009 // minimum dataset set
2011 for (int i = 0; i < sequences.length; i++)
2015 newDs.addElement(null);
2017 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2019 if (importDs && ds != null)
2021 if (!newDs.contains(ds))
2023 newDs.setElementAt(ds, i);
2024 ds = new Sequence(ds);
2025 // update with new dataset sequence
2026 sequences[i].setDatasetSequence(ds);
2030 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2035 // copy and derive new dataset sequence
2036 sequences[i] = sequences[i].deriveSequence();
2037 alignment.getDataset().addSequence(
2038 sequences[i].getDatasetSequence());
2039 // TODO: avoid creation of duplicate dataset sequences with a
2040 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2042 alignment.addSequence(sequences[i]); // merges dataset
2046 newDs.clear(); // tidy up
2048 if (alignment.getAlignmentAnnotation() != null)
2050 for (AlignmentAnnotation alan : alignment
2051 .getAlignmentAnnotation())
2053 if (alan.graphGroup > fgroup)
2055 fgroup = alan.graphGroup;
2059 if (pastedal.getAlignmentAnnotation() != null)
2061 // Add any annotation attached to alignment.
2062 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2063 for (int i = 0; i < alann.length; i++)
2065 annotationAdded = true;
2066 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2068 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2069 if (newann.graphGroup > -1)
2071 if (newGraphGroups.size() <= newann.graphGroup
2072 || newGraphGroups.get(newann.graphGroup) == null)
2074 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2076 newGraphGroups.add(q, null);
2078 newGraphGroups.set(newann.graphGroup, new Integer(
2081 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2085 newann.padAnnotation(alwidth);
2086 alignment.addAnnotation(newann);
2096 addHistoryItem(new EditCommand(
2097 MessageManager.getString("label.add_sequences"),
2098 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2100 // Add any annotations attached to sequences
2101 for (int i = 0; i < sequences.length; i++)
2103 if (sequences[i].getAnnotation() != null)
2105 AlignmentAnnotation newann;
2106 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2108 annotationAdded = true;
2109 newann = sequences[i].getAnnotation()[a];
2110 newann.adjustForAlignment();
2111 newann.padAnnotation(alwidth);
2112 if (newann.graphGroup > -1)
2114 if (newann.graphGroup > -1)
2116 if (newGraphGroups.size() <= newann.graphGroup
2117 || newGraphGroups.get(newann.graphGroup) == null)
2119 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2121 newGraphGroups.add(q, null);
2123 newGraphGroups.set(newann.graphGroup, new Integer(
2126 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2130 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2135 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2142 // propagate alignment changed.
2143 viewport.setEndSeq(alignment.getHeight());
2144 if (annotationAdded)
2146 // Duplicate sequence annotation in all views.
2147 AlignmentI[] alview = this.getViewAlignments();
2148 for (int i = 0; i < sequences.length; i++)
2150 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2155 for (int avnum = 0; avnum < alview.length; avnum++)
2157 if (alview[avnum] != alignment)
2159 // duplicate in a view other than the one with input focus
2160 int avwidth = alview[avnum].getWidth() + 1;
2161 // this relies on sann being preserved after we
2162 // modify the sequence's annotation array for each duplication
2163 for (int a = 0; a < sann.length; a++)
2165 AlignmentAnnotation newann = new AlignmentAnnotation(
2167 sequences[i].addAlignmentAnnotation(newann);
2168 newann.padAnnotation(avwidth);
2169 alview[avnum].addAnnotation(newann); // annotation was
2170 // duplicated earlier
2171 // TODO JAL-1145 graphGroups are not updated for sequence
2172 // annotation added to several views. This may cause
2174 alview[avnum].setAnnotationIndex(newann, a);
2179 buildSortByAnnotationScoresMenu();
2181 viewport.firePropertyChange("alignment", null,
2182 alignment.getSequences());
2183 if (alignPanels != null)
2185 for (AlignmentPanel ap : alignPanels)
2187 ap.validateAnnotationDimensions(false);
2192 alignPanel.validateAnnotationDimensions(false);
2198 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2200 String newtitle = new String("Copied sequences");
2202 if (Desktop.jalviewClipboard != null
2203 && Desktop.jalviewClipboard[2] != null)
2205 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2206 for (int[] region : hc)
2208 af.viewport.hideColumns(region[0], region[1]);
2212 // >>>This is a fix for the moment, until a better solution is
2214 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2216 alignPanel.getSeqPanel().seqCanvas
2217 .getFeatureRenderer());
2219 // TODO: maintain provenance of an alignment, rather than just make the
2220 // title a concatenation of operations.
2223 if (title.startsWith("Copied sequences"))
2229 newtitle = newtitle.concat("- from " + title);
2234 newtitle = new String("Pasted sequences");
2237 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2242 } catch (Exception ex)
2244 ex.printStackTrace();
2245 System.out.println("Exception whilst pasting: " + ex);
2246 // could be anything being pasted in here
2252 protected void expand_newalign(ActionEvent e)
2256 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2257 .getAlignment(), -1);
2258 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2260 String newtitle = new String("Flanking alignment");
2262 if (Desktop.jalviewClipboard != null
2263 && Desktop.jalviewClipboard[2] != null)
2265 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2266 for (int region[] : hc)
2268 af.viewport.hideColumns(region[0], region[1]);
2272 // >>>This is a fix for the moment, until a better solution is
2274 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2276 alignPanel.getSeqPanel().seqCanvas
2277 .getFeatureRenderer());
2279 // TODO: maintain provenance of an alignment, rather than just make the
2280 // title a concatenation of operations.
2282 if (title.startsWith("Copied sequences"))
2288 newtitle = newtitle.concat("- from " + title);
2292 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2294 } catch (Exception ex)
2296 ex.printStackTrace();
2297 System.out.println("Exception whilst pasting: " + ex);
2298 // could be anything being pasted in here
2299 } catch (OutOfMemoryError oom)
2301 new OOMWarning("Viewing flanking region of alignment", oom);
2312 protected void cut_actionPerformed(ActionEvent e)
2314 copy_actionPerformed(null);
2315 delete_actionPerformed(null);
2325 protected void delete_actionPerformed(ActionEvent evt)
2328 SequenceGroup sg = viewport.getSelectionGroup();
2335 * If the cut affects all sequences, warn, remove highlighted columns
2337 if (sg.getSize() == viewport.getAlignment().getHeight())
2339 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2340 .getAlignment().getWidth()) ? true : false;
2341 if (isEntireAlignWidth)
2343 int confirm = JvOptionPane.showConfirmDialog(this,
2344 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2345 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2346 JvOptionPane.OK_CANCEL_OPTION);
2348 if (confirm == JvOptionPane.CANCEL_OPTION
2349 || confirm == JvOptionPane.CLOSED_OPTION)
2354 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2355 sg.getEndRes() + 1);
2357 SequenceI[] cut = sg.getSequences()
2358 .toArray(new SequenceI[sg.getSize()]);
2360 addHistoryItem(new EditCommand(
2361 MessageManager.getString("label.cut_sequences"), Action.CUT,
2362 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2363 viewport.getAlignment()));
2365 viewport.setSelectionGroup(null);
2366 viewport.sendSelection();
2367 viewport.getAlignment().deleteGroup(sg);
2369 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2371 if (viewport.getAlignment().getHeight() < 1)
2375 this.setClosed(true);
2376 } catch (Exception ex)
2389 protected void deleteGroups_actionPerformed(ActionEvent e)
2391 if (avc.deleteGroups())
2393 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2394 alignPanel.updateAnnotation();
2395 alignPanel.paintAlignment(true);
2406 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2408 SequenceGroup sg = new SequenceGroup();
2410 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2412 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2415 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2416 viewport.setSelectionGroup(sg);
2417 viewport.sendSelection();
2418 // JAL-2034 - should delegate to
2419 // alignPanel to decide if overview needs
2421 alignPanel.paintAlignment(false);
2422 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2432 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2434 if (viewport.cursorMode)
2436 alignPanel.getSeqPanel().keyboardNo1 = null;
2437 alignPanel.getSeqPanel().keyboardNo2 = null;
2439 viewport.setSelectionGroup(null);
2440 viewport.getColumnSelection().clear();
2441 viewport.setSelectionGroup(null);
2442 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2443 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2444 // JAL-2034 - should delegate to
2445 // alignPanel to decide if overview needs
2447 alignPanel.paintAlignment(false);
2448 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2449 viewport.sendSelection();
2459 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2461 SequenceGroup sg = viewport.getSelectionGroup();
2465 selectAllSequenceMenuItem_actionPerformed(null);
2470 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2472 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2474 // JAL-2034 - should delegate to
2475 // alignPanel to decide if overview needs
2478 alignPanel.paintAlignment(true);
2479 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2480 viewport.sendSelection();
2484 public void invertColSel_actionPerformed(ActionEvent e)
2486 viewport.invertColumnSelection();
2487 alignPanel.paintAlignment(true);
2488 viewport.sendSelection();
2498 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2500 trimAlignment(true);
2510 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2512 trimAlignment(false);
2515 void trimAlignment(boolean trimLeft)
2517 ColumnSelection colSel = viewport.getColumnSelection();
2520 if (!colSel.isEmpty())
2524 column = colSel.getMin();
2528 column = colSel.getMax();
2532 if (viewport.getSelectionGroup() != null)
2534 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2535 viewport.getHiddenRepSequences());
2539 seqs = viewport.getAlignment().getSequencesArray();
2542 TrimRegionCommand trimRegion;
2545 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2546 column, viewport.getAlignment());
2547 viewport.setStartRes(0);
2551 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2552 column, viewport.getAlignment());
2555 statusBar.setText(MessageManager.formatMessage(
2556 "label.removed_columns",
2557 new String[] { Integer.valueOf(trimRegion.getSize())
2560 addHistoryItem(trimRegion);
2562 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2564 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2565 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2567 viewport.getAlignment().deleteGroup(sg);
2571 viewport.firePropertyChange("alignment", null, viewport
2572 .getAlignment().getSequences());
2583 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2585 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2588 if (viewport.getSelectionGroup() != null)
2590 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2591 viewport.getHiddenRepSequences());
2592 start = viewport.getSelectionGroup().getStartRes();
2593 end = viewport.getSelectionGroup().getEndRes();
2597 seqs = viewport.getAlignment().getSequencesArray();
2600 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2601 "Remove Gapped Columns", seqs, start, end,
2602 viewport.getAlignment());
2604 addHistoryItem(removeGapCols);
2606 statusBar.setText(MessageManager.formatMessage(
2607 "label.removed_empty_columns",
2608 new Object[] { Integer.valueOf(removeGapCols.getSize())
2611 // This is to maintain viewport position on first residue
2612 // of first sequence
2613 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2614 int startRes = seq.findPosition(viewport.startRes);
2615 // ShiftList shifts;
2616 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2617 // edit.alColumnChanges=shifts.getInverse();
2618 // if (viewport.hasHiddenColumns)
2619 // viewport.getColumnSelection().compensateForEdits(shifts);
2620 viewport.setStartRes(seq.findIndex(startRes) - 1);
2621 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2633 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2635 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2638 if (viewport.getSelectionGroup() != null)
2640 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2641 viewport.getHiddenRepSequences());
2642 start = viewport.getSelectionGroup().getStartRes();
2643 end = viewport.getSelectionGroup().getEndRes();
2647 seqs = viewport.getAlignment().getSequencesArray();
2650 // This is to maintain viewport position on first residue
2651 // of first sequence
2652 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2653 int startRes = seq.findPosition(viewport.startRes);
2655 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2656 viewport.getAlignment()));
2658 viewport.setStartRes(seq.findIndex(startRes) - 1);
2660 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2672 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2674 viewport.setPadGaps(padGapsMenuitem.isSelected());
2675 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2686 public void findMenuItem_actionPerformed(ActionEvent e)
2692 * Create a new view of the current alignment.
2695 public void newView_actionPerformed(ActionEvent e)
2697 newView(null, true);
2701 * Creates and shows a new view of the current alignment.
2704 * title of newly created view; if null, one will be generated
2705 * @param copyAnnotation
2706 * if true then duplicate all annnotation, groups and settings
2707 * @return new alignment panel, already displayed.
2709 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2712 * Create a new AlignmentPanel (with its own, new Viewport)
2714 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2716 if (!copyAnnotation)
2719 * remove all groups and annotation except for the automatic stuff
2721 newap.av.getAlignment().deleteAllGroups();
2722 newap.av.getAlignment().deleteAllAnnotations(false);
2725 newap.av.setGatherViewsHere(false);
2727 if (viewport.viewName == null)
2729 viewport.viewName = MessageManager
2730 .getString("label.view_name_original");
2734 * Views share the same edits undo and redo stacks
2736 newap.av.setHistoryList(viewport.getHistoryList());
2737 newap.av.setRedoList(viewport.getRedoList());
2740 * Views share the same mappings; need to deregister any new mappings
2741 * created by copyAlignPanel, and register the new reference to the shared
2744 newap.av.replaceMappings(viewport.getAlignment());
2746 newap.av.viewName = getNewViewName(viewTitle);
2748 addAlignmentPanel(newap, true);
2749 newap.alignmentChanged();
2751 if (alignPanels.size() == 2)
2753 viewport.setGatherViewsHere(true);
2755 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2760 * Make a new name for the view, ensuring it is unique within the current
2761 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2762 * these now use viewId. Unique view names are still desirable for usability.)
2767 protected String getNewViewName(String viewTitle)
2769 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2770 boolean addFirstIndex = false;
2771 if (viewTitle == null || viewTitle.trim().length() == 0)
2773 viewTitle = MessageManager.getString("action.view");
2774 addFirstIndex = true;
2778 index = 1;// we count from 1 if given a specific name
2780 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2782 List<Component> comps = PaintRefresher.components.get(viewport
2783 .getSequenceSetId());
2785 List<String> existingNames = getExistingViewNames(comps);
2787 while (existingNames.contains(newViewName))
2789 newViewName = viewTitle + " " + (++index);
2795 * Returns a list of distinct view names found in the given list of
2796 * components. View names are held on the viewport of an AlignmentPanel.
2801 protected List<String> getExistingViewNames(List<Component> comps)
2803 List<String> existingNames = new ArrayList<String>();
2804 for (Component comp : comps)
2806 if (comp instanceof AlignmentPanel)
2808 AlignmentPanel ap = (AlignmentPanel) comp;
2809 if (!existingNames.contains(ap.av.viewName))
2811 existingNames.add(ap.av.viewName);
2815 return existingNames;
2819 * Explode tabbed views into separate windows.
2822 public void expandViews_actionPerformed(ActionEvent e)
2824 Desktop.explodeViews(this);
2828 * Gather views in separate windows back into a tabbed presentation.
2831 public void gatherViews_actionPerformed(ActionEvent e)
2833 Desktop.instance.gatherViews(this);
2843 public void font_actionPerformed(ActionEvent e)
2845 new FontChooser(alignPanel);
2855 protected void seqLimit_actionPerformed(ActionEvent e)
2857 viewport.setShowJVSuffix(seqLimits.isSelected());
2859 alignPanel.getIdPanel().getIdCanvas()
2860 .setPreferredSize(alignPanel.calculateIdWidth());
2861 alignPanel.paintAlignment(true);
2865 public void idRightAlign_actionPerformed(ActionEvent e)
2867 viewport.setRightAlignIds(idRightAlign.isSelected());
2868 alignPanel.paintAlignment(true);
2872 public void centreColumnLabels_actionPerformed(ActionEvent e)
2874 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2875 alignPanel.paintAlignment(true);
2881 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2884 protected void followHighlight_actionPerformed()
2887 * Set the 'follow' flag on the Viewport (and scroll to position if now
2890 final boolean state = this.followHighlightMenuItem.getState();
2891 viewport.setFollowHighlight(state);
2894 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2905 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2907 viewport.setColourText(colourTextMenuItem.isSelected());
2908 alignPanel.paintAlignment(true);
2918 public void wrapMenuItem_actionPerformed(ActionEvent e)
2920 scaleAbove.setVisible(wrapMenuItem.isSelected());
2921 scaleLeft.setVisible(wrapMenuItem.isSelected());
2922 scaleRight.setVisible(wrapMenuItem.isSelected());
2923 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2924 alignPanel.updateLayout();
2928 public void showAllSeqs_actionPerformed(ActionEvent e)
2930 viewport.showAllHiddenSeqs();
2934 public void showAllColumns_actionPerformed(ActionEvent e)
2936 viewport.showAllHiddenColumns();
2938 viewport.sendSelection();
2942 public void hideSelSequences_actionPerformed(ActionEvent e)
2944 viewport.hideAllSelectedSeqs();
2945 // alignPanel.paintAlignment(true);
2949 * called by key handler and the hide all/show all menu items
2954 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2957 boolean hide = false;
2958 SequenceGroup sg = viewport.getSelectionGroup();
2959 if (!toggleSeqs && !toggleCols)
2961 // Hide everything by the current selection - this is a hack - we do the
2962 // invert and then hide
2963 // first check that there will be visible columns after the invert.
2964 if (viewport.hasSelectedColumns()
2965 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2968 // now invert the sequence set, if required - empty selection implies
2969 // that no hiding is required.
2972 invertSequenceMenuItem_actionPerformed(null);
2973 sg = viewport.getSelectionGroup();
2977 viewport.expandColSelection(sg, true);
2978 // finally invert the column selection and get the new sequence
2980 invertColSel_actionPerformed(null);
2987 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2989 hideSelSequences_actionPerformed(null);
2992 else if (!(toggleCols && viewport.hasSelectedColumns()))
2994 showAllSeqs_actionPerformed(null);
3000 if (viewport.hasSelectedColumns())
3002 hideSelColumns_actionPerformed(null);
3005 viewport.setSelectionGroup(sg);
3010 showAllColumns_actionPerformed(null);
3019 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3020 * event.ActionEvent)
3023 public void hideAllButSelection_actionPerformed(ActionEvent e)
3025 toggleHiddenRegions(false, false);
3026 viewport.sendSelection();
3033 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3037 public void hideAllSelection_actionPerformed(ActionEvent e)
3039 SequenceGroup sg = viewport.getSelectionGroup();
3040 viewport.expandColSelection(sg, false);
3041 viewport.hideAllSelectedSeqs();
3042 viewport.hideSelectedColumns();
3043 alignPanel.paintAlignment(true);
3044 viewport.sendSelection();
3051 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3055 public void showAllhidden_actionPerformed(ActionEvent e)
3057 viewport.showAllHiddenColumns();
3058 viewport.showAllHiddenSeqs();
3059 alignPanel.paintAlignment(true);
3060 viewport.sendSelection();
3064 public void hideSelColumns_actionPerformed(ActionEvent e)
3066 viewport.hideSelectedColumns();
3067 alignPanel.paintAlignment(true);
3068 viewport.sendSelection();
3072 public void hiddenMarkers_actionPerformed(ActionEvent e)
3074 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3085 protected void scaleAbove_actionPerformed(ActionEvent e)
3087 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3088 alignPanel.paintAlignment(true);
3098 protected void scaleLeft_actionPerformed(ActionEvent e)
3100 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3101 alignPanel.paintAlignment(true);
3111 protected void scaleRight_actionPerformed(ActionEvent e)
3113 viewport.setScaleRightWrapped(scaleRight.isSelected());
3114 alignPanel.paintAlignment(true);
3124 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3126 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3127 alignPanel.paintAlignment(true);
3137 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3139 viewport.setShowText(viewTextMenuItem.isSelected());
3140 alignPanel.paintAlignment(true);
3150 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3152 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3153 alignPanel.paintAlignment(true);
3156 public FeatureSettings featureSettings;
3159 public FeatureSettingsControllerI getFeatureSettingsUI()
3161 return featureSettings;
3165 public void featureSettings_actionPerformed(ActionEvent e)
3167 if (featureSettings != null)
3169 featureSettings.close();
3170 featureSettings = null;
3172 if (!showSeqFeatures.isSelected())
3174 // make sure features are actually displayed
3175 showSeqFeatures.setSelected(true);
3176 showSeqFeatures_actionPerformed(null);
3178 featureSettings = new FeatureSettings(this);
3182 * Set or clear 'Show Sequence Features'
3188 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3190 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3191 alignPanel.paintAlignment(true);
3192 if (alignPanel.getOverviewPanel() != null)
3194 alignPanel.getOverviewPanel().updateOverviewImage();
3199 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3200 * the annotations panel as a whole.
3202 * The options to show/hide all annotations should be enabled when the panel
3203 * is shown, and disabled when the panel is hidden.
3208 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3210 final boolean setVisible = annotationPanelMenuItem.isSelected();
3211 viewport.setShowAnnotation(setVisible);
3212 this.showAllSeqAnnotations.setEnabled(setVisible);
3213 this.hideAllSeqAnnotations.setEnabled(setVisible);
3214 this.showAllAlAnnotations.setEnabled(setVisible);
3215 this.hideAllAlAnnotations.setEnabled(setVisible);
3216 alignPanel.updateLayout();
3220 public void alignmentProperties()
3222 JEditorPane editPane = new JEditorPane("text/html", "");
3223 editPane.setEditable(false);
3224 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3226 editPane.setText(MessageManager.formatMessage("label.html_content",
3227 new Object[] { contents.toString() }));
3228 JInternalFrame frame = new JInternalFrame();
3229 frame.getContentPane().add(new JScrollPane(editPane));
3231 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3232 "label.alignment_properties", new Object[] { getTitle() }),
3243 public void overviewMenuItem_actionPerformed(ActionEvent e)
3245 if (alignPanel.overviewPanel != null)
3250 JInternalFrame frame = new JInternalFrame();
3251 OverviewPanel overview = new OverviewPanel(alignPanel);
3252 frame.setContentPane(overview);
3253 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3254 "label.overview_params", new Object[] { this.getTitle() }),
3255 frame.getWidth(), frame.getHeight());
3257 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3258 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3261 public void internalFrameClosed(
3262 javax.swing.event.InternalFrameEvent evt)
3264 alignPanel.setOverviewPanel(null);
3268 alignPanel.setOverviewPanel(overview);
3272 public void textColour_actionPerformed()
3274 new TextColourChooser().chooseColour(alignPanel, null);
3278 * public void covariationColour_actionPerformed() {
3280 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3284 public void annotationColour_actionPerformed()
3286 new AnnotationColourChooser(viewport, alignPanel);
3290 public void annotationColumn_actionPerformed(ActionEvent e)
3292 new AnnotationColumnChooser(viewport, alignPanel);
3296 * Action on the user checking or unchecking the option to apply the selected
3297 * colour scheme to all groups. If unchecked, groups may have their own
3298 * independent colour schemes.
3302 protected void applyToAllGroups_actionPerformed()
3304 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3308 * Action on user selecting a colour from the colour menu
3311 * the name (not the menu item label!) of the colour scheme
3314 public void changeColour_actionPerformed(String name)
3317 * 'User Defined' opens a panel to configure or load a
3318 * user-defined colour scheme
3320 if (ResidueColourScheme.USER_DEFINED.equals(name))
3322 new UserDefinedColours(alignPanel, null);
3327 * otherwise set the chosen colour scheme (or null for 'None')
3329 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3330 viewport.getAlignment(), viewport.getHiddenRepSequences());
3335 * Actions on setting or changing the alignment colour scheme
3340 public void changeColour(ColourSchemeI cs)
3342 // TODO: pull up to controller method
3345 ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
3346 // Make sure viewport is up to date w.r.t. any sliders
3347 if (viewport.getAbovePIDThreshold())
3349 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3351 viewport.setThreshold(threshold);
3354 if (viewport.getConservationSelected())
3356 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3361 viewport.setGlobalColourScheme(cs);
3363 alignPanel.paintAlignment(true);
3373 protected void modifyPID_actionPerformed()
3375 if (viewport.getAbovePIDThreshold()
3376 && viewport.getGlobalColourScheme() != null)
3378 SliderPanel.setPIDSliderSource(alignPanel,
3379 viewport.getGlobalColourScheme(), "Background");
3380 SliderPanel.showPIDSlider();
3391 protected void modifyConservation_actionPerformed()
3393 if (viewport.getConservationSelected()
3394 && viewport.getGlobalColourScheme() != null)
3396 SliderPanel.setConservationSlider(alignPanel,
3397 viewport.getGlobalColourScheme(), "Background");
3398 SliderPanel.showConservationSlider();
3409 protected void conservationMenuItem_actionPerformed()
3411 viewport.setConservationSelected(conservationMenuItem.isSelected());
3413 viewport.setAbovePIDThreshold(false);
3414 abovePIDThreshold.setSelected(false);
3416 changeColour(viewport.getGlobalColourScheme());
3418 modifyConservation_actionPerformed();
3428 public void abovePIDThreshold_actionPerformed()
3430 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3432 conservationMenuItem.setSelected(false);
3433 viewport.setConservationSelected(false);
3435 changeColour(viewport.getGlobalColourScheme());
3437 modifyPID_actionPerformed();
3447 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3449 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3450 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3451 .getAlignment().getSequenceAt(0), null);
3452 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3453 viewport.getAlignment()));
3454 alignPanel.paintAlignment(true);
3464 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3466 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3467 AlignmentSorter.sortByID(viewport.getAlignment());
3468 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3469 viewport.getAlignment()));
3470 alignPanel.paintAlignment(true);
3480 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3482 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3483 AlignmentSorter.sortByLength(viewport.getAlignment());
3484 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3485 viewport.getAlignment()));
3486 alignPanel.paintAlignment(true);
3496 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3498 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3499 AlignmentSorter.sortByGroup(viewport.getAlignment());
3500 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3501 viewport.getAlignment()));
3503 alignPanel.paintAlignment(true);
3513 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3515 new RedundancyPanel(alignPanel, this);
3525 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3527 if ((viewport.getSelectionGroup() == null)
3528 || (viewport.getSelectionGroup().getSize() < 2))
3530 JvOptionPane.showInternalMessageDialog(this, MessageManager
3531 .getString("label.you_must_select_least_two_sequences"),
3532 MessageManager.getString("label.invalid_selection"),
3533 JvOptionPane.WARNING_MESSAGE);
3537 JInternalFrame frame = new JInternalFrame();
3538 frame.setContentPane(new PairwiseAlignPanel(viewport));
3539 Desktop.addInternalFrame(frame,
3540 MessageManager.getString("action.pairwise_alignment"), 600,
3552 public void PCAMenuItem_actionPerformed(ActionEvent e)
3554 if (((viewport.getSelectionGroup() != null)
3555 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3556 .getSelectionGroup().getSize() > 0))
3557 || (viewport.getAlignment().getHeight() < 4))
3560 .showInternalMessageDialog(
3563 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3565 .getString("label.sequence_selection_insufficient"),
3566 JvOptionPane.WARNING_MESSAGE);
3571 new PCAPanel(alignPanel);
3575 public void autoCalculate_actionPerformed(ActionEvent e)
3577 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3578 if (viewport.autoCalculateConsensus)
3580 viewport.firePropertyChange("alignment", null, viewport
3581 .getAlignment().getSequences());
3586 public void sortByTreeOption_actionPerformed(ActionEvent e)
3588 viewport.sortByTree = sortByTree.isSelected();
3592 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3594 viewport.followSelection = listenToViewSelections.isSelected();
3604 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3606 newTreePanel("AV", "PID", "Average distance tree using PID");
3616 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3618 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3628 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3630 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3640 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3642 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3655 void newTreePanel(String type, String pwType, String title)
3659 if (viewport.getSelectionGroup() != null
3660 && viewport.getSelectionGroup().getSize() > 0)
3662 if (viewport.getSelectionGroup().getSize() < 3)
3668 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3670 .getString("label.not_enough_sequences"),
3671 JvOptionPane.WARNING_MESSAGE);
3675 SequenceGroup sg = viewport.getSelectionGroup();
3677 /* Decide if the selection is a column region */
3678 for (SequenceI _s : sg.getSequences())
3680 if (_s.getLength() < sg.getEndRes())
3686 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3688 .getString("label.sequences_selection_not_aligned"),
3689 JvOptionPane.WARNING_MESSAGE);
3695 title = title + " on region";
3696 tp = new TreePanel(alignPanel, type, pwType);
3700 // are the visible sequences aligned?
3701 if (!viewport.getAlignment().isAligned(false))
3707 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3709 .getString("label.sequences_not_aligned"),
3710 JvOptionPane.WARNING_MESSAGE);
3715 if (viewport.getAlignment().getHeight() < 2)
3720 tp = new TreePanel(alignPanel, type, pwType);
3725 if (viewport.viewName != null)
3727 title += viewport.viewName + " of ";
3730 title += this.title;
3732 Desktop.addInternalFrame(tp, title, 600, 500);
3743 public void addSortByOrderMenuItem(String title,
3744 final AlignmentOrder order)
3746 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3747 "action.by_title_param", new Object[] { title }));
3749 item.addActionListener(new java.awt.event.ActionListener()
3752 public void actionPerformed(ActionEvent e)
3754 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3756 // TODO: JBPNote - have to map order entries to curent SequenceI
3758 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3760 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3763 alignPanel.paintAlignment(true);
3769 * Add a new sort by annotation score menu item
3772 * the menu to add the option to
3774 * the label used to retrieve scores for each sequence on the
3777 public void addSortByAnnotScoreMenuItem(JMenu sort,
3778 final String scoreLabel)
3780 final JMenuItem item = new JMenuItem(scoreLabel);
3782 item.addActionListener(new java.awt.event.ActionListener()
3785 public void actionPerformed(ActionEvent e)
3787 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3788 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3789 viewport.getAlignment());// ,viewport.getSelectionGroup());
3790 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3791 viewport.getAlignment()));
3792 alignPanel.paintAlignment(true);
3798 * last hash for alignment's annotation array - used to minimise cost of
3801 protected int _annotationScoreVectorHash;
3804 * search the alignment and rebuild the sort by annotation score submenu the
3805 * last alignment annotation vector hash is stored to minimize cost of
3806 * rebuilding in subsequence calls.
3810 public void buildSortByAnnotationScoresMenu()
3812 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3817 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3819 sortByAnnotScore.removeAll();
3820 // almost certainly a quicker way to do this - but we keep it simple
3821 Hashtable scoreSorts = new Hashtable();
3822 AlignmentAnnotation aann[];
3823 for (SequenceI sqa : viewport.getAlignment().getSequences())
3825 aann = sqa.getAnnotation();
3826 for (int i = 0; aann != null && i < aann.length; i++)
3828 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3830 scoreSorts.put(aann[i].label, aann[i].label);
3834 Enumeration labels = scoreSorts.keys();
3835 while (labels.hasMoreElements())
3837 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3838 (String) labels.nextElement());
3840 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3843 _annotationScoreVectorHash = viewport.getAlignment()
3844 .getAlignmentAnnotation().hashCode();
3849 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3850 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3851 * call. Listeners are added to remove the menu item when the treePanel is
3852 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3856 * Displayed tree window.
3858 * SortBy menu item title.
3861 public void buildTreeMenu()
3863 calculateTree.removeAll();
3864 // build the calculate menu
3866 for (final String type : new String[] { "NJ", "AV" })
3868 String treecalcnm = MessageManager.getString("label.tree_calc_"
3869 + type.toLowerCase());
3870 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
3872 JMenuItem tm = new JMenuItem();
3873 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
3874 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
3875 || sm.isProtein() == !viewport.getAlignment()
3878 String smn = MessageManager.getStringOrReturn(
3879 "label.score_model_", sm.getName());
3880 final String title = MessageManager.formatMessage(
3881 "label.treecalc_title", treecalcnm, smn);
3882 tm.setText(title);//
3883 tm.addActionListener(new java.awt.event.ActionListener()
3886 public void actionPerformed(ActionEvent e)
3888 newTreePanel(type, pwtype, title);
3891 calculateTree.add(tm);
3896 sortByTreeMenu.removeAll();
3898 List<Component> comps = PaintRefresher.components.get(viewport
3899 .getSequenceSetId());
3900 List<TreePanel> treePanels = new ArrayList<TreePanel>();
3901 for (Component comp : comps)
3903 if (comp instanceof TreePanel)
3905 treePanels.add((TreePanel) comp);
3909 if (treePanels.size() < 1)
3911 sortByTreeMenu.setVisible(false);
3915 sortByTreeMenu.setVisible(true);
3917 for (final TreePanel tp : treePanels)
3919 final JMenuItem item = new JMenuItem(tp.getTitle());
3920 item.addActionListener(new java.awt.event.ActionListener()
3923 public void actionPerformed(ActionEvent e)
3925 tp.sortByTree_actionPerformed();
3926 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3931 sortByTreeMenu.add(item);
3935 public boolean sortBy(AlignmentOrder alorder, String undoname)
3937 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3938 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3939 if (undoname != null)
3941 addHistoryItem(new OrderCommand(undoname, oldOrder,
3942 viewport.getAlignment()));
3944 alignPanel.paintAlignment(true);
3949 * Work out whether the whole set of sequences or just the selected set will
3950 * be submitted for multiple alignment.
3953 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3955 // Now, check we have enough sequences
3956 AlignmentView msa = null;
3958 if ((viewport.getSelectionGroup() != null)
3959 && (viewport.getSelectionGroup().getSize() > 1))
3961 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3962 // some common interface!
3964 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3965 * SequenceI[sz = seqs.getSize(false)];
3967 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3968 * seqs.getSequenceAt(i); }
3970 msa = viewport.getAlignmentView(true);
3972 else if (viewport.getSelectionGroup() != null
3973 && viewport.getSelectionGroup().getSize() == 1)
3975 int option = JvOptionPane.showConfirmDialog(this,
3976 MessageManager.getString("warn.oneseq_msainput_selection"),
3977 MessageManager.getString("label.invalid_selection"),
3978 JvOptionPane.OK_CANCEL_OPTION);
3979 if (option == JvOptionPane.OK_OPTION)
3981 msa = viewport.getAlignmentView(false);
3986 msa = viewport.getAlignmentView(false);
3992 * Decides what is submitted to a secondary structure prediction service: the
3993 * first sequence in the alignment, or in the current selection, or, if the
3994 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3995 * region or the whole alignment. (where the first sequence in the set is the
3996 * one that the prediction will be for).
3998 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4000 AlignmentView seqs = null;
4002 if ((viewport.getSelectionGroup() != null)
4003 && (viewport.getSelectionGroup().getSize() > 0))
4005 seqs = viewport.getAlignmentView(true);
4009 seqs = viewport.getAlignmentView(false);
4011 // limit sequences - JBPNote in future - could spawn multiple prediction
4013 // TODO: viewport.getAlignment().isAligned is a global state - the local
4014 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4015 if (!viewport.getAlignment().isAligned(false))
4017 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4018 // TODO: if seqs.getSequences().length>1 then should really have warned
4032 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4034 // Pick the tree file
4035 JalviewFileChooser chooser = new JalviewFileChooser(
4036 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4037 chooser.setFileView(new JalviewFileView());
4038 chooser.setDialogTitle(MessageManager
4039 .getString("label.select_newick_like_tree_file"));
4040 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4042 int value = chooser.showOpenDialog(null);
4044 if (value == JalviewFileChooser.APPROVE_OPTION)
4046 String choice = chooser.getSelectedFile().getPath();
4047 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4048 jalview.io.NewickFile fin = null;
4051 fin = new NewickFile(choice, DataSourceType.FILE);
4052 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4053 } catch (Exception ex)
4060 .getString("label.problem_reading_tree_file"),
4061 JvOptionPane.WARNING_MESSAGE);
4062 ex.printStackTrace();
4064 if (fin != null && fin.hasWarningMessage())
4066 JvOptionPane.showMessageDialog(Desktop.desktop, fin
4067 .getWarningMessage(), MessageManager
4068 .getString("label.possible_problem_with_tree_file"),
4069 JvOptionPane.WARNING_MESSAGE);
4074 public TreePanel ShowNewickTree(NewickFile nf, String title)
4076 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4079 public TreePanel ShowNewickTree(NewickFile nf, String title,
4080 AlignmentView input)
4082 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4085 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4086 int h, int x, int y)
4088 return ShowNewickTree(nf, title, null, w, h, x, y);
4092 * Add a treeviewer for the tree extracted from a newick file object to the
4093 * current alignment view
4100 * Associated alignment input data (or null)
4109 * @return TreePanel handle
4111 public TreePanel ShowNewickTree(NewickFile nf, String title,
4112 AlignmentView input, int w, int h, int x, int y)
4114 TreePanel tp = null;
4120 if (nf.getTree() != null)
4122 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4128 tp.setLocation(x, y);
4131 Desktop.addInternalFrame(tp, title, w, h);
4133 } catch (Exception ex)
4135 ex.printStackTrace();
4141 private boolean buildingMenu = false;
4144 * Generates menu items and listener event actions for web service clients
4147 public void BuildWebServiceMenu()
4149 while (buildingMenu)
4153 System.err.println("Waiting for building menu to finish.");
4155 } catch (Exception e)
4159 final AlignFrame me = this;
4160 buildingMenu = true;
4161 new Thread(new Runnable()
4166 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4169 // System.err.println("Building ws menu again "
4170 // + Thread.currentThread());
4171 // TODO: add support for context dependent disabling of services based
4173 // alignment and current selection
4174 // TODO: add additional serviceHandle parameter to specify abstract
4176 // class independently of AbstractName
4177 // TODO: add in rediscovery GUI function to restart discoverer
4178 // TODO: group services by location as well as function and/or
4180 // object broker mechanism.
4181 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4182 final IProgressIndicator af = me;
4185 * do not i18n these strings - they are hard-coded in class
4186 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4187 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4189 final JMenu msawsmenu = new JMenu("Alignment");
4190 final JMenu secstrmenu = new JMenu(
4191 "Secondary Structure Prediction");
4192 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4193 final JMenu analymenu = new JMenu("Analysis");
4194 final JMenu dismenu = new JMenu("Protein Disorder");
4195 // JAL-940 - only show secondary structure prediction services from
4196 // the legacy server
4197 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4199 Discoverer.services != null && (Discoverer.services.size() > 0))
4201 // TODO: refactor to allow list of AbstractName/Handler bindings to
4203 // stored or retrieved from elsewhere
4204 // No MSAWS used any more:
4205 // Vector msaws = null; // (Vector)
4206 // Discoverer.services.get("MsaWS");
4207 Vector secstrpr = (Vector) Discoverer.services
4209 if (secstrpr != null)
4211 // Add any secondary structure prediction services
4212 for (int i = 0, j = secstrpr.size(); i < j; i++)
4214 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4216 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4217 .getServiceClient(sh);
4218 int p = secstrmenu.getItemCount();
4219 impl.attachWSMenuEntry(secstrmenu, me);
4220 int q = secstrmenu.getItemCount();
4221 for (int litm = p; litm < q; litm++)
4223 legacyItems.add(secstrmenu.getItem(litm));
4229 // Add all submenus in the order they should appear on the web
4231 wsmenu.add(msawsmenu);
4232 wsmenu.add(secstrmenu);
4233 wsmenu.add(dismenu);
4234 wsmenu.add(analymenu);
4235 // No search services yet
4236 // wsmenu.add(seqsrchmenu);
4238 javax.swing.SwingUtilities.invokeLater(new Runnable()
4245 webService.removeAll();
4246 // first, add discovered services onto the webservices menu
4247 if (wsmenu.size() > 0)
4249 for (int i = 0, j = wsmenu.size(); i < j; i++)
4251 webService.add(wsmenu.get(i));
4256 webService.add(me.webServiceNoServices);
4258 // TODO: move into separate menu builder class.
4259 boolean new_sspred = false;
4260 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4262 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4263 if (jws2servs != null)
4265 if (jws2servs.hasServices())
4267 jws2servs.attachWSMenuEntry(webService, me);
4268 for (Jws2Instance sv : jws2servs.getServices())
4270 if (sv.description.toLowerCase().contains("jpred"))
4272 for (JMenuItem jmi : legacyItems)
4274 jmi.setVisible(false);
4280 if (jws2servs.isRunning())
4282 JMenuItem tm = new JMenuItem(
4283 "Still discovering JABA Services");
4284 tm.setEnabled(false);
4289 build_urlServiceMenu(me.webService);
4290 build_fetchdbmenu(webService);
4291 for (JMenu item : wsmenu)
4293 if (item.getItemCount() == 0)
4295 item.setEnabled(false);
4299 item.setEnabled(true);
4302 } catch (Exception e)
4305 .debug("Exception during web service menu building process.",
4310 } catch (Exception e)
4313 buildingMenu = false;
4320 * construct any groupURL type service menu entries.
4324 private void build_urlServiceMenu(JMenu webService)
4326 // TODO: remove this code when 2.7 is released
4327 // DEBUG - alignmentView
4329 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4330 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4332 * @Override public void actionPerformed(ActionEvent e) {
4333 * jalview.datamodel.AlignmentView
4334 * .testSelectionViews(af.viewport.getAlignment(),
4335 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4337 * }); webService.add(testAlView);
4339 // TODO: refactor to RestClient discoverer and merge menu entries for
4340 // rest-style services with other types of analysis/calculation service
4341 // SHmmr test client - still being implemented.
4342 // DEBUG - alignmentView
4344 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4347 client.attachWSMenuEntry(
4348 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4354 * Searches the alignment sequences for xRefs and builds the Show
4355 * Cross-References menu (formerly called Show Products), with database
4356 * sources for which cross-references are found (protein sources for a
4357 * nucleotide alignment and vice versa)
4359 * @return true if Show Cross-references menu should be enabled
4361 public boolean canShowProducts()
4363 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4364 AlignmentI dataset = viewport.getAlignment().getDataset();
4366 showProducts.removeAll();
4367 final boolean dna = viewport.getAlignment().isNucleotide();
4369 if (seqs == null || seqs.length == 0)
4371 // nothing to see here.
4375 boolean showp = false;
4378 List<String> ptypes = new CrossRef(seqs, dataset)
4379 .findXrefSourcesForSequences(dna);
4381 for (final String source : ptypes)
4384 final AlignFrame af = this;
4385 JMenuItem xtype = new JMenuItem(source);
4386 xtype.addActionListener(new ActionListener()
4389 public void actionPerformed(ActionEvent e)
4391 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4394 showProducts.add(xtype);
4396 showProducts.setVisible(showp);
4397 showProducts.setEnabled(showp);
4398 } catch (Exception e)
4401 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4409 * Finds and displays cross-references for the selected sequences (protein
4410 * products for nucleotide sequences, dna coding sequences for peptides).
4413 * the sequences to show cross-references for
4415 * true if from a nucleotide alignment (so showing proteins)
4417 * the database to show cross-references for
4419 protected void showProductsFor(final SequenceI[] sel,
4420 final boolean _odna, final String source)
4422 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4427 * Construct and display a new frame containing the translation of this
4428 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4431 public void showTranslation_actionPerformed(ActionEvent e)
4433 AlignmentI al = null;
4436 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4438 al = dna.translateCdna();
4439 } catch (Exception ex)
4441 jalview.bin.Cache.log.error(
4442 "Exception during translation. Please report this !", ex);
4443 final String msg = MessageManager
4444 .getString("label.error_when_translating_sequences_submit_bug_report");
4445 final String errorTitle = MessageManager
4446 .getString("label.implementation_error")
4447 + MessageManager.getString("label.translation_failed");
4448 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4449 JvOptionPane.ERROR_MESSAGE);
4452 if (al == null || al.getHeight() == 0)
4454 final String msg = MessageManager
4455 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4456 final String errorTitle = MessageManager
4457 .getString("label.translation_failed");
4458 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4459 JvOptionPane.WARNING_MESSAGE);
4463 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4464 af.setFileFormat(this.currentFileFormat);
4465 final String newTitle = MessageManager.formatMessage(
4466 "label.translation_of_params",
4467 new Object[] { this.getTitle() });
4468 af.setTitle(newTitle);
4469 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4471 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4472 viewport.openSplitFrame(af, new Alignment(seqs));
4476 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4483 * Set the file format
4487 public void setFileFormat(FileFormatI format)
4489 this.currentFileFormat = format;
4493 * Try to load a features file onto the alignment.
4496 * contents or path to retrieve file
4498 * access mode of file (see jalview.io.AlignFile)
4499 * @return true if features file was parsed correctly.
4501 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4503 return avc.parseFeaturesFile(file, sourceType,
4504 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4509 public void refreshFeatureUI(boolean enableIfNecessary)
4511 // note - currently this is only still here rather than in the controller
4512 // because of the featureSettings hard reference that is yet to be
4514 if (enableIfNecessary)
4516 viewport.setShowSequenceFeatures(true);
4517 showSeqFeatures.setSelected(true);
4523 public void dragEnter(DropTargetDragEvent evt)
4528 public void dragExit(DropTargetEvent evt)
4533 public void dragOver(DropTargetDragEvent evt)
4538 public void dropActionChanged(DropTargetDragEvent evt)
4543 public void drop(DropTargetDropEvent evt)
4545 // JAL-1552 - acceptDrop required before getTransferable call for
4546 // Java's Transferable for native dnd
4547 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4548 Transferable t = evt.getTransferable();
4549 List<String> files = new ArrayList<String>();
4550 List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4554 Desktop.transferFromDropTarget(files, protocols, evt, t);
4555 } catch (Exception e)
4557 e.printStackTrace();
4563 // check to see if any of these files have names matching sequences in
4565 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4566 .getAlignment().getSequencesArray());
4568 * Object[] { String,SequenceI}
4570 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4571 ArrayList<String> filesnotmatched = new ArrayList<String>();
4572 for (int i = 0; i < files.size(); i++)
4574 String file = files.get(i).toString();
4576 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4577 if (protocol == DataSourceType.FILE)
4579 File fl = new File(file);
4580 pdbfn = fl.getName();
4582 else if (protocol == DataSourceType.URL)
4584 URL url = new URL(file);
4585 pdbfn = url.getFile();
4587 if (pdbfn.length() > 0)
4589 // attempt to find a match in the alignment
4590 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4591 int l = 0, c = pdbfn.indexOf(".");
4592 while (mtch == null && c != -1)
4597 } while ((c = pdbfn.indexOf(".", l)) > l);
4600 pdbfn = pdbfn.substring(0, l);
4602 mtch = idm.findAllIdMatches(pdbfn);
4606 FileFormatI type = null;
4609 type = new IdentifyFile().identify(file, protocol);
4610 } catch (Exception ex)
4614 if (type != null && type.isStructureFile())
4616 filesmatched.add(new Object[] { file, protocol, mtch });
4620 // File wasn't named like one of the sequences or wasn't a PDB file.
4621 filesnotmatched.add(file);
4625 if (filesmatched.size() > 0)
4627 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4633 "label.automatically_associate_structure_files_with_sequences_same_name",
4634 new Object[] { Integer
4640 .getString("label.automatically_associate_structure_files_by_name"),
4641 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4644 for (Object[] fm : filesmatched)
4646 // try and associate
4647 // TODO: may want to set a standard ID naming formalism for
4648 // associating PDB files which have no IDs.
4649 for (SequenceI toassoc : (SequenceI[]) fm[2])
4651 PDBEntry pe = new AssociatePdbFileWithSeq()
4652 .associatePdbWithSeq((String) fm[0],
4653 (DataSourceType) fm[1], toassoc, false,
4657 System.err.println("Associated file : "
4658 + ((String) fm[0]) + " with "
4659 + toassoc.getDisplayId(true));
4663 alignPanel.paintAlignment(true);
4667 if (filesnotmatched.size() > 0)
4670 && (Cache.getDefault(
4671 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4677 "label.ignore_unmatched_dropped_files_info",
4678 new Object[] { Integer
4685 .getString("label.ignore_unmatched_dropped_files"),
4686 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4690 for (String fn : filesnotmatched)
4692 loadJalviewDataFile(fn, null, null, null);
4696 } catch (Exception ex)
4698 ex.printStackTrace();
4704 * Attempt to load a "dropped" file or URL string: First by testing whether
4705 * it's an Annotation file, then a JNet file, and finally a features file. If
4706 * all are false then the user may have dropped an alignment file onto this
4710 * either a filename or a URL string.
4712 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4713 FileFormatI format, SequenceI assocSeq)
4717 if (sourceType == null)
4719 sourceType = FormatAdapter.checkProtocol(file);
4721 // if the file isn't identified, or not positively identified as some
4722 // other filetype (PFAM is default unidentified alignment file type) then
4723 // try to parse as annotation.
4724 boolean isAnnotation = (format == null || FileFormat.Pfam
4725 .equals(format)) ? new AnnotationFile()
4726 .annotateAlignmentView(viewport, file, sourceType) : false;
4730 // first see if its a T-COFFEE score file
4731 TCoffeeScoreFile tcf = null;
4734 tcf = new TCoffeeScoreFile(file, sourceType);
4737 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4740 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4741 isAnnotation = true;
4743 .setText(MessageManager
4744 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4748 // some problem - if no warning its probable that the ID matching
4749 // process didn't work
4753 tcf.getWarningMessage() == null ? MessageManager
4754 .getString("label.check_file_matches_sequence_ids_alignment")
4755 : tcf.getWarningMessage(),
4757 .getString("label.problem_reading_tcoffee_score_file"),
4758 JvOptionPane.WARNING_MESSAGE);
4765 } catch (Exception x)
4768 .debug("Exception when processing data source as T-COFFEE score file",
4774 // try to see if its a JNet 'concise' style annotation file *before*
4776 // try to parse it as a features file
4779 format = new IdentifyFile().identify(file, sourceType);
4781 if (FileFormat.Jnet.equals(format))
4783 JPredFile predictions = new JPredFile(
4785 new JnetAnnotationMaker();
4786 JnetAnnotationMaker.add_annotation(predictions,
4787 viewport.getAlignment(), 0, false);
4788 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4789 viewport.getAlignment().setSeqrep(repseq);
4790 ColumnSelection cs = new ColumnSelection();
4791 cs.hideInsertionsFor(repseq);
4792 viewport.setColumnSelection(cs);
4793 isAnnotation = true;
4795 // else if (IdentifyFile.FeaturesFile.equals(format))
4796 else if (FileFormat.Features.equals(format))
4798 if (parseFeaturesFile(file, sourceType))
4800 alignPanel.paintAlignment(true);
4805 new FileLoader().LoadFile(viewport, file, sourceType, format);
4812 alignPanel.adjustAnnotationHeight();
4813 viewport.updateSequenceIdColours();
4814 buildSortByAnnotationScoresMenu();
4815 alignPanel.paintAlignment(true);
4817 } catch (Exception ex)
4819 ex.printStackTrace();
4820 } catch (OutOfMemoryError oom)
4825 } catch (Exception x)
4830 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4831 : "using " + sourceType + " from " + file)
4833 + (format != null ? "(parsing as '" + format
4834 + "' file)" : ""), oom, Desktop.desktop);
4839 * Method invoked by the ChangeListener on the tabbed pane, in other words
4840 * when a different tabbed pane is selected by the user or programmatically.
4843 public void tabSelectionChanged(int index)
4847 alignPanel = alignPanels.get(index);
4848 viewport = alignPanel.av;
4849 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4850 setMenusFromViewport(viewport);
4854 * If there is a frame linked to this one in a SplitPane, switch it to the
4855 * same view tab index. No infinite recursion of calls should happen, since
4856 * tabSelectionChanged() should not get invoked on setting the selected
4857 * index to an unchanged value. Guard against setting an invalid index
4858 * before the new view peer tab has been created.
4860 final AlignViewportI peer = viewport.getCodingComplement();
4863 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4864 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4866 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4872 * On right mouse click on view tab, prompt for and set new view name.
4875 public void tabbedPane_mousePressed(MouseEvent e)
4877 if (e.isPopupTrigger())
4879 String msg = MessageManager.getString("label.enter_view_name");
4880 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4881 JvOptionPane.QUESTION_MESSAGE);
4885 viewport.viewName = reply;
4886 // TODO warn if reply is in getExistingViewNames()?
4887 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4892 public AlignViewport getCurrentView()
4898 * Open the dialog for regex description parsing.
4901 protected void extractScores_actionPerformed(ActionEvent e)
4903 ParseProperties pp = new jalview.analysis.ParseProperties(
4904 viewport.getAlignment());
4905 // TODO: verify regex and introduce GUI dialog for version 2.5
4906 // if (pp.getScoresFromDescription("col", "score column ",
4907 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4909 if (pp.getScoresFromDescription("description column",
4910 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4912 buildSortByAnnotationScoresMenu();
4920 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4924 protected void showDbRefs_actionPerformed(ActionEvent e)
4926 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4932 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4936 protected void showNpFeats_actionPerformed(ActionEvent e)
4938 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4942 * find the viewport amongst the tabs in this alignment frame and close that
4947 public boolean closeView(AlignViewportI av)
4951 this.closeMenuItem_actionPerformed(false);
4954 Component[] comp = tabbedPane.getComponents();
4955 for (int i = 0; comp != null && i < comp.length; i++)
4957 if (comp[i] instanceof AlignmentPanel)
4959 if (((AlignmentPanel) comp[i]).av == av)
4962 closeView((AlignmentPanel) comp[i]);
4970 protected void build_fetchdbmenu(JMenu webService)
4972 // Temporary hack - DBRef Fetcher always top level ws entry.
4973 // TODO We probably want to store a sequence database checklist in
4974 // preferences and have checkboxes.. rather than individual sources selected
4976 final JMenu rfetch = new JMenu(
4977 MessageManager.getString("action.fetch_db_references"));
4978 rfetch.setToolTipText(MessageManager
4979 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4980 webService.add(rfetch);
4982 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4983 MessageManager.getString("option.trim_retrieved_seqs"));
4984 trimrs.setToolTipText(MessageManager
4985 .getString("label.trim_retrieved_sequences"));
4986 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4987 trimrs.addActionListener(new ActionListener()
4990 public void actionPerformed(ActionEvent e)
4992 trimrs.setSelected(trimrs.isSelected());
4993 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4994 Boolean.valueOf(trimrs.isSelected()).toString());
4998 JMenuItem fetchr = new JMenuItem(
4999 MessageManager.getString("label.standard_databases"));
5000 fetchr.setToolTipText(MessageManager
5001 .getString("label.fetch_embl_uniprot"));
5002 fetchr.addActionListener(new ActionListener()
5006 public void actionPerformed(ActionEvent e)
5008 new Thread(new Runnable()
5013 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5014 .getAlignment().isNucleotide();
5015 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5016 .getSequenceSelection(), alignPanel.alignFrame, null,
5017 alignPanel.alignFrame.featureSettings, isNucleotide);
5018 dbRefFetcher.addListener(new FetchFinishedListenerI()
5021 public void finished()
5023 AlignFrame.this.setMenusForViewport();
5026 dbRefFetcher.fetchDBRefs(false);
5034 final AlignFrame me = this;
5035 new Thread(new Runnable()
5040 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5041 .getSequenceFetcherSingleton(me);
5042 javax.swing.SwingUtilities.invokeLater(new Runnable()
5047 String[] dbclasses = sf.getOrderedSupportedSources();
5048 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5049 // jalview.util.QuickSort.sort(otherdb, otherdb);
5050 List<DbSourceProxy> otherdb;
5051 JMenu dfetch = new JMenu();
5052 JMenu ifetch = new JMenu();
5053 JMenuItem fetchr = null;
5054 int comp = 0, icomp = 0, mcomp = 15;
5055 String mname = null;
5057 for (String dbclass : dbclasses)
5059 otherdb = sf.getSourceProxy(dbclass);
5060 // add a single entry for this class, or submenu allowing 'fetch
5062 if (otherdb == null || otherdb.size() < 1)
5066 // List<DbSourceProxy> dbs=otherdb;
5067 // otherdb=new ArrayList<DbSourceProxy>();
5068 // for (DbSourceProxy db:dbs)
5070 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5074 mname = "From " + dbclass;
5076 if (otherdb.size() == 1)
5078 final DbSourceProxy[] dassource = otherdb
5079 .toArray(new DbSourceProxy[0]);
5080 DbSourceProxy src = otherdb.get(0);
5081 fetchr = new JMenuItem(src.getDbSource());
5082 fetchr.addActionListener(new ActionListener()
5086 public void actionPerformed(ActionEvent e)
5088 new Thread(new Runnable()
5094 boolean isNucleotide = alignPanel.alignFrame
5095 .getViewport().getAlignment()
5097 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5098 alignPanel.av.getSequenceSelection(),
5099 alignPanel.alignFrame, dassource,
5100 alignPanel.alignFrame.featureSettings,
5103 .addListener(new FetchFinishedListenerI()
5106 public void finished()
5108 AlignFrame.this.setMenusForViewport();
5111 dbRefFetcher.fetchDBRefs(false);
5117 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5118 MessageManager.formatMessage(
5119 "label.fetch_retrieve_from",
5120 new Object[] { src.getDbName() })));
5126 final DbSourceProxy[] dassource = otherdb
5127 .toArray(new DbSourceProxy[0]);
5129 DbSourceProxy src = otherdb.get(0);
5130 fetchr = new JMenuItem(MessageManager.formatMessage(
5131 "label.fetch_all_param",
5132 new Object[] { src.getDbSource() }));
5133 fetchr.addActionListener(new ActionListener()
5136 public void actionPerformed(ActionEvent e)
5138 new Thread(new Runnable()
5144 boolean isNucleotide = alignPanel.alignFrame
5145 .getViewport().getAlignment()
5147 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5148 alignPanel.av.getSequenceSelection(),
5149 alignPanel.alignFrame, dassource,
5150 alignPanel.alignFrame.featureSettings,
5153 .addListener(new FetchFinishedListenerI()
5156 public void finished()
5158 AlignFrame.this.setMenusForViewport();
5161 dbRefFetcher.fetchDBRefs(false);
5167 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5168 MessageManager.formatMessage(
5169 "label.fetch_retrieve_from_all_sources",
5171 Integer.valueOf(otherdb.size())
5172 .toString(), src.getDbSource(),
5173 src.getDbName() })));
5176 // and then build the rest of the individual menus
5177 ifetch = new JMenu(MessageManager.formatMessage(
5178 "label.source_from_db_source",
5179 new Object[] { src.getDbSource() }));
5181 String imname = null;
5183 for (DbSourceProxy sproxy : otherdb)
5185 String dbname = sproxy.getDbName();
5186 String sname = dbname.length() > 5 ? dbname.substring(0,
5187 5) + "..." : dbname;
5188 String msname = dbname.length() > 10 ? dbname.substring(
5189 0, 10) + "..." : dbname;
5192 imname = MessageManager.formatMessage(
5193 "label.from_msname", new Object[] { sname });
5195 fetchr = new JMenuItem(msname);
5196 final DbSourceProxy[] dassrc = { sproxy };
5197 fetchr.addActionListener(new ActionListener()
5201 public void actionPerformed(ActionEvent e)
5203 new Thread(new Runnable()
5209 boolean isNucleotide = alignPanel.alignFrame
5210 .getViewport().getAlignment()
5212 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5213 alignPanel.av.getSequenceSelection(),
5214 alignPanel.alignFrame, dassrc,
5215 alignPanel.alignFrame.featureSettings,
5218 .addListener(new FetchFinishedListenerI()
5221 public void finished()
5223 AlignFrame.this.setMenusForViewport();
5226 dbRefFetcher.fetchDBRefs(false);
5232 fetchr.setToolTipText("<html>"
5233 + MessageManager.formatMessage(
5234 "label.fetch_retrieve_from", new Object[]
5238 if (++icomp >= mcomp || i == (otherdb.size()))
5240 ifetch.setText(MessageManager.formatMessage(
5241 "label.source_to_target", imname, sname));
5243 ifetch = new JMenu();
5251 if (comp >= mcomp || dbi >= (dbclasses.length))
5253 dfetch.setText(MessageManager.formatMessage(
5254 "label.source_to_target", mname, dbclass));
5256 dfetch = new JMenu();
5269 * Left justify the whole alignment.
5272 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5274 AlignmentI al = viewport.getAlignment();
5276 viewport.firePropertyChange("alignment", null, al);
5280 * Right justify the whole alignment.
5283 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5285 AlignmentI al = viewport.getAlignment();
5287 viewport.firePropertyChange("alignment", null, al);
5291 public void setShowSeqFeatures(boolean b)
5293 showSeqFeatures.setSelected(b);
5294 viewport.setShowSequenceFeatures(b);
5301 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5302 * awt.event.ActionEvent)
5305 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5307 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5308 alignPanel.paintAlignment(true);
5315 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5319 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5321 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5322 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5330 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5331 * .event.ActionEvent)
5334 protected void showGroupConservation_actionPerformed(ActionEvent e)
5336 viewport.setShowGroupConservation(showGroupConservation.getState());
5337 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5344 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5345 * .event.ActionEvent)
5348 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5350 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5351 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5358 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5359 * .event.ActionEvent)
5362 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5364 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5365 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5369 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5371 showSequenceLogo.setState(true);
5372 viewport.setShowSequenceLogo(true);
5373 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5374 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5378 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5380 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5387 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5388 * .event.ActionEvent)
5391 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5393 if (avc.makeGroupsFromSelection())
5395 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5396 alignPanel.updateAnnotation();
5397 alignPanel.paintAlignment(true);
5401 public void clearAlignmentSeqRep()
5403 // TODO refactor alignmentseqrep to controller
5404 if (viewport.getAlignment().hasSeqrep())
5406 viewport.getAlignment().setSeqrep(null);
5407 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5408 alignPanel.updateAnnotation();
5409 alignPanel.paintAlignment(true);
5414 protected void createGroup_actionPerformed(ActionEvent e)
5416 if (avc.createGroup())
5418 alignPanel.alignmentChanged();
5423 protected void unGroup_actionPerformed(ActionEvent e)
5427 alignPanel.alignmentChanged();
5432 * make the given alignmentPanel the currently selected tab
5434 * @param alignmentPanel
5436 public void setDisplayedView(AlignmentPanel alignmentPanel)
5438 if (!viewport.getSequenceSetId().equals(
5439 alignmentPanel.av.getSequenceSetId()))
5443 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5445 if (tabbedPane != null
5446 && tabbedPane.getTabCount() > 0
5447 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5448 .getSelectedIndex())
5450 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5455 * Action on selection of menu options to Show or Hide annotations.
5458 * @param forSequences
5459 * update sequence-related annotations
5460 * @param forAlignment
5461 * update non-sequence-related annotations
5464 protected void setAnnotationsVisibility(boolean visible,
5465 boolean forSequences, boolean forAlignment)
5467 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5468 .getAlignmentAnnotation();
5473 for (AlignmentAnnotation aa : anns)
5476 * don't display non-positional annotations on an alignment
5478 if (aa.annotations == null)
5482 boolean apply = (aa.sequenceRef == null && forAlignment)
5483 || (aa.sequenceRef != null && forSequences);
5486 aa.visible = visible;
5489 alignPanel.validateAnnotationDimensions(true);
5490 alignPanel.alignmentChanged();
5494 * Store selected annotation sort order for the view and repaint.
5497 protected void sortAnnotations_actionPerformed()
5499 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5501 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5502 alignPanel.paintAlignment(true);
5507 * @return alignment panels in this alignment frame
5509 public List<? extends AlignmentViewPanel> getAlignPanels()
5511 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5515 * Open a new alignment window, with the cDNA associated with this (protein)
5516 * alignment, aligned as is the protein.
5518 protected void viewAsCdna_actionPerformed()
5520 // TODO no longer a menu action - refactor as required
5521 final AlignmentI alignment = getViewport().getAlignment();
5522 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5523 if (mappings == null)
5527 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5528 for (SequenceI aaSeq : alignment.getSequences())
5530 for (AlignedCodonFrame acf : mappings)
5532 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5536 * There is a cDNA mapping for this protein sequence - add to new
5537 * alignment. It will share the same dataset sequence as other mapped
5538 * cDNA (no new mappings need to be created).
5540 final Sequence newSeq = new Sequence(dnaSeq);
5541 newSeq.setDatasetSequence(dnaSeq);
5542 cdnaSeqs.add(newSeq);
5546 if (cdnaSeqs.size() == 0)
5548 // show a warning dialog no mapped cDNA
5551 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5553 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5554 AlignFrame.DEFAULT_HEIGHT);
5555 cdna.alignAs(alignment);
5556 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5558 Desktop.addInternalFrame(alignFrame, newtitle,
5559 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5563 * Set visibility of dna/protein complement view (available when shown in a
5569 protected void showComplement_actionPerformed(boolean show)
5571 SplitContainerI sf = getSplitViewContainer();
5574 sf.setComplementVisible(this, show);
5579 * Generate the reverse (optionally complemented) of the selected sequences,
5580 * and add them to the alignment
5583 protected void showReverse_actionPerformed(boolean complement)
5585 AlignmentI al = null;
5588 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5589 al = dna.reverseCdna(complement);
5590 viewport.addAlignment(al, "");
5591 addHistoryItem(new EditCommand(
5592 MessageManager.getString("label.add_sequences"),
5593 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5594 viewport.getAlignment()));
5595 } catch (Exception ex)
5597 System.err.println(ex.getMessage());
5603 * Try to run a script in the Groovy console, having first ensured that this
5604 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5605 * be targeted at this alignment.
5608 protected void runGroovy_actionPerformed()
5610 Jalview.setCurrentAlignFrame(this);
5611 groovy.ui.Console console = Desktop.getGroovyConsole();
5612 if (console != null)
5616 console.runScript();
5617 } catch (Exception ex)
5619 System.err.println((ex.toString()));
5621 .showInternalMessageDialog(Desktop.desktop, MessageManager
5622 .getString("label.couldnt_run_groovy_script"),
5624 .getString("label.groovy_support_failed"),
5625 JvOptionPane.ERROR_MESSAGE);
5630 System.err.println("Can't run Groovy script as console not found");
5635 * Hides columns containing (or not containing) a specified feature, provided
5636 * that would not leave all columns hidden
5638 * @param featureType
5639 * @param columnsContaining
5642 public boolean hideFeatureColumns(String featureType,
5643 boolean columnsContaining)
5645 boolean notForHiding = avc.markColumnsContainingFeatures(
5646 columnsContaining, false, false, featureType);
5649 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5650 false, featureType))
5652 getViewport().hideSelectedColumns();
5660 protected void selectHighlightedColumns_actionPerformed(
5661 ActionEvent actionEvent)
5663 // include key modifier check in case user selects from menu
5664 avc.markHighlightedColumns(
5665 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5667 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5671 * Rebuilds the Colour menu, including any user-defined colours which have
5672 * been loaded either on startup or during the session
5674 public void buildColourMenu()
5676 colourMenu.removeAll();
5678 colourMenu.add(applyToAllGroups);
5679 colourMenu.add(textColour);
5680 colourMenu.addSeparator();
5682 ColourMenuHelper.addMenuItems(colourMenu, this,
5683 viewport.getAlignment(), false);
5685 colourMenu.addSeparator();
5686 colourMenu.add(conservationMenuItem);
5687 colourMenu.add(modifyConservation);
5688 colourMenu.add(abovePIDThreshold);
5689 colourMenu.add(modifyPID);
5690 colourMenu.add(annotationColour);
5693 * select the default colour for the alignment (this may be
5696 boolean nucleotide = viewport.getAlignment().isNucleotide();
5697 String defaultColourScheme = Cache.getDefault(
5698 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
5699 : Preferences.DEFAULT_COLOUR_PROT,
5700 ResidueColourScheme.NONE);
5702 ColourMenuHelper.setColourSelected(colourMenu, defaultColourScheme);
5706 class PrintThread extends Thread
5710 public PrintThread(AlignmentPanel ap)
5715 static PageFormat pf;
5720 PrinterJob printJob = PrinterJob.getPrinterJob();
5724 printJob.setPrintable(ap, pf);
5728 printJob.setPrintable(ap);
5731 if (printJob.printDialog())
5736 } catch (Exception PrintException)
5738 PrintException.printStackTrace();