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 && conservationMenuItem.isSelected());
850 showGroupConservation.setEnabled(!nucleotide);
852 showComplementMenuItem.setText(nucleotide ? MessageManager
853 .getString("label.protein") : MessageManager
854 .getString("label.nucleotide"));
858 * set up menus for the current viewport. This may be called after any
859 * operation that affects the data in the current view (selection changed,
860 * etc) to update the menus to reflect the new state.
863 public void setMenusForViewport()
865 setMenusFromViewport(viewport);
869 * Need to call this method when tabs are selected for multiple views, or when
870 * loading from Jalview2XML.java
875 void setMenusFromViewport(AlignViewport av)
877 padGapsMenuitem.setSelected(av.isPadGaps());
878 colourTextMenuItem.setSelected(av.isShowColourText());
879 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
880 modifyPID.setEnabled(abovePIDThreshold.isSelected());
881 conservationMenuItem.setSelected(av.getConservationSelected());
882 modifyConservation.setEnabled(conservationMenuItem.isSelected());
883 seqLimits.setSelected(av.getShowJVSuffix());
884 idRightAlign.setSelected(av.isRightAlignIds());
885 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
886 renderGapsMenuItem.setSelected(av.isRenderGaps());
887 wrapMenuItem.setSelected(av.getWrapAlignment());
888 scaleAbove.setVisible(av.getWrapAlignment());
889 scaleLeft.setVisible(av.getWrapAlignment());
890 scaleRight.setVisible(av.getWrapAlignment());
891 annotationPanelMenuItem.setState(av.isShowAnnotation());
893 * Show/hide annotations only enabled if annotation panel is shown
895 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
896 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
897 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
898 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
899 viewBoxesMenuItem.setSelected(av.getShowBoxes());
900 viewTextMenuItem.setSelected(av.getShowText());
901 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
902 showGroupConsensus.setSelected(av.isShowGroupConsensus());
903 showGroupConservation.setSelected(av.isShowGroupConservation());
904 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
905 showSequenceLogo.setSelected(av.isShowSequenceLogo());
906 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
908 ColourMenuHelper.setColourSelected(colourMenu,
909 av.getGlobalColourScheme());
911 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
912 hiddenMarkers.setState(av.getShowHiddenMarkers());
913 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
914 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
915 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
916 autoCalculate.setSelected(av.autoCalculateConsensus);
917 sortByTree.setSelected(av.sortByTree);
918 listenToViewSelections.setSelected(av.followSelection);
920 showProducts.setEnabled(canShowProducts());
921 setGroovyEnabled(Desktop.getGroovyConsole() != null);
927 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
931 public void setGroovyEnabled(boolean b)
933 runGroovy.setEnabled(b);
936 private IProgressIndicator progressBar;
941 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
944 public void setProgressBar(String message, long id)
946 progressBar.setProgressBar(message, id);
950 public void registerHandler(final long id,
951 final IProgressIndicatorHandler handler)
953 progressBar.registerHandler(id, handler);
958 * @return true if any progress bars are still active
961 public boolean operationInProgress()
963 return progressBar.operationInProgress();
967 public void setStatus(String text)
969 statusBar.setText(text);
973 * Added so Castor Mapping file can obtain Jalview Version
975 public String getVersion()
977 return jalview.bin.Cache.getProperty("VERSION");
980 public FeatureRenderer getFeatureRenderer()
982 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
986 public void fetchSequence_actionPerformed(ActionEvent e)
988 new jalview.gui.SequenceFetcher(this);
992 public void addFromFile_actionPerformed(ActionEvent e)
994 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
998 public void reload_actionPerformed(ActionEvent e)
1000 if (fileName != null)
1002 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1003 // originating file's format
1004 // TODO: work out how to recover feature settings for correct view(s) when
1005 // file is reloaded.
1006 if (FileFormat.Jalview.equals(currentFileFormat))
1008 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1009 for (int i = 0; i < frames.length; i++)
1011 if (frames[i] instanceof AlignFrame && frames[i] != this
1012 && ((AlignFrame) frames[i]).fileName != null
1013 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1017 frames[i].setSelected(true);
1018 Desktop.instance.closeAssociatedWindows();
1019 } catch (java.beans.PropertyVetoException ex)
1025 Desktop.instance.closeAssociatedWindows();
1027 FileLoader loader = new FileLoader();
1028 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1029 : DataSourceType.FILE;
1030 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1034 Rectangle bounds = this.getBounds();
1036 FileLoader loader = new FileLoader();
1037 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1038 : DataSourceType.FILE;
1039 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1040 protocol, currentFileFormat);
1042 newframe.setBounds(bounds);
1043 if (featureSettings != null && featureSettings.isShowing())
1045 final Rectangle fspos = featureSettings.frame.getBounds();
1046 // TODO: need a 'show feature settings' function that takes bounds -
1047 // need to refactor Desktop.addFrame
1048 newframe.featureSettings_actionPerformed(null);
1049 final FeatureSettings nfs = newframe.featureSettings;
1050 SwingUtilities.invokeLater(new Runnable()
1055 nfs.frame.setBounds(fspos);
1058 this.featureSettings.close();
1059 this.featureSettings = null;
1061 this.closeMenuItem_actionPerformed(true);
1067 public void addFromText_actionPerformed(ActionEvent e)
1069 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1074 public void addFromURL_actionPerformed(ActionEvent e)
1076 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1080 public void save_actionPerformed(ActionEvent e)
1082 if (fileName == null || (currentFileFormat == null)
1083 || fileName.startsWith("http"))
1085 saveAs_actionPerformed(null);
1089 saveAlignment(fileName, currentFileFormat);
1100 public void saveAs_actionPerformed(ActionEvent e)
1102 String format = currentFileFormat == null ? null : currentFileFormat
1104 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1105 Cache.getProperty("LAST_DIRECTORY"), format);
1107 chooser.setFileView(new JalviewFileView());
1108 chooser.setDialogTitle(MessageManager
1109 .getString("label.save_alignment_to_file"));
1110 chooser.setToolTipText(MessageManager.getString("action.save"));
1112 int value = chooser.showSaveDialog(this);
1114 if (value == JalviewFileChooser.APPROVE_OPTION)
1116 currentFileFormat = chooser.getSelectedFormat();
1117 while (currentFileFormat == null)
1120 .showInternalMessageDialog(
1123 .getString("label.select_file_format_before_saving"),
1125 .getString("label.file_format_not_specified"),
1126 JvOptionPane.WARNING_MESSAGE);
1127 currentFileFormat = chooser.getSelectedFormat();
1128 value = chooser.showSaveDialog(this);
1129 if (value != JalviewFileChooser.APPROVE_OPTION)
1135 fileName = chooser.getSelectedFile().getPath();
1137 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1139 Cache.setProperty("LAST_DIRECTORY", fileName);
1140 saveAlignment(fileName, currentFileFormat);
1144 public boolean saveAlignment(String file, FileFormatI format)
1146 boolean success = true;
1148 if (FileFormat.Jalview.equals(format))
1150 String shortName = title;
1152 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1154 shortName = shortName.substring(shortName
1155 .lastIndexOf(java.io.File.separatorChar) + 1);
1158 success = new Jalview2XML().saveAlignment(this, file, shortName);
1160 statusBar.setText(MessageManager.formatMessage(
1161 "label.successfully_saved_to_file_in_format", new Object[] {
1162 fileName, format }));
1167 AlignmentExportData exportData = getAlignmentForExport(format,
1169 if (exportData.getSettings().isCancelled())
1173 FormatAdapter f = new FormatAdapter(alignPanel,
1174 exportData.getSettings());
1175 String output = f.formatSequences(
1177 exportData.getAlignment(), // class cast exceptions will
1178 // occur in the distant future
1179 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1180 f.getCacheSuffixDefault(format),
1181 viewport.getColumnSelection());
1191 PrintWriter out = new PrintWriter(new FileWriter(file));
1195 this.setTitle(file);
1196 statusBar.setText(MessageManager.formatMessage(
1197 "label.successfully_saved_to_file_in_format",
1198 new Object[] { fileName, format.getName() }));
1199 } catch (Exception ex)
1202 ex.printStackTrace();
1209 JvOptionPane.showInternalMessageDialog(this, MessageManager
1210 .formatMessage("label.couldnt_save_file",
1211 new Object[] { fileName }), MessageManager
1212 .getString("label.error_saving_file"),
1213 JvOptionPane.WARNING_MESSAGE);
1219 private void warningMessage(String warning, String title)
1221 if (new jalview.util.Platform().isHeadless())
1223 System.err.println("Warning: " + title + "\nWarning: " + warning);
1228 JvOptionPane.showInternalMessageDialog(this, warning, title,
1229 JvOptionPane.WARNING_MESSAGE);
1241 protected void outputText_actionPerformed(ActionEvent e)
1243 FileFormatI fileFormat = FileFormats.getInstance().forName(
1244 e.getActionCommand());
1245 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1247 if (exportData.getSettings().isCancelled())
1251 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1252 cap.setForInput(null);
1255 FileFormatI format = fileFormat;
1256 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1257 .formatSequences(format, exportData.getAlignment(),
1258 exportData.getOmitHidden(),
1259 exportData.getStartEndPostions(),
1260 viewport.getColumnSelection()));
1261 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1262 "label.alignment_output_command",
1263 new Object[] { e.getActionCommand() }), 600, 500);
1264 } catch (OutOfMemoryError oom)
1266 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1272 public static AlignmentExportData getAlignmentForExport(
1273 FileFormatI format, AlignViewportI viewport,
1274 AlignExportSettingI exportSettings)
1276 AlignmentI alignmentToExport = null;
1277 AlignExportSettingI settings = exportSettings;
1278 String[] omitHidden = null;
1280 HiddenSequences hiddenSeqs = viewport.getAlignment()
1281 .getHiddenSequences();
1283 alignmentToExport = viewport.getAlignment();
1285 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1286 if (settings == null)
1288 settings = new AlignExportSettings(hasHiddenSeqs,
1289 viewport.hasHiddenColumns(), format);
1291 // settings.isExportAnnotations();
1293 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1295 omitHidden = viewport.getViewAsString(false,
1296 settings.isExportHiddenSequences());
1299 int[] alignmentStartEnd = new int[2];
1300 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1302 alignmentToExport = hiddenSeqs.getFullAlignment();
1306 alignmentToExport = viewport.getAlignment();
1308 alignmentStartEnd = alignmentToExport
1309 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1310 .getHiddenColumns());
1311 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1312 omitHidden, alignmentStartEnd, settings);
1323 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1325 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1326 htmlSVG.exportHTML(null);
1330 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1332 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1333 bjs.exportHTML(null);
1336 public void createImageMap(File file, String image)
1338 alignPanel.makePNGImageMap(file, image);
1348 public void createPNG(File f)
1350 alignPanel.makePNG(f);
1360 public void createEPS(File f)
1362 alignPanel.makeEPS(f);
1366 public void createSVG(File f)
1368 alignPanel.makeSVG(f);
1372 public void pageSetup_actionPerformed(ActionEvent e)
1374 PrinterJob printJob = PrinterJob.getPrinterJob();
1375 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1385 public void printMenuItem_actionPerformed(ActionEvent e)
1387 // Putting in a thread avoids Swing painting problems
1388 PrintThread thread = new PrintThread(alignPanel);
1393 public void exportFeatures_actionPerformed(ActionEvent e)
1395 new AnnotationExporter().exportFeatures(alignPanel);
1399 public void exportAnnotations_actionPerformed(ActionEvent e)
1401 new AnnotationExporter().exportAnnotations(alignPanel);
1405 public void associatedData_actionPerformed(ActionEvent e)
1407 // Pick the tree file
1408 JalviewFileChooser chooser = new JalviewFileChooser(
1409 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1410 chooser.setFileView(new JalviewFileView());
1411 chooser.setDialogTitle(MessageManager
1412 .getString("label.load_jalview_annotations"));
1413 chooser.setToolTipText(MessageManager
1414 .getString("label.load_jalview_annotations"));
1416 int value = chooser.showOpenDialog(null);
1418 if (value == JalviewFileChooser.APPROVE_OPTION)
1420 String choice = chooser.getSelectedFile().getPath();
1421 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1422 loadJalviewDataFile(choice, null, null, null);
1428 * Close the current view or all views in the alignment frame. If the frame
1429 * only contains one view then the alignment will be removed from memory.
1431 * @param closeAllTabs
1434 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1436 if (alignPanels != null && alignPanels.size() < 2)
1438 closeAllTabs = true;
1443 if (alignPanels != null)
1447 if (this.isClosed())
1449 // really close all the windows - otherwise wait till
1450 // setClosed(true) is called
1451 for (int i = 0; i < alignPanels.size(); i++)
1453 AlignmentPanel ap = alignPanels.get(i);
1460 closeView(alignPanel);
1467 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1468 * be called recursively, with the frame now in 'closed' state
1470 this.setClosed(true);
1472 } catch (Exception ex)
1474 ex.printStackTrace();
1479 * Close the specified panel and close up tabs appropriately.
1481 * @param panelToClose
1483 public void closeView(AlignmentPanel panelToClose)
1485 int index = tabbedPane.getSelectedIndex();
1486 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1487 alignPanels.remove(panelToClose);
1488 panelToClose.closePanel();
1489 panelToClose = null;
1491 tabbedPane.removeTabAt(closedindex);
1492 tabbedPane.validate();
1494 if (index > closedindex || index == tabbedPane.getTabCount())
1496 // modify currently selected tab index if necessary.
1500 this.tabSelectionChanged(index);
1506 void updateEditMenuBar()
1509 if (viewport.getHistoryList().size() > 0)
1511 undoMenuItem.setEnabled(true);
1512 CommandI command = viewport.getHistoryList().peek();
1513 undoMenuItem.setText(MessageManager.formatMessage(
1514 "label.undo_command",
1515 new Object[] { command.getDescription() }));
1519 undoMenuItem.setEnabled(false);
1520 undoMenuItem.setText(MessageManager.getString("action.undo"));
1523 if (viewport.getRedoList().size() > 0)
1525 redoMenuItem.setEnabled(true);
1527 CommandI command = viewport.getRedoList().peek();
1528 redoMenuItem.setText(MessageManager.formatMessage(
1529 "label.redo_command",
1530 new Object[] { command.getDescription() }));
1534 redoMenuItem.setEnabled(false);
1535 redoMenuItem.setText(MessageManager.getString("action.redo"));
1540 public void addHistoryItem(CommandI command)
1542 if (command.getSize() > 0)
1544 viewport.addToHistoryList(command);
1545 viewport.clearRedoList();
1546 updateEditMenuBar();
1547 viewport.updateHiddenColumns();
1548 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1549 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1550 // viewport.getColumnSelection()
1551 // .getHiddenColumns().size() > 0);
1557 * @return alignment objects for all views
1559 AlignmentI[] getViewAlignments()
1561 if (alignPanels != null)
1563 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1565 for (AlignmentPanel ap : alignPanels)
1567 als[i++] = ap.av.getAlignment();
1571 if (viewport != null)
1573 return new AlignmentI[] { viewport.getAlignment() };
1585 protected void undoMenuItem_actionPerformed(ActionEvent e)
1587 if (viewport.getHistoryList().isEmpty())
1591 CommandI command = viewport.getHistoryList().pop();
1592 viewport.addToRedoList(command);
1593 command.undoCommand(getViewAlignments());
1595 AlignmentViewport originalSource = getOriginatingSource(command);
1596 updateEditMenuBar();
1598 if (originalSource != null)
1600 if (originalSource != viewport)
1603 .warn("Implementation worry: mismatch of viewport origin for undo");
1605 originalSource.updateHiddenColumns();
1606 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1608 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1609 // viewport.getColumnSelection()
1610 // .getHiddenColumns().size() > 0);
1611 originalSource.firePropertyChange("alignment", null, originalSource
1612 .getAlignment().getSequences());
1623 protected void redoMenuItem_actionPerformed(ActionEvent e)
1625 if (viewport.getRedoList().size() < 1)
1630 CommandI command = viewport.getRedoList().pop();
1631 viewport.addToHistoryList(command);
1632 command.doCommand(getViewAlignments());
1634 AlignmentViewport originalSource = getOriginatingSource(command);
1635 updateEditMenuBar();
1637 if (originalSource != null)
1640 if (originalSource != viewport)
1643 .warn("Implementation worry: mismatch of viewport origin for redo");
1645 originalSource.updateHiddenColumns();
1646 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1648 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1649 // viewport.getColumnSelection()
1650 // .getHiddenColumns().size() > 0);
1651 originalSource.firePropertyChange("alignment", null, originalSource
1652 .getAlignment().getSequences());
1656 AlignmentViewport getOriginatingSource(CommandI command)
1658 AlignmentViewport originalSource = null;
1659 // For sequence removal and addition, we need to fire
1660 // the property change event FROM the viewport where the
1661 // original alignment was altered
1662 AlignmentI al = null;
1663 if (command instanceof EditCommand)
1665 EditCommand editCommand = (EditCommand) command;
1666 al = editCommand.getAlignment();
1667 List<Component> comps = PaintRefresher.components.get(viewport
1668 .getSequenceSetId());
1670 for (Component comp : comps)
1672 if (comp instanceof AlignmentPanel)
1674 if (al == ((AlignmentPanel) comp).av.getAlignment())
1676 originalSource = ((AlignmentPanel) comp).av;
1683 if (originalSource == null)
1685 // The original view is closed, we must validate
1686 // the current view against the closed view first
1689 PaintRefresher.validateSequences(al, viewport.getAlignment());
1692 originalSource = viewport;
1695 return originalSource;
1704 public void moveSelectedSequences(boolean up)
1706 SequenceGroup sg = viewport.getSelectionGroup();
1712 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1713 viewport.getHiddenRepSequences(), up);
1714 alignPanel.paintAlignment(true);
1717 synchronized void slideSequences(boolean right, int size)
1719 List<SequenceI> sg = new ArrayList<SequenceI>();
1720 if (viewport.cursorMode)
1722 sg.add(viewport.getAlignment().getSequenceAt(
1723 alignPanel.getSeqPanel().seqCanvas.cursorY));
1725 else if (viewport.getSelectionGroup() != null
1726 && viewport.getSelectionGroup().getSize() != viewport
1727 .getAlignment().getHeight())
1729 sg = viewport.getSelectionGroup().getSequences(
1730 viewport.getHiddenRepSequences());
1738 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1740 for (SequenceI seq : viewport.getAlignment().getSequences())
1742 if (!sg.contains(seq))
1744 invertGroup.add(seq);
1748 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1750 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1751 for (int i = 0; i < invertGroup.size(); i++)
1753 seqs2[i] = invertGroup.get(i);
1756 SlideSequencesCommand ssc;
1759 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1760 size, viewport.getGapCharacter());
1764 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1765 size, viewport.getGapCharacter());
1768 int groupAdjustment = 0;
1769 if (ssc.getGapsInsertedBegin() && right)
1771 if (viewport.cursorMode)
1773 alignPanel.getSeqPanel().moveCursor(size, 0);
1777 groupAdjustment = size;
1780 else if (!ssc.getGapsInsertedBegin() && !right)
1782 if (viewport.cursorMode)
1784 alignPanel.getSeqPanel().moveCursor(-size, 0);
1788 groupAdjustment = -size;
1792 if (groupAdjustment != 0)
1794 viewport.getSelectionGroup().setStartRes(
1795 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1796 viewport.getSelectionGroup().setEndRes(
1797 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1801 * just extend the last slide command if compatible; but not if in
1802 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1804 boolean appendHistoryItem = false;
1805 Deque<CommandI> historyList = viewport.getHistoryList();
1806 boolean inSplitFrame = getSplitViewContainer() != null;
1807 if (!inSplitFrame && historyList != null && historyList.size() > 0
1808 && historyList.peek() instanceof SlideSequencesCommand)
1810 appendHistoryItem = ssc
1811 .appendSlideCommand((SlideSequencesCommand) historyList
1815 if (!appendHistoryItem)
1817 addHistoryItem(ssc);
1830 protected void copy_actionPerformed(ActionEvent e)
1833 if (viewport.getSelectionGroup() == null)
1837 // TODO: preserve the ordering of displayed alignment annotation in any
1838 // internal paste (particularly sequence associated annotation)
1839 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1840 String[] omitHidden = null;
1842 if (viewport.hasHiddenColumns())
1844 omitHidden = viewport.getViewAsString(true);
1847 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1848 seqs, omitHidden, null);
1850 StringSelection ss = new StringSelection(output);
1854 jalview.gui.Desktop.internalCopy = true;
1855 // Its really worth setting the clipboard contents
1856 // to empty before setting the large StringSelection!!
1857 Toolkit.getDefaultToolkit().getSystemClipboard()
1858 .setContents(new StringSelection(""), null);
1860 Toolkit.getDefaultToolkit().getSystemClipboard()
1861 .setContents(ss, Desktop.instance);
1862 } catch (OutOfMemoryError er)
1864 new OOMWarning("copying region", er);
1868 ArrayList<int[]> hiddenColumns = null;
1869 if (viewport.hasHiddenColumns())
1871 hiddenColumns = new ArrayList<int[]>();
1872 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1873 .getSelectionGroup().getEndRes();
1874 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1876 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1878 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1879 region[1] - hiddenOffset });
1884 Desktop.jalviewClipboard = new Object[] { seqs,
1885 viewport.getAlignment().getDataset(), hiddenColumns };
1886 statusBar.setText(MessageManager.formatMessage(
1887 "label.copied_sequences_to_clipboard", new Object[] { Integer
1888 .valueOf(seqs.length).toString() }));
1898 protected void pasteNew_actionPerformed(ActionEvent e)
1910 protected void pasteThis_actionPerformed(ActionEvent e)
1916 * Paste contents of Jalview clipboard
1918 * @param newAlignment
1919 * true to paste to a new alignment, otherwise add to this.
1921 void paste(boolean newAlignment)
1923 boolean externalPaste = true;
1926 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1927 Transferable contents = c.getContents(this);
1929 if (contents == null)
1938 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1939 if (str.length() < 1)
1944 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1946 } catch (OutOfMemoryError er)
1948 new OOMWarning("Out of memory pasting sequences!!", er);
1952 SequenceI[] sequences;
1953 boolean annotationAdded = false;
1954 AlignmentI alignment = null;
1956 if (Desktop.jalviewClipboard != null)
1958 // The clipboard was filled from within Jalview, we must use the
1960 // And dataset from the copied alignment
1961 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1962 // be doubly sure that we create *new* sequence objects.
1963 sequences = new SequenceI[newseq.length];
1964 for (int i = 0; i < newseq.length; i++)
1966 sequences[i] = new Sequence(newseq[i]);
1968 alignment = new Alignment(sequences);
1969 externalPaste = false;
1973 // parse the clipboard as an alignment.
1974 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1976 sequences = alignment.getSequencesArray();
1980 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1986 if (Desktop.jalviewClipboard != null)
1988 // dataset is inherited
1989 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1993 // new dataset is constructed
1994 alignment.setDataset(null);
1996 alwidth = alignment.getWidth() + 1;
2000 AlignmentI pastedal = alignment; // preserve pasted alignment object
2001 // Add pasted sequences and dataset into existing alignment.
2002 alignment = viewport.getAlignment();
2003 alwidth = alignment.getWidth() + 1;
2004 // decide if we need to import sequences from an existing dataset
2005 boolean importDs = Desktop.jalviewClipboard != null
2006 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2007 // importDs==true instructs us to copy over new dataset sequences from
2008 // an existing alignment
2009 Vector newDs = (importDs) ? new Vector() : null; // used to create
2010 // minimum dataset set
2012 for (int i = 0; i < sequences.length; i++)
2016 newDs.addElement(null);
2018 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2020 if (importDs && ds != null)
2022 if (!newDs.contains(ds))
2024 newDs.setElementAt(ds, i);
2025 ds = new Sequence(ds);
2026 // update with new dataset sequence
2027 sequences[i].setDatasetSequence(ds);
2031 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2036 // copy and derive new dataset sequence
2037 sequences[i] = sequences[i].deriveSequence();
2038 alignment.getDataset().addSequence(
2039 sequences[i].getDatasetSequence());
2040 // TODO: avoid creation of duplicate dataset sequences with a
2041 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2043 alignment.addSequence(sequences[i]); // merges dataset
2047 newDs.clear(); // tidy up
2049 if (alignment.getAlignmentAnnotation() != null)
2051 for (AlignmentAnnotation alan : alignment
2052 .getAlignmentAnnotation())
2054 if (alan.graphGroup > fgroup)
2056 fgroup = alan.graphGroup;
2060 if (pastedal.getAlignmentAnnotation() != null)
2062 // Add any annotation attached to alignment.
2063 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2064 for (int i = 0; i < alann.length; i++)
2066 annotationAdded = true;
2067 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2069 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2070 if (newann.graphGroup > -1)
2072 if (newGraphGroups.size() <= newann.graphGroup
2073 || newGraphGroups.get(newann.graphGroup) == null)
2075 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2077 newGraphGroups.add(q, null);
2079 newGraphGroups.set(newann.graphGroup, new Integer(
2082 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2086 newann.padAnnotation(alwidth);
2087 alignment.addAnnotation(newann);
2097 addHistoryItem(new EditCommand(
2098 MessageManager.getString("label.add_sequences"),
2099 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2101 // Add any annotations attached to sequences
2102 for (int i = 0; i < sequences.length; i++)
2104 if (sequences[i].getAnnotation() != null)
2106 AlignmentAnnotation newann;
2107 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2109 annotationAdded = true;
2110 newann = sequences[i].getAnnotation()[a];
2111 newann.adjustForAlignment();
2112 newann.padAnnotation(alwidth);
2113 if (newann.graphGroup > -1)
2115 if (newann.graphGroup > -1)
2117 if (newGraphGroups.size() <= newann.graphGroup
2118 || newGraphGroups.get(newann.graphGroup) == null)
2120 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2122 newGraphGroups.add(q, null);
2124 newGraphGroups.set(newann.graphGroup, new Integer(
2127 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2131 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2136 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2143 // propagate alignment changed.
2144 viewport.setEndSeq(alignment.getHeight());
2145 if (annotationAdded)
2147 // Duplicate sequence annotation in all views.
2148 AlignmentI[] alview = this.getViewAlignments();
2149 for (int i = 0; i < sequences.length; i++)
2151 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2156 for (int avnum = 0; avnum < alview.length; avnum++)
2158 if (alview[avnum] != alignment)
2160 // duplicate in a view other than the one with input focus
2161 int avwidth = alview[avnum].getWidth() + 1;
2162 // this relies on sann being preserved after we
2163 // modify the sequence's annotation array for each duplication
2164 for (int a = 0; a < sann.length; a++)
2166 AlignmentAnnotation newann = new AlignmentAnnotation(
2168 sequences[i].addAlignmentAnnotation(newann);
2169 newann.padAnnotation(avwidth);
2170 alview[avnum].addAnnotation(newann); // annotation was
2171 // duplicated earlier
2172 // TODO JAL-1145 graphGroups are not updated for sequence
2173 // annotation added to several views. This may cause
2175 alview[avnum].setAnnotationIndex(newann, a);
2180 buildSortByAnnotationScoresMenu();
2182 viewport.firePropertyChange("alignment", null,
2183 alignment.getSequences());
2184 if (alignPanels != null)
2186 for (AlignmentPanel ap : alignPanels)
2188 ap.validateAnnotationDimensions(false);
2193 alignPanel.validateAnnotationDimensions(false);
2199 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2201 String newtitle = new String("Copied sequences");
2203 if (Desktop.jalviewClipboard != null
2204 && Desktop.jalviewClipboard[2] != null)
2206 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2207 for (int[] region : hc)
2209 af.viewport.hideColumns(region[0], region[1]);
2213 // >>>This is a fix for the moment, until a better solution is
2215 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2217 alignPanel.getSeqPanel().seqCanvas
2218 .getFeatureRenderer());
2220 // TODO: maintain provenance of an alignment, rather than just make the
2221 // title a concatenation of operations.
2224 if (title.startsWith("Copied sequences"))
2230 newtitle = newtitle.concat("- from " + title);
2235 newtitle = new String("Pasted sequences");
2238 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2243 } catch (Exception ex)
2245 ex.printStackTrace();
2246 System.out.println("Exception whilst pasting: " + ex);
2247 // could be anything being pasted in here
2253 protected void expand_newalign(ActionEvent e)
2257 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2258 .getAlignment(), -1);
2259 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2261 String newtitle = new String("Flanking alignment");
2263 if (Desktop.jalviewClipboard != null
2264 && Desktop.jalviewClipboard[2] != null)
2266 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2267 for (int region[] : hc)
2269 af.viewport.hideColumns(region[0], region[1]);
2273 // >>>This is a fix for the moment, until a better solution is
2275 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2277 alignPanel.getSeqPanel().seqCanvas
2278 .getFeatureRenderer());
2280 // TODO: maintain provenance of an alignment, rather than just make the
2281 // title a concatenation of operations.
2283 if (title.startsWith("Copied sequences"))
2289 newtitle = newtitle.concat("- from " + title);
2293 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2295 } catch (Exception ex)
2297 ex.printStackTrace();
2298 System.out.println("Exception whilst pasting: " + ex);
2299 // could be anything being pasted in here
2300 } catch (OutOfMemoryError oom)
2302 new OOMWarning("Viewing flanking region of alignment", oom);
2313 protected void cut_actionPerformed(ActionEvent e)
2315 copy_actionPerformed(null);
2316 delete_actionPerformed(null);
2326 protected void delete_actionPerformed(ActionEvent evt)
2329 SequenceGroup sg = viewport.getSelectionGroup();
2336 * If the cut affects all sequences, warn, remove highlighted columns
2338 if (sg.getSize() == viewport.getAlignment().getHeight())
2340 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2341 .getAlignment().getWidth()) ? true : false;
2342 if (isEntireAlignWidth)
2344 int confirm = JvOptionPane.showConfirmDialog(this,
2345 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2346 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2347 JvOptionPane.OK_CANCEL_OPTION);
2349 if (confirm == JvOptionPane.CANCEL_OPTION
2350 || confirm == JvOptionPane.CLOSED_OPTION)
2355 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2356 sg.getEndRes() + 1);
2358 SequenceI[] cut = sg.getSequences()
2359 .toArray(new SequenceI[sg.getSize()]);
2361 addHistoryItem(new EditCommand(
2362 MessageManager.getString("label.cut_sequences"), Action.CUT,
2363 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2364 viewport.getAlignment()));
2366 viewport.setSelectionGroup(null);
2367 viewport.sendSelection();
2368 viewport.getAlignment().deleteGroup(sg);
2370 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2372 if (viewport.getAlignment().getHeight() < 1)
2376 this.setClosed(true);
2377 } catch (Exception ex)
2390 protected void deleteGroups_actionPerformed(ActionEvent e)
2392 if (avc.deleteGroups())
2394 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2395 alignPanel.updateAnnotation();
2396 alignPanel.paintAlignment(true);
2407 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2409 SequenceGroup sg = new SequenceGroup();
2411 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2413 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2416 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2417 viewport.setSelectionGroup(sg);
2418 viewport.sendSelection();
2419 // JAL-2034 - should delegate to
2420 // alignPanel to decide if overview needs
2422 alignPanel.paintAlignment(false);
2423 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2433 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2435 if (viewport.cursorMode)
2437 alignPanel.getSeqPanel().keyboardNo1 = null;
2438 alignPanel.getSeqPanel().keyboardNo2 = null;
2440 viewport.setSelectionGroup(null);
2441 viewport.getColumnSelection().clear();
2442 viewport.setSelectionGroup(null);
2443 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2444 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2445 // JAL-2034 - should delegate to
2446 // alignPanel to decide if overview needs
2448 alignPanel.paintAlignment(false);
2449 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2450 viewport.sendSelection();
2460 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2462 SequenceGroup sg = viewport.getSelectionGroup();
2466 selectAllSequenceMenuItem_actionPerformed(null);
2471 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2473 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2475 // JAL-2034 - should delegate to
2476 // alignPanel to decide if overview needs
2479 alignPanel.paintAlignment(true);
2480 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2481 viewport.sendSelection();
2485 public void invertColSel_actionPerformed(ActionEvent e)
2487 viewport.invertColumnSelection();
2488 alignPanel.paintAlignment(true);
2489 viewport.sendSelection();
2499 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2501 trimAlignment(true);
2511 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2513 trimAlignment(false);
2516 void trimAlignment(boolean trimLeft)
2518 ColumnSelection colSel = viewport.getColumnSelection();
2521 if (!colSel.isEmpty())
2525 column = colSel.getMin();
2529 column = colSel.getMax();
2533 if (viewport.getSelectionGroup() != null)
2535 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2536 viewport.getHiddenRepSequences());
2540 seqs = viewport.getAlignment().getSequencesArray();
2543 TrimRegionCommand trimRegion;
2546 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2547 column, viewport.getAlignment());
2548 viewport.setStartRes(0);
2552 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2553 column, viewport.getAlignment());
2556 statusBar.setText(MessageManager.formatMessage(
2557 "label.removed_columns",
2558 new String[] { Integer.valueOf(trimRegion.getSize())
2561 addHistoryItem(trimRegion);
2563 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2565 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2566 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2568 viewport.getAlignment().deleteGroup(sg);
2572 viewport.firePropertyChange("alignment", null, viewport
2573 .getAlignment().getSequences());
2584 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2586 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2589 if (viewport.getSelectionGroup() != null)
2591 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2592 viewport.getHiddenRepSequences());
2593 start = viewport.getSelectionGroup().getStartRes();
2594 end = viewport.getSelectionGroup().getEndRes();
2598 seqs = viewport.getAlignment().getSequencesArray();
2601 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2602 "Remove Gapped Columns", seqs, start, end,
2603 viewport.getAlignment());
2605 addHistoryItem(removeGapCols);
2607 statusBar.setText(MessageManager.formatMessage(
2608 "label.removed_empty_columns",
2609 new Object[] { Integer.valueOf(removeGapCols.getSize())
2612 // This is to maintain viewport position on first residue
2613 // of first sequence
2614 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2615 int startRes = seq.findPosition(viewport.startRes);
2616 // ShiftList shifts;
2617 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2618 // edit.alColumnChanges=shifts.getInverse();
2619 // if (viewport.hasHiddenColumns)
2620 // viewport.getColumnSelection().compensateForEdits(shifts);
2621 viewport.setStartRes(seq.findIndex(startRes) - 1);
2622 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2634 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2636 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2639 if (viewport.getSelectionGroup() != null)
2641 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2642 viewport.getHiddenRepSequences());
2643 start = viewport.getSelectionGroup().getStartRes();
2644 end = viewport.getSelectionGroup().getEndRes();
2648 seqs = viewport.getAlignment().getSequencesArray();
2651 // This is to maintain viewport position on first residue
2652 // of first sequence
2653 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2654 int startRes = seq.findPosition(viewport.startRes);
2656 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2657 viewport.getAlignment()));
2659 viewport.setStartRes(seq.findIndex(startRes) - 1);
2661 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2673 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2675 viewport.setPadGaps(padGapsMenuitem.isSelected());
2676 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2687 public void findMenuItem_actionPerformed(ActionEvent e)
2693 * Create a new view of the current alignment.
2696 public void newView_actionPerformed(ActionEvent e)
2698 newView(null, true);
2702 * Creates and shows a new view of the current alignment.
2705 * title of newly created view; if null, one will be generated
2706 * @param copyAnnotation
2707 * if true then duplicate all annnotation, groups and settings
2708 * @return new alignment panel, already displayed.
2710 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2713 * Create a new AlignmentPanel (with its own, new Viewport)
2715 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2717 if (!copyAnnotation)
2720 * remove all groups and annotation except for the automatic stuff
2722 newap.av.getAlignment().deleteAllGroups();
2723 newap.av.getAlignment().deleteAllAnnotations(false);
2726 newap.av.setGatherViewsHere(false);
2728 if (viewport.viewName == null)
2730 viewport.viewName = MessageManager
2731 .getString("label.view_name_original");
2735 * Views share the same edits undo and redo stacks
2737 newap.av.setHistoryList(viewport.getHistoryList());
2738 newap.av.setRedoList(viewport.getRedoList());
2741 * Views share the same mappings; need to deregister any new mappings
2742 * created by copyAlignPanel, and register the new reference to the shared
2745 newap.av.replaceMappings(viewport.getAlignment());
2748 * start up cDNA consensus (if applicable) now mappings are in place
2750 if (newap.av.initComplementConsensus())
2752 newap.refresh(true); // adjust layout of annotations
2755 newap.av.viewName = getNewViewName(viewTitle);
2757 addAlignmentPanel(newap, true);
2758 newap.alignmentChanged();
2760 if (alignPanels.size() == 2)
2762 viewport.setGatherViewsHere(true);
2764 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2769 * Make a new name for the view, ensuring it is unique within the current
2770 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2771 * these now use viewId. Unique view names are still desirable for usability.)
2776 protected String getNewViewName(String viewTitle)
2778 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2779 boolean addFirstIndex = false;
2780 if (viewTitle == null || viewTitle.trim().length() == 0)
2782 viewTitle = MessageManager.getString("action.view");
2783 addFirstIndex = true;
2787 index = 1;// we count from 1 if given a specific name
2789 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2791 List<Component> comps = PaintRefresher.components.get(viewport
2792 .getSequenceSetId());
2794 List<String> existingNames = getExistingViewNames(comps);
2796 while (existingNames.contains(newViewName))
2798 newViewName = viewTitle + " " + (++index);
2804 * Returns a list of distinct view names found in the given list of
2805 * components. View names are held on the viewport of an AlignmentPanel.
2810 protected List<String> getExistingViewNames(List<Component> comps)
2812 List<String> existingNames = new ArrayList<String>();
2813 for (Component comp : comps)
2815 if (comp instanceof AlignmentPanel)
2817 AlignmentPanel ap = (AlignmentPanel) comp;
2818 if (!existingNames.contains(ap.av.viewName))
2820 existingNames.add(ap.av.viewName);
2824 return existingNames;
2828 * Explode tabbed views into separate windows.
2831 public void expandViews_actionPerformed(ActionEvent e)
2833 Desktop.explodeViews(this);
2837 * Gather views in separate windows back into a tabbed presentation.
2840 public void gatherViews_actionPerformed(ActionEvent e)
2842 Desktop.instance.gatherViews(this);
2852 public void font_actionPerformed(ActionEvent e)
2854 new FontChooser(alignPanel);
2864 protected void seqLimit_actionPerformed(ActionEvent e)
2866 viewport.setShowJVSuffix(seqLimits.isSelected());
2868 alignPanel.getIdPanel().getIdCanvas()
2869 .setPreferredSize(alignPanel.calculateIdWidth());
2870 alignPanel.paintAlignment(true);
2874 public void idRightAlign_actionPerformed(ActionEvent e)
2876 viewport.setRightAlignIds(idRightAlign.isSelected());
2877 alignPanel.paintAlignment(true);
2881 public void centreColumnLabels_actionPerformed(ActionEvent e)
2883 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2884 alignPanel.paintAlignment(true);
2890 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2893 protected void followHighlight_actionPerformed()
2896 * Set the 'follow' flag on the Viewport (and scroll to position if now
2899 final boolean state = this.followHighlightMenuItem.getState();
2900 viewport.setFollowHighlight(state);
2903 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2914 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2916 viewport.setColourText(colourTextMenuItem.isSelected());
2917 alignPanel.paintAlignment(true);
2927 public void wrapMenuItem_actionPerformed(ActionEvent e)
2929 scaleAbove.setVisible(wrapMenuItem.isSelected());
2930 scaleLeft.setVisible(wrapMenuItem.isSelected());
2931 scaleRight.setVisible(wrapMenuItem.isSelected());
2932 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2933 alignPanel.updateLayout();
2937 public void showAllSeqs_actionPerformed(ActionEvent e)
2939 viewport.showAllHiddenSeqs();
2943 public void showAllColumns_actionPerformed(ActionEvent e)
2945 viewport.showAllHiddenColumns();
2947 viewport.sendSelection();
2951 public void hideSelSequences_actionPerformed(ActionEvent e)
2953 viewport.hideAllSelectedSeqs();
2954 // alignPanel.paintAlignment(true);
2958 * called by key handler and the hide all/show all menu items
2963 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2966 boolean hide = false;
2967 SequenceGroup sg = viewport.getSelectionGroup();
2968 if (!toggleSeqs && !toggleCols)
2970 // Hide everything by the current selection - this is a hack - we do the
2971 // invert and then hide
2972 // first check that there will be visible columns after the invert.
2973 if (viewport.hasSelectedColumns()
2974 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2977 // now invert the sequence set, if required - empty selection implies
2978 // that no hiding is required.
2981 invertSequenceMenuItem_actionPerformed(null);
2982 sg = viewport.getSelectionGroup();
2986 viewport.expandColSelection(sg, true);
2987 // finally invert the column selection and get the new sequence
2989 invertColSel_actionPerformed(null);
2996 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2998 hideSelSequences_actionPerformed(null);
3001 else if (!(toggleCols && viewport.hasSelectedColumns()))
3003 showAllSeqs_actionPerformed(null);
3009 if (viewport.hasSelectedColumns())
3011 hideSelColumns_actionPerformed(null);
3014 viewport.setSelectionGroup(sg);
3019 showAllColumns_actionPerformed(null);
3028 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3029 * event.ActionEvent)
3032 public void hideAllButSelection_actionPerformed(ActionEvent e)
3034 toggleHiddenRegions(false, false);
3035 viewport.sendSelection();
3042 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3046 public void hideAllSelection_actionPerformed(ActionEvent e)
3048 SequenceGroup sg = viewport.getSelectionGroup();
3049 viewport.expandColSelection(sg, false);
3050 viewport.hideAllSelectedSeqs();
3051 viewport.hideSelectedColumns();
3052 alignPanel.paintAlignment(true);
3053 viewport.sendSelection();
3060 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3064 public void showAllhidden_actionPerformed(ActionEvent e)
3066 viewport.showAllHiddenColumns();
3067 viewport.showAllHiddenSeqs();
3068 alignPanel.paintAlignment(true);
3069 viewport.sendSelection();
3073 public void hideSelColumns_actionPerformed(ActionEvent e)
3075 viewport.hideSelectedColumns();
3076 alignPanel.paintAlignment(true);
3077 viewport.sendSelection();
3081 public void hiddenMarkers_actionPerformed(ActionEvent e)
3083 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3094 protected void scaleAbove_actionPerformed(ActionEvent e)
3096 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3097 alignPanel.paintAlignment(true);
3107 protected void scaleLeft_actionPerformed(ActionEvent e)
3109 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3110 alignPanel.paintAlignment(true);
3120 protected void scaleRight_actionPerformed(ActionEvent e)
3122 viewport.setScaleRightWrapped(scaleRight.isSelected());
3123 alignPanel.paintAlignment(true);
3133 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3135 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3136 alignPanel.paintAlignment(true);
3146 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3148 viewport.setShowText(viewTextMenuItem.isSelected());
3149 alignPanel.paintAlignment(true);
3159 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3161 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3162 alignPanel.paintAlignment(true);
3165 public FeatureSettings featureSettings;
3168 public FeatureSettingsControllerI getFeatureSettingsUI()
3170 return featureSettings;
3174 public void featureSettings_actionPerformed(ActionEvent e)
3176 if (featureSettings != null)
3178 featureSettings.close();
3179 featureSettings = null;
3181 if (!showSeqFeatures.isSelected())
3183 // make sure features are actually displayed
3184 showSeqFeatures.setSelected(true);
3185 showSeqFeatures_actionPerformed(null);
3187 featureSettings = new FeatureSettings(this);
3191 * Set or clear 'Show Sequence Features'
3197 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3199 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3200 alignPanel.paintAlignment(true);
3201 if (alignPanel.getOverviewPanel() != null)
3203 alignPanel.getOverviewPanel().updateOverviewImage();
3208 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3209 * the annotations panel as a whole.
3211 * The options to show/hide all annotations should be enabled when the panel
3212 * is shown, and disabled when the panel is hidden.
3217 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3219 final boolean setVisible = annotationPanelMenuItem.isSelected();
3220 viewport.setShowAnnotation(setVisible);
3221 this.showAllSeqAnnotations.setEnabled(setVisible);
3222 this.hideAllSeqAnnotations.setEnabled(setVisible);
3223 this.showAllAlAnnotations.setEnabled(setVisible);
3224 this.hideAllAlAnnotations.setEnabled(setVisible);
3225 alignPanel.updateLayout();
3229 public void alignmentProperties()
3231 JEditorPane editPane = new JEditorPane("text/html", "");
3232 editPane.setEditable(false);
3233 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3235 editPane.setText(MessageManager.formatMessage("label.html_content",
3236 new Object[] { contents.toString() }));
3237 JInternalFrame frame = new JInternalFrame();
3238 frame.getContentPane().add(new JScrollPane(editPane));
3240 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3241 "label.alignment_properties", new Object[] { getTitle() }),
3252 public void overviewMenuItem_actionPerformed(ActionEvent e)
3254 if (alignPanel.overviewPanel != null)
3259 JInternalFrame frame = new JInternalFrame();
3260 OverviewPanel overview = new OverviewPanel(alignPanel);
3261 frame.setContentPane(overview);
3262 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3263 "label.overview_params", new Object[] { this.getTitle() }),
3264 frame.getWidth(), frame.getHeight());
3266 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3267 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3270 public void internalFrameClosed(
3271 javax.swing.event.InternalFrameEvent evt)
3273 alignPanel.setOverviewPanel(null);
3277 alignPanel.setOverviewPanel(overview);
3281 public void textColour_actionPerformed()
3283 new TextColourChooser().chooseColour(alignPanel, null);
3287 * public void covariationColour_actionPerformed() {
3289 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3293 public void annotationColour_actionPerformed()
3295 new AnnotationColourChooser(viewport, alignPanel);
3299 public void annotationColumn_actionPerformed(ActionEvent e)
3301 new AnnotationColumnChooser(viewport, alignPanel);
3305 * Action on the user checking or unchecking the option to apply the selected
3306 * colour scheme to all groups. If unchecked, groups may have their own
3307 * independent colour schemes.
3312 public void applyToAllGroups_actionPerformed(boolean selected)
3314 viewport.setColourAppliesToAllGroups(selected);
3318 * Action on user selecting a colour from the colour menu
3321 * the name (not the menu item label!) of the colour scheme
3324 public void changeColour_actionPerformed(String name)
3327 * 'User Defined' opens a panel to configure or load a
3328 * user-defined colour scheme
3330 if (ResidueColourScheme.USER_DEFINED.equals(name))
3332 new UserDefinedColours(alignPanel, null);
3337 * otherwise set the chosen colour scheme (or null for 'None')
3339 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3340 viewport.getAlignment(), viewport.getHiddenRepSequences());
3345 * Actions on setting or changing the alignment colour scheme
3350 public void changeColour(ColourSchemeI cs)
3352 // TODO: pull up to controller method
3355 ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
3358 viewport.setGlobalColourScheme(cs);
3360 alignPanel.paintAlignment(true);
3364 * Show the PID threshold slider panel
3367 protected void modifyPID_actionPerformed()
3369 SliderPanel.setPIDSliderSource(alignPanel,
3370 viewport.getResidueShading(), alignPanel.getViewName());
3371 SliderPanel.showPIDSlider();
3375 * Show the Conservation slider panel
3378 protected void modifyConservation_actionPerformed()
3380 SliderPanel.setConservationSlider(alignPanel,
3381 viewport.getResidueShading(), alignPanel.getViewName());
3382 SliderPanel.showConservationSlider();
3386 * Action on selecting or deselecting (Colour) By Conservation
3389 public void conservationMenuItem_actionPerformed(boolean selected)
3391 modifyConservation.setEnabled(selected);
3392 viewport.setConservationSelected(selected);
3393 viewport.getResidueShading().setConservationApplied(selected);
3395 changeColour(viewport.getGlobalColourScheme());
3398 modifyConservation_actionPerformed();
3402 SliderPanel.hideConservationSlider();
3407 * Action on selecting or deselecting (Colour) Above PID Threshold
3410 public void abovePIDThreshold_actionPerformed(boolean selected)
3412 modifyPID.setEnabled(selected);
3413 viewport.setAbovePIDThreshold(selected);
3416 viewport.getResidueShading().setThreshold(0,
3417 viewport.isIgnoreGapsConsensus());
3420 changeColour(viewport.getGlobalColourScheme());
3423 modifyPID_actionPerformed();
3427 SliderPanel.hidePIDSlider();
3438 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3440 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3441 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3442 .getAlignment().getSequenceAt(0), null);
3443 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3444 viewport.getAlignment()));
3445 alignPanel.paintAlignment(true);
3455 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3457 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3458 AlignmentSorter.sortByID(viewport.getAlignment());
3459 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3460 viewport.getAlignment()));
3461 alignPanel.paintAlignment(true);
3471 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3473 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3474 AlignmentSorter.sortByLength(viewport.getAlignment());
3475 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3476 viewport.getAlignment()));
3477 alignPanel.paintAlignment(true);
3487 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3489 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3490 AlignmentSorter.sortByGroup(viewport.getAlignment());
3491 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3492 viewport.getAlignment()));
3494 alignPanel.paintAlignment(true);
3504 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3506 new RedundancyPanel(alignPanel, this);
3516 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3518 if ((viewport.getSelectionGroup() == null)
3519 || (viewport.getSelectionGroup().getSize() < 2))
3521 JvOptionPane.showInternalMessageDialog(this, MessageManager
3522 .getString("label.you_must_select_least_two_sequences"),
3523 MessageManager.getString("label.invalid_selection"),
3524 JvOptionPane.WARNING_MESSAGE);
3528 JInternalFrame frame = new JInternalFrame();
3529 frame.setContentPane(new PairwiseAlignPanel(viewport));
3530 Desktop.addInternalFrame(frame,
3531 MessageManager.getString("action.pairwise_alignment"), 600,
3543 public void PCAMenuItem_actionPerformed(ActionEvent e)
3545 if (((viewport.getSelectionGroup() != null)
3546 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3547 .getSelectionGroup().getSize() > 0))
3548 || (viewport.getAlignment().getHeight() < 4))
3551 .showInternalMessageDialog(
3554 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3556 .getString("label.sequence_selection_insufficient"),
3557 JvOptionPane.WARNING_MESSAGE);
3562 new PCAPanel(alignPanel);
3566 public void autoCalculate_actionPerformed(ActionEvent e)
3568 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3569 if (viewport.autoCalculateConsensus)
3571 viewport.firePropertyChange("alignment", null, viewport
3572 .getAlignment().getSequences());
3577 public void sortByTreeOption_actionPerformed(ActionEvent e)
3579 viewport.sortByTree = sortByTree.isSelected();
3583 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3585 viewport.followSelection = listenToViewSelections.isSelected();
3595 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3597 newTreePanel("AV", "PID", "Average distance tree using PID");
3607 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3609 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3619 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3621 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3631 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3633 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3646 void newTreePanel(String type, String pwType, String title)
3650 if (viewport.getSelectionGroup() != null
3651 && viewport.getSelectionGroup().getSize() > 0)
3653 if (viewport.getSelectionGroup().getSize() < 3)
3659 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3661 .getString("label.not_enough_sequences"),
3662 JvOptionPane.WARNING_MESSAGE);
3666 SequenceGroup sg = viewport.getSelectionGroup();
3668 /* Decide if the selection is a column region */
3669 for (SequenceI _s : sg.getSequences())
3671 if (_s.getLength() < sg.getEndRes())
3677 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3679 .getString("label.sequences_selection_not_aligned"),
3680 JvOptionPane.WARNING_MESSAGE);
3686 title = title + " on region";
3687 tp = new TreePanel(alignPanel, type, pwType);
3691 // are the visible sequences aligned?
3692 if (!viewport.getAlignment().isAligned(false))
3698 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3700 .getString("label.sequences_not_aligned"),
3701 JvOptionPane.WARNING_MESSAGE);
3706 if (viewport.getAlignment().getHeight() < 2)
3711 tp = new TreePanel(alignPanel, type, pwType);
3716 if (viewport.viewName != null)
3718 title += viewport.viewName + " of ";
3721 title += this.title;
3723 Desktop.addInternalFrame(tp, title, 600, 500);
3734 public void addSortByOrderMenuItem(String title,
3735 final AlignmentOrder order)
3737 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3738 "action.by_title_param", new Object[] { title }));
3740 item.addActionListener(new java.awt.event.ActionListener()
3743 public void actionPerformed(ActionEvent e)
3745 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3747 // TODO: JBPNote - have to map order entries to curent SequenceI
3749 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3751 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3754 alignPanel.paintAlignment(true);
3760 * Add a new sort by annotation score menu item
3763 * the menu to add the option to
3765 * the label used to retrieve scores for each sequence on the
3768 public void addSortByAnnotScoreMenuItem(JMenu sort,
3769 final String scoreLabel)
3771 final JMenuItem item = new JMenuItem(scoreLabel);
3773 item.addActionListener(new java.awt.event.ActionListener()
3776 public void actionPerformed(ActionEvent e)
3778 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3779 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3780 viewport.getAlignment());// ,viewport.getSelectionGroup());
3781 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3782 viewport.getAlignment()));
3783 alignPanel.paintAlignment(true);
3789 * last hash for alignment's annotation array - used to minimise cost of
3792 protected int _annotationScoreVectorHash;
3795 * search the alignment and rebuild the sort by annotation score submenu the
3796 * last alignment annotation vector hash is stored to minimize cost of
3797 * rebuilding in subsequence calls.
3801 public void buildSortByAnnotationScoresMenu()
3803 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3808 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3810 sortByAnnotScore.removeAll();
3811 // almost certainly a quicker way to do this - but we keep it simple
3812 Hashtable scoreSorts = new Hashtable();
3813 AlignmentAnnotation aann[];
3814 for (SequenceI sqa : viewport.getAlignment().getSequences())
3816 aann = sqa.getAnnotation();
3817 for (int i = 0; aann != null && i < aann.length; i++)
3819 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3821 scoreSorts.put(aann[i].label, aann[i].label);
3825 Enumeration labels = scoreSorts.keys();
3826 while (labels.hasMoreElements())
3828 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3829 (String) labels.nextElement());
3831 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3834 _annotationScoreVectorHash = viewport.getAlignment()
3835 .getAlignmentAnnotation().hashCode();
3840 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3841 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3842 * call. Listeners are added to remove the menu item when the treePanel is
3843 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3847 * Displayed tree window.
3849 * SortBy menu item title.
3852 public void buildTreeMenu()
3854 calculateTree.removeAll();
3855 // build the calculate menu
3857 for (final String type : new String[] { "NJ", "AV" })
3859 String treecalcnm = MessageManager.getString("label.tree_calc_"
3860 + type.toLowerCase());
3861 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
3863 JMenuItem tm = new JMenuItem();
3864 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
3865 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
3866 || sm.isProtein() == !viewport.getAlignment()
3869 String smn = MessageManager.getStringOrReturn(
3870 "label.score_model_", sm.getName());
3871 final String title = MessageManager.formatMessage(
3872 "label.treecalc_title", treecalcnm, smn);
3873 tm.setText(title);//
3874 tm.addActionListener(new java.awt.event.ActionListener()
3877 public void actionPerformed(ActionEvent e)
3879 newTreePanel(type, pwtype, title);
3882 calculateTree.add(tm);
3887 sortByTreeMenu.removeAll();
3889 List<Component> comps = PaintRefresher.components.get(viewport
3890 .getSequenceSetId());
3891 List<TreePanel> treePanels = new ArrayList<TreePanel>();
3892 for (Component comp : comps)
3894 if (comp instanceof TreePanel)
3896 treePanels.add((TreePanel) comp);
3900 if (treePanels.size() < 1)
3902 sortByTreeMenu.setVisible(false);
3906 sortByTreeMenu.setVisible(true);
3908 for (final TreePanel tp : treePanels)
3910 final JMenuItem item = new JMenuItem(tp.getTitle());
3911 item.addActionListener(new java.awt.event.ActionListener()
3914 public void actionPerformed(ActionEvent e)
3916 tp.sortByTree_actionPerformed();
3917 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3922 sortByTreeMenu.add(item);
3926 public boolean sortBy(AlignmentOrder alorder, String undoname)
3928 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3929 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3930 if (undoname != null)
3932 addHistoryItem(new OrderCommand(undoname, oldOrder,
3933 viewport.getAlignment()));
3935 alignPanel.paintAlignment(true);
3940 * Work out whether the whole set of sequences or just the selected set will
3941 * be submitted for multiple alignment.
3944 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3946 // Now, check we have enough sequences
3947 AlignmentView msa = null;
3949 if ((viewport.getSelectionGroup() != null)
3950 && (viewport.getSelectionGroup().getSize() > 1))
3952 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3953 // some common interface!
3955 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3956 * SequenceI[sz = seqs.getSize(false)];
3958 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3959 * seqs.getSequenceAt(i); }
3961 msa = viewport.getAlignmentView(true);
3963 else if (viewport.getSelectionGroup() != null
3964 && viewport.getSelectionGroup().getSize() == 1)
3966 int option = JvOptionPane.showConfirmDialog(this,
3967 MessageManager.getString("warn.oneseq_msainput_selection"),
3968 MessageManager.getString("label.invalid_selection"),
3969 JvOptionPane.OK_CANCEL_OPTION);
3970 if (option == JvOptionPane.OK_OPTION)
3972 msa = viewport.getAlignmentView(false);
3977 msa = viewport.getAlignmentView(false);
3983 * Decides what is submitted to a secondary structure prediction service: the
3984 * first sequence in the alignment, or in the current selection, or, if the
3985 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3986 * region or the whole alignment. (where the first sequence in the set is the
3987 * one that the prediction will be for).
3989 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3991 AlignmentView seqs = null;
3993 if ((viewport.getSelectionGroup() != null)
3994 && (viewport.getSelectionGroup().getSize() > 0))
3996 seqs = viewport.getAlignmentView(true);
4000 seqs = viewport.getAlignmentView(false);
4002 // limit sequences - JBPNote in future - could spawn multiple prediction
4004 // TODO: viewport.getAlignment().isAligned is a global state - the local
4005 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4006 if (!viewport.getAlignment().isAligned(false))
4008 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4009 // TODO: if seqs.getSequences().length>1 then should really have warned
4023 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4025 // Pick the tree file
4026 JalviewFileChooser chooser = new JalviewFileChooser(
4027 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4028 chooser.setFileView(new JalviewFileView());
4029 chooser.setDialogTitle(MessageManager
4030 .getString("label.select_newick_like_tree_file"));
4031 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4033 int value = chooser.showOpenDialog(null);
4035 if (value == JalviewFileChooser.APPROVE_OPTION)
4037 String choice = chooser.getSelectedFile().getPath();
4038 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4039 jalview.io.NewickFile fin = null;
4042 fin = new NewickFile(choice, DataSourceType.FILE);
4043 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4044 } catch (Exception ex)
4051 .getString("label.problem_reading_tree_file"),
4052 JvOptionPane.WARNING_MESSAGE);
4053 ex.printStackTrace();
4055 if (fin != null && fin.hasWarningMessage())
4057 JvOptionPane.showMessageDialog(Desktop.desktop, fin
4058 .getWarningMessage(), MessageManager
4059 .getString("label.possible_problem_with_tree_file"),
4060 JvOptionPane.WARNING_MESSAGE);
4065 public TreePanel ShowNewickTree(NewickFile nf, String title)
4067 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4070 public TreePanel ShowNewickTree(NewickFile nf, String title,
4071 AlignmentView input)
4073 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4076 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4077 int h, int x, int y)
4079 return ShowNewickTree(nf, title, null, w, h, x, y);
4083 * Add a treeviewer for the tree extracted from a newick file object to the
4084 * current alignment view
4091 * Associated alignment input data (or null)
4100 * @return TreePanel handle
4102 public TreePanel ShowNewickTree(NewickFile nf, String title,
4103 AlignmentView input, int w, int h, int x, int y)
4105 TreePanel tp = null;
4111 if (nf.getTree() != null)
4113 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4119 tp.setLocation(x, y);
4122 Desktop.addInternalFrame(tp, title, w, h);
4124 } catch (Exception ex)
4126 ex.printStackTrace();
4132 private boolean buildingMenu = false;
4135 * Generates menu items and listener event actions for web service clients
4138 public void BuildWebServiceMenu()
4140 while (buildingMenu)
4144 System.err.println("Waiting for building menu to finish.");
4146 } catch (Exception e)
4150 final AlignFrame me = this;
4151 buildingMenu = true;
4152 new Thread(new Runnable()
4157 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4160 // System.err.println("Building ws menu again "
4161 // + Thread.currentThread());
4162 // TODO: add support for context dependent disabling of services based
4164 // alignment and current selection
4165 // TODO: add additional serviceHandle parameter to specify abstract
4167 // class independently of AbstractName
4168 // TODO: add in rediscovery GUI function to restart discoverer
4169 // TODO: group services by location as well as function and/or
4171 // object broker mechanism.
4172 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4173 final IProgressIndicator af = me;
4176 * do not i18n these strings - they are hard-coded in class
4177 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4178 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4180 final JMenu msawsmenu = new JMenu("Alignment");
4181 final JMenu secstrmenu = new JMenu(
4182 "Secondary Structure Prediction");
4183 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4184 final JMenu analymenu = new JMenu("Analysis");
4185 final JMenu dismenu = new JMenu("Protein Disorder");
4186 // JAL-940 - only show secondary structure prediction services from
4187 // the legacy server
4188 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4190 Discoverer.services != null && (Discoverer.services.size() > 0))
4192 // TODO: refactor to allow list of AbstractName/Handler bindings to
4194 // stored or retrieved from elsewhere
4195 // No MSAWS used any more:
4196 // Vector msaws = null; // (Vector)
4197 // Discoverer.services.get("MsaWS");
4198 Vector secstrpr = (Vector) Discoverer.services
4200 if (secstrpr != null)
4202 // Add any secondary structure prediction services
4203 for (int i = 0, j = secstrpr.size(); i < j; i++)
4205 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4207 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4208 .getServiceClient(sh);
4209 int p = secstrmenu.getItemCount();
4210 impl.attachWSMenuEntry(secstrmenu, me);
4211 int q = secstrmenu.getItemCount();
4212 for (int litm = p; litm < q; litm++)
4214 legacyItems.add(secstrmenu.getItem(litm));
4220 // Add all submenus in the order they should appear on the web
4222 wsmenu.add(msawsmenu);
4223 wsmenu.add(secstrmenu);
4224 wsmenu.add(dismenu);
4225 wsmenu.add(analymenu);
4226 // No search services yet
4227 // wsmenu.add(seqsrchmenu);
4229 javax.swing.SwingUtilities.invokeLater(new Runnable()
4236 webService.removeAll();
4237 // first, add discovered services onto the webservices menu
4238 if (wsmenu.size() > 0)
4240 for (int i = 0, j = wsmenu.size(); i < j; i++)
4242 webService.add(wsmenu.get(i));
4247 webService.add(me.webServiceNoServices);
4249 // TODO: move into separate menu builder class.
4250 boolean new_sspred = false;
4251 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4253 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4254 if (jws2servs != null)
4256 if (jws2servs.hasServices())
4258 jws2servs.attachWSMenuEntry(webService, me);
4259 for (Jws2Instance sv : jws2servs.getServices())
4261 if (sv.description.toLowerCase().contains("jpred"))
4263 for (JMenuItem jmi : legacyItems)
4265 jmi.setVisible(false);
4271 if (jws2servs.isRunning())
4273 JMenuItem tm = new JMenuItem(
4274 "Still discovering JABA Services");
4275 tm.setEnabled(false);
4280 build_urlServiceMenu(me.webService);
4281 build_fetchdbmenu(webService);
4282 for (JMenu item : wsmenu)
4284 if (item.getItemCount() == 0)
4286 item.setEnabled(false);
4290 item.setEnabled(true);
4293 } catch (Exception e)
4296 .debug("Exception during web service menu building process.",
4301 } catch (Exception e)
4304 buildingMenu = false;
4311 * construct any groupURL type service menu entries.
4315 private void build_urlServiceMenu(JMenu webService)
4317 // TODO: remove this code when 2.7 is released
4318 // DEBUG - alignmentView
4320 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4321 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4323 * @Override public void actionPerformed(ActionEvent e) {
4324 * jalview.datamodel.AlignmentView
4325 * .testSelectionViews(af.viewport.getAlignment(),
4326 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4328 * }); webService.add(testAlView);
4330 // TODO: refactor to RestClient discoverer and merge menu entries for
4331 // rest-style services with other types of analysis/calculation service
4332 // SHmmr test client - still being implemented.
4333 // DEBUG - alignmentView
4335 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4338 client.attachWSMenuEntry(
4339 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4345 * Searches the alignment sequences for xRefs and builds the Show
4346 * Cross-References menu (formerly called Show Products), with database
4347 * sources for which cross-references are found (protein sources for a
4348 * nucleotide alignment and vice versa)
4350 * @return true if Show Cross-references menu should be enabled
4352 public boolean canShowProducts()
4354 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4355 AlignmentI dataset = viewport.getAlignment().getDataset();
4357 showProducts.removeAll();
4358 final boolean dna = viewport.getAlignment().isNucleotide();
4360 if (seqs == null || seqs.length == 0)
4362 // nothing to see here.
4366 boolean showp = false;
4369 List<String> ptypes = new CrossRef(seqs, dataset)
4370 .findXrefSourcesForSequences(dna);
4372 for (final String source : ptypes)
4375 final AlignFrame af = this;
4376 JMenuItem xtype = new JMenuItem(source);
4377 xtype.addActionListener(new ActionListener()
4380 public void actionPerformed(ActionEvent e)
4382 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4385 showProducts.add(xtype);
4387 showProducts.setVisible(showp);
4388 showProducts.setEnabled(showp);
4389 } catch (Exception e)
4392 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4400 * Finds and displays cross-references for the selected sequences (protein
4401 * products for nucleotide sequences, dna coding sequences for peptides).
4404 * the sequences to show cross-references for
4406 * true if from a nucleotide alignment (so showing proteins)
4408 * the database to show cross-references for
4410 protected void showProductsFor(final SequenceI[] sel,
4411 final boolean _odna, final String source)
4413 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4418 * Construct and display a new frame containing the translation of this
4419 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4422 public void showTranslation_actionPerformed(ActionEvent e)
4424 AlignmentI al = null;
4427 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4429 al = dna.translateCdna();
4430 } catch (Exception ex)
4432 jalview.bin.Cache.log.error(
4433 "Exception during translation. Please report this !", ex);
4434 final String msg = MessageManager
4435 .getString("label.error_when_translating_sequences_submit_bug_report");
4436 final String errorTitle = MessageManager
4437 .getString("label.implementation_error")
4438 + MessageManager.getString("label.translation_failed");
4439 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4440 JvOptionPane.ERROR_MESSAGE);
4443 if (al == null || al.getHeight() == 0)
4445 final String msg = MessageManager
4446 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4447 final String errorTitle = MessageManager
4448 .getString("label.translation_failed");
4449 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4450 JvOptionPane.WARNING_MESSAGE);
4454 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4455 af.setFileFormat(this.currentFileFormat);
4456 final String newTitle = MessageManager.formatMessage(
4457 "label.translation_of_params",
4458 new Object[] { this.getTitle() });
4459 af.setTitle(newTitle);
4460 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4462 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4463 viewport.openSplitFrame(af, new Alignment(seqs));
4467 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4474 * Set the file format
4478 public void setFileFormat(FileFormatI format)
4480 this.currentFileFormat = format;
4484 * Try to load a features file onto the alignment.
4487 * contents or path to retrieve file
4489 * access mode of file (see jalview.io.AlignFile)
4490 * @return true if features file was parsed correctly.
4492 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4494 return avc.parseFeaturesFile(file, sourceType,
4495 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4500 public void refreshFeatureUI(boolean enableIfNecessary)
4502 // note - currently this is only still here rather than in the controller
4503 // because of the featureSettings hard reference that is yet to be
4505 if (enableIfNecessary)
4507 viewport.setShowSequenceFeatures(true);
4508 showSeqFeatures.setSelected(true);
4514 public void dragEnter(DropTargetDragEvent evt)
4519 public void dragExit(DropTargetEvent evt)
4524 public void dragOver(DropTargetDragEvent evt)
4529 public void dropActionChanged(DropTargetDragEvent evt)
4534 public void drop(DropTargetDropEvent evt)
4536 // JAL-1552 - acceptDrop required before getTransferable call for
4537 // Java's Transferable for native dnd
4538 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4539 Transferable t = evt.getTransferable();
4540 List<String> files = new ArrayList<String>();
4541 List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4545 Desktop.transferFromDropTarget(files, protocols, evt, t);
4546 } catch (Exception e)
4548 e.printStackTrace();
4554 // check to see if any of these files have names matching sequences in
4556 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4557 .getAlignment().getSequencesArray());
4559 * Object[] { String,SequenceI}
4561 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4562 ArrayList<String> filesnotmatched = new ArrayList<String>();
4563 for (int i = 0; i < files.size(); i++)
4565 String file = files.get(i).toString();
4567 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4568 if (protocol == DataSourceType.FILE)
4570 File fl = new File(file);
4571 pdbfn = fl.getName();
4573 else if (protocol == DataSourceType.URL)
4575 URL url = new URL(file);
4576 pdbfn = url.getFile();
4578 if (pdbfn.length() > 0)
4580 // attempt to find a match in the alignment
4581 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4582 int l = 0, c = pdbfn.indexOf(".");
4583 while (mtch == null && c != -1)
4588 } while ((c = pdbfn.indexOf(".", l)) > l);
4591 pdbfn = pdbfn.substring(0, l);
4593 mtch = idm.findAllIdMatches(pdbfn);
4597 FileFormatI type = null;
4600 type = new IdentifyFile().identify(file, protocol);
4601 } catch (Exception ex)
4605 if (type != null && type.isStructureFile())
4607 filesmatched.add(new Object[] { file, protocol, mtch });
4611 // File wasn't named like one of the sequences or wasn't a PDB file.
4612 filesnotmatched.add(file);
4616 if (filesmatched.size() > 0)
4618 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4624 "label.automatically_associate_structure_files_with_sequences_same_name",
4625 new Object[] { Integer
4631 .getString("label.automatically_associate_structure_files_by_name"),
4632 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4635 for (Object[] fm : filesmatched)
4637 // try and associate
4638 // TODO: may want to set a standard ID naming formalism for
4639 // associating PDB files which have no IDs.
4640 for (SequenceI toassoc : (SequenceI[]) fm[2])
4642 PDBEntry pe = new AssociatePdbFileWithSeq()
4643 .associatePdbWithSeq((String) fm[0],
4644 (DataSourceType) fm[1], toassoc, false,
4648 System.err.println("Associated file : "
4649 + ((String) fm[0]) + " with "
4650 + toassoc.getDisplayId(true));
4654 alignPanel.paintAlignment(true);
4658 if (filesnotmatched.size() > 0)
4661 && (Cache.getDefault(
4662 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4668 "label.ignore_unmatched_dropped_files_info",
4669 new Object[] { Integer
4676 .getString("label.ignore_unmatched_dropped_files"),
4677 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4681 for (String fn : filesnotmatched)
4683 loadJalviewDataFile(fn, null, null, null);
4687 } catch (Exception ex)
4689 ex.printStackTrace();
4695 * Attempt to load a "dropped" file or URL string: First by testing whether
4696 * it's an Annotation file, then a JNet file, and finally a features file. If
4697 * all are false then the user may have dropped an alignment file onto this
4701 * either a filename or a URL string.
4703 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4704 FileFormatI format, SequenceI assocSeq)
4708 if (sourceType == null)
4710 sourceType = FormatAdapter.checkProtocol(file);
4712 // if the file isn't identified, or not positively identified as some
4713 // other filetype (PFAM is default unidentified alignment file type) then
4714 // try to parse as annotation.
4715 boolean isAnnotation = (format == null || FileFormat.Pfam
4716 .equals(format)) ? new AnnotationFile()
4717 .annotateAlignmentView(viewport, file, sourceType) : false;
4721 // first see if its a T-COFFEE score file
4722 TCoffeeScoreFile tcf = null;
4725 tcf = new TCoffeeScoreFile(file, sourceType);
4728 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4731 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4732 isAnnotation = true;
4734 .setText(MessageManager
4735 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4739 // some problem - if no warning its probable that the ID matching
4740 // process didn't work
4744 tcf.getWarningMessage() == null ? MessageManager
4745 .getString("label.check_file_matches_sequence_ids_alignment")
4746 : tcf.getWarningMessage(),
4748 .getString("label.problem_reading_tcoffee_score_file"),
4749 JvOptionPane.WARNING_MESSAGE);
4756 } catch (Exception x)
4759 .debug("Exception when processing data source as T-COFFEE score file",
4765 // try to see if its a JNet 'concise' style annotation file *before*
4767 // try to parse it as a features file
4770 format = new IdentifyFile().identify(file, sourceType);
4772 if (FileFormat.Jnet.equals(format))
4774 JPredFile predictions = new JPredFile(file, sourceType);
4775 new JnetAnnotationMaker();
4776 JnetAnnotationMaker.add_annotation(predictions,
4777 viewport.getAlignment(), 0, false);
4778 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4779 viewport.getAlignment().setSeqrep(repseq);
4780 ColumnSelection cs = new ColumnSelection();
4781 cs.hideInsertionsFor(repseq);
4782 viewport.setColumnSelection(cs);
4783 isAnnotation = true;
4785 // else if (IdentifyFile.FeaturesFile.equals(format))
4786 else if (FileFormat.Features.equals(format))
4788 if (parseFeaturesFile(file, sourceType))
4790 alignPanel.paintAlignment(true);
4795 new FileLoader().LoadFile(viewport, file, sourceType, format);
4802 alignPanel.adjustAnnotationHeight();
4803 viewport.updateSequenceIdColours();
4804 buildSortByAnnotationScoresMenu();
4805 alignPanel.paintAlignment(true);
4807 } catch (Exception ex)
4809 ex.printStackTrace();
4810 } catch (OutOfMemoryError oom)
4815 } catch (Exception x)
4820 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4821 : "using " + sourceType + " from " + file)
4823 + (format != null ? "(parsing as '" + format
4824 + "' file)" : ""), oom, Desktop.desktop);
4829 * Method invoked by the ChangeListener on the tabbed pane, in other words
4830 * when a different tabbed pane is selected by the user or programmatically.
4833 public void tabSelectionChanged(int index)
4837 alignPanel = alignPanels.get(index);
4838 viewport = alignPanel.av;
4839 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4840 setMenusFromViewport(viewport);
4844 * 'focus' any colour slider that is open to the selected viewport
4846 if (viewport.getConservationSelected())
4848 SliderPanel.setConservationSlider(alignPanel,
4849 viewport.getResidueShading(), alignPanel.getViewName());
4853 SliderPanel.hideConservationSlider();
4855 if (viewport.getAbovePIDThreshold())
4857 SliderPanel.setPIDSliderSource(alignPanel,
4858 viewport.getResidueShading(), alignPanel.getViewName());
4862 SliderPanel.hidePIDSlider();
4866 * If there is a frame linked to this one in a SplitPane, switch it to the
4867 * same view tab index. No infinite recursion of calls should happen, since
4868 * tabSelectionChanged() should not get invoked on setting the selected
4869 * index to an unchanged value. Guard against setting an invalid index
4870 * before the new view peer tab has been created.
4872 final AlignViewportI peer = viewport.getCodingComplement();
4875 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4876 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4878 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4884 * On right mouse click on view tab, prompt for and set new view name.
4887 public void tabbedPane_mousePressed(MouseEvent e)
4889 if (e.isPopupTrigger())
4891 String msg = MessageManager.getString("label.enter_view_name");
4892 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4893 JvOptionPane.QUESTION_MESSAGE);
4897 viewport.viewName = reply;
4898 // TODO warn if reply is in getExistingViewNames()?
4899 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4904 public AlignViewport getCurrentView()
4910 * Open the dialog for regex description parsing.
4913 protected void extractScores_actionPerformed(ActionEvent e)
4915 ParseProperties pp = new jalview.analysis.ParseProperties(
4916 viewport.getAlignment());
4917 // TODO: verify regex and introduce GUI dialog for version 2.5
4918 // if (pp.getScoresFromDescription("col", "score column ",
4919 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4921 if (pp.getScoresFromDescription("description column",
4922 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4924 buildSortByAnnotationScoresMenu();
4932 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4936 protected void showDbRefs_actionPerformed(ActionEvent e)
4938 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4944 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4948 protected void showNpFeats_actionPerformed(ActionEvent e)
4950 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4954 * find the viewport amongst the tabs in this alignment frame and close that
4959 public boolean closeView(AlignViewportI av)
4963 this.closeMenuItem_actionPerformed(false);
4966 Component[] comp = tabbedPane.getComponents();
4967 for (int i = 0; comp != null && i < comp.length; i++)
4969 if (comp[i] instanceof AlignmentPanel)
4971 if (((AlignmentPanel) comp[i]).av == av)
4974 closeView((AlignmentPanel) comp[i]);
4982 protected void build_fetchdbmenu(JMenu webService)
4984 // Temporary hack - DBRef Fetcher always top level ws entry.
4985 // TODO We probably want to store a sequence database checklist in
4986 // preferences and have checkboxes.. rather than individual sources selected
4988 final JMenu rfetch = new JMenu(
4989 MessageManager.getString("action.fetch_db_references"));
4990 rfetch.setToolTipText(MessageManager
4991 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4992 webService.add(rfetch);
4994 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4995 MessageManager.getString("option.trim_retrieved_seqs"));
4996 trimrs.setToolTipText(MessageManager
4997 .getString("label.trim_retrieved_sequences"));
4998 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4999 trimrs.addActionListener(new ActionListener()
5002 public void actionPerformed(ActionEvent e)
5004 trimrs.setSelected(trimrs.isSelected());
5005 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5006 Boolean.valueOf(trimrs.isSelected()).toString());
5010 JMenuItem fetchr = new JMenuItem(
5011 MessageManager.getString("label.standard_databases"));
5012 fetchr.setToolTipText(MessageManager
5013 .getString("label.fetch_embl_uniprot"));
5014 fetchr.addActionListener(new ActionListener()
5018 public void actionPerformed(ActionEvent e)
5020 new Thread(new Runnable()
5025 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5026 .getAlignment().isNucleotide();
5027 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5028 .getSequenceSelection(), alignPanel.alignFrame, null,
5029 alignPanel.alignFrame.featureSettings, isNucleotide);
5030 dbRefFetcher.addListener(new FetchFinishedListenerI()
5033 public void finished()
5035 AlignFrame.this.setMenusForViewport();
5038 dbRefFetcher.fetchDBRefs(false);
5046 final AlignFrame me = this;
5047 new Thread(new Runnable()
5052 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5053 .getSequenceFetcherSingleton(me);
5054 javax.swing.SwingUtilities.invokeLater(new Runnable()
5059 String[] dbclasses = sf.getOrderedSupportedSources();
5060 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5061 // jalview.util.QuickSort.sort(otherdb, otherdb);
5062 List<DbSourceProxy> otherdb;
5063 JMenu dfetch = new JMenu();
5064 JMenu ifetch = new JMenu();
5065 JMenuItem fetchr = null;
5066 int comp = 0, icomp = 0, mcomp = 15;
5067 String mname = null;
5069 for (String dbclass : dbclasses)
5071 otherdb = sf.getSourceProxy(dbclass);
5072 // add a single entry for this class, or submenu allowing 'fetch
5074 if (otherdb == null || otherdb.size() < 1)
5078 // List<DbSourceProxy> dbs=otherdb;
5079 // otherdb=new ArrayList<DbSourceProxy>();
5080 // for (DbSourceProxy db:dbs)
5082 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5086 mname = "From " + dbclass;
5088 if (otherdb.size() == 1)
5090 final DbSourceProxy[] dassource = otherdb
5091 .toArray(new DbSourceProxy[0]);
5092 DbSourceProxy src = otherdb.get(0);
5093 fetchr = new JMenuItem(src.getDbSource());
5094 fetchr.addActionListener(new ActionListener()
5098 public void actionPerformed(ActionEvent e)
5100 new Thread(new Runnable()
5106 boolean isNucleotide = alignPanel.alignFrame
5107 .getViewport().getAlignment()
5109 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5110 alignPanel.av.getSequenceSelection(),
5111 alignPanel.alignFrame, dassource,
5112 alignPanel.alignFrame.featureSettings,
5115 .addListener(new FetchFinishedListenerI()
5118 public void finished()
5120 AlignFrame.this.setMenusForViewport();
5123 dbRefFetcher.fetchDBRefs(false);
5129 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5130 MessageManager.formatMessage(
5131 "label.fetch_retrieve_from",
5132 new Object[] { src.getDbName() })));
5138 final DbSourceProxy[] dassource = otherdb
5139 .toArray(new DbSourceProxy[0]);
5141 DbSourceProxy src = otherdb.get(0);
5142 fetchr = new JMenuItem(MessageManager.formatMessage(
5143 "label.fetch_all_param",
5144 new Object[] { src.getDbSource() }));
5145 fetchr.addActionListener(new ActionListener()
5148 public void actionPerformed(ActionEvent e)
5150 new Thread(new Runnable()
5156 boolean isNucleotide = alignPanel.alignFrame
5157 .getViewport().getAlignment()
5159 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5160 alignPanel.av.getSequenceSelection(),
5161 alignPanel.alignFrame, dassource,
5162 alignPanel.alignFrame.featureSettings,
5165 .addListener(new FetchFinishedListenerI()
5168 public void finished()
5170 AlignFrame.this.setMenusForViewport();
5173 dbRefFetcher.fetchDBRefs(false);
5179 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5180 MessageManager.formatMessage(
5181 "label.fetch_retrieve_from_all_sources",
5183 Integer.valueOf(otherdb.size())
5184 .toString(), src.getDbSource(),
5185 src.getDbName() })));
5188 // and then build the rest of the individual menus
5189 ifetch = new JMenu(MessageManager.formatMessage(
5190 "label.source_from_db_source",
5191 new Object[] { src.getDbSource() }));
5193 String imname = null;
5195 for (DbSourceProxy sproxy : otherdb)
5197 String dbname = sproxy.getDbName();
5198 String sname = dbname.length() > 5 ? dbname.substring(0,
5199 5) + "..." : dbname;
5200 String msname = dbname.length() > 10 ? dbname.substring(
5201 0, 10) + "..." : dbname;
5204 imname = MessageManager.formatMessage(
5205 "label.from_msname", new Object[] { sname });
5207 fetchr = new JMenuItem(msname);
5208 final DbSourceProxy[] dassrc = { sproxy };
5209 fetchr.addActionListener(new ActionListener()
5213 public void actionPerformed(ActionEvent e)
5215 new Thread(new Runnable()
5221 boolean isNucleotide = alignPanel.alignFrame
5222 .getViewport().getAlignment()
5224 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5225 alignPanel.av.getSequenceSelection(),
5226 alignPanel.alignFrame, dassrc,
5227 alignPanel.alignFrame.featureSettings,
5230 .addListener(new FetchFinishedListenerI()
5233 public void finished()
5235 AlignFrame.this.setMenusForViewport();
5238 dbRefFetcher.fetchDBRefs(false);
5244 fetchr.setToolTipText("<html>"
5245 + MessageManager.formatMessage(
5246 "label.fetch_retrieve_from", new Object[]
5250 if (++icomp >= mcomp || i == (otherdb.size()))
5252 ifetch.setText(MessageManager.formatMessage(
5253 "label.source_to_target", imname, sname));
5255 ifetch = new JMenu();
5263 if (comp >= mcomp || dbi >= (dbclasses.length))
5265 dfetch.setText(MessageManager.formatMessage(
5266 "label.source_to_target", mname, dbclass));
5268 dfetch = new JMenu();
5281 * Left justify the whole alignment.
5284 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5286 AlignmentI al = viewport.getAlignment();
5288 viewport.firePropertyChange("alignment", null, al);
5292 * Right justify the whole alignment.
5295 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5297 AlignmentI al = viewport.getAlignment();
5299 viewport.firePropertyChange("alignment", null, al);
5303 public void setShowSeqFeatures(boolean b)
5305 showSeqFeatures.setSelected(b);
5306 viewport.setShowSequenceFeatures(b);
5313 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5314 * awt.event.ActionEvent)
5317 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5319 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5320 alignPanel.paintAlignment(true);
5327 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5331 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5333 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5334 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5342 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5343 * .event.ActionEvent)
5346 protected void showGroupConservation_actionPerformed(ActionEvent e)
5348 viewport.setShowGroupConservation(showGroupConservation.getState());
5349 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5356 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5357 * .event.ActionEvent)
5360 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5362 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5363 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5370 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5371 * .event.ActionEvent)
5374 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5376 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5377 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5381 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5383 showSequenceLogo.setState(true);
5384 viewport.setShowSequenceLogo(true);
5385 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5386 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5390 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5392 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5399 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5400 * .event.ActionEvent)
5403 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5405 if (avc.makeGroupsFromSelection())
5407 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5408 alignPanel.updateAnnotation();
5409 alignPanel.paintAlignment(true);
5413 public void clearAlignmentSeqRep()
5415 // TODO refactor alignmentseqrep to controller
5416 if (viewport.getAlignment().hasSeqrep())
5418 viewport.getAlignment().setSeqrep(null);
5419 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5420 alignPanel.updateAnnotation();
5421 alignPanel.paintAlignment(true);
5426 protected void createGroup_actionPerformed(ActionEvent e)
5428 if (avc.createGroup())
5430 alignPanel.alignmentChanged();
5435 protected void unGroup_actionPerformed(ActionEvent e)
5439 alignPanel.alignmentChanged();
5444 * make the given alignmentPanel the currently selected tab
5446 * @param alignmentPanel
5448 public void setDisplayedView(AlignmentPanel alignmentPanel)
5450 if (!viewport.getSequenceSetId().equals(
5451 alignmentPanel.av.getSequenceSetId()))
5455 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5457 if (tabbedPane != null
5458 && tabbedPane.getTabCount() > 0
5459 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5460 .getSelectedIndex())
5462 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5467 * Action on selection of menu options to Show or Hide annotations.
5470 * @param forSequences
5471 * update sequence-related annotations
5472 * @param forAlignment
5473 * update non-sequence-related annotations
5476 protected void setAnnotationsVisibility(boolean visible,
5477 boolean forSequences, boolean forAlignment)
5479 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5480 .getAlignmentAnnotation();
5485 for (AlignmentAnnotation aa : anns)
5488 * don't display non-positional annotations on an alignment
5490 if (aa.annotations == null)
5494 boolean apply = (aa.sequenceRef == null && forAlignment)
5495 || (aa.sequenceRef != null && forSequences);
5498 aa.visible = visible;
5501 alignPanel.validateAnnotationDimensions(true);
5502 alignPanel.alignmentChanged();
5506 * Store selected annotation sort order for the view and repaint.
5509 protected void sortAnnotations_actionPerformed()
5511 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5513 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5514 alignPanel.paintAlignment(true);
5519 * @return alignment panels in this alignment frame
5521 public List<? extends AlignmentViewPanel> getAlignPanels()
5523 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5527 * Open a new alignment window, with the cDNA associated with this (protein)
5528 * alignment, aligned as is the protein.
5530 protected void viewAsCdna_actionPerformed()
5532 // TODO no longer a menu action - refactor as required
5533 final AlignmentI alignment = getViewport().getAlignment();
5534 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5535 if (mappings == null)
5539 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5540 for (SequenceI aaSeq : alignment.getSequences())
5542 for (AlignedCodonFrame acf : mappings)
5544 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5548 * There is a cDNA mapping for this protein sequence - add to new
5549 * alignment. It will share the same dataset sequence as other mapped
5550 * cDNA (no new mappings need to be created).
5552 final Sequence newSeq = new Sequence(dnaSeq);
5553 newSeq.setDatasetSequence(dnaSeq);
5554 cdnaSeqs.add(newSeq);
5558 if (cdnaSeqs.size() == 0)
5560 // show a warning dialog no mapped cDNA
5563 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5565 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5566 AlignFrame.DEFAULT_HEIGHT);
5567 cdna.alignAs(alignment);
5568 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5570 Desktop.addInternalFrame(alignFrame, newtitle,
5571 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5575 * Set visibility of dna/protein complement view (available when shown in a
5581 protected void showComplement_actionPerformed(boolean show)
5583 SplitContainerI sf = getSplitViewContainer();
5586 sf.setComplementVisible(this, show);
5591 * Generate the reverse (optionally complemented) of the selected sequences,
5592 * and add them to the alignment
5595 protected void showReverse_actionPerformed(boolean complement)
5597 AlignmentI al = null;
5600 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5601 al = dna.reverseCdna(complement);
5602 viewport.addAlignment(al, "");
5603 addHistoryItem(new EditCommand(
5604 MessageManager.getString("label.add_sequences"),
5605 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5606 viewport.getAlignment()));
5607 } catch (Exception ex)
5609 System.err.println(ex.getMessage());
5615 * Try to run a script in the Groovy console, having first ensured that this
5616 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5617 * be targeted at this alignment.
5620 protected void runGroovy_actionPerformed()
5622 Jalview.setCurrentAlignFrame(this);
5623 groovy.ui.Console console = Desktop.getGroovyConsole();
5624 if (console != null)
5628 console.runScript();
5629 } catch (Exception ex)
5631 System.err.println((ex.toString()));
5633 .showInternalMessageDialog(Desktop.desktop, MessageManager
5634 .getString("label.couldnt_run_groovy_script"),
5636 .getString("label.groovy_support_failed"),
5637 JvOptionPane.ERROR_MESSAGE);
5642 System.err.println("Can't run Groovy script as console not found");
5647 * Hides columns containing (or not containing) a specified feature, provided
5648 * that would not leave all columns hidden
5650 * @param featureType
5651 * @param columnsContaining
5654 public boolean hideFeatureColumns(String featureType,
5655 boolean columnsContaining)
5657 boolean notForHiding = avc.markColumnsContainingFeatures(
5658 columnsContaining, false, false, featureType);
5661 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5662 false, featureType))
5664 getViewport().hideSelectedColumns();
5672 protected void selectHighlightedColumns_actionPerformed(
5673 ActionEvent actionEvent)
5675 // include key modifier check in case user selects from menu
5676 avc.markHighlightedColumns(
5677 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5679 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5683 * Rebuilds the Colour menu, including any user-defined colours which have
5684 * been loaded either on startup or during the session
5686 public void buildColourMenu()
5688 colourMenu.removeAll();
5690 colourMenu.add(applyToAllGroups);
5691 colourMenu.add(textColour);
5692 colourMenu.addSeparator();
5694 ColourMenuHelper.addMenuItems(colourMenu, this,
5695 viewport.getAlignment(), false);
5697 colourMenu.addSeparator();
5698 colourMenu.add(conservationMenuItem);
5699 colourMenu.add(modifyConservation);
5700 colourMenu.add(abovePIDThreshold);
5701 colourMenu.add(modifyPID);
5702 colourMenu.add(annotationColour);
5704 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5705 String schemeName = colourScheme == null ? null : colourScheme
5708 ColourMenuHelper.setColourSelected(colourMenu, schemeName);
5712 class PrintThread extends Thread
5716 public PrintThread(AlignmentPanel ap)
5721 static PageFormat pf;
5726 PrinterJob printJob = PrinterJob.getPrinterJob();
5730 printJob.setPrintable(ap, pf);
5734 printJob.setPrintable(ap);
5737 if (printJob.printDialog())
5742 } catch (Exception PrintException)
5744 PrintException.printStackTrace();