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,
1258 exportData.getAlignment(),
1259 exportData.getOmitHidden(),
1260 exportData.getStartEndPostions(),
1261 viewport.getColumnSelection()));
1262 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1263 "label.alignment_output_command",
1264 new Object[] { e.getActionCommand() }), 600, 500);
1265 } catch (OutOfMemoryError oom)
1267 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1273 public static AlignmentExportData getAlignmentForExport(
1274 FileFormatI format, AlignViewportI viewport,
1275 AlignExportSettingI exportSettings)
1277 AlignmentI alignmentToExport = null;
1278 AlignExportSettingI settings = exportSettings;
1279 String[] omitHidden = null;
1281 HiddenSequences hiddenSeqs = viewport.getAlignment()
1282 .getHiddenSequences();
1284 alignmentToExport = viewport.getAlignment();
1286 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1287 if (settings == null)
1289 settings = new AlignExportSettings(hasHiddenSeqs,
1290 viewport.hasHiddenColumns(), format);
1292 // settings.isExportAnnotations();
1294 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1296 omitHidden = viewport.getViewAsString(false,
1297 settings.isExportHiddenSequences());
1300 int[] alignmentStartEnd = new int[2];
1301 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1303 alignmentToExport = hiddenSeqs.getFullAlignment();
1307 alignmentToExport = viewport.getAlignment();
1309 alignmentStartEnd = alignmentToExport
1310 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1311 .getHiddenColumns());
1312 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1313 omitHidden, alignmentStartEnd, settings);
1324 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1326 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1327 htmlSVG.exportHTML(null);
1331 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1333 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1334 bjs.exportHTML(null);
1337 public void createImageMap(File file, String image)
1339 alignPanel.makePNGImageMap(file, image);
1349 public void createPNG(File f)
1351 alignPanel.makePNG(f);
1361 public void createEPS(File f)
1363 alignPanel.makeEPS(f);
1367 public void createSVG(File f)
1369 alignPanel.makeSVG(f);
1373 public void pageSetup_actionPerformed(ActionEvent e)
1375 PrinterJob printJob = PrinterJob.getPrinterJob();
1376 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1386 public void printMenuItem_actionPerformed(ActionEvent e)
1388 // Putting in a thread avoids Swing painting problems
1389 PrintThread thread = new PrintThread(alignPanel);
1394 public void exportFeatures_actionPerformed(ActionEvent e)
1396 new AnnotationExporter().exportFeatures(alignPanel);
1400 public void exportAnnotations_actionPerformed(ActionEvent e)
1402 new AnnotationExporter().exportAnnotations(alignPanel);
1406 public void associatedData_actionPerformed(ActionEvent e)
1408 // Pick the tree file
1409 JalviewFileChooser chooser = new JalviewFileChooser(
1410 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1411 chooser.setFileView(new JalviewFileView());
1412 chooser.setDialogTitle(MessageManager
1413 .getString("label.load_jalview_annotations"));
1414 chooser.setToolTipText(MessageManager
1415 .getString("label.load_jalview_annotations"));
1417 int value = chooser.showOpenDialog(null);
1419 if (value == JalviewFileChooser.APPROVE_OPTION)
1421 String choice = chooser.getSelectedFile().getPath();
1422 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1423 loadJalviewDataFile(choice, null, null, null);
1429 * Close the current view or all views in the alignment frame. If the frame
1430 * only contains one view then the alignment will be removed from memory.
1432 * @param closeAllTabs
1435 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1437 if (alignPanels != null && alignPanels.size() < 2)
1439 closeAllTabs = true;
1444 if (alignPanels != null)
1448 if (this.isClosed())
1450 // really close all the windows - otherwise wait till
1451 // setClosed(true) is called
1452 for (int i = 0; i < alignPanels.size(); i++)
1454 AlignmentPanel ap = alignPanels.get(i);
1461 closeView(alignPanel);
1468 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1469 * be called recursively, with the frame now in 'closed' state
1471 this.setClosed(true);
1473 } catch (Exception ex)
1475 ex.printStackTrace();
1480 * Close the specified panel and close up tabs appropriately.
1482 * @param panelToClose
1484 public void closeView(AlignmentPanel panelToClose)
1486 int index = tabbedPane.getSelectedIndex();
1487 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1488 alignPanels.remove(panelToClose);
1489 panelToClose.closePanel();
1490 panelToClose = null;
1492 tabbedPane.removeTabAt(closedindex);
1493 tabbedPane.validate();
1495 if (index > closedindex || index == tabbedPane.getTabCount())
1497 // modify currently selected tab index if necessary.
1501 this.tabSelectionChanged(index);
1507 void updateEditMenuBar()
1510 if (viewport.getHistoryList().size() > 0)
1512 undoMenuItem.setEnabled(true);
1513 CommandI command = viewport.getHistoryList().peek();
1514 undoMenuItem.setText(MessageManager.formatMessage(
1515 "label.undo_command",
1516 new Object[] { command.getDescription() }));
1520 undoMenuItem.setEnabled(false);
1521 undoMenuItem.setText(MessageManager.getString("action.undo"));
1524 if (viewport.getRedoList().size() > 0)
1526 redoMenuItem.setEnabled(true);
1528 CommandI command = viewport.getRedoList().peek();
1529 redoMenuItem.setText(MessageManager.formatMessage(
1530 "label.redo_command",
1531 new Object[] { command.getDescription() }));
1535 redoMenuItem.setEnabled(false);
1536 redoMenuItem.setText(MessageManager.getString("action.redo"));
1541 public void addHistoryItem(CommandI command)
1543 if (command.getSize() > 0)
1545 viewport.addToHistoryList(command);
1546 viewport.clearRedoList();
1547 updateEditMenuBar();
1548 viewport.updateHiddenColumns();
1549 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1550 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1551 // viewport.getColumnSelection()
1552 // .getHiddenColumns().size() > 0);
1558 * @return alignment objects for all views
1560 AlignmentI[] getViewAlignments()
1562 if (alignPanels != null)
1564 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1566 for (AlignmentPanel ap : alignPanels)
1568 als[i++] = ap.av.getAlignment();
1572 if (viewport != null)
1574 return new AlignmentI[] { viewport.getAlignment() };
1586 protected void undoMenuItem_actionPerformed(ActionEvent e)
1588 if (viewport.getHistoryList().isEmpty())
1592 CommandI command = viewport.getHistoryList().pop();
1593 viewport.addToRedoList(command);
1594 command.undoCommand(getViewAlignments());
1596 AlignmentViewport originalSource = getOriginatingSource(command);
1597 updateEditMenuBar();
1599 if (originalSource != null)
1601 if (originalSource != viewport)
1604 .warn("Implementation worry: mismatch of viewport origin for undo");
1606 originalSource.updateHiddenColumns();
1607 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1609 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1610 // viewport.getColumnSelection()
1611 // .getHiddenColumns().size() > 0);
1612 originalSource.firePropertyChange("alignment", null, originalSource
1613 .getAlignment().getSequences());
1624 protected void redoMenuItem_actionPerformed(ActionEvent e)
1626 if (viewport.getRedoList().size() < 1)
1631 CommandI command = viewport.getRedoList().pop();
1632 viewport.addToHistoryList(command);
1633 command.doCommand(getViewAlignments());
1635 AlignmentViewport originalSource = getOriginatingSource(command);
1636 updateEditMenuBar();
1638 if (originalSource != null)
1641 if (originalSource != viewport)
1644 .warn("Implementation worry: mismatch of viewport origin for redo");
1646 originalSource.updateHiddenColumns();
1647 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1649 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1650 // viewport.getColumnSelection()
1651 // .getHiddenColumns().size() > 0);
1652 originalSource.firePropertyChange("alignment", null, originalSource
1653 .getAlignment().getSequences());
1657 AlignmentViewport getOriginatingSource(CommandI command)
1659 AlignmentViewport originalSource = null;
1660 // For sequence removal and addition, we need to fire
1661 // the property change event FROM the viewport where the
1662 // original alignment was altered
1663 AlignmentI al = null;
1664 if (command instanceof EditCommand)
1666 EditCommand editCommand = (EditCommand) command;
1667 al = editCommand.getAlignment();
1668 List<Component> comps = PaintRefresher.components.get(viewport
1669 .getSequenceSetId());
1671 for (Component comp : comps)
1673 if (comp instanceof AlignmentPanel)
1675 if (al == ((AlignmentPanel) comp).av.getAlignment())
1677 originalSource = ((AlignmentPanel) comp).av;
1684 if (originalSource == null)
1686 // The original view is closed, we must validate
1687 // the current view against the closed view first
1690 PaintRefresher.validateSequences(al, viewport.getAlignment());
1693 originalSource = viewport;
1696 return originalSource;
1705 public void moveSelectedSequences(boolean up)
1707 SequenceGroup sg = viewport.getSelectionGroup();
1713 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1714 viewport.getHiddenRepSequences(), up);
1715 alignPanel.paintAlignment(true);
1718 synchronized void slideSequences(boolean right, int size)
1720 List<SequenceI> sg = new ArrayList<SequenceI>();
1721 if (viewport.cursorMode)
1723 sg.add(viewport.getAlignment().getSequenceAt(
1724 alignPanel.getSeqPanel().seqCanvas.cursorY));
1726 else if (viewport.getSelectionGroup() != null
1727 && viewport.getSelectionGroup().getSize() != viewport
1728 .getAlignment().getHeight())
1730 sg = viewport.getSelectionGroup().getSequences(
1731 viewport.getHiddenRepSequences());
1739 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1741 for (SequenceI seq : viewport.getAlignment().getSequences())
1743 if (!sg.contains(seq))
1745 invertGroup.add(seq);
1749 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1751 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1752 for (int i = 0; i < invertGroup.size(); i++)
1754 seqs2[i] = invertGroup.get(i);
1757 SlideSequencesCommand ssc;
1760 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1761 size, viewport.getGapCharacter());
1765 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1766 size, viewport.getGapCharacter());
1769 int groupAdjustment = 0;
1770 if (ssc.getGapsInsertedBegin() && right)
1772 if (viewport.cursorMode)
1774 alignPanel.getSeqPanel().moveCursor(size, 0);
1778 groupAdjustment = size;
1781 else if (!ssc.getGapsInsertedBegin() && !right)
1783 if (viewport.cursorMode)
1785 alignPanel.getSeqPanel().moveCursor(-size, 0);
1789 groupAdjustment = -size;
1793 if (groupAdjustment != 0)
1795 viewport.getSelectionGroup().setStartRes(
1796 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1797 viewport.getSelectionGroup().setEndRes(
1798 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1802 * just extend the last slide command if compatible; but not if in
1803 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1805 boolean appendHistoryItem = false;
1806 Deque<CommandI> historyList = viewport.getHistoryList();
1807 boolean inSplitFrame = getSplitViewContainer() != null;
1808 if (!inSplitFrame && historyList != null && historyList.size() > 0
1809 && historyList.peek() instanceof SlideSequencesCommand)
1811 appendHistoryItem = ssc
1812 .appendSlideCommand((SlideSequencesCommand) historyList
1816 if (!appendHistoryItem)
1818 addHistoryItem(ssc);
1831 protected void copy_actionPerformed(ActionEvent e)
1834 if (viewport.getSelectionGroup() == null)
1838 // TODO: preserve the ordering of displayed alignment annotation in any
1839 // internal paste (particularly sequence associated annotation)
1840 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1841 String[] omitHidden = null;
1843 if (viewport.hasHiddenColumns())
1845 omitHidden = viewport.getViewAsString(true);
1848 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1852 StringSelection ss = new StringSelection(output);
1856 jalview.gui.Desktop.internalCopy = true;
1857 // Its really worth setting the clipboard contents
1858 // to empty before setting the large StringSelection!!
1859 Toolkit.getDefaultToolkit().getSystemClipboard()
1860 .setContents(new StringSelection(""), null);
1862 Toolkit.getDefaultToolkit().getSystemClipboard()
1863 .setContents(ss, Desktop.instance);
1864 } catch (OutOfMemoryError er)
1866 new OOMWarning("copying region", er);
1870 ArrayList<int[]> hiddenColumns = null;
1871 if (viewport.hasHiddenColumns())
1873 hiddenColumns = new ArrayList<int[]>();
1874 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1875 .getSelectionGroup().getEndRes();
1876 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1878 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1880 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1881 region[1] - hiddenOffset });
1886 Desktop.jalviewClipboard = new Object[] { seqs,
1887 viewport.getAlignment().getDataset(), hiddenColumns };
1888 statusBar.setText(MessageManager.formatMessage(
1889 "label.copied_sequences_to_clipboard", new Object[] { Integer
1890 .valueOf(seqs.length).toString() }));
1900 protected void pasteNew_actionPerformed(ActionEvent e)
1912 protected void pasteThis_actionPerformed(ActionEvent e)
1918 * Paste contents of Jalview clipboard
1920 * @param newAlignment
1921 * true to paste to a new alignment, otherwise add to this.
1923 void paste(boolean newAlignment)
1925 boolean externalPaste = true;
1928 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1929 Transferable contents = c.getContents(this);
1931 if (contents == null)
1940 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1941 if (str.length() < 1)
1946 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1948 } catch (OutOfMemoryError er)
1950 new OOMWarning("Out of memory pasting sequences!!", er);
1954 SequenceI[] sequences;
1955 boolean annotationAdded = false;
1956 AlignmentI alignment = null;
1958 if (Desktop.jalviewClipboard != null)
1960 // The clipboard was filled from within Jalview, we must use the
1962 // And dataset from the copied alignment
1963 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1964 // be doubly sure that we create *new* sequence objects.
1965 sequences = new SequenceI[newseq.length];
1966 for (int i = 0; i < newseq.length; i++)
1968 sequences[i] = new Sequence(newseq[i]);
1970 alignment = new Alignment(sequences);
1971 externalPaste = false;
1975 // parse the clipboard as an alignment.
1976 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1978 sequences = alignment.getSequencesArray();
1982 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1988 if (Desktop.jalviewClipboard != null)
1990 // dataset is inherited
1991 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1995 // new dataset is constructed
1996 alignment.setDataset(null);
1998 alwidth = alignment.getWidth() + 1;
2002 AlignmentI pastedal = alignment; // preserve pasted alignment object
2003 // Add pasted sequences and dataset into existing alignment.
2004 alignment = viewport.getAlignment();
2005 alwidth = alignment.getWidth() + 1;
2006 // decide if we need to import sequences from an existing dataset
2007 boolean importDs = Desktop.jalviewClipboard != null
2008 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2009 // importDs==true instructs us to copy over new dataset sequences from
2010 // an existing alignment
2011 Vector newDs = (importDs) ? new Vector() : null; // used to create
2012 // minimum dataset set
2014 for (int i = 0; i < sequences.length; i++)
2018 newDs.addElement(null);
2020 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2022 if (importDs && ds != null)
2024 if (!newDs.contains(ds))
2026 newDs.setElementAt(ds, i);
2027 ds = new Sequence(ds);
2028 // update with new dataset sequence
2029 sequences[i].setDatasetSequence(ds);
2033 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2038 // copy and derive new dataset sequence
2039 sequences[i] = sequences[i].deriveSequence();
2040 alignment.getDataset().addSequence(
2041 sequences[i].getDatasetSequence());
2042 // TODO: avoid creation of duplicate dataset sequences with a
2043 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2045 alignment.addSequence(sequences[i]); // merges dataset
2049 newDs.clear(); // tidy up
2051 if (alignment.getAlignmentAnnotation() != null)
2053 for (AlignmentAnnotation alan : alignment
2054 .getAlignmentAnnotation())
2056 if (alan.graphGroup > fgroup)
2058 fgroup = alan.graphGroup;
2062 if (pastedal.getAlignmentAnnotation() != null)
2064 // Add any annotation attached to alignment.
2065 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2066 for (int i = 0; i < alann.length; i++)
2068 annotationAdded = true;
2069 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2071 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2072 if (newann.graphGroup > -1)
2074 if (newGraphGroups.size() <= newann.graphGroup
2075 || newGraphGroups.get(newann.graphGroup) == null)
2077 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2079 newGraphGroups.add(q, null);
2081 newGraphGroups.set(newann.graphGroup, new Integer(
2084 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2088 newann.padAnnotation(alwidth);
2089 alignment.addAnnotation(newann);
2099 addHistoryItem(new EditCommand(
2100 MessageManager.getString("label.add_sequences"),
2101 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2103 // Add any annotations attached to sequences
2104 for (int i = 0; i < sequences.length; i++)
2106 if (sequences[i].getAnnotation() != null)
2108 AlignmentAnnotation newann;
2109 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2111 annotationAdded = true;
2112 newann = sequences[i].getAnnotation()[a];
2113 newann.adjustForAlignment();
2114 newann.padAnnotation(alwidth);
2115 if (newann.graphGroup > -1)
2117 if (newann.graphGroup > -1)
2119 if (newGraphGroups.size() <= newann.graphGroup
2120 || newGraphGroups.get(newann.graphGroup) == null)
2122 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2124 newGraphGroups.add(q, null);
2126 newGraphGroups.set(newann.graphGroup, new Integer(
2129 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2133 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2138 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2145 // propagate alignment changed.
2146 viewport.setEndSeq(alignment.getHeight());
2147 if (annotationAdded)
2149 // Duplicate sequence annotation in all views.
2150 AlignmentI[] alview = this.getViewAlignments();
2151 for (int i = 0; i < sequences.length; i++)
2153 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2158 for (int avnum = 0; avnum < alview.length; avnum++)
2160 if (alview[avnum] != alignment)
2162 // duplicate in a view other than the one with input focus
2163 int avwidth = alview[avnum].getWidth() + 1;
2164 // this relies on sann being preserved after we
2165 // modify the sequence's annotation array for each duplication
2166 for (int a = 0; a < sann.length; a++)
2168 AlignmentAnnotation newann = new AlignmentAnnotation(
2170 sequences[i].addAlignmentAnnotation(newann);
2171 newann.padAnnotation(avwidth);
2172 alview[avnum].addAnnotation(newann); // annotation was
2173 // duplicated earlier
2174 // TODO JAL-1145 graphGroups are not updated for sequence
2175 // annotation added to several views. This may cause
2177 alview[avnum].setAnnotationIndex(newann, a);
2182 buildSortByAnnotationScoresMenu();
2184 viewport.firePropertyChange("alignment", null,
2185 alignment.getSequences());
2186 if (alignPanels != null)
2188 for (AlignmentPanel ap : alignPanels)
2190 ap.validateAnnotationDimensions(false);
2195 alignPanel.validateAnnotationDimensions(false);
2201 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2203 String newtitle = new String("Copied sequences");
2205 if (Desktop.jalviewClipboard != null
2206 && Desktop.jalviewClipboard[2] != null)
2208 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2209 for (int[] region : hc)
2211 af.viewport.hideColumns(region[0], region[1]);
2215 // >>>This is a fix for the moment, until a better solution is
2217 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2219 alignPanel.getSeqPanel().seqCanvas
2220 .getFeatureRenderer());
2222 // TODO: maintain provenance of an alignment, rather than just make the
2223 // title a concatenation of operations.
2226 if (title.startsWith("Copied sequences"))
2232 newtitle = newtitle.concat("- from " + title);
2237 newtitle = new String("Pasted sequences");
2240 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2245 } catch (Exception ex)
2247 ex.printStackTrace();
2248 System.out.println("Exception whilst pasting: " + ex);
2249 // could be anything being pasted in here
2255 protected void expand_newalign(ActionEvent e)
2259 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2260 .getAlignment(), -1);
2261 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2263 String newtitle = new String("Flanking alignment");
2265 if (Desktop.jalviewClipboard != null
2266 && Desktop.jalviewClipboard[2] != null)
2268 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2269 for (int region[] : hc)
2271 af.viewport.hideColumns(region[0], region[1]);
2275 // >>>This is a fix for the moment, until a better solution is
2277 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2279 alignPanel.getSeqPanel().seqCanvas
2280 .getFeatureRenderer());
2282 // TODO: maintain provenance of an alignment, rather than just make the
2283 // title a concatenation of operations.
2285 if (title.startsWith("Copied sequences"))
2291 newtitle = newtitle.concat("- from " + title);
2295 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2297 } catch (Exception ex)
2299 ex.printStackTrace();
2300 System.out.println("Exception whilst pasting: " + ex);
2301 // could be anything being pasted in here
2302 } catch (OutOfMemoryError oom)
2304 new OOMWarning("Viewing flanking region of alignment", oom);
2315 protected void cut_actionPerformed(ActionEvent e)
2317 copy_actionPerformed(null);
2318 delete_actionPerformed(null);
2328 protected void delete_actionPerformed(ActionEvent evt)
2331 SequenceGroup sg = viewport.getSelectionGroup();
2338 * If the cut affects all sequences, warn, remove highlighted columns
2340 if (sg.getSize() == viewport.getAlignment().getHeight())
2342 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2343 .getAlignment().getWidth()) ? true : false;
2344 if (isEntireAlignWidth)
2346 int confirm = JvOptionPane.showConfirmDialog(this,
2347 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2348 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2349 JvOptionPane.OK_CANCEL_OPTION);
2351 if (confirm == JvOptionPane.CANCEL_OPTION
2352 || confirm == JvOptionPane.CLOSED_OPTION)
2357 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2358 sg.getEndRes() + 1);
2360 SequenceI[] cut = sg.getSequences()
2361 .toArray(new SequenceI[sg.getSize()]);
2363 addHistoryItem(new EditCommand(
2364 MessageManager.getString("label.cut_sequences"), Action.CUT,
2365 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2366 viewport.getAlignment()));
2368 viewport.setSelectionGroup(null);
2369 viewport.sendSelection();
2370 viewport.getAlignment().deleteGroup(sg);
2372 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2374 if (viewport.getAlignment().getHeight() < 1)
2378 this.setClosed(true);
2379 } catch (Exception ex)
2392 protected void deleteGroups_actionPerformed(ActionEvent e)
2394 if (avc.deleteGroups())
2396 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2397 alignPanel.updateAnnotation();
2398 alignPanel.paintAlignment(true);
2409 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2411 SequenceGroup sg = new SequenceGroup();
2413 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2415 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2418 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2419 viewport.setSelectionGroup(sg);
2420 viewport.sendSelection();
2421 // JAL-2034 - should delegate to
2422 // alignPanel to decide if overview needs
2424 alignPanel.paintAlignment(false);
2425 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2435 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2437 if (viewport.cursorMode)
2439 alignPanel.getSeqPanel().keyboardNo1 = null;
2440 alignPanel.getSeqPanel().keyboardNo2 = null;
2442 viewport.setSelectionGroup(null);
2443 viewport.getColumnSelection().clear();
2444 viewport.setSelectionGroup(null);
2445 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2446 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2447 // JAL-2034 - should delegate to
2448 // alignPanel to decide if overview needs
2450 alignPanel.paintAlignment(false);
2451 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2452 viewport.sendSelection();
2462 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2464 SequenceGroup sg = viewport.getSelectionGroup();
2468 selectAllSequenceMenuItem_actionPerformed(null);
2473 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2475 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2477 // JAL-2034 - should delegate to
2478 // alignPanel to decide if overview needs
2481 alignPanel.paintAlignment(true);
2482 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2483 viewport.sendSelection();
2487 public void invertColSel_actionPerformed(ActionEvent e)
2489 viewport.invertColumnSelection();
2490 alignPanel.paintAlignment(true);
2491 viewport.sendSelection();
2501 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2503 trimAlignment(true);
2513 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2515 trimAlignment(false);
2518 void trimAlignment(boolean trimLeft)
2520 ColumnSelection colSel = viewport.getColumnSelection();
2523 if (!colSel.isEmpty())
2527 column = colSel.getMin();
2531 column = colSel.getMax();
2535 if (viewport.getSelectionGroup() != null)
2537 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2538 viewport.getHiddenRepSequences());
2542 seqs = viewport.getAlignment().getSequencesArray();
2545 TrimRegionCommand trimRegion;
2548 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2549 column, viewport.getAlignment());
2550 viewport.setStartRes(0);
2554 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2555 column, viewport.getAlignment());
2558 statusBar.setText(MessageManager.formatMessage(
2559 "label.removed_columns",
2560 new String[] { Integer.valueOf(trimRegion.getSize())
2563 addHistoryItem(trimRegion);
2565 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2567 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2568 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2570 viewport.getAlignment().deleteGroup(sg);
2574 viewport.firePropertyChange("alignment", null, viewport
2575 .getAlignment().getSequences());
2586 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2588 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2591 if (viewport.getSelectionGroup() != null)
2593 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2594 viewport.getHiddenRepSequences());
2595 start = viewport.getSelectionGroup().getStartRes();
2596 end = viewport.getSelectionGroup().getEndRes();
2600 seqs = viewport.getAlignment().getSequencesArray();
2603 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2604 "Remove Gapped Columns", seqs, start, end,
2605 viewport.getAlignment());
2607 addHistoryItem(removeGapCols);
2609 statusBar.setText(MessageManager.formatMessage(
2610 "label.removed_empty_columns",
2611 new Object[] { Integer.valueOf(removeGapCols.getSize())
2614 // This is to maintain viewport position on first residue
2615 // of first sequence
2616 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2617 int startRes = seq.findPosition(viewport.startRes);
2618 // ShiftList shifts;
2619 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2620 // edit.alColumnChanges=shifts.getInverse();
2621 // if (viewport.hasHiddenColumns)
2622 // viewport.getColumnSelection().compensateForEdits(shifts);
2623 viewport.setStartRes(seq.findIndex(startRes) - 1);
2624 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2636 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2638 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2641 if (viewport.getSelectionGroup() != null)
2643 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2644 viewport.getHiddenRepSequences());
2645 start = viewport.getSelectionGroup().getStartRes();
2646 end = viewport.getSelectionGroup().getEndRes();
2650 seqs = viewport.getAlignment().getSequencesArray();
2653 // This is to maintain viewport position on first residue
2654 // of first sequence
2655 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2656 int startRes = seq.findPosition(viewport.startRes);
2658 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2659 viewport.getAlignment()));
2661 viewport.setStartRes(seq.findIndex(startRes) - 1);
2663 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2675 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2677 viewport.setPadGaps(padGapsMenuitem.isSelected());
2678 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2689 public void findMenuItem_actionPerformed(ActionEvent e)
2695 * Create a new view of the current alignment.
2698 public void newView_actionPerformed(ActionEvent e)
2700 newView(null, true);
2704 * Creates and shows a new view of the current alignment.
2707 * title of newly created view; if null, one will be generated
2708 * @param copyAnnotation
2709 * if true then duplicate all annnotation, groups and settings
2710 * @return new alignment panel, already displayed.
2712 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2715 * Create a new AlignmentPanel (with its own, new Viewport)
2717 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2719 if (!copyAnnotation)
2722 * remove all groups and annotation except for the automatic stuff
2724 newap.av.getAlignment().deleteAllGroups();
2725 newap.av.getAlignment().deleteAllAnnotations(false);
2728 newap.av.setGatherViewsHere(false);
2730 if (viewport.viewName == null)
2732 viewport.viewName = MessageManager
2733 .getString("label.view_name_original");
2737 * Views share the same edits undo and redo stacks
2739 newap.av.setHistoryList(viewport.getHistoryList());
2740 newap.av.setRedoList(viewport.getRedoList());
2743 * Views share the same mappings; need to deregister any new mappings
2744 * created by copyAlignPanel, and register the new reference to the shared
2747 newap.av.replaceMappings(viewport.getAlignment());
2749 newap.av.viewName = getNewViewName(viewTitle);
2751 addAlignmentPanel(newap, true);
2752 newap.alignmentChanged();
2754 if (alignPanels.size() == 2)
2756 viewport.setGatherViewsHere(true);
2758 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2763 * Make a new name for the view, ensuring it is unique within the current
2764 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2765 * these now use viewId. Unique view names are still desirable for usability.)
2770 protected String getNewViewName(String viewTitle)
2772 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2773 boolean addFirstIndex = false;
2774 if (viewTitle == null || viewTitle.trim().length() == 0)
2776 viewTitle = MessageManager.getString("action.view");
2777 addFirstIndex = true;
2781 index = 1;// we count from 1 if given a specific name
2783 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2785 List<Component> comps = PaintRefresher.components.get(viewport
2786 .getSequenceSetId());
2788 List<String> existingNames = getExistingViewNames(comps);
2790 while (existingNames.contains(newViewName))
2792 newViewName = viewTitle + " " + (++index);
2798 * Returns a list of distinct view names found in the given list of
2799 * components. View names are held on the viewport of an AlignmentPanel.
2804 protected List<String> getExistingViewNames(List<Component> comps)
2806 List<String> existingNames = new ArrayList<String>();
2807 for (Component comp : comps)
2809 if (comp instanceof AlignmentPanel)
2811 AlignmentPanel ap = (AlignmentPanel) comp;
2812 if (!existingNames.contains(ap.av.viewName))
2814 existingNames.add(ap.av.viewName);
2818 return existingNames;
2822 * Explode tabbed views into separate windows.
2825 public void expandViews_actionPerformed(ActionEvent e)
2827 Desktop.explodeViews(this);
2831 * Gather views in separate windows back into a tabbed presentation.
2834 public void gatherViews_actionPerformed(ActionEvent e)
2836 Desktop.instance.gatherViews(this);
2846 public void font_actionPerformed(ActionEvent e)
2848 new FontChooser(alignPanel);
2858 protected void seqLimit_actionPerformed(ActionEvent e)
2860 viewport.setShowJVSuffix(seqLimits.isSelected());
2862 alignPanel.getIdPanel().getIdCanvas()
2863 .setPreferredSize(alignPanel.calculateIdWidth());
2864 alignPanel.paintAlignment(true);
2868 public void idRightAlign_actionPerformed(ActionEvent e)
2870 viewport.setRightAlignIds(idRightAlign.isSelected());
2871 alignPanel.paintAlignment(true);
2875 public void centreColumnLabels_actionPerformed(ActionEvent e)
2877 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2878 alignPanel.paintAlignment(true);
2884 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2887 protected void followHighlight_actionPerformed()
2890 * Set the 'follow' flag on the Viewport (and scroll to position if now
2893 final boolean state = this.followHighlightMenuItem.getState();
2894 viewport.setFollowHighlight(state);
2897 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2908 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2910 viewport.setColourText(colourTextMenuItem.isSelected());
2911 alignPanel.paintAlignment(true);
2921 public void wrapMenuItem_actionPerformed(ActionEvent e)
2923 scaleAbove.setVisible(wrapMenuItem.isSelected());
2924 scaleLeft.setVisible(wrapMenuItem.isSelected());
2925 scaleRight.setVisible(wrapMenuItem.isSelected());
2926 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2927 alignPanel.updateLayout();
2931 public void showAllSeqs_actionPerformed(ActionEvent e)
2933 viewport.showAllHiddenSeqs();
2937 public void showAllColumns_actionPerformed(ActionEvent e)
2939 viewport.showAllHiddenColumns();
2941 viewport.sendSelection();
2945 public void hideSelSequences_actionPerformed(ActionEvent e)
2947 viewport.hideAllSelectedSeqs();
2948 // alignPanel.paintAlignment(true);
2952 * called by key handler and the hide all/show all menu items
2957 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2960 boolean hide = false;
2961 SequenceGroup sg = viewport.getSelectionGroup();
2962 if (!toggleSeqs && !toggleCols)
2964 // Hide everything by the current selection - this is a hack - we do the
2965 // invert and then hide
2966 // first check that there will be visible columns after the invert.
2967 if (viewport.hasSelectedColumns()
2968 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2971 // now invert the sequence set, if required - empty selection implies
2972 // that no hiding is required.
2975 invertSequenceMenuItem_actionPerformed(null);
2976 sg = viewport.getSelectionGroup();
2980 viewport.expandColSelection(sg, true);
2981 // finally invert the column selection and get the new sequence
2983 invertColSel_actionPerformed(null);
2990 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2992 hideSelSequences_actionPerformed(null);
2995 else if (!(toggleCols && viewport.hasSelectedColumns()))
2997 showAllSeqs_actionPerformed(null);
3003 if (viewport.hasSelectedColumns())
3005 hideSelColumns_actionPerformed(null);
3008 viewport.setSelectionGroup(sg);
3013 showAllColumns_actionPerformed(null);
3022 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3023 * event.ActionEvent)
3026 public void hideAllButSelection_actionPerformed(ActionEvent e)
3028 toggleHiddenRegions(false, false);
3029 viewport.sendSelection();
3036 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3040 public void hideAllSelection_actionPerformed(ActionEvent e)
3042 SequenceGroup sg = viewport.getSelectionGroup();
3043 viewport.expandColSelection(sg, false);
3044 viewport.hideAllSelectedSeqs();
3045 viewport.hideSelectedColumns();
3046 alignPanel.paintAlignment(true);
3047 viewport.sendSelection();
3054 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3058 public void showAllhidden_actionPerformed(ActionEvent e)
3060 viewport.showAllHiddenColumns();
3061 viewport.showAllHiddenSeqs();
3062 alignPanel.paintAlignment(true);
3063 viewport.sendSelection();
3067 public void hideSelColumns_actionPerformed(ActionEvent e)
3069 viewport.hideSelectedColumns();
3070 alignPanel.paintAlignment(true);
3071 viewport.sendSelection();
3075 public void hiddenMarkers_actionPerformed(ActionEvent e)
3077 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3088 protected void scaleAbove_actionPerformed(ActionEvent e)
3090 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3091 alignPanel.paintAlignment(true);
3101 protected void scaleLeft_actionPerformed(ActionEvent e)
3103 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3104 alignPanel.paintAlignment(true);
3114 protected void scaleRight_actionPerformed(ActionEvent e)
3116 viewport.setScaleRightWrapped(scaleRight.isSelected());
3117 alignPanel.paintAlignment(true);
3127 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3129 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3130 alignPanel.paintAlignment(true);
3140 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3142 viewport.setShowText(viewTextMenuItem.isSelected());
3143 alignPanel.paintAlignment(true);
3153 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3155 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3156 alignPanel.paintAlignment(true);
3159 public FeatureSettings featureSettings;
3162 public FeatureSettingsControllerI getFeatureSettingsUI()
3164 return featureSettings;
3168 public void featureSettings_actionPerformed(ActionEvent e)
3170 if (featureSettings != null)
3172 featureSettings.close();
3173 featureSettings = null;
3175 if (!showSeqFeatures.isSelected())
3177 // make sure features are actually displayed
3178 showSeqFeatures.setSelected(true);
3179 showSeqFeatures_actionPerformed(null);
3181 featureSettings = new FeatureSettings(this);
3185 * Set or clear 'Show Sequence Features'
3191 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3193 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3194 alignPanel.paintAlignment(true);
3195 if (alignPanel.getOverviewPanel() != null)
3197 alignPanel.getOverviewPanel().updateOverviewImage();
3202 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3203 * the annotations panel as a whole.
3205 * The options to show/hide all annotations should be enabled when the panel
3206 * is shown, and disabled when the panel is hidden.
3211 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3213 final boolean setVisible = annotationPanelMenuItem.isSelected();
3214 viewport.setShowAnnotation(setVisible);
3215 this.showAllSeqAnnotations.setEnabled(setVisible);
3216 this.hideAllSeqAnnotations.setEnabled(setVisible);
3217 this.showAllAlAnnotations.setEnabled(setVisible);
3218 this.hideAllAlAnnotations.setEnabled(setVisible);
3219 alignPanel.updateLayout();
3223 public void alignmentProperties()
3225 JEditorPane editPane = new JEditorPane("text/html", "");
3226 editPane.setEditable(false);
3227 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3229 editPane.setText(MessageManager.formatMessage("label.html_content",
3230 new Object[] { contents.toString() }));
3231 JInternalFrame frame = new JInternalFrame();
3232 frame.getContentPane().add(new JScrollPane(editPane));
3234 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3235 "label.alignment_properties", new Object[] { getTitle() }),
3246 public void overviewMenuItem_actionPerformed(ActionEvent e)
3248 if (alignPanel.overviewPanel != null)
3253 JInternalFrame frame = new JInternalFrame();
3254 OverviewPanel overview = new OverviewPanel(alignPanel);
3255 frame.setContentPane(overview);
3256 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3257 "label.overview_params", new Object[] { this.getTitle() }),
3258 frame.getWidth(), frame.getHeight());
3260 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3261 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3264 public void internalFrameClosed(
3265 javax.swing.event.InternalFrameEvent evt)
3267 alignPanel.setOverviewPanel(null);
3271 alignPanel.setOverviewPanel(overview);
3275 public void textColour_actionPerformed()
3277 new TextColourChooser().chooseColour(alignPanel, null);
3281 * public void covariationColour_actionPerformed() {
3283 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3287 public void annotationColour_actionPerformed()
3289 new AnnotationColourChooser(viewport, alignPanel);
3293 public void annotationColumn_actionPerformed(ActionEvent e)
3295 new AnnotationColumnChooser(viewport, alignPanel);
3299 * Action on the user checking or unchecking the option to apply the selected
3300 * colour scheme to all groups. If unchecked, groups may have their own
3301 * independent colour schemes.
3305 protected void applyToAllGroups_actionPerformed()
3307 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3311 * Action on user selecting a colour from the colour menu
3314 * the name (not the menu item label!) of the colour scheme
3317 public void changeColour_actionPerformed(String name)
3320 * 'User Defined' opens a panel to configure or load a
3321 * user-defined colour scheme
3323 if (ResidueColourScheme.USER_DEFINED.equals(name))
3325 new UserDefinedColours(alignPanel, null);
3330 * otherwise set the chosen colour scheme (or null for 'None')
3332 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3333 viewport.getAlignment(), viewport.getHiddenRepSequences());
3338 * Actions on setting or changing the alignment colour scheme
3343 public void changeColour(ColourSchemeI cs)
3345 // TODO: pull up to controller method
3348 ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
3349 // Make sure viewport is up to date w.r.t. any sliders
3350 if (viewport.getAbovePIDThreshold())
3352 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3354 viewport.setThreshold(threshold);
3357 if (viewport.getConservationSelected())
3359 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3364 viewport.setGlobalColourScheme(cs);
3366 alignPanel.paintAlignment(true);
3376 protected void modifyPID_actionPerformed()
3378 if (viewport.getAbovePIDThreshold()
3379 && viewport.getGlobalColourScheme() != null)
3381 SliderPanel.setPIDSliderSource(alignPanel,
3382 viewport.getGlobalColourScheme(), "Background");
3383 SliderPanel.showPIDSlider();
3394 protected void modifyConservation_actionPerformed()
3396 if (viewport.getConservationSelected()
3397 && viewport.getGlobalColourScheme() != null)
3399 SliderPanel.setConservationSlider(alignPanel,
3400 viewport.getGlobalColourScheme(), "Background");
3401 SliderPanel.showConservationSlider();
3406 * Action on selecting or deselecting (Colour) By Conservation
3409 protected void conservationMenuItem_actionPerformed()
3411 boolean selected = conservationMenuItem.isSelected();
3412 modifyConservation.setEnabled(selected);
3413 viewport.setConservationSelected(selected);
3415 changeColour(viewport.getGlobalColourScheme());
3418 modifyConservation_actionPerformed();
3422 SliderPanel.hideConservationSlider();
3427 * Action on selecting or deselecting (Colour) Above PID Threshold
3430 public void abovePIDThreshold_actionPerformed()
3432 boolean selected = abovePIDThreshold.isSelected();
3433 modifyPID.setEnabled(selected);
3434 viewport.setAbovePIDThreshold(selected);
3436 changeColour(viewport.getGlobalColourScheme());
3439 modifyPID_actionPerformed();
3443 SliderPanel.hidePIDSlider();
3454 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3456 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3457 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3458 .getAlignment().getSequenceAt(0), null);
3459 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3460 viewport.getAlignment()));
3461 alignPanel.paintAlignment(true);
3471 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3473 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3474 AlignmentSorter.sortByID(viewport.getAlignment());
3475 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3476 viewport.getAlignment()));
3477 alignPanel.paintAlignment(true);
3487 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3489 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3490 AlignmentSorter.sortByLength(viewport.getAlignment());
3491 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3492 viewport.getAlignment()));
3493 alignPanel.paintAlignment(true);
3503 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3505 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3506 AlignmentSorter.sortByGroup(viewport.getAlignment());
3507 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3508 viewport.getAlignment()));
3510 alignPanel.paintAlignment(true);
3520 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3522 new RedundancyPanel(alignPanel, this);
3532 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3534 if ((viewport.getSelectionGroup() == null)
3535 || (viewport.getSelectionGroup().getSize() < 2))
3537 JvOptionPane.showInternalMessageDialog(this, MessageManager
3538 .getString("label.you_must_select_least_two_sequences"),
3539 MessageManager.getString("label.invalid_selection"),
3540 JvOptionPane.WARNING_MESSAGE);
3544 JInternalFrame frame = new JInternalFrame();
3545 frame.setContentPane(new PairwiseAlignPanel(viewport));
3546 Desktop.addInternalFrame(frame,
3547 MessageManager.getString("action.pairwise_alignment"), 600,
3559 public void PCAMenuItem_actionPerformed(ActionEvent e)
3561 if (((viewport.getSelectionGroup() != null)
3562 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3563 .getSelectionGroup().getSize() > 0))
3564 || (viewport.getAlignment().getHeight() < 4))
3567 .showInternalMessageDialog(
3570 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3572 .getString("label.sequence_selection_insufficient"),
3573 JvOptionPane.WARNING_MESSAGE);
3578 new PCAPanel(alignPanel);
3582 public void autoCalculate_actionPerformed(ActionEvent e)
3584 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3585 if (viewport.autoCalculateConsensus)
3587 viewport.firePropertyChange("alignment", null, viewport
3588 .getAlignment().getSequences());
3593 public void sortByTreeOption_actionPerformed(ActionEvent e)
3595 viewport.sortByTree = sortByTree.isSelected();
3599 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3601 viewport.followSelection = listenToViewSelections.isSelected();
3611 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3613 newTreePanel("AV", "PID", "Average distance tree using PID");
3623 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3625 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3635 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3637 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3647 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3649 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3662 void newTreePanel(String type, String pwType, String title)
3666 if (viewport.getSelectionGroup() != null
3667 && viewport.getSelectionGroup().getSize() > 0)
3669 if (viewport.getSelectionGroup().getSize() < 3)
3675 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3677 .getString("label.not_enough_sequences"),
3678 JvOptionPane.WARNING_MESSAGE);
3682 SequenceGroup sg = viewport.getSelectionGroup();
3684 /* Decide if the selection is a column region */
3685 for (SequenceI _s : sg.getSequences())
3687 if (_s.getLength() < sg.getEndRes())
3693 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3695 .getString("label.sequences_selection_not_aligned"),
3696 JvOptionPane.WARNING_MESSAGE);
3702 title = title + " on region";
3703 tp = new TreePanel(alignPanel, type, pwType);
3707 // are the visible sequences aligned?
3708 if (!viewport.getAlignment().isAligned(false))
3714 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3716 .getString("label.sequences_not_aligned"),
3717 JvOptionPane.WARNING_MESSAGE);
3722 if (viewport.getAlignment().getHeight() < 2)
3727 tp = new TreePanel(alignPanel, type, pwType);
3732 if (viewport.viewName != null)
3734 title += viewport.viewName + " of ";
3737 title += this.title;
3739 Desktop.addInternalFrame(tp, title, 600, 500);
3750 public void addSortByOrderMenuItem(String title,
3751 final AlignmentOrder order)
3753 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3754 "action.by_title_param", new Object[] { title }));
3756 item.addActionListener(new java.awt.event.ActionListener()
3759 public void actionPerformed(ActionEvent e)
3761 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3763 // TODO: JBPNote - have to map order entries to curent SequenceI
3765 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3767 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3770 alignPanel.paintAlignment(true);
3776 * Add a new sort by annotation score menu item
3779 * the menu to add the option to
3781 * the label used to retrieve scores for each sequence on the
3784 public void addSortByAnnotScoreMenuItem(JMenu sort,
3785 final String scoreLabel)
3787 final JMenuItem item = new JMenuItem(scoreLabel);
3789 item.addActionListener(new java.awt.event.ActionListener()
3792 public void actionPerformed(ActionEvent e)
3794 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3795 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3796 viewport.getAlignment());// ,viewport.getSelectionGroup());
3797 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3798 viewport.getAlignment()));
3799 alignPanel.paintAlignment(true);
3805 * last hash for alignment's annotation array - used to minimise cost of
3808 protected int _annotationScoreVectorHash;
3811 * search the alignment and rebuild the sort by annotation score submenu the
3812 * last alignment annotation vector hash is stored to minimize cost of
3813 * rebuilding in subsequence calls.
3817 public void buildSortByAnnotationScoresMenu()
3819 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3824 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3826 sortByAnnotScore.removeAll();
3827 // almost certainly a quicker way to do this - but we keep it simple
3828 Hashtable scoreSorts = new Hashtable();
3829 AlignmentAnnotation aann[];
3830 for (SequenceI sqa : viewport.getAlignment().getSequences())
3832 aann = sqa.getAnnotation();
3833 for (int i = 0; aann != null && i < aann.length; i++)
3835 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3837 scoreSorts.put(aann[i].label, aann[i].label);
3841 Enumeration labels = scoreSorts.keys();
3842 while (labels.hasMoreElements())
3844 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3845 (String) labels.nextElement());
3847 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3850 _annotationScoreVectorHash = viewport.getAlignment()
3851 .getAlignmentAnnotation().hashCode();
3856 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3857 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3858 * call. Listeners are added to remove the menu item when the treePanel is
3859 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3863 * Displayed tree window.
3865 * SortBy menu item title.
3868 public void buildTreeMenu()
3870 calculateTree.removeAll();
3871 // build the calculate menu
3873 for (final String type : new String[] { "NJ", "AV" })
3875 String treecalcnm = MessageManager.getString("label.tree_calc_"
3876 + type.toLowerCase());
3877 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
3879 JMenuItem tm = new JMenuItem();
3880 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
3881 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
3882 || sm.isProtein() == !viewport.getAlignment()
3885 String smn = MessageManager.getStringOrReturn(
3886 "label.score_model_", sm.getName());
3887 final String title = MessageManager.formatMessage(
3888 "label.treecalc_title", treecalcnm, smn);
3889 tm.setText(title);//
3890 tm.addActionListener(new java.awt.event.ActionListener()
3893 public void actionPerformed(ActionEvent e)
3895 newTreePanel(type, pwtype, title);
3898 calculateTree.add(tm);
3903 sortByTreeMenu.removeAll();
3905 List<Component> comps = PaintRefresher.components.get(viewport
3906 .getSequenceSetId());
3907 List<TreePanel> treePanels = new ArrayList<TreePanel>();
3908 for (Component comp : comps)
3910 if (comp instanceof TreePanel)
3912 treePanels.add((TreePanel) comp);
3916 if (treePanels.size() < 1)
3918 sortByTreeMenu.setVisible(false);
3922 sortByTreeMenu.setVisible(true);
3924 for (final TreePanel tp : treePanels)
3926 final JMenuItem item = new JMenuItem(tp.getTitle());
3927 item.addActionListener(new java.awt.event.ActionListener()
3930 public void actionPerformed(ActionEvent e)
3932 tp.sortByTree_actionPerformed();
3933 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3938 sortByTreeMenu.add(item);
3942 public boolean sortBy(AlignmentOrder alorder, String undoname)
3944 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3945 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3946 if (undoname != null)
3948 addHistoryItem(new OrderCommand(undoname, oldOrder,
3949 viewport.getAlignment()));
3951 alignPanel.paintAlignment(true);
3956 * Work out whether the whole set of sequences or just the selected set will
3957 * be submitted for multiple alignment.
3960 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3962 // Now, check we have enough sequences
3963 AlignmentView msa = null;
3965 if ((viewport.getSelectionGroup() != null)
3966 && (viewport.getSelectionGroup().getSize() > 1))
3968 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3969 // some common interface!
3971 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3972 * SequenceI[sz = seqs.getSize(false)];
3974 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3975 * seqs.getSequenceAt(i); }
3977 msa = viewport.getAlignmentView(true);
3979 else if (viewport.getSelectionGroup() != null
3980 && viewport.getSelectionGroup().getSize() == 1)
3982 int option = JvOptionPane.showConfirmDialog(this,
3983 MessageManager.getString("warn.oneseq_msainput_selection"),
3984 MessageManager.getString("label.invalid_selection"),
3985 JvOptionPane.OK_CANCEL_OPTION);
3986 if (option == JvOptionPane.OK_OPTION)
3988 msa = viewport.getAlignmentView(false);
3993 msa = viewport.getAlignmentView(false);
3999 * Decides what is submitted to a secondary structure prediction service: the
4000 * first sequence in the alignment, or in the current selection, or, if the
4001 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4002 * region or the whole alignment. (where the first sequence in the set is the
4003 * one that the prediction will be for).
4005 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4007 AlignmentView seqs = null;
4009 if ((viewport.getSelectionGroup() != null)
4010 && (viewport.getSelectionGroup().getSize() > 0))
4012 seqs = viewport.getAlignmentView(true);
4016 seqs = viewport.getAlignmentView(false);
4018 // limit sequences - JBPNote in future - could spawn multiple prediction
4020 // TODO: viewport.getAlignment().isAligned is a global state - the local
4021 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4022 if (!viewport.getAlignment().isAligned(false))
4024 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4025 // TODO: if seqs.getSequences().length>1 then should really have warned
4039 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4041 // Pick the tree file
4042 JalviewFileChooser chooser = new JalviewFileChooser(
4043 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4044 chooser.setFileView(new JalviewFileView());
4045 chooser.setDialogTitle(MessageManager
4046 .getString("label.select_newick_like_tree_file"));
4047 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4049 int value = chooser.showOpenDialog(null);
4051 if (value == JalviewFileChooser.APPROVE_OPTION)
4053 String choice = chooser.getSelectedFile().getPath();
4054 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4055 jalview.io.NewickFile fin = null;
4058 fin = new NewickFile(choice, DataSourceType.FILE);
4059 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4060 } catch (Exception ex)
4067 .getString("label.problem_reading_tree_file"),
4068 JvOptionPane.WARNING_MESSAGE);
4069 ex.printStackTrace();
4071 if (fin != null && fin.hasWarningMessage())
4073 JvOptionPane.showMessageDialog(Desktop.desktop, fin
4074 .getWarningMessage(), MessageManager
4075 .getString("label.possible_problem_with_tree_file"),
4076 JvOptionPane.WARNING_MESSAGE);
4081 public TreePanel ShowNewickTree(NewickFile nf, String title)
4083 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4086 public TreePanel ShowNewickTree(NewickFile nf, String title,
4087 AlignmentView input)
4089 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4092 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4093 int h, int x, int y)
4095 return ShowNewickTree(nf, title, null, w, h, x, y);
4099 * Add a treeviewer for the tree extracted from a newick file object to the
4100 * current alignment view
4107 * Associated alignment input data (or null)
4116 * @return TreePanel handle
4118 public TreePanel ShowNewickTree(NewickFile nf, String title,
4119 AlignmentView input, int w, int h, int x, int y)
4121 TreePanel tp = null;
4127 if (nf.getTree() != null)
4129 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4135 tp.setLocation(x, y);
4138 Desktop.addInternalFrame(tp, title, w, h);
4140 } catch (Exception ex)
4142 ex.printStackTrace();
4148 private boolean buildingMenu = false;
4151 * Generates menu items and listener event actions for web service clients
4154 public void BuildWebServiceMenu()
4156 while (buildingMenu)
4160 System.err.println("Waiting for building menu to finish.");
4162 } catch (Exception e)
4166 final AlignFrame me = this;
4167 buildingMenu = true;
4168 new Thread(new Runnable()
4173 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4176 // System.err.println("Building ws menu again "
4177 // + Thread.currentThread());
4178 // TODO: add support for context dependent disabling of services based
4180 // alignment and current selection
4181 // TODO: add additional serviceHandle parameter to specify abstract
4183 // class independently of AbstractName
4184 // TODO: add in rediscovery GUI function to restart discoverer
4185 // TODO: group services by location as well as function and/or
4187 // object broker mechanism.
4188 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4189 final IProgressIndicator af = me;
4192 * do not i18n these strings - they are hard-coded in class
4193 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4194 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4196 final JMenu msawsmenu = new JMenu("Alignment");
4197 final JMenu secstrmenu = new JMenu(
4198 "Secondary Structure Prediction");
4199 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4200 final JMenu analymenu = new JMenu("Analysis");
4201 final JMenu dismenu = new JMenu("Protein Disorder");
4202 // JAL-940 - only show secondary structure prediction services from
4203 // the legacy server
4204 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4206 Discoverer.services != null && (Discoverer.services.size() > 0))
4208 // TODO: refactor to allow list of AbstractName/Handler bindings to
4210 // stored or retrieved from elsewhere
4211 // No MSAWS used any more:
4212 // Vector msaws = null; // (Vector)
4213 // Discoverer.services.get("MsaWS");
4214 Vector secstrpr = (Vector) Discoverer.services
4216 if (secstrpr != null)
4218 // Add any secondary structure prediction services
4219 for (int i = 0, j = secstrpr.size(); i < j; i++)
4221 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4223 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4224 .getServiceClient(sh);
4225 int p = secstrmenu.getItemCount();
4226 impl.attachWSMenuEntry(secstrmenu, me);
4227 int q = secstrmenu.getItemCount();
4228 for (int litm = p; litm < q; litm++)
4230 legacyItems.add(secstrmenu.getItem(litm));
4236 // Add all submenus in the order they should appear on the web
4238 wsmenu.add(msawsmenu);
4239 wsmenu.add(secstrmenu);
4240 wsmenu.add(dismenu);
4241 wsmenu.add(analymenu);
4242 // No search services yet
4243 // wsmenu.add(seqsrchmenu);
4245 javax.swing.SwingUtilities.invokeLater(new Runnable()
4252 webService.removeAll();
4253 // first, add discovered services onto the webservices menu
4254 if (wsmenu.size() > 0)
4256 for (int i = 0, j = wsmenu.size(); i < j; i++)
4258 webService.add(wsmenu.get(i));
4263 webService.add(me.webServiceNoServices);
4265 // TODO: move into separate menu builder class.
4266 boolean new_sspred = false;
4267 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4269 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4270 if (jws2servs != null)
4272 if (jws2servs.hasServices())
4274 jws2servs.attachWSMenuEntry(webService, me);
4275 for (Jws2Instance sv : jws2servs.getServices())
4277 if (sv.description.toLowerCase().contains("jpred"))
4279 for (JMenuItem jmi : legacyItems)
4281 jmi.setVisible(false);
4287 if (jws2servs.isRunning())
4289 JMenuItem tm = new JMenuItem(
4290 "Still discovering JABA Services");
4291 tm.setEnabled(false);
4296 build_urlServiceMenu(me.webService);
4297 build_fetchdbmenu(webService);
4298 for (JMenu item : wsmenu)
4300 if (item.getItemCount() == 0)
4302 item.setEnabled(false);
4306 item.setEnabled(true);
4309 } catch (Exception e)
4312 .debug("Exception during web service menu building process.",
4317 } catch (Exception e)
4320 buildingMenu = false;
4327 * construct any groupURL type service menu entries.
4331 private void build_urlServiceMenu(JMenu webService)
4333 // TODO: remove this code when 2.7 is released
4334 // DEBUG - alignmentView
4336 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4337 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4339 * @Override public void actionPerformed(ActionEvent e) {
4340 * jalview.datamodel.AlignmentView
4341 * .testSelectionViews(af.viewport.getAlignment(),
4342 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4344 * }); webService.add(testAlView);
4346 // TODO: refactor to RestClient discoverer and merge menu entries for
4347 // rest-style services with other types of analysis/calculation service
4348 // SHmmr test client - still being implemented.
4349 // DEBUG - alignmentView
4351 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4354 client.attachWSMenuEntry(
4355 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4361 * Searches the alignment sequences for xRefs and builds the Show
4362 * Cross-References menu (formerly called Show Products), with database
4363 * sources for which cross-references are found (protein sources for a
4364 * nucleotide alignment and vice versa)
4366 * @return true if Show Cross-references menu should be enabled
4368 public boolean canShowProducts()
4370 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4371 AlignmentI dataset = viewport.getAlignment().getDataset();
4373 showProducts.removeAll();
4374 final boolean dna = viewport.getAlignment().isNucleotide();
4376 if (seqs == null || seqs.length == 0)
4378 // nothing to see here.
4382 boolean showp = false;
4385 List<String> ptypes = new CrossRef(seqs, dataset)
4386 .findXrefSourcesForSequences(dna);
4388 for (final String source : ptypes)
4391 final AlignFrame af = this;
4392 JMenuItem xtype = new JMenuItem(source);
4393 xtype.addActionListener(new ActionListener()
4396 public void actionPerformed(ActionEvent e)
4398 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4401 showProducts.add(xtype);
4403 showProducts.setVisible(showp);
4404 showProducts.setEnabled(showp);
4405 } catch (Exception e)
4408 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4416 * Finds and displays cross-references for the selected sequences (protein
4417 * products for nucleotide sequences, dna coding sequences for peptides).
4420 * the sequences to show cross-references for
4422 * true if from a nucleotide alignment (so showing proteins)
4424 * the database to show cross-references for
4426 protected void showProductsFor(final SequenceI[] sel,
4427 final boolean _odna, final String source)
4429 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4434 * Construct and display a new frame containing the translation of this
4435 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4438 public void showTranslation_actionPerformed(ActionEvent e)
4440 AlignmentI al = null;
4443 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4445 al = dna.translateCdna();
4446 } catch (Exception ex)
4448 jalview.bin.Cache.log.error(
4449 "Exception during translation. Please report this !", ex);
4450 final String msg = MessageManager
4451 .getString("label.error_when_translating_sequences_submit_bug_report");
4452 final String errorTitle = MessageManager
4453 .getString("label.implementation_error")
4454 + MessageManager.getString("label.translation_failed");
4455 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4456 JvOptionPane.ERROR_MESSAGE);
4459 if (al == null || al.getHeight() == 0)
4461 final String msg = MessageManager
4462 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4463 final String errorTitle = MessageManager
4464 .getString("label.translation_failed");
4465 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4466 JvOptionPane.WARNING_MESSAGE);
4470 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4471 af.setFileFormat(this.currentFileFormat);
4472 final String newTitle = MessageManager.formatMessage(
4473 "label.translation_of_params",
4474 new Object[] { this.getTitle() });
4475 af.setTitle(newTitle);
4476 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4478 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4479 viewport.openSplitFrame(af, new Alignment(seqs));
4483 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4490 * Set the file format
4494 public void setFileFormat(FileFormatI format)
4496 this.currentFileFormat = format;
4500 * Try to load a features file onto the alignment.
4503 * contents or path to retrieve file
4505 * access mode of file (see jalview.io.AlignFile)
4506 * @return true if features file was parsed correctly.
4508 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4510 return avc.parseFeaturesFile(file, sourceType,
4511 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4516 public void refreshFeatureUI(boolean enableIfNecessary)
4518 // note - currently this is only still here rather than in the controller
4519 // because of the featureSettings hard reference that is yet to be
4521 if (enableIfNecessary)
4523 viewport.setShowSequenceFeatures(true);
4524 showSeqFeatures.setSelected(true);
4530 public void dragEnter(DropTargetDragEvent evt)
4535 public void dragExit(DropTargetEvent evt)
4540 public void dragOver(DropTargetDragEvent evt)
4545 public void dropActionChanged(DropTargetDragEvent evt)
4550 public void drop(DropTargetDropEvent evt)
4552 // JAL-1552 - acceptDrop required before getTransferable call for
4553 // Java's Transferable for native dnd
4554 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4555 Transferable t = evt.getTransferable();
4556 List<String> files = new ArrayList<String>();
4557 List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4561 Desktop.transferFromDropTarget(files, protocols, evt, t);
4562 } catch (Exception e)
4564 e.printStackTrace();
4570 // check to see if any of these files have names matching sequences in
4572 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4573 .getAlignment().getSequencesArray());
4575 * Object[] { String,SequenceI}
4577 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4578 ArrayList<String> filesnotmatched = new ArrayList<String>();
4579 for (int i = 0; i < files.size(); i++)
4581 String file = files.get(i).toString();
4583 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4584 if (protocol == DataSourceType.FILE)
4586 File fl = new File(file);
4587 pdbfn = fl.getName();
4589 else if (protocol == DataSourceType.URL)
4591 URL url = new URL(file);
4592 pdbfn = url.getFile();
4594 if (pdbfn.length() > 0)
4596 // attempt to find a match in the alignment
4597 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4598 int l = 0, c = pdbfn.indexOf(".");
4599 while (mtch == null && c != -1)
4604 } while ((c = pdbfn.indexOf(".", l)) > l);
4607 pdbfn = pdbfn.substring(0, l);
4609 mtch = idm.findAllIdMatches(pdbfn);
4613 FileFormatI type = null;
4616 type = new IdentifyFile().identify(file, protocol);
4617 } catch (Exception ex)
4621 if (type != null && type.isStructureFile())
4623 filesmatched.add(new Object[] { file, protocol, mtch });
4627 // File wasn't named like one of the sequences or wasn't a PDB file.
4628 filesnotmatched.add(file);
4632 if (filesmatched.size() > 0)
4634 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4640 "label.automatically_associate_structure_files_with_sequences_same_name",
4641 new Object[] { Integer
4647 .getString("label.automatically_associate_structure_files_by_name"),
4648 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4651 for (Object[] fm : filesmatched)
4653 // try and associate
4654 // TODO: may want to set a standard ID naming formalism for
4655 // associating PDB files which have no IDs.
4656 for (SequenceI toassoc : (SequenceI[]) fm[2])
4658 PDBEntry pe = new AssociatePdbFileWithSeq()
4659 .associatePdbWithSeq((String) fm[0],
4660 (DataSourceType) fm[1], toassoc, false,
4664 System.err.println("Associated file : "
4665 + ((String) fm[0]) + " with "
4666 + toassoc.getDisplayId(true));
4670 alignPanel.paintAlignment(true);
4674 if (filesnotmatched.size() > 0)
4677 && (Cache.getDefault(
4678 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4684 "label.ignore_unmatched_dropped_files_info",
4685 new Object[] { Integer
4692 .getString("label.ignore_unmatched_dropped_files"),
4693 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4697 for (String fn : filesnotmatched)
4699 loadJalviewDataFile(fn, null, null, null);
4703 } catch (Exception ex)
4705 ex.printStackTrace();
4711 * Attempt to load a "dropped" file or URL string: First by testing whether
4712 * it's an Annotation file, then a JNet file, and finally a features file. If
4713 * all are false then the user may have dropped an alignment file onto this
4717 * either a filename or a URL string.
4719 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4720 FileFormatI format, SequenceI assocSeq)
4724 if (sourceType == null)
4726 sourceType = FormatAdapter.checkProtocol(file);
4728 // if the file isn't identified, or not positively identified as some
4729 // other filetype (PFAM is default unidentified alignment file type) then
4730 // try to parse as annotation.
4731 boolean isAnnotation = (format == null || FileFormat.Pfam
4732 .equals(format)) ? new AnnotationFile()
4733 .annotateAlignmentView(viewport, file, sourceType) : false;
4737 // first see if its a T-COFFEE score file
4738 TCoffeeScoreFile tcf = null;
4741 tcf = new TCoffeeScoreFile(file, sourceType);
4744 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4747 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4748 isAnnotation = true;
4750 .setText(MessageManager
4751 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4755 // some problem - if no warning its probable that the ID matching
4756 // process didn't work
4760 tcf.getWarningMessage() == null ? MessageManager
4761 .getString("label.check_file_matches_sequence_ids_alignment")
4762 : tcf.getWarningMessage(),
4764 .getString("label.problem_reading_tcoffee_score_file"),
4765 JvOptionPane.WARNING_MESSAGE);
4772 } catch (Exception x)
4775 .debug("Exception when processing data source as T-COFFEE score file",
4781 // try to see if its a JNet 'concise' style annotation file *before*
4783 // try to parse it as a features file
4786 format = new IdentifyFile().identify(file, sourceType);
4788 if (FileFormat.Jnet.equals(format))
4790 JPredFile predictions = new JPredFile(
4792 new JnetAnnotationMaker();
4793 JnetAnnotationMaker.add_annotation(predictions,
4794 viewport.getAlignment(), 0, false);
4795 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4796 viewport.getAlignment().setSeqrep(repseq);
4797 ColumnSelection cs = new ColumnSelection();
4798 cs.hideInsertionsFor(repseq);
4799 viewport.setColumnSelection(cs);
4800 isAnnotation = true;
4802 // else if (IdentifyFile.FeaturesFile.equals(format))
4803 else if (FileFormat.Features.equals(format))
4805 if (parseFeaturesFile(file, sourceType))
4807 alignPanel.paintAlignment(true);
4812 new FileLoader().LoadFile(viewport, file, sourceType, format);
4819 alignPanel.adjustAnnotationHeight();
4820 viewport.updateSequenceIdColours();
4821 buildSortByAnnotationScoresMenu();
4822 alignPanel.paintAlignment(true);
4824 } catch (Exception ex)
4826 ex.printStackTrace();
4827 } catch (OutOfMemoryError oom)
4832 } catch (Exception x)
4837 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4838 : "using " + sourceType + " from " + file)
4840 + (format != null ? "(parsing as '" + format
4841 + "' file)" : ""), oom, Desktop.desktop);
4846 * Method invoked by the ChangeListener on the tabbed pane, in other words
4847 * when a different tabbed pane is selected by the user or programmatically.
4850 public void tabSelectionChanged(int index)
4854 alignPanel = alignPanels.get(index);
4855 viewport = alignPanel.av;
4856 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4857 setMenusFromViewport(viewport);
4861 * If there is a frame linked to this one in a SplitPane, switch it to the
4862 * same view tab index. No infinite recursion of calls should happen, since
4863 * tabSelectionChanged() should not get invoked on setting the selected
4864 * index to an unchanged value. Guard against setting an invalid index
4865 * before the new view peer tab has been created.
4867 final AlignViewportI peer = viewport.getCodingComplement();
4870 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4871 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4873 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4879 * On right mouse click on view tab, prompt for and set new view name.
4882 public void tabbedPane_mousePressed(MouseEvent e)
4884 if (e.isPopupTrigger())
4886 String msg = MessageManager.getString("label.enter_view_name");
4887 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4888 JvOptionPane.QUESTION_MESSAGE);
4892 viewport.viewName = reply;
4893 // TODO warn if reply is in getExistingViewNames()?
4894 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4899 public AlignViewport getCurrentView()
4905 * Open the dialog for regex description parsing.
4908 protected void extractScores_actionPerformed(ActionEvent e)
4910 ParseProperties pp = new jalview.analysis.ParseProperties(
4911 viewport.getAlignment());
4912 // TODO: verify regex and introduce GUI dialog for version 2.5
4913 // if (pp.getScoresFromDescription("col", "score column ",
4914 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4916 if (pp.getScoresFromDescription("description column",
4917 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4919 buildSortByAnnotationScoresMenu();
4927 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4931 protected void showDbRefs_actionPerformed(ActionEvent e)
4933 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4939 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4943 protected void showNpFeats_actionPerformed(ActionEvent e)
4945 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4949 * find the viewport amongst the tabs in this alignment frame and close that
4954 public boolean closeView(AlignViewportI av)
4958 this.closeMenuItem_actionPerformed(false);
4961 Component[] comp = tabbedPane.getComponents();
4962 for (int i = 0; comp != null && i < comp.length; i++)
4964 if (comp[i] instanceof AlignmentPanel)
4966 if (((AlignmentPanel) comp[i]).av == av)
4969 closeView((AlignmentPanel) comp[i]);
4977 protected void build_fetchdbmenu(JMenu webService)
4979 // Temporary hack - DBRef Fetcher always top level ws entry.
4980 // TODO We probably want to store a sequence database checklist in
4981 // preferences and have checkboxes.. rather than individual sources selected
4983 final JMenu rfetch = new JMenu(
4984 MessageManager.getString("action.fetch_db_references"));
4985 rfetch.setToolTipText(MessageManager
4986 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4987 webService.add(rfetch);
4989 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4990 MessageManager.getString("option.trim_retrieved_seqs"));
4991 trimrs.setToolTipText(MessageManager
4992 .getString("label.trim_retrieved_sequences"));
4993 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4994 trimrs.addActionListener(new ActionListener()
4997 public void actionPerformed(ActionEvent e)
4999 trimrs.setSelected(trimrs.isSelected());
5000 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5001 Boolean.valueOf(trimrs.isSelected()).toString());
5005 JMenuItem fetchr = new JMenuItem(
5006 MessageManager.getString("label.standard_databases"));
5007 fetchr.setToolTipText(MessageManager
5008 .getString("label.fetch_embl_uniprot"));
5009 fetchr.addActionListener(new ActionListener()
5013 public void actionPerformed(ActionEvent e)
5015 new Thread(new Runnable()
5020 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5021 .getAlignment().isNucleotide();
5022 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5023 .getSequenceSelection(), alignPanel.alignFrame, null,
5024 alignPanel.alignFrame.featureSettings, isNucleotide);
5025 dbRefFetcher.addListener(new FetchFinishedListenerI()
5028 public void finished()
5030 AlignFrame.this.setMenusForViewport();
5033 dbRefFetcher.fetchDBRefs(false);
5041 final AlignFrame me = this;
5042 new Thread(new Runnable()
5047 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5048 .getSequenceFetcherSingleton(me);
5049 javax.swing.SwingUtilities.invokeLater(new Runnable()
5054 String[] dbclasses = sf.getOrderedSupportedSources();
5055 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5056 // jalview.util.QuickSort.sort(otherdb, otherdb);
5057 List<DbSourceProxy> otherdb;
5058 JMenu dfetch = new JMenu();
5059 JMenu ifetch = new JMenu();
5060 JMenuItem fetchr = null;
5061 int comp = 0, icomp = 0, mcomp = 15;
5062 String mname = null;
5064 for (String dbclass : dbclasses)
5066 otherdb = sf.getSourceProxy(dbclass);
5067 // add a single entry for this class, or submenu allowing 'fetch
5069 if (otherdb == null || otherdb.size() < 1)
5073 // List<DbSourceProxy> dbs=otherdb;
5074 // otherdb=new ArrayList<DbSourceProxy>();
5075 // for (DbSourceProxy db:dbs)
5077 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5081 mname = "From " + dbclass;
5083 if (otherdb.size() == 1)
5085 final DbSourceProxy[] dassource = otherdb
5086 .toArray(new DbSourceProxy[0]);
5087 DbSourceProxy src = otherdb.get(0);
5088 fetchr = new JMenuItem(src.getDbSource());
5089 fetchr.addActionListener(new ActionListener()
5093 public void actionPerformed(ActionEvent e)
5095 new Thread(new Runnable()
5101 boolean isNucleotide = alignPanel.alignFrame
5102 .getViewport().getAlignment()
5104 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5105 alignPanel.av.getSequenceSelection(),
5106 alignPanel.alignFrame, dassource,
5107 alignPanel.alignFrame.featureSettings,
5110 .addListener(new FetchFinishedListenerI()
5113 public void finished()
5115 AlignFrame.this.setMenusForViewport();
5118 dbRefFetcher.fetchDBRefs(false);
5124 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5125 MessageManager.formatMessage(
5126 "label.fetch_retrieve_from",
5127 new Object[] { src.getDbName() })));
5133 final DbSourceProxy[] dassource = otherdb
5134 .toArray(new DbSourceProxy[0]);
5136 DbSourceProxy src = otherdb.get(0);
5137 fetchr = new JMenuItem(MessageManager.formatMessage(
5138 "label.fetch_all_param",
5139 new Object[] { src.getDbSource() }));
5140 fetchr.addActionListener(new ActionListener()
5143 public void actionPerformed(ActionEvent e)
5145 new Thread(new Runnable()
5151 boolean isNucleotide = alignPanel.alignFrame
5152 .getViewport().getAlignment()
5154 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5155 alignPanel.av.getSequenceSelection(),
5156 alignPanel.alignFrame, dassource,
5157 alignPanel.alignFrame.featureSettings,
5160 .addListener(new FetchFinishedListenerI()
5163 public void finished()
5165 AlignFrame.this.setMenusForViewport();
5168 dbRefFetcher.fetchDBRefs(false);
5174 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5175 MessageManager.formatMessage(
5176 "label.fetch_retrieve_from_all_sources",
5178 Integer.valueOf(otherdb.size())
5179 .toString(), src.getDbSource(),
5180 src.getDbName() })));
5183 // and then build the rest of the individual menus
5184 ifetch = new JMenu(MessageManager.formatMessage(
5185 "label.source_from_db_source",
5186 new Object[] { src.getDbSource() }));
5188 String imname = null;
5190 for (DbSourceProxy sproxy : otherdb)
5192 String dbname = sproxy.getDbName();
5193 String sname = dbname.length() > 5 ? dbname.substring(0,
5194 5) + "..." : dbname;
5195 String msname = dbname.length() > 10 ? dbname.substring(
5196 0, 10) + "..." : dbname;
5199 imname = MessageManager.formatMessage(
5200 "label.from_msname", new Object[] { sname });
5202 fetchr = new JMenuItem(msname);
5203 final DbSourceProxy[] dassrc = { sproxy };
5204 fetchr.addActionListener(new ActionListener()
5208 public void actionPerformed(ActionEvent e)
5210 new Thread(new Runnable()
5216 boolean isNucleotide = alignPanel.alignFrame
5217 .getViewport().getAlignment()
5219 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5220 alignPanel.av.getSequenceSelection(),
5221 alignPanel.alignFrame, dassrc,
5222 alignPanel.alignFrame.featureSettings,
5225 .addListener(new FetchFinishedListenerI()
5228 public void finished()
5230 AlignFrame.this.setMenusForViewport();
5233 dbRefFetcher.fetchDBRefs(false);
5239 fetchr.setToolTipText("<html>"
5240 + MessageManager.formatMessage(
5241 "label.fetch_retrieve_from", new Object[]
5245 if (++icomp >= mcomp || i == (otherdb.size()))
5247 ifetch.setText(MessageManager.formatMessage(
5248 "label.source_to_target", imname, sname));
5250 ifetch = new JMenu();
5258 if (comp >= mcomp || dbi >= (dbclasses.length))
5260 dfetch.setText(MessageManager.formatMessage(
5261 "label.source_to_target", mname, dbclass));
5263 dfetch = new JMenu();
5276 * Left justify the whole alignment.
5279 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5281 AlignmentI al = viewport.getAlignment();
5283 viewport.firePropertyChange("alignment", null, al);
5287 * Right justify the whole alignment.
5290 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5292 AlignmentI al = viewport.getAlignment();
5294 viewport.firePropertyChange("alignment", null, al);
5298 public void setShowSeqFeatures(boolean b)
5300 showSeqFeatures.setSelected(b);
5301 viewport.setShowSequenceFeatures(b);
5308 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5309 * awt.event.ActionEvent)
5312 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5314 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5315 alignPanel.paintAlignment(true);
5322 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5326 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5328 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5329 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5337 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5338 * .event.ActionEvent)
5341 protected void showGroupConservation_actionPerformed(ActionEvent e)
5343 viewport.setShowGroupConservation(showGroupConservation.getState());
5344 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5351 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5352 * .event.ActionEvent)
5355 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5357 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5358 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5365 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5366 * .event.ActionEvent)
5369 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5371 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5372 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5376 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5378 showSequenceLogo.setState(true);
5379 viewport.setShowSequenceLogo(true);
5380 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5381 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5385 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5387 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5394 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5395 * .event.ActionEvent)
5398 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5400 if (avc.makeGroupsFromSelection())
5402 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5403 alignPanel.updateAnnotation();
5404 alignPanel.paintAlignment(true);
5408 public void clearAlignmentSeqRep()
5410 // TODO refactor alignmentseqrep to controller
5411 if (viewport.getAlignment().hasSeqrep())
5413 viewport.getAlignment().setSeqrep(null);
5414 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5415 alignPanel.updateAnnotation();
5416 alignPanel.paintAlignment(true);
5421 protected void createGroup_actionPerformed(ActionEvent e)
5423 if (avc.createGroup())
5425 alignPanel.alignmentChanged();
5430 protected void unGroup_actionPerformed(ActionEvent e)
5434 alignPanel.alignmentChanged();
5439 * make the given alignmentPanel the currently selected tab
5441 * @param alignmentPanel
5443 public void setDisplayedView(AlignmentPanel alignmentPanel)
5445 if (!viewport.getSequenceSetId().equals(
5446 alignmentPanel.av.getSequenceSetId()))
5450 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5452 if (tabbedPane != null
5453 && tabbedPane.getTabCount() > 0
5454 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5455 .getSelectedIndex())
5457 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5462 * Action on selection of menu options to Show or Hide annotations.
5465 * @param forSequences
5466 * update sequence-related annotations
5467 * @param forAlignment
5468 * update non-sequence-related annotations
5471 protected void setAnnotationsVisibility(boolean visible,
5472 boolean forSequences, boolean forAlignment)
5474 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5475 .getAlignmentAnnotation();
5480 for (AlignmentAnnotation aa : anns)
5483 * don't display non-positional annotations on an alignment
5485 if (aa.annotations == null)
5489 boolean apply = (aa.sequenceRef == null && forAlignment)
5490 || (aa.sequenceRef != null && forSequences);
5493 aa.visible = visible;
5496 alignPanel.validateAnnotationDimensions(true);
5497 alignPanel.alignmentChanged();
5501 * Store selected annotation sort order for the view and repaint.
5504 protected void sortAnnotations_actionPerformed()
5506 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5508 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5509 alignPanel.paintAlignment(true);
5514 * @return alignment panels in this alignment frame
5516 public List<? extends AlignmentViewPanel> getAlignPanels()
5518 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5522 * Open a new alignment window, with the cDNA associated with this (protein)
5523 * alignment, aligned as is the protein.
5525 protected void viewAsCdna_actionPerformed()
5527 // TODO no longer a menu action - refactor as required
5528 final AlignmentI alignment = getViewport().getAlignment();
5529 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5530 if (mappings == null)
5534 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5535 for (SequenceI aaSeq : alignment.getSequences())
5537 for (AlignedCodonFrame acf : mappings)
5539 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5543 * There is a cDNA mapping for this protein sequence - add to new
5544 * alignment. It will share the same dataset sequence as other mapped
5545 * cDNA (no new mappings need to be created).
5547 final Sequence newSeq = new Sequence(dnaSeq);
5548 newSeq.setDatasetSequence(dnaSeq);
5549 cdnaSeqs.add(newSeq);
5553 if (cdnaSeqs.size() == 0)
5555 // show a warning dialog no mapped cDNA
5558 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5560 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5561 AlignFrame.DEFAULT_HEIGHT);
5562 cdna.alignAs(alignment);
5563 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5565 Desktop.addInternalFrame(alignFrame, newtitle,
5566 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5570 * Set visibility of dna/protein complement view (available when shown in a
5576 protected void showComplement_actionPerformed(boolean show)
5578 SplitContainerI sf = getSplitViewContainer();
5581 sf.setComplementVisible(this, show);
5586 * Generate the reverse (optionally complemented) of the selected sequences,
5587 * and add them to the alignment
5590 protected void showReverse_actionPerformed(boolean complement)
5592 AlignmentI al = null;
5595 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5596 al = dna.reverseCdna(complement);
5597 viewport.addAlignment(al, "");
5598 addHistoryItem(new EditCommand(
5599 MessageManager.getString("label.add_sequences"),
5600 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5601 viewport.getAlignment()));
5602 } catch (Exception ex)
5604 System.err.println(ex.getMessage());
5610 * Try to run a script in the Groovy console, having first ensured that this
5611 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5612 * be targeted at this alignment.
5615 protected void runGroovy_actionPerformed()
5617 Jalview.setCurrentAlignFrame(this);
5618 groovy.ui.Console console = Desktop.getGroovyConsole();
5619 if (console != null)
5623 console.runScript();
5624 } catch (Exception ex)
5626 System.err.println((ex.toString()));
5628 .showInternalMessageDialog(Desktop.desktop, MessageManager
5629 .getString("label.couldnt_run_groovy_script"),
5631 .getString("label.groovy_support_failed"),
5632 JvOptionPane.ERROR_MESSAGE);
5637 System.err.println("Can't run Groovy script as console not found");
5642 * Hides columns containing (or not containing) a specified feature, provided
5643 * that would not leave all columns hidden
5645 * @param featureType
5646 * @param columnsContaining
5649 public boolean hideFeatureColumns(String featureType,
5650 boolean columnsContaining)
5652 boolean notForHiding = avc.markColumnsContainingFeatures(
5653 columnsContaining, false, false, featureType);
5656 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5657 false, featureType))
5659 getViewport().hideSelectedColumns();
5667 protected void selectHighlightedColumns_actionPerformed(
5668 ActionEvent actionEvent)
5670 // include key modifier check in case user selects from menu
5671 avc.markHighlightedColumns(
5672 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5674 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5678 * Rebuilds the Colour menu, including any user-defined colours which have
5679 * been loaded either on startup or during the session
5681 public void buildColourMenu()
5683 colourMenu.removeAll();
5685 colourMenu.add(applyToAllGroups);
5686 colourMenu.add(textColour);
5687 colourMenu.addSeparator();
5689 ColourMenuHelper.addMenuItems(colourMenu, this,
5690 viewport.getAlignment(), false);
5692 colourMenu.addSeparator();
5693 colourMenu.add(conservationMenuItem);
5694 colourMenu.add(modifyConservation);
5695 colourMenu.add(abovePIDThreshold);
5696 colourMenu.add(modifyPID);
5697 colourMenu.add(annotationColour);
5700 * select the default colour for the alignment (this may be
5703 boolean nucleotide = viewport.getAlignment().isNucleotide();
5704 String defaultColourScheme = Cache.getDefault(
5705 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
5706 : Preferences.DEFAULT_COLOUR_PROT,
5707 ResidueColourScheme.NONE);
5709 ColourMenuHelper.setColourSelected(colourMenu, defaultColourScheme);
5713 class PrintThread extends Thread
5717 public PrintThread(AlignmentPanel ap)
5722 static PageFormat pf;
5727 PrinterJob printJob = PrinterJob.getPrinterJob();
5731 printJob.setPrintable(ap, pf);
5735 printJob.setPrintable(ap);
5738 if (printJob.printDialog())
5743 } catch (Exception PrintException)
5745 PrintException.printStackTrace();