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.AnnotationSorter.SequenceAnnotationOrder;
26 import jalview.analysis.CrossRef;
27 import jalview.analysis.Dna;
28 import jalview.analysis.GeneticCodeI;
29 import jalview.analysis.ParseProperties;
30 import jalview.analysis.SequenceIdMatcher;
31 import jalview.api.AlignExportSettingI;
32 import jalview.api.AlignViewControllerGuiI;
33 import jalview.api.AlignViewControllerI;
34 import jalview.api.AlignViewportI;
35 import jalview.api.AlignmentViewPanel;
36 import jalview.api.FeatureSettingsControllerI;
37 import jalview.api.SplitContainerI;
38 import jalview.api.ViewStyleI;
39 import jalview.api.analysis.SimilarityParamsI;
40 import jalview.bin.Cache;
41 import jalview.bin.Jalview;
42 import jalview.commands.CommandI;
43 import jalview.commands.EditCommand;
44 import jalview.commands.EditCommand.Action;
45 import jalview.commands.OrderCommand;
46 import jalview.commands.RemoveGapColCommand;
47 import jalview.commands.RemoveGapsCommand;
48 import jalview.commands.SlideSequencesCommand;
49 import jalview.commands.TrimRegionCommand;
50 import jalview.datamodel.AlignedCodonFrame;
51 import jalview.datamodel.Alignment;
52 import jalview.datamodel.AlignmentAnnotation;
53 import jalview.datamodel.AlignmentExportData;
54 import jalview.datamodel.AlignmentI;
55 import jalview.datamodel.AlignmentOrder;
56 import jalview.datamodel.AlignmentView;
57 import jalview.datamodel.ColumnSelection;
58 import jalview.datamodel.HiddenColumns;
59 import jalview.datamodel.HiddenSequences;
60 import jalview.datamodel.PDBEntry;
61 import jalview.datamodel.SeqCigar;
62 import jalview.datamodel.Sequence;
63 import jalview.datamodel.SequenceGroup;
64 import jalview.datamodel.SequenceI;
65 import jalview.gui.ColourMenuHelper.ColourChangeListener;
66 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
67 import jalview.io.AlignmentProperties;
68 import jalview.io.AnnotationFile;
69 import jalview.io.BackupFiles;
70 import jalview.io.BioJsHTMLOutput;
71 import jalview.io.DataSourceType;
72 import jalview.io.FileFormat;
73 import jalview.io.FileFormatI;
74 import jalview.io.FileFormats;
75 import jalview.io.FileLoader;
76 import jalview.io.FileParse;
77 import jalview.io.FormatAdapter;
78 import jalview.io.HtmlSvgOutput;
79 import jalview.io.IdentifyFile;
80 import jalview.io.JPredFile;
81 import jalview.io.JalviewFileChooser;
82 import jalview.io.JalviewFileView;
83 import jalview.io.JnetAnnotationMaker;
84 import jalview.io.NewickFile;
85 import jalview.io.ScoreMatrixFile;
86 import jalview.io.TCoffeeScoreFile;
87 import jalview.io.vcf.VCFLoader;
88 import jalview.jbgui.GAlignFrame;
89 import jalview.schemes.ColourSchemeI;
90 import jalview.schemes.ColourSchemes;
91 import jalview.schemes.ResidueColourScheme;
92 import jalview.schemes.TCoffeeColourScheme;
93 import jalview.util.MessageManager;
94 import jalview.viewmodel.AlignmentViewport;
95 import jalview.viewmodel.ViewportRanges;
96 import jalview.ws.DBRefFetcher;
97 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
98 import jalview.ws.jws1.Discoverer;
99 import jalview.ws.jws2.Jws2Discoverer;
100 import jalview.ws.jws2.jabaws2.Jws2Instance;
101 import jalview.ws.seqfetcher.DbSourceProxy;
103 import java.awt.BorderLayout;
104 import java.awt.Component;
105 import java.awt.Rectangle;
106 import java.awt.Toolkit;
107 import java.awt.datatransfer.Clipboard;
108 import java.awt.datatransfer.DataFlavor;
109 import java.awt.datatransfer.StringSelection;
110 import java.awt.datatransfer.Transferable;
111 import java.awt.dnd.DnDConstants;
112 import java.awt.dnd.DropTargetDragEvent;
113 import java.awt.dnd.DropTargetDropEvent;
114 import java.awt.dnd.DropTargetEvent;
115 import java.awt.dnd.DropTargetListener;
116 import java.awt.event.ActionEvent;
117 import java.awt.event.ActionListener;
118 import java.awt.event.FocusAdapter;
119 import java.awt.event.FocusEvent;
120 import java.awt.event.ItemEvent;
121 import java.awt.event.ItemListener;
122 import java.awt.event.KeyAdapter;
123 import java.awt.event.KeyEvent;
124 import java.awt.event.MouseEvent;
125 import java.awt.print.PageFormat;
126 import java.awt.print.PrinterJob;
127 import java.beans.PropertyChangeEvent;
129 import java.io.FileWriter;
130 import java.io.PrintWriter;
132 import java.util.ArrayList;
133 import java.util.Arrays;
134 import java.util.Deque;
135 import java.util.Enumeration;
136 import java.util.Hashtable;
137 import java.util.List;
138 import java.util.Vector;
140 import javax.swing.ButtonGroup;
141 import javax.swing.JCheckBoxMenuItem;
142 import javax.swing.JEditorPane;
143 import javax.swing.JInternalFrame;
144 import javax.swing.JLayeredPane;
145 import javax.swing.JMenu;
146 import javax.swing.JMenuItem;
147 import javax.swing.JScrollPane;
148 import javax.swing.SwingUtilities;
154 * @version $Revision$
156 public class AlignFrame extends GAlignFrame implements DropTargetListener,
157 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
160 public static final int DEFAULT_WIDTH = 700;
162 public static final int DEFAULT_HEIGHT = 500;
165 * The currently displayed panel (selected tabbed view if more than one)
167 public AlignmentPanel alignPanel;
169 AlignViewport viewport;
171 public AlignViewControllerI avc;
173 List<AlignmentPanel> alignPanels = new ArrayList<>();
176 * Last format used to load or save alignments in this window
178 FileFormatI currentFileFormat = null;
181 * Current filename for this alignment
183 String fileName = null;
186 * Creates a new AlignFrame object with specific width and height.
192 public AlignFrame(AlignmentI al, int width, int height)
194 this(al, null, width, height);
198 * Creates a new AlignFrame object with specific width, height and
204 * @param sequenceSetId
206 public AlignFrame(AlignmentI al, int width, int height,
207 String sequenceSetId)
209 this(al, null, width, height, sequenceSetId);
213 * Creates a new AlignFrame object with specific width, height and
219 * @param sequenceSetId
222 public AlignFrame(AlignmentI al, int width, int height,
223 String sequenceSetId, String viewId)
225 this(al, null, width, height, sequenceSetId, viewId);
229 * new alignment window with hidden columns
233 * @param hiddenColumns
234 * ColumnSelection or null
236 * Width of alignment frame
240 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
243 this(al, hiddenColumns, width, height, null);
247 * Create alignment frame for al with hiddenColumns, a specific width and
248 * height, and specific sequenceId
251 * @param hiddenColumns
254 * @param sequenceSetId
257 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
258 int height, String sequenceSetId)
260 this(al, hiddenColumns, width, height, sequenceSetId, null);
264 * Create alignment frame for al with hiddenColumns, a specific width and
265 * height, and specific sequenceId
268 * @param hiddenColumns
271 * @param sequenceSetId
276 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
277 int height, String sequenceSetId, String viewId)
279 setSize(width, height);
281 if (al.getDataset() == null)
286 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
288 alignPanel = new AlignmentPanel(this, viewport);
290 addAlignmentPanel(alignPanel, true);
294 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
295 HiddenColumns hiddenColumns, int width, int height)
297 setSize(width, height);
299 if (al.getDataset() == null)
304 viewport = new AlignViewport(al, hiddenColumns);
306 if (hiddenSeqs != null && hiddenSeqs.length > 0)
308 viewport.hideSequence(hiddenSeqs);
310 alignPanel = new AlignmentPanel(this, viewport);
311 addAlignmentPanel(alignPanel, true);
316 * Make a new AlignFrame from existing alignmentPanels
323 public AlignFrame(AlignmentPanel ap)
327 addAlignmentPanel(ap, false);
332 * initalise the alignframe from the underlying viewport data and the
337 if (!Jalview.isHeadlessMode())
339 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
342 avc = new jalview.controller.AlignViewController(this, viewport,
344 if (viewport.getAlignmentConservationAnnotation() == null)
346 // BLOSUM62Colour.setEnabled(false);
347 conservationMenuItem.setEnabled(false);
348 modifyConservation.setEnabled(false);
349 // PIDColour.setEnabled(false);
350 // abovePIDThreshold.setEnabled(false);
351 // modifyPID.setEnabled(false);
354 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
357 if (sortby.equals("Id"))
359 sortIDMenuItem_actionPerformed(null);
361 else if (sortby.equals("Pairwise Identity"))
363 sortPairwiseMenuItem_actionPerformed(null);
366 setMenusFromViewport(viewport);
367 buildSortByAnnotationScoresMenu();
368 calculateTree.addActionListener(new ActionListener()
372 public void actionPerformed(ActionEvent e)
379 if (Desktop.desktop != null)
381 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
382 addServiceListeners();
386 if (viewport.getWrapAlignment())
388 wrapMenuItem_actionPerformed(null);
391 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
393 this.overviewMenuItem_actionPerformed(null);
398 final List<AlignmentPanel> selviews = new ArrayList<>();
399 final List<AlignmentPanel> origview = new ArrayList<>();
400 final String menuLabel = MessageManager
401 .getString("label.copy_format_from");
402 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
403 new ViewSetProvider()
407 public AlignmentPanel[] getAllAlignmentPanels()
410 origview.add(alignPanel);
411 // make an array of all alignment panels except for this one
412 List<AlignmentPanel> aps = new ArrayList<>(
413 Arrays.asList(Desktop.getAlignmentPanels(null)));
414 aps.remove(AlignFrame.this.alignPanel);
415 return aps.toArray(new AlignmentPanel[aps.size()]);
417 }, selviews, new ItemListener()
421 public void itemStateChanged(ItemEvent e)
423 if (origview.size() > 0)
425 final AlignmentPanel ap = origview.get(0);
428 * Copy the ViewStyle of the selected panel to 'this one'.
429 * Don't change value of 'scaleProteinAsCdna' unless copying
432 ViewStyleI vs = selviews.get(0).getAlignViewport()
434 boolean fromSplitFrame = selviews.get(0)
435 .getAlignViewport().getCodingComplement() != null;
438 vs.setScaleProteinAsCdna(ap.getAlignViewport()
439 .getViewStyle().isScaleProteinAsCdna());
441 ap.getAlignViewport().setViewStyle(vs);
444 * Also rescale ViewStyle of SplitFrame complement if there is
445 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
446 * the whole ViewStyle (allow cDNA protein to have different
449 AlignViewportI complement = ap.getAlignViewport()
450 .getCodingComplement();
451 if (complement != null && vs.isScaleProteinAsCdna())
453 AlignFrame af = Desktop.getAlignFrameFor(complement);
454 ((SplitFrame) af.getSplitViewContainer())
456 af.setMenusForViewport();
460 ap.setSelected(true);
461 ap.alignFrame.setMenusForViewport();
466 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
467 .indexOf("devel") > -1
468 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
469 .indexOf("test") > -1)
471 formatMenu.add(vsel);
473 addFocusListener(new FocusAdapter()
476 public void focusGained(FocusEvent e)
478 Jalview.setCurrentAlignFrame(AlignFrame.this);
482 alignPanel.sortAnnotations(false);
486 * Change the filename and format for the alignment, and enable the 'reload'
487 * button functionality.
494 public void setFileName(String file, FileFormatI format)
497 setFileFormat(format);
498 reload.setEnabled(true);
502 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
505 void addKeyListener()
507 addKeyListener(new KeyAdapter()
510 public void keyPressed(KeyEvent evt)
512 if (viewport.cursorMode
513 && ((evt.getKeyCode() >= KeyEvent.VK_0
514 && evt.getKeyCode() <= KeyEvent.VK_9)
515 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
516 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
517 && Character.isDigit(evt.getKeyChar()))
519 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
522 switch (evt.getKeyCode())
525 case 27: // escape key
526 deselectAllSequenceMenuItem_actionPerformed(null);
530 case KeyEvent.VK_DOWN:
531 if (evt.isAltDown() || !viewport.cursorMode)
533 moveSelectedSequences(false);
535 if (viewport.cursorMode)
537 alignPanel.getSeqPanel().moveCursor(0, 1);
542 if (evt.isAltDown() || !viewport.cursorMode)
544 moveSelectedSequences(true);
546 if (viewport.cursorMode)
548 alignPanel.getSeqPanel().moveCursor(0, -1);
553 case KeyEvent.VK_LEFT:
554 if (evt.isAltDown() || !viewport.cursorMode)
556 slideSequences(false,
557 alignPanel.getSeqPanel().getKeyboardNo1());
561 alignPanel.getSeqPanel().moveCursor(-1, 0);
566 case KeyEvent.VK_RIGHT:
567 if (evt.isAltDown() || !viewport.cursorMode)
569 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
573 alignPanel.getSeqPanel().moveCursor(1, 0);
577 case KeyEvent.VK_SPACE:
578 if (viewport.cursorMode)
580 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
581 || evt.isShiftDown() || evt.isAltDown());
585 // case KeyEvent.VK_A:
586 // if (viewport.cursorMode)
588 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
589 // //System.out.println("A");
593 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
594 * System.out.println("closing bracket"); } break;
596 case KeyEvent.VK_DELETE:
597 case KeyEvent.VK_BACK_SPACE:
598 if (!viewport.cursorMode)
600 cut_actionPerformed(null);
604 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
605 || evt.isShiftDown() || evt.isAltDown());
611 if (viewport.cursorMode)
613 alignPanel.getSeqPanel().setCursorRow();
617 if (viewport.cursorMode && !evt.isControlDown())
619 alignPanel.getSeqPanel().setCursorColumn();
623 if (viewport.cursorMode)
625 alignPanel.getSeqPanel().setCursorPosition();
629 case KeyEvent.VK_ENTER:
630 case KeyEvent.VK_COMMA:
631 if (viewport.cursorMode)
633 alignPanel.getSeqPanel().setCursorRowAndColumn();
638 if (viewport.cursorMode)
640 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
644 if (viewport.cursorMode)
646 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
651 viewport.cursorMode = !viewport.cursorMode;
652 statusBar.setText(MessageManager
653 .formatMessage("label.keyboard_editing_mode", new String[]
654 { (viewport.cursorMode ? "on" : "off") }));
655 if (viewport.cursorMode)
657 ViewportRanges ranges = viewport.getRanges();
658 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
660 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
663 alignPanel.getSeqPanel().seqCanvas.repaint();
669 Help.showHelpWindow();
670 } catch (Exception ex)
672 ex.printStackTrace();
677 boolean toggleSeqs = !evt.isControlDown();
678 boolean toggleCols = !evt.isShiftDown();
679 toggleHiddenRegions(toggleSeqs, toggleCols);
684 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
685 boolean modifyExisting = true; // always modify, don't clear
686 // evt.isShiftDown();
687 boolean invertHighlighted = evt.isAltDown();
688 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
692 case KeyEvent.VK_PAGE_UP:
693 viewport.getRanges().pageUp();
695 case KeyEvent.VK_PAGE_DOWN:
696 viewport.getRanges().pageDown();
702 public void keyReleased(KeyEvent evt)
704 switch (evt.getKeyCode())
706 case KeyEvent.VK_LEFT:
707 if (evt.isAltDown() || !viewport.cursorMode)
709 viewport.firePropertyChange("alignment", null,
710 viewport.getAlignment().getSequences());
714 case KeyEvent.VK_RIGHT:
715 if (evt.isAltDown() || !viewport.cursorMode)
717 viewport.firePropertyChange("alignment", null,
718 viewport.getAlignment().getSequences());
726 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
728 ap.alignFrame = this;
729 avc = new jalview.controller.AlignViewController(this, viewport,
734 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
736 int aSize = alignPanels.size();
738 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
740 if (aSize == 1 && ap.av.getViewName() == null)
742 this.getContentPane().add(ap, BorderLayout.CENTER);
748 setInitialTabVisible();
751 expandViews.setEnabled(true);
752 gatherViews.setEnabled(true);
753 tabbedPane.addTab(ap.av.getViewName(), ap);
755 ap.setVisible(false);
760 if (ap.av.isPadGaps())
762 ap.av.getAlignment().padGaps();
764 ap.av.updateConservation(ap);
765 ap.av.updateConsensus(ap);
766 ap.av.updateStrucConsensus(ap);
770 public void setInitialTabVisible()
772 expandViews.setEnabled(true);
773 gatherViews.setEnabled(true);
774 tabbedPane.setVisible(true);
775 AlignmentPanel first = alignPanels.get(0);
776 tabbedPane.addTab(first.av.getViewName(), first);
777 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
780 public AlignViewport getViewport()
785 /* Set up intrinsic listeners for dynamically generated GUI bits. */
786 private void addServiceListeners()
788 final java.beans.PropertyChangeListener thisListener;
789 Desktop.instance.addJalviewPropertyChangeListener("services",
790 thisListener = new java.beans.PropertyChangeListener()
793 public void propertyChange(PropertyChangeEvent evt)
795 // // System.out.println("Discoverer property change.");
796 // if (evt.getPropertyName().equals("services"))
798 SwingUtilities.invokeLater(new Runnable()
805 "Rebuild WS Menu for service change");
806 BuildWebServiceMenu();
813 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
816 public void internalFrameClosed(
817 javax.swing.event.InternalFrameEvent evt)
819 // System.out.println("deregistering discoverer listener");
820 Desktop.instance.removeJalviewPropertyChangeListener("services",
822 closeMenuItem_actionPerformed(true);
825 // Finally, build the menu once to get current service state
826 new Thread(new Runnable()
831 BuildWebServiceMenu();
837 * Configure menu items that vary according to whether the alignment is
838 * nucleotide or protein
840 public void setGUINucleotide()
842 AlignmentI al = getViewport().getAlignment();
843 boolean nucleotide = al.isNucleotide();
845 loadVcf.setVisible(nucleotide);
846 showTranslation.setVisible(nucleotide);
847 showReverse.setVisible(nucleotide);
848 showReverseComplement.setVisible(nucleotide);
849 conservationMenuItem.setEnabled(!nucleotide);
851 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
852 showGroupConservation.setEnabled(!nucleotide);
854 showComplementMenuItem
855 .setText(nucleotide ? MessageManager.getString("label.protein")
856 : MessageManager.getString("label.nucleotide"));
860 * set up menus for the current viewport. This may be called after any
861 * operation that affects the data in the current view (selection changed,
862 * etc) to update the menus to reflect the new state.
865 public void setMenusForViewport()
867 setMenusFromViewport(viewport);
871 * Need to call this method when tabs are selected for multiple views, or when
872 * loading from Jalview2XML.java
877 public void setMenusFromViewport(AlignViewport av)
879 padGapsMenuitem.setSelected(av.isPadGaps());
880 colourTextMenuItem.setSelected(av.isShowColourText());
881 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
882 modifyPID.setEnabled(abovePIDThreshold.isSelected());
883 conservationMenuItem.setSelected(av.getConservationSelected());
884 modifyConservation.setEnabled(conservationMenuItem.isSelected());
885 seqLimits.setSelected(av.getShowJVSuffix());
886 idRightAlign.setSelected(av.isRightAlignIds());
887 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
888 renderGapsMenuItem.setSelected(av.isRenderGaps());
889 wrapMenuItem.setSelected(av.getWrapAlignment());
890 scaleAbove.setVisible(av.getWrapAlignment());
891 scaleLeft.setVisible(av.getWrapAlignment());
892 scaleRight.setVisible(av.getWrapAlignment());
893 annotationPanelMenuItem.setState(av.isShowAnnotation());
895 * Show/hide annotations only enabled if annotation panel is shown
897 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
898 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
899 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
900 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
901 viewBoxesMenuItem.setSelected(av.getShowBoxes());
902 viewTextMenuItem.setSelected(av.getShowText());
903 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
904 showGroupConsensus.setSelected(av.isShowGroupConsensus());
905 showGroupConservation.setSelected(av.isShowGroupConservation());
906 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
907 showSequenceLogo.setSelected(av.isShowSequenceLogo());
908 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
910 ColourMenuHelper.setColourSelected(colourMenu,
911 av.getGlobalColourScheme());
913 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
914 hiddenMarkers.setState(av.getShowHiddenMarkers());
915 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
916 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
917 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
918 autoCalculate.setSelected(av.autoCalculateConsensus);
919 sortByTree.setSelected(av.sortByTree);
920 listenToViewSelections.setSelected(av.followSelection);
922 showProducts.setEnabled(canShowProducts());
923 setGroovyEnabled(Desktop.getGroovyConsole() != null);
929 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
933 public void setGroovyEnabled(boolean b)
935 runGroovy.setEnabled(b);
938 private IProgressIndicator progressBar;
943 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
946 public void setProgressBar(String message, long id)
948 progressBar.setProgressBar(message, id);
952 public void registerHandler(final long id,
953 final IProgressIndicatorHandler handler)
955 progressBar.registerHandler(id, handler);
960 * @return true if any progress bars are still active
963 public boolean operationInProgress()
965 return progressBar.operationInProgress();
969 * Sets the text of the status bar. Note that setting a null or empty value
970 * will cause the status bar to be hidden, with possibly undesirable flicker
971 * of the screen layout.
974 public void setStatus(String text)
976 statusBar.setText(text == null || text.isEmpty() ? " " : text);
980 * Added so Castor Mapping file can obtain Jalview Version
982 public String getVersion()
984 return jalview.bin.Cache.getProperty("VERSION");
987 public FeatureRenderer getFeatureRenderer()
989 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
993 public void fetchSequence_actionPerformed(ActionEvent e)
995 new jalview.gui.SequenceFetcher(this);
999 public void addFromFile_actionPerformed(ActionEvent e)
1001 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1005 public void reload_actionPerformed(ActionEvent e)
1007 if (fileName != null)
1009 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1010 // originating file's format
1011 // TODO: work out how to recover feature settings for correct view(s) when
1012 // file is reloaded.
1013 if (FileFormat.Jalview.equals(currentFileFormat))
1015 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1016 for (int i = 0; i < frames.length; i++)
1018 if (frames[i] instanceof AlignFrame && frames[i] != this
1019 && ((AlignFrame) frames[i]).fileName != null
1020 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1024 frames[i].setSelected(true);
1025 Desktop.instance.closeAssociatedWindows();
1026 } catch (java.beans.PropertyVetoException ex)
1032 Desktop.instance.closeAssociatedWindows();
1034 FileLoader loader = new FileLoader();
1035 DataSourceType protocol = fileName.startsWith("http:")
1036 ? DataSourceType.URL
1037 : DataSourceType.FILE;
1038 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1042 Rectangle bounds = this.getBounds();
1044 FileLoader loader = new FileLoader();
1045 DataSourceType protocol = fileName.startsWith("http:")
1046 ? DataSourceType.URL
1047 : DataSourceType.FILE;
1048 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1049 protocol, currentFileFormat);
1051 newframe.setBounds(bounds);
1052 if (featureSettings != null && featureSettings.isShowing())
1054 final Rectangle fspos = featureSettings.frame.getBounds();
1055 // TODO: need a 'show feature settings' function that takes bounds -
1056 // need to refactor Desktop.addFrame
1057 newframe.featureSettings_actionPerformed(null);
1058 final FeatureSettings nfs = newframe.featureSettings;
1059 SwingUtilities.invokeLater(new Runnable()
1064 nfs.frame.setBounds(fspos);
1067 this.featureSettings.close();
1068 this.featureSettings = null;
1070 this.closeMenuItem_actionPerformed(true);
1076 public void addFromText_actionPerformed(ActionEvent e)
1079 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1083 public void addFromURL_actionPerformed(ActionEvent e)
1085 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1089 public void save_actionPerformed(ActionEvent e)
1091 if (fileName == null || (currentFileFormat == null)
1092 || fileName.startsWith("http"))
1094 saveAs_actionPerformed(null);
1098 saveAlignment(fileName, currentFileFormat);
1109 public void saveAs_actionPerformed(ActionEvent e)
1111 String format = currentFileFormat == null ? null
1112 : currentFileFormat.getName();
1113 JalviewFileChooser chooser = JalviewFileChooser
1114 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1116 chooser.setFileView(new JalviewFileView());
1117 chooser.setDialogTitle(
1118 MessageManager.getString("label.save_alignment_to_file"));
1119 chooser.setToolTipText(MessageManager.getString("action.save"));
1121 int value = chooser.showSaveDialog(this);
1123 if (value == JalviewFileChooser.APPROVE_OPTION)
1125 currentFileFormat = chooser.getSelectedFormat();
1126 while (currentFileFormat == null)
1128 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1129 MessageManager.getString(
1130 "label.select_file_format_before_saving"),
1131 MessageManager.getString("label.file_format_not_specified"),
1132 JvOptionPane.WARNING_MESSAGE);
1133 currentFileFormat = chooser.getSelectedFormat();
1134 value = chooser.showSaveDialog(this);
1135 if (value != JalviewFileChooser.APPROVE_OPTION)
1141 fileName = chooser.getSelectedFile().getPath();
1143 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1145 Cache.setProperty("LAST_DIRECTORY", fileName);
1146 saveAlignment(fileName, currentFileFormat);
1150 public boolean saveAlignment(String file, FileFormatI format)
1152 boolean success = true;
1154 if (FileFormat.Jalview.equals(format))
1156 String shortName = title;
1158 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1160 shortName = shortName.substring(
1161 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1164 success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1167 statusBar.setText(MessageManager.formatMessage(
1168 "label.successfully_saved_to_file_in_format", new Object[]
1169 { fileName, format }));
1174 AlignmentExportData exportData = getAlignmentForExport(format,
1176 if (exportData.getSettings().isCancelled())
1180 FormatAdapter f = new FormatAdapter(alignPanel,
1181 exportData.getSettings());
1182 String output = f.formatSequences(format, exportData.getAlignment(), // class
1186 // occur in the distant future
1187 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1188 f.getCacheSuffixDefault(format),
1189 viewport.getAlignment().getHiddenColumns());
1197 // create backupfiles object and get new temp filename destination
1198 BackupFiles backupfiles = new BackupFiles(file);
1202 PrintWriter out = new PrintWriter(
1203 new FileWriter(backupfiles.getTempFilePath()));
1207 this.setTitle(file);
1208 statusBar.setText(MessageManager.formatMessage(
1209 "label.successfully_saved_to_file_in_format", new Object[]
1210 { fileName, format.getName() }));
1211 } catch (Exception ex)
1214 ex.printStackTrace();
1217 backupfiles.setWriteSuccess(success);
1218 // do the backup file roll and rename the temp file to actual file
1219 success = backupfiles.rollBackupsAndRenameTempFile();
1226 JvOptionPane.showInternalMessageDialog(this, MessageManager
1227 .formatMessage("label.couldnt_save_file", new Object[]
1229 MessageManager.getString("label.error_saving_file"),
1230 JvOptionPane.WARNING_MESSAGE);
1236 private void warningMessage(String warning, String title)
1238 if (new jalview.util.Platform().isHeadless())
1240 System.err.println("Warning: " + title + "\nWarning: " + warning);
1245 JvOptionPane.showInternalMessageDialog(this, warning, title,
1246 JvOptionPane.WARNING_MESSAGE);
1258 protected void outputText_actionPerformed(ActionEvent e)
1260 FileFormatI fileFormat = FileFormats.getInstance()
1261 .forName(e.getActionCommand());
1262 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1264 if (exportData.getSettings().isCancelled())
1268 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1269 cap.setForInput(null);
1272 FileFormatI format = fileFormat;
1273 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1274 .formatSequences(format, exportData.getAlignment(),
1275 exportData.getOmitHidden(),
1276 exportData.getStartEndPostions(),
1277 viewport.getAlignment().getHiddenColumns()));
1278 Desktop.addInternalFrame(cap, MessageManager
1279 .formatMessage("label.alignment_output_command", new Object[]
1280 { e.getActionCommand() }), 600, 500);
1281 } catch (OutOfMemoryError oom)
1283 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1290 public static AlignmentExportData getAlignmentForExport(
1291 FileFormatI format, AlignViewportI viewport,
1292 AlignExportSettingI exportSettings)
1294 AlignmentI alignmentToExport = null;
1295 AlignExportSettingI settings = exportSettings;
1296 String[] omitHidden = null;
1298 HiddenSequences hiddenSeqs = viewport.getAlignment()
1299 .getHiddenSequences();
1301 alignmentToExport = viewport.getAlignment();
1303 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1304 if (settings == null)
1306 settings = new AlignExportSettings(hasHiddenSeqs,
1307 viewport.hasHiddenColumns(), format);
1309 // settings.isExportAnnotations();
1311 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1313 omitHidden = viewport.getViewAsString(false,
1314 settings.isExportHiddenSequences());
1317 int[] alignmentStartEnd = new int[2];
1318 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1320 alignmentToExport = hiddenSeqs.getFullAlignment();
1324 alignmentToExport = viewport.getAlignment();
1326 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1327 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1328 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1329 omitHidden, alignmentStartEnd, settings);
1340 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1342 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1343 htmlSVG.exportHTML(null);
1347 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1349 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1350 bjs.exportHTML(null);
1353 public void createImageMap(File file, String image)
1355 alignPanel.makePNGImageMap(file, image);
1365 public void createPNG(File f)
1367 alignPanel.makePNG(f);
1377 public void createEPS(File f)
1379 alignPanel.makeEPS(f);
1383 public void createSVG(File f)
1385 alignPanel.makeSVG(f);
1389 public void pageSetup_actionPerformed(ActionEvent e)
1391 PrinterJob printJob = PrinterJob.getPrinterJob();
1392 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1402 public void printMenuItem_actionPerformed(ActionEvent e)
1404 // Putting in a thread avoids Swing painting problems
1405 PrintThread thread = new PrintThread(alignPanel);
1410 public void exportFeatures_actionPerformed(ActionEvent e)
1412 new AnnotationExporter(alignPanel).exportFeatures();
1416 public void exportAnnotations_actionPerformed(ActionEvent e)
1418 new AnnotationExporter(alignPanel).exportAnnotations();
1422 public void associatedData_actionPerformed(ActionEvent e)
1424 // Pick the tree file
1425 JalviewFileChooser chooser = new JalviewFileChooser(
1426 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1427 chooser.setFileView(new JalviewFileView());
1428 chooser.setDialogTitle(
1429 MessageManager.getString("label.load_jalview_annotations"));
1430 chooser.setToolTipText(
1431 MessageManager.getString("label.load_jalview_annotations"));
1433 int value = chooser.showOpenDialog(null);
1435 if (value == JalviewFileChooser.APPROVE_OPTION)
1437 String choice = chooser.getSelectedFile().getPath();
1438 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1439 loadJalviewDataFile(choice, null, null, null);
1445 * Close the current view or all views in the alignment frame. If the frame
1446 * only contains one view then the alignment will be removed from memory.
1448 * @param closeAllTabs
1451 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1453 if (alignPanels != null && alignPanels.size() < 2)
1455 closeAllTabs = true;
1460 if (alignPanels != null)
1464 if (this.isClosed())
1466 // really close all the windows - otherwise wait till
1467 // setClosed(true) is called
1468 for (int i = 0; i < alignPanels.size(); i++)
1470 AlignmentPanel ap = alignPanels.get(i);
1477 closeView(alignPanel);
1484 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1485 * be called recursively, with the frame now in 'closed' state
1487 this.setClosed(true);
1489 } catch (Exception ex)
1491 ex.printStackTrace();
1496 * Close the specified panel and close up tabs appropriately.
1498 * @param panelToClose
1500 public void closeView(AlignmentPanel panelToClose)
1502 int index = tabbedPane.getSelectedIndex();
1503 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1504 alignPanels.remove(panelToClose);
1505 panelToClose.closePanel();
1506 panelToClose = null;
1508 tabbedPane.removeTabAt(closedindex);
1509 tabbedPane.validate();
1511 if (index > closedindex || index == tabbedPane.getTabCount())
1513 // modify currently selected tab index if necessary.
1517 this.tabSelectionChanged(index);
1523 void updateEditMenuBar()
1526 if (viewport.getHistoryList().size() > 0)
1528 undoMenuItem.setEnabled(true);
1529 CommandI command = viewport.getHistoryList().peek();
1530 undoMenuItem.setText(MessageManager
1531 .formatMessage("label.undo_command", new Object[]
1532 { command.getDescription() }));
1536 undoMenuItem.setEnabled(false);
1537 undoMenuItem.setText(MessageManager.getString("action.undo"));
1540 if (viewport.getRedoList().size() > 0)
1542 redoMenuItem.setEnabled(true);
1544 CommandI command = viewport.getRedoList().peek();
1545 redoMenuItem.setText(MessageManager
1546 .formatMessage("label.redo_command", new Object[]
1547 { command.getDescription() }));
1551 redoMenuItem.setEnabled(false);
1552 redoMenuItem.setText(MessageManager.getString("action.redo"));
1557 public void addHistoryItem(CommandI command)
1559 if (command.getSize() > 0)
1561 viewport.addToHistoryList(command);
1562 viewport.clearRedoList();
1563 updateEditMenuBar();
1564 viewport.updateHiddenColumns();
1565 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1566 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1567 // viewport.getColumnSelection()
1568 // .getHiddenColumns().size() > 0);
1574 * @return alignment objects for all views
1576 AlignmentI[] getViewAlignments()
1578 if (alignPanels != null)
1580 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1582 for (AlignmentPanel ap : alignPanels)
1584 als[i++] = ap.av.getAlignment();
1588 if (viewport != null)
1590 return new AlignmentI[] { viewport.getAlignment() };
1602 protected void undoMenuItem_actionPerformed(ActionEvent e)
1604 if (viewport.getHistoryList().isEmpty())
1608 CommandI command = viewport.getHistoryList().pop();
1609 viewport.addToRedoList(command);
1610 command.undoCommand(getViewAlignments());
1612 AlignmentViewport originalSource = getOriginatingSource(command);
1613 updateEditMenuBar();
1615 if (originalSource != null)
1617 if (originalSource != viewport)
1620 "Implementation worry: mismatch of viewport origin for undo");
1622 originalSource.updateHiddenColumns();
1623 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1625 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1626 // viewport.getColumnSelection()
1627 // .getHiddenColumns().size() > 0);
1628 originalSource.firePropertyChange("alignment", null,
1629 originalSource.getAlignment().getSequences());
1640 protected void redoMenuItem_actionPerformed(ActionEvent e)
1642 if (viewport.getRedoList().size() < 1)
1647 CommandI command = viewport.getRedoList().pop();
1648 viewport.addToHistoryList(command);
1649 command.doCommand(getViewAlignments());
1651 AlignmentViewport originalSource = getOriginatingSource(command);
1652 updateEditMenuBar();
1654 if (originalSource != null)
1657 if (originalSource != viewport)
1660 "Implementation worry: mismatch of viewport origin for redo");
1662 originalSource.updateHiddenColumns();
1663 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1665 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1666 // viewport.getColumnSelection()
1667 // .getHiddenColumns().size() > 0);
1668 originalSource.firePropertyChange("alignment", null,
1669 originalSource.getAlignment().getSequences());
1673 AlignmentViewport getOriginatingSource(CommandI command)
1675 AlignmentViewport originalSource = null;
1676 // For sequence removal and addition, we need to fire
1677 // the property change event FROM the viewport where the
1678 // original alignment was altered
1679 AlignmentI al = null;
1680 if (command instanceof EditCommand)
1682 EditCommand editCommand = (EditCommand) command;
1683 al = editCommand.getAlignment();
1684 List<Component> comps = PaintRefresher.components
1685 .get(viewport.getSequenceSetId());
1687 for (Component comp : comps)
1689 if (comp instanceof AlignmentPanel)
1691 if (al == ((AlignmentPanel) comp).av.getAlignment())
1693 originalSource = ((AlignmentPanel) comp).av;
1700 if (originalSource == null)
1702 // The original view is closed, we must validate
1703 // the current view against the closed view first
1706 PaintRefresher.validateSequences(al, viewport.getAlignment());
1709 originalSource = viewport;
1712 return originalSource;
1721 public void moveSelectedSequences(boolean up)
1723 SequenceGroup sg = viewport.getSelectionGroup();
1729 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1730 viewport.getHiddenRepSequences(), up);
1731 alignPanel.paintAlignment(true, false);
1734 synchronized void slideSequences(boolean right, int size)
1736 List<SequenceI> sg = new ArrayList<>();
1737 if (viewport.cursorMode)
1739 sg.add(viewport.getAlignment()
1740 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1742 else if (viewport.getSelectionGroup() != null
1743 && viewport.getSelectionGroup().getSize() != viewport
1744 .getAlignment().getHeight())
1746 sg = viewport.getSelectionGroup()
1747 .getSequences(viewport.getHiddenRepSequences());
1755 List<SequenceI> invertGroup = new ArrayList<>();
1757 for (SequenceI seq : viewport.getAlignment().getSequences())
1759 if (!sg.contains(seq))
1761 invertGroup.add(seq);
1765 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1767 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1768 for (int i = 0; i < invertGroup.size(); i++)
1770 seqs2[i] = invertGroup.get(i);
1773 SlideSequencesCommand ssc;
1776 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1777 viewport.getGapCharacter());
1781 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1782 viewport.getGapCharacter());
1785 int groupAdjustment = 0;
1786 if (ssc.getGapsInsertedBegin() && right)
1788 if (viewport.cursorMode)
1790 alignPanel.getSeqPanel().moveCursor(size, 0);
1794 groupAdjustment = size;
1797 else if (!ssc.getGapsInsertedBegin() && !right)
1799 if (viewport.cursorMode)
1801 alignPanel.getSeqPanel().moveCursor(-size, 0);
1805 groupAdjustment = -size;
1809 if (groupAdjustment != 0)
1811 viewport.getSelectionGroup().setStartRes(
1812 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1813 viewport.getSelectionGroup().setEndRes(
1814 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1818 * just extend the last slide command if compatible; but not if in
1819 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1821 boolean appendHistoryItem = false;
1822 Deque<CommandI> historyList = viewport.getHistoryList();
1823 boolean inSplitFrame = getSplitViewContainer() != null;
1824 if (!inSplitFrame && historyList != null && historyList.size() > 0
1825 && historyList.peek() instanceof SlideSequencesCommand)
1827 appendHistoryItem = ssc.appendSlideCommand(
1828 (SlideSequencesCommand) historyList.peek());
1831 if (!appendHistoryItem)
1833 addHistoryItem(ssc);
1846 protected void copy_actionPerformed(ActionEvent e)
1848 if (viewport.getSelectionGroup() == null)
1852 // TODO: preserve the ordering of displayed alignment annotation in any
1853 // internal paste (particularly sequence associated annotation)
1854 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1855 String[] omitHidden = null;
1857 if (viewport.hasHiddenColumns())
1859 omitHidden = viewport.getViewAsString(true);
1862 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1863 seqs, omitHidden, null);
1865 StringSelection ss = new StringSelection(output);
1869 jalview.gui.Desktop.internalCopy = true;
1870 // Its really worth setting the clipboard contents
1871 // to empty before setting the large StringSelection!!
1872 Toolkit.getDefaultToolkit().getSystemClipboard()
1873 .setContents(new StringSelection(""), null);
1875 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1877 } catch (OutOfMemoryError er)
1879 new OOMWarning("copying region", er);
1883 HiddenColumns hiddenColumns = null;
1884 if (viewport.hasHiddenColumns())
1886 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1887 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1889 // create new HiddenColumns object with copy of hidden regions
1890 // between startRes and endRes, offset by startRes
1891 hiddenColumns = new HiddenColumns(
1892 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1893 hiddenCutoff, hiddenOffset);
1896 Desktop.jalviewClipboard = new Object[] { seqs,
1897 viewport.getAlignment().getDataset(), hiddenColumns };
1898 statusBar.setText(MessageManager.formatMessage(
1899 "label.copied_sequences_to_clipboard", new Object[]
1900 { Integer.valueOf(seqs.length).toString() }));
1910 protected void pasteNew_actionPerformed(ActionEvent e)
1922 protected void pasteThis_actionPerformed(ActionEvent e)
1928 * Paste contents of Jalview clipboard
1930 * @param newAlignment
1931 * true to paste to a new alignment, otherwise add to this.
1933 void paste(boolean newAlignment)
1935 boolean externalPaste = true;
1938 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1939 Transferable contents = c.getContents(this);
1941 if (contents == null)
1950 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1951 if (str.length() < 1)
1956 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1958 } catch (OutOfMemoryError er)
1960 new OOMWarning("Out of memory pasting sequences!!", er);
1964 SequenceI[] sequences;
1965 boolean annotationAdded = false;
1966 AlignmentI alignment = null;
1968 if (Desktop.jalviewClipboard != null)
1970 // The clipboard was filled from within Jalview, we must use the
1972 // And dataset from the copied alignment
1973 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1974 // be doubly sure that we create *new* sequence objects.
1975 sequences = new SequenceI[newseq.length];
1976 for (int i = 0; i < newseq.length; i++)
1978 sequences[i] = new Sequence(newseq[i]);
1980 alignment = new Alignment(sequences);
1981 externalPaste = false;
1985 // parse the clipboard as an alignment.
1986 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1988 sequences = alignment.getSequencesArray();
1992 ArrayList<Integer> newGraphGroups = new ArrayList<>();
1998 if (Desktop.jalviewClipboard != null)
2000 // dataset is inherited
2001 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2005 // new dataset is constructed
2006 alignment.setDataset(null);
2008 alwidth = alignment.getWidth() + 1;
2012 AlignmentI pastedal = alignment; // preserve pasted alignment object
2013 // Add pasted sequences and dataset into existing alignment.
2014 alignment = viewport.getAlignment();
2015 alwidth = alignment.getWidth() + 1;
2016 // decide if we need to import sequences from an existing dataset
2017 boolean importDs = Desktop.jalviewClipboard != null
2018 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2019 // importDs==true instructs us to copy over new dataset sequences from
2020 // an existing alignment
2021 Vector newDs = (importDs) ? new Vector() : null; // used to create
2022 // minimum dataset set
2024 for (int i = 0; i < sequences.length; i++)
2028 newDs.addElement(null);
2030 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2032 if (importDs && ds != null)
2034 if (!newDs.contains(ds))
2036 newDs.setElementAt(ds, i);
2037 ds = new Sequence(ds);
2038 // update with new dataset sequence
2039 sequences[i].setDatasetSequence(ds);
2043 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2048 // copy and derive new dataset sequence
2049 sequences[i] = sequences[i].deriveSequence();
2050 alignment.getDataset()
2051 .addSequence(sequences[i].getDatasetSequence());
2052 // TODO: avoid creation of duplicate dataset sequences with a
2053 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2055 alignment.addSequence(sequences[i]); // merges dataset
2059 newDs.clear(); // tidy up
2061 if (alignment.getAlignmentAnnotation() != null)
2063 for (AlignmentAnnotation alan : alignment
2064 .getAlignmentAnnotation())
2066 if (alan.graphGroup > fgroup)
2068 fgroup = alan.graphGroup;
2072 if (pastedal.getAlignmentAnnotation() != null)
2074 // Add any annotation attached to alignment.
2075 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2076 for (int i = 0; i < alann.length; i++)
2078 annotationAdded = true;
2079 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2081 AlignmentAnnotation newann = new AlignmentAnnotation(
2083 if (newann.graphGroup > -1)
2085 if (newGraphGroups.size() <= newann.graphGroup
2086 || newGraphGroups.get(newann.graphGroup) == null)
2088 for (int q = newGraphGroups
2089 .size(); q <= newann.graphGroup; q++)
2091 newGraphGroups.add(q, null);
2093 newGraphGroups.set(newann.graphGroup,
2094 new Integer(++fgroup));
2096 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2100 newann.padAnnotation(alwidth);
2101 alignment.addAnnotation(newann);
2111 addHistoryItem(new EditCommand(
2112 MessageManager.getString("label.add_sequences"),
2113 Action.PASTE, sequences, 0, alignment.getWidth(),
2116 // Add any annotations attached to sequences
2117 for (int i = 0; i < sequences.length; i++)
2119 if (sequences[i].getAnnotation() != null)
2121 AlignmentAnnotation newann;
2122 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2124 annotationAdded = true;
2125 newann = sequences[i].getAnnotation()[a];
2126 newann.adjustForAlignment();
2127 newann.padAnnotation(alwidth);
2128 if (newann.graphGroup > -1)
2130 if (newann.graphGroup > -1)
2132 if (newGraphGroups.size() <= newann.graphGroup
2133 || newGraphGroups.get(newann.graphGroup) == null)
2135 for (int q = newGraphGroups
2136 .size(); q <= newann.graphGroup; q++)
2138 newGraphGroups.add(q, null);
2140 newGraphGroups.set(newann.graphGroup,
2141 new Integer(++fgroup));
2143 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2147 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2151 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2159 // propagate alignment changed.
2160 viewport.getRanges().setEndSeq(alignment.getHeight());
2161 if (annotationAdded)
2163 // Duplicate sequence annotation in all views.
2164 AlignmentI[] alview = this.getViewAlignments();
2165 for (int i = 0; i < sequences.length; i++)
2167 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2172 for (int avnum = 0; avnum < alview.length; avnum++)
2174 if (alview[avnum] != alignment)
2176 // duplicate in a view other than the one with input focus
2177 int avwidth = alview[avnum].getWidth() + 1;
2178 // this relies on sann being preserved after we
2179 // modify the sequence's annotation array for each duplication
2180 for (int a = 0; a < sann.length; a++)
2182 AlignmentAnnotation newann = new AlignmentAnnotation(
2184 sequences[i].addAlignmentAnnotation(newann);
2185 newann.padAnnotation(avwidth);
2186 alview[avnum].addAnnotation(newann); // annotation was
2187 // duplicated earlier
2188 // TODO JAL-1145 graphGroups are not updated for sequence
2189 // annotation added to several views. This may cause
2191 alview[avnum].setAnnotationIndex(newann, a);
2196 buildSortByAnnotationScoresMenu();
2198 viewport.firePropertyChange("alignment", null,
2199 alignment.getSequences());
2200 if (alignPanels != null)
2202 for (AlignmentPanel ap : alignPanels)
2204 ap.validateAnnotationDimensions(false);
2209 alignPanel.validateAnnotationDimensions(false);
2215 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2217 String newtitle = new String("Copied sequences");
2219 if (Desktop.jalviewClipboard != null
2220 && Desktop.jalviewClipboard[2] != null)
2222 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2223 af.viewport.setHiddenColumns(hc);
2226 // >>>This is a fix for the moment, until a better solution is
2228 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2229 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2230 .getFeatureRenderer());
2232 // TODO: maintain provenance of an alignment, rather than just make the
2233 // title a concatenation of operations.
2236 if (title.startsWith("Copied sequences"))
2242 newtitle = newtitle.concat("- from " + title);
2247 newtitle = new String("Pasted sequences");
2250 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2255 } catch (Exception ex)
2257 ex.printStackTrace();
2258 System.out.println("Exception whilst pasting: " + ex);
2259 // could be anything being pasted in here
2265 protected void expand_newalign(ActionEvent e)
2269 AlignmentI alignment = AlignmentUtils
2270 .expandContext(getViewport().getAlignment(), -1);
2271 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2273 String newtitle = new String("Flanking alignment");
2275 if (Desktop.jalviewClipboard != null
2276 && Desktop.jalviewClipboard[2] != null)
2278 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2279 af.viewport.setHiddenColumns(hc);
2282 // >>>This is a fix for the moment, until a better solution is
2284 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2285 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2286 .getFeatureRenderer());
2288 // TODO: maintain provenance of an alignment, rather than just make the
2289 // title a concatenation of operations.
2291 if (title.startsWith("Copied sequences"))
2297 newtitle = newtitle.concat("- from " + title);
2301 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2303 } catch (Exception ex)
2305 ex.printStackTrace();
2306 System.out.println("Exception whilst pasting: " + ex);
2307 // could be anything being pasted in here
2308 } catch (OutOfMemoryError oom)
2310 new OOMWarning("Viewing flanking region of alignment", oom);
2321 protected void cut_actionPerformed(ActionEvent e)
2323 copy_actionPerformed(null);
2324 delete_actionPerformed(null);
2334 protected void delete_actionPerformed(ActionEvent evt)
2337 SequenceGroup sg = viewport.getSelectionGroup();
2344 * If the cut affects all sequences, warn, remove highlighted columns
2346 if (sg.getSize() == viewport.getAlignment().getHeight())
2348 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2349 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2350 if (isEntireAlignWidth)
2352 int confirm = JvOptionPane.showConfirmDialog(this,
2353 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2354 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2355 JvOptionPane.OK_CANCEL_OPTION);
2357 if (confirm == JvOptionPane.CANCEL_OPTION
2358 || confirm == JvOptionPane.CLOSED_OPTION)
2363 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2364 sg.getEndRes() + 1);
2366 SequenceI[] cut = sg.getSequences()
2367 .toArray(new SequenceI[sg.getSize()]);
2369 addHistoryItem(new EditCommand(
2370 MessageManager.getString("label.cut_sequences"), Action.CUT,
2371 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2372 viewport.getAlignment()));
2374 viewport.setSelectionGroup(null);
2375 viewport.sendSelection();
2376 viewport.getAlignment().deleteGroup(sg);
2378 viewport.firePropertyChange("alignment", null,
2379 viewport.getAlignment().getSequences());
2380 if (viewport.getAlignment().getHeight() < 1)
2384 this.setClosed(true);
2385 } catch (Exception ex)
2398 protected void deleteGroups_actionPerformed(ActionEvent e)
2400 if (avc.deleteGroups())
2402 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2403 alignPanel.updateAnnotation();
2404 alignPanel.paintAlignment(true, true);
2415 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2417 SequenceGroup sg = new SequenceGroup(
2418 viewport.getAlignment().getSequences());
2420 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2421 viewport.setSelectionGroup(sg);
2422 viewport.isSelectionGroupChanged(true);
2423 viewport.sendSelection();
2424 // JAL-2034 - should delegate to
2425 // alignPanel to decide if overview needs
2427 alignPanel.paintAlignment(false, false);
2428 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2438 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2440 if (viewport.cursorMode)
2442 alignPanel.getSeqPanel().keyboardNo1 = null;
2443 alignPanel.getSeqPanel().keyboardNo2 = null;
2445 viewport.setSelectionGroup(null);
2446 viewport.getColumnSelection().clear();
2447 viewport.setSelectionGroup(null);
2448 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2449 // JAL-2034 - should delegate to
2450 // alignPanel to decide if overview needs
2452 alignPanel.paintAlignment(false, false);
2453 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2454 viewport.sendSelection();
2464 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2466 SequenceGroup sg = viewport.getSelectionGroup();
2470 selectAllSequenceMenuItem_actionPerformed(null);
2475 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2477 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2479 // JAL-2034 - should delegate to
2480 // alignPanel to decide if overview needs
2483 alignPanel.paintAlignment(true, false);
2484 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2485 viewport.sendSelection();
2489 public void invertColSel_actionPerformed(ActionEvent e)
2491 viewport.invertColumnSelection();
2492 alignPanel.paintAlignment(true, false);
2493 viewport.sendSelection();
2503 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2505 trimAlignment(true);
2515 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2517 trimAlignment(false);
2520 void trimAlignment(boolean trimLeft)
2522 ColumnSelection colSel = viewport.getColumnSelection();
2525 if (!colSel.isEmpty())
2529 column = colSel.getMin();
2533 column = colSel.getMax();
2537 if (viewport.getSelectionGroup() != null)
2539 seqs = viewport.getSelectionGroup()
2540 .getSequencesAsArray(viewport.getHiddenRepSequences());
2544 seqs = viewport.getAlignment().getSequencesArray();
2547 TrimRegionCommand trimRegion;
2550 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2551 column, viewport.getAlignment());
2552 viewport.getRanges().setStartRes(0);
2556 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2557 column, viewport.getAlignment());
2560 statusBar.setText(MessageManager
2561 .formatMessage("label.removed_columns", new String[]
2562 { Integer.valueOf(trimRegion.getSize()).toString() }));
2564 addHistoryItem(trimRegion);
2566 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2568 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2569 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2571 viewport.getAlignment().deleteGroup(sg);
2575 viewport.firePropertyChange("alignment", null,
2576 viewport.getAlignment().getSequences());
2587 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2589 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2592 if (viewport.getSelectionGroup() != null)
2594 seqs = viewport.getSelectionGroup()
2595 .getSequencesAsArray(viewport.getHiddenRepSequences());
2596 start = viewport.getSelectionGroup().getStartRes();
2597 end = viewport.getSelectionGroup().getEndRes();
2601 seqs = viewport.getAlignment().getSequencesArray();
2604 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2605 "Remove Gapped Columns", seqs, start, end,
2606 viewport.getAlignment());
2608 addHistoryItem(removeGapCols);
2610 statusBar.setText(MessageManager
2611 .formatMessage("label.removed_empty_columns", new Object[]
2612 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2614 // This is to maintain viewport position on first residue
2615 // of first sequence
2616 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2617 ViewportRanges ranges = viewport.getRanges();
2618 int startRes = seq.findPosition(ranges.getStartRes());
2619 // ShiftList shifts;
2620 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2621 // edit.alColumnChanges=shifts.getInverse();
2622 // if (viewport.hasHiddenColumns)
2623 // viewport.getColumnSelection().compensateForEdits(shifts);
2624 ranges.setStartRes(seq.findIndex(startRes) - 1);
2625 viewport.firePropertyChange("alignment", null,
2626 viewport.getAlignment().getSequences());
2637 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2639 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2642 if (viewport.getSelectionGroup() != null)
2644 seqs = viewport.getSelectionGroup()
2645 .getSequencesAsArray(viewport.getHiddenRepSequences());
2646 start = viewport.getSelectionGroup().getStartRes();
2647 end = viewport.getSelectionGroup().getEndRes();
2651 seqs = viewport.getAlignment().getSequencesArray();
2654 // This is to maintain viewport position on first residue
2655 // of first sequence
2656 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2657 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2659 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2660 viewport.getAlignment()));
2662 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2664 viewport.firePropertyChange("alignment", null,
2665 viewport.getAlignment().getSequences());
2676 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2678 viewport.setPadGaps(padGapsMenuitem.isSelected());
2679 viewport.firePropertyChange("alignment", null,
2680 viewport.getAlignment().getSequences());
2690 public void findMenuItem_actionPerformed(ActionEvent e)
2696 * Create a new view of the current alignment.
2699 public void newView_actionPerformed(ActionEvent e)
2701 newView(null, true);
2705 * Creates and shows a new view of the current alignment.
2708 * title of newly created view; if null, one will be generated
2709 * @param copyAnnotation
2710 * if true then duplicate all annnotation, groups and settings
2711 * @return new alignment panel, already displayed.
2713 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2716 * Create a new AlignmentPanel (with its own, new Viewport)
2718 AlignmentPanel newap = new jalview.project.Jalview2XML()
2719 .copyAlignPanel(alignPanel);
2720 if (!copyAnnotation)
2723 * remove all groups and annotation except for the automatic stuff
2725 newap.av.getAlignment().deleteAllGroups();
2726 newap.av.getAlignment().deleteAllAnnotations(false);
2729 newap.av.setGatherViewsHere(false);
2731 if (viewport.getViewName() == null)
2733 viewport.setViewName(MessageManager
2734 .getString("label.view_name_original"));
2738 * Views share the same edits undo and redo stacks
2740 newap.av.setHistoryList(viewport.getHistoryList());
2741 newap.av.setRedoList(viewport.getRedoList());
2744 * copy any visualisation settings that are not saved in the project
2746 newap.av.setColourAppliesToAllGroups(
2747 viewport.getColourAppliesToAllGroups());
2750 * Views share the same mappings; need to deregister any new mappings
2751 * created by copyAlignPanel, and register the new reference to the shared
2754 newap.av.replaceMappings(viewport.getAlignment());
2757 * start up cDNA consensus (if applicable) now mappings are in place
2759 if (newap.av.initComplementConsensus())
2761 newap.refresh(true); // adjust layout of annotations
2764 newap.av.setViewName(getNewViewName(viewTitle));
2766 addAlignmentPanel(newap, true);
2767 newap.alignmentChanged();
2769 if (alignPanels.size() == 2)
2771 viewport.setGatherViewsHere(true);
2773 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2778 * Make a new name for the view, ensuring it is unique within the current
2779 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2780 * these now use viewId. Unique view names are still desirable for usability.)
2785 protected String getNewViewName(String viewTitle)
2787 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2788 boolean addFirstIndex = false;
2789 if (viewTitle == null || viewTitle.trim().length() == 0)
2791 viewTitle = MessageManager.getString("action.view");
2792 addFirstIndex = true;
2796 index = 1;// we count from 1 if given a specific name
2798 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2800 List<Component> comps = PaintRefresher.components
2801 .get(viewport.getSequenceSetId());
2803 List<String> existingNames = getExistingViewNames(comps);
2805 while (existingNames.contains(newViewName))
2807 newViewName = viewTitle + " " + (++index);
2813 * Returns a list of distinct view names found in the given list of
2814 * components. View names are held on the viewport of an AlignmentPanel.
2819 protected List<String> getExistingViewNames(List<Component> comps)
2821 List<String> existingNames = new ArrayList<>();
2822 for (Component comp : comps)
2824 if (comp instanceof AlignmentPanel)
2826 AlignmentPanel ap = (AlignmentPanel) comp;
2827 if (!existingNames.contains(ap.av.getViewName()))
2829 existingNames.add(ap.av.getViewName());
2833 return existingNames;
2837 * Explode tabbed views into separate windows.
2840 public void expandViews_actionPerformed(ActionEvent e)
2842 Desktop.explodeViews(this);
2846 * Gather views in separate windows back into a tabbed presentation.
2849 public void gatherViews_actionPerformed(ActionEvent e)
2851 Desktop.instance.gatherViews(this);
2861 public void font_actionPerformed(ActionEvent e)
2863 new FontChooser(alignPanel);
2873 protected void seqLimit_actionPerformed(ActionEvent e)
2875 viewport.setShowJVSuffix(seqLimits.isSelected());
2877 alignPanel.getIdPanel().getIdCanvas()
2878 .setPreferredSize(alignPanel.calculateIdWidth());
2879 alignPanel.paintAlignment(true, false);
2883 public void idRightAlign_actionPerformed(ActionEvent e)
2885 viewport.setRightAlignIds(idRightAlign.isSelected());
2886 alignPanel.paintAlignment(false, false);
2890 public void centreColumnLabels_actionPerformed(ActionEvent e)
2892 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2893 alignPanel.paintAlignment(false, false);
2899 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2902 protected void followHighlight_actionPerformed()
2905 * Set the 'follow' flag on the Viewport (and scroll to position if now
2908 final boolean state = this.followHighlightMenuItem.getState();
2909 viewport.setFollowHighlight(state);
2912 alignPanel.scrollToPosition(viewport.getSearchResults());
2923 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2925 viewport.setColourText(colourTextMenuItem.isSelected());
2926 alignPanel.paintAlignment(false, false);
2936 public void wrapMenuItem_actionPerformed(ActionEvent e)
2938 scaleAbove.setVisible(wrapMenuItem.isSelected());
2939 scaleLeft.setVisible(wrapMenuItem.isSelected());
2940 scaleRight.setVisible(wrapMenuItem.isSelected());
2941 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2942 alignPanel.updateLayout();
2946 public void showAllSeqs_actionPerformed(ActionEvent e)
2948 viewport.showAllHiddenSeqs();
2952 public void showAllColumns_actionPerformed(ActionEvent e)
2954 viewport.showAllHiddenColumns();
2955 alignPanel.paintAlignment(true, true);
2956 viewport.sendSelection();
2960 public void hideSelSequences_actionPerformed(ActionEvent e)
2962 viewport.hideAllSelectedSeqs();
2966 * called by key handler and the hide all/show all menu items
2971 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2974 boolean hide = false;
2975 SequenceGroup sg = viewport.getSelectionGroup();
2976 if (!toggleSeqs && !toggleCols)
2978 // Hide everything by the current selection - this is a hack - we do the
2979 // invert and then hide
2980 // first check that there will be visible columns after the invert.
2981 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2982 && sg.getStartRes() <= sg.getEndRes()))
2984 // now invert the sequence set, if required - empty selection implies
2985 // that no hiding is required.
2988 invertSequenceMenuItem_actionPerformed(null);
2989 sg = viewport.getSelectionGroup();
2993 viewport.expandColSelection(sg, true);
2994 // finally invert the column selection and get the new sequence
2996 invertColSel_actionPerformed(null);
3003 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3005 hideSelSequences_actionPerformed(null);
3008 else if (!(toggleCols && viewport.hasSelectedColumns()))
3010 showAllSeqs_actionPerformed(null);
3016 if (viewport.hasSelectedColumns())
3018 hideSelColumns_actionPerformed(null);
3021 viewport.setSelectionGroup(sg);
3026 showAllColumns_actionPerformed(null);
3035 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3036 * event.ActionEvent)
3039 public void hideAllButSelection_actionPerformed(ActionEvent e)
3041 toggleHiddenRegions(false, false);
3042 viewport.sendSelection();
3049 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3053 public void hideAllSelection_actionPerformed(ActionEvent e)
3055 SequenceGroup sg = viewport.getSelectionGroup();
3056 viewport.expandColSelection(sg, false);
3057 viewport.hideAllSelectedSeqs();
3058 viewport.hideSelectedColumns();
3059 alignPanel.updateLayout();
3060 alignPanel.paintAlignment(true, true);
3061 viewport.sendSelection();
3068 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3072 public void showAllhidden_actionPerformed(ActionEvent e)
3074 viewport.showAllHiddenColumns();
3075 viewport.showAllHiddenSeqs();
3076 alignPanel.paintAlignment(true, true);
3077 viewport.sendSelection();
3081 public void hideSelColumns_actionPerformed(ActionEvent e)
3083 viewport.hideSelectedColumns();
3084 alignPanel.updateLayout();
3085 alignPanel.paintAlignment(true, true);
3086 viewport.sendSelection();
3090 public void hiddenMarkers_actionPerformed(ActionEvent e)
3092 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3103 protected void scaleAbove_actionPerformed(ActionEvent e)
3105 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3106 alignPanel.updateLayout();
3107 alignPanel.paintAlignment(true, false);
3117 protected void scaleLeft_actionPerformed(ActionEvent e)
3119 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3120 alignPanel.updateLayout();
3121 alignPanel.paintAlignment(true, false);
3131 protected void scaleRight_actionPerformed(ActionEvent e)
3133 viewport.setScaleRightWrapped(scaleRight.isSelected());
3134 alignPanel.updateLayout();
3135 alignPanel.paintAlignment(true, false);
3145 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3147 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3148 alignPanel.paintAlignment(false, false);
3158 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3160 viewport.setShowText(viewTextMenuItem.isSelected());
3161 alignPanel.paintAlignment(false, false);
3171 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3173 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3174 alignPanel.paintAlignment(false, false);
3177 public FeatureSettings featureSettings;
3180 public FeatureSettingsControllerI getFeatureSettingsUI()
3182 return featureSettings;
3186 public void featureSettings_actionPerformed(ActionEvent e)
3188 if (featureSettings != null)
3190 featureSettings.close();
3191 featureSettings = null;
3193 if (!showSeqFeatures.isSelected())
3195 // make sure features are actually displayed
3196 showSeqFeatures.setSelected(true);
3197 showSeqFeatures_actionPerformed(null);
3199 featureSettings = new FeatureSettings(this);
3203 * Set or clear 'Show Sequence Features'
3209 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3211 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3212 alignPanel.paintAlignment(true, true);
3216 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3217 * the annotations panel as a whole.
3219 * The options to show/hide all annotations should be enabled when the panel
3220 * is shown, and disabled when the panel is hidden.
3225 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3227 final boolean setVisible = annotationPanelMenuItem.isSelected();
3228 viewport.setShowAnnotation(setVisible);
3229 this.showAllSeqAnnotations.setEnabled(setVisible);
3230 this.hideAllSeqAnnotations.setEnabled(setVisible);
3231 this.showAllAlAnnotations.setEnabled(setVisible);
3232 this.hideAllAlAnnotations.setEnabled(setVisible);
3233 alignPanel.updateLayout();
3237 public void alignmentProperties()
3239 JEditorPane editPane = new JEditorPane("text/html", "");
3240 editPane.setEditable(false);
3241 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3244 MessageManager.formatMessage("label.html_content", new Object[]
3245 { contents.toString() }));
3246 JInternalFrame frame = new JInternalFrame();
3247 frame.getContentPane().add(new JScrollPane(editPane));
3249 Desktop.addInternalFrame(frame, MessageManager
3250 .formatMessage("label.alignment_properties", new Object[]
3251 { getTitle() }), 500, 400);
3261 public void overviewMenuItem_actionPerformed(ActionEvent e)
3263 if (alignPanel.overviewPanel != null)
3268 JInternalFrame frame = new JInternalFrame();
3269 final OverviewPanel overview = new OverviewPanel(alignPanel);
3270 frame.setContentPane(overview);
3271 Desktop.addInternalFrame(frame, MessageManager
3272 .formatMessage("label.overview_params", new Object[]
3273 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3276 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3277 frame.addInternalFrameListener(
3278 new javax.swing.event.InternalFrameAdapter()
3281 public void internalFrameClosed(
3282 javax.swing.event.InternalFrameEvent evt)
3285 alignPanel.setOverviewPanel(null);
3288 if (getKeyListeners().length > 0)
3290 frame.addKeyListener(getKeyListeners()[0]);
3293 alignPanel.setOverviewPanel(overview);
3297 public void textColour_actionPerformed()
3299 new TextColourChooser().chooseColour(alignPanel, null);
3303 * public void covariationColour_actionPerformed() {
3305 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3309 public void annotationColour_actionPerformed()
3311 new AnnotationColourChooser(viewport, alignPanel);
3315 public void annotationColumn_actionPerformed(ActionEvent e)
3317 new AnnotationColumnChooser(viewport, alignPanel);
3321 * Action on the user checking or unchecking the option to apply the selected
3322 * colour scheme to all groups. If unchecked, groups may have their own
3323 * independent colour schemes.
3328 public void applyToAllGroups_actionPerformed(boolean selected)
3330 viewport.setColourAppliesToAllGroups(selected);
3334 * Action on user selecting a colour from the colour menu
3337 * the name (not the menu item label!) of the colour scheme
3340 public void changeColour_actionPerformed(String name)
3343 * 'User Defined' opens a panel to configure or load a
3344 * user-defined colour scheme
3346 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3348 new UserDefinedColours(alignPanel);
3353 * otherwise set the chosen colour scheme (or null for 'None')
3355 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3357 viewport.getAlignment(), viewport.getHiddenRepSequences());
3362 * Actions on setting or changing the alignment colour scheme
3367 public void changeColour(ColourSchemeI cs)
3369 // TODO: pull up to controller method
3370 ColourMenuHelper.setColourSelected(colourMenu, cs);
3372 viewport.setGlobalColourScheme(cs);
3374 alignPanel.paintAlignment(true, true);
3378 * Show the PID threshold slider panel
3381 protected void modifyPID_actionPerformed()
3383 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3384 alignPanel.getViewName());
3385 SliderPanel.showPIDSlider();
3389 * Show the Conservation slider panel
3392 protected void modifyConservation_actionPerformed()
3394 SliderPanel.setConservationSlider(alignPanel,
3395 viewport.getResidueShading(), alignPanel.getViewName());
3396 SliderPanel.showConservationSlider();
3400 * Action on selecting or deselecting (Colour) By Conservation
3403 public void conservationMenuItem_actionPerformed(boolean selected)
3405 modifyConservation.setEnabled(selected);
3406 viewport.setConservationSelected(selected);
3407 viewport.getResidueShading().setConservationApplied(selected);
3409 changeColour(viewport.getGlobalColourScheme());
3412 modifyConservation_actionPerformed();
3416 SliderPanel.hideConservationSlider();
3421 * Action on selecting or deselecting (Colour) Above PID Threshold
3424 public void abovePIDThreshold_actionPerformed(boolean selected)
3426 modifyPID.setEnabled(selected);
3427 viewport.setAbovePIDThreshold(selected);
3430 viewport.getResidueShading().setThreshold(0,
3431 viewport.isIgnoreGapsConsensus());
3434 changeColour(viewport.getGlobalColourScheme());
3437 modifyPID_actionPerformed();
3441 SliderPanel.hidePIDSlider();
3452 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3454 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3455 AlignmentSorter.sortByPID(viewport.getAlignment(),
3456 viewport.getAlignment().getSequenceAt(0));
3457 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3458 viewport.getAlignment()));
3459 alignPanel.paintAlignment(true, false);
3469 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3471 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3472 AlignmentSorter.sortByID(viewport.getAlignment());
3474 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3475 alignPanel.paintAlignment(true, false);
3485 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3487 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3488 AlignmentSorter.sortByLength(viewport.getAlignment());
3489 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3490 viewport.getAlignment()));
3491 alignPanel.paintAlignment(true, false);
3501 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3503 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3504 AlignmentSorter.sortByGroup(viewport.getAlignment());
3505 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3506 viewport.getAlignment()));
3508 alignPanel.paintAlignment(true, false);
3518 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3520 new RedundancyPanel(alignPanel, this);
3530 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3532 if ((viewport.getSelectionGroup() == null)
3533 || (viewport.getSelectionGroup().getSize() < 2))
3535 JvOptionPane.showInternalMessageDialog(this,
3536 MessageManager.getString(
3537 "label.you_must_select_least_two_sequences"),
3538 MessageManager.getString("label.invalid_selection"),
3539 JvOptionPane.WARNING_MESSAGE);
3543 JInternalFrame frame = new JInternalFrame();
3544 frame.setContentPane(new PairwiseAlignPanel(viewport));
3545 Desktop.addInternalFrame(frame,
3546 MessageManager.getString("action.pairwise_alignment"), 600,
3552 public void autoCalculate_actionPerformed(ActionEvent e)
3554 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3555 if (viewport.autoCalculateConsensus)
3557 viewport.firePropertyChange("alignment", null,
3558 viewport.getAlignment().getSequences());
3563 public void sortByTreeOption_actionPerformed(ActionEvent e)
3565 viewport.sortByTree = sortByTree.isSelected();
3569 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3571 viewport.followSelection = listenToViewSelections.isSelected();
3575 * Constructs a tree panel and adds it to the desktop
3578 * tree type (NJ or AV)
3580 * name of score model used to compute the tree
3582 * parameters for the distance or similarity calculation
3584 void newTreePanel(String type, String modelName,
3585 SimilarityParamsI options)
3587 String frameTitle = "";
3590 boolean onSelection = false;
3591 if (viewport.getSelectionGroup() != null
3592 && viewport.getSelectionGroup().getSize() > 0)
3594 SequenceGroup sg = viewport.getSelectionGroup();
3596 /* Decide if the selection is a column region */
3597 for (SequenceI _s : sg.getSequences())
3599 if (_s.getLength() < sg.getEndRes())
3601 JvOptionPane.showMessageDialog(Desktop.desktop,
3602 MessageManager.getString(
3603 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3604 MessageManager.getString(
3605 "label.sequences_selection_not_aligned"),
3606 JvOptionPane.WARNING_MESSAGE);
3615 if (viewport.getAlignment().getHeight() < 2)
3621 tp = new TreePanel(alignPanel, type, modelName, options);
3622 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3624 frameTitle += " from ";
3626 if (viewport.getViewName() != null)
3628 frameTitle += viewport.getViewName() + " of ";
3631 frameTitle += this.title;
3633 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3644 public void addSortByOrderMenuItem(String title,
3645 final AlignmentOrder order)
3647 final JMenuItem item = new JMenuItem(MessageManager
3648 .formatMessage("action.by_title_param", new Object[]
3651 item.addActionListener(new java.awt.event.ActionListener()
3654 public void actionPerformed(ActionEvent e)
3656 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3658 // TODO: JBPNote - have to map order entries to curent SequenceI
3660 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3662 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3663 viewport.getAlignment()));
3665 alignPanel.paintAlignment(true, false);
3671 * Add a new sort by annotation score menu item
3674 * the menu to add the option to
3676 * the label used to retrieve scores for each sequence on the
3679 public void addSortByAnnotScoreMenuItem(JMenu sort,
3680 final String scoreLabel)
3682 final JMenuItem item = new JMenuItem(scoreLabel);
3684 item.addActionListener(new java.awt.event.ActionListener()
3687 public void actionPerformed(ActionEvent e)
3689 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3690 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3691 viewport.getAlignment());// ,viewport.getSelectionGroup());
3692 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3693 viewport.getAlignment()));
3694 alignPanel.paintAlignment(true, false);
3700 * last hash for alignment's annotation array - used to minimise cost of
3703 protected int _annotationScoreVectorHash;
3706 * search the alignment and rebuild the sort by annotation score submenu the
3707 * last alignment annotation vector hash is stored to minimize cost of
3708 * rebuilding in subsequence calls.
3712 public void buildSortByAnnotationScoresMenu()
3714 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3719 if (viewport.getAlignment().getAlignmentAnnotation()
3720 .hashCode() != _annotationScoreVectorHash)
3722 sortByAnnotScore.removeAll();
3723 // almost certainly a quicker way to do this - but we keep it simple
3724 Hashtable scoreSorts = new Hashtable();
3725 AlignmentAnnotation aann[];
3726 for (SequenceI sqa : viewport.getAlignment().getSequences())
3728 aann = sqa.getAnnotation();
3729 for (int i = 0; aann != null && i < aann.length; i++)
3731 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3733 scoreSorts.put(aann[i].label, aann[i].label);
3737 Enumeration labels = scoreSorts.keys();
3738 while (labels.hasMoreElements())
3740 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3741 (String) labels.nextElement());
3743 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3746 _annotationScoreVectorHash = viewport.getAlignment()
3747 .getAlignmentAnnotation().hashCode();
3752 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3753 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3754 * call. Listeners are added to remove the menu item when the treePanel is
3755 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3759 public void buildTreeSortMenu()
3761 sortByTreeMenu.removeAll();
3763 List<Component> comps = PaintRefresher.components
3764 .get(viewport.getSequenceSetId());
3765 List<TreePanel> treePanels = new ArrayList<>();
3766 for (Component comp : comps)
3768 if (comp instanceof TreePanel)
3770 treePanels.add((TreePanel) comp);
3774 if (treePanels.size() < 1)
3776 sortByTreeMenu.setVisible(false);
3780 sortByTreeMenu.setVisible(true);
3782 for (final TreePanel tp : treePanels)
3784 final JMenuItem item = new JMenuItem(tp.getTitle());
3785 item.addActionListener(new java.awt.event.ActionListener()
3788 public void actionPerformed(ActionEvent e)
3790 tp.sortByTree_actionPerformed();
3791 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3796 sortByTreeMenu.add(item);
3800 public boolean sortBy(AlignmentOrder alorder, String undoname)
3802 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3803 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3804 if (undoname != null)
3806 addHistoryItem(new OrderCommand(undoname, oldOrder,
3807 viewport.getAlignment()));
3809 alignPanel.paintAlignment(true, false);
3814 * Work out whether the whole set of sequences or just the selected set will
3815 * be submitted for multiple alignment.
3818 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3820 // Now, check we have enough sequences
3821 AlignmentView msa = null;
3823 if ((viewport.getSelectionGroup() != null)
3824 && (viewport.getSelectionGroup().getSize() > 1))
3826 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3827 // some common interface!
3829 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3830 * SequenceI[sz = seqs.getSize(false)];
3832 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3833 * seqs.getSequenceAt(i); }
3835 msa = viewport.getAlignmentView(true);
3837 else if (viewport.getSelectionGroup() != null
3838 && viewport.getSelectionGroup().getSize() == 1)
3840 int option = JvOptionPane.showConfirmDialog(this,
3841 MessageManager.getString("warn.oneseq_msainput_selection"),
3842 MessageManager.getString("label.invalid_selection"),
3843 JvOptionPane.OK_CANCEL_OPTION);
3844 if (option == JvOptionPane.OK_OPTION)
3846 msa = viewport.getAlignmentView(false);
3851 msa = viewport.getAlignmentView(false);
3857 * Decides what is submitted to a secondary structure prediction service: the
3858 * first sequence in the alignment, or in the current selection, or, if the
3859 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3860 * region or the whole alignment. (where the first sequence in the set is the
3861 * one that the prediction will be for).
3863 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3865 AlignmentView seqs = null;
3867 if ((viewport.getSelectionGroup() != null)
3868 && (viewport.getSelectionGroup().getSize() > 0))
3870 seqs = viewport.getAlignmentView(true);
3874 seqs = viewport.getAlignmentView(false);
3876 // limit sequences - JBPNote in future - could spawn multiple prediction
3878 // TODO: viewport.getAlignment().isAligned is a global state - the local
3879 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3880 if (!viewport.getAlignment().isAligned(false))
3882 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3883 // TODO: if seqs.getSequences().length>1 then should really have warned
3897 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3899 // Pick the tree file
3900 JalviewFileChooser chooser = new JalviewFileChooser(
3901 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3902 chooser.setFileView(new JalviewFileView());
3903 chooser.setDialogTitle(
3904 MessageManager.getString("label.select_newick_like_tree_file"));
3905 chooser.setToolTipText(
3906 MessageManager.getString("label.load_tree_file"));
3908 int value = chooser.showOpenDialog(null);
3910 if (value == JalviewFileChooser.APPROVE_OPTION)
3912 String filePath = chooser.getSelectedFile().getPath();
3913 Cache.setProperty("LAST_DIRECTORY", filePath);
3914 NewickFile fin = null;
3917 fin = new NewickFile(filePath, DataSourceType.FILE);
3918 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3919 } catch (Exception ex)
3921 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3922 MessageManager.getString("label.problem_reading_tree_file"),
3923 JvOptionPane.WARNING_MESSAGE);
3924 ex.printStackTrace();
3926 if (fin != null && fin.hasWarningMessage())
3928 JvOptionPane.showMessageDialog(Desktop.desktop,
3929 fin.getWarningMessage(),
3931 .getString("label.possible_problem_with_tree_file"),
3932 JvOptionPane.WARNING_MESSAGE);
3937 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3939 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3942 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3943 int h, int x, int y)
3945 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3949 * Add a treeviewer for the tree extracted from a Newick file object to the
3950 * current alignment view
3957 * Associated alignment input data (or null)
3966 * @return TreePanel handle
3968 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3969 AlignmentView input, int w, int h, int x, int y)
3971 TreePanel tp = null;
3977 if (nf.getTree() != null)
3979 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3985 tp.setLocation(x, y);
3988 Desktop.addInternalFrame(tp, treeTitle, w, h);
3990 } catch (Exception ex)
3992 ex.printStackTrace();
3998 private boolean buildingMenu = false;
4001 * Generates menu items and listener event actions for web service clients
4004 public void BuildWebServiceMenu()
4006 while (buildingMenu)
4010 System.err.println("Waiting for building menu to finish.");
4012 } catch (Exception e)
4016 final AlignFrame me = this;
4017 buildingMenu = true;
4018 new Thread(new Runnable()
4023 final List<JMenuItem> legacyItems = new ArrayList<>();
4026 // System.err.println("Building ws menu again "
4027 // + Thread.currentThread());
4028 // TODO: add support for context dependent disabling of services based
4030 // alignment and current selection
4031 // TODO: add additional serviceHandle parameter to specify abstract
4033 // class independently of AbstractName
4034 // TODO: add in rediscovery GUI function to restart discoverer
4035 // TODO: group services by location as well as function and/or
4037 // object broker mechanism.
4038 final Vector<JMenu> wsmenu = new Vector<>();
4039 final IProgressIndicator af = me;
4042 * do not i18n these strings - they are hard-coded in class
4043 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4044 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4046 final JMenu msawsmenu = new JMenu("Alignment");
4047 final JMenu secstrmenu = new JMenu(
4048 "Secondary Structure Prediction");
4049 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4050 final JMenu analymenu = new JMenu("Analysis");
4051 final JMenu dismenu = new JMenu("Protein Disorder");
4052 // JAL-940 - only show secondary structure prediction services from
4053 // the legacy server
4054 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4056 Discoverer.services != null && (Discoverer.services.size() > 0))
4058 // TODO: refactor to allow list of AbstractName/Handler bindings to
4060 // stored or retrieved from elsewhere
4061 // No MSAWS used any more:
4062 // Vector msaws = null; // (Vector)
4063 // Discoverer.services.get("MsaWS");
4064 Vector secstrpr = (Vector) Discoverer.services
4066 if (secstrpr != null)
4068 // Add any secondary structure prediction services
4069 for (int i = 0, j = secstrpr.size(); i < j; i++)
4071 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4073 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4074 .getServiceClient(sh);
4075 int p = secstrmenu.getItemCount();
4076 impl.attachWSMenuEntry(secstrmenu, me);
4077 int q = secstrmenu.getItemCount();
4078 for (int litm = p; litm < q; litm++)
4080 legacyItems.add(secstrmenu.getItem(litm));
4086 // Add all submenus in the order they should appear on the web
4088 wsmenu.add(msawsmenu);
4089 wsmenu.add(secstrmenu);
4090 wsmenu.add(dismenu);
4091 wsmenu.add(analymenu);
4092 // No search services yet
4093 // wsmenu.add(seqsrchmenu);
4095 javax.swing.SwingUtilities.invokeLater(new Runnable()
4102 webService.removeAll();
4103 // first, add discovered services onto the webservices menu
4104 if (wsmenu.size() > 0)
4106 for (int i = 0, j = wsmenu.size(); i < j; i++)
4108 webService.add(wsmenu.get(i));
4113 webService.add(me.webServiceNoServices);
4115 // TODO: move into separate menu builder class.
4116 boolean new_sspred = false;
4117 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4119 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4120 if (jws2servs != null)
4122 if (jws2servs.hasServices())
4124 jws2servs.attachWSMenuEntry(webService, me);
4125 for (Jws2Instance sv : jws2servs.getServices())
4127 if (sv.description.toLowerCase().contains("jpred"))
4129 for (JMenuItem jmi : legacyItems)
4131 jmi.setVisible(false);
4137 if (jws2servs.isRunning())
4139 JMenuItem tm = new JMenuItem(
4140 "Still discovering JABA Services");
4141 tm.setEnabled(false);
4146 build_urlServiceMenu(me.webService);
4147 build_fetchdbmenu(webService);
4148 for (JMenu item : wsmenu)
4150 if (item.getItemCount() == 0)
4152 item.setEnabled(false);
4156 item.setEnabled(true);
4159 } catch (Exception e)
4162 "Exception during web service menu building process.",
4167 } catch (Exception e)
4170 buildingMenu = false;
4177 * construct any groupURL type service menu entries.
4181 private void build_urlServiceMenu(JMenu webService)
4183 // TODO: remove this code when 2.7 is released
4184 // DEBUG - alignmentView
4186 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4187 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4189 * @Override public void actionPerformed(ActionEvent e) {
4190 * jalview.datamodel.AlignmentView
4191 * .testSelectionViews(af.viewport.getAlignment(),
4192 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4194 * }); webService.add(testAlView);
4196 // TODO: refactor to RestClient discoverer and merge menu entries for
4197 // rest-style services with other types of analysis/calculation service
4198 // SHmmr test client - still being implemented.
4199 // DEBUG - alignmentView
4201 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4204 client.attachWSMenuEntry(
4205 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4211 * Searches the alignment sequences for xRefs and builds the Show
4212 * Cross-References menu (formerly called Show Products), with database
4213 * sources for which cross-references are found (protein sources for a
4214 * nucleotide alignment and vice versa)
4216 * @return true if Show Cross-references menu should be enabled
4218 public boolean canShowProducts()
4220 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4221 AlignmentI dataset = viewport.getAlignment().getDataset();
4223 showProducts.removeAll();
4224 final boolean dna = viewport.getAlignment().isNucleotide();
4226 if (seqs == null || seqs.length == 0)
4228 // nothing to see here.
4232 boolean showp = false;
4235 List<String> ptypes = new CrossRef(seqs, dataset)
4236 .findXrefSourcesForSequences(dna);
4238 for (final String source : ptypes)
4241 final AlignFrame af = this;
4242 JMenuItem xtype = new JMenuItem(source);
4243 xtype.addActionListener(new ActionListener()
4246 public void actionPerformed(ActionEvent e)
4248 showProductsFor(af.viewport.getSequenceSelection(), dna,
4252 showProducts.add(xtype);
4254 showProducts.setVisible(showp);
4255 showProducts.setEnabled(showp);
4256 } catch (Exception e)
4259 "canShowProducts threw an exception - please report to help@jalview.org",
4267 * Finds and displays cross-references for the selected sequences (protein
4268 * products for nucleotide sequences, dna coding sequences for peptides).
4271 * the sequences to show cross-references for
4273 * true if from a nucleotide alignment (so showing proteins)
4275 * the database to show cross-references for
4277 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4278 final String source)
4280 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4285 * Construct and display a new frame containing the translation of this
4286 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4289 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4291 AlignmentI al = null;
4294 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4296 al = dna.translateCdna(codeTable);
4297 } catch (Exception ex)
4299 jalview.bin.Cache.log.error(
4300 "Exception during translation. Please report this !", ex);
4301 final String msg = MessageManager.getString(
4302 "label.error_when_translating_sequences_submit_bug_report");
4303 final String errorTitle = MessageManager
4304 .getString("label.implementation_error")
4305 + MessageManager.getString("label.translation_failed");
4306 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4307 JvOptionPane.ERROR_MESSAGE);
4310 if (al == null || al.getHeight() == 0)
4312 final String msg = MessageManager.getString(
4313 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4314 final String errorTitle = MessageManager
4315 .getString("label.translation_failed");
4316 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4317 JvOptionPane.WARNING_MESSAGE);
4321 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4322 af.setFileFormat(this.currentFileFormat);
4323 final String newTitle = MessageManager
4324 .formatMessage("label.translation_of_params", new Object[]
4325 { this.getTitle(), codeTable.getId() });
4326 af.setTitle(newTitle);
4327 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4329 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4330 viewport.openSplitFrame(af, new Alignment(seqs));
4334 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4341 * Set the file format
4345 public void setFileFormat(FileFormatI format)
4347 this.currentFileFormat = format;
4351 * Try to load a features file onto the alignment.
4354 * contents or path to retrieve file
4356 * access mode of file (see jalview.io.AlignFile)
4357 * @return true if features file was parsed correctly.
4359 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4361 return avc.parseFeaturesFile(file, sourceType,
4362 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4367 public void refreshFeatureUI(boolean enableIfNecessary)
4369 // note - currently this is only still here rather than in the controller
4370 // because of the featureSettings hard reference that is yet to be
4372 if (enableIfNecessary)
4374 viewport.setShowSequenceFeatures(true);
4375 showSeqFeatures.setSelected(true);
4381 public void dragEnter(DropTargetDragEvent evt)
4386 public void dragExit(DropTargetEvent evt)
4391 public void dragOver(DropTargetDragEvent evt)
4396 public void dropActionChanged(DropTargetDragEvent evt)
4401 public void drop(DropTargetDropEvent evt)
4403 // JAL-1552 - acceptDrop required before getTransferable call for
4404 // Java's Transferable for native dnd
4405 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4406 Transferable t = evt.getTransferable();
4407 final AlignFrame thisaf = this;
4408 final List<String> files = new ArrayList<>();
4409 List<DataSourceType> protocols = new ArrayList<>();
4413 Desktop.transferFromDropTarget(files, protocols, evt, t);
4414 } catch (Exception e)
4416 e.printStackTrace();
4420 new Thread(new Runnable()
4427 // check to see if any of these files have names matching sequences
4430 SequenceIdMatcher idm = new SequenceIdMatcher(
4431 viewport.getAlignment().getSequencesArray());
4433 * Object[] { String,SequenceI}
4435 ArrayList<Object[]> filesmatched = new ArrayList<>();
4436 ArrayList<String> filesnotmatched = new ArrayList<>();
4437 for (int i = 0; i < files.size(); i++)
4439 String file = files.get(i).toString();
4441 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4442 if (protocol == DataSourceType.FILE)
4444 File fl = new File(file);
4445 pdbfn = fl.getName();
4447 else if (protocol == DataSourceType.URL)
4449 URL url = new URL(file);
4450 pdbfn = url.getFile();
4452 if (pdbfn.length() > 0)
4454 // attempt to find a match in the alignment
4455 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4456 int l = 0, c = pdbfn.indexOf(".");
4457 while (mtch == null && c != -1)
4462 } while ((c = pdbfn.indexOf(".", l)) > l);
4465 pdbfn = pdbfn.substring(0, l);
4467 mtch = idm.findAllIdMatches(pdbfn);
4471 FileFormatI type = null;
4474 type = new IdentifyFile().identify(file, protocol);
4475 } catch (Exception ex)
4479 if (type != null && type.isStructureFile())
4481 filesmatched.add(new Object[] { file, protocol, mtch });
4485 // File wasn't named like one of the sequences or wasn't a PDB
4487 filesnotmatched.add(file);
4491 if (filesmatched.size() > 0)
4493 boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4496 String msg = MessageManager.formatMessage(
4497 "label.automatically_associate_structure_files_with_sequences_same_name",
4499 { Integer.valueOf(filesmatched.size())
4501 String ttl = MessageManager.getString(
4502 "label.automatically_associate_structure_files_by_name");
4503 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4504 ttl, JvOptionPane.YES_NO_OPTION);
4505 autoAssociate = choice == JvOptionPane.YES_OPTION;
4509 for (Object[] fm : filesmatched)
4511 // try and associate
4512 // TODO: may want to set a standard ID naming formalism for
4513 // associating PDB files which have no IDs.
4514 for (SequenceI toassoc : (SequenceI[]) fm[2])
4516 PDBEntry pe = new AssociatePdbFileWithSeq()
4517 .associatePdbWithSeq((String) fm[0],
4518 (DataSourceType) fm[1], toassoc, false,
4522 System.err.println("Associated file : "
4523 + ((String) fm[0]) + " with "
4524 + toassoc.getDisplayId(true));
4528 // TODO: do we need to update overview ? only if features are
4530 alignPanel.paintAlignment(true, false);
4536 * add declined structures as sequences
4538 for (Object[] o : filesmatched)
4540 filesnotmatched.add((String) o[0]);
4544 if (filesnotmatched.size() > 0)
4546 if (assocfiles > 0 && (Cache.getDefault(
4547 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4548 || JvOptionPane.showConfirmDialog(thisaf,
4549 "<html>" + MessageManager.formatMessage(
4550 "label.ignore_unmatched_dropped_files_info",
4553 filesnotmatched.size())
4556 MessageManager.getString(
4557 "label.ignore_unmatched_dropped_files"),
4558 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4562 for (String fn : filesnotmatched)
4564 loadJalviewDataFile(fn, null, null, null);
4568 } catch (Exception ex)
4570 ex.printStackTrace();
4578 * Attempt to load a "dropped" file or URL string, by testing in turn for
4580 * <li>an Annotation file</li>
4581 * <li>a JNet file</li>
4582 * <li>a features file</li>
4583 * <li>else try to interpret as an alignment file</li>
4587 * either a filename or a URL string.
4589 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4590 FileFormatI format, SequenceI assocSeq)
4594 if (sourceType == null)
4596 sourceType = FormatAdapter.checkProtocol(file);
4598 // if the file isn't identified, or not positively identified as some
4599 // other filetype (PFAM is default unidentified alignment file type) then
4600 // try to parse as annotation.
4601 boolean isAnnotation = (format == null
4602 || FileFormat.Pfam.equals(format))
4603 ? new AnnotationFile().annotateAlignmentView(viewport,
4609 // first see if its a T-COFFEE score file
4610 TCoffeeScoreFile tcf = null;
4613 tcf = new TCoffeeScoreFile(file, sourceType);
4616 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4620 new TCoffeeColourScheme(viewport.getAlignment()));
4621 isAnnotation = true;
4622 statusBar.setText(MessageManager.getString(
4623 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4627 // some problem - if no warning its probable that the ID matching
4628 // process didn't work
4629 JvOptionPane.showMessageDialog(Desktop.desktop,
4630 tcf.getWarningMessage() == null
4631 ? MessageManager.getString(
4632 "label.check_file_matches_sequence_ids_alignment")
4633 : tcf.getWarningMessage(),
4634 MessageManager.getString(
4635 "label.problem_reading_tcoffee_score_file"),
4636 JvOptionPane.WARNING_MESSAGE);
4643 } catch (Exception x)
4646 "Exception when processing data source as T-COFFEE score file",
4652 // try to see if its a JNet 'concise' style annotation file *before*
4654 // try to parse it as a features file
4657 format = new IdentifyFile().identify(file, sourceType);
4659 if (FileFormat.ScoreMatrix == format)
4661 ScoreMatrixFile sm = new ScoreMatrixFile(
4662 new FileParse(file, sourceType));
4664 // todo: i18n this message
4665 statusBar.setText(MessageManager.formatMessage(
4666 "label.successfully_loaded_matrix",
4667 sm.getMatrixName()));
4669 else if (FileFormat.Jnet.equals(format))
4671 JPredFile predictions = new JPredFile(file, sourceType);
4672 new JnetAnnotationMaker();
4673 JnetAnnotationMaker.add_annotation(predictions,
4674 viewport.getAlignment(), 0, false);
4675 viewport.getAlignment().setupJPredAlignment();
4676 isAnnotation = true;
4678 // else if (IdentifyFile.FeaturesFile.equals(format))
4679 else if (FileFormat.Features.equals(format))
4681 if (parseFeaturesFile(file, sourceType))
4683 alignPanel.paintAlignment(true, true);
4688 new FileLoader().LoadFile(viewport, file, sourceType, format);
4694 alignPanel.sortAnnotations(false);
4695 alignPanel.adjustAnnotationHeight();
4696 viewport.updateSequenceIdColours();
4697 buildSortByAnnotationScoresMenu();
4698 alignPanel.paintAlignment(true, true);
4700 } catch (Exception ex)
4702 ex.printStackTrace();
4703 } catch (OutOfMemoryError oom)
4708 } catch (Exception x)
4713 + (sourceType != null
4714 ? (sourceType == DataSourceType.PASTE
4716 : "using " + sourceType + " from "
4720 ? "(parsing as '" + format + "' file)"
4722 oom, Desktop.desktop);
4727 * Method invoked by the ChangeListener on the tabbed pane, in other words
4728 * when a different tabbed pane is selected by the user or programmatically.
4731 public void tabSelectionChanged(int index)
4735 alignPanel = alignPanels.get(index);
4736 viewport = alignPanel.av;
4737 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4738 setMenusFromViewport(viewport);
4742 * 'focus' any colour slider that is open to the selected viewport
4744 if (viewport.getConservationSelected())
4746 SliderPanel.setConservationSlider(alignPanel,
4747 viewport.getResidueShading(), alignPanel.getViewName());
4751 SliderPanel.hideConservationSlider();
4753 if (viewport.getAbovePIDThreshold())
4755 SliderPanel.setPIDSliderSource(alignPanel,
4756 viewport.getResidueShading(), alignPanel.getViewName());
4760 SliderPanel.hidePIDSlider();
4764 * If there is a frame linked to this one in a SplitPane, switch it to the
4765 * same view tab index. No infinite recursion of calls should happen, since
4766 * tabSelectionChanged() should not get invoked on setting the selected
4767 * index to an unchanged value. Guard against setting an invalid index
4768 * before the new view peer tab has been created.
4770 final AlignViewportI peer = viewport.getCodingComplement();
4773 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4774 .getAlignPanel().alignFrame;
4775 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4777 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4783 * On right mouse click on view tab, prompt for and set new view name.
4786 public void tabbedPane_mousePressed(MouseEvent e)
4788 if (e.isPopupTrigger())
4790 String msg = MessageManager.getString("label.enter_view_name");
4791 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4792 JvOptionPane.QUESTION_MESSAGE);
4796 viewport.setViewName(reply);
4797 // TODO warn if reply is in getExistingViewNames()?
4798 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4803 public AlignViewport getCurrentView()
4809 * Open the dialog for regex description parsing.
4812 protected void extractScores_actionPerformed(ActionEvent e)
4814 ParseProperties pp = new jalview.analysis.ParseProperties(
4815 viewport.getAlignment());
4816 // TODO: verify regex and introduce GUI dialog for version 2.5
4817 // if (pp.getScoresFromDescription("col", "score column ",
4818 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4820 if (pp.getScoresFromDescription("description column",
4821 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4823 buildSortByAnnotationScoresMenu();
4831 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4835 protected void showDbRefs_actionPerformed(ActionEvent e)
4837 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4843 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4847 protected void showNpFeats_actionPerformed(ActionEvent e)
4849 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4853 * find the viewport amongst the tabs in this alignment frame and close that
4858 public boolean closeView(AlignViewportI av)
4862 this.closeMenuItem_actionPerformed(false);
4865 Component[] comp = tabbedPane.getComponents();
4866 for (int i = 0; comp != null && i < comp.length; i++)
4868 if (comp[i] instanceof AlignmentPanel)
4870 if (((AlignmentPanel) comp[i]).av == av)
4873 closeView((AlignmentPanel) comp[i]);
4881 protected void build_fetchdbmenu(JMenu webService)
4883 // Temporary hack - DBRef Fetcher always top level ws entry.
4884 // TODO We probably want to store a sequence database checklist in
4885 // preferences and have checkboxes.. rather than individual sources selected
4887 final JMenu rfetch = new JMenu(
4888 MessageManager.getString("action.fetch_db_references"));
4889 rfetch.setToolTipText(MessageManager.getString(
4890 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4891 webService.add(rfetch);
4893 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4894 MessageManager.getString("option.trim_retrieved_seqs"));
4895 trimrs.setToolTipText(
4896 MessageManager.getString("label.trim_retrieved_sequences"));
4898 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4899 trimrs.addActionListener(new ActionListener()
4902 public void actionPerformed(ActionEvent e)
4904 trimrs.setSelected(trimrs.isSelected());
4905 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4906 Boolean.valueOf(trimrs.isSelected()).toString());
4910 JMenuItem fetchr = new JMenuItem(
4911 MessageManager.getString("label.standard_databases"));
4912 fetchr.setToolTipText(
4913 MessageManager.getString("label.fetch_embl_uniprot"));
4914 fetchr.addActionListener(new ActionListener()
4918 public void actionPerformed(ActionEvent e)
4920 new Thread(new Runnable()
4925 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4926 .getAlignment().isNucleotide();
4927 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4928 alignPanel.av.getSequenceSelection(),
4929 alignPanel.alignFrame, null,
4930 alignPanel.alignFrame.featureSettings, isNucleotide);
4931 dbRefFetcher.addListener(new FetchFinishedListenerI()
4934 public void finished()
4936 AlignFrame.this.setMenusForViewport();
4939 dbRefFetcher.fetchDBRefs(false);
4947 final AlignFrame me = this;
4948 new Thread(new Runnable()
4953 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4954 .getSequenceFetcherSingleton(me);
4955 javax.swing.SwingUtilities.invokeLater(new Runnable()
4960 String[] dbclasses = sf.getOrderedSupportedSources();
4961 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4962 // jalview.util.QuickSort.sort(otherdb, otherdb);
4963 List<DbSourceProxy> otherdb;
4964 JMenu dfetch = new JMenu();
4965 JMenu ifetch = new JMenu();
4966 JMenuItem fetchr = null;
4967 int comp = 0, icomp = 0, mcomp = 15;
4968 String mname = null;
4970 for (String dbclass : dbclasses)
4972 otherdb = sf.getSourceProxy(dbclass);
4973 // add a single entry for this class, or submenu allowing 'fetch
4975 if (otherdb == null || otherdb.size() < 1)
4979 // List<DbSourceProxy> dbs=otherdb;
4980 // otherdb=new ArrayList<DbSourceProxy>();
4981 // for (DbSourceProxy db:dbs)
4983 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4987 mname = "From " + dbclass;
4989 if (otherdb.size() == 1)
4991 final DbSourceProxy[] dassource = otherdb
4992 .toArray(new DbSourceProxy[0]);
4993 DbSourceProxy src = otherdb.get(0);
4994 fetchr = new JMenuItem(src.getDbSource());
4995 fetchr.addActionListener(new ActionListener()
4999 public void actionPerformed(ActionEvent e)
5001 new Thread(new Runnable()
5007 boolean isNucleotide = alignPanel.alignFrame
5008 .getViewport().getAlignment()
5010 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5011 alignPanel.av.getSequenceSelection(),
5012 alignPanel.alignFrame, dassource,
5013 alignPanel.alignFrame.featureSettings,
5016 .addListener(new FetchFinishedListenerI()
5019 public void finished()
5021 AlignFrame.this.setMenusForViewport();
5024 dbRefFetcher.fetchDBRefs(false);
5030 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5031 MessageManager.formatMessage(
5032 "label.fetch_retrieve_from", new Object[]
5033 { src.getDbName() })));
5039 final DbSourceProxy[] dassource = otherdb
5040 .toArray(new DbSourceProxy[0]);
5042 DbSourceProxy src = otherdb.get(0);
5043 fetchr = new JMenuItem(MessageManager
5044 .formatMessage("label.fetch_all_param", new Object[]
5045 { src.getDbSource() }));
5046 fetchr.addActionListener(new ActionListener()
5049 public void actionPerformed(ActionEvent e)
5051 new Thread(new Runnable()
5057 boolean isNucleotide = alignPanel.alignFrame
5058 .getViewport().getAlignment()
5060 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5061 alignPanel.av.getSequenceSelection(),
5062 alignPanel.alignFrame, dassource,
5063 alignPanel.alignFrame.featureSettings,
5066 .addListener(new FetchFinishedListenerI()
5069 public void finished()
5071 AlignFrame.this.setMenusForViewport();
5074 dbRefFetcher.fetchDBRefs(false);
5080 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5081 MessageManager.formatMessage(
5082 "label.fetch_retrieve_from_all_sources",
5084 { Integer.valueOf(otherdb.size())
5086 src.getDbSource(), src.getDbName() })));
5089 // and then build the rest of the individual menus
5090 ifetch = new JMenu(MessageManager.formatMessage(
5091 "label.source_from_db_source", new Object[]
5092 { src.getDbSource() }));
5094 String imname = null;
5096 for (DbSourceProxy sproxy : otherdb)
5098 String dbname = sproxy.getDbName();
5099 String sname = dbname.length() > 5
5100 ? dbname.substring(0, 5) + "..."
5102 String msname = dbname.length() > 10
5103 ? dbname.substring(0, 10) + "..."
5107 imname = MessageManager
5108 .formatMessage("label.from_msname", new Object[]
5111 fetchr = new JMenuItem(msname);
5112 final DbSourceProxy[] dassrc = { sproxy };
5113 fetchr.addActionListener(new ActionListener()
5117 public void actionPerformed(ActionEvent e)
5119 new Thread(new Runnable()
5125 boolean isNucleotide = alignPanel.alignFrame
5126 .getViewport().getAlignment()
5128 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5129 alignPanel.av.getSequenceSelection(),
5130 alignPanel.alignFrame, dassrc,
5131 alignPanel.alignFrame.featureSettings,
5134 .addListener(new FetchFinishedListenerI()
5137 public void finished()
5139 AlignFrame.this.setMenusForViewport();
5142 dbRefFetcher.fetchDBRefs(false);
5148 fetchr.setToolTipText(
5149 "<html>" + MessageManager.formatMessage(
5150 "label.fetch_retrieve_from", new Object[]
5154 if (++icomp >= mcomp || i == (otherdb.size()))
5156 ifetch.setText(MessageManager.formatMessage(
5157 "label.source_to_target", imname, sname));
5159 ifetch = new JMenu();
5167 if (comp >= mcomp || dbi >= (dbclasses.length))
5169 dfetch.setText(MessageManager.formatMessage(
5170 "label.source_to_target", mname, dbclass));
5172 dfetch = new JMenu();
5185 * Left justify the whole alignment.
5188 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5190 AlignmentI al = viewport.getAlignment();
5192 viewport.firePropertyChange("alignment", null, al);
5196 * Right justify the whole alignment.
5199 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5201 AlignmentI al = viewport.getAlignment();
5203 viewport.firePropertyChange("alignment", null, al);
5207 public void setShowSeqFeatures(boolean b)
5209 showSeqFeatures.setSelected(b);
5210 viewport.setShowSequenceFeatures(b);
5217 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5218 * awt.event.ActionEvent)
5221 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5223 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5224 alignPanel.paintAlignment(false, false);
5231 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5235 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5237 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5238 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5246 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5247 * .event.ActionEvent)
5250 protected void showGroupConservation_actionPerformed(ActionEvent e)
5252 viewport.setShowGroupConservation(showGroupConservation.getState());
5253 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5260 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5261 * .event.ActionEvent)
5264 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5266 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5267 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5274 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5275 * .event.ActionEvent)
5278 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5280 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5281 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5285 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5287 showSequenceLogo.setState(true);
5288 viewport.setShowSequenceLogo(true);
5289 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5290 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5294 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5296 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5303 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5304 * .event.ActionEvent)
5307 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5309 if (avc.makeGroupsFromSelection())
5311 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5312 alignPanel.updateAnnotation();
5313 alignPanel.paintAlignment(true,
5314 viewport.needToUpdateStructureViews());
5318 public void clearAlignmentSeqRep()
5320 // TODO refactor alignmentseqrep to controller
5321 if (viewport.getAlignment().hasSeqrep())
5323 viewport.getAlignment().setSeqrep(null);
5324 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5325 alignPanel.updateAnnotation();
5326 alignPanel.paintAlignment(true, true);
5331 protected void createGroup_actionPerformed(ActionEvent e)
5333 if (avc.createGroup())
5335 if (applyAutoAnnotationSettings.isSelected())
5337 alignPanel.updateAnnotation(true, false);
5339 alignPanel.alignmentChanged();
5344 protected void unGroup_actionPerformed(ActionEvent e)
5348 alignPanel.alignmentChanged();
5353 * make the given alignmentPanel the currently selected tab
5355 * @param alignmentPanel
5357 public void setDisplayedView(AlignmentPanel alignmentPanel)
5359 if (!viewport.getSequenceSetId()
5360 .equals(alignmentPanel.av.getSequenceSetId()))
5362 throw new Error(MessageManager.getString(
5363 "error.implementation_error_cannot_show_view_alignment_frame"));
5365 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5366 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5368 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5373 * Action on selection of menu options to Show or Hide annotations.
5376 * @param forSequences
5377 * update sequence-related annotations
5378 * @param forAlignment
5379 * update non-sequence-related annotations
5382 protected void setAnnotationsVisibility(boolean visible,
5383 boolean forSequences, boolean forAlignment)
5385 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5386 .getAlignmentAnnotation();
5391 for (AlignmentAnnotation aa : anns)
5394 * don't display non-positional annotations on an alignment
5396 if (aa.annotations == null)
5400 boolean apply = (aa.sequenceRef == null && forAlignment)
5401 || (aa.sequenceRef != null && forSequences);
5404 aa.visible = visible;
5407 alignPanel.validateAnnotationDimensions(true);
5408 alignPanel.alignmentChanged();
5412 * Sorts annotations and repaints the alignment
5415 public void sortAnnotations(boolean autoCalcOnly)
5417 alignPanel.sortAnnotations(autoCalcOnly);
5418 alignPanel.paintAlignment(false, false);
5423 * @return alignment panels in this alignment frame
5425 public List<? extends AlignmentViewPanel> getAlignPanels()
5427 // alignPanels is never null
5428 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5433 * Open a new alignment window, with the cDNA associated with this (protein)
5434 * alignment, aligned as is the protein.
5436 protected void viewAsCdna_actionPerformed()
5438 // TODO no longer a menu action - refactor as required
5439 final AlignmentI alignment = getViewport().getAlignment();
5440 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5441 if (mappings == null)
5445 List<SequenceI> cdnaSeqs = new ArrayList<>();
5446 for (SequenceI aaSeq : alignment.getSequences())
5448 for (AlignedCodonFrame acf : mappings)
5450 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5454 * There is a cDNA mapping for this protein sequence - add to new
5455 * alignment. It will share the same dataset sequence as other mapped
5456 * cDNA (no new mappings need to be created).
5458 final Sequence newSeq = new Sequence(dnaSeq);
5459 newSeq.setDatasetSequence(dnaSeq);
5460 cdnaSeqs.add(newSeq);
5464 if (cdnaSeqs.size() == 0)
5466 // show a warning dialog no mapped cDNA
5469 AlignmentI cdna = new Alignment(
5470 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5471 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5472 AlignFrame.DEFAULT_HEIGHT);
5473 cdna.alignAs(alignment);
5474 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5476 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5477 AlignFrame.DEFAULT_HEIGHT);
5481 * Set visibility of dna/protein complement view (available when shown in a
5487 protected void showComplement_actionPerformed(boolean show)
5489 SplitContainerI sf = getSplitViewContainer();
5492 sf.setComplementVisible(this, show);
5497 * Generate the reverse (optionally complemented) of the selected sequences,
5498 * and add them to the alignment
5501 protected void showReverse_actionPerformed(boolean complement)
5503 AlignmentI al = null;
5506 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5507 al = dna.reverseCdna(complement);
5508 viewport.addAlignment(al, "");
5509 addHistoryItem(new EditCommand(
5510 MessageManager.getString("label.add_sequences"), Action.PASTE,
5511 al.getSequencesArray(), 0, al.getWidth(),
5512 viewport.getAlignment()));
5513 } catch (Exception ex)
5515 System.err.println(ex.getMessage());
5521 * Try to run a script in the Groovy console, having first ensured that this
5522 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5523 * be targeted at this alignment.
5526 protected void runGroovy_actionPerformed()
5528 Jalview.setCurrentAlignFrame(this);
5529 groovy.ui.Console console = Desktop.getGroovyConsole();
5530 if (console != null)
5534 console.runScript();
5535 } catch (Exception ex)
5537 System.err.println((ex.toString()));
5538 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5539 MessageManager.getString("label.couldnt_run_groovy_script"),
5540 MessageManager.getString("label.groovy_support_failed"),
5541 JvOptionPane.ERROR_MESSAGE);
5546 System.err.println("Can't run Groovy script as console not found");
5551 * Hides columns containing (or not containing) a specified feature, provided
5552 * that would not leave all columns hidden
5554 * @param featureType
5555 * @param columnsContaining
5558 public boolean hideFeatureColumns(String featureType,
5559 boolean columnsContaining)
5561 boolean notForHiding = avc.markColumnsContainingFeatures(
5562 columnsContaining, false, false, featureType);
5565 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5566 false, featureType))
5568 getViewport().hideSelectedColumns();
5576 protected void selectHighlightedColumns_actionPerformed(
5577 ActionEvent actionEvent)
5579 // include key modifier check in case user selects from menu
5580 avc.markHighlightedColumns(
5581 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5582 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5583 | ActionEvent.CTRL_MASK)) != 0);
5587 * Rebuilds the Colour menu, including any user-defined colours which have
5588 * been loaded either on startup or during the session
5590 public void buildColourMenu()
5592 colourMenu.removeAll();
5594 colourMenu.add(applyToAllGroups);
5595 colourMenu.add(textColour);
5596 colourMenu.addSeparator();
5598 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5599 viewport.getAlignment(), false);
5601 colourMenu.add(annotationColour);
5602 bg.add(annotationColour);
5603 colourMenu.addSeparator();
5604 colourMenu.add(conservationMenuItem);
5605 colourMenu.add(modifyConservation);
5606 colourMenu.add(abovePIDThreshold);
5607 colourMenu.add(modifyPID);
5609 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5610 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5614 * Open a dialog (if not already open) that allows the user to select and
5615 * calculate PCA or Tree analysis
5617 protected void openTreePcaDialog()
5619 if (alignPanel.getCalculationDialog() == null)
5621 new CalculationChooser(AlignFrame.this);
5626 protected void loadVcf_actionPerformed()
5628 JalviewFileChooser chooser = new JalviewFileChooser(
5629 Cache.getProperty("LAST_DIRECTORY"));
5630 chooser.setFileView(new JalviewFileView());
5631 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5632 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5634 int value = chooser.showOpenDialog(null);
5636 if (value == JalviewFileChooser.APPROVE_OPTION)
5638 String choice = chooser.getSelectedFile().getPath();
5639 Cache.setProperty("LAST_DIRECTORY", choice);
5640 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5641 new VCFLoader(choice).loadVCF(seqs, this);
5647 * Sets the flag for whether auto-calculated annotations should be shown above
5648 * other annotations. If the given value is the same as the current setting,
5649 * simply returns false. Otherwise updates the setting, and returns true. If
5650 * annotation sort order is currently set to 'Custom', this is changed to
5651 * 'None', because 'Custom' ordering ignores all sort options.
5654 public boolean setShowAutoCalculatedAbove(boolean b)
5656 if (viewport.isShowAutocalculatedAbove() != b)
5658 viewport.setShowAutocalculatedAbove(b);
5661 * change CUSTOM annotation ordering to NONE
5662 * so that sorting actually does something
5664 if (viewport.getSortAnnotationsBy() == SequenceAnnotationOrder.CUSTOM)
5666 viewport.setSortAnnotationsBy(SequenceAnnotationOrder.NONE);
5674 public void setAnnotationSortOrder(
5675 SequenceAnnotationOrder annotationSortOrder)
5677 viewport.setSortAnnotationsBy(annotationSortOrder);
5681 class PrintThread extends Thread
5685 public PrintThread(AlignmentPanel ap)
5690 static PageFormat pf;
5695 PrinterJob printJob = PrinterJob.getPrinterJob();
5699 printJob.setPrintable(ap, pf);
5703 printJob.setPrintable(ap);
5706 if (printJob.printDialog())
5711 } catch (Exception PrintException)
5713 PrintException.printStackTrace();