2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.GeneticCodeI;
28 import jalview.analysis.ParseProperties;
29 import jalview.analysis.SequenceIdMatcher;
30 import jalview.api.AlignExportSettingsI;
31 import jalview.api.AlignViewControllerGuiI;
32 import jalview.api.AlignViewControllerI;
33 import jalview.api.AlignViewportI;
34 import jalview.api.AlignmentViewPanel;
35 import jalview.api.FeatureSettingsControllerI;
36 import jalview.api.SplitContainerI;
37 import jalview.api.ViewStyleI;
38 import jalview.api.analysis.SimilarityParamsI;
39 import jalview.bin.Cache;
40 import jalview.bin.Jalview;
41 import jalview.commands.CommandI;
42 import jalview.commands.EditCommand;
43 import jalview.commands.EditCommand.Action;
44 import jalview.commands.OrderCommand;
45 import jalview.commands.RemoveGapColCommand;
46 import jalview.commands.RemoveGapsCommand;
47 import jalview.commands.SlideSequencesCommand;
48 import jalview.commands.TrimRegionCommand;
49 import jalview.datamodel.AlignExportSettingsAdapter;
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.PDBEntry;
60 import jalview.datamodel.SeqCigar;
61 import jalview.datamodel.Sequence;
62 import jalview.datamodel.SequenceGroup;
63 import jalview.datamodel.SequenceI;
64 import jalview.gui.ColourMenuHelper.ColourChangeListener;
65 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
66 import jalview.io.AlignmentProperties;
67 import jalview.io.AnnotationFile;
68 import jalview.io.BackupFiles;
69 import jalview.io.BioJsHTMLOutput;
70 import jalview.io.DataSourceType;
71 import jalview.io.FileFormat;
72 import jalview.io.FileFormatI;
73 import jalview.io.FileFormats;
74 import jalview.io.FileLoader;
75 import jalview.io.FileParse;
76 import jalview.io.FormatAdapter;
77 import jalview.io.HtmlSvgOutput;
78 import jalview.io.IdentifyFile;
79 import jalview.io.JPredFile;
80 import jalview.io.JalviewFileChooser;
81 import jalview.io.JalviewFileView;
82 import jalview.io.JnetAnnotationMaker;
83 import jalview.io.NewickFile;
84 import jalview.io.ScoreMatrixFile;
85 import jalview.io.TCoffeeScoreFile;
86 import jalview.io.vcf.VCFLoader;
87 import jalview.jbgui.GAlignFrame;
88 import jalview.project.Jalview2XML;
89 import jalview.schemes.ColourSchemeI;
90 import jalview.schemes.ColourSchemes;
91 import jalview.schemes.ResidueColourScheme;
92 import jalview.schemes.TCoffeeColourScheme;
93 import jalview.util.ImageMaker.TYPE;
94 import jalview.util.MessageManager;
95 import jalview.util.Platform;
96 import jalview.viewmodel.AlignmentViewport;
97 import jalview.viewmodel.ViewportRanges;
98 import jalview.ws.DBRefFetcher;
99 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
100 import jalview.ws.jws1.Discoverer;
101 import jalview.ws.jws2.Jws2Discoverer;
102 import jalview.ws.jws2.jabaws2.Jws2Instance;
103 import jalview.ws.seqfetcher.DbSourceProxy;
105 import java.awt.BorderLayout;
106 import java.awt.Color;
107 import java.awt.Component;
108 import java.awt.Rectangle;
109 import java.awt.Toolkit;
110 import java.awt.datatransfer.Clipboard;
111 import java.awt.datatransfer.DataFlavor;
112 import java.awt.datatransfer.StringSelection;
113 import java.awt.datatransfer.Transferable;
114 import java.awt.dnd.DnDConstants;
115 import java.awt.dnd.DropTargetDragEvent;
116 import java.awt.dnd.DropTargetDropEvent;
117 import java.awt.dnd.DropTargetEvent;
118 import java.awt.dnd.DropTargetListener;
119 import java.awt.event.ActionEvent;
120 import java.awt.event.ActionListener;
121 import java.awt.event.FocusAdapter;
122 import java.awt.event.FocusEvent;
123 import java.awt.event.ItemEvent;
124 import java.awt.event.ItemListener;
125 import java.awt.event.KeyAdapter;
126 import java.awt.event.KeyEvent;
127 import java.awt.event.MouseEvent;
128 import java.awt.print.PageFormat;
129 import java.awt.print.PrinterJob;
130 import java.beans.PropertyChangeEvent;
132 import java.io.FileWriter;
133 import java.io.PrintWriter;
135 import java.util.ArrayList;
136 import java.util.Arrays;
137 import java.util.Deque;
138 import java.util.Enumeration;
139 import java.util.Hashtable;
140 import java.util.List;
141 import java.util.Vector;
143 import javax.swing.ButtonGroup;
144 import javax.swing.JCheckBoxMenuItem;
145 import javax.swing.JComponent;
146 import javax.swing.JEditorPane;
147 import javax.swing.JInternalFrame;
148 import javax.swing.JLabel;
149 import javax.swing.JLayeredPane;
150 import javax.swing.JMenu;
151 import javax.swing.JMenuItem;
152 import javax.swing.JPanel;
153 import javax.swing.JScrollPane;
154 import javax.swing.SwingUtilities;
160 * @version $Revision$
162 public class AlignFrame extends GAlignFrame implements DropTargetListener,
163 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
166 public static final int DEFAULT_WIDTH = 700;
168 public static final int DEFAULT_HEIGHT = 500;
171 * The currently displayed panel (selected tabbed view if more than one)
173 public AlignmentPanel alignPanel;
175 AlignViewport viewport;
177 public AlignViewControllerI avc;
179 List<AlignmentPanel> alignPanels = new ArrayList<>();
182 * Last format used to load or save alignments in this window
184 FileFormatI currentFileFormat = null;
187 * Current filename for this alignment
189 String fileName = null;
194 * Creates a new AlignFrame object with specific width and height.
200 public AlignFrame(AlignmentI al, int width, int height)
202 this(al, null, width, height);
206 * Creates a new AlignFrame object with specific width, height and
212 * @param sequenceSetId
214 public AlignFrame(AlignmentI al, int width, int height,
215 String sequenceSetId)
217 this(al, null, width, height, sequenceSetId);
221 * Creates a new AlignFrame object with specific width, height and
227 * @param sequenceSetId
230 public AlignFrame(AlignmentI al, int width, int height,
231 String sequenceSetId, String viewId)
233 this(al, null, width, height, sequenceSetId, viewId);
237 * new alignment window with hidden columns
241 * @param hiddenColumns
242 * ColumnSelection or null
244 * Width of alignment frame
248 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
251 this(al, hiddenColumns, width, height, null);
255 * Create alignment frame for al with hiddenColumns, a specific width and
256 * height, and specific sequenceId
259 * @param hiddenColumns
262 * @param sequenceSetId
265 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
266 int height, String sequenceSetId)
268 this(al, hiddenColumns, width, height, sequenceSetId, null);
272 * Create alignment frame for al with hiddenColumns, a specific width and
273 * height, and specific sequenceId
276 * @param hiddenColumns
279 * @param sequenceSetId
284 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
285 int height, String sequenceSetId, String viewId)
287 setSize(width, height);
289 if (al.getDataset() == null)
294 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
296 alignPanel = new AlignmentPanel(this, viewport);
298 addAlignmentPanel(alignPanel, true);
302 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
303 HiddenColumns hiddenColumns, int width, int height)
305 setSize(width, height);
307 if (al.getDataset() == null)
312 viewport = new AlignViewport(al, hiddenColumns);
314 if (hiddenSeqs != null && hiddenSeqs.length > 0)
316 viewport.hideSequence(hiddenSeqs);
318 alignPanel = new AlignmentPanel(this, viewport);
319 addAlignmentPanel(alignPanel, true);
324 * Make a new AlignFrame from existing alignmentPanels
331 public AlignFrame(AlignmentPanel ap)
335 addAlignmentPanel(ap, false);
340 * initalise the alignframe from the underlying viewport data and the
345 // setBackground(Color.white); // BH 2019
347 if (!Jalview.isHeadlessMode())
349 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
352 avc = new jalview.controller.AlignViewController(this, viewport,
354 if (viewport.getAlignmentConservationAnnotation() == null)
356 // BLOSUM62Colour.setEnabled(false);
357 conservationMenuItem.setEnabled(false);
358 modifyConservation.setEnabled(false);
359 // PIDColour.setEnabled(false);
360 // abovePIDThreshold.setEnabled(false);
361 // modifyPID.setEnabled(false);
364 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
367 if (sortby.equals("Id"))
369 sortIDMenuItem_actionPerformed(null);
371 else if (sortby.equals("Pairwise Identity"))
373 sortPairwiseMenuItem_actionPerformed(null);
377 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
379 setMenusFromViewport(viewport);
380 buildSortByAnnotationScoresMenu();
381 calculateTree.addActionListener(new ActionListener()
385 public void actionPerformed(ActionEvent e)
392 if (Desktop.desktop != null)
394 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
395 if (!Platform.isJS())
397 addServiceListeners();
402 if (viewport.getWrapAlignment())
404 wrapMenuItem_actionPerformed(null);
407 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
409 this.overviewMenuItem_actionPerformed(null);
414 final List<AlignmentPanel> selviews = new ArrayList<>();
415 final List<AlignmentPanel> origview = new ArrayList<>();
416 final String menuLabel = MessageManager
417 .getString("label.copy_format_from");
418 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
419 new ViewSetProvider()
423 public AlignmentPanel[] getAllAlignmentPanels()
426 origview.add(alignPanel);
427 // make an array of all alignment panels except for this one
428 List<AlignmentPanel> aps = new ArrayList<>(
429 Arrays.asList(Desktop.getAlignmentPanels(null)));
430 aps.remove(AlignFrame.this.alignPanel);
431 return aps.toArray(new AlignmentPanel[aps.size()]);
433 }, selviews, new ItemListener()
437 public void itemStateChanged(ItemEvent e)
439 if (origview.size() > 0)
441 final AlignmentPanel ap = origview.get(0);
444 * Copy the ViewStyle of the selected panel to 'this one'.
445 * Don't change value of 'scaleProteinAsCdna' unless copying
448 ViewStyleI vs = selviews.get(0).getAlignViewport()
450 boolean fromSplitFrame = selviews.get(0)
451 .getAlignViewport().getCodingComplement() != null;
454 vs.setScaleProteinAsCdna(ap.getAlignViewport()
455 .getViewStyle().isScaleProteinAsCdna());
457 ap.getAlignViewport().setViewStyle(vs);
460 * Also rescale ViewStyle of SplitFrame complement if there is
461 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
462 * the whole ViewStyle (allow cDNA protein to have different
465 AlignViewportI complement = ap.getAlignViewport()
466 .getCodingComplement();
467 if (complement != null && vs.isScaleProteinAsCdna())
469 AlignFrame af = Desktop.getAlignFrameFor(complement);
470 ((SplitFrame) af.getSplitViewContainer())
472 af.setMenusForViewport();
476 ap.setSelected(true);
477 ap.alignFrame.setMenusForViewport();
482 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
483 .indexOf("devel") > -1
484 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
485 .indexOf("test") > -1)
487 formatMenu.add(vsel);
489 addFocusListener(new FocusAdapter()
492 public void focusGained(FocusEvent e)
494 Jalview.setCurrentAlignFrame(AlignFrame.this);
501 * Change the filename and format for the alignment, and enable the 'reload'
502 * button functionality.
509 public void setFileName(String file, FileFormatI format)
512 setFileFormat(format);
513 reload.setEnabled(true);
517 * JavaScript will have this, maybe others. More dependable than a file name
518 * and maintains a reference to the actual bytes loaded.
522 public void setFileObject(File file)
524 this.fileObject = file;
528 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
531 void addKeyListener()
533 addKeyListener(new KeyAdapter()
536 public void keyPressed(KeyEvent evt)
538 if (viewport.cursorMode
539 && ((evt.getKeyCode() >= KeyEvent.VK_0
540 && evt.getKeyCode() <= KeyEvent.VK_9)
541 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
542 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
543 && Character.isDigit(evt.getKeyChar()))
545 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
548 switch (evt.getKeyCode())
551 case 27: // escape key
552 deselectAllSequenceMenuItem_actionPerformed(null);
556 case KeyEvent.VK_DOWN:
557 if (evt.isAltDown() || !viewport.cursorMode)
559 moveSelectedSequences(false);
561 if (viewport.cursorMode)
563 alignPanel.getSeqPanel().moveCursor(0, 1);
568 if (evt.isAltDown() || !viewport.cursorMode)
570 moveSelectedSequences(true);
572 if (viewport.cursorMode)
574 alignPanel.getSeqPanel().moveCursor(0, -1);
579 case KeyEvent.VK_LEFT:
580 if (evt.isAltDown() || !viewport.cursorMode)
582 slideSequences(false,
583 alignPanel.getSeqPanel().getKeyboardNo1());
587 alignPanel.getSeqPanel().moveCursor(-1, 0);
592 case KeyEvent.VK_RIGHT:
593 if (evt.isAltDown() || !viewport.cursorMode)
595 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
599 alignPanel.getSeqPanel().moveCursor(1, 0);
603 case KeyEvent.VK_SPACE:
604 if (viewport.cursorMode)
606 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
607 || evt.isShiftDown() || evt.isAltDown());
611 // case KeyEvent.VK_A:
612 // if (viewport.cursorMode)
614 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
615 // //System.out.println("A");
619 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
620 * System.out.println("closing bracket"); } break;
622 case KeyEvent.VK_DELETE:
623 case KeyEvent.VK_BACK_SPACE:
624 if (!viewport.cursorMode)
626 cut_actionPerformed();
630 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
631 || evt.isShiftDown() || evt.isAltDown());
637 if (viewport.cursorMode)
639 alignPanel.getSeqPanel().setCursorRow();
643 if (viewport.cursorMode && !evt.isControlDown())
645 alignPanel.getSeqPanel().setCursorColumn();
649 if (viewport.cursorMode)
651 alignPanel.getSeqPanel().setCursorPosition();
655 case KeyEvent.VK_ENTER:
656 case KeyEvent.VK_COMMA:
657 if (viewport.cursorMode)
659 alignPanel.getSeqPanel().setCursorRowAndColumn();
664 if (viewport.cursorMode)
666 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
670 if (viewport.cursorMode)
672 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
677 viewport.cursorMode = !viewport.cursorMode;
678 setStatus(MessageManager
679 .formatMessage("label.keyboard_editing_mode", new String[]
680 { (viewport.cursorMode ? "on" : "off") }));
681 if (viewport.cursorMode)
683 ViewportRanges ranges = viewport.getRanges();
684 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
686 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
689 alignPanel.getSeqPanel().seqCanvas.repaint();
695 Help.showHelpWindow();
696 } catch (Exception ex)
698 ex.printStackTrace();
703 boolean toggleSeqs = !evt.isControlDown();
704 boolean toggleCols = !evt.isShiftDown();
705 toggleHiddenRegions(toggleSeqs, toggleCols);
710 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
711 boolean modifyExisting = true; // always modify, don't clear
712 // evt.isShiftDown();
713 boolean invertHighlighted = evt.isAltDown();
714 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
718 case KeyEvent.VK_PAGE_UP:
719 viewport.getRanges().pageUp();
721 case KeyEvent.VK_PAGE_DOWN:
722 viewport.getRanges().pageDown();
728 public void keyReleased(KeyEvent evt)
730 switch (evt.getKeyCode())
732 case KeyEvent.VK_LEFT:
733 if (evt.isAltDown() || !viewport.cursorMode)
735 viewport.firePropertyChange("alignment", null,
736 viewport.getAlignment().getSequences());
740 case KeyEvent.VK_RIGHT:
741 if (evt.isAltDown() || !viewport.cursorMode)
743 viewport.firePropertyChange("alignment", null,
744 viewport.getAlignment().getSequences());
752 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
754 ap.alignFrame = this;
755 avc = new jalview.controller.AlignViewController(this, viewport,
760 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
762 int aSize = alignPanels.size();
764 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
766 if (aSize == 1 && ap.av.getViewName() == null)
768 this.getContentPane().add(ap, BorderLayout.CENTER);
774 setInitialTabVisible();
777 expandViews.setEnabled(true);
778 gatherViews.setEnabled(true);
779 tabbedPane.addTab(ap.av.getViewName(), ap);
781 ap.setVisible(false);
786 if (ap.av.isPadGaps())
788 ap.av.getAlignment().padGaps();
790 ap.av.updateConservation(ap);
791 ap.av.updateConsensus(ap);
792 ap.av.updateStrucConsensus(ap);
796 public void setInitialTabVisible()
798 expandViews.setEnabled(true);
799 gatherViews.setEnabled(true);
800 tabbedPane.setVisible(true);
801 AlignmentPanel first = alignPanels.get(0);
802 tabbedPane.addTab(first.av.getViewName(), first);
803 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
806 public AlignViewport getViewport()
811 /* Set up intrinsic listeners for dynamically generated GUI bits. */
812 private void addServiceListeners()
814 final java.beans.PropertyChangeListener thisListener;
815 Desktop.instance.addJalviewPropertyChangeListener("services",
816 thisListener = new java.beans.PropertyChangeListener()
819 public void propertyChange(PropertyChangeEvent evt)
821 // // System.out.println("Discoverer property change.");
822 // if (evt.getPropertyName().equals("services"))
824 SwingUtilities.invokeLater(new Runnable()
831 "Rebuild WS Menu for service change");
832 BuildWebServiceMenu();
839 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
842 public void internalFrameClosed(
843 javax.swing.event.InternalFrameEvent evt)
845 // System.out.println("deregistering discoverer listener");
846 Desktop.instance.removeJalviewPropertyChangeListener("services",
848 closeMenuItem_actionPerformed(true);
851 // Finally, build the menu once to get current service state
852 new Thread(new Runnable()
857 BuildWebServiceMenu();
863 * Configure menu items that vary according to whether the alignment is
864 * nucleotide or protein
866 public void setGUINucleotide()
868 AlignmentI al = getViewport().getAlignment();
869 boolean nucleotide = al.isNucleotide();
871 loadVcf.setVisible(nucleotide);
872 showTranslation.setVisible(nucleotide);
873 showReverse.setVisible(nucleotide);
874 showReverseComplement.setVisible(nucleotide);
875 conservationMenuItem.setEnabled(!nucleotide);
877 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
878 showGroupConservation.setEnabled(!nucleotide);
880 showComplementMenuItem
881 .setText(nucleotide ? MessageManager.getString("label.protein")
882 : MessageManager.getString("label.nucleotide"));
886 * set up menus for the current viewport. This may be called after any
887 * operation that affects the data in the current view (selection changed,
888 * etc) to update the menus to reflect the new state.
891 public void setMenusForViewport()
893 setMenusFromViewport(viewport);
897 * Need to call this method when tabs are selected for multiple views, or when
898 * loading from Jalview2XML.java
903 public void setMenusFromViewport(AlignViewport av)
905 padGapsMenuitem.setSelected(av.isPadGaps());
906 colourTextMenuItem.setSelected(av.isShowColourText());
907 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
908 modifyPID.setEnabled(abovePIDThreshold.isSelected());
909 conservationMenuItem.setSelected(av.getConservationSelected());
910 modifyConservation.setEnabled(conservationMenuItem.isSelected());
911 seqLimits.setSelected(av.getShowJVSuffix());
912 idRightAlign.setSelected(av.isRightAlignIds());
913 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
914 renderGapsMenuItem.setSelected(av.isRenderGaps());
915 wrapMenuItem.setSelected(av.getWrapAlignment());
916 scaleAbove.setVisible(av.getWrapAlignment());
917 scaleLeft.setVisible(av.getWrapAlignment());
918 scaleRight.setVisible(av.getWrapAlignment());
919 annotationPanelMenuItem.setState(av.isShowAnnotation());
921 * Show/hide annotations only enabled if annotation panel is shown
923 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
924 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
925 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
926 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
927 viewBoxesMenuItem.setSelected(av.getShowBoxes());
928 viewTextMenuItem.setSelected(av.getShowText());
929 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
930 showGroupConsensus.setSelected(av.isShowGroupConsensus());
931 showGroupConservation.setSelected(av.isShowGroupConservation());
932 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
933 showSequenceLogo.setSelected(av.isShowSequenceLogo());
934 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
936 ColourMenuHelper.setColourSelected(colourMenu,
937 av.getGlobalColourScheme());
939 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
940 hiddenMarkers.setState(av.getShowHiddenMarkers());
941 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
942 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
943 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
944 autoCalculate.setSelected(av.autoCalculateConsensus);
945 sortByTree.setSelected(av.sortByTree);
946 listenToViewSelections.setSelected(av.followSelection);
948 showProducts.setEnabled(canShowProducts());
949 setGroovyEnabled(Desktop.getGroovyConsole() != null);
955 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
959 public void setGroovyEnabled(boolean b)
961 runGroovy.setEnabled(b);
964 private IProgressIndicator progressBar;
969 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
972 public void setProgressBar(String message, long id)
974 progressBar.setProgressBar(message, id);
978 public void registerHandler(final long id,
979 final IProgressIndicatorHandler handler)
981 progressBar.registerHandler(id, handler);
986 * @return true if any progress bars are still active
989 public boolean operationInProgress()
991 return progressBar.operationInProgress();
995 * Sets the text of the status bar. Note that setting a null or empty value
996 * will cause the status bar to be hidden, with possibly undesirable flicker
997 * of the screen layout.
1000 public void setStatus(String text)
1002 statusBar.setText(text == null || text.isEmpty() ? " " : text);
1006 * Added so Castor Mapping file can obtain Jalview Version
1008 public String getVersion()
1010 return jalview.bin.Cache.getProperty("VERSION");
1013 public FeatureRenderer getFeatureRenderer()
1015 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1019 public void fetchSequence_actionPerformed()
1021 new SequenceFetcher(this);
1025 public void addFromFile_actionPerformed(ActionEvent e)
1027 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1031 public void reload_actionPerformed(ActionEvent e)
1033 if (fileName != null)
1035 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1036 // originating file's format
1037 // TODO: work out how to recover feature settings for correct view(s) when
1038 // file is reloaded.
1039 if (FileFormat.Jalview.equals(currentFileFormat))
1041 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1042 for (int i = 0; i < frames.length; i++)
1044 if (frames[i] instanceof AlignFrame && frames[i] != this
1045 && ((AlignFrame) frames[i]).fileName != null
1046 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1050 frames[i].setSelected(true);
1051 Desktop.instance.closeAssociatedWindows();
1052 } catch (java.beans.PropertyVetoException ex)
1058 Desktop.instance.closeAssociatedWindows();
1060 FileLoader loader = new FileLoader();
1061 DataSourceType protocol = fileName.startsWith("http:")
1062 ? DataSourceType.URL
1063 : DataSourceType.FILE;
1064 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1068 Rectangle bounds = this.getBounds();
1070 FileLoader loader = new FileLoader();
1072 AlignFrame newframe = null;
1074 if (fileObject == null)
1077 DataSourceType protocol = (fileName.startsWith("http:")
1078 ? DataSourceType.URL
1079 : DataSourceType.FILE);
1080 newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1085 newframe = loader.LoadFileWaitTillLoaded(fileObject,
1086 DataSourceType.FILE, currentFileFormat);
1089 newframe.setBounds(bounds);
1090 if (featureSettings != null && featureSettings.isShowing())
1092 final Rectangle fspos = featureSettings.frame.getBounds();
1093 // TODO: need a 'show feature settings' function that takes bounds -
1094 // need to refactor Desktop.addFrame
1095 newframe.featureSettings_actionPerformed(null);
1096 final FeatureSettings nfs = newframe.featureSettings;
1097 SwingUtilities.invokeLater(new Runnable()
1102 nfs.frame.setBounds(fspos);
1105 this.featureSettings.close();
1106 this.featureSettings = null;
1108 this.closeMenuItem_actionPerformed(true);
1114 public void addFromText_actionPerformed(ActionEvent e)
1117 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1121 public void addFromURL_actionPerformed(ActionEvent e)
1123 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1127 public void save_actionPerformed(ActionEvent e)
1129 if (fileName == null || (currentFileFormat == null)
1130 || fileName.startsWith("http"))
1132 saveAs_actionPerformed();
1136 saveAlignment(fileName, currentFileFormat);
1141 * Saves the alignment to a file with a name chosen by the user, if necessary
1142 * warning if a file would be overwritten
1145 public void saveAs_actionPerformed()
1147 String format = currentFileFormat == null ? null
1148 : currentFileFormat.getName();
1149 JalviewFileChooser chooser = JalviewFileChooser
1150 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1152 chooser.setFileView(new JalviewFileView());
1153 chooser.setDialogTitle(
1154 MessageManager.getString("label.save_alignment_to_file"));
1155 chooser.setToolTipText(MessageManager.getString("action.save"));
1157 int value = chooser.showSaveDialog(this);
1159 if (value != JalviewFileChooser.APPROVE_OPTION)
1163 currentFileFormat = chooser.getSelectedFormat();
1164 // todo is this (2005) test now obsolete - value is never null?
1165 while (currentFileFormat == null)
1167 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1169 .getString("label.select_file_format_before_saving"),
1170 MessageManager.getString("label.file_format_not_specified"),
1171 JvOptionPane.WARNING_MESSAGE);
1172 currentFileFormat = chooser.getSelectedFormat();
1173 value = chooser.showSaveDialog(this);
1174 if (value != JalviewFileChooser.APPROVE_OPTION)
1180 fileName = chooser.getSelectedFile().getPath();
1182 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1183 Cache.setProperty("LAST_DIRECTORY", fileName);
1184 saveAlignment(fileName, currentFileFormat);
1187 boolean lastSaveSuccessful = false;
1189 FileFormatI lastFormatSaved;
1191 String lastFilenameSaved;
1194 * Raise a dialog or status message for the last call to saveAlignment.
1196 * @return true if last call to saveAlignment(file, format) was successful.
1198 public boolean isSaveAlignmentSuccessful()
1201 if (!lastSaveSuccessful)
1203 JvOptionPane.showInternalMessageDialog(this, MessageManager
1204 .formatMessage("label.couldnt_save_file", new Object[]
1205 { lastFilenameSaved }),
1206 MessageManager.getString("label.error_saving_file"),
1207 JvOptionPane.WARNING_MESSAGE);
1212 setStatus(MessageManager.formatMessage(
1213 "label.successfully_saved_to_file_in_format", new Object[]
1214 { lastFilenameSaved, lastFormatSaved }));
1217 return lastSaveSuccessful;
1221 * Saves the alignment to the specified file path, in the specified format,
1222 * which may be an alignment format, or Jalview project format. If the
1223 * alignment has hidden regions, or the format is one capable of including
1224 * non-sequence data (features, annotations, groups), then the user may be
1225 * prompted to specify what to include in the output.
1230 public void saveAlignment(String file, FileFormatI format)
1232 lastSaveSuccessful = true;
1233 lastFilenameSaved = file;
1234 lastFormatSaved = format;
1236 if (FileFormat.Jalview.equals(format))
1238 String shortName = title;
1239 if (shortName.indexOf(File.separatorChar) > -1)
1241 shortName = shortName.substring(
1242 shortName.lastIndexOf(File.separatorChar) + 1);
1244 lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName);
1246 statusBar.setText(MessageManager.formatMessage(
1247 "label.successfully_saved_to_file_in_format", new Object[]
1248 { fileName, format }));
1253 AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1254 Runnable cancelAction = new Runnable()
1259 lastSaveSuccessful = false;
1262 Runnable outputAction = new Runnable()
1267 // todo defer this to inside formatSequences (or later)
1268 AlignmentExportData exportData = viewport
1269 .getAlignExportData(options);
1270 String output = new FormatAdapter(alignPanel, options)
1271 .formatSequences(format, exportData.getAlignment(),
1272 exportData.getOmitHidden(),
1273 exportData.getStartEndPostions(),
1274 viewport.getAlignment().getHiddenColumns());
1277 lastSaveSuccessful = false;
1281 // create backupfiles object and get new temp filename destination
1282 boolean doBackup = BackupFiles.getEnabled();
1283 BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
1286 String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
1287 PrintWriter out = new PrintWriter(
1288 new FileWriter(tempFilePath));
1292 AlignFrame.this.setTitle(file);
1293 statusBar.setText(MessageManager.formatMessage(
1294 "label.successfully_saved_to_file_in_format", new Object[]
1295 { fileName, format.getName() }));
1296 lastSaveSuccessful = true;
1297 } catch (Exception ex)
1299 lastSaveSuccessful = false;
1300 ex.printStackTrace();
1305 backupfiles.setWriteSuccess(lastSaveSuccessful);
1306 // do the backup file roll and rename the temp file to actual file
1307 lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1314 * show dialog with export options if applicable; else just do it
1316 if (AlignExportOptions.isNeeded(viewport, format))
1318 AlignExportOptions choices = new AlignExportOptions(
1319 alignPanel.getAlignViewport(), format, options);
1320 choices.setResponseAction(0, outputAction);
1321 choices.setResponseAction(1, cancelAction);
1322 choices.showDialog();
1331 * Outputs the alignment to textbox in the requested format, if necessary
1332 * first prompting the user for whether to include hidden regions or
1335 * @param fileFormatName
1338 protected void outputText_actionPerformed(String fileFormatName)
1340 FileFormatI fileFormat = FileFormats.getInstance()
1341 .forName(fileFormatName);
1342 AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1343 Runnable outputAction = new Runnable()
1348 // todo defer this to inside formatSequences (or later)
1349 AlignmentExportData exportData = viewport
1350 .getAlignExportData(options);
1351 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1352 cap.setForInput(null);
1355 FileFormatI format = fileFormat;
1356 cap.setText(new FormatAdapter(alignPanel, options)
1357 .formatSequences(format, exportData.getAlignment(),
1358 exportData.getOmitHidden(),
1359 exportData.getStartEndPostions(),
1360 viewport.getAlignment().getHiddenColumns()));
1361 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1362 "label.alignment_output_command", new Object[]
1363 { fileFormat.getName() }), 600, 500);
1364 } catch (OutOfMemoryError oom)
1366 new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1374 * show dialog with export options if applicable; else just do it
1376 if (AlignExportOptions.isNeeded(viewport, fileFormat))
1378 AlignExportOptions choices = new AlignExportOptions(
1379 alignPanel.getAlignViewport(), fileFormat, options);
1380 choices.setResponseAction(0, outputAction);
1381 choices.showDialog();
1396 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1398 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1399 htmlSVG.exportHTML(null);
1403 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1405 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1406 bjs.exportHTML(null);
1409 public void createImageMap(File file, String image)
1411 alignPanel.makePNGImageMap(file, image);
1415 * Creates a PNG image of the alignment and writes it to the given file. If
1416 * the file is null, the user is prompted to choose a file.
1421 public void createPNG(File f)
1423 alignPanel.makeAlignmentImage(TYPE.PNG, f);
1427 * Creates an EPS image of the alignment and writes it to the given file. If
1428 * the file is null, the user is prompted to choose a file.
1433 public void createEPS(File f)
1435 alignPanel.makeAlignmentImage(TYPE.EPS, f);
1439 * Creates an SVG image of the alignment and writes it to the given file. If
1440 * the file is null, the user is prompted to choose a file.
1445 public void createSVG(File f)
1447 alignPanel.makeAlignmentImage(TYPE.SVG, f);
1451 public void pageSetup_actionPerformed(ActionEvent e)
1453 PrinterJob printJob = PrinterJob.getPrinterJob();
1454 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1464 public void printMenuItem_actionPerformed(ActionEvent e)
1466 // Putting in a thread avoids Swing painting problems
1467 PrintThread thread = new PrintThread(alignPanel);
1472 public void exportFeatures_actionPerformed(ActionEvent e)
1474 new AnnotationExporter(alignPanel).exportFeatures();
1478 public void exportAnnotations_actionPerformed(ActionEvent e)
1480 new AnnotationExporter(alignPanel).exportAnnotations();
1484 public void associatedData_actionPerformed(ActionEvent e)
1486 final JalviewFileChooser chooser = new JalviewFileChooser(
1487 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1488 chooser.setFileView(new JalviewFileView());
1489 chooser.setDialogTitle(
1490 MessageManager.getString("label.load_jalview_annotations"));
1491 chooser.setToolTipText(
1492 MessageManager.getString("label.load_jalview_annotations"));
1493 chooser.setResponseHandler(0, new Runnable()
1498 String choice = chooser.getSelectedFile().getPath();
1499 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1500 loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1504 chooser.showOpenDialog(this);
1508 * Close the current view or all views in the alignment frame. If the frame
1509 * only contains one view then the alignment will be removed from memory.
1511 * @param closeAllTabs
1514 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1516 if (alignPanels != null && alignPanels.size() < 2)
1518 closeAllTabs = true;
1523 if (alignPanels != null)
1527 if (this.isClosed())
1529 // really close all the windows - otherwise wait till
1530 // setClosed(true) is called
1531 for (int i = 0; i < alignPanels.size(); i++)
1533 AlignmentPanel ap = alignPanels.get(i);
1540 closeView(alignPanel);
1547 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1548 * be called recursively, with the frame now in 'closed' state
1550 this.setClosed(true);
1552 } catch (Exception ex)
1554 ex.printStackTrace();
1559 * Close the specified panel and close up tabs appropriately.
1561 * @param panelToClose
1563 public void closeView(AlignmentPanel panelToClose)
1565 int index = tabbedPane.getSelectedIndex();
1566 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1567 alignPanels.remove(panelToClose);
1568 panelToClose.closePanel();
1569 panelToClose = null;
1571 tabbedPane.removeTabAt(closedindex);
1572 tabbedPane.validate();
1574 if (index > closedindex || index == tabbedPane.getTabCount())
1576 // modify currently selected tab index if necessary.
1580 this.tabSelectionChanged(index);
1586 void updateEditMenuBar()
1589 if (viewport.getHistoryList().size() > 0)
1591 undoMenuItem.setEnabled(true);
1592 CommandI command = viewport.getHistoryList().peek();
1593 undoMenuItem.setText(MessageManager
1594 .formatMessage("label.undo_command", new Object[]
1595 { command.getDescription() }));
1599 undoMenuItem.setEnabled(false);
1600 undoMenuItem.setText(MessageManager.getString("action.undo"));
1603 if (viewport.getRedoList().size() > 0)
1605 redoMenuItem.setEnabled(true);
1607 CommandI command = viewport.getRedoList().peek();
1608 redoMenuItem.setText(MessageManager
1609 .formatMessage("label.redo_command", new Object[]
1610 { command.getDescription() }));
1614 redoMenuItem.setEnabled(false);
1615 redoMenuItem.setText(MessageManager.getString("action.redo"));
1620 public void addHistoryItem(CommandI command)
1622 if (command.getSize() > 0)
1624 viewport.addToHistoryList(command);
1625 viewport.clearRedoList();
1626 updateEditMenuBar();
1627 viewport.updateHiddenColumns();
1628 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1629 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1630 // viewport.getColumnSelection()
1631 // .getHiddenColumns().size() > 0);
1637 * @return alignment objects for all views
1639 AlignmentI[] getViewAlignments()
1641 if (alignPanels != null)
1643 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1645 for (AlignmentPanel ap : alignPanels)
1647 als[i++] = ap.av.getAlignment();
1651 if (viewport != null)
1653 return new AlignmentI[] { viewport.getAlignment() };
1665 protected void undoMenuItem_actionPerformed(ActionEvent e)
1667 if (viewport.getHistoryList().isEmpty())
1671 CommandI command = viewport.getHistoryList().pop();
1672 viewport.addToRedoList(command);
1673 command.undoCommand(getViewAlignments());
1675 AlignmentViewport originalSource = getOriginatingSource(command);
1676 updateEditMenuBar();
1678 if (originalSource != null)
1680 if (originalSource != viewport)
1683 "Implementation worry: mismatch of viewport origin for undo");
1685 originalSource.updateHiddenColumns();
1686 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1688 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1689 // viewport.getColumnSelection()
1690 // .getHiddenColumns().size() > 0);
1691 originalSource.firePropertyChange("alignment", null,
1692 originalSource.getAlignment().getSequences());
1703 protected void redoMenuItem_actionPerformed(ActionEvent e)
1705 if (viewport.getRedoList().size() < 1)
1710 CommandI command = viewport.getRedoList().pop();
1711 viewport.addToHistoryList(command);
1712 command.doCommand(getViewAlignments());
1714 AlignmentViewport originalSource = getOriginatingSource(command);
1715 updateEditMenuBar();
1717 if (originalSource != null)
1720 if (originalSource != viewport)
1723 "Implementation worry: mismatch of viewport origin for redo");
1725 originalSource.updateHiddenColumns();
1726 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1728 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1729 // viewport.getColumnSelection()
1730 // .getHiddenColumns().size() > 0);
1731 originalSource.firePropertyChange("alignment", null,
1732 originalSource.getAlignment().getSequences());
1736 AlignmentViewport getOriginatingSource(CommandI command)
1738 AlignmentViewport originalSource = null;
1739 // For sequence removal and addition, we need to fire
1740 // the property change event FROM the viewport where the
1741 // original alignment was altered
1742 AlignmentI al = null;
1743 if (command instanceof EditCommand)
1745 EditCommand editCommand = (EditCommand) command;
1746 al = editCommand.getAlignment();
1747 List<Component> comps = PaintRefresher.components
1748 .get(viewport.getSequenceSetId());
1750 for (Component comp : comps)
1752 if (comp instanceof AlignmentPanel)
1754 if (al == ((AlignmentPanel) comp).av.getAlignment())
1756 originalSource = ((AlignmentPanel) comp).av;
1763 if (originalSource == null)
1765 // The original view is closed, we must validate
1766 // the current view against the closed view first
1769 PaintRefresher.validateSequences(al, viewport.getAlignment());
1772 originalSource = viewport;
1775 return originalSource;
1784 public void moveSelectedSequences(boolean up)
1786 SequenceGroup sg = viewport.getSelectionGroup();
1792 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1793 viewport.getHiddenRepSequences(), up);
1794 alignPanel.paintAlignment(true, false);
1797 synchronized void slideSequences(boolean right, int size)
1799 List<SequenceI> sg = new ArrayList<>();
1800 if (viewport.cursorMode)
1802 sg.add(viewport.getAlignment()
1803 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1805 else if (viewport.getSelectionGroup() != null
1806 && viewport.getSelectionGroup().getSize() != viewport
1807 .getAlignment().getHeight())
1809 sg = viewport.getSelectionGroup()
1810 .getSequences(viewport.getHiddenRepSequences());
1818 List<SequenceI> invertGroup = new ArrayList<>();
1820 for (SequenceI seq : viewport.getAlignment().getSequences())
1822 if (!sg.contains(seq))
1824 invertGroup.add(seq);
1828 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1830 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1831 for (int i = 0; i < invertGroup.size(); i++)
1833 seqs2[i] = invertGroup.get(i);
1836 SlideSequencesCommand ssc;
1839 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1840 viewport.getGapCharacter());
1844 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1845 viewport.getGapCharacter());
1848 int groupAdjustment = 0;
1849 if (ssc.getGapsInsertedBegin() && right)
1851 if (viewport.cursorMode)
1853 alignPanel.getSeqPanel().moveCursor(size, 0);
1857 groupAdjustment = size;
1860 else if (!ssc.getGapsInsertedBegin() && !right)
1862 if (viewport.cursorMode)
1864 alignPanel.getSeqPanel().moveCursor(-size, 0);
1868 groupAdjustment = -size;
1872 if (groupAdjustment != 0)
1874 viewport.getSelectionGroup().setStartRes(
1875 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1876 viewport.getSelectionGroup().setEndRes(
1877 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1881 * just extend the last slide command if compatible; but not if in
1882 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1884 boolean appendHistoryItem = false;
1885 Deque<CommandI> historyList = viewport.getHistoryList();
1886 boolean inSplitFrame = getSplitViewContainer() != null;
1887 if (!inSplitFrame && historyList != null && historyList.size() > 0
1888 && historyList.peek() instanceof SlideSequencesCommand)
1890 appendHistoryItem = ssc.appendSlideCommand(
1891 (SlideSequencesCommand) historyList.peek());
1894 if (!appendHistoryItem)
1896 addHistoryItem(ssc);
1909 protected void copy_actionPerformed()
1911 if (viewport.getSelectionGroup() == null)
1915 // TODO: preserve the ordering of displayed alignment annotation in any
1916 // internal paste (particularly sequence associated annotation)
1917 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1918 String[] omitHidden = null;
1920 if (viewport.hasHiddenColumns())
1922 omitHidden = viewport.getViewAsString(true);
1925 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1926 seqs, omitHidden, null);
1928 StringSelection ss = new StringSelection(output);
1932 jalview.gui.Desktop.internalCopy = true;
1933 // Its really worth setting the clipboard contents
1934 // to empty before setting the large StringSelection!!
1935 Toolkit.getDefaultToolkit().getSystemClipboard()
1936 .setContents(new StringSelection(""), null);
1938 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1940 } catch (OutOfMemoryError er)
1942 new OOMWarning("copying region", er);
1946 HiddenColumns hiddenColumns = null;
1947 if (viewport.hasHiddenColumns())
1949 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1950 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1952 // create new HiddenColumns object with copy of hidden regions
1953 // between startRes and endRes, offset by startRes
1954 hiddenColumns = new HiddenColumns(
1955 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1956 hiddenCutoff, hiddenOffset);
1959 Desktop.jalviewClipboard = new Object[] { seqs,
1960 viewport.getAlignment().getDataset(), hiddenColumns };
1961 setStatus(MessageManager.formatMessage(
1962 "label.copied_sequences_to_clipboard", new Object[]
1963 { Integer.valueOf(seqs.length).toString() }));
1973 protected void pasteNew_actionPerformed(ActionEvent e)
1985 protected void pasteThis_actionPerformed(ActionEvent e)
1991 * Paste contents of Jalview clipboard
1993 * @param newAlignment
1994 * true to paste to a new alignment, otherwise add to this.
1996 void paste(boolean newAlignment)
1998 boolean externalPaste = true;
2001 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2002 Transferable contents = c.getContents(this);
2004 if (contents == null)
2013 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2014 if (str.length() < 1)
2019 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2021 } catch (OutOfMemoryError er)
2023 new OOMWarning("Out of memory pasting sequences!!", er);
2027 SequenceI[] sequences;
2028 boolean annotationAdded = false;
2029 AlignmentI alignment = null;
2031 if (Desktop.jalviewClipboard != null)
2033 // The clipboard was filled from within Jalview, we must use the
2035 // And dataset from the copied alignment
2036 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2037 // be doubly sure that we create *new* sequence objects.
2038 sequences = new SequenceI[newseq.length];
2039 for (int i = 0; i < newseq.length; i++)
2041 sequences[i] = new Sequence(newseq[i]);
2043 alignment = new Alignment(sequences);
2044 externalPaste = false;
2048 // parse the clipboard as an alignment.
2049 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2051 sequences = alignment.getSequencesArray();
2055 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2061 if (Desktop.jalviewClipboard != null)
2063 // dataset is inherited
2064 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2068 // new dataset is constructed
2069 alignment.setDataset(null);
2071 alwidth = alignment.getWidth() + 1;
2075 AlignmentI pastedal = alignment; // preserve pasted alignment object
2076 // Add pasted sequences and dataset into existing alignment.
2077 alignment = viewport.getAlignment();
2078 alwidth = alignment.getWidth() + 1;
2079 // decide if we need to import sequences from an existing dataset
2080 boolean importDs = Desktop.jalviewClipboard != null
2081 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2082 // importDs==true instructs us to copy over new dataset sequences from
2083 // an existing alignment
2084 Vector newDs = (importDs) ? new Vector() : null; // used to create
2085 // minimum dataset set
2087 for (int i = 0; i < sequences.length; i++)
2091 newDs.addElement(null);
2093 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2095 if (importDs && ds != null)
2097 if (!newDs.contains(ds))
2099 newDs.setElementAt(ds, i);
2100 ds = new Sequence(ds);
2101 // update with new dataset sequence
2102 sequences[i].setDatasetSequence(ds);
2106 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2111 // copy and derive new dataset sequence
2112 sequences[i] = sequences[i].deriveSequence();
2113 alignment.getDataset()
2114 .addSequence(sequences[i].getDatasetSequence());
2115 // TODO: avoid creation of duplicate dataset sequences with a
2116 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2118 alignment.addSequence(sequences[i]); // merges dataset
2122 newDs.clear(); // tidy up
2124 if (alignment.getAlignmentAnnotation() != null)
2126 for (AlignmentAnnotation alan : alignment
2127 .getAlignmentAnnotation())
2129 if (alan.graphGroup > fgroup)
2131 fgroup = alan.graphGroup;
2135 if (pastedal.getAlignmentAnnotation() != null)
2137 // Add any annotation attached to alignment.
2138 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2139 for (int i = 0; i < alann.length; i++)
2141 annotationAdded = true;
2142 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2144 AlignmentAnnotation newann = new AlignmentAnnotation(
2146 if (newann.graphGroup > -1)
2148 if (newGraphGroups.size() <= newann.graphGroup
2149 || newGraphGroups.get(newann.graphGroup) == null)
2151 for (int q = newGraphGroups
2152 .size(); q <= newann.graphGroup; q++)
2154 newGraphGroups.add(q, null);
2156 newGraphGroups.set(newann.graphGroup,
2157 new Integer(++fgroup));
2159 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2163 newann.padAnnotation(alwidth);
2164 alignment.addAnnotation(newann);
2174 addHistoryItem(new EditCommand(
2175 MessageManager.getString("label.add_sequences"),
2176 Action.PASTE, sequences, 0, alignment.getWidth(),
2179 // Add any annotations attached to sequences
2180 for (int i = 0; i < sequences.length; i++)
2182 if (sequences[i].getAnnotation() != null)
2184 AlignmentAnnotation newann;
2185 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2187 annotationAdded = true;
2188 newann = sequences[i].getAnnotation()[a];
2189 newann.adjustForAlignment();
2190 newann.padAnnotation(alwidth);
2191 if (newann.graphGroup > -1)
2193 if (newann.graphGroup > -1)
2195 if (newGraphGroups.size() <= newann.graphGroup
2196 || newGraphGroups.get(newann.graphGroup) == null)
2198 for (int q = newGraphGroups
2199 .size(); q <= newann.graphGroup; q++)
2201 newGraphGroups.add(q, null);
2203 newGraphGroups.set(newann.graphGroup,
2204 new Integer(++fgroup));
2206 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2210 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2214 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2222 // propagate alignment changed.
2223 viewport.getRanges().setEndSeq(alignment.getHeight());
2224 if (annotationAdded)
2226 // Duplicate sequence annotation in all views.
2227 AlignmentI[] alview = this.getViewAlignments();
2228 for (int i = 0; i < sequences.length; i++)
2230 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2235 for (int avnum = 0; avnum < alview.length; avnum++)
2237 if (alview[avnum] != alignment)
2239 // duplicate in a view other than the one with input focus
2240 int avwidth = alview[avnum].getWidth() + 1;
2241 // this relies on sann being preserved after we
2242 // modify the sequence's annotation array for each duplication
2243 for (int a = 0; a < sann.length; a++)
2245 AlignmentAnnotation newann = new AlignmentAnnotation(
2247 sequences[i].addAlignmentAnnotation(newann);
2248 newann.padAnnotation(avwidth);
2249 alview[avnum].addAnnotation(newann); // annotation was
2250 // duplicated earlier
2251 // TODO JAL-1145 graphGroups are not updated for sequence
2252 // annotation added to several views. This may cause
2254 alview[avnum].setAnnotationIndex(newann, a);
2259 buildSortByAnnotationScoresMenu();
2261 viewport.firePropertyChange("alignment", null,
2262 alignment.getSequences());
2263 if (alignPanels != null)
2265 for (AlignmentPanel ap : alignPanels)
2267 ap.validateAnnotationDimensions(false);
2272 alignPanel.validateAnnotationDimensions(false);
2278 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2280 String newtitle = new String("Copied sequences");
2282 if (Desktop.jalviewClipboard != null
2283 && Desktop.jalviewClipboard[2] != null)
2285 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2286 af.viewport.setHiddenColumns(hc);
2289 // >>>This is a fix for the moment, until a better solution is
2291 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2292 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2293 .getFeatureRenderer());
2295 // TODO: maintain provenance of an alignment, rather than just make the
2296 // title a concatenation of operations.
2299 if (title.startsWith("Copied sequences"))
2305 newtitle = newtitle.concat("- from " + title);
2310 newtitle = new String("Pasted sequences");
2313 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2318 } catch (Exception ex)
2320 ex.printStackTrace();
2321 System.out.println("Exception whilst pasting: " + ex);
2322 // could be anything being pasted in here
2328 protected void expand_newalign(ActionEvent e)
2332 AlignmentI alignment = AlignmentUtils
2333 .expandContext(getViewport().getAlignment(), -1);
2334 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2336 String newtitle = new String("Flanking alignment");
2338 if (Desktop.jalviewClipboard != null
2339 && Desktop.jalviewClipboard[2] != null)
2341 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2342 af.viewport.setHiddenColumns(hc);
2345 // >>>This is a fix for the moment, until a better solution is
2347 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2348 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2349 .getFeatureRenderer());
2351 // TODO: maintain provenance of an alignment, rather than just make the
2352 // title a concatenation of operations.
2354 if (title.startsWith("Copied sequences"))
2360 newtitle = newtitle.concat("- from " + title);
2364 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2366 } catch (Exception ex)
2368 ex.printStackTrace();
2369 System.out.println("Exception whilst pasting: " + ex);
2370 // could be anything being pasted in here
2371 } catch (OutOfMemoryError oom)
2373 new OOMWarning("Viewing flanking region of alignment", oom);
2378 * Action Cut (delete and copy) the selected region
2381 protected void cut_actionPerformed()
2383 copy_actionPerformed();
2384 delete_actionPerformed();
2388 * Performs menu option to Delete the currently selected region
2391 protected void delete_actionPerformed()
2394 SequenceGroup sg = viewport.getSelectionGroup();
2400 Runnable okAction = new Runnable()
2405 SequenceI[] cut = sg.getSequences()
2406 .toArray(new SequenceI[sg.getSize()]);
2408 addHistoryItem(new EditCommand(
2409 MessageManager.getString("label.cut_sequences"), Action.CUT,
2410 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2411 viewport.getAlignment()));
2413 viewport.setSelectionGroup(null);
2414 viewport.sendSelection();
2415 viewport.getAlignment().deleteGroup(sg);
2417 viewport.firePropertyChange("alignment", null,
2418 viewport.getAlignment().getSequences());
2419 if (viewport.getAlignment().getHeight() < 1)
2423 AlignFrame.this.setClosed(true);
2424 } catch (Exception ex)
2431 * If the cut affects all sequences, prompt for confirmation
2433 boolean wholeHeight = sg.getSize() == viewport.getAlignment().getHeight();
2434 boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2435 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2436 if (wholeHeight && wholeWidth)
2438 JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2439 dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2440 Object[] options = new Object[] { MessageManager.getString("action.ok"),
2441 MessageManager.getString("action.cancel") };
2442 dialog.showDialog(MessageManager.getString("warn.delete_all"),
2443 MessageManager.getString("label.delete_all"),
2444 JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2445 options, options[0]);
2459 protected void deleteGroups_actionPerformed(ActionEvent e)
2461 if (avc.deleteGroups())
2463 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2464 alignPanel.updateAnnotation();
2465 alignPanel.paintAlignment(true, true);
2476 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2478 SequenceGroup sg = new SequenceGroup(
2479 viewport.getAlignment().getSequences());
2481 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2482 viewport.setSelectionGroup(sg);
2483 viewport.isSelectionGroupChanged(true);
2484 viewport.sendSelection();
2485 // JAL-2034 - should delegate to
2486 // alignPanel to decide if overview needs
2488 alignPanel.paintAlignment(false, false);
2489 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2499 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2501 if (viewport.cursorMode)
2503 alignPanel.getSeqPanel().keyboardNo1 = null;
2504 alignPanel.getSeqPanel().keyboardNo2 = null;
2506 viewport.setSelectionGroup(null);
2507 viewport.getColumnSelection().clear();
2508 viewport.setSelectionGroup(null);
2509 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2510 // JAL-2034 - should delegate to
2511 // alignPanel to decide if overview needs
2513 alignPanel.paintAlignment(false, false);
2514 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2515 viewport.sendSelection();
2525 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2527 SequenceGroup sg = viewport.getSelectionGroup();
2531 selectAllSequenceMenuItem_actionPerformed(null);
2536 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2538 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2540 // JAL-2034 - should delegate to
2541 // alignPanel to decide if overview needs
2544 alignPanel.paintAlignment(true, false);
2545 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2546 viewport.sendSelection();
2550 public void invertColSel_actionPerformed(ActionEvent e)
2552 viewport.invertColumnSelection();
2553 alignPanel.paintAlignment(true, false);
2554 viewport.sendSelection();
2564 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2566 trimAlignment(true);
2576 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2578 trimAlignment(false);
2581 void trimAlignment(boolean trimLeft)
2583 ColumnSelection colSel = viewport.getColumnSelection();
2586 if (!colSel.isEmpty())
2590 column = colSel.getMin();
2594 column = colSel.getMax();
2598 if (viewport.getSelectionGroup() != null)
2600 seqs = viewport.getSelectionGroup()
2601 .getSequencesAsArray(viewport.getHiddenRepSequences());
2605 seqs = viewport.getAlignment().getSequencesArray();
2608 TrimRegionCommand trimRegion;
2611 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2612 column, viewport.getAlignment());
2613 viewport.getRanges().setStartRes(0);
2617 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2618 column, viewport.getAlignment());
2621 setStatus(MessageManager
2622 .formatMessage("label.removed_columns", new String[]
2623 { Integer.valueOf(trimRegion.getSize()).toString() }));
2625 addHistoryItem(trimRegion);
2627 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2629 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2630 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2632 viewport.getAlignment().deleteGroup(sg);
2636 viewport.firePropertyChange("alignment", null,
2637 viewport.getAlignment().getSequences());
2648 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2650 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2653 if (viewport.getSelectionGroup() != null)
2655 seqs = viewport.getSelectionGroup()
2656 .getSequencesAsArray(viewport.getHiddenRepSequences());
2657 start = viewport.getSelectionGroup().getStartRes();
2658 end = viewport.getSelectionGroup().getEndRes();
2662 seqs = viewport.getAlignment().getSequencesArray();
2665 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2666 "Remove Gapped Columns", seqs, start, end,
2667 viewport.getAlignment());
2669 addHistoryItem(removeGapCols);
2671 setStatus(MessageManager
2672 .formatMessage("label.removed_empty_columns", new Object[]
2673 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2675 // This is to maintain viewport position on first residue
2676 // of first sequence
2677 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2678 ViewportRanges ranges = viewport.getRanges();
2679 int startRes = seq.findPosition(ranges.getStartRes());
2680 // ShiftList shifts;
2681 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2682 // edit.alColumnChanges=shifts.getInverse();
2683 // if (viewport.hasHiddenColumns)
2684 // viewport.getColumnSelection().compensateForEdits(shifts);
2685 ranges.setStartRes(seq.findIndex(startRes) - 1);
2686 viewport.firePropertyChange("alignment", null,
2687 viewport.getAlignment().getSequences());
2698 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2700 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2703 if (viewport.getSelectionGroup() != null)
2705 seqs = viewport.getSelectionGroup()
2706 .getSequencesAsArray(viewport.getHiddenRepSequences());
2707 start = viewport.getSelectionGroup().getStartRes();
2708 end = viewport.getSelectionGroup().getEndRes();
2712 seqs = viewport.getAlignment().getSequencesArray();
2715 // This is to maintain viewport position on first residue
2716 // of first sequence
2717 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2718 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2720 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2721 viewport.getAlignment()));
2723 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2725 viewport.firePropertyChange("alignment", null,
2726 viewport.getAlignment().getSequences());
2737 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2739 viewport.setPadGaps(padGapsMenuitem.isSelected());
2740 viewport.firePropertyChange("alignment", null,
2741 viewport.getAlignment().getSequences());
2751 public void findMenuItem_actionPerformed(ActionEvent e)
2757 * Create a new view of the current alignment.
2760 public void newView_actionPerformed(ActionEvent e)
2762 newView(null, true);
2766 * Creates and shows a new view of the current alignment.
2769 * title of newly created view; if null, one will be generated
2770 * @param copyAnnotation
2771 * if true then duplicate all annnotation, groups and settings
2772 * @return new alignment panel, already displayed.
2774 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2777 * Create a new AlignmentPanel (with its own, new Viewport)
2779 AlignmentPanel newap = new jalview.project.Jalview2XML()
2780 .copyAlignPanel(alignPanel);
2781 if (!copyAnnotation)
2784 * remove all groups and annotation except for the automatic stuff
2786 newap.av.getAlignment().deleteAllGroups();
2787 newap.av.getAlignment().deleteAllAnnotations(false);
2790 newap.av.setGatherViewsHere(false);
2792 if (viewport.getViewName() == null)
2794 viewport.setViewName(MessageManager
2795 .getString("label.view_name_original"));
2799 * Views share the same edits undo and redo stacks
2801 newap.av.setHistoryList(viewport.getHistoryList());
2802 newap.av.setRedoList(viewport.getRedoList());
2805 * copy any visualisation settings that are not saved in the project
2807 newap.av.setColourAppliesToAllGroups(
2808 viewport.getColourAppliesToAllGroups());
2811 * Views share the same mappings; need to deregister any new mappings
2812 * created by copyAlignPanel, and register the new reference to the shared
2815 newap.av.replaceMappings(viewport.getAlignment());
2818 * start up cDNA consensus (if applicable) now mappings are in place
2820 if (newap.av.initComplementConsensus())
2822 newap.refresh(true); // adjust layout of annotations
2825 newap.av.setViewName(getNewViewName(viewTitle));
2827 addAlignmentPanel(newap, true);
2828 newap.alignmentChanged();
2830 if (alignPanels.size() == 2)
2832 viewport.setGatherViewsHere(true);
2834 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2839 * Make a new name for the view, ensuring it is unique within the current
2840 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2841 * these now use viewId. Unique view names are still desirable for usability.)
2846 protected String getNewViewName(String viewTitle)
2848 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2849 boolean addFirstIndex = false;
2850 if (viewTitle == null || viewTitle.trim().length() == 0)
2852 viewTitle = MessageManager.getString("action.view");
2853 addFirstIndex = true;
2857 index = 1;// we count from 1 if given a specific name
2859 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2861 List<Component> comps = PaintRefresher.components
2862 .get(viewport.getSequenceSetId());
2864 List<String> existingNames = getExistingViewNames(comps);
2866 while (existingNames.contains(newViewName))
2868 newViewName = viewTitle + " " + (++index);
2874 * Returns a list of distinct view names found in the given list of
2875 * components. View names are held on the viewport of an AlignmentPanel.
2880 protected List<String> getExistingViewNames(List<Component> comps)
2882 List<String> existingNames = new ArrayList<>();
2883 for (Component comp : comps)
2885 if (comp instanceof AlignmentPanel)
2887 AlignmentPanel ap = (AlignmentPanel) comp;
2888 if (!existingNames.contains(ap.av.getViewName()))
2890 existingNames.add(ap.av.getViewName());
2894 return existingNames;
2898 * Explode tabbed views into separate windows.
2901 public void expandViews_actionPerformed(ActionEvent e)
2903 Desktop.explodeViews(this);
2907 * Gather views in separate windows back into a tabbed presentation.
2910 public void gatherViews_actionPerformed(ActionEvent e)
2912 Desktop.instance.gatherViews(this);
2922 public void font_actionPerformed(ActionEvent e)
2924 new FontChooser(alignPanel);
2934 protected void seqLimit_actionPerformed(ActionEvent e)
2936 viewport.setShowJVSuffix(seqLimits.isSelected());
2938 alignPanel.getIdPanel().getIdCanvas()
2939 .setPreferredSize(alignPanel.calculateIdWidth());
2940 alignPanel.paintAlignment(true, false);
2944 public void idRightAlign_actionPerformed(ActionEvent e)
2946 viewport.setRightAlignIds(idRightAlign.isSelected());
2947 alignPanel.paintAlignment(false, false);
2951 public void centreColumnLabels_actionPerformed(ActionEvent e)
2953 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2954 alignPanel.paintAlignment(false, false);
2960 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2963 protected void followHighlight_actionPerformed()
2966 * Set the 'follow' flag on the Viewport (and scroll to position if now
2969 final boolean state = this.followHighlightMenuItem.getState();
2970 viewport.setFollowHighlight(state);
2973 alignPanel.scrollToPosition(viewport.getSearchResults());
2984 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2986 viewport.setColourText(colourTextMenuItem.isSelected());
2987 alignPanel.paintAlignment(false, false);
2997 public void wrapMenuItem_actionPerformed(ActionEvent e)
2999 scaleAbove.setVisible(wrapMenuItem.isSelected());
3000 scaleLeft.setVisible(wrapMenuItem.isSelected());
3001 scaleRight.setVisible(wrapMenuItem.isSelected());
3002 viewport.setWrapAlignment(wrapMenuItem.isSelected());
3003 alignPanel.updateLayout();
3007 public void showAllSeqs_actionPerformed(ActionEvent e)
3009 viewport.showAllHiddenSeqs();
3013 public void showAllColumns_actionPerformed(ActionEvent e)
3015 viewport.showAllHiddenColumns();
3016 alignPanel.paintAlignment(true, true);
3017 viewport.sendSelection();
3021 public void hideSelSequences_actionPerformed(ActionEvent e)
3023 viewport.hideAllSelectedSeqs();
3027 * called by key handler and the hide all/show all menu items
3032 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3035 boolean hide = false;
3036 SequenceGroup sg = viewport.getSelectionGroup();
3037 if (!toggleSeqs && !toggleCols)
3039 // Hide everything by the current selection - this is a hack - we do the
3040 // invert and then hide
3041 // first check that there will be visible columns after the invert.
3042 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3043 && sg.getStartRes() <= sg.getEndRes()))
3045 // now invert the sequence set, if required - empty selection implies
3046 // that no hiding is required.
3049 invertSequenceMenuItem_actionPerformed(null);
3050 sg = viewport.getSelectionGroup();
3054 viewport.expandColSelection(sg, true);
3055 // finally invert the column selection and get the new sequence
3057 invertColSel_actionPerformed(null);
3064 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3066 hideSelSequences_actionPerformed(null);
3069 else if (!(toggleCols && viewport.hasSelectedColumns()))
3071 showAllSeqs_actionPerformed(null);
3077 if (viewport.hasSelectedColumns())
3079 hideSelColumns_actionPerformed(null);
3082 viewport.setSelectionGroup(sg);
3087 showAllColumns_actionPerformed(null);
3096 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3097 * event.ActionEvent)
3100 public void hideAllButSelection_actionPerformed(ActionEvent e)
3102 toggleHiddenRegions(false, false);
3103 viewport.sendSelection();
3110 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3114 public void hideAllSelection_actionPerformed(ActionEvent e)
3116 SequenceGroup sg = viewport.getSelectionGroup();
3117 viewport.expandColSelection(sg, false);
3118 viewport.hideAllSelectedSeqs();
3119 viewport.hideSelectedColumns();
3120 alignPanel.updateLayout();
3121 alignPanel.paintAlignment(true, true);
3122 viewport.sendSelection();
3129 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3133 public void showAllhidden_actionPerformed(ActionEvent e)
3135 viewport.showAllHiddenColumns();
3136 viewport.showAllHiddenSeqs();
3137 alignPanel.paintAlignment(true, true);
3138 viewport.sendSelection();
3142 public void hideSelColumns_actionPerformed(ActionEvent e)
3144 viewport.hideSelectedColumns();
3145 alignPanel.updateLayout();
3146 alignPanel.paintAlignment(true, true);
3147 viewport.sendSelection();
3151 public void hiddenMarkers_actionPerformed(ActionEvent e)
3153 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3164 protected void scaleAbove_actionPerformed(ActionEvent e)
3166 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3167 alignPanel.updateLayout();
3168 alignPanel.paintAlignment(true, false);
3178 protected void scaleLeft_actionPerformed(ActionEvent e)
3180 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3181 alignPanel.updateLayout();
3182 alignPanel.paintAlignment(true, false);
3192 protected void scaleRight_actionPerformed(ActionEvent e)
3194 viewport.setScaleRightWrapped(scaleRight.isSelected());
3195 alignPanel.updateLayout();
3196 alignPanel.paintAlignment(true, false);
3206 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3208 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3209 alignPanel.paintAlignment(false, false);
3219 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3221 viewport.setShowText(viewTextMenuItem.isSelected());
3222 alignPanel.paintAlignment(false, false);
3232 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3234 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3235 alignPanel.paintAlignment(false, false);
3238 public FeatureSettings featureSettings;
3241 public FeatureSettingsControllerI getFeatureSettingsUI()
3243 return featureSettings;
3247 public void featureSettings_actionPerformed(ActionEvent e)
3249 if (featureSettings != null)
3251 featureSettings.close();
3252 featureSettings = null;
3254 if (!showSeqFeatures.isSelected())
3256 // make sure features are actually displayed
3257 showSeqFeatures.setSelected(true);
3258 showSeqFeatures_actionPerformed(null);
3260 featureSettings = new FeatureSettings(this);
3264 * Set or clear 'Show Sequence Features'
3270 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3272 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3273 alignPanel.paintAlignment(true, true);
3277 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3278 * the annotations panel as a whole.
3280 * The options to show/hide all annotations should be enabled when the panel
3281 * is shown, and disabled when the panel is hidden.
3286 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3288 final boolean setVisible = annotationPanelMenuItem.isSelected();
3289 viewport.setShowAnnotation(setVisible);
3290 this.showAllSeqAnnotations.setEnabled(setVisible);
3291 this.hideAllSeqAnnotations.setEnabled(setVisible);
3292 this.showAllAlAnnotations.setEnabled(setVisible);
3293 this.hideAllAlAnnotations.setEnabled(setVisible);
3294 alignPanel.updateLayout();
3298 public void alignmentProperties()
3301 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3304 String content = MessageManager.formatMessage("label.html_content",
3306 { contents.toString() });
3309 if (Platform.isJS())
3311 JLabel textLabel = new JLabel();
3312 textLabel.setText(content);
3313 textLabel.setBackground(Color.WHITE);
3315 pane = new JPanel(new BorderLayout());
3316 ((JPanel) pane).setOpaque(true);
3317 pane.setBackground(Color.WHITE);
3318 ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3327 JEditorPane editPane = new JEditorPane("text/html", "");
3328 editPane.setEditable(false);
3329 editPane.setText(content);
3333 JInternalFrame frame = new JInternalFrame();
3335 frame.getContentPane().add(new JScrollPane(pane));
3337 Desktop.addInternalFrame(frame, MessageManager
3338 .formatMessage("label.alignment_properties", new Object[]
3339 { getTitle() }), 500, 400);
3349 public void overviewMenuItem_actionPerformed(ActionEvent e)
3351 if (alignPanel.overviewPanel != null)
3356 JInternalFrame frame = new JInternalFrame();
3357 final OverviewPanel overview = new OverviewPanel(alignPanel);
3358 frame.setContentPane(overview);
3359 Desktop.addInternalFrame(frame, MessageManager
3360 .formatMessage("label.overview_params", new Object[]
3361 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3364 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3365 frame.addInternalFrameListener(
3366 new javax.swing.event.InternalFrameAdapter()
3369 public void internalFrameClosed(
3370 javax.swing.event.InternalFrameEvent evt)
3373 alignPanel.setOverviewPanel(null);
3376 if (getKeyListeners().length > 0)
3378 frame.addKeyListener(getKeyListeners()[0]);
3381 alignPanel.setOverviewPanel(overview);
3385 public void textColour_actionPerformed()
3387 new TextColourChooser().chooseColour(alignPanel, null);
3391 * public void covariationColour_actionPerformed() {
3393 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3397 public void annotationColour_actionPerformed()
3399 new AnnotationColourChooser(viewport, alignPanel);
3403 public void annotationColumn_actionPerformed(ActionEvent e)
3405 new AnnotationColumnChooser(viewport, alignPanel);
3409 * Action on the user checking or unchecking the option to apply the selected
3410 * colour scheme to all groups. If unchecked, groups may have their own
3411 * independent colour schemes.
3416 public void applyToAllGroups_actionPerformed(boolean selected)
3418 viewport.setColourAppliesToAllGroups(selected);
3422 * Action on user selecting a colour from the colour menu
3425 * the name (not the menu item label!) of the colour scheme
3428 public void changeColour_actionPerformed(String name)
3431 * 'User Defined' opens a panel to configure or load a
3432 * user-defined colour scheme
3434 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3436 new UserDefinedColours(alignPanel);
3441 * otherwise set the chosen colour scheme (or null for 'None')
3443 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3445 viewport.getAlignment(), viewport.getHiddenRepSequences());
3450 * Actions on setting or changing the alignment colour scheme
3455 public void changeColour(ColourSchemeI cs)
3457 // TODO: pull up to controller method
3458 ColourMenuHelper.setColourSelected(colourMenu, cs);
3460 viewport.setGlobalColourScheme(cs);
3462 alignPanel.paintAlignment(true, true);
3466 * Show the PID threshold slider panel
3469 protected void modifyPID_actionPerformed()
3471 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3472 alignPanel.getViewName());
3473 SliderPanel.showPIDSlider();
3477 * Show the Conservation slider panel
3480 protected void modifyConservation_actionPerformed()
3482 SliderPanel.setConservationSlider(alignPanel,
3483 viewport.getResidueShading(), alignPanel.getViewName());
3484 SliderPanel.showConservationSlider();
3488 * Action on selecting or deselecting (Colour) By Conservation
3491 public void conservationMenuItem_actionPerformed(boolean selected)
3493 modifyConservation.setEnabled(selected);
3494 viewport.setConservationSelected(selected);
3495 viewport.getResidueShading().setConservationApplied(selected);
3497 changeColour(viewport.getGlobalColourScheme());
3500 modifyConservation_actionPerformed();
3504 SliderPanel.hideConservationSlider();
3509 * Action on selecting or deselecting (Colour) Above PID Threshold
3512 public void abovePIDThreshold_actionPerformed(boolean selected)
3514 modifyPID.setEnabled(selected);
3515 viewport.setAbovePIDThreshold(selected);
3518 viewport.getResidueShading().setThreshold(0,
3519 viewport.isIgnoreGapsConsensus());
3522 changeColour(viewport.getGlobalColourScheme());
3525 modifyPID_actionPerformed();
3529 SliderPanel.hidePIDSlider();
3540 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3542 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3543 AlignmentSorter.sortByPID(viewport.getAlignment(),
3544 viewport.getAlignment().getSequenceAt(0));
3545 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3546 viewport.getAlignment()));
3547 alignPanel.paintAlignment(true, false);
3557 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3559 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3560 AlignmentSorter.sortByID(viewport.getAlignment());
3562 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3563 alignPanel.paintAlignment(true, false);
3573 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3575 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3576 AlignmentSorter.sortByLength(viewport.getAlignment());
3577 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3578 viewport.getAlignment()));
3579 alignPanel.paintAlignment(true, false);
3589 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3591 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3592 AlignmentSorter.sortByGroup(viewport.getAlignment());
3593 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3594 viewport.getAlignment()));
3596 alignPanel.paintAlignment(true, false);
3606 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3608 new RedundancyPanel(alignPanel, this);
3618 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3620 if ((viewport.getSelectionGroup() == null)
3621 || (viewport.getSelectionGroup().getSize() < 2))
3623 JvOptionPane.showInternalMessageDialog(this,
3624 MessageManager.getString(
3625 "label.you_must_select_least_two_sequences"),
3626 MessageManager.getString("label.invalid_selection"),
3627 JvOptionPane.WARNING_MESSAGE);
3631 JInternalFrame frame = new JInternalFrame();
3632 frame.setContentPane(new PairwiseAlignPanel(viewport));
3633 Desktop.addInternalFrame(frame,
3634 MessageManager.getString("action.pairwise_alignment"), 600,
3640 public void autoCalculate_actionPerformed(ActionEvent e)
3642 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3643 if (viewport.autoCalculateConsensus)
3645 viewport.firePropertyChange("alignment", null,
3646 viewport.getAlignment().getSequences());
3651 public void sortByTreeOption_actionPerformed(ActionEvent e)
3653 viewport.sortByTree = sortByTree.isSelected();
3657 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3659 viewport.followSelection = listenToViewSelections.isSelected();
3663 * Constructs a tree panel and adds it to the desktop
3666 * tree type (NJ or AV)
3668 * name of score model used to compute the tree
3670 * parameters for the distance or similarity calculation
3672 void newTreePanel(String type, String modelName,
3673 SimilarityParamsI options)
3675 String frameTitle = "";
3678 boolean onSelection = false;
3679 if (viewport.getSelectionGroup() != null
3680 && viewport.getSelectionGroup().getSize() > 0)
3682 SequenceGroup sg = viewport.getSelectionGroup();
3684 /* Decide if the selection is a column region */
3685 for (SequenceI _s : sg.getSequences())
3687 if (_s.getLength() < sg.getEndRes())
3689 JvOptionPane.showMessageDialog(Desktop.desktop,
3690 MessageManager.getString(
3691 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3692 MessageManager.getString(
3693 "label.sequences_selection_not_aligned"),
3694 JvOptionPane.WARNING_MESSAGE);
3703 if (viewport.getAlignment().getHeight() < 2)
3709 tp = new TreePanel(alignPanel, type, modelName, options);
3710 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3712 frameTitle += " from ";
3714 if (viewport.getViewName() != null)
3716 frameTitle += viewport.getViewName() + " of ";
3719 frameTitle += this.title;
3721 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3732 public void addSortByOrderMenuItem(String title,
3733 final AlignmentOrder order)
3735 final JMenuItem item = new JMenuItem(MessageManager
3736 .formatMessage("action.by_title_param", new Object[]
3739 item.addActionListener(new java.awt.event.ActionListener()
3742 public void actionPerformed(ActionEvent e)
3744 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3746 // TODO: JBPNote - have to map order entries to curent SequenceI
3748 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3750 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3751 viewport.getAlignment()));
3753 alignPanel.paintAlignment(true, false);
3759 * Add a new sort by annotation score menu item
3762 * the menu to add the option to
3764 * the label used to retrieve scores for each sequence on the
3767 public void addSortByAnnotScoreMenuItem(JMenu sort,
3768 final String scoreLabel)
3770 final JMenuItem item = new JMenuItem(scoreLabel);
3772 item.addActionListener(new java.awt.event.ActionListener()
3775 public void actionPerformed(ActionEvent e)
3777 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3778 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3779 viewport.getAlignment());// ,viewport.getSelectionGroup());
3780 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3781 viewport.getAlignment()));
3782 alignPanel.paintAlignment(true, false);
3788 * last hash for alignment's annotation array - used to minimise cost of
3791 protected int _annotationScoreVectorHash;
3794 * search the alignment and rebuild the sort by annotation score submenu the
3795 * last alignment annotation vector hash is stored to minimize cost of
3796 * rebuilding in subsequence calls.
3800 public void buildSortByAnnotationScoresMenu()
3802 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3807 if (viewport.getAlignment().getAlignmentAnnotation()
3808 .hashCode() != _annotationScoreVectorHash)
3810 sortByAnnotScore.removeAll();
3811 // almost certainly a quicker way to do this - but we keep it simple
3812 Hashtable scoreSorts = new Hashtable();
3813 AlignmentAnnotation aann[];
3814 for (SequenceI sqa : viewport.getAlignment().getSequences())
3816 aann = sqa.getAnnotation();
3817 for (int i = 0; aann != null && i < aann.length; i++)
3819 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3821 scoreSorts.put(aann[i].label, aann[i].label);
3825 Enumeration labels = scoreSorts.keys();
3826 while (labels.hasMoreElements())
3828 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3829 (String) labels.nextElement());
3831 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3834 _annotationScoreVectorHash = viewport.getAlignment()
3835 .getAlignmentAnnotation().hashCode();
3840 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3841 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3842 * call. Listeners are added to remove the menu item when the treePanel is
3843 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3847 public void buildTreeSortMenu()
3849 sortByTreeMenu.removeAll();
3851 List<Component> comps = PaintRefresher.components
3852 .get(viewport.getSequenceSetId());
3853 List<TreePanel> treePanels = new ArrayList<>();
3854 for (Component comp : comps)
3856 if (comp instanceof TreePanel)
3858 treePanels.add((TreePanel) comp);
3862 if (treePanels.size() < 1)
3864 sortByTreeMenu.setVisible(false);
3868 sortByTreeMenu.setVisible(true);
3870 for (final TreePanel tp : treePanels)
3872 final JMenuItem item = new JMenuItem(tp.getTitle());
3873 item.addActionListener(new java.awt.event.ActionListener()
3876 public void actionPerformed(ActionEvent e)
3878 tp.sortByTree_actionPerformed();
3879 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3884 sortByTreeMenu.add(item);
3888 public boolean sortBy(AlignmentOrder alorder, String undoname)
3890 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3891 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3892 if (undoname != null)
3894 addHistoryItem(new OrderCommand(undoname, oldOrder,
3895 viewport.getAlignment()));
3897 alignPanel.paintAlignment(true, false);
3902 * Work out whether the whole set of sequences or just the selected set will
3903 * be submitted for multiple alignment.
3906 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3908 // Now, check we have enough sequences
3909 AlignmentView msa = null;
3911 if ((viewport.getSelectionGroup() != null)
3912 && (viewport.getSelectionGroup().getSize() > 1))
3914 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3915 // some common interface!
3917 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3918 * SequenceI[sz = seqs.getSize(false)];
3920 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3921 * seqs.getSequenceAt(i); }
3923 msa = viewport.getAlignmentView(true);
3925 else if (viewport.getSelectionGroup() != null
3926 && viewport.getSelectionGroup().getSize() == 1)
3928 int option = JvOptionPane.showConfirmDialog(this,
3929 MessageManager.getString("warn.oneseq_msainput_selection"),
3930 MessageManager.getString("label.invalid_selection"),
3931 JvOptionPane.OK_CANCEL_OPTION);
3932 if (option == JvOptionPane.OK_OPTION)
3934 msa = viewport.getAlignmentView(false);
3939 msa = viewport.getAlignmentView(false);
3945 * Decides what is submitted to a secondary structure prediction service: the
3946 * first sequence in the alignment, or in the current selection, or, if the
3947 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3948 * region or the whole alignment. (where the first sequence in the set is the
3949 * one that the prediction will be for).
3951 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3953 AlignmentView seqs = null;
3955 if ((viewport.getSelectionGroup() != null)
3956 && (viewport.getSelectionGroup().getSize() > 0))
3958 seqs = viewport.getAlignmentView(true);
3962 seqs = viewport.getAlignmentView(false);
3964 // limit sequences - JBPNote in future - could spawn multiple prediction
3966 // TODO: viewport.getAlignment().isAligned is a global state - the local
3967 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3968 if (!viewport.getAlignment().isAligned(false))
3970 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3971 // TODO: if seqs.getSequences().length>1 then should really have warned
3985 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3987 // Pick the tree file
3988 JalviewFileChooser chooser = new JalviewFileChooser(
3989 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3990 chooser.setFileView(new JalviewFileView());
3991 chooser.setDialogTitle(
3992 MessageManager.getString("label.select_newick_like_tree_file"));
3993 chooser.setToolTipText(
3994 MessageManager.getString("label.load_tree_file"));
3996 chooser.setResponseHandler(0,new Runnable()
4001 String filePath = chooser.getSelectedFile().getPath();
4002 Cache.setProperty("LAST_DIRECTORY", filePath);
4003 NewickFile fin = null;
4006 fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4007 DataSourceType.FILE));
4008 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4009 } catch (Exception ex)
4011 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4013 .getString("label.problem_reading_tree_file"),
4014 JvOptionPane.WARNING_MESSAGE);
4015 ex.printStackTrace();
4017 if (fin != null && fin.hasWarningMessage())
4019 JvOptionPane.showMessageDialog(Desktop.desktop,
4020 fin.getWarningMessage(),
4021 MessageManager.getString(
4022 "label.possible_problem_with_tree_file"),
4023 JvOptionPane.WARNING_MESSAGE);
4027 chooser.showOpenDialog(this);
4030 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4032 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4035 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4036 int h, int x, int y)
4038 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4042 * Add a treeviewer for the tree extracted from a Newick file object to the
4043 * current alignment view
4050 * Associated alignment input data (or null)
4059 * @return TreePanel handle
4061 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4062 AlignmentView input, int w, int h, int x, int y)
4064 TreePanel tp = null;
4070 if (nf.getTree() != null)
4072 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4078 tp.setLocation(x, y);
4081 Desktop.addInternalFrame(tp, treeTitle, w, h);
4083 } catch (Exception ex)
4085 ex.printStackTrace();
4091 private boolean buildingMenu = false;
4094 * Generates menu items and listener event actions for web service clients
4097 public void BuildWebServiceMenu()
4099 while (buildingMenu)
4103 System.err.println("Waiting for building menu to finish.");
4105 } catch (Exception e)
4109 final AlignFrame me = this;
4110 buildingMenu = true;
4111 new Thread(new Runnable()
4116 final List<JMenuItem> legacyItems = new ArrayList<>();
4119 // System.err.println("Building ws menu again "
4120 // + Thread.currentThread());
4121 // TODO: add support for context dependent disabling of services based
4123 // alignment and current selection
4124 // TODO: add additional serviceHandle parameter to specify abstract
4126 // class independently of AbstractName
4127 // TODO: add in rediscovery GUI function to restart discoverer
4128 // TODO: group services by location as well as function and/or
4130 // object broker mechanism.
4131 final Vector<JMenu> wsmenu = new Vector<>();
4132 final IProgressIndicator af = me;
4135 * do not i18n these strings - they are hard-coded in class
4136 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4137 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4139 final JMenu msawsmenu = new JMenu("Alignment");
4140 final JMenu secstrmenu = new JMenu(
4141 "Secondary Structure Prediction");
4142 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4143 final JMenu analymenu = new JMenu("Analysis");
4144 final JMenu dismenu = new JMenu("Protein Disorder");
4145 // JAL-940 - only show secondary structure prediction services from
4146 // the legacy server
4147 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4149 Discoverer.services != null && (Discoverer.services.size() > 0))
4151 // TODO: refactor to allow list of AbstractName/Handler bindings to
4153 // stored or retrieved from elsewhere
4154 // No MSAWS used any more:
4155 // Vector msaws = null; // (Vector)
4156 // Discoverer.services.get("MsaWS");
4157 Vector secstrpr = (Vector) Discoverer.services
4159 if (secstrpr != null)
4161 // Add any secondary structure prediction services
4162 for (int i = 0, j = secstrpr.size(); i < j; i++)
4164 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4166 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4167 .getServiceClient(sh);
4168 int p = secstrmenu.getItemCount();
4169 impl.attachWSMenuEntry(secstrmenu, me);
4170 int q = secstrmenu.getItemCount();
4171 for (int litm = p; litm < q; litm++)
4173 legacyItems.add(secstrmenu.getItem(litm));
4179 // Add all submenus in the order they should appear on the web
4181 wsmenu.add(msawsmenu);
4182 wsmenu.add(secstrmenu);
4183 wsmenu.add(dismenu);
4184 wsmenu.add(analymenu);
4185 // No search services yet
4186 // wsmenu.add(seqsrchmenu);
4188 javax.swing.SwingUtilities.invokeLater(new Runnable()
4195 webService.removeAll();
4196 // first, add discovered services onto the webservices menu
4197 if (wsmenu.size() > 0)
4199 for (int i = 0, j = wsmenu.size(); i < j; i++)
4201 webService.add(wsmenu.get(i));
4206 webService.add(me.webServiceNoServices);
4208 // TODO: move into separate menu builder class.
4209 boolean new_sspred = false;
4210 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4212 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4213 if (jws2servs != null)
4215 if (jws2servs.hasServices())
4217 jws2servs.attachWSMenuEntry(webService, me);
4218 for (Jws2Instance sv : jws2servs.getServices())
4220 if (sv.description.toLowerCase().contains("jpred"))
4222 for (JMenuItem jmi : legacyItems)
4224 jmi.setVisible(false);
4230 if (jws2servs.isRunning())
4232 JMenuItem tm = new JMenuItem(
4233 "Still discovering JABA Services");
4234 tm.setEnabled(false);
4239 build_urlServiceMenu(me.webService);
4240 build_fetchdbmenu(webService);
4241 for (JMenu item : wsmenu)
4243 if (item.getItemCount() == 0)
4245 item.setEnabled(false);
4249 item.setEnabled(true);
4252 } catch (Exception e)
4255 "Exception during web service menu building process.",
4260 } catch (Exception e)
4263 buildingMenu = false;
4270 * construct any groupURL type service menu entries.
4274 private void build_urlServiceMenu(JMenu webService)
4276 // TODO: remove this code when 2.7 is released
4277 // DEBUG - alignmentView
4279 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4280 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4282 * @Override public void actionPerformed(ActionEvent e) {
4283 * jalview.datamodel.AlignmentView
4284 * .testSelectionViews(af.viewport.getAlignment(),
4285 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4287 * }); webService.add(testAlView);
4289 // TODO: refactor to RestClient discoverer and merge menu entries for
4290 // rest-style services with other types of analysis/calculation service
4291 // SHmmr test client - still being implemented.
4292 // DEBUG - alignmentView
4294 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4297 client.attachWSMenuEntry(
4298 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4304 * Searches the alignment sequences for xRefs and builds the Show
4305 * Cross-References menu (formerly called Show Products), with database
4306 * sources for which cross-references are found (protein sources for a
4307 * nucleotide alignment and vice versa)
4309 * @return true if Show Cross-references menu should be enabled
4311 public boolean canShowProducts()
4313 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4314 AlignmentI dataset = viewport.getAlignment().getDataset();
4316 showProducts.removeAll();
4317 final boolean dna = viewport.getAlignment().isNucleotide();
4319 if (seqs == null || seqs.length == 0)
4321 // nothing to see here.
4325 boolean showp = false;
4328 List<String> ptypes = new CrossRef(seqs, dataset)
4329 .findXrefSourcesForSequences(dna);
4331 for (final String source : ptypes)
4334 final AlignFrame af = this;
4335 JMenuItem xtype = new JMenuItem(source);
4336 xtype.addActionListener(new ActionListener()
4339 public void actionPerformed(ActionEvent e)
4341 showProductsFor(af.viewport.getSequenceSelection(), dna,
4345 showProducts.add(xtype);
4347 showProducts.setVisible(showp);
4348 showProducts.setEnabled(showp);
4349 } catch (Exception e)
4352 "canShowProducts threw an exception - please report to help@jalview.org",
4360 * Finds and displays cross-references for the selected sequences (protein
4361 * products for nucleotide sequences, dna coding sequences for peptides).
4364 * the sequences to show cross-references for
4366 * true if from a nucleotide alignment (so showing proteins)
4368 * the database to show cross-references for
4370 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4371 final String source)
4373 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4378 * Construct and display a new frame containing the translation of this
4379 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4382 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4384 AlignmentI al = null;
4387 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4389 al = dna.translateCdna(codeTable);
4390 } catch (Exception ex)
4392 jalview.bin.Cache.log.error(
4393 "Exception during translation. Please report this !", ex);
4394 final String msg = MessageManager.getString(
4395 "label.error_when_translating_sequences_submit_bug_report");
4396 final String errorTitle = MessageManager
4397 .getString("label.implementation_error")
4398 + MessageManager.getString("label.translation_failed");
4399 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4400 JvOptionPane.ERROR_MESSAGE);
4403 if (al == null || al.getHeight() == 0)
4405 final String msg = MessageManager.getString(
4406 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4407 final String errorTitle = MessageManager
4408 .getString("label.translation_failed");
4409 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4410 JvOptionPane.WARNING_MESSAGE);
4414 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4415 af.setFileFormat(this.currentFileFormat);
4416 final String newTitle = MessageManager
4417 .formatMessage("label.translation_of_params", new Object[]
4418 { this.getTitle(), codeTable.getId() });
4419 af.setTitle(newTitle);
4420 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4422 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4423 viewport.openSplitFrame(af, new Alignment(seqs));
4427 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4434 * Set the file format
4438 public void setFileFormat(FileFormatI format)
4440 this.currentFileFormat = format;
4444 * Try to load a features file onto the alignment.
4447 * contents or path to retrieve file or a File object
4449 * access mode of file (see jalview.io.AlignFile)
4450 * @return true if features file was parsed correctly.
4452 public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4455 return avc.parseFeaturesFile(file, sourceType,
4456 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4461 public void refreshFeatureUI(boolean enableIfNecessary)
4463 // note - currently this is only still here rather than in the controller
4464 // because of the featureSettings hard reference that is yet to be
4466 if (enableIfNecessary)
4468 viewport.setShowSequenceFeatures(true);
4469 showSeqFeatures.setSelected(true);
4475 public void dragEnter(DropTargetDragEvent evt)
4480 public void dragExit(DropTargetEvent evt)
4485 public void dragOver(DropTargetDragEvent evt)
4490 public void dropActionChanged(DropTargetDragEvent evt)
4495 public void drop(DropTargetDropEvent evt)
4497 // JAL-1552 - acceptDrop required before getTransferable call for
4498 // Java's Transferable for native dnd
4499 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4500 Transferable t = evt.getTransferable();
4502 final AlignFrame thisaf = this;
4503 final List<Object> files = new ArrayList<>();
4504 List<DataSourceType> protocols = new ArrayList<>();
4508 Desktop.transferFromDropTarget(files, protocols, evt, t);
4509 } catch (Exception e)
4511 e.printStackTrace();
4515 new Thread(new Runnable()
4522 // check to see if any of these files have names matching sequences
4525 SequenceIdMatcher idm = new SequenceIdMatcher(
4526 viewport.getAlignment().getSequencesArray());
4528 * Object[] { String,SequenceI}
4530 ArrayList<Object[]> filesmatched = new ArrayList<>();
4531 ArrayList<Object> filesnotmatched = new ArrayList<>();
4532 for (int i = 0; i < files.size(); i++)
4535 Object file = files.get(i);
4536 String fileName = file.toString();
4538 DataSourceType protocol = (file instanceof File
4539 ? DataSourceType.FILE
4540 : FormatAdapter.checkProtocol(fileName));
4541 if (protocol == DataSourceType.FILE)
4543 File fl = (file instanceof File ? (File) file
4544 : new File(fileName));
4545 pdbfn = fl.getName();
4547 else if (protocol == DataSourceType.URL)
4549 URL url = new URL(fileName);
4550 pdbfn = url.getFile();
4552 if (pdbfn.length() > 0)
4554 // attempt to find a match in the alignment
4555 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4556 int l = 0, c = pdbfn.indexOf(".");
4557 while (mtch == null && c != -1)
4562 } while ((c = pdbfn.indexOf(".", l)) > l);
4565 pdbfn = pdbfn.substring(0, l);
4567 mtch = idm.findAllIdMatches(pdbfn);
4574 type = new IdentifyFile().identify(file, protocol);
4575 } catch (Exception ex)
4579 if (type != null && type.isStructureFile())
4581 filesmatched.add(new Object[] { file, protocol, mtch });
4585 // File wasn't named like one of the sequences or wasn't a PDB
4587 filesnotmatched.add(file);
4591 if (filesmatched.size() > 0)
4593 boolean autoAssociate = Cache
4594 .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4597 String msg = MessageManager.formatMessage(
4598 "label.automatically_associate_structure_files_with_sequences_same_name",
4600 { Integer.valueOf(filesmatched.size())
4602 String ttl = MessageManager.getString(
4603 "label.automatically_associate_structure_files_by_name");
4604 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4605 ttl, JvOptionPane.YES_NO_OPTION);
4606 autoAssociate = choice == JvOptionPane.YES_OPTION;
4610 for (Object[] fm : filesmatched)
4612 // try and associate
4613 // TODO: may want to set a standard ID naming formalism for
4614 // associating PDB files which have no IDs.
4615 for (SequenceI toassoc : (SequenceI[]) fm[2])
4617 PDBEntry pe = new AssociatePdbFileWithSeq()
4618 .associatePdbWithSeq(fm[0].toString(),
4619 (DataSourceType) fm[1], toassoc, false,
4623 System.err.println("Associated file : "
4624 + (fm[0].toString()) + " with "
4625 + toassoc.getDisplayId(true));
4629 // TODO: do we need to update overview ? only if features are
4631 alignPanel.paintAlignment(true, false);
4637 * add declined structures as sequences
4639 for (Object[] o : filesmatched)
4641 filesnotmatched.add(o[0]);
4645 if (filesnotmatched.size() > 0)
4647 if (assocfiles > 0 && (Cache.getDefault(
4648 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4649 || JvOptionPane.showConfirmDialog(thisaf,
4650 "<html>" + MessageManager.formatMessage(
4651 "label.ignore_unmatched_dropped_files_info",
4654 filesnotmatched.size())
4657 MessageManager.getString(
4658 "label.ignore_unmatched_dropped_files"),
4659 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4663 for (Object fn : filesnotmatched)
4665 loadJalviewDataFile(fn, null, null, null);
4669 } catch (Exception ex)
4671 ex.printStackTrace();
4679 * Attempt to load a "dropped" file or URL string, by testing in turn for
4681 * <li>an Annotation file</li>
4682 * <li>a JNet file</li>
4683 * <li>a features file</li>
4684 * <li>else try to interpret as an alignment file</li>
4688 * either a filename or a URL string.
4690 public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4691 FileFormatI format, SequenceI assocSeq)
4693 // BH 2018 was String file
4696 if (sourceType == null)
4698 sourceType = FormatAdapter.checkProtocol(file);
4700 // if the file isn't identified, or not positively identified as some
4701 // other filetype (PFAM is default unidentified alignment file type) then
4702 // try to parse as annotation.
4703 boolean isAnnotation = (format == null
4704 || FileFormat.Pfam.equals(format))
4705 ? new AnnotationFile().annotateAlignmentView(viewport,
4711 // first see if its a T-COFFEE score file
4712 TCoffeeScoreFile tcf = null;
4715 tcf = new TCoffeeScoreFile(file, sourceType);
4718 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4722 new TCoffeeColourScheme(viewport.getAlignment()));
4723 isAnnotation = true;
4724 setStatus(MessageManager.getString(
4725 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4729 // some problem - if no warning its probable that the ID matching
4730 // process didn't work
4731 JvOptionPane.showMessageDialog(Desktop.desktop,
4732 tcf.getWarningMessage() == null
4733 ? MessageManager.getString(
4734 "label.check_file_matches_sequence_ids_alignment")
4735 : tcf.getWarningMessage(),
4736 MessageManager.getString(
4737 "label.problem_reading_tcoffee_score_file"),
4738 JvOptionPane.WARNING_MESSAGE);
4745 } catch (Exception x)
4748 "Exception when processing data source as T-COFFEE score file",
4754 // try to see if its a JNet 'concise' style annotation file *before*
4756 // try to parse it as a features file
4759 format = new IdentifyFile().identify(file, sourceType);
4761 if (FileFormat.ScoreMatrix == format)
4763 ScoreMatrixFile sm = new ScoreMatrixFile(
4764 new FileParse(file, sourceType));
4766 // todo: i18n this message
4767 setStatus(MessageManager.formatMessage(
4768 "label.successfully_loaded_matrix",
4769 sm.getMatrixName()));
4771 else if (FileFormat.Jnet.equals(format))
4773 JPredFile predictions = new JPredFile(file, sourceType);
4774 new JnetAnnotationMaker();
4775 JnetAnnotationMaker.add_annotation(predictions,
4776 viewport.getAlignment(), 0, false);
4777 viewport.getAlignment().setupJPredAlignment();
4778 isAnnotation = true;
4780 // else if (IdentifyFile.FeaturesFile.equals(format))
4781 else if (FileFormat.Features.equals(format))
4783 if (parseFeaturesFile(file, sourceType))
4785 alignPanel.paintAlignment(true, true);
4790 new FileLoader().LoadFile(viewport, file, sourceType, format);
4797 alignPanel.adjustAnnotationHeight();
4798 viewport.updateSequenceIdColours();
4799 buildSortByAnnotationScoresMenu();
4800 alignPanel.paintAlignment(true, true);
4802 } catch (Exception ex)
4804 ex.printStackTrace();
4805 } catch (OutOfMemoryError oom)
4810 } catch (Exception x)
4815 + (sourceType != null
4816 ? (sourceType == DataSourceType.PASTE
4818 : "using " + sourceType + " from "
4822 ? "(parsing as '" + format + "' file)"
4824 oom, Desktop.desktop);
4829 * Method invoked by the ChangeListener on the tabbed pane, in other words
4830 * when a different tabbed pane is selected by the user or programmatically.
4833 public void tabSelectionChanged(int index)
4837 alignPanel = alignPanels.get(index);
4838 viewport = alignPanel.av;
4839 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4840 setMenusFromViewport(viewport);
4844 * 'focus' any colour slider that is open to the selected viewport
4846 if (viewport.getConservationSelected())
4848 SliderPanel.setConservationSlider(alignPanel,
4849 viewport.getResidueShading(), alignPanel.getViewName());
4853 SliderPanel.hideConservationSlider();
4855 if (viewport.getAbovePIDThreshold())
4857 SliderPanel.setPIDSliderSource(alignPanel,
4858 viewport.getResidueShading(), alignPanel.getViewName());
4862 SliderPanel.hidePIDSlider();
4866 * If there is a frame linked to this one in a SplitPane, switch it to the
4867 * same view tab index. No infinite recursion of calls should happen, since
4868 * tabSelectionChanged() should not get invoked on setting the selected
4869 * index to an unchanged value. Guard against setting an invalid index
4870 * before the new view peer tab has been created.
4872 final AlignViewportI peer = viewport.getCodingComplement();
4875 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4876 .getAlignPanel().alignFrame;
4877 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4879 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4885 * On right mouse click on view tab, prompt for and set new view name.
4888 public void tabbedPane_mousePressed(MouseEvent e)
4890 if (e.isPopupTrigger())
4892 String msg = MessageManager.getString("label.enter_view_name");
4893 String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
4894 String reply = JvOptionPane.showInputDialog(msg, ttl);
4898 viewport.setViewName(reply);
4899 // TODO warn if reply is in getExistingViewNames()?
4900 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4905 public AlignViewport getCurrentView()
4911 * Open the dialog for regex description parsing.
4914 protected void extractScores_actionPerformed(ActionEvent e)
4916 ParseProperties pp = new jalview.analysis.ParseProperties(
4917 viewport.getAlignment());
4918 // TODO: verify regex and introduce GUI dialog for version 2.5
4919 // if (pp.getScoresFromDescription("col", "score column ",
4920 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4922 if (pp.getScoresFromDescription("description column",
4923 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4925 buildSortByAnnotationScoresMenu();
4933 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4937 protected void showDbRefs_actionPerformed(ActionEvent e)
4939 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4945 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4949 protected void showNpFeats_actionPerformed(ActionEvent e)
4951 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4955 * find the viewport amongst the tabs in this alignment frame and close that
4960 public boolean closeView(AlignViewportI av)
4964 this.closeMenuItem_actionPerformed(false);
4967 Component[] comp = tabbedPane.getComponents();
4968 for (int i = 0; comp != null && i < comp.length; i++)
4970 if (comp[i] instanceof AlignmentPanel)
4972 if (((AlignmentPanel) comp[i]).av == av)
4975 closeView((AlignmentPanel) comp[i]);
4983 protected void build_fetchdbmenu(JMenu webService)
4985 // Temporary hack - DBRef Fetcher always top level ws entry.
4986 // TODO We probably want to store a sequence database checklist in
4987 // preferences and have checkboxes.. rather than individual sources selected
4989 final JMenu rfetch = new JMenu(
4990 MessageManager.getString("action.fetch_db_references"));
4991 rfetch.setToolTipText(MessageManager.getString(
4992 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4993 webService.add(rfetch);
4995 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4996 MessageManager.getString("option.trim_retrieved_seqs"));
4997 trimrs.setToolTipText(
4998 MessageManager.getString("label.trim_retrieved_sequences"));
5000 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5001 trimrs.addActionListener(new ActionListener()
5004 public void actionPerformed(ActionEvent e)
5006 trimrs.setSelected(trimrs.isSelected());
5007 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5008 Boolean.valueOf(trimrs.isSelected()).toString());
5012 JMenuItem fetchr = new JMenuItem(
5013 MessageManager.getString("label.standard_databases"));
5014 fetchr.setToolTipText(
5015 MessageManager.getString("label.fetch_embl_uniprot"));
5016 fetchr.addActionListener(new ActionListener()
5020 public void actionPerformed(ActionEvent e)
5022 new Thread(new Runnable()
5027 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5028 .getAlignment().isNucleotide();
5029 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5030 alignPanel.av.getSequenceSelection(),
5031 alignPanel.alignFrame, null,
5032 alignPanel.alignFrame.featureSettings, isNucleotide);
5033 dbRefFetcher.addListener(new FetchFinishedListenerI()
5036 public void finished()
5038 AlignFrame.this.setMenusForViewport();
5041 dbRefFetcher.fetchDBRefs(false);
5049 new Thread(new Runnable()
5054 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5055 .getSequenceFetcherSingleton();
5056 javax.swing.SwingUtilities.invokeLater(new Runnable()
5061 String[] dbclasses = sf.getNonAlignmentSources();
5062 List<DbSourceProxy> otherdb;
5063 JMenu dfetch = new JMenu();
5064 JMenu ifetch = new JMenu();
5065 JMenuItem fetchr = null;
5066 int comp = 0, icomp = 0, mcomp = 15;
5067 String mname = null;
5069 for (String dbclass : dbclasses)
5071 otherdb = sf.getSourceProxy(dbclass);
5072 // add a single entry for this class, or submenu allowing 'fetch
5074 if (otherdb == null || otherdb.size() < 1)
5080 mname = "From " + dbclass;
5082 if (otherdb.size() == 1)
5084 final DbSourceProxy[] dassource = otherdb
5085 .toArray(new DbSourceProxy[0]);
5086 DbSourceProxy src = otherdb.get(0);
5087 fetchr = new JMenuItem(src.getDbSource());
5088 fetchr.addActionListener(new ActionListener()
5092 public void actionPerformed(ActionEvent e)
5094 new Thread(new Runnable()
5100 boolean isNucleotide = alignPanel.alignFrame
5101 .getViewport().getAlignment()
5103 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5104 alignPanel.av.getSequenceSelection(),
5105 alignPanel.alignFrame, dassource,
5106 alignPanel.alignFrame.featureSettings,
5109 .addListener(new FetchFinishedListenerI()
5112 public void finished()
5114 AlignFrame.this.setMenusForViewport();
5117 dbRefFetcher.fetchDBRefs(false);
5123 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5124 MessageManager.formatMessage(
5125 "label.fetch_retrieve_from", new Object[]
5126 { src.getDbName() })));
5132 final DbSourceProxy[] dassource = otherdb
5133 .toArray(new DbSourceProxy[0]);
5135 DbSourceProxy src = otherdb.get(0);
5136 fetchr = new JMenuItem(MessageManager
5137 .formatMessage("label.fetch_all_param", new Object[]
5138 { src.getDbSource() }));
5139 fetchr.addActionListener(new ActionListener()
5142 public void actionPerformed(ActionEvent e)
5144 new Thread(new Runnable()
5150 boolean isNucleotide = alignPanel.alignFrame
5151 .getViewport().getAlignment()
5153 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5154 alignPanel.av.getSequenceSelection(),
5155 alignPanel.alignFrame, dassource,
5156 alignPanel.alignFrame.featureSettings,
5159 .addListener(new FetchFinishedListenerI()
5162 public void finished()
5164 AlignFrame.this.setMenusForViewport();
5167 dbRefFetcher.fetchDBRefs(false);
5173 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5174 MessageManager.formatMessage(
5175 "label.fetch_retrieve_from_all_sources",
5177 { Integer.valueOf(otherdb.size())
5179 src.getDbSource(), src.getDbName() })));
5182 // and then build the rest of the individual menus
5183 ifetch = new JMenu(MessageManager.formatMessage(
5184 "label.source_from_db_source", new Object[]
5185 { src.getDbSource() }));
5187 String imname = null;
5189 for (DbSourceProxy sproxy : otherdb)
5191 String dbname = sproxy.getDbName();
5192 String sname = dbname.length() > 5
5193 ? dbname.substring(0, 5) + "..."
5195 String msname = dbname.length() > 10
5196 ? dbname.substring(0, 10) + "..."
5200 imname = MessageManager
5201 .formatMessage("label.from_msname", new Object[]
5204 fetchr = new JMenuItem(msname);
5205 final DbSourceProxy[] dassrc = { sproxy };
5206 fetchr.addActionListener(new ActionListener()
5210 public void actionPerformed(ActionEvent e)
5212 new Thread(new Runnable()
5218 boolean isNucleotide = alignPanel.alignFrame
5219 .getViewport().getAlignment()
5221 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5222 alignPanel.av.getSequenceSelection(),
5223 alignPanel.alignFrame, dassrc,
5224 alignPanel.alignFrame.featureSettings,
5227 .addListener(new FetchFinishedListenerI()
5230 public void finished()
5232 AlignFrame.this.setMenusForViewport();
5235 dbRefFetcher.fetchDBRefs(false);
5241 fetchr.setToolTipText(
5242 "<html>" + MessageManager.formatMessage(
5243 "label.fetch_retrieve_from", new Object[]
5247 if (++icomp >= mcomp || i == (otherdb.size()))
5249 ifetch.setText(MessageManager.formatMessage(
5250 "label.source_to_target", imname, sname));
5252 ifetch = new JMenu();
5260 if (comp >= mcomp || dbi >= (dbclasses.length))
5262 dfetch.setText(MessageManager.formatMessage(
5263 "label.source_to_target", mname, dbclass));
5265 dfetch = new JMenu();
5278 * Left justify the whole alignment.
5281 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5283 AlignmentI al = viewport.getAlignment();
5285 viewport.firePropertyChange("alignment", null, al);
5289 * Right justify the whole alignment.
5292 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5294 AlignmentI al = viewport.getAlignment();
5296 viewport.firePropertyChange("alignment", null, al);
5300 public void setShowSeqFeatures(boolean b)
5302 showSeqFeatures.setSelected(b);
5303 viewport.setShowSequenceFeatures(b);
5310 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5311 * awt.event.ActionEvent)
5314 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5316 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5317 alignPanel.paintAlignment(false, false);
5324 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5328 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5330 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5331 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5339 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5340 * .event.ActionEvent)
5343 protected void showGroupConservation_actionPerformed(ActionEvent e)
5345 viewport.setShowGroupConservation(showGroupConservation.getState());
5346 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5353 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5354 * .event.ActionEvent)
5357 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5359 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5360 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5367 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5368 * .event.ActionEvent)
5371 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5373 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5374 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5378 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5380 showSequenceLogo.setState(true);
5381 viewport.setShowSequenceLogo(true);
5382 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5383 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5387 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5389 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5396 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5397 * .event.ActionEvent)
5400 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5402 if (avc.makeGroupsFromSelection())
5404 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5405 alignPanel.updateAnnotation();
5406 alignPanel.paintAlignment(true,
5407 viewport.needToUpdateStructureViews());
5411 public void clearAlignmentSeqRep()
5413 // TODO refactor alignmentseqrep to controller
5414 if (viewport.getAlignment().hasSeqrep())
5416 viewport.getAlignment().setSeqrep(null);
5417 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5418 alignPanel.updateAnnotation();
5419 alignPanel.paintAlignment(true, true);
5424 protected void createGroup_actionPerformed(ActionEvent e)
5426 if (avc.createGroup())
5428 if (applyAutoAnnotationSettings.isSelected())
5430 alignPanel.updateAnnotation(true, false);
5432 alignPanel.alignmentChanged();
5437 protected void unGroup_actionPerformed(ActionEvent e)
5441 alignPanel.alignmentChanged();
5446 * make the given alignmentPanel the currently selected tab
5448 * @param alignmentPanel
5450 public void setDisplayedView(AlignmentPanel alignmentPanel)
5452 if (!viewport.getSequenceSetId()
5453 .equals(alignmentPanel.av.getSequenceSetId()))
5455 throw new Error(MessageManager.getString(
5456 "error.implementation_error_cannot_show_view_alignment_frame"));
5458 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5459 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5461 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5466 * Action on selection of menu options to Show or Hide annotations.
5469 * @param forSequences
5470 * update sequence-related annotations
5471 * @param forAlignment
5472 * update non-sequence-related annotations
5475 protected void setAnnotationsVisibility(boolean visible,
5476 boolean forSequences, boolean forAlignment)
5478 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5479 .getAlignmentAnnotation();
5484 for (AlignmentAnnotation aa : anns)
5487 * don't display non-positional annotations on an alignment
5489 if (aa.annotations == null)
5493 boolean apply = (aa.sequenceRef == null && forAlignment)
5494 || (aa.sequenceRef != null && forSequences);
5497 aa.visible = visible;
5500 alignPanel.validateAnnotationDimensions(true);
5501 alignPanel.alignmentChanged();
5505 * Store selected annotation sort order for the view and repaint.
5508 protected void sortAnnotations_actionPerformed()
5510 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5512 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5513 alignPanel.paintAlignment(false, false);
5518 * @return alignment panels in this alignment frame
5520 public List<? extends AlignmentViewPanel> getAlignPanels()
5522 // alignPanels is never null
5523 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5528 * Open a new alignment window, with the cDNA associated with this (protein)
5529 * alignment, aligned as is the protein.
5531 protected void viewAsCdna_actionPerformed()
5533 // TODO no longer a menu action - refactor as required
5534 final AlignmentI alignment = getViewport().getAlignment();
5535 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5536 if (mappings == null)
5540 List<SequenceI> cdnaSeqs = new ArrayList<>();
5541 for (SequenceI aaSeq : alignment.getSequences())
5543 for (AlignedCodonFrame acf : mappings)
5545 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5549 * There is a cDNA mapping for this protein sequence - add to new
5550 * alignment. It will share the same dataset sequence as other mapped
5551 * cDNA (no new mappings need to be created).
5553 final Sequence newSeq = new Sequence(dnaSeq);
5554 newSeq.setDatasetSequence(dnaSeq);
5555 cdnaSeqs.add(newSeq);
5559 if (cdnaSeqs.size() == 0)
5561 // show a warning dialog no mapped cDNA
5564 AlignmentI cdna = new Alignment(
5565 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5566 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5567 AlignFrame.DEFAULT_HEIGHT);
5568 cdna.alignAs(alignment);
5569 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5571 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5572 AlignFrame.DEFAULT_HEIGHT);
5576 * Set visibility of dna/protein complement view (available when shown in a
5582 protected void showComplement_actionPerformed(boolean show)
5584 SplitContainerI sf = getSplitViewContainer();
5587 sf.setComplementVisible(this, show);
5592 * Generate the reverse (optionally complemented) of the selected sequences,
5593 * and add them to the alignment
5596 protected void showReverse_actionPerformed(boolean complement)
5598 AlignmentI al = null;
5601 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5602 al = dna.reverseCdna(complement);
5603 viewport.addAlignment(al, "");
5604 addHistoryItem(new EditCommand(
5605 MessageManager.getString("label.add_sequences"), Action.PASTE,
5606 al.getSequencesArray(), 0, al.getWidth(),
5607 viewport.getAlignment()));
5608 } catch (Exception ex)
5610 System.err.println(ex.getMessage());
5616 * Try to run a script in the Groovy console, having first ensured that this
5617 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5618 * be targeted at this alignment.
5621 protected void runGroovy_actionPerformed()
5623 Jalview.setCurrentAlignFrame(this);
5624 groovy.ui.Console console = Desktop.getGroovyConsole();
5625 if (console != null)
5629 console.runScript();
5630 } catch (Exception ex)
5632 System.err.println((ex.toString()));
5633 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5634 MessageManager.getString("label.couldnt_run_groovy_script"),
5635 MessageManager.getString("label.groovy_support_failed"),
5636 JvOptionPane.ERROR_MESSAGE);
5641 System.err.println("Can't run Groovy script as console not found");
5646 * Hides columns containing (or not containing) a specified feature, provided
5647 * that would not leave all columns hidden
5649 * @param featureType
5650 * @param columnsContaining
5653 public boolean hideFeatureColumns(String featureType,
5654 boolean columnsContaining)
5656 boolean notForHiding = avc.markColumnsContainingFeatures(
5657 columnsContaining, false, false, featureType);
5660 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5661 false, featureType))
5663 getViewport().hideSelectedColumns();
5671 protected void selectHighlightedColumns_actionPerformed(
5672 ActionEvent actionEvent)
5674 // include key modifier check in case user selects from menu
5675 avc.markHighlightedColumns(
5676 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5677 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5678 | ActionEvent.CTRL_MASK)) != 0);
5682 * Rebuilds the Colour menu, including any user-defined colours which have
5683 * been loaded either on startup or during the session
5685 public void buildColourMenu()
5687 colourMenu.removeAll();
5689 colourMenu.add(applyToAllGroups);
5690 colourMenu.add(textColour);
5691 colourMenu.addSeparator();
5693 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5694 viewport.getAlignment(), false);
5696 colourMenu.add(annotationColour);
5697 bg.add(annotationColour);
5698 colourMenu.addSeparator();
5699 colourMenu.add(conservationMenuItem);
5700 colourMenu.add(modifyConservation);
5701 colourMenu.add(abovePIDThreshold);
5702 colourMenu.add(modifyPID);
5704 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5705 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5709 * Open a dialog (if not already open) that allows the user to select and
5710 * calculate PCA or Tree analysis
5712 protected void openTreePcaDialog()
5714 if (alignPanel.getCalculationDialog() == null)
5716 new CalculationChooser(AlignFrame.this);
5721 protected void loadVcf_actionPerformed()
5723 JalviewFileChooser chooser = new JalviewFileChooser(
5724 Cache.getProperty("LAST_DIRECTORY"));
5725 chooser.setFileView(new JalviewFileView());
5726 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5727 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5728 final AlignFrame us = this;
5729 chooser.setResponseHandler(0, new Runnable()
5734 String choice = chooser.getSelectedFile().getPath();
5735 Cache.setProperty("LAST_DIRECTORY", choice);
5736 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5737 new VCFLoader(choice).loadVCF(seqs, us);
5740 chooser.showOpenDialog(null);
5746 class PrintThread extends Thread
5750 public PrintThread(AlignmentPanel ap)
5755 static PageFormat pf;
5760 PrinterJob printJob = PrinterJob.getPrinterJob();
5764 printJob.setPrintable(ap, pf);
5768 printJob.setPrintable(ap);
5771 if (printJob.printDialog())
5776 } catch (Exception PrintException)
5778 PrintException.printStackTrace();