2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingsI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.SimilarityParamsI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignExportSettingsAdapter;
49 import jalview.datamodel.AlignedCodonFrame;
50 import jalview.datamodel.Alignment;
51 import jalview.datamodel.AlignmentAnnotation;
52 import jalview.datamodel.AlignmentExportData;
53 import jalview.datamodel.AlignmentI;
54 import jalview.datamodel.AlignmentOrder;
55 import jalview.datamodel.AlignmentView;
56 import jalview.datamodel.ColumnSelection;
57 import jalview.datamodel.HiddenColumns;
58 import jalview.datamodel.PDBEntry;
59 import jalview.datamodel.SeqCigar;
60 import jalview.datamodel.Sequence;
61 import jalview.datamodel.SequenceGroup;
62 import jalview.datamodel.SequenceI;
63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.DataSourceType;
69 import jalview.io.FileFormat;
70 import jalview.io.FileFormatI;
71 import jalview.io.FileFormats;
72 import jalview.io.FileLoader;
73 import jalview.io.FileParse;
74 import jalview.io.FormatAdapter;
75 import jalview.io.HtmlSvgOutput;
76 import jalview.io.IdentifyFile;
77 import jalview.io.JPredFile;
78 import jalview.io.JalviewFileChooser;
79 import jalview.io.JalviewFileView;
80 import jalview.io.JnetAnnotationMaker;
81 import jalview.io.NewickFile;
82 import jalview.io.ScoreMatrixFile;
83 import jalview.io.TCoffeeScoreFile;
84 import jalview.io.vcf.VCFLoader;
85 import jalview.jbgui.GAlignFrame;
86 import jalview.schemes.ColourSchemeI;
87 import jalview.schemes.ColourSchemes;
88 import jalview.schemes.ResidueColourScheme;
89 import jalview.schemes.TCoffeeColourScheme;
90 import jalview.util.ImageMaker.TYPE;
91 import jalview.util.MessageManager;
92 import jalview.util.dialogrunner.RunResponse;
93 import jalview.viewmodel.AlignmentViewport;
94 import jalview.viewmodel.ViewportRanges;
95 import jalview.ws.DBRefFetcher;
96 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
97 import jalview.ws.jws1.Discoverer;
98 import jalview.ws.jws2.Jws2Discoverer;
99 import jalview.ws.jws2.jabaws2.Jws2Instance;
100 import jalview.ws.seqfetcher.DbSourceProxy;
102 import java.awt.BorderLayout;
103 import java.awt.Color;
104 import java.awt.Component;
105 import java.awt.Rectangle;
106 import java.awt.Toolkit;
107 import java.awt.datatransfer.Clipboard;
108 import java.awt.datatransfer.DataFlavor;
109 import java.awt.datatransfer.StringSelection;
110 import java.awt.datatransfer.Transferable;
111 import java.awt.dnd.DnDConstants;
112 import java.awt.dnd.DropTargetDragEvent;
113 import java.awt.dnd.DropTargetDropEvent;
114 import java.awt.dnd.DropTargetEvent;
115 import java.awt.dnd.DropTargetListener;
116 import java.awt.event.ActionEvent;
117 import java.awt.event.ActionListener;
118 import java.awt.event.FocusAdapter;
119 import java.awt.event.FocusEvent;
120 import java.awt.event.ItemEvent;
121 import java.awt.event.ItemListener;
122 import java.awt.event.KeyAdapter;
123 import java.awt.event.KeyEvent;
124 import java.awt.event.MouseEvent;
125 import java.awt.print.PageFormat;
126 import java.awt.print.PrinterJob;
127 import java.beans.PropertyChangeEvent;
128 import java.beans.PropertyChangeListener;
130 import java.io.FileWriter;
131 import java.io.PrintWriter;
133 import java.util.ArrayList;
134 import java.util.Arrays;
135 import java.util.Deque;
136 import java.util.Enumeration;
137 import java.util.Hashtable;
138 import java.util.List;
139 import java.util.Vector;
141 import javax.swing.JCheckBoxMenuItem;
142 import javax.swing.JComponent;
143 import javax.swing.JEditorPane;
144 import javax.swing.JInternalFrame;
145 import javax.swing.JLabel;
146 import javax.swing.JLayeredPane;
147 import javax.swing.JMenu;
148 import javax.swing.JMenuItem;
149 import javax.swing.JPanel;
150 import javax.swing.JScrollPane;
151 import javax.swing.SwingUtilities;
157 * @version $Revision$
159 public class AlignFrame extends GAlignFrame implements DropTargetListener,
160 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
163 public static final int DEFAULT_WIDTH = 700;
165 public static final int DEFAULT_HEIGHT = 500;
168 * The currently displayed panel (selected tabbed view if more than one)
170 public AlignmentPanel alignPanel;
172 AlignViewport viewport;
174 public AlignViewControllerI avc;
176 List<AlignmentPanel> alignPanels = new ArrayList<>();
179 * Last format used to load or save alignments in this window
181 FileFormatI currentFileFormat = null;
184 * Current filename for this alignment
186 String fileName = null;
191 * Creates a new AlignFrame object with specific width and height.
197 public AlignFrame(AlignmentI al, int width, int height)
199 this(al, null, width, height);
203 * Creates a new AlignFrame object with specific width, height and
209 * @param sequenceSetId
211 public AlignFrame(AlignmentI al, int width, int height,
212 String sequenceSetId)
214 this(al, null, width, height, sequenceSetId);
218 * Creates a new AlignFrame object with specific width, height and
224 * @param sequenceSetId
227 public AlignFrame(AlignmentI al, int width, int height,
228 String sequenceSetId, String viewId)
230 this(al, null, width, height, sequenceSetId, viewId);
234 * new alignment window with hidden columns
238 * @param hiddenColumns
239 * ColumnSelection or null
241 * Width of alignment frame
245 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
248 this(al, hiddenColumns, width, height, null);
252 * Create alignment frame for al with hiddenColumns, a specific width and
253 * height, and specific sequenceId
256 * @param hiddenColumns
259 * @param sequenceSetId
262 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
263 int height, String sequenceSetId)
265 this(al, hiddenColumns, width, height, sequenceSetId, null);
269 * Create alignment frame for al with hiddenColumns, a specific width and
270 * height, and specific sequenceId
273 * @param hiddenColumns
276 * @param sequenceSetId
281 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
282 int height, String sequenceSetId, String viewId)
284 setSize(width, height);
286 if (al.getDataset() == null)
291 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
293 alignPanel = new AlignmentPanel(this, viewport);
295 addAlignmentPanel(alignPanel, true);
299 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
300 HiddenColumns hiddenColumns, int width, int height)
302 setSize(width, height);
304 if (al.getDataset() == null)
309 viewport = new AlignViewport(al, hiddenColumns);
311 if (hiddenSeqs != null && hiddenSeqs.length > 0)
313 viewport.hideSequence(hiddenSeqs);
315 alignPanel = new AlignmentPanel(this, viewport);
316 addAlignmentPanel(alignPanel, true);
321 * Make a new AlignFrame from existing alignmentPanels
328 public AlignFrame(AlignmentPanel ap)
332 addAlignmentPanel(ap, false);
337 * initalise the alignframe from the underlying viewport data and the
342 if (!Jalview.isHeadlessMode())
344 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
347 avc = new jalview.controller.AlignViewController(this, viewport,
349 if (viewport.getAlignmentConservationAnnotation() == null)
351 // BLOSUM62Colour.setEnabled(false);
352 conservationMenuItem.setEnabled(false);
353 modifyConservation.setEnabled(false);
354 // PIDColour.setEnabled(false);
355 // abovePIDThreshold.setEnabled(false);
356 // modifyPID.setEnabled(false);
359 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
362 if (sortby.equals("Id"))
364 sortIDMenuItem_actionPerformed(null);
366 else if (sortby.equals("Pairwise Identity"))
368 sortPairwiseMenuItem_actionPerformed(null);
372 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
374 setMenusFromViewport(viewport);
375 buildSortByAnnotationScoresMenu();
376 calculateTree.addActionListener(new ActionListener()
380 public void actionPerformed(ActionEvent e)
387 if (Desktop.desktop != null)
389 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
391 * BH 2018 ignore service listeners
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(null);
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 statusBar.setText(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.viewName != null);
766 if (aSize == 1 && ap.av.viewName == null)
768 this.getContentPane().add(ap, BorderLayout.CENTER);
774 setInitialTabVisible();
777 expandViews.setEnabled(true);
778 gatherViews.setEnabled(true);
779 tabbedPane.addTab(ap.av.viewName, 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.viewName, 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 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 public void setStatus(String text)
997 statusBar.setText(text);
1001 * Added so Castor Mapping file can obtain Jalview Version
1003 public String getVersion()
1005 return jalview.bin.Cache.getProperty("VERSION");
1008 public FeatureRenderer getFeatureRenderer()
1010 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1014 public void fetchSequence_actionPerformed(ActionEvent e)
1016 new jalview.gui.SequenceFetcher(this);
1020 public void addFromFile_actionPerformed(ActionEvent e)
1022 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1026 public void reload_actionPerformed(ActionEvent e)
1028 if (fileName != null)
1030 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1031 // originating file's format
1032 // TODO: work out how to recover feature settings for correct view(s) when
1033 // file is reloaded.
1034 if (FileFormat.Jalview.equals(currentFileFormat))
1036 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1037 for (int i = 0; i < frames.length; i++)
1039 if (frames[i] instanceof AlignFrame && frames[i] != this
1040 && ((AlignFrame) frames[i]).fileName != null
1041 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1045 frames[i].setSelected(true);
1046 Desktop.instance.closeAssociatedWindows();
1047 } catch (java.beans.PropertyVetoException ex)
1053 Desktop.instance.closeAssociatedWindows();
1055 FileLoader loader = new FileLoader();
1056 DataSourceType protocol = fileName.startsWith("http:")
1057 ? DataSourceType.URL
1058 : DataSourceType.FILE;
1059 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1063 Rectangle bounds = this.getBounds();
1065 FileLoader loader = new FileLoader();
1067 AlignFrame newframe = null;
1069 if (fileObject == null)
1072 DataSourceType protocol = (fileName.startsWith("http:")
1073 ? DataSourceType.URL
1074 : DataSourceType.FILE);
1075 newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1080 newframe = loader.LoadFileWaitTillLoaded(fileObject,
1081 DataSourceType.FILE, currentFileFormat);
1084 newframe.setBounds(bounds);
1085 if (featureSettings != null && featureSettings.isShowing())
1087 final Rectangle fspos = featureSettings.frame.getBounds();
1088 // TODO: need a 'show feature settings' function that takes bounds -
1089 // need to refactor Desktop.addFrame
1090 newframe.featureSettings_actionPerformed(null);
1091 final FeatureSettings nfs = newframe.featureSettings;
1092 SwingUtilities.invokeLater(new Runnable()
1097 nfs.frame.setBounds(fspos);
1100 this.featureSettings.close();
1101 this.featureSettings = null;
1103 this.closeMenuItem_actionPerformed(true);
1109 public void addFromText_actionPerformed(ActionEvent e)
1112 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1116 public void addFromURL_actionPerformed(ActionEvent e)
1118 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1122 public void save_actionPerformed(ActionEvent e)
1124 if (fileName == null || (currentFileFormat == null)
1125 || fileName.startsWith("http"))
1127 saveAs_actionPerformed();
1131 saveAlignment(fileName, currentFileFormat);
1136 * Saves the alignment to a file with a name chosen by the user, if necessary
1137 * warning if a file would be overwritten
1140 public void saveAs_actionPerformed()
1142 String format = currentFileFormat == null ? null
1143 : currentFileFormat.getName();
1144 JalviewFileChooser chooser = JalviewFileChooser
1145 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1147 chooser.setFileView(new JalviewFileView());
1148 chooser.setDialogTitle(
1149 MessageManager.getString("label.save_alignment_to_file"));
1150 chooser.setToolTipText(MessageManager.getString("action.save"));
1152 int value = chooser.showSaveDialog(this);
1154 if (value != JalviewFileChooser.APPROVE_OPTION)
1158 currentFileFormat = chooser.getSelectedFormat();
1159 // todo is this (2005) test now obsolete - value is never null?
1160 while (currentFileFormat == null)
1162 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1164 .getString("label.select_file_format_before_saving"),
1165 MessageManager.getString("label.file_format_not_specified"),
1166 JvOptionPane.WARNING_MESSAGE);
1167 currentFileFormat = chooser.getSelectedFormat();
1168 value = chooser.showSaveDialog(this);
1169 if (value != JalviewFileChooser.APPROVE_OPTION)
1175 fileName = chooser.getSelectedFile().getPath();
1177 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1178 Cache.setProperty("LAST_DIRECTORY", fileName);
1179 saveAlignment(fileName, currentFileFormat);
1182 boolean lastSaveSuccessful = false;
1184 FileFormatI lastFormatSaved;
1186 String lastFilenameSaved;
1189 * Raise a dialog or status message for the last call to saveAlignment.
1191 * @return true if last call to saveAlignment(file, format) was successful.
1193 public boolean isSaveAlignmentSuccessful()
1196 if (!lastSaveSuccessful)
1198 JvOptionPane.showInternalMessageDialog(this, MessageManager
1199 .formatMessage("label.couldnt_save_file", new Object[]
1200 { lastFilenameSaved }),
1201 MessageManager.getString("label.error_saving_file"),
1202 JvOptionPane.WARNING_MESSAGE);
1207 statusBar.setText(MessageManager.formatMessage(
1208 "label.successfully_saved_to_file_in_format", new Object[]
1209 { lastFilenameSaved, lastFormatSaved }));
1212 return lastSaveSuccessful;
1216 * Saves the alignment to the specified file path, in the specified format,
1217 * which may be an alignment format, or Jalview project format. If the
1218 * alignment has hidden regions, or the format is one capable of including
1219 * non-sequence data (features, annotations, groups), then the user may be
1220 * prompted to specify what to include in the output.
1225 public void saveAlignment(String file, FileFormatI format)
1227 lastSaveSuccessful = false;
1228 lastFilenameSaved = file;
1229 lastFormatSaved = format;
1231 if (FileFormat.Jalview.equals(format))
1233 String shortName = title;
1234 if (shortName.indexOf(File.separatorChar) > -1)
1236 shortName = shortName.substring(
1237 shortName.lastIndexOf(File.separatorChar) + 1);
1239 lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
1244 AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1245 RunResponse cancelAction = new RunResponse(JvOptionPane.CANCEL_OPTION)
1250 lastSaveSuccessful = false;
1253 RunResponse outputAction = new RunResponse(JvOptionPane.OK_OPTION)
1258 // todo defer this to inside formatSequences (or later)
1259 AlignmentExportData exportData = viewport
1260 .getAlignExportData(options);
1261 String output = new FormatAdapter(alignPanel, options)
1262 .formatSequences(format, exportData.getAlignment(),
1263 exportData.getOmitHidden(),
1264 exportData.getStartEndPostions(),
1265 viewport.getAlignment().getHiddenColumns());
1268 lastSaveSuccessful = false;
1274 PrintWriter out = new PrintWriter(new FileWriter(file));
1277 AlignFrame.this.setTitle(file);
1278 statusBar.setText(MessageManager.formatMessage(
1279 "label.successfully_saved_to_file_in_format",
1281 { fileName, format.getName() }));
1282 } catch (Exception ex)
1284 lastSaveSuccessful = false;
1285 ex.printStackTrace();
1292 * show dialog with export options if applicable; else just do it
1294 if (AlignExportOptions.isNeeded(viewport, format))
1296 AlignExportOptions choices = new AlignExportOptions(
1297 alignPanel.getAlignViewport(), format, options);
1298 choices.setResponseAction(outputAction);
1299 choices.setResponseAction(cancelAction);
1300 choices.showDialog();
1309 * Outputs the alignment to textbox in the requested format, if necessary
1310 * first prompting the user for whether to include hidden regions or
1313 * @param fileFormatName
1316 protected void outputText_actionPerformed(String fileFormatName)
1318 FileFormatI fileFormat = FileFormats.getInstance()
1319 .forName(fileFormatName);
1320 AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1321 RunResponse outputAction = new RunResponse(JvOptionPane.OK_OPTION)
1326 // todo defer this to inside formatSequences (or later)
1327 AlignmentExportData exportData = viewport
1328 .getAlignExportData(options);
1329 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1330 cap.setForInput(null);
1333 FileFormatI format = fileFormat;
1334 cap.setText(new FormatAdapter(alignPanel, options)
1335 .formatSequences(format, exportData.getAlignment(),
1336 exportData.getOmitHidden(),
1337 exportData.getStartEndPostions(),
1338 viewport.getAlignment().getHiddenColumns()));
1339 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1340 "label.alignment_output_command", new Object[]
1341 { fileFormat.getName() }), 600, 500);
1342 } catch (OutOfMemoryError oom)
1344 new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1352 * show dialog with export options if applicable; else just do it
1354 if (AlignExportOptions.isNeeded(viewport, fileFormat))
1356 AlignExportOptions choices = new AlignExportOptions(
1357 alignPanel.getAlignViewport(), fileFormat, options);
1358 choices.setResponseAction(outputAction);
1359 choices.showDialog();
1374 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1376 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1377 htmlSVG.exportHTML(null);
1381 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1383 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1384 bjs.exportHTML(null);
1387 public void createImageMap(File file, String image)
1389 alignPanel.makePNGImageMap(file, image);
1393 * Creates a PNG image of the alignment and writes it to the given file. If
1394 * the file is null, the user is prompted to choose a file.
1399 public void createPNG(File f)
1401 alignPanel.makeAlignmentImage(TYPE.PNG, f);
1405 * Creates an EPS image of the alignment and writes it to the given file. If
1406 * the file is null, the user is prompted to choose a file.
1411 public void createEPS(File f)
1413 alignPanel.makeAlignmentImage(TYPE.EPS, f);
1417 * Creates an SVG image of the alignment and writes it to the given file. If
1418 * the file is null, the user is prompted to choose a file.
1423 public void createSVG(File f)
1425 alignPanel.makeAlignmentImage(TYPE.SVG, f);
1429 public void pageSetup_actionPerformed(ActionEvent e)
1431 PrinterJob printJob = PrinterJob.getPrinterJob();
1432 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1442 public void printMenuItem_actionPerformed(ActionEvent e)
1444 // Putting in a thread avoids Swing painting problems
1445 PrintThread thread = new PrintThread(alignPanel);
1450 public void exportFeatures_actionPerformed(ActionEvent e)
1452 new AnnotationExporter(alignPanel).exportFeatures();
1456 public void exportAnnotations_actionPerformed(ActionEvent e)
1458 new AnnotationExporter(alignPanel).exportAnnotations();
1462 public void associatedData_actionPerformed(ActionEvent e)
1464 final JalviewFileChooser chooser = new JalviewFileChooser(
1465 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1466 chooser.setFileView(new JalviewFileView());
1467 chooser.setDialogTitle(
1468 MessageManager.getString("label.load_jalview_annotations"));
1469 chooser.setToolTipText(
1470 MessageManager.getString("label.load_jalview_annotations"));
1471 chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
1477 String choice = chooser.getSelectedFile().getPath();
1478 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1479 loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1484 chooser.openDialog(this);
1488 * Close the current view or all views in the alignment frame. If the frame
1489 * only contains one view then the alignment will be removed from memory.
1491 * @param closeAllTabs
1494 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1496 if (alignPanels != null && alignPanels.size() < 2)
1498 closeAllTabs = true;
1503 if (alignPanels != null)
1507 if (this.isClosed())
1509 // really close all the windows - otherwise wait till
1510 // setClosed(true) is called
1511 for (int i = 0; i < alignPanels.size(); i++)
1513 AlignmentPanel ap = alignPanels.get(i);
1520 closeView(alignPanel);
1527 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1528 * be called recursively, with the frame now in 'closed' state
1530 this.setClosed(true);
1532 } catch (Exception ex)
1534 ex.printStackTrace();
1539 * Close the specified panel and close up tabs appropriately.
1541 * @param panelToClose
1543 public void closeView(AlignmentPanel panelToClose)
1545 int index = tabbedPane.getSelectedIndex();
1546 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1547 alignPanels.remove(panelToClose);
1548 panelToClose.closePanel();
1549 panelToClose = null;
1551 tabbedPane.removeTabAt(closedindex);
1552 tabbedPane.validate();
1554 if (index > closedindex || index == tabbedPane.getTabCount())
1556 // modify currently selected tab index if necessary.
1560 this.tabSelectionChanged(index);
1566 void updateEditMenuBar()
1569 if (viewport.getHistoryList().size() > 0)
1571 undoMenuItem.setEnabled(true);
1572 CommandI command = viewport.getHistoryList().peek();
1573 undoMenuItem.setText(MessageManager
1574 .formatMessage("label.undo_command", new Object[]
1575 { command.getDescription() }));
1579 undoMenuItem.setEnabled(false);
1580 undoMenuItem.setText(MessageManager.getString("action.undo"));
1583 if (viewport.getRedoList().size() > 0)
1585 redoMenuItem.setEnabled(true);
1587 CommandI command = viewport.getRedoList().peek();
1588 redoMenuItem.setText(MessageManager
1589 .formatMessage("label.redo_command", new Object[]
1590 { command.getDescription() }));
1594 redoMenuItem.setEnabled(false);
1595 redoMenuItem.setText(MessageManager.getString("action.redo"));
1600 public void addHistoryItem(CommandI command)
1602 if (command.getSize() > 0)
1604 viewport.addToHistoryList(command);
1605 viewport.clearRedoList();
1606 updateEditMenuBar();
1607 viewport.updateHiddenColumns();
1608 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1609 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1610 // viewport.getColumnSelection()
1611 // .getHiddenColumns().size() > 0);
1617 * @return alignment objects for all views
1619 AlignmentI[] getViewAlignments()
1621 if (alignPanels != null)
1623 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1625 for (AlignmentPanel ap : alignPanels)
1627 als[i++] = ap.av.getAlignment();
1631 if (viewport != null)
1633 return new AlignmentI[] { viewport.getAlignment() };
1645 protected void undoMenuItem_actionPerformed(ActionEvent e)
1647 if (viewport.getHistoryList().isEmpty())
1651 CommandI command = viewport.getHistoryList().pop();
1652 viewport.addToRedoList(command);
1653 command.undoCommand(getViewAlignments());
1655 AlignmentViewport originalSource = getOriginatingSource(command);
1656 updateEditMenuBar();
1658 if (originalSource != null)
1660 if (originalSource != viewport)
1663 "Implementation worry: mismatch of viewport origin for undo");
1665 originalSource.updateHiddenColumns();
1666 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1668 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1669 // viewport.getColumnSelection()
1670 // .getHiddenColumns().size() > 0);
1671 originalSource.firePropertyChange("alignment", null,
1672 originalSource.getAlignment().getSequences());
1683 protected void redoMenuItem_actionPerformed(ActionEvent e)
1685 if (viewport.getRedoList().size() < 1)
1690 CommandI command = viewport.getRedoList().pop();
1691 viewport.addToHistoryList(command);
1692 command.doCommand(getViewAlignments());
1694 AlignmentViewport originalSource = getOriginatingSource(command);
1695 updateEditMenuBar();
1697 if (originalSource != null)
1700 if (originalSource != viewport)
1703 "Implementation worry: mismatch of viewport origin for redo");
1705 originalSource.updateHiddenColumns();
1706 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1708 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1709 // viewport.getColumnSelection()
1710 // .getHiddenColumns().size() > 0);
1711 originalSource.firePropertyChange("alignment", null,
1712 originalSource.getAlignment().getSequences());
1716 AlignmentViewport getOriginatingSource(CommandI command)
1718 AlignmentViewport originalSource = null;
1719 // For sequence removal and addition, we need to fire
1720 // the property change event FROM the viewport where the
1721 // original alignment was altered
1722 AlignmentI al = null;
1723 if (command instanceof EditCommand)
1725 EditCommand editCommand = (EditCommand) command;
1726 al = editCommand.getAlignment();
1727 List<Component> comps = PaintRefresher.components
1728 .get(viewport.getSequenceSetId());
1730 for (Component comp : comps)
1732 if (comp instanceof AlignmentPanel)
1734 if (al == ((AlignmentPanel) comp).av.getAlignment())
1736 originalSource = ((AlignmentPanel) comp).av;
1743 if (originalSource == null)
1745 // The original view is closed, we must validate
1746 // the current view against the closed view first
1749 PaintRefresher.validateSequences(al, viewport.getAlignment());
1752 originalSource = viewport;
1755 return originalSource;
1764 public void moveSelectedSequences(boolean up)
1766 SequenceGroup sg = viewport.getSelectionGroup();
1772 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1773 viewport.getHiddenRepSequences(), up);
1774 alignPanel.paintAlignment(true, false);
1777 synchronized void slideSequences(boolean right, int size)
1779 List<SequenceI> sg = new ArrayList<>();
1780 if (viewport.cursorMode)
1782 sg.add(viewport.getAlignment()
1783 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1785 else if (viewport.getSelectionGroup() != null
1786 && viewport.getSelectionGroup().getSize() != viewport
1787 .getAlignment().getHeight())
1789 sg = viewport.getSelectionGroup()
1790 .getSequences(viewport.getHiddenRepSequences());
1798 List<SequenceI> invertGroup = new ArrayList<>();
1800 for (SequenceI seq : viewport.getAlignment().getSequences())
1802 if (!sg.contains(seq))
1804 invertGroup.add(seq);
1808 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1810 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1811 for (int i = 0; i < invertGroup.size(); i++)
1813 seqs2[i] = invertGroup.get(i);
1816 SlideSequencesCommand ssc;
1819 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1820 viewport.getGapCharacter());
1824 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1825 viewport.getGapCharacter());
1828 int groupAdjustment = 0;
1829 if (ssc.getGapsInsertedBegin() && right)
1831 if (viewport.cursorMode)
1833 alignPanel.getSeqPanel().moveCursor(size, 0);
1837 groupAdjustment = size;
1840 else if (!ssc.getGapsInsertedBegin() && !right)
1842 if (viewport.cursorMode)
1844 alignPanel.getSeqPanel().moveCursor(-size, 0);
1848 groupAdjustment = -size;
1852 if (groupAdjustment != 0)
1854 viewport.getSelectionGroup().setStartRes(
1855 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1856 viewport.getSelectionGroup().setEndRes(
1857 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1861 * just extend the last slide command if compatible; but not if in
1862 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1864 boolean appendHistoryItem = false;
1865 Deque<CommandI> historyList = viewport.getHistoryList();
1866 boolean inSplitFrame = getSplitViewContainer() != null;
1867 if (!inSplitFrame && historyList != null && historyList.size() > 0
1868 && historyList.peek() instanceof SlideSequencesCommand)
1870 appendHistoryItem = ssc.appendSlideCommand(
1871 (SlideSequencesCommand) historyList.peek());
1874 if (!appendHistoryItem)
1876 addHistoryItem(ssc);
1889 protected void copy_actionPerformed(ActionEvent e)
1891 if (viewport.getSelectionGroup() == null)
1895 // TODO: preserve the ordering of displayed alignment annotation in any
1896 // internal paste (particularly sequence associated annotation)
1897 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1898 String[] omitHidden = null;
1900 if (viewport.hasHiddenColumns())
1902 omitHidden = viewport.getViewAsString(true);
1905 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1906 seqs, omitHidden, null);
1908 StringSelection ss = new StringSelection(output);
1912 jalview.gui.Desktop.internalCopy = true;
1913 // Its really worth setting the clipboard contents
1914 // to empty before setting the large StringSelection!!
1915 Toolkit.getDefaultToolkit().getSystemClipboard()
1916 .setContents(new StringSelection(""), null);
1918 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1920 } catch (OutOfMemoryError er)
1922 new OOMWarning("copying region", er);
1926 HiddenColumns hiddenColumns = null;
1927 if (viewport.hasHiddenColumns())
1929 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1930 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1932 // create new HiddenColumns object with copy of hidden regions
1933 // between startRes and endRes, offset by startRes
1934 hiddenColumns = new HiddenColumns(
1935 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1936 hiddenCutoff, hiddenOffset);
1939 Desktop.jalviewClipboard = new Object[] { seqs,
1940 viewport.getAlignment().getDataset(), hiddenColumns };
1941 statusBar.setText(MessageManager.formatMessage(
1942 "label.copied_sequences_to_clipboard", new Object[]
1943 { Integer.valueOf(seqs.length).toString() }));
1953 protected void pasteNew_actionPerformed(ActionEvent e)
1965 protected void pasteThis_actionPerformed(ActionEvent e)
1971 * Paste contents of Jalview clipboard
1973 * @param newAlignment
1974 * true to paste to a new alignment, otherwise add to this.
1976 void paste(boolean newAlignment)
1978 boolean externalPaste = true;
1981 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1982 Transferable contents = c.getContents(this);
1984 if (contents == null)
1993 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1994 if (str.length() < 1)
1999 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2001 } catch (OutOfMemoryError er)
2003 new OOMWarning("Out of memory pasting sequences!!", er);
2007 SequenceI[] sequences;
2008 boolean annotationAdded = false;
2009 AlignmentI alignment = null;
2011 if (Desktop.jalviewClipboard != null)
2013 // The clipboard was filled from within Jalview, we must use the
2015 // And dataset from the copied alignment
2016 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2017 // be doubly sure that we create *new* sequence objects.
2018 sequences = new SequenceI[newseq.length];
2019 for (int i = 0; i < newseq.length; i++)
2021 sequences[i] = new Sequence(newseq[i]);
2023 alignment = new Alignment(sequences);
2024 externalPaste = false;
2028 // parse the clipboard as an alignment.
2029 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2031 sequences = alignment.getSequencesArray();
2035 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2041 if (Desktop.jalviewClipboard != null)
2043 // dataset is inherited
2044 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2048 // new dataset is constructed
2049 alignment.setDataset(null);
2051 alwidth = alignment.getWidth() + 1;
2055 AlignmentI pastedal = alignment; // preserve pasted alignment object
2056 // Add pasted sequences and dataset into existing alignment.
2057 alignment = viewport.getAlignment();
2058 alwidth = alignment.getWidth() + 1;
2059 // decide if we need to import sequences from an existing dataset
2060 boolean importDs = Desktop.jalviewClipboard != null
2061 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2062 // importDs==true instructs us to copy over new dataset sequences from
2063 // an existing alignment
2064 Vector newDs = (importDs) ? new Vector() : null; // used to create
2065 // minimum dataset set
2067 for (int i = 0; i < sequences.length; i++)
2071 newDs.addElement(null);
2073 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2075 if (importDs && ds != null)
2077 if (!newDs.contains(ds))
2079 newDs.setElementAt(ds, i);
2080 ds = new Sequence(ds);
2081 // update with new dataset sequence
2082 sequences[i].setDatasetSequence(ds);
2086 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2091 // copy and derive new dataset sequence
2092 sequences[i] = sequences[i].deriveSequence();
2093 alignment.getDataset()
2094 .addSequence(sequences[i].getDatasetSequence());
2095 // TODO: avoid creation of duplicate dataset sequences with a
2096 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2098 alignment.addSequence(sequences[i]); // merges dataset
2102 newDs.clear(); // tidy up
2104 if (alignment.getAlignmentAnnotation() != null)
2106 for (AlignmentAnnotation alan : alignment
2107 .getAlignmentAnnotation())
2109 if (alan.graphGroup > fgroup)
2111 fgroup = alan.graphGroup;
2115 if (pastedal.getAlignmentAnnotation() != null)
2117 // Add any annotation attached to alignment.
2118 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2119 for (int i = 0; i < alann.length; i++)
2121 annotationAdded = true;
2122 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2124 AlignmentAnnotation newann = new AlignmentAnnotation(
2126 if (newann.graphGroup > -1)
2128 if (newGraphGroups.size() <= newann.graphGroup
2129 || newGraphGroups.get(newann.graphGroup) == null)
2131 for (int q = newGraphGroups
2132 .size(); q <= newann.graphGroup; q++)
2134 newGraphGroups.add(q, null);
2136 newGraphGroups.set(newann.graphGroup,
2137 new Integer(++fgroup));
2139 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2143 newann.padAnnotation(alwidth);
2144 alignment.addAnnotation(newann);
2154 addHistoryItem(new EditCommand(
2155 MessageManager.getString("label.add_sequences"),
2156 Action.PASTE, sequences, 0, alignment.getWidth(),
2159 // Add any annotations attached to sequences
2160 for (int i = 0; i < sequences.length; i++)
2162 if (sequences[i].getAnnotation() != null)
2164 AlignmentAnnotation newann;
2165 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2167 annotationAdded = true;
2168 newann = sequences[i].getAnnotation()[a];
2169 newann.adjustForAlignment();
2170 newann.padAnnotation(alwidth);
2171 if (newann.graphGroup > -1)
2173 if (newann.graphGroup > -1)
2175 if (newGraphGroups.size() <= newann.graphGroup
2176 || newGraphGroups.get(newann.graphGroup) == null)
2178 for (int q = newGraphGroups
2179 .size(); q <= newann.graphGroup; q++)
2181 newGraphGroups.add(q, null);
2183 newGraphGroups.set(newann.graphGroup,
2184 new Integer(++fgroup));
2186 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2190 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2194 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2202 // propagate alignment changed.
2203 viewport.getRanges().setEndSeq(alignment.getHeight());
2204 if (annotationAdded)
2206 // Duplicate sequence annotation in all views.
2207 AlignmentI[] alview = this.getViewAlignments();
2208 for (int i = 0; i < sequences.length; i++)
2210 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2215 for (int avnum = 0; avnum < alview.length; avnum++)
2217 if (alview[avnum] != alignment)
2219 // duplicate in a view other than the one with input focus
2220 int avwidth = alview[avnum].getWidth() + 1;
2221 // this relies on sann being preserved after we
2222 // modify the sequence's annotation array for each duplication
2223 for (int a = 0; a < sann.length; a++)
2225 AlignmentAnnotation newann = new AlignmentAnnotation(
2227 sequences[i].addAlignmentAnnotation(newann);
2228 newann.padAnnotation(avwidth);
2229 alview[avnum].addAnnotation(newann); // annotation was
2230 // duplicated earlier
2231 // TODO JAL-1145 graphGroups are not updated for sequence
2232 // annotation added to several views. This may cause
2234 alview[avnum].setAnnotationIndex(newann, a);
2239 buildSortByAnnotationScoresMenu();
2241 viewport.firePropertyChange("alignment", null,
2242 alignment.getSequences());
2243 if (alignPanels != null)
2245 for (AlignmentPanel ap : alignPanels)
2247 ap.validateAnnotationDimensions(false);
2252 alignPanel.validateAnnotationDimensions(false);
2258 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2260 String newtitle = new String("Copied sequences");
2262 if (Desktop.jalviewClipboard != null
2263 && Desktop.jalviewClipboard[2] != null)
2265 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2266 af.viewport.setHiddenColumns(hc);
2269 // >>>This is a fix for the moment, until a better solution is
2271 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2272 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2273 .getFeatureRenderer());
2275 // TODO: maintain provenance of an alignment, rather than just make the
2276 // title a concatenation of operations.
2279 if (title.startsWith("Copied sequences"))
2285 newtitle = newtitle.concat("- from " + title);
2290 newtitle = new String("Pasted sequences");
2293 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2298 } catch (Exception ex)
2300 ex.printStackTrace();
2301 System.out.println("Exception whilst pasting: " + ex);
2302 // could be anything being pasted in here
2308 protected void expand_newalign(ActionEvent e)
2312 AlignmentI alignment = AlignmentUtils
2313 .expandContext(getViewport().getAlignment(), -1);
2314 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2316 String newtitle = new String("Flanking alignment");
2318 if (Desktop.jalviewClipboard != null
2319 && Desktop.jalviewClipboard[2] != null)
2321 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2322 af.viewport.setHiddenColumns(hc);
2325 // >>>This is a fix for the moment, until a better solution is
2327 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2328 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2329 .getFeatureRenderer());
2331 // TODO: maintain provenance of an alignment, rather than just make the
2332 // title a concatenation of operations.
2334 if (title.startsWith("Copied sequences"))
2340 newtitle = newtitle.concat("- from " + title);
2344 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2346 } catch (Exception ex)
2348 ex.printStackTrace();
2349 System.out.println("Exception whilst pasting: " + ex);
2350 // could be anything being pasted in here
2351 } catch (OutOfMemoryError oom)
2353 new OOMWarning("Viewing flanking region of alignment", oom);
2364 protected void cut_actionPerformed(ActionEvent e)
2366 copy_actionPerformed(null);
2367 delete_actionPerformed(null);
2377 protected void delete_actionPerformed(ActionEvent evt)
2380 SequenceGroup sg = viewport.getSelectionGroup();
2387 * If the cut affects all sequences, warn, remove highlighted columns
2389 if (sg.getSize() == viewport.getAlignment().getHeight())
2391 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2392 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2393 if (isEntireAlignWidth)
2395 int confirm = JvOptionPane.showConfirmDialog(this,
2396 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2397 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2398 JvOptionPane.OK_CANCEL_OPTION);
2400 if (confirm == JvOptionPane.CANCEL_OPTION
2401 || confirm == JvOptionPane.CLOSED_OPTION)
2406 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2407 sg.getEndRes() + 1);
2409 SequenceI[] cut = sg.getSequences()
2410 .toArray(new SequenceI[sg.getSize()]);
2412 addHistoryItem(new EditCommand(
2413 MessageManager.getString("label.cut_sequences"), Action.CUT,
2414 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2415 viewport.getAlignment()));
2417 viewport.setSelectionGroup(null);
2418 viewport.sendSelection();
2419 viewport.getAlignment().deleteGroup(sg);
2421 viewport.firePropertyChange("alignment", null,
2422 viewport.getAlignment().getSequences());
2423 if (viewport.getAlignment().getHeight() < 1)
2427 this.setClosed(true);
2428 } catch (Exception ex)
2441 protected void deleteGroups_actionPerformed(ActionEvent e)
2443 if (avc.deleteGroups())
2445 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2446 alignPanel.updateAnnotation();
2447 alignPanel.paintAlignment(true, true);
2458 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2460 SequenceGroup sg = new SequenceGroup();
2462 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2464 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2467 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2468 viewport.setSelectionGroup(sg);
2469 viewport.sendSelection();
2470 // JAL-2034 - should delegate to
2471 // alignPanel to decide if overview needs
2473 alignPanel.paintAlignment(false, false);
2474 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2484 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2486 if (viewport.cursorMode)
2488 alignPanel.getSeqPanel().keyboardNo1 = null;
2489 alignPanel.getSeqPanel().keyboardNo2 = null;
2491 viewport.setSelectionGroup(null);
2492 viewport.getColumnSelection().clear();
2493 viewport.setSelectionGroup(null);
2494 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2495 // JAL-2034 - should delegate to
2496 // alignPanel to decide if overview needs
2498 alignPanel.paintAlignment(false, false);
2499 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2500 viewport.sendSelection();
2510 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2512 SequenceGroup sg = viewport.getSelectionGroup();
2516 selectAllSequenceMenuItem_actionPerformed(null);
2521 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2523 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2525 // JAL-2034 - should delegate to
2526 // alignPanel to decide if overview needs
2529 alignPanel.paintAlignment(true, false);
2530 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2531 viewport.sendSelection();
2535 public void invertColSel_actionPerformed(ActionEvent e)
2537 viewport.invertColumnSelection();
2538 alignPanel.paintAlignment(true, false);
2539 viewport.sendSelection();
2549 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2551 trimAlignment(true);
2561 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2563 trimAlignment(false);
2566 void trimAlignment(boolean trimLeft)
2568 ColumnSelection colSel = viewport.getColumnSelection();
2571 if (!colSel.isEmpty())
2575 column = colSel.getMin();
2579 column = colSel.getMax();
2583 if (viewport.getSelectionGroup() != null)
2585 seqs = viewport.getSelectionGroup()
2586 .getSequencesAsArray(viewport.getHiddenRepSequences());
2590 seqs = viewport.getAlignment().getSequencesArray();
2593 TrimRegionCommand trimRegion;
2596 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2597 column, viewport.getAlignment());
2598 viewport.getRanges().setStartRes(0);
2602 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2603 column, viewport.getAlignment());
2606 statusBar.setText(MessageManager
2607 .formatMessage("label.removed_columns", new String[]
2608 { Integer.valueOf(trimRegion.getSize()).toString() }));
2610 addHistoryItem(trimRegion);
2612 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2614 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2615 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2617 viewport.getAlignment().deleteGroup(sg);
2621 viewport.firePropertyChange("alignment", null,
2622 viewport.getAlignment().getSequences());
2633 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2635 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2638 if (viewport.getSelectionGroup() != null)
2640 seqs = viewport.getSelectionGroup()
2641 .getSequencesAsArray(viewport.getHiddenRepSequences());
2642 start = viewport.getSelectionGroup().getStartRes();
2643 end = viewport.getSelectionGroup().getEndRes();
2647 seqs = viewport.getAlignment().getSequencesArray();
2650 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2651 "Remove Gapped Columns", seqs, start, end,
2652 viewport.getAlignment());
2654 addHistoryItem(removeGapCols);
2656 statusBar.setText(MessageManager
2657 .formatMessage("label.removed_empty_columns", new Object[]
2658 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2660 // This is to maintain viewport position on first residue
2661 // of first sequence
2662 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2663 ViewportRanges ranges = viewport.getRanges();
2664 int startRes = seq.findPosition(ranges.getStartRes());
2665 // ShiftList shifts;
2666 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2667 // edit.alColumnChanges=shifts.getInverse();
2668 // if (viewport.hasHiddenColumns)
2669 // viewport.getColumnSelection().compensateForEdits(shifts);
2670 ranges.setStartRes(seq.findIndex(startRes) - 1);
2671 viewport.firePropertyChange("alignment", null,
2672 viewport.getAlignment().getSequences());
2683 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2685 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2688 if (viewport.getSelectionGroup() != null)
2690 seqs = viewport.getSelectionGroup()
2691 .getSequencesAsArray(viewport.getHiddenRepSequences());
2692 start = viewport.getSelectionGroup().getStartRes();
2693 end = viewport.getSelectionGroup().getEndRes();
2697 seqs = viewport.getAlignment().getSequencesArray();
2700 // This is to maintain viewport position on first residue
2701 // of first sequence
2702 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2703 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2705 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2706 viewport.getAlignment()));
2708 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2710 viewport.firePropertyChange("alignment", null,
2711 viewport.getAlignment().getSequences());
2722 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2724 viewport.setPadGaps(padGapsMenuitem.isSelected());
2725 viewport.firePropertyChange("alignment", null,
2726 viewport.getAlignment().getSequences());
2736 public void findMenuItem_actionPerformed(ActionEvent e)
2742 * Create a new view of the current alignment.
2745 public void newView_actionPerformed(ActionEvent e)
2747 newView(null, true);
2751 * Creates and shows a new view of the current alignment.
2754 * title of newly created view; if null, one will be generated
2755 * @param copyAnnotation
2756 * if true then duplicate all annnotation, groups and settings
2757 * @return new alignment panel, already displayed.
2759 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2762 * Create a new AlignmentPanel (with its own, new Viewport)
2764 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2765 if (!copyAnnotation)
2768 * remove all groups and annotation except for the automatic stuff
2770 newap.av.getAlignment().deleteAllGroups();
2771 newap.av.getAlignment().deleteAllAnnotations(false);
2774 newap.av.setGatherViewsHere(false);
2776 if (viewport.viewName == null)
2778 viewport.viewName = MessageManager
2779 .getString("label.view_name_original");
2783 * Views share the same edits undo and redo stacks
2785 newap.av.setHistoryList(viewport.getHistoryList());
2786 newap.av.setRedoList(viewport.getRedoList());
2789 * Views share the same mappings; need to deregister any new mappings
2790 * created by copyAlignPanel, and register the new reference to the shared
2793 newap.av.replaceMappings(viewport.getAlignment());
2796 * start up cDNA consensus (if applicable) now mappings are in place
2798 if (newap.av.initComplementConsensus())
2800 newap.refresh(true); // adjust layout of annotations
2803 newap.av.viewName = getNewViewName(viewTitle);
2805 addAlignmentPanel(newap, true);
2806 newap.alignmentChanged();
2808 if (alignPanels.size() == 2)
2810 viewport.setGatherViewsHere(true);
2812 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2817 * Make a new name for the view, ensuring it is unique within the current
2818 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2819 * these now use viewId. Unique view names are still desirable for usability.)
2824 protected String getNewViewName(String viewTitle)
2826 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2827 boolean addFirstIndex = false;
2828 if (viewTitle == null || viewTitle.trim().length() == 0)
2830 viewTitle = MessageManager.getString("action.view");
2831 addFirstIndex = true;
2835 index = 1;// we count from 1 if given a specific name
2837 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2839 List<Component> comps = PaintRefresher.components
2840 .get(viewport.getSequenceSetId());
2842 List<String> existingNames = getExistingViewNames(comps);
2844 while (existingNames.contains(newViewName))
2846 newViewName = viewTitle + " " + (++index);
2852 * Returns a list of distinct view names found in the given list of
2853 * components. View names are held on the viewport of an AlignmentPanel.
2858 protected List<String> getExistingViewNames(List<Component> comps)
2860 List<String> existingNames = new ArrayList<>();
2861 for (Component comp : comps)
2863 if (comp instanceof AlignmentPanel)
2865 AlignmentPanel ap = (AlignmentPanel) comp;
2866 if (!existingNames.contains(ap.av.viewName))
2868 existingNames.add(ap.av.viewName);
2872 return existingNames;
2876 * Explode tabbed views into separate windows.
2879 public void expandViews_actionPerformed(ActionEvent e)
2881 Desktop.explodeViews(this);
2885 * Gather views in separate windows back into a tabbed presentation.
2888 public void gatherViews_actionPerformed(ActionEvent e)
2890 Desktop.instance.gatherViews(this);
2900 public void font_actionPerformed(ActionEvent e)
2902 new FontChooser(alignPanel);
2912 protected void seqLimit_actionPerformed(ActionEvent e)
2914 viewport.setShowJVSuffix(seqLimits.isSelected());
2916 alignPanel.getIdPanel().getIdCanvas()
2917 .setPreferredSize(alignPanel.calculateIdWidth());
2918 alignPanel.paintAlignment(true, false);
2922 public void idRightAlign_actionPerformed(ActionEvent e)
2924 viewport.setRightAlignIds(idRightAlign.isSelected());
2925 alignPanel.paintAlignment(false, false);
2929 public void centreColumnLabels_actionPerformed(ActionEvent e)
2931 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2932 alignPanel.paintAlignment(false, false);
2938 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2941 protected void followHighlight_actionPerformed()
2944 * Set the 'follow' flag on the Viewport (and scroll to position if now
2947 final boolean state = this.followHighlightMenuItem.getState();
2948 viewport.setFollowHighlight(state);
2951 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2962 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2964 viewport.setColourText(colourTextMenuItem.isSelected());
2965 alignPanel.paintAlignment(false, false);
2975 public void wrapMenuItem_actionPerformed(ActionEvent e)
2977 scaleAbove.setVisible(wrapMenuItem.isSelected());
2978 scaleLeft.setVisible(wrapMenuItem.isSelected());
2979 scaleRight.setVisible(wrapMenuItem.isSelected());
2980 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2981 alignPanel.updateLayout();
2985 public void showAllSeqs_actionPerformed(ActionEvent e)
2987 viewport.showAllHiddenSeqs();
2991 public void showAllColumns_actionPerformed(ActionEvent e)
2993 viewport.showAllHiddenColumns();
2994 alignPanel.paintAlignment(true, true);
2995 viewport.sendSelection();
2999 public void hideSelSequences_actionPerformed(ActionEvent e)
3001 viewport.hideAllSelectedSeqs();
3005 * called by key handler and the hide all/show all menu items
3010 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3013 boolean hide = false;
3014 SequenceGroup sg = viewport.getSelectionGroup();
3015 if (!toggleSeqs && !toggleCols)
3017 // Hide everything by the current selection - this is a hack - we do the
3018 // invert and then hide
3019 // first check that there will be visible columns after the invert.
3020 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3021 && sg.getStartRes() <= sg.getEndRes()))
3023 // now invert the sequence set, if required - empty selection implies
3024 // that no hiding is required.
3027 invertSequenceMenuItem_actionPerformed(null);
3028 sg = viewport.getSelectionGroup();
3032 viewport.expandColSelection(sg, true);
3033 // finally invert the column selection and get the new sequence
3035 invertColSel_actionPerformed(null);
3042 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3044 hideSelSequences_actionPerformed(null);
3047 else if (!(toggleCols && viewport.hasSelectedColumns()))
3049 showAllSeqs_actionPerformed(null);
3055 if (viewport.hasSelectedColumns())
3057 hideSelColumns_actionPerformed(null);
3060 viewport.setSelectionGroup(sg);
3065 showAllColumns_actionPerformed(null);
3074 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3075 * event.ActionEvent)
3078 public void hideAllButSelection_actionPerformed(ActionEvent e)
3080 toggleHiddenRegions(false, false);
3081 viewport.sendSelection();
3088 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3092 public void hideAllSelection_actionPerformed(ActionEvent e)
3094 SequenceGroup sg = viewport.getSelectionGroup();
3095 viewport.expandColSelection(sg, false);
3096 viewport.hideAllSelectedSeqs();
3097 viewport.hideSelectedColumns();
3098 alignPanel.paintAlignment(true, true);
3099 viewport.sendSelection();
3106 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3110 public void showAllhidden_actionPerformed(ActionEvent e)
3112 viewport.showAllHiddenColumns();
3113 viewport.showAllHiddenSeqs();
3114 alignPanel.paintAlignment(true, true);
3115 viewport.sendSelection();
3119 public void hideSelColumns_actionPerformed(ActionEvent e)
3121 viewport.hideSelectedColumns();
3122 alignPanel.paintAlignment(true, true);
3123 viewport.sendSelection();
3127 public void hiddenMarkers_actionPerformed(ActionEvent e)
3129 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3140 protected void scaleAbove_actionPerformed(ActionEvent e)
3142 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3143 // TODO: do we actually need to update overview for scale above change ?
3144 alignPanel.paintAlignment(true, false);
3154 protected void scaleLeft_actionPerformed(ActionEvent e)
3156 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3157 alignPanel.paintAlignment(true, false);
3167 protected void scaleRight_actionPerformed(ActionEvent e)
3169 viewport.setScaleRightWrapped(scaleRight.isSelected());
3170 alignPanel.paintAlignment(true, false);
3180 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3182 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3183 alignPanel.paintAlignment(false, false);
3193 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3195 viewport.setShowText(viewTextMenuItem.isSelected());
3196 alignPanel.paintAlignment(false, false);
3206 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3208 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3209 alignPanel.paintAlignment(false, false);
3212 public FeatureSettings featureSettings;
3215 public FeatureSettingsControllerI getFeatureSettingsUI()
3217 return featureSettings;
3221 public void featureSettings_actionPerformed(ActionEvent e)
3223 if (featureSettings != null)
3225 featureSettings.close();
3226 featureSettings = null;
3228 if (!showSeqFeatures.isSelected())
3230 // make sure features are actually displayed
3231 showSeqFeatures.setSelected(true);
3232 showSeqFeatures_actionPerformed(null);
3234 featureSettings = new FeatureSettings(this);
3238 * Set or clear 'Show Sequence Features'
3244 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3246 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3247 alignPanel.paintAlignment(true, true);
3251 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3252 * the annotations panel as a whole.
3254 * The options to show/hide all annotations should be enabled when the panel
3255 * is shown, and disabled when the panel is hidden.
3260 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3262 final boolean setVisible = annotationPanelMenuItem.isSelected();
3263 viewport.setShowAnnotation(setVisible);
3264 this.showAllSeqAnnotations.setEnabled(setVisible);
3265 this.hideAllSeqAnnotations.setEnabled(setVisible);
3266 this.showAllAlAnnotations.setEnabled(setVisible);
3267 this.hideAllAlAnnotations.setEnabled(setVisible);
3268 alignPanel.updateLayout();
3272 public void alignmentProperties()
3275 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3278 String content = MessageManager.formatMessage("label.html_content",
3280 { contents.toString() });
3285 JLabel textLabel = new JLabel();
3286 textLabel.setText(content);
3287 textLabel.setBackground(Color.WHITE);
3289 pane = new JPanel(new BorderLayout());
3290 ((JPanel) pane).setOpaque(true);
3291 pane.setBackground(Color.WHITE);
3292 ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3296 JEditorPane editPane = new JEditorPane("text/html", "");
3297 editPane.setEditable(false);
3298 editPane.setText(content);
3302 JInternalFrame frame = new JInternalFrame();
3304 frame.getContentPane().add(new JScrollPane(pane));
3306 Desktop.addInternalFrame(frame, MessageManager
3307 .formatMessage("label.alignment_properties", new Object[]
3308 { getTitle() }), 500, 400);
3318 public void overviewMenuItem_actionPerformed(ActionEvent e)
3320 if (alignPanel.overviewPanel != null)
3325 JInternalFrame frame = new JInternalFrame();
3326 final OverviewPanel overview = new OverviewPanel(alignPanel);
3327 frame.setContentPane(overview);
3328 Desktop.addInternalFrame(frame, MessageManager
3329 .formatMessage("label.overview_params", new Object[]
3330 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3333 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3334 frame.addInternalFrameListener(
3335 new javax.swing.event.InternalFrameAdapter()
3338 public void internalFrameClosed(
3339 javax.swing.event.InternalFrameEvent evt)
3342 alignPanel.setOverviewPanel(null);
3345 if (getKeyListeners().length > 0)
3347 frame.addKeyListener(getKeyListeners()[0]);
3350 alignPanel.setOverviewPanel(overview);
3354 public void textColour_actionPerformed()
3356 new TextColourChooser().chooseColour(alignPanel, null);
3360 * public void covariationColour_actionPerformed() {
3362 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3366 public void annotationColour_actionPerformed()
3368 new AnnotationColourChooser(viewport, alignPanel);
3372 public void annotationColumn_actionPerformed(ActionEvent e)
3374 new AnnotationColumnChooser(viewport, alignPanel);
3378 * Action on the user checking or unchecking the option to apply the selected
3379 * colour scheme to all groups. If unchecked, groups may have their own
3380 * independent colour schemes.
3385 public void applyToAllGroups_actionPerformed(boolean selected)
3387 viewport.setColourAppliesToAllGroups(selected);
3391 * Action on user selecting a colour from the colour menu
3394 * the name (not the menu item label!) of the colour scheme
3397 public void changeColour_actionPerformed(String name)
3400 * 'User Defined' opens a panel to configure or load a
3401 * user-defined colour scheme
3403 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3405 new UserDefinedColours(alignPanel);
3410 * otherwise set the chosen colour scheme (or null for 'None')
3412 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3413 viewport.getAlignment(), viewport.getHiddenRepSequences());
3418 * Actions on setting or changing the alignment colour scheme
3423 public void changeColour(ColourSchemeI cs)
3425 // TODO: pull up to controller method
3426 ColourMenuHelper.setColourSelected(colourMenu, cs);
3428 viewport.setGlobalColourScheme(cs);
3430 alignPanel.paintAlignment(true, true);
3434 * Show the PID threshold slider panel
3437 protected void modifyPID_actionPerformed()
3439 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3440 alignPanel.getViewName());
3441 SliderPanel.showPIDSlider();
3445 * Show the Conservation slider panel
3448 protected void modifyConservation_actionPerformed()
3450 SliderPanel.setConservationSlider(alignPanel,
3451 viewport.getResidueShading(), alignPanel.getViewName());
3452 SliderPanel.showConservationSlider();
3456 * Action on selecting or deselecting (Colour) By Conservation
3459 public void conservationMenuItem_actionPerformed(boolean selected)
3461 modifyConservation.setEnabled(selected);
3462 viewport.setConservationSelected(selected);
3463 viewport.getResidueShading().setConservationApplied(selected);
3465 changeColour(viewport.getGlobalColourScheme());
3468 modifyConservation_actionPerformed();
3472 SliderPanel.hideConservationSlider();
3477 * Action on selecting or deselecting (Colour) Above PID Threshold
3480 public void abovePIDThreshold_actionPerformed(boolean selected)
3482 modifyPID.setEnabled(selected);
3483 viewport.setAbovePIDThreshold(selected);
3486 viewport.getResidueShading().setThreshold(0,
3487 viewport.isIgnoreGapsConsensus());
3490 changeColour(viewport.getGlobalColourScheme());
3493 modifyPID_actionPerformed();
3497 SliderPanel.hidePIDSlider();
3508 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3510 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3511 AlignmentSorter.sortByPID(viewport.getAlignment(),
3512 viewport.getAlignment().getSequenceAt(0));
3513 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3514 viewport.getAlignment()));
3515 alignPanel.paintAlignment(true, false);
3525 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3527 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3528 AlignmentSorter.sortByID(viewport.getAlignment());
3530 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3531 alignPanel.paintAlignment(true, false);
3541 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3543 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3544 AlignmentSorter.sortByLength(viewport.getAlignment());
3545 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3546 viewport.getAlignment()));
3547 alignPanel.paintAlignment(true, false);
3557 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3559 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3560 AlignmentSorter.sortByGroup(viewport.getAlignment());
3561 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3562 viewport.getAlignment()));
3564 alignPanel.paintAlignment(true, false);
3574 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3576 new RedundancyPanel(alignPanel, this);
3586 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3588 if ((viewport.getSelectionGroup() == null)
3589 || (viewport.getSelectionGroup().getSize() < 2))
3591 JvOptionPane.showInternalMessageDialog(this,
3592 MessageManager.getString(
3593 "label.you_must_select_least_two_sequences"),
3594 MessageManager.getString("label.invalid_selection"),
3595 JvOptionPane.WARNING_MESSAGE);
3599 JInternalFrame frame = new JInternalFrame();
3600 frame.setContentPane(new PairwiseAlignPanel(viewport));
3601 Desktop.addInternalFrame(frame,
3602 MessageManager.getString("action.pairwise_alignment"), 600,
3608 public void autoCalculate_actionPerformed(ActionEvent e)
3610 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3611 if (viewport.autoCalculateConsensus)
3613 viewport.firePropertyChange("alignment", null,
3614 viewport.getAlignment().getSequences());
3619 public void sortByTreeOption_actionPerformed(ActionEvent e)
3621 viewport.sortByTree = sortByTree.isSelected();
3625 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3627 viewport.followSelection = listenToViewSelections.isSelected();
3631 * Constructs a tree panel and adds it to the desktop
3634 * tree type (NJ or AV)
3636 * name of score model used to compute the tree
3638 * parameters for the distance or similarity calculation
3640 void newTreePanel(String type, String modelName,
3641 SimilarityParamsI options)
3643 String frameTitle = "";
3646 boolean onSelection = false;
3647 if (viewport.getSelectionGroup() != null
3648 && viewport.getSelectionGroup().getSize() > 0)
3650 SequenceGroup sg = viewport.getSelectionGroup();
3652 /* Decide if the selection is a column region */
3653 for (SequenceI _s : sg.getSequences())
3655 if (_s.getLength() < sg.getEndRes())
3657 JvOptionPane.showMessageDialog(Desktop.desktop,
3658 MessageManager.getString(
3659 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3660 MessageManager.getString(
3661 "label.sequences_selection_not_aligned"),
3662 JvOptionPane.WARNING_MESSAGE);
3671 if (viewport.getAlignment().getHeight() < 2)
3677 tp = new TreePanel(alignPanel, type, modelName, options);
3678 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3680 frameTitle += " from ";
3682 if (viewport.viewName != null)
3684 frameTitle += viewport.viewName + " of ";
3687 frameTitle += this.title;
3689 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3700 public void addSortByOrderMenuItem(String title,
3701 final AlignmentOrder order)
3703 final JMenuItem item = new JMenuItem(MessageManager
3704 .formatMessage("action.by_title_param", new Object[]
3707 item.addActionListener(new java.awt.event.ActionListener()
3710 public void actionPerformed(ActionEvent e)
3712 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3714 // TODO: JBPNote - have to map order entries to curent SequenceI
3716 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3718 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3719 viewport.getAlignment()));
3721 alignPanel.paintAlignment(true, false);
3727 * Add a new sort by annotation score menu item
3730 * the menu to add the option to
3732 * the label used to retrieve scores for each sequence on the
3735 public void addSortByAnnotScoreMenuItem(JMenu sort,
3736 final String scoreLabel)
3738 final JMenuItem item = new JMenuItem(scoreLabel);
3740 item.addActionListener(new java.awt.event.ActionListener()
3743 public void actionPerformed(ActionEvent e)
3745 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3746 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3747 viewport.getAlignment());// ,viewport.getSelectionGroup());
3748 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3749 viewport.getAlignment()));
3750 alignPanel.paintAlignment(true, false);
3756 * last hash for alignment's annotation array - used to minimise cost of
3759 protected int _annotationScoreVectorHash;
3762 * search the alignment and rebuild the sort by annotation score submenu the
3763 * last alignment annotation vector hash is stored to minimize cost of
3764 * rebuilding in subsequence calls.
3768 public void buildSortByAnnotationScoresMenu()
3770 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3775 if (viewport.getAlignment().getAlignmentAnnotation()
3776 .hashCode() != _annotationScoreVectorHash)
3778 sortByAnnotScore.removeAll();
3779 // almost certainly a quicker way to do this - but we keep it simple
3780 Hashtable scoreSorts = new Hashtable();
3781 AlignmentAnnotation aann[];
3782 for (SequenceI sqa : viewport.getAlignment().getSequences())
3784 aann = sqa.getAnnotation();
3785 for (int i = 0; aann != null && i < aann.length; i++)
3787 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3789 scoreSorts.put(aann[i].label, aann[i].label);
3793 Enumeration labels = scoreSorts.keys();
3794 while (labels.hasMoreElements())
3796 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3797 (String) labels.nextElement());
3799 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3802 _annotationScoreVectorHash = viewport.getAlignment()
3803 .getAlignmentAnnotation().hashCode();
3808 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3809 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3810 * call. Listeners are added to remove the menu item when the treePanel is
3811 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3815 public void buildTreeSortMenu()
3817 sortByTreeMenu.removeAll();
3819 List<Component> comps = PaintRefresher.components
3820 .get(viewport.getSequenceSetId());
3821 List<TreePanel> treePanels = new ArrayList<>();
3822 for (Component comp : comps)
3824 if (comp instanceof TreePanel)
3826 treePanels.add((TreePanel) comp);
3830 if (treePanels.size() < 1)
3832 sortByTreeMenu.setVisible(false);
3836 sortByTreeMenu.setVisible(true);
3838 for (final TreePanel tp : treePanels)
3840 final JMenuItem item = new JMenuItem(tp.getTitle());
3841 item.addActionListener(new java.awt.event.ActionListener()
3844 public void actionPerformed(ActionEvent e)
3846 tp.sortByTree_actionPerformed();
3847 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3852 sortByTreeMenu.add(item);
3856 public boolean sortBy(AlignmentOrder alorder, String undoname)
3858 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3859 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3860 if (undoname != null)
3862 addHistoryItem(new OrderCommand(undoname, oldOrder,
3863 viewport.getAlignment()));
3865 alignPanel.paintAlignment(true, false);
3870 * Work out whether the whole set of sequences or just the selected set will
3871 * be submitted for multiple alignment.
3874 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3876 // Now, check we have enough sequences
3877 AlignmentView msa = null;
3879 if ((viewport.getSelectionGroup() != null)
3880 && (viewport.getSelectionGroup().getSize() > 1))
3882 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3883 // some common interface!
3885 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3886 * SequenceI[sz = seqs.getSize(false)];
3888 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3889 * seqs.getSequenceAt(i); }
3891 msa = viewport.getAlignmentView(true);
3893 else if (viewport.getSelectionGroup() != null
3894 && viewport.getSelectionGroup().getSize() == 1)
3896 int option = JvOptionPane.showConfirmDialog(this,
3897 MessageManager.getString("warn.oneseq_msainput_selection"),
3898 MessageManager.getString("label.invalid_selection"),
3899 JvOptionPane.OK_CANCEL_OPTION);
3900 if (option == JvOptionPane.OK_OPTION)
3902 msa = viewport.getAlignmentView(false);
3907 msa = viewport.getAlignmentView(false);
3913 * Decides what is submitted to a secondary structure prediction service: the
3914 * first sequence in the alignment, or in the current selection, or, if the
3915 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3916 * region or the whole alignment. (where the first sequence in the set is the
3917 * one that the prediction will be for).
3919 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3921 AlignmentView seqs = null;
3923 if ((viewport.getSelectionGroup() != null)
3924 && (viewport.getSelectionGroup().getSize() > 0))
3926 seqs = viewport.getAlignmentView(true);
3930 seqs = viewport.getAlignmentView(false);
3932 // limit sequences - JBPNote in future - could spawn multiple prediction
3934 // TODO: viewport.getAlignment().isAligned is a global state - the local
3935 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3936 if (!viewport.getAlignment().isAligned(false))
3938 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3939 // TODO: if seqs.getSequences().length>1 then should really have warned
3953 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3955 // Pick the tree file
3956 JalviewFileChooser chooser = new JalviewFileChooser(
3957 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3958 chooser.setFileView(new JalviewFileView());
3959 chooser.setDialogTitle(
3960 MessageManager.getString("label.select_newick_like_tree_file"));
3961 chooser.setToolTipText(
3962 MessageManager.getString("label.load_tree_file"));
3964 chooser.response(new jalview.util.dialogrunner.RunResponse(
3965 JalviewFileChooser.APPROVE_OPTION)
3970 String filePath = chooser.getSelectedFile().getPath();
3971 Cache.setProperty("LAST_DIRECTORY", filePath);
3972 NewickFile fin = null;
3975 fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
3976 DataSourceType.FILE));
3977 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3978 } catch (Exception ex)
3980 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3982 .getString("label.problem_reading_tree_file"),
3983 JvOptionPane.WARNING_MESSAGE);
3984 ex.printStackTrace();
3986 if (fin != null && fin.hasWarningMessage())
3988 JvOptionPane.showMessageDialog(Desktop.desktop,
3989 fin.getWarningMessage(),
3990 MessageManager.getString(
3991 "label.possible_problem_with_tree_file"),
3992 JvOptionPane.WARNING_MESSAGE);
3995 }).openDialog(this);
3998 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4000 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4003 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4004 int h, int x, int y)
4006 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4010 * Add a treeviewer for the tree extracted from a Newick file object to the
4011 * current alignment view
4018 * Associated alignment input data (or null)
4027 * @return TreePanel handle
4029 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4030 AlignmentView input, int w, int h, int x, int y)
4032 TreePanel tp = null;
4038 if (nf.getTree() != null)
4040 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4046 tp.setLocation(x, y);
4049 Desktop.addInternalFrame(tp, treeTitle, w, h);
4051 } catch (Exception ex)
4053 ex.printStackTrace();
4059 private boolean buildingMenu = false;
4062 * Generates menu items and listener event actions for web service clients
4065 public void BuildWebServiceMenu()
4067 while (buildingMenu)
4071 System.err.println("Waiting for building menu to finish.");
4073 } catch (Exception e)
4077 final AlignFrame me = this;
4078 buildingMenu = true;
4079 new Thread(new Runnable()
4084 final List<JMenuItem> legacyItems = new ArrayList<>();
4087 // System.err.println("Building ws menu again "
4088 // + Thread.currentThread());
4089 // TODO: add support for context dependent disabling of services based
4091 // alignment and current selection
4092 // TODO: add additional serviceHandle parameter to specify abstract
4094 // class independently of AbstractName
4095 // TODO: add in rediscovery GUI function to restart discoverer
4096 // TODO: group services by location as well as function and/or
4098 // object broker mechanism.
4099 final Vector<JMenu> wsmenu = new Vector<>();
4100 final IProgressIndicator af = me;
4103 * do not i18n these strings - they are hard-coded in class
4104 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4105 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4107 final JMenu msawsmenu = new JMenu("Alignment");
4108 final JMenu secstrmenu = new JMenu(
4109 "Secondary Structure Prediction");
4110 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4111 final JMenu analymenu = new JMenu("Analysis");
4112 final JMenu dismenu = new JMenu("Protein Disorder");
4113 // JAL-940 - only show secondary structure prediction services from
4114 // the legacy server
4115 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4117 Discoverer.services != null && (Discoverer.services.size() > 0))
4119 // TODO: refactor to allow list of AbstractName/Handler bindings to
4121 // stored or retrieved from elsewhere
4122 // No MSAWS used any more:
4123 // Vector msaws = null; // (Vector)
4124 // Discoverer.services.get("MsaWS");
4125 Vector secstrpr = (Vector) Discoverer.services
4127 if (secstrpr != null)
4129 // Add any secondary structure prediction services
4130 for (int i = 0, j = secstrpr.size(); i < j; i++)
4132 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4134 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4135 .getServiceClient(sh);
4136 int p = secstrmenu.getItemCount();
4137 impl.attachWSMenuEntry(secstrmenu, me);
4138 int q = secstrmenu.getItemCount();
4139 for (int litm = p; litm < q; litm++)
4141 legacyItems.add(secstrmenu.getItem(litm));
4147 // Add all submenus in the order they should appear on the web
4149 wsmenu.add(msawsmenu);
4150 wsmenu.add(secstrmenu);
4151 wsmenu.add(dismenu);
4152 wsmenu.add(analymenu);
4153 // No search services yet
4154 // wsmenu.add(seqsrchmenu);
4156 javax.swing.SwingUtilities.invokeLater(new Runnable()
4163 webService.removeAll();
4164 // first, add discovered services onto the webservices menu
4165 if (wsmenu.size() > 0)
4167 for (int i = 0, j = wsmenu.size(); i < j; i++)
4169 webService.add(wsmenu.get(i));
4174 webService.add(me.webServiceNoServices);
4176 // TODO: move into separate menu builder class.
4177 boolean new_sspred = false;
4178 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4180 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4181 if (jws2servs != null)
4183 if (jws2servs.hasServices())
4185 jws2servs.attachWSMenuEntry(webService, me);
4186 for (Jws2Instance sv : jws2servs.getServices())
4188 if (sv.description.toLowerCase().contains("jpred"))
4190 for (JMenuItem jmi : legacyItems)
4192 jmi.setVisible(false);
4198 if (jws2servs.isRunning())
4200 JMenuItem tm = new JMenuItem(
4201 "Still discovering JABA Services");
4202 tm.setEnabled(false);
4207 build_urlServiceMenu(me.webService);
4208 build_fetchdbmenu(webService);
4209 for (JMenu item : wsmenu)
4211 if (item.getItemCount() == 0)
4213 item.setEnabled(false);
4217 item.setEnabled(true);
4220 } catch (Exception e)
4223 "Exception during web service menu building process.",
4228 } catch (Exception e)
4231 buildingMenu = false;
4238 * construct any groupURL type service menu entries.
4242 private void build_urlServiceMenu(JMenu webService)
4244 // TODO: remove this code when 2.7 is released
4245 // DEBUG - alignmentView
4247 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4248 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4250 * @Override public void actionPerformed(ActionEvent e) {
4251 * jalview.datamodel.AlignmentView
4252 * .testSelectionViews(af.viewport.getAlignment(),
4253 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4255 * }); webService.add(testAlView);
4257 // TODO: refactor to RestClient discoverer and merge menu entries for
4258 // rest-style services with other types of analysis/calculation service
4259 // SHmmr test client - still being implemented.
4260 // DEBUG - alignmentView
4262 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4265 client.attachWSMenuEntry(
4266 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4272 * Searches the alignment sequences for xRefs and builds the Show
4273 * Cross-References menu (formerly called Show Products), with database
4274 * sources for which cross-references are found (protein sources for a
4275 * nucleotide alignment and vice versa)
4277 * @return true if Show Cross-references menu should be enabled
4279 public boolean canShowProducts()
4281 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4282 AlignmentI dataset = viewport.getAlignment().getDataset();
4284 showProducts.removeAll();
4285 final boolean dna = viewport.getAlignment().isNucleotide();
4287 if (seqs == null || seqs.length == 0)
4289 // nothing to see here.
4293 boolean showp = false;
4296 List<String> ptypes = new CrossRef(seqs, dataset)
4297 .findXrefSourcesForSequences(dna);
4299 for (final String source : ptypes)
4302 final AlignFrame af = this;
4303 JMenuItem xtype = new JMenuItem(source);
4304 xtype.addActionListener(new ActionListener()
4307 public void actionPerformed(ActionEvent e)
4309 showProductsFor(af.viewport.getSequenceSelection(), dna,
4313 showProducts.add(xtype);
4315 showProducts.setVisible(showp);
4316 showProducts.setEnabled(showp);
4317 } catch (Exception e)
4320 "canShowProducts threw an exception - please report to help@jalview.org",
4328 * Finds and displays cross-references for the selected sequences (protein
4329 * products for nucleotide sequences, dna coding sequences for peptides).
4332 * the sequences to show cross-references for
4334 * true if from a nucleotide alignment (so showing proteins)
4336 * the database to show cross-references for
4338 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4339 final String source)
4341 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4346 * Construct and display a new frame containing the translation of this
4347 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4350 public void showTranslation_actionPerformed(ActionEvent e)
4352 AlignmentI al = null;
4355 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4357 al = dna.translateCdna();
4358 } catch (Exception ex)
4360 jalview.bin.Cache.log.error(
4361 "Exception during translation. Please report this !", ex);
4362 final String msg = MessageManager.getString(
4363 "label.error_when_translating_sequences_submit_bug_report");
4364 final String errorTitle = MessageManager
4365 .getString("label.implementation_error")
4366 + MessageManager.getString("label.translation_failed");
4367 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4368 JvOptionPane.ERROR_MESSAGE);
4371 if (al == null || al.getHeight() == 0)
4373 final String msg = MessageManager.getString(
4374 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4375 final String errorTitle = MessageManager
4376 .getString("label.translation_failed");
4377 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4378 JvOptionPane.WARNING_MESSAGE);
4382 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4383 af.setFileFormat(this.currentFileFormat);
4384 final String newTitle = MessageManager
4385 .formatMessage("label.translation_of_params", new Object[]
4386 { this.getTitle() });
4387 af.setTitle(newTitle);
4388 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4390 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4391 viewport.openSplitFrame(af, new Alignment(seqs));
4395 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4402 * Set the file format
4406 public void setFileFormat(FileFormatI format)
4408 this.currentFileFormat = format;
4412 * Try to load a features file onto the alignment.
4415 * contents or path to retrieve file or a File object
4417 * access mode of file (see jalview.io.AlignFile)
4418 * @return true if features file was parsed correctly.
4420 public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4423 return avc.parseFeaturesFile(file, sourceType,
4424 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4429 public void refreshFeatureUI(boolean enableIfNecessary)
4431 // note - currently this is only still here rather than in the controller
4432 // because of the featureSettings hard reference that is yet to be
4434 if (enableIfNecessary)
4436 viewport.setShowSequenceFeatures(true);
4437 showSeqFeatures.setSelected(true);
4443 public void dragEnter(DropTargetDragEvent evt)
4448 public void dragExit(DropTargetEvent evt)
4453 public void dragOver(DropTargetDragEvent evt)
4458 public void dropActionChanged(DropTargetDragEvent evt)
4463 public void drop(DropTargetDropEvent evt)
4465 // JAL-1552 - acceptDrop required before getTransferable call for
4466 // Java's Transferable for native dnd
4467 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4468 Transferable t = evt.getTransferable();
4470 final AlignFrame thisaf = this;
4471 final List<Object> files = new ArrayList<>();
4472 List<DataSourceType> protocols = new ArrayList<>();
4476 Desktop.transferFromDropTarget(files, protocols, evt, t);
4477 } catch (Exception e)
4479 e.printStackTrace();
4483 new Thread(new Runnable()
4490 // check to see if any of these files have names matching sequences
4493 SequenceIdMatcher idm = new SequenceIdMatcher(
4494 viewport.getAlignment().getSequencesArray());
4496 * Object[] { String,SequenceI}
4498 ArrayList<Object[]> filesmatched = new ArrayList<>();
4499 ArrayList<Object> filesnotmatched = new ArrayList<>();
4500 for (int i = 0; i < files.size(); i++)
4503 Object file = files.get(i);
4504 String fileName = file.toString();
4506 DataSourceType protocol = (file instanceof File
4507 ? DataSourceType.FILE
4508 : FormatAdapter.checkProtocol(fileName));
4509 if (protocol == DataSourceType.FILE)
4511 File fl = (file instanceof File ? (File) file
4512 : new File(fileName));
4513 pdbfn = fl.getName();
4515 else if (protocol == DataSourceType.URL)
4517 URL url = new URL(fileName);
4518 pdbfn = url.getFile();
4520 if (pdbfn.length() > 0)
4522 // attempt to find a match in the alignment
4523 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4524 int l = 0, c = pdbfn.indexOf(".");
4525 while (mtch == null && c != -1)
4530 } while ((c = pdbfn.indexOf(".", l)) > l);
4533 pdbfn = pdbfn.substring(0, l);
4535 mtch = idm.findAllIdMatches(pdbfn);
4542 type = new IdentifyFile().identify(file, protocol);
4543 } catch (Exception ex)
4547 if (type != null && type.isStructureFile())
4549 filesmatched.add(new Object[] { file, protocol, mtch });
4553 // File wasn't named like one of the sequences or wasn't a PDB
4555 filesnotmatched.add(file);
4559 if (filesmatched.size() > 0)
4561 boolean autoAssociate = Cache
4562 .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4565 String msg = MessageManager.formatMessage(
4566 "label.automatically_associate_structure_files_with_sequences_same_name",
4568 { Integer.valueOf(filesmatched.size())
4570 String ttl = MessageManager.getString(
4571 "label.automatically_associate_structure_files_by_name");
4572 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4573 ttl, JvOptionPane.YES_NO_OPTION);
4574 autoAssociate = choice == JvOptionPane.YES_OPTION;
4578 for (Object[] fm : filesmatched)
4580 // try and associate
4581 // TODO: may want to set a standard ID naming formalism for
4582 // associating PDB files which have no IDs.
4583 for (SequenceI toassoc : (SequenceI[]) fm[2])
4585 PDBEntry pe = new AssociatePdbFileWithSeq()
4586 .associatePdbWithSeq((String) fm[0],
4587 (DataSourceType) fm[1], toassoc, false,
4591 System.err.println("Associated file : "
4592 + ((String) fm[0]) + " with "
4593 + toassoc.getDisplayId(true));
4597 // TODO: do we need to update overview ? only if features are
4599 alignPanel.paintAlignment(true, false);
4605 * add declined structures as sequences
4607 for (Object[] o : filesmatched)
4609 filesnotmatched.add(o[0]);
4613 if (filesnotmatched.size() > 0)
4615 if (assocfiles > 0 && (Cache.getDefault(
4616 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4617 || JvOptionPane.showConfirmDialog(thisaf,
4618 "<html>" + MessageManager.formatMessage(
4619 "label.ignore_unmatched_dropped_files_info",
4622 filesnotmatched.size())
4625 MessageManager.getString(
4626 "label.ignore_unmatched_dropped_files"),
4627 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4631 for (Object fn : filesnotmatched)
4633 loadJalviewDataFile(fn, null, null, null);
4637 } catch (Exception ex)
4639 ex.printStackTrace();
4647 * Attempt to load a "dropped" file or URL string, by testing in turn for
4649 * <li>an Annotation file</li>
4650 * <li>a JNet file</li>
4651 * <li>a features file</li>
4652 * <li>else try to interpret as an alignment file</li>
4656 * either a filename or a URL string.
4658 public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4659 FileFormatI format, SequenceI assocSeq)
4661 // BH 2018 was String file
4664 if (sourceType == null)
4666 sourceType = FormatAdapter.checkProtocol(file);
4668 // if the file isn't identified, or not positively identified as some
4669 // other filetype (PFAM is default unidentified alignment file type) then
4670 // try to parse as annotation.
4671 boolean isAnnotation = (format == null
4672 || FileFormat.Pfam.equals(format))
4673 ? new AnnotationFile().annotateAlignmentView(viewport,
4679 // first see if its a T-COFFEE score file
4680 TCoffeeScoreFile tcf = null;
4683 tcf = new TCoffeeScoreFile(file, sourceType);
4686 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4690 new TCoffeeColourScheme(viewport.getAlignment()));
4691 isAnnotation = true;
4692 statusBar.setText(MessageManager.getString(
4693 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4697 // some problem - if no warning its probable that the ID matching
4698 // process didn't work
4699 JvOptionPane.showMessageDialog(Desktop.desktop,
4700 tcf.getWarningMessage() == null
4701 ? MessageManager.getString(
4702 "label.check_file_matches_sequence_ids_alignment")
4703 : tcf.getWarningMessage(),
4704 MessageManager.getString(
4705 "label.problem_reading_tcoffee_score_file"),
4706 JvOptionPane.WARNING_MESSAGE);
4713 } catch (Exception x)
4716 "Exception when processing data source as T-COFFEE score file",
4722 // try to see if its a JNet 'concise' style annotation file *before*
4724 // try to parse it as a features file
4727 format = new IdentifyFile().identify(file, sourceType);
4729 if (FileFormat.ScoreMatrix == format)
4731 ScoreMatrixFile sm = new ScoreMatrixFile(
4732 new FileParse(file, sourceType));
4734 // todo: i18n this message
4735 statusBar.setText(MessageManager.formatMessage(
4736 "label.successfully_loaded_matrix",
4737 sm.getMatrixName()));
4739 else if (FileFormat.Jnet.equals(format))
4741 JPredFile predictions = new JPredFile(file, sourceType);
4742 new JnetAnnotationMaker();
4743 JnetAnnotationMaker.add_annotation(predictions,
4744 viewport.getAlignment(), 0, false);
4745 viewport.getAlignment().setupJPredAlignment();
4746 isAnnotation = true;
4748 // else if (IdentifyFile.FeaturesFile.equals(format))
4749 else if (FileFormat.Features.equals(format))
4751 if (parseFeaturesFile(file, sourceType))
4753 alignPanel.paintAlignment(true, true);
4758 new FileLoader().LoadFile(viewport, file, sourceType, format);
4765 alignPanel.adjustAnnotationHeight();
4766 viewport.updateSequenceIdColours();
4767 buildSortByAnnotationScoresMenu();
4768 alignPanel.paintAlignment(true, true);
4770 } catch (Exception ex)
4772 ex.printStackTrace();
4773 } catch (OutOfMemoryError oom)
4778 } catch (Exception x)
4783 + (sourceType != null
4784 ? (sourceType == DataSourceType.PASTE
4786 : "using " + sourceType + " from "
4790 ? "(parsing as '" + format + "' file)"
4792 oom, Desktop.desktop);
4797 * Method invoked by the ChangeListener on the tabbed pane, in other words
4798 * when a different tabbed pane is selected by the user or programmatically.
4801 public void tabSelectionChanged(int index)
4805 alignPanel = alignPanels.get(index);
4806 viewport = alignPanel.av;
4807 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4808 setMenusFromViewport(viewport);
4812 * 'focus' any colour slider that is open to the selected viewport
4814 if (viewport.getConservationSelected())
4816 SliderPanel.setConservationSlider(alignPanel,
4817 viewport.getResidueShading(), alignPanel.getViewName());
4821 SliderPanel.hideConservationSlider();
4823 if (viewport.getAbovePIDThreshold())
4825 SliderPanel.setPIDSliderSource(alignPanel,
4826 viewport.getResidueShading(), alignPanel.getViewName());
4830 SliderPanel.hidePIDSlider();
4834 * If there is a frame linked to this one in a SplitPane, switch it to the
4835 * same view tab index. No infinite recursion of calls should happen, since
4836 * tabSelectionChanged() should not get invoked on setting the selected
4837 * index to an unchanged value. Guard against setting an invalid index
4838 * before the new view peer tab has been created.
4840 final AlignViewportI peer = viewport.getCodingComplement();
4843 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4844 .getAlignPanel().alignFrame;
4845 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4847 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4853 * On right mouse click on view tab, prompt for and set new view name.
4856 public void tabbedPane_mousePressed(MouseEvent e)
4858 if (e.isPopupTrigger())
4860 String msg = MessageManager.getString("label.enter_view_name");
4861 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4862 JvOptionPane.QUESTION_MESSAGE);
4866 viewport.viewName = reply;
4867 // TODO warn if reply is in getExistingViewNames()?
4868 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4873 public AlignViewport getCurrentView()
4879 * Open the dialog for regex description parsing.
4882 protected void extractScores_actionPerformed(ActionEvent e)
4884 ParseProperties pp = new jalview.analysis.ParseProperties(
4885 viewport.getAlignment());
4886 // TODO: verify regex and introduce GUI dialog for version 2.5
4887 // if (pp.getScoresFromDescription("col", "score column ",
4888 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4890 if (pp.getScoresFromDescription("description column",
4891 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4893 buildSortByAnnotationScoresMenu();
4901 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4905 protected void showDbRefs_actionPerformed(ActionEvent e)
4907 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4913 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4917 protected void showNpFeats_actionPerformed(ActionEvent e)
4919 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4923 * find the viewport amongst the tabs in this alignment frame and close that
4928 public boolean closeView(AlignViewportI av)
4932 this.closeMenuItem_actionPerformed(false);
4935 Component[] comp = tabbedPane.getComponents();
4936 for (int i = 0; comp != null && i < comp.length; i++)
4938 if (comp[i] instanceof AlignmentPanel)
4940 if (((AlignmentPanel) comp[i]).av == av)
4943 closeView((AlignmentPanel) comp[i]);
4951 protected void build_fetchdbmenu(JMenu webService)
4953 // Temporary hack - DBRef Fetcher always top level ws entry.
4954 // TODO We probably want to store a sequence database checklist in
4955 // preferences and have checkboxes.. rather than individual sources selected
4957 final JMenu rfetch = new JMenu(
4958 MessageManager.getString("action.fetch_db_references"));
4959 rfetch.setToolTipText(MessageManager.getString(
4960 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4961 webService.add(rfetch);
4963 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4964 MessageManager.getString("option.trim_retrieved_seqs"));
4965 trimrs.setToolTipText(
4966 MessageManager.getString("label.trim_retrieved_sequences"));
4968 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4969 trimrs.addActionListener(new ActionListener()
4972 public void actionPerformed(ActionEvent e)
4974 trimrs.setSelected(trimrs.isSelected());
4975 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4976 Boolean.valueOf(trimrs.isSelected()).toString());
4980 JMenuItem fetchr = new JMenuItem(
4981 MessageManager.getString("label.standard_databases"));
4982 fetchr.setToolTipText(
4983 MessageManager.getString("label.fetch_embl_uniprot"));
4984 fetchr.addActionListener(new ActionListener()
4988 public void actionPerformed(ActionEvent e)
4990 new Thread(new Runnable()
4995 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4996 .getAlignment().isNucleotide();
4997 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4998 alignPanel.av.getSequenceSelection(),
4999 alignPanel.alignFrame, null,
5000 alignPanel.alignFrame.featureSettings, isNucleotide);
5001 dbRefFetcher.addListener(new FetchFinishedListenerI()
5004 public void finished()
5006 AlignFrame.this.setMenusForViewport();
5009 dbRefFetcher.fetchDBRefs(false);
5017 final AlignFrame me = this;
5018 new Thread(new Runnable()
5023 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5024 .getSequenceFetcherSingleton(me);
5025 javax.swing.SwingUtilities.invokeLater(new Runnable()
5030 String[] dbclasses = sf.getOrderedSupportedSources();
5031 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5032 // jalview.util.QuickSort.sort(otherdb, otherdb);
5033 List<DbSourceProxy> otherdb;
5034 JMenu dfetch = new JMenu();
5035 JMenu ifetch = new JMenu();
5036 JMenuItem fetchr = null;
5037 int comp = 0, icomp = 0, mcomp = 15;
5038 String mname = null;
5040 for (String dbclass : dbclasses)
5042 otherdb = sf.getSourceProxy(dbclass);
5043 // add a single entry for this class, or submenu allowing 'fetch
5045 if (otherdb == null || otherdb.size() < 1)
5049 // List<DbSourceProxy> dbs=otherdb;
5050 // otherdb=new ArrayList<DbSourceProxy>();
5051 // for (DbSourceProxy db:dbs)
5053 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5057 mname = "From " + dbclass;
5059 if (otherdb.size() == 1)
5061 final DbSourceProxy[] dassource = otherdb
5062 .toArray(new DbSourceProxy[0]);
5063 DbSourceProxy src = otherdb.get(0);
5064 fetchr = new JMenuItem(src.getDbSource());
5065 fetchr.addActionListener(new ActionListener()
5069 public void actionPerformed(ActionEvent e)
5071 new Thread(new Runnable()
5077 boolean isNucleotide = alignPanel.alignFrame
5078 .getViewport().getAlignment()
5080 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5081 alignPanel.av.getSequenceSelection(),
5082 alignPanel.alignFrame, dassource,
5083 alignPanel.alignFrame.featureSettings,
5086 .addListener(new FetchFinishedListenerI()
5089 public void finished()
5091 AlignFrame.this.setMenusForViewport();
5094 dbRefFetcher.fetchDBRefs(false);
5100 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5101 MessageManager.formatMessage(
5102 "label.fetch_retrieve_from", new Object[]
5103 { src.getDbName() })));
5109 final DbSourceProxy[] dassource = otherdb
5110 .toArray(new DbSourceProxy[0]);
5112 DbSourceProxy src = otherdb.get(0);
5113 fetchr = new JMenuItem(MessageManager
5114 .formatMessage("label.fetch_all_param", new Object[]
5115 { src.getDbSource() }));
5116 fetchr.addActionListener(new ActionListener()
5119 public void actionPerformed(ActionEvent e)
5121 new Thread(new Runnable()
5127 boolean isNucleotide = alignPanel.alignFrame
5128 .getViewport().getAlignment()
5130 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5131 alignPanel.av.getSequenceSelection(),
5132 alignPanel.alignFrame, dassource,
5133 alignPanel.alignFrame.featureSettings,
5136 .addListener(new FetchFinishedListenerI()
5139 public void finished()
5141 AlignFrame.this.setMenusForViewport();
5144 dbRefFetcher.fetchDBRefs(false);
5150 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5151 MessageManager.formatMessage(
5152 "label.fetch_retrieve_from_all_sources",
5154 { Integer.valueOf(otherdb.size())
5156 src.getDbSource(), src.getDbName() })));
5159 // and then build the rest of the individual menus
5160 ifetch = new JMenu(MessageManager.formatMessage(
5161 "label.source_from_db_source", new Object[]
5162 { src.getDbSource() }));
5164 String imname = null;
5166 for (DbSourceProxy sproxy : otherdb)
5168 String dbname = sproxy.getDbName();
5169 String sname = dbname.length() > 5
5170 ? dbname.substring(0, 5) + "..."
5172 String msname = dbname.length() > 10
5173 ? dbname.substring(0, 10) + "..."
5177 imname = MessageManager
5178 .formatMessage("label.from_msname", new Object[]
5181 fetchr = new JMenuItem(msname);
5182 final DbSourceProxy[] dassrc = { sproxy };
5183 fetchr.addActionListener(new ActionListener()
5187 public void actionPerformed(ActionEvent e)
5189 new Thread(new Runnable()
5195 boolean isNucleotide = alignPanel.alignFrame
5196 .getViewport().getAlignment()
5198 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5199 alignPanel.av.getSequenceSelection(),
5200 alignPanel.alignFrame, dassrc,
5201 alignPanel.alignFrame.featureSettings,
5204 .addListener(new FetchFinishedListenerI()
5207 public void finished()
5209 AlignFrame.this.setMenusForViewport();
5212 dbRefFetcher.fetchDBRefs(false);
5218 fetchr.setToolTipText(
5219 "<html>" + MessageManager.formatMessage(
5220 "label.fetch_retrieve_from", new Object[]
5224 if (++icomp >= mcomp || i == (otherdb.size()))
5226 ifetch.setText(MessageManager.formatMessage(
5227 "label.source_to_target", imname, sname));
5229 ifetch = new JMenu();
5237 if (comp >= mcomp || dbi >= (dbclasses.length))
5239 dfetch.setText(MessageManager.formatMessage(
5240 "label.source_to_target", mname, dbclass));
5242 dfetch = new JMenu();
5255 * Left justify the whole alignment.
5258 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5260 AlignmentI al = viewport.getAlignment();
5262 viewport.firePropertyChange("alignment", null, al);
5266 * Right justify the whole alignment.
5269 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5271 AlignmentI al = viewport.getAlignment();
5273 viewport.firePropertyChange("alignment", null, al);
5277 public void setShowSeqFeatures(boolean b)
5279 showSeqFeatures.setSelected(b);
5280 viewport.setShowSequenceFeatures(b);
5287 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5288 * awt.event.ActionEvent)
5291 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5293 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5294 alignPanel.paintAlignment(false, false);
5301 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5305 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5307 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5308 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5316 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5317 * .event.ActionEvent)
5320 protected void showGroupConservation_actionPerformed(ActionEvent e)
5322 viewport.setShowGroupConservation(showGroupConservation.getState());
5323 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5330 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5331 * .event.ActionEvent)
5334 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5336 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5337 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5344 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5345 * .event.ActionEvent)
5348 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5350 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5351 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5355 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5357 showSequenceLogo.setState(true);
5358 viewport.setShowSequenceLogo(true);
5359 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5360 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5364 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5366 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5373 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5374 * .event.ActionEvent)
5377 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5379 if (avc.makeGroupsFromSelection())
5381 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5382 alignPanel.updateAnnotation();
5383 alignPanel.paintAlignment(true, true);
5387 public void clearAlignmentSeqRep()
5389 // TODO refactor alignmentseqrep to controller
5390 if (viewport.getAlignment().hasSeqrep())
5392 viewport.getAlignment().setSeqrep(null);
5393 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5394 alignPanel.updateAnnotation();
5395 alignPanel.paintAlignment(true, true);
5400 protected void createGroup_actionPerformed(ActionEvent e)
5402 if (avc.createGroup())
5404 alignPanel.alignmentChanged();
5409 protected void unGroup_actionPerformed(ActionEvent e)
5413 alignPanel.alignmentChanged();
5418 * make the given alignmentPanel the currently selected tab
5420 * @param alignmentPanel
5422 public void setDisplayedView(AlignmentPanel alignmentPanel)
5424 if (!viewport.getSequenceSetId()
5425 .equals(alignmentPanel.av.getSequenceSetId()))
5427 throw new Error(MessageManager.getString(
5428 "error.implementation_error_cannot_show_view_alignment_frame"));
5430 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5431 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5433 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5438 * Action on selection of menu options to Show or Hide annotations.
5441 * @param forSequences
5442 * update sequence-related annotations
5443 * @param forAlignment
5444 * update non-sequence-related annotations
5447 protected void setAnnotationsVisibility(boolean visible,
5448 boolean forSequences, boolean forAlignment)
5450 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5451 .getAlignmentAnnotation();
5456 for (AlignmentAnnotation aa : anns)
5459 * don't display non-positional annotations on an alignment
5461 if (aa.annotations == null)
5465 boolean apply = (aa.sequenceRef == null && forAlignment)
5466 || (aa.sequenceRef != null && forSequences);
5469 aa.visible = visible;
5472 alignPanel.validateAnnotationDimensions(true);
5473 alignPanel.alignmentChanged();
5477 * Store selected annotation sort order for the view and repaint.
5480 protected void sortAnnotations_actionPerformed()
5482 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5484 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5485 alignPanel.paintAlignment(false, false);
5490 * @return alignment panels in this alignment frame
5492 public List<? extends AlignmentViewPanel> getAlignPanels()
5494 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5498 * Open a new alignment window, with the cDNA associated with this (protein)
5499 * alignment, aligned as is the protein.
5501 protected void viewAsCdna_actionPerformed()
5503 // TODO no longer a menu action - refactor as required
5504 final AlignmentI alignment = getViewport().getAlignment();
5505 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5506 if (mappings == null)
5510 List<SequenceI> cdnaSeqs = new ArrayList<>();
5511 for (SequenceI aaSeq : alignment.getSequences())
5513 for (AlignedCodonFrame acf : mappings)
5515 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5519 * There is a cDNA mapping for this protein sequence - add to new
5520 * alignment. It will share the same dataset sequence as other mapped
5521 * cDNA (no new mappings need to be created).
5523 final Sequence newSeq = new Sequence(dnaSeq);
5524 newSeq.setDatasetSequence(dnaSeq);
5525 cdnaSeqs.add(newSeq);
5529 if (cdnaSeqs.size() == 0)
5531 // show a warning dialog no mapped cDNA
5534 AlignmentI cdna = new Alignment(
5535 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5536 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5537 AlignFrame.DEFAULT_HEIGHT);
5538 cdna.alignAs(alignment);
5539 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5541 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5542 AlignFrame.DEFAULT_HEIGHT);
5546 * Set visibility of dna/protein complement view (available when shown in a
5552 protected void showComplement_actionPerformed(boolean show)
5554 SplitContainerI sf = getSplitViewContainer();
5557 sf.setComplementVisible(this, show);
5562 * Generate the reverse (optionally complemented) of the selected sequences,
5563 * and add them to the alignment
5566 protected void showReverse_actionPerformed(boolean complement)
5568 AlignmentI al = null;
5571 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5572 al = dna.reverseCdna(complement);
5573 viewport.addAlignment(al, "");
5574 addHistoryItem(new EditCommand(
5575 MessageManager.getString("label.add_sequences"), Action.PASTE,
5576 al.getSequencesArray(), 0, al.getWidth(),
5577 viewport.getAlignment()));
5578 } catch (Exception ex)
5580 System.err.println(ex.getMessage());
5586 * Try to run a script in the Groovy console, having first ensured that this
5587 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5588 * be targeted at this alignment.
5591 protected void runGroovy_actionPerformed()
5593 Jalview.setCurrentAlignFrame(this);
5594 groovy.ui.Console console = Desktop.getGroovyConsole();
5595 if (console != null)
5599 console.runScript();
5600 } catch (Exception ex)
5602 System.err.println((ex.toString()));
5603 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5604 MessageManager.getString("label.couldnt_run_groovy_script"),
5605 MessageManager.getString("label.groovy_support_failed"),
5606 JvOptionPane.ERROR_MESSAGE);
5611 System.err.println("Can't run Groovy script as console not found");
5616 * Hides columns containing (or not containing) a specified feature, provided
5617 * that would not leave all columns hidden
5619 * @param featureType
5620 * @param columnsContaining
5623 public boolean hideFeatureColumns(String featureType,
5624 boolean columnsContaining)
5626 boolean notForHiding = avc.markColumnsContainingFeatures(
5627 columnsContaining, false, false, featureType);
5630 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5631 false, featureType))
5633 getViewport().hideSelectedColumns();
5641 protected void selectHighlightedColumns_actionPerformed(
5642 ActionEvent actionEvent)
5644 // include key modifier check in case user selects from menu
5645 avc.markHighlightedColumns(
5646 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5647 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5648 | ActionEvent.CTRL_MASK)) != 0);
5652 * Rebuilds the Colour menu, including any user-defined colours which have
5653 * been loaded either on startup or during the session
5655 public void buildColourMenu()
5657 colourMenu.removeAll();
5659 colourMenu.add(applyToAllGroups);
5660 colourMenu.add(textColour);
5661 colourMenu.addSeparator();
5663 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5666 colourMenu.addSeparator();
5667 colourMenu.add(conservationMenuItem);
5668 colourMenu.add(modifyConservation);
5669 colourMenu.add(abovePIDThreshold);
5670 colourMenu.add(modifyPID);
5671 colourMenu.add(annotationColour);
5673 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5674 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5678 * Open a dialog (if not already open) that allows the user to select and
5679 * calculate PCA or Tree analysis
5681 protected void openTreePcaDialog()
5683 if (alignPanel.getCalculationDialog() == null)
5685 new CalculationChooser(AlignFrame.this);
5690 protected void loadVcf_actionPerformed()
5692 JalviewFileChooser chooser = new JalviewFileChooser(
5693 Cache.getProperty("LAST_DIRECTORY"));
5694 chooser.setFileView(new JalviewFileView());
5695 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5696 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5697 final AlignFrame us = this;
5698 chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
5705 String choice = chooser.getSelectedFile().getPath();
5706 Cache.setProperty("LAST_DIRECTORY", choice);
5707 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5708 new VCFLoader(choice).loadVCF(seqs, us);
5712 }).openDialog(null);
5718 class PrintThread extends Thread
5722 public PrintThread(AlignmentPanel ap)
5727 static PageFormat pf;
5732 PrinterJob printJob = PrinterJob.getPrinterJob();
5736 printJob.setPrintable(ap, pf);
5740 printJob.setPrintable(ap);
5743 if (printJob.printDialog())
5748 } catch (Exception PrintException)
5750 PrintException.printStackTrace();