2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.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.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenColumns;
57 import jalview.datamodel.HiddenMarkovModel;
58 import jalview.datamodel.HiddenSequences;
59 import jalview.datamodel.PDBEntry;
60 import jalview.datamodel.SeqCigar;
61 import jalview.datamodel.Sequence;
62 import jalview.datamodel.SequenceGroup;
63 import jalview.datamodel.SequenceI;
64 import jalview.gui.ColourMenuHelper.ColourChangeListener;
65 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
66 import jalview.hmmer.HMMERCommands;
67 import jalview.io.AlignmentProperties;
68 import jalview.io.AnnotationFile;
69 import jalview.io.BioJsHTMLOutput;
70 import jalview.io.DataSourceType;
71 import jalview.io.FileFormat;
72 import jalview.io.FileFormatI;
73 import jalview.io.FileFormats;
74 import jalview.io.FileLoader;
75 import jalview.io.FileParse;
76 import jalview.io.FormatAdapter;
77 import jalview.io.HMMFile;
78 import jalview.io.HtmlSvgOutput;
79 import jalview.io.IdentifyFile;
80 import jalview.io.JPredFile;
81 import jalview.io.JalviewFileChooser;
82 import jalview.io.JalviewFileView;
83 import jalview.io.JnetAnnotationMaker;
84 import jalview.io.NewickFile;
85 import jalview.io.ScoreMatrixFile;
86 import jalview.io.TCoffeeScoreFile;
87 import jalview.jbgui.GAlignFrame;
88 import jalview.schemes.ColourSchemeI;
89 import jalview.schemes.ColourSchemes;
90 import jalview.schemes.ResidueColourScheme;
91 import jalview.schemes.TCoffeeColourScheme;
92 import jalview.util.MessageManager;
93 import jalview.viewmodel.AlignmentViewport;
94 import jalview.viewmodel.ViewportRanges;
95 import jalview.workers.InformationThread;
96 import jalview.ws.DBRefFetcher;
97 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
98 import jalview.ws.jws1.Discoverer;
99 import jalview.ws.jws2.Jws2Discoverer;
100 import jalview.ws.jws2.jabaws2.Jws2Instance;
101 import jalview.ws.seqfetcher.DbSourceProxy;
103 import java.awt.BorderLayout;
104 import java.awt.Component;
105 import java.awt.Rectangle;
106 import java.awt.Toolkit;
107 import java.awt.datatransfer.Clipboard;
108 import java.awt.datatransfer.DataFlavor;
109 import java.awt.datatransfer.StringSelection;
110 import java.awt.datatransfer.Transferable;
111 import java.awt.dnd.DnDConstants;
112 import java.awt.dnd.DropTargetDragEvent;
113 import java.awt.dnd.DropTargetDropEvent;
114 import java.awt.dnd.DropTargetEvent;
115 import java.awt.dnd.DropTargetListener;
116 import java.awt.event.ActionEvent;
117 import java.awt.event.ActionListener;
118 import java.awt.event.FocusAdapter;
119 import java.awt.event.FocusEvent;
120 import java.awt.event.ItemEvent;
121 import java.awt.event.ItemListener;
122 import java.awt.event.KeyAdapter;
123 import java.awt.event.KeyEvent;
124 import java.awt.event.MouseEvent;
125 import java.awt.print.PageFormat;
126 import java.awt.print.PrinterJob;
127 import java.beans.PropertyChangeEvent;
129 import java.io.FileWriter;
130 import java.io.IOException;
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.HashMap;
138 import java.util.Hashtable;
139 import java.util.List;
140 import java.util.Map;
141 import java.util.Vector;
143 import javax.swing.JCheckBoxMenuItem;
144 import javax.swing.JEditorPane;
145 import javax.swing.JInternalFrame;
146 import javax.swing.JLayeredPane;
147 import javax.swing.JMenu;
148 import javax.swing.JMenuItem;
149 import javax.swing.JScrollPane;
150 import javax.swing.SwingUtilities;
156 * @version $Revision$
158 public class AlignFrame extends GAlignFrame implements DropTargetListener,
159 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
162 Map<String, Float> distribution = new HashMap<>(); // temporary
164 public static final int DEFAULT_WIDTH = 700;
166 public static final int DEFAULT_HEIGHT = 500;
168 boolean autoAlignNewSequences;
173 * The currently displayed panel (selected tabbed view if more than one)
175 public AlignmentPanel alignPanel;
177 AlignViewport viewport;
179 ViewportRanges vpRanges;
181 public AlignViewControllerI avc;
183 List<AlignmentPanel> alignPanels = new ArrayList<>();
186 * Last format used to load or save alignments in this window
188 FileFormatI currentFileFormat = null;
191 * Current filename for this alignment
193 String fileName = null;
197 * Creates a new AlignFrame object with specific width and height.
203 public AlignFrame(AlignmentI al, int width, int height)
205 this(al, null, width, height);
209 * Creates a new AlignFrame object with specific width, height and
215 * @param sequenceSetId
217 public AlignFrame(AlignmentI al, int width, int height,
218 String sequenceSetId)
220 this(al, null, width, height, sequenceSetId);
224 * Creates a new AlignFrame object with specific width, height and
230 * @param sequenceSetId
233 public AlignFrame(AlignmentI al, int width, int height,
234 String sequenceSetId, String viewId)
236 this(al, null, width, height, sequenceSetId, viewId);
240 * new alignment window with hidden columns
244 * @param hiddenColumns
245 * ColumnSelection or null
247 * Width of alignment frame
251 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
252 int width, int height)
254 this(al, hiddenColumns, width, height, null);
258 * Create alignment frame for al with hiddenColumns, a specific width and
259 * height, and specific sequenceId
262 * @param hiddenColumns
265 * @param sequenceSetId
268 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
269 int width, int height, String sequenceSetId)
271 this(al, hiddenColumns, width, height, sequenceSetId, null);
275 * Create alignment frame for al with hiddenColumns, a specific width and
276 * height, and specific sequenceId
279 * @param hiddenColumns
282 * @param sequenceSetId
287 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
288 int width, int height, String sequenceSetId, String viewId)
290 setSize(width, height);
292 if (al.getDataset() == null)
297 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
299 alignPanel = new AlignmentPanel(this, viewport);
301 addAlignmentPanel(alignPanel, true);
305 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
306 HiddenColumns hiddenColumns, int width, int height)
308 setSize(width, height);
310 if (al.getDataset() == null)
315 viewport = new AlignViewport(al, hiddenColumns);
317 if (hiddenSeqs != null && hiddenSeqs.length > 0)
319 viewport.hideSequence(hiddenSeqs);
321 alignPanel = new AlignmentPanel(this, viewport);
322 addAlignmentPanel(alignPanel, true);
327 * Make a new AlignFrame from existing alignmentPanels
334 public AlignFrame(AlignmentPanel ap)
338 addAlignmentPanel(ap, false);
343 * initalise the alignframe from the underlying viewport data and the
348 if (!Jalview.isHeadlessMode())
350 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
353 vpRanges = viewport.getRanges();
354 avc = new jalview.controller.AlignViewController(this, viewport,
356 if (viewport.getAlignmentConservationAnnotation() == null)
358 // BLOSUM62Colour.setEnabled(false);
359 conservationMenuItem.setEnabled(false);
360 modifyConservation.setEnabled(false);
361 // PIDColour.setEnabled(false);
362 // abovePIDThreshold.setEnabled(false);
363 // modifyPID.setEnabled(false);
366 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
369 if (sortby.equals("Id"))
371 sortIDMenuItem_actionPerformed(null);
373 else if (sortby.equals("Pairwise Identity"))
375 sortPairwiseMenuItem_actionPerformed(null);
379 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
381 setMenusFromViewport(viewport);
382 buildSortByAnnotationScoresMenu();
383 calculateTree.addActionListener(new ActionListener()
387 public void actionPerformed(ActionEvent e)
395 if (Desktop.desktop != null)
397 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
398 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);
500 private void buildHMMERMenu()
502 hmmerMenu.removeAll();
504 hmmerMenu.add(autoAlignSeqs);
505 hmmerMenu.addSeparator();
507 hmmerMenu.add(hmmAlign);
508 hmmerMenu.add(hmmBuild);
509 hmmerMenu.add(hmmSearch);
514 * Change the filename and format for the alignment, and enable the 'reload'
515 * button functionality.
522 public void setFileName(String file, FileFormatI format)
525 setFileFormat(format);
526 reload.setEnabled(true);
530 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
533 void addKeyListener()
535 addKeyListener(new KeyAdapter()
538 public void keyPressed(KeyEvent evt)
540 if (viewport.cursorMode
541 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
542 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
543 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
544 && Character.isDigit(evt.getKeyChar()))
546 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
549 switch (evt.getKeyCode())
552 case 27: // escape key
553 deselectAllSequenceMenuItem_actionPerformed(null);
557 case KeyEvent.VK_DOWN:
558 if (evt.isAltDown() || !viewport.cursorMode)
560 moveSelectedSequences(false);
562 if (viewport.cursorMode)
564 alignPanel.getSeqPanel().moveCursor(0, 1);
569 if (evt.isAltDown() || !viewport.cursorMode)
571 moveSelectedSequences(true);
573 if (viewport.cursorMode)
575 alignPanel.getSeqPanel().moveCursor(0, -1);
580 case KeyEvent.VK_LEFT:
581 if (evt.isAltDown() || !viewport.cursorMode)
583 slideSequences(false, 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(
607 evt.isControlDown() || evt.isShiftDown()
612 // case KeyEvent.VK_A:
613 // if (viewport.cursorMode)
615 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
616 // //System.out.println("A");
620 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
621 * System.out.println("closing bracket"); } break;
623 case KeyEvent.VK_DELETE:
624 case KeyEvent.VK_BACK_SPACE:
625 if (!viewport.cursorMode)
627 cut_actionPerformed(null);
631 alignPanel.getSeqPanel().deleteGapAtCursor(
632 evt.isControlDown() || evt.isShiftDown()
639 if (viewport.cursorMode)
641 alignPanel.getSeqPanel().setCursorRow();
645 if (viewport.cursorMode && !evt.isControlDown())
647 alignPanel.getSeqPanel().setCursorColumn();
651 if (viewport.cursorMode)
653 alignPanel.getSeqPanel().setCursorPosition();
657 case KeyEvent.VK_ENTER:
658 case KeyEvent.VK_COMMA:
659 if (viewport.cursorMode)
661 alignPanel.getSeqPanel().setCursorRowAndColumn();
666 if (viewport.cursorMode)
668 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
672 if (viewport.cursorMode)
674 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
679 viewport.cursorMode = !viewport.cursorMode;
680 statusBar.setText(MessageManager.formatMessage(
681 "label.keyboard_editing_mode",
682 new String[] { (viewport.cursorMode ? "on" : "off") }));
683 if (viewport.cursorMode)
685 alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
687 alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
690 alignPanel.getSeqPanel().seqCanvas.repaint();
696 Help.showHelpWindow();
697 } catch (Exception ex)
699 ex.printStackTrace();
704 boolean toggleSeqs = !evt.isControlDown();
705 boolean toggleCols = !evt.isShiftDown();
706 toggleHiddenRegions(toggleSeqs, toggleCols);
711 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
712 boolean modifyExisting = true; // always modify, don't clear
713 // evt.isShiftDown();
714 boolean invertHighlighted = evt.isAltDown();
715 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
719 case KeyEvent.VK_PAGE_UP:
720 if (viewport.getWrapAlignment())
722 vpRanges.scrollUp(true);
729 case KeyEvent.VK_PAGE_DOWN:
730 if (viewport.getWrapAlignment())
732 vpRanges.scrollUp(false);
743 public void keyReleased(KeyEvent evt)
745 switch (evt.getKeyCode())
747 case KeyEvent.VK_LEFT:
748 if (evt.isAltDown() || !viewport.cursorMode)
750 viewport.firePropertyChange("alignment", null, viewport
751 .getAlignment().getSequences());
755 case KeyEvent.VK_RIGHT:
756 if (evt.isAltDown() || !viewport.cursorMode)
758 viewport.firePropertyChange("alignment", null, viewport
759 .getAlignment().getSequences());
767 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
769 ap.alignFrame = this;
770 avc = new jalview.controller.AlignViewController(this, viewport,
775 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
777 int aSize = alignPanels.size();
779 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
781 if (aSize == 1 && ap.av.viewName == null)
783 this.getContentPane().add(ap, BorderLayout.CENTER);
789 setInitialTabVisible();
792 expandViews.setEnabled(true);
793 gatherViews.setEnabled(true);
794 tabbedPane.addTab(ap.av.viewName, ap);
796 ap.setVisible(false);
801 if (ap.av.isPadGaps())
803 ap.av.getAlignment().padGaps();
805 ap.av.updateConservation(ap);
806 ap.av.updateConsensus(ap);
807 ap.av.updateStrucConsensus(ap);
808 ap.av.updateInformation(ap);
812 public void setInitialTabVisible()
814 expandViews.setEnabled(true);
815 gatherViews.setEnabled(true);
816 tabbedPane.setVisible(true);
817 AlignmentPanel first = alignPanels.get(0);
818 tabbedPane.addTab(first.av.viewName, first);
819 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
822 public AlignViewport getViewport()
827 /* Set up intrinsic listeners for dynamically generated GUI bits. */
828 private void addServiceListeners()
830 final java.beans.PropertyChangeListener thisListener;
831 Desktop.instance.addJalviewPropertyChangeListener("services",
832 thisListener = new java.beans.PropertyChangeListener()
835 public void propertyChange(PropertyChangeEvent evt)
837 // // System.out.println("Discoverer property change.");
838 // if (evt.getPropertyName().equals("services"))
840 SwingUtilities.invokeLater(new Runnable()
847 .println("Rebuild WS Menu for service change");
848 BuildWebServiceMenu();
855 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
858 public void internalFrameClosed(
859 javax.swing.event.InternalFrameEvent evt)
861 // System.out.println("deregistering discoverer listener");
862 Desktop.instance.removeJalviewPropertyChangeListener("services",
864 closeMenuItem_actionPerformed(true);
867 // Finally, build the menu once to get current service state
868 new Thread(new Runnable()
873 BuildWebServiceMenu();
879 * Configure menu items that vary according to whether the alignment is
880 * nucleotide or protein
882 public void setGUINucleotide()
884 AlignmentI al = getViewport().getAlignment();
885 boolean nucleotide = al.isNucleotide();
887 showTranslation.setVisible(nucleotide);
888 showReverse.setVisible(nucleotide);
889 showReverseComplement.setVisible(nucleotide);
890 conservationMenuItem.setEnabled(!nucleotide);
891 modifyConservation.setEnabled(!nucleotide
892 && conservationMenuItem.isSelected());
893 showGroupConservation.setEnabled(!nucleotide);
895 showComplementMenuItem.setText(nucleotide ? MessageManager
896 .getString("label.protein") : MessageManager
897 .getString("label.nucleotide"));
901 * set up menus for the current viewport. This may be called after any
902 * operation that affects the data in the current view (selection changed,
903 * etc) to update the menus to reflect the new state.
906 public void setMenusForViewport()
908 setMenusFromViewport(viewport);
912 * Need to call this method when tabs are selected for multiple views, or when
913 * loading from Jalview2XML.java
918 void setMenusFromViewport(AlignViewport av)
920 padGapsMenuitem.setSelected(av.isPadGaps());
921 colourTextMenuItem.setSelected(av.isShowColourText());
922 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
923 modifyPID.setEnabled(abovePIDThreshold.isSelected());
924 conservationMenuItem.setSelected(av.getConservationSelected());
925 modifyConservation.setEnabled(conservationMenuItem.isSelected());
926 seqLimits.setSelected(av.getShowJVSuffix());
927 idRightAlign.setSelected(av.isRightAlignIds());
928 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
929 renderGapsMenuItem.setSelected(av.isRenderGaps());
930 wrapMenuItem.setSelected(av.getWrapAlignment());
931 scaleAbove.setVisible(av.getWrapAlignment());
932 scaleLeft.setVisible(av.getWrapAlignment());
933 scaleRight.setVisible(av.getWrapAlignment());
934 annotationPanelMenuItem.setState(av.isShowAnnotation());
936 * Show/hide annotations only enabled if annotation panel is shown
938 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
939 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
940 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
941 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
942 viewBoxesMenuItem.setSelected(av.getShowBoxes());
943 viewTextMenuItem.setSelected(av.getShowText());
944 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
945 showGroupConsensus.setSelected(av.isShowGroupConsensus());
946 showGroupConservation.setSelected(av.isShowGroupConservation());
947 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
948 showSequenceLogo.setSelected(av.isShowSequenceLogo());
949 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
950 showInformationHistogram.setSelected(av.isShowInformationHistogram());
951 showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
952 normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
954 ColourMenuHelper.setColourSelected(colourMenu,
955 av.getGlobalColourScheme());
957 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
958 hiddenMarkers.setState(av.getShowHiddenMarkers());
959 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
960 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
961 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
962 autoCalculate.setSelected(av.autoCalculateConsensus);
963 sortByTree.setSelected(av.sortByTree);
964 listenToViewSelections.setSelected(av.followSelection);
966 showProducts.setEnabled(canShowProducts());
967 setGroovyEnabled(Desktop.getGroovyConsole() != null);
973 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
977 public void setGroovyEnabled(boolean b)
979 runGroovy.setEnabled(b);
982 private IProgressIndicator progressBar;
987 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
990 public void setProgressBar(String message, long id)
992 progressBar.setProgressBar(message, id);
996 public void registerHandler(final long id,
997 final IProgressIndicatorHandler handler)
999 progressBar.registerHandler(id, handler);
1004 * @return true if any progress bars are still active
1007 public boolean operationInProgress()
1009 return progressBar.operationInProgress();
1013 public void setStatus(String text)
1015 statusBar.setText(text);
1019 * Added so Castor Mapping file can obtain Jalview Version
1021 public String getVersion()
1023 return jalview.bin.Cache.getProperty("VERSION");
1026 public FeatureRenderer getFeatureRenderer()
1028 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1032 public void fetchSequence_actionPerformed(ActionEvent e)
1034 new jalview.gui.SequenceFetcher(this);
1038 public void addFromFile_actionPerformed(ActionEvent e)
1040 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1044 public void hmmBuild_actionPerformed(ActionEvent e)
1045 throws IOException, InterruptedException
1048 HMMERCommands.hmmBuild(this);
1049 alignPanel.repaint();
1054 public void hmmAlign_actionPerformed(ActionEvent e)
1055 throws IOException, InterruptedException
1057 SequenceI seq = getViewport().getAlignment()
1058 .getHMMConsensusSequences(false).get(0);
1059 HMMERCommands.hmmAlign(this, true, seq.getHMM());
1060 alignPanel.repaint();
1064 public void autoAlignSeqs_actionPerformed(boolean autoAlignSeqs)
1066 autoAlignNewSequences = autoAlignSeqs;
1067 alignPanel.repaint();
1071 public void hmmSearch_actionPerformed(ActionEvent e)
1073 alignPanel.repaint();
1077 public void reload_actionPerformed(ActionEvent e)
1079 if (fileName != null)
1081 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1082 // originating file's format
1083 // TODO: work out how to recover feature settings for correct view(s) when
1084 // file is reloaded.
1085 if (FileFormat.Jalview.equals(currentFileFormat))
1087 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1088 for (int i = 0; i < frames.length; i++)
1090 if (frames[i] instanceof AlignFrame && frames[i] != this
1091 && ((AlignFrame) frames[i]).fileName != null
1092 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1096 frames[i].setSelected(true);
1097 Desktop.instance.closeAssociatedWindows();
1098 } catch (java.beans.PropertyVetoException ex)
1104 Desktop.instance.closeAssociatedWindows();
1106 FileLoader loader = new FileLoader();
1107 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1108 : DataSourceType.FILE;
1109 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1113 Rectangle bounds = this.getBounds();
1115 FileLoader loader = new FileLoader();
1116 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1117 : DataSourceType.FILE;
1118 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1119 protocol, currentFileFormat);
1121 newframe.setBounds(bounds);
1122 if (featureSettings != null && featureSettings.isShowing())
1124 final Rectangle fspos = featureSettings.frame.getBounds();
1125 // TODO: need a 'show feature settings' function that takes bounds -
1126 // need to refactor Desktop.addFrame
1127 newframe.featureSettings_actionPerformed(null);
1128 final FeatureSettings nfs = newframe.featureSettings;
1129 SwingUtilities.invokeLater(new Runnable()
1134 nfs.frame.setBounds(fspos);
1137 this.featureSettings.close();
1138 this.featureSettings = null;
1140 this.closeMenuItem_actionPerformed(true);
1146 public void addFromText_actionPerformed(ActionEvent e)
1148 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1153 public void addFromURL_actionPerformed(ActionEvent e)
1155 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1159 public void save_actionPerformed(ActionEvent e)
1161 if (fileName == null || (currentFileFormat == null)
1162 || fileName.startsWith("http"))
1164 saveAs_actionPerformed(null);
1168 saveAlignment(fileName, currentFileFormat);
1179 public void saveAs_actionPerformed(ActionEvent e)
1181 String format = currentFileFormat == null ? null : currentFileFormat
1183 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1184 Cache.getProperty("LAST_DIRECTORY"), format);
1186 chooser.setFileView(new JalviewFileView());
1187 chooser.setDialogTitle(MessageManager
1188 .getString("label.save_alignment_to_file"));
1189 chooser.setToolTipText(MessageManager.getString("action.save"));
1191 int value = chooser.showSaveDialog(this);
1193 if (value == JalviewFileChooser.APPROVE_OPTION)
1195 currentFileFormat = chooser.getSelectedFormat();
1196 while (currentFileFormat == null)
1199 .showInternalMessageDialog(
1202 .getString("label.select_file_format_before_saving"),
1204 .getString("label.file_format_not_specified"),
1205 JvOptionPane.WARNING_MESSAGE);
1206 currentFileFormat = chooser.getSelectedFormat();
1207 value = chooser.showSaveDialog(this);
1208 if (value != JalviewFileChooser.APPROVE_OPTION)
1214 fileName = chooser.getSelectedFile().getPath();
1216 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1218 Cache.setProperty("LAST_DIRECTORY", fileName);
1219 saveAlignment(fileName, currentFileFormat);
1223 public boolean saveAlignment(String file, FileFormatI format)
1225 boolean success = true;
1227 if (FileFormat.Jalview.equals(format))
1229 String shortName = title;
1231 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1233 shortName = shortName.substring(shortName
1234 .lastIndexOf(java.io.File.separatorChar) + 1);
1237 success = new Jalview2XML().saveAlignment(this, file, shortName);
1239 statusBar.setText(MessageManager.formatMessage(
1240 "label.successfully_saved_to_file_in_format", new Object[] {
1241 fileName, format }));
1246 AlignmentExportData exportData = getAlignmentForExport(format,
1248 if (exportData.getSettings().isCancelled())
1252 FormatAdapter f = new FormatAdapter(alignPanel,
1253 exportData.getSettings());
1254 String output = f.formatSequences(
1256 exportData.getAlignment(), // class cast exceptions will
1257 // occur in the distant future
1258 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1259 f.getCacheSuffixDefault(format), viewport.getAlignment()
1260 .getHiddenColumns());
1270 PrintWriter out = new PrintWriter(new FileWriter(file));
1274 this.setTitle(file);
1275 statusBar.setText(MessageManager.formatMessage(
1276 "label.successfully_saved_to_file_in_format",
1277 new Object[] { fileName, format.getName() }));
1278 } catch (Exception ex)
1281 ex.printStackTrace();
1288 JvOptionPane.showInternalMessageDialog(this, MessageManager
1289 .formatMessage("label.couldnt_save_file",
1290 new Object[] { fileName }), MessageManager
1291 .getString("label.error_saving_file"),
1292 JvOptionPane.WARNING_MESSAGE);
1298 private void warningMessage(String warning, String title)
1300 if (new jalview.util.Platform().isHeadless())
1302 System.err.println("Warning: " + title + "\nWarning: " + warning);
1307 JvOptionPane.showInternalMessageDialog(this, warning, title,
1308 JvOptionPane.WARNING_MESSAGE);
1320 protected void outputText_actionPerformed(ActionEvent e)
1322 FileFormatI fileFormat = FileFormats.getInstance().forName(
1323 e.getActionCommand());
1324 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1326 if (exportData.getSettings().isCancelled())
1330 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1331 cap.setForInput(null);
1334 FileFormatI format = fileFormat;
1335 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1336 .formatSequences(format, exportData.getAlignment(),
1337 exportData.getOmitHidden(),
1339 .getStartEndPostions(), viewport
1340 .getAlignment().getHiddenColumns()));
1341 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1342 "label.alignment_output_command",
1343 new Object[] { e.getActionCommand() }), 600, 500);
1344 } catch (OutOfMemoryError oom)
1346 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1352 public static AlignmentExportData getAlignmentForExport(
1353 FileFormatI format, AlignViewportI viewport,
1354 AlignExportSettingI exportSettings)
1356 AlignmentI alignmentToExport = null;
1357 AlignExportSettingI settings = exportSettings;
1358 String[] omitHidden = null;
1360 HiddenSequences hiddenSeqs = viewport.getAlignment()
1361 .getHiddenSequences();
1363 alignmentToExport = viewport.getAlignment();
1365 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1366 if (settings == null)
1368 settings = new AlignExportSettings(hasHiddenSeqs,
1369 viewport.hasHiddenColumns(), format);
1371 // settings.isExportAnnotations();
1373 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1375 omitHidden = viewport.getViewAsString(false,
1376 settings.isExportHiddenSequences());
1379 int[] alignmentStartEnd = new int[2];
1380 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1382 alignmentToExport = hiddenSeqs.getFullAlignment();
1386 alignmentToExport = viewport.getAlignment();
1388 alignmentStartEnd = alignmentToExport
1389 .getVisibleStartAndEndIndex(viewport.getAlignment()
1391 .getHiddenRegions());
1392 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1393 omitHidden, alignmentStartEnd, settings);
1404 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1406 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1407 htmlSVG.exportHTML(null);
1411 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1413 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1414 bjs.exportHTML(null);
1417 public void createImageMap(File file, String image)
1419 alignPanel.makePNGImageMap(file, image);
1429 public void createPNG(File f)
1431 alignPanel.makePNG(f);
1441 public void createEPS(File f)
1443 alignPanel.makeEPS(f);
1447 public void createSVG(File f)
1449 alignPanel.makeSVG(f);
1453 public void pageSetup_actionPerformed(ActionEvent e)
1455 PrinterJob printJob = PrinterJob.getPrinterJob();
1456 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1466 public void printMenuItem_actionPerformed(ActionEvent e)
1468 // Putting in a thread avoids Swing painting problems
1469 PrintThread thread = new PrintThread(alignPanel);
1474 public void exportFeatures_actionPerformed(ActionEvent e)
1476 new AnnotationExporter().exportFeatures(alignPanel);
1480 public void exportAnnotations_actionPerformed(ActionEvent e)
1482 new AnnotationExporter().exportAnnotations(alignPanel);
1486 public void associatedData_actionPerformed(ActionEvent e)
1487 throws IOException, InterruptedException
1489 // Pick the tree file
1490 JalviewFileChooser chooser = new JalviewFileChooser(
1491 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1492 chooser.setFileView(new JalviewFileView());
1493 chooser.setDialogTitle(MessageManager
1494 .getString("label.load_jalview_annotations"));
1495 chooser.setToolTipText(MessageManager
1496 .getString("label.load_jalview_annotations"));
1498 int value = chooser.showOpenDialog(null);
1500 if (value == JalviewFileChooser.APPROVE_OPTION)
1502 String choice = chooser.getSelectedFile().getPath();
1503 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1504 loadJalviewDataFile(choice, null, null, null);
1510 * Close the current view or all views in the alignment frame. If the frame
1511 * only contains one view then the alignment will be removed from memory.
1513 * @param closeAllTabs
1516 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1518 if (alignPanels != null && alignPanels.size() < 2)
1520 closeAllTabs = true;
1525 if (alignPanels != null)
1529 if (this.isClosed())
1531 // really close all the windows - otherwise wait till
1532 // setClosed(true) is called
1533 for (int i = 0; i < alignPanels.size(); i++)
1535 AlignmentPanel ap = alignPanels.get(i);
1542 closeView(alignPanel);
1549 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1550 * be called recursively, with the frame now in 'closed' state
1552 this.setClosed(true);
1554 } catch (Exception ex)
1556 ex.printStackTrace();
1561 * Close the specified panel and close up tabs appropriately.
1563 * @param panelToClose
1565 public void closeView(AlignmentPanel panelToClose)
1567 int index = tabbedPane.getSelectedIndex();
1568 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1569 alignPanels.remove(panelToClose);
1570 panelToClose.closePanel();
1571 panelToClose = null;
1573 tabbedPane.removeTabAt(closedindex);
1574 tabbedPane.validate();
1576 if (index > closedindex || index == tabbedPane.getTabCount())
1578 // modify currently selected tab index if necessary.
1582 this.tabSelectionChanged(index);
1588 void updateEditMenuBar()
1591 if (viewport.getHistoryList().size() > 0)
1593 undoMenuItem.setEnabled(true);
1594 CommandI command = viewport.getHistoryList().peek();
1595 undoMenuItem.setText(MessageManager.formatMessage(
1596 "label.undo_command",
1597 new Object[] { command.getDescription() }));
1601 undoMenuItem.setEnabled(false);
1602 undoMenuItem.setText(MessageManager.getString("action.undo"));
1605 if (viewport.getRedoList().size() > 0)
1607 redoMenuItem.setEnabled(true);
1609 CommandI command = viewport.getRedoList().peek();
1610 redoMenuItem.setText(MessageManager.formatMessage(
1611 "label.redo_command",
1612 new Object[] { command.getDescription() }));
1616 redoMenuItem.setEnabled(false);
1617 redoMenuItem.setText(MessageManager.getString("action.redo"));
1622 public void addHistoryItem(CommandI command)
1624 if (command.getSize() > 0)
1626 viewport.addToHistoryList(command);
1627 viewport.clearRedoList();
1628 updateEditMenuBar();
1629 viewport.updateHiddenColumns();
1630 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1631 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1632 // viewport.getColumnSelection()
1633 // .getHiddenColumns().size() > 0);
1639 * @return alignment objects for all views
1641 AlignmentI[] getViewAlignments()
1643 if (alignPanels != null)
1645 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1647 for (AlignmentPanel ap : alignPanels)
1649 als[i++] = ap.av.getAlignment();
1653 if (viewport != null)
1655 return new AlignmentI[] { viewport.getAlignment() };
1667 protected void undoMenuItem_actionPerformed(ActionEvent e)
1669 if (viewport.getHistoryList().isEmpty())
1673 CommandI command = viewport.getHistoryList().pop();
1674 viewport.addToRedoList(command);
1675 command.undoCommand(getViewAlignments());
1677 AlignmentViewport originalSource = getOriginatingSource(command);
1678 updateEditMenuBar();
1680 if (originalSource != null)
1682 if (originalSource != viewport)
1685 .warn("Implementation worry: mismatch of viewport origin for undo");
1687 originalSource.updateHiddenColumns();
1688 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1690 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1691 // viewport.getColumnSelection()
1692 // .getHiddenColumns().size() > 0);
1693 originalSource.firePropertyChange("alignment", null, originalSource
1694 .getAlignment().getSequences());
1705 protected void redoMenuItem_actionPerformed(ActionEvent e)
1707 if (viewport.getRedoList().size() < 1)
1712 CommandI command = viewport.getRedoList().pop();
1713 viewport.addToHistoryList(command);
1714 command.doCommand(getViewAlignments());
1716 AlignmentViewport originalSource = getOriginatingSource(command);
1717 updateEditMenuBar();
1719 if (originalSource != null)
1722 if (originalSource != viewport)
1725 .warn("Implementation worry: mismatch of viewport origin for redo");
1727 originalSource.updateHiddenColumns();
1728 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1730 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1731 // viewport.getColumnSelection()
1732 // .getHiddenColumns().size() > 0);
1733 originalSource.firePropertyChange("alignment", null, originalSource
1734 .getAlignment().getSequences());
1738 AlignmentViewport getOriginatingSource(CommandI command)
1740 AlignmentViewport originalSource = null;
1741 // For sequence removal and addition, we need to fire
1742 // the property change event FROM the viewport where the
1743 // original alignment was altered
1744 AlignmentI al = null;
1745 if (command instanceof EditCommand)
1747 EditCommand editCommand = (EditCommand) command;
1748 al = editCommand.getAlignment();
1749 List<Component> comps = PaintRefresher.components.get(viewport
1750 .getSequenceSetId());
1752 for (Component comp : comps)
1754 if (comp instanceof AlignmentPanel)
1756 if (al == ((AlignmentPanel) comp).av.getAlignment())
1758 originalSource = ((AlignmentPanel) comp).av;
1765 if (originalSource == null)
1767 // The original view is closed, we must validate
1768 // the current view against the closed view first
1771 PaintRefresher.validateSequences(al, viewport.getAlignment());
1774 originalSource = viewport;
1777 return originalSource;
1786 public void moveSelectedSequences(boolean up)
1788 SequenceGroup sg = viewport.getSelectionGroup();
1794 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1795 viewport.getHiddenRepSequences(), up);
1796 alignPanel.paintAlignment(true);
1799 synchronized void slideSequences(boolean right, int size)
1801 List<SequenceI> sg = new ArrayList<>();
1802 if (viewport.cursorMode)
1804 sg.add(viewport.getAlignment().getSequenceAt(
1805 alignPanel.getSeqPanel().seqCanvas.cursorY));
1807 else if (viewport.getSelectionGroup() != null
1808 && viewport.getSelectionGroup().getSize() != viewport
1809 .getAlignment().getHeight())
1811 sg = viewport.getSelectionGroup().getSequences(
1812 viewport.getHiddenRepSequences());
1820 List<SequenceI> invertGroup = new ArrayList<>();
1822 for (SequenceI seq : viewport.getAlignment().getSequences())
1824 if (!sg.contains(seq))
1826 invertGroup.add(seq);
1830 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1832 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1833 for (int i = 0; i < invertGroup.size(); i++)
1835 seqs2[i] = invertGroup.get(i);
1838 SlideSequencesCommand ssc;
1841 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1842 size, viewport.getGapCharacter());
1846 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1847 size, viewport.getGapCharacter());
1850 int groupAdjustment = 0;
1851 if (ssc.getGapsInsertedBegin() && right)
1853 if (viewport.cursorMode)
1855 alignPanel.getSeqPanel().moveCursor(size, 0);
1859 groupAdjustment = size;
1862 else if (!ssc.getGapsInsertedBegin() && !right)
1864 if (viewport.cursorMode)
1866 alignPanel.getSeqPanel().moveCursor(-size, 0);
1870 groupAdjustment = -size;
1874 if (groupAdjustment != 0)
1876 viewport.getSelectionGroup().setStartRes(
1877 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1878 viewport.getSelectionGroup().setEndRes(
1879 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1883 * just extend the last slide command if compatible; but not if in
1884 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1886 boolean appendHistoryItem = false;
1887 Deque<CommandI> historyList = viewport.getHistoryList();
1888 boolean inSplitFrame = getSplitViewContainer() != null;
1889 if (!inSplitFrame && historyList != null && historyList.size() > 0
1890 && historyList.peek() instanceof SlideSequencesCommand)
1892 appendHistoryItem = ssc
1893 .appendSlideCommand((SlideSequencesCommand) historyList
1897 if (!appendHistoryItem)
1899 addHistoryItem(ssc);
1912 protected void copy_actionPerformed(ActionEvent e)
1915 if (viewport.getSelectionGroup() == null)
1919 // TODO: preserve the ordering of displayed alignment annotation in any
1920 // internal paste (particularly sequence associated annotation)
1921 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1922 String[] omitHidden = null;
1924 if (viewport.hasHiddenColumns())
1926 omitHidden = viewport.getViewAsString(true);
1929 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1930 seqs, omitHidden, null);
1932 StringSelection ss = new StringSelection(output);
1936 jalview.gui.Desktop.internalCopy = true;
1937 // Its really worth setting the clipboard contents
1938 // to empty before setting the large StringSelection!!
1939 Toolkit.getDefaultToolkit().getSystemClipboard()
1940 .setContents(new StringSelection(""), null);
1942 Toolkit.getDefaultToolkit().getSystemClipboard()
1943 .setContents(ss, Desktop.instance);
1944 } catch (OutOfMemoryError er)
1946 new OOMWarning("copying region", er);
1950 ArrayList<int[]> hiddenColumns = null;
1951 if (viewport.hasHiddenColumns())
1953 hiddenColumns = new ArrayList<>();
1954 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1955 .getSelectionGroup().getEndRes();
1956 for (int[] region : viewport.getAlignment().getHiddenColumns()
1957 .getHiddenRegions())
1959 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1961 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1962 region[1] - hiddenOffset });
1967 Desktop.jalviewClipboard = new Object[] { seqs,
1968 viewport.getAlignment().getDataset(), hiddenColumns };
1969 statusBar.setText(MessageManager.formatMessage(
1970 "label.copied_sequences_to_clipboard", new Object[] { Integer
1971 .valueOf(seqs.length).toString() }));
1979 * @throws InterruptedException
1980 * @throws IOException
1983 protected void pasteNew_actionPerformed(ActionEvent e)
1984 throws IOException, InterruptedException
1994 * @throws InterruptedException
1995 * @throws IOException
1998 protected void pasteThis_actionPerformed(ActionEvent e)
1999 throws IOException, InterruptedException
2005 * Paste contents of Jalview clipboard
2007 * @param newAlignment
2008 * true to paste to a new alignment, otherwise add to this.
2009 * @throws InterruptedException
2010 * @throws IOException
2012 void paste(boolean newAlignment) throws IOException, InterruptedException
2014 boolean externalPaste = true;
2017 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2018 Transferable contents = c.getContents(this);
2020 if (contents == null)
2029 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2030 if (str.length() < 1)
2035 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2037 } catch (OutOfMemoryError er)
2039 new OOMWarning("Out of memory pasting sequences!!", er);
2043 SequenceI[] sequences;
2044 boolean annotationAdded = false;
2045 AlignmentI alignment = null;
2047 if (Desktop.jalviewClipboard != null)
2049 // The clipboard was filled from within Jalview, we must use the
2051 // And dataset from the copied alignment
2052 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2053 // be doubly sure that we create *new* sequence objects.
2054 sequences = new SequenceI[newseq.length];
2055 for (int i = 0; i < newseq.length; i++)
2057 sequences[i] = new Sequence(newseq[i]);
2059 alignment = new Alignment(sequences);
2060 externalPaste = false;
2064 // parse the clipboard as an alignment.
2065 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2067 sequences = alignment.getSequencesArray();
2071 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2077 if (Desktop.jalviewClipboard != null)
2079 // dataset is inherited
2080 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2084 // new dataset is constructed
2085 alignment.setDataset(null);
2087 alwidth = alignment.getWidth() + 1;
2091 AlignmentI pastedal = alignment; // preserve pasted alignment object
2092 // Add pasted sequences and dataset into existing alignment.
2093 alignment = viewport.getAlignment();
2094 alwidth = alignment.getWidth() + 1;
2095 // decide if we need to import sequences from an existing dataset
2096 boolean importDs = Desktop.jalviewClipboard != null
2097 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2098 // importDs==true instructs us to copy over new dataset sequences from
2099 // an existing alignment
2100 Vector newDs = (importDs) ? new Vector() : null; // used to create
2101 // minimum dataset set
2103 for (int i = 0; i < sequences.length; i++)
2107 newDs.addElement(null);
2109 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2111 if (importDs && ds != null)
2113 if (!newDs.contains(ds))
2115 newDs.setElementAt(ds, i);
2116 ds = new Sequence(ds);
2117 // update with new dataset sequence
2118 sequences[i].setDatasetSequence(ds);
2122 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2127 // copy and derive new dataset sequence
2128 sequences[i] = sequences[i].deriveSequence();
2129 alignment.getDataset().addSequence(
2130 sequences[i].getDatasetSequence());
2131 // TODO: avoid creation of duplicate dataset sequences with a
2132 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2134 alignment.addSequence(sequences[i]); // merges dataset
2138 newDs.clear(); // tidy up
2140 if (alignment.getAlignmentAnnotation() != null)
2142 for (AlignmentAnnotation alan : alignment
2143 .getAlignmentAnnotation())
2145 if (alan.graphGroup > fgroup)
2147 fgroup = alan.graphGroup;
2151 if (pastedal.getAlignmentAnnotation() != null)
2153 // Add any annotation attached to alignment.
2154 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2155 for (int i = 0; i < alann.length; i++)
2157 annotationAdded = true;
2158 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2160 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2161 if (newann.graphGroup > -1)
2163 if (newGraphGroups.size() <= newann.graphGroup
2164 || newGraphGroups.get(newann.graphGroup) == null)
2166 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2168 newGraphGroups.add(q, null);
2170 newGraphGroups.set(newann.graphGroup, new Integer(
2173 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2177 newann.padAnnotation(alwidth);
2178 alignment.addAnnotation(newann);
2188 addHistoryItem(new EditCommand(
2189 MessageManager.getString("label.add_sequences"),
2190 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2192 // Add any annotations attached to sequences
2193 for (int i = 0; i < sequences.length; i++)
2195 if (sequences[i].getAnnotation() != null)
2197 AlignmentAnnotation newann;
2198 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2200 annotationAdded = true;
2201 newann = sequences[i].getAnnotation()[a];
2202 newann.adjustForAlignment();
2203 newann.padAnnotation(alwidth);
2204 if (newann.graphGroup > -1)
2206 if (newann.graphGroup > -1)
2208 if (newGraphGroups.size() <= newann.graphGroup
2209 || newGraphGroups.get(newann.graphGroup) == null)
2211 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2213 newGraphGroups.add(q, null);
2215 newGraphGroups.set(newann.graphGroup, new Integer(
2218 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2222 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2227 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2234 // propagate alignment changed.
2235 vpRanges.setEndSeq(alignment.getHeight());
2236 if (annotationAdded)
2238 // Duplicate sequence annotation in all views.
2239 AlignmentI[] alview = this.getViewAlignments();
2240 for (int i = 0; i < sequences.length; i++)
2242 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2247 for (int avnum = 0; avnum < alview.length; avnum++)
2249 if (alview[avnum] != alignment)
2251 // duplicate in a view other than the one with input focus
2252 int avwidth = alview[avnum].getWidth() + 1;
2253 // this relies on sann being preserved after we
2254 // modify the sequence's annotation array for each duplication
2255 for (int a = 0; a < sann.length; a++)
2257 AlignmentAnnotation newann = new AlignmentAnnotation(
2259 sequences[i].addAlignmentAnnotation(newann);
2260 newann.padAnnotation(avwidth);
2261 alview[avnum].addAnnotation(newann); // annotation was
2262 // duplicated earlier
2263 // TODO JAL-1145 graphGroups are not updated for sequence
2264 // annotation added to several views. This may cause
2266 alview[avnum].setAnnotationIndex(newann, a);
2271 buildSortByAnnotationScoresMenu();
2273 viewport.firePropertyChange("alignment", null,
2274 alignment.getSequences());
2275 if (alignPanels != null)
2277 for (AlignmentPanel ap : alignPanels)
2279 ap.validateAnnotationDimensions(false);
2284 alignPanel.validateAnnotationDimensions(false);
2290 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2292 String newtitle = new String("Copied sequences");
2294 if (Desktop.jalviewClipboard != null
2295 && Desktop.jalviewClipboard[2] != null)
2297 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2298 for (int[] region : hc)
2300 af.viewport.hideColumns(region[0], region[1]);
2304 // >>>This is a fix for the moment, until a better solution is
2306 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2308 alignPanel.getSeqPanel().seqCanvas
2309 .getFeatureRenderer());
2311 // TODO: maintain provenance of an alignment, rather than just make the
2312 // title a concatenation of operations.
2315 if (title.startsWith("Copied sequences"))
2321 newtitle = newtitle.concat("- from " + title);
2326 newtitle = new String("Pasted sequences");
2329 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2334 } catch (Exception ex)
2336 ex.printStackTrace();
2337 System.out.println("Exception whilst pasting: " + ex);
2338 // could be anything being pasted in here
2343 protected void expand_newalign(ActionEvent e)
2347 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2348 .getAlignment(), -1);
2349 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2351 String newtitle = new String("Flanking alignment");
2353 if (Desktop.jalviewClipboard != null
2354 && Desktop.jalviewClipboard[2] != null)
2356 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2357 for (int region[] : hc)
2359 af.viewport.hideColumns(region[0], region[1]);
2363 // >>>This is a fix for the moment, until a better solution is
2365 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2367 alignPanel.getSeqPanel().seqCanvas
2368 .getFeatureRenderer());
2370 // TODO: maintain provenance of an alignment, rather than just make the
2371 // title a concatenation of operations.
2373 if (title.startsWith("Copied sequences"))
2379 newtitle = newtitle.concat("- from " + title);
2383 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2385 } catch (Exception ex)
2387 ex.printStackTrace();
2388 System.out.println("Exception whilst pasting: " + ex);
2389 // could be anything being pasted in here
2390 } catch (OutOfMemoryError oom)
2392 new OOMWarning("Viewing flanking region of alignment", oom);
2403 protected void cut_actionPerformed(ActionEvent e)
2405 copy_actionPerformed(null);
2406 delete_actionPerformed(null);
2416 protected void delete_actionPerformed(ActionEvent evt)
2419 SequenceGroup sg = viewport.getSelectionGroup();
2426 * If the cut affects all sequences, warn, remove highlighted columns
2428 if (sg.getSize() == viewport.getAlignment().getHeight())
2430 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2431 .getAlignment().getWidth()) ? true : false;
2432 if (isEntireAlignWidth)
2434 int confirm = JvOptionPane.showConfirmDialog(this,
2435 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2436 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2437 JvOptionPane.OK_CANCEL_OPTION);
2439 if (confirm == JvOptionPane.CANCEL_OPTION
2440 || confirm == JvOptionPane.CLOSED_OPTION)
2445 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2446 sg.getEndRes() + 1);
2448 SequenceI[] cut = sg.getSequences()
2449 .toArray(new SequenceI[sg.getSize()]);
2451 addHistoryItem(new EditCommand(
2452 MessageManager.getString("label.cut_sequences"), Action.CUT,
2453 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2454 viewport.getAlignment()));
2456 viewport.setSelectionGroup(null);
2457 viewport.sendSelection();
2458 viewport.getAlignment().deleteGroup(sg);
2460 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2462 if (viewport.getAlignment().getHeight() < 1)
2466 this.setClosed(true);
2467 } catch (Exception ex)
2480 protected void deleteGroups_actionPerformed(ActionEvent e)
2482 if (avc.deleteGroups())
2484 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2485 alignPanel.updateAnnotation();
2486 alignPanel.paintAlignment(true);
2497 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2499 SequenceGroup sg = new SequenceGroup();
2501 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2503 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2506 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2507 viewport.setSelectionGroup(sg);
2508 viewport.sendSelection();
2509 // JAL-2034 - should delegate to
2510 // alignPanel to decide if overview needs
2512 alignPanel.paintAlignment(false);
2513 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2523 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2525 if (viewport.cursorMode)
2527 alignPanel.getSeqPanel().keyboardNo1 = null;
2528 alignPanel.getSeqPanel().keyboardNo2 = null;
2530 viewport.setSelectionGroup(null);
2531 viewport.getColumnSelection().clear();
2532 viewport.setSelectionGroup(null);
2533 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2534 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2535 // JAL-2034 - should delegate to
2536 // alignPanel to decide if overview needs
2538 alignPanel.paintAlignment(false);
2539 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2540 viewport.sendSelection();
2550 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2552 SequenceGroup sg = viewport.getSelectionGroup();
2556 selectAllSequenceMenuItem_actionPerformed(null);
2561 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2563 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2565 // JAL-2034 - should delegate to
2566 // alignPanel to decide if overview needs
2569 alignPanel.paintAlignment(true);
2570 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2571 viewport.sendSelection();
2575 public void invertColSel_actionPerformed(ActionEvent e)
2577 viewport.invertColumnSelection();
2578 alignPanel.paintAlignment(true);
2579 viewport.sendSelection();
2589 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2591 trimAlignment(true);
2601 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2603 trimAlignment(false);
2606 void trimAlignment(boolean trimLeft)
2608 ColumnSelection colSel = viewport.getColumnSelection();
2611 if (!colSel.isEmpty())
2615 column = colSel.getMin();
2619 column = colSel.getMax();
2623 if (viewport.getSelectionGroup() != null)
2625 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2626 viewport.getHiddenRepSequences());
2630 seqs = viewport.getAlignment().getSequencesArray();
2633 TrimRegionCommand trimRegion;
2636 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2637 column, viewport.getAlignment());
2638 vpRanges.setStartRes(0);
2642 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2643 column, viewport.getAlignment());
2646 statusBar.setText(MessageManager.formatMessage(
2647 "label.removed_columns",
2648 new String[] { Integer.valueOf(trimRegion.getSize())
2651 addHistoryItem(trimRegion);
2653 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2655 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2656 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2658 viewport.getAlignment().deleteGroup(sg);
2662 viewport.firePropertyChange("alignment", null, viewport
2663 .getAlignment().getSequences());
2674 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2676 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2679 if (viewport.getSelectionGroup() != null)
2681 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2682 viewport.getHiddenRepSequences());
2683 start = viewport.getSelectionGroup().getStartRes();
2684 end = viewport.getSelectionGroup().getEndRes();
2688 seqs = viewport.getAlignment().getSequencesArray();
2691 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2692 "Remove Gapped Columns", seqs, start, end,
2693 viewport.getAlignment());
2695 addHistoryItem(removeGapCols);
2697 statusBar.setText(MessageManager.formatMessage(
2698 "label.removed_empty_columns",
2699 new Object[] { Integer.valueOf(removeGapCols.getSize())
2702 // This is to maintain viewport position on first residue
2703 // of first sequence
2704 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2705 int startRes = seq.findPosition(vpRanges.getStartRes());
2706 // ShiftList shifts;
2707 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2708 // edit.alColumnChanges=shifts.getInverse();
2709 // if (viewport.hasHiddenColumns)
2710 // viewport.getColumnSelection().compensateForEdits(shifts);
2711 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2712 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2724 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2726 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2729 if (viewport.getSelectionGroup() != null)
2731 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2732 viewport.getHiddenRepSequences());
2733 start = viewport.getSelectionGroup().getStartRes();
2734 end = viewport.getSelectionGroup().getEndRes();
2738 seqs = viewport.getAlignment().getSequencesArray();
2741 // This is to maintain viewport position on first residue
2742 // of first sequence
2743 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2744 int startRes = seq.findPosition(vpRanges.getStartRes());
2746 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2747 viewport.getAlignment()));
2749 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2751 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2763 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2765 viewport.setPadGaps(padGapsMenuitem.isSelected());
2766 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2777 public void findMenuItem_actionPerformed(ActionEvent e)
2783 * Create a new view of the current alignment.
2786 public void newView_actionPerformed(ActionEvent e)
2788 newView(null, true);
2792 * Creates and shows a new view of the current alignment.
2795 * title of newly created view; if null, one will be generated
2796 * @param copyAnnotation
2797 * if true then duplicate all annnotation, groups and settings
2798 * @return new alignment panel, already displayed.
2800 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2803 * Create a new AlignmentPanel (with its own, new Viewport)
2805 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2807 if (!copyAnnotation)
2810 * remove all groups and annotation except for the automatic stuff
2812 newap.av.getAlignment().deleteAllGroups();
2813 newap.av.getAlignment().deleteAllAnnotations(false);
2816 newap.av.setGatherViewsHere(false);
2818 if (viewport.viewName == null)
2820 viewport.viewName = MessageManager
2821 .getString("label.view_name_original");
2825 * Views share the same edits undo and redo stacks
2827 newap.av.setHistoryList(viewport.getHistoryList());
2828 newap.av.setRedoList(viewport.getRedoList());
2831 * Views share the same mappings; need to deregister any new mappings
2832 * created by copyAlignPanel, and register the new reference to the shared
2835 newap.av.replaceMappings(viewport.getAlignment());
2838 * start up cDNA consensus (if applicable) now mappings are in place
2840 if (newap.av.initComplementConsensus())
2842 newap.refresh(true); // adjust layout of annotations
2845 newap.av.viewName = getNewViewName(viewTitle);
2847 addAlignmentPanel(newap, true);
2848 newap.alignmentChanged();
2850 if (alignPanels.size() == 2)
2852 viewport.setGatherViewsHere(true);
2854 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2859 * Make a new name for the view, ensuring it is unique within the current
2860 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2861 * these now use viewId. Unique view names are still desirable for usability.)
2866 protected String getNewViewName(String viewTitle)
2868 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2869 boolean addFirstIndex = false;
2870 if (viewTitle == null || viewTitle.trim().length() == 0)
2872 viewTitle = MessageManager.getString("action.view");
2873 addFirstIndex = true;
2877 index = 1;// we count from 1 if given a specific name
2879 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2881 List<Component> comps = PaintRefresher.components.get(viewport
2882 .getSequenceSetId());
2884 List<String> existingNames = getExistingViewNames(comps);
2886 while (existingNames.contains(newViewName))
2888 newViewName = viewTitle + " " + (++index);
2894 * Returns a list of distinct view names found in the given list of
2895 * components. View names are held on the viewport of an AlignmentPanel.
2900 protected List<String> getExistingViewNames(List<Component> comps)
2902 List<String> existingNames = new ArrayList<>();
2903 for (Component comp : comps)
2905 if (comp instanceof AlignmentPanel)
2907 AlignmentPanel ap = (AlignmentPanel) comp;
2908 if (!existingNames.contains(ap.av.viewName))
2910 existingNames.add(ap.av.viewName);
2914 return existingNames;
2918 * Explode tabbed views into separate windows.
2921 public void expandViews_actionPerformed(ActionEvent e)
2923 Desktop.explodeViews(this);
2927 * Gather views in separate windows back into a tabbed presentation.
2930 public void gatherViews_actionPerformed(ActionEvent e)
2932 Desktop.instance.gatherViews(this);
2942 public void font_actionPerformed(ActionEvent e)
2944 new FontChooser(alignPanel);
2954 protected void seqLimit_actionPerformed(ActionEvent e)
2956 viewport.setShowJVSuffix(seqLimits.isSelected());
2958 alignPanel.getIdPanel().getIdCanvas()
2959 .setPreferredSize(alignPanel.calculateIdWidth());
2960 alignPanel.paintAlignment(true);
2964 public void idRightAlign_actionPerformed(ActionEvent e)
2966 viewport.setRightAlignIds(idRightAlign.isSelected());
2967 alignPanel.paintAlignment(true);
2971 public void centreColumnLabels_actionPerformed(ActionEvent e)
2973 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2974 alignPanel.paintAlignment(true);
2980 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2983 protected void followHighlight_actionPerformed()
2986 * Set the 'follow' flag on the Viewport (and scroll to position if now
2989 final boolean state = this.followHighlightMenuItem.getState();
2990 viewport.setFollowHighlight(state);
2993 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
3004 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3006 viewport.setColourText(colourTextMenuItem.isSelected());
3007 alignPanel.paintAlignment(true);
3017 public void wrapMenuItem_actionPerformed(ActionEvent e)
3019 scaleAbove.setVisible(wrapMenuItem.isSelected());
3020 scaleLeft.setVisible(wrapMenuItem.isSelected());
3021 scaleRight.setVisible(wrapMenuItem.isSelected());
3022 viewport.setWrapAlignment(wrapMenuItem.isSelected());
3023 alignPanel.updateLayout();
3027 public void showAllSeqs_actionPerformed(ActionEvent e)
3029 viewport.showAllHiddenSeqs();
3033 public void showAllColumns_actionPerformed(ActionEvent e)
3035 viewport.showAllHiddenColumns();
3037 viewport.sendSelection();
3041 public void hideSelSequences_actionPerformed(ActionEvent e)
3043 viewport.hideAllSelectedSeqs();
3044 // alignPanel.paintAlignment(true);
3048 * called by key handler and the hide all/show all menu items
3053 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3056 boolean hide = false;
3057 SequenceGroup sg = viewport.getSelectionGroup();
3058 if (!toggleSeqs && !toggleCols)
3060 // Hide everything by the current selection - this is a hack - we do the
3061 // invert and then hide
3062 // first check that there will be visible columns after the invert.
3063 if (viewport.hasSelectedColumns()
3064 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3067 // now invert the sequence set, if required - empty selection implies
3068 // that no hiding is required.
3071 invertSequenceMenuItem_actionPerformed(null);
3072 sg = viewport.getSelectionGroup();
3076 viewport.expandColSelection(sg, true);
3077 // finally invert the column selection and get the new sequence
3079 invertColSel_actionPerformed(null);
3086 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3088 hideSelSequences_actionPerformed(null);
3091 else if (!(toggleCols && viewport.hasSelectedColumns()))
3093 showAllSeqs_actionPerformed(null);
3099 if (viewport.hasSelectedColumns())
3101 hideSelColumns_actionPerformed(null);
3104 viewport.setSelectionGroup(sg);
3109 showAllColumns_actionPerformed(null);
3118 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3119 * event.ActionEvent)
3122 public void hideAllButSelection_actionPerformed(ActionEvent e)
3124 toggleHiddenRegions(false, false);
3125 viewport.sendSelection();
3132 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3136 public void hideAllSelection_actionPerformed(ActionEvent e)
3138 SequenceGroup sg = viewport.getSelectionGroup();
3139 viewport.expandColSelection(sg, false);
3140 viewport.hideAllSelectedSeqs();
3141 viewport.hideSelectedColumns();
3142 alignPanel.paintAlignment(true);
3143 viewport.sendSelection();
3150 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3154 public void showAllhidden_actionPerformed(ActionEvent e)
3156 viewport.showAllHiddenColumns();
3157 viewport.showAllHiddenSeqs();
3158 alignPanel.paintAlignment(true);
3159 viewport.sendSelection();
3163 public void hideSelColumns_actionPerformed(ActionEvent e)
3165 viewport.hideSelectedColumns();
3166 alignPanel.paintAlignment(true);
3167 viewport.sendSelection();
3171 public void hiddenMarkers_actionPerformed(ActionEvent e)
3173 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3184 protected void scaleAbove_actionPerformed(ActionEvent e)
3186 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3187 alignPanel.paintAlignment(true);
3197 protected void scaleLeft_actionPerformed(ActionEvent e)
3199 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3200 alignPanel.paintAlignment(true);
3210 protected void scaleRight_actionPerformed(ActionEvent e)
3212 viewport.setScaleRightWrapped(scaleRight.isSelected());
3213 alignPanel.paintAlignment(true);
3223 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3225 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3226 alignPanel.paintAlignment(true);
3236 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3238 viewport.setShowText(viewTextMenuItem.isSelected());
3239 alignPanel.paintAlignment(true);
3249 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3251 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3252 alignPanel.paintAlignment(true);
3255 public FeatureSettings featureSettings;
3258 public FeatureSettingsControllerI getFeatureSettingsUI()
3260 return featureSettings;
3264 public void featureSettings_actionPerformed(ActionEvent e)
3266 if (featureSettings != null)
3268 featureSettings.close();
3269 featureSettings = null;
3271 if (!showSeqFeatures.isSelected())
3273 // make sure features are actually displayed
3274 showSeqFeatures.setSelected(true);
3275 showSeqFeatures_actionPerformed(null);
3277 featureSettings = new FeatureSettings(this);
3281 * Set or clear 'Show Sequence Features'
3287 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3289 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3290 alignPanel.paintAlignment(true);
3291 if (alignPanel.getOverviewPanel() != null)
3293 alignPanel.getOverviewPanel().updateOverviewImage();
3298 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3299 * the annotations panel as a whole.
3301 * The options to show/hide all annotations should be enabled when the panel
3302 * is shown, and disabled when the panel is hidden.
3307 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3309 final boolean setVisible = annotationPanelMenuItem.isSelected();
3310 viewport.setShowAnnotation(setVisible);
3311 this.showAllSeqAnnotations.setEnabled(setVisible);
3312 this.hideAllSeqAnnotations.setEnabled(setVisible);
3313 this.showAllAlAnnotations.setEnabled(setVisible);
3314 this.hideAllAlAnnotations.setEnabled(setVisible);
3315 alignPanel.updateLayout();
3319 public void alignmentProperties()
3321 JEditorPane editPane = new JEditorPane("text/html", "");
3322 editPane.setEditable(false);
3323 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3325 editPane.setText(MessageManager.formatMessage("label.html_content",
3326 new Object[] { contents.toString() }));
3327 JInternalFrame frame = new JInternalFrame();
3328 frame.getContentPane().add(new JScrollPane(editPane));
3330 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3331 "label.alignment_properties", new Object[] { getTitle() }),
3342 public void overviewMenuItem_actionPerformed(ActionEvent e)
3344 if (alignPanel.overviewPanel != null)
3349 JInternalFrame frame = new JInternalFrame();
3350 OverviewPanel overview = new OverviewPanel(alignPanel);
3351 frame.setContentPane(overview);
3352 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3353 "label.overview_params", new Object[] { this.getTitle() }),
3354 true, frame.getWidth(), frame.getHeight(), true, true);
3356 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3357 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3360 public void internalFrameClosed(
3361 javax.swing.event.InternalFrameEvent evt)
3363 alignPanel.setOverviewPanel(null);
3367 alignPanel.setOverviewPanel(overview);
3371 public void textColour_actionPerformed()
3373 new TextColourChooser().chooseColour(alignPanel, null);
3377 * public void covariationColour_actionPerformed() {
3379 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3383 public void annotationColour_actionPerformed()
3385 new AnnotationColourChooser(viewport, alignPanel);
3389 public void annotationColumn_actionPerformed(ActionEvent e)
3391 new AnnotationColumnChooser(viewport, alignPanel);
3395 * Action on the user checking or unchecking the option to apply the selected
3396 * colour scheme to all groups. If unchecked, groups may have their own
3397 * independent colour schemes.
3402 public void applyToAllGroups_actionPerformed(boolean selected)
3404 viewport.setColourAppliesToAllGroups(selected);
3408 * Action on user selecting a colour from the colour menu
3411 * the name (not the menu item label!) of the colour scheme
3414 public void changeColour_actionPerformed(String name)
3417 * 'User Defined' opens a panel to configure or load a
3418 * user-defined colour scheme
3420 if (ResidueColourScheme.USER_DEFINED.equals(name))
3422 new UserDefinedColours(alignPanel);
3427 * otherwise set the chosen colour scheme (or null for 'None')
3429 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3430 viewport.getAlignment(), viewport.getHiddenRepSequences());
3435 * Actions on setting or changing the alignment colour scheme
3440 public void changeColour(ColourSchemeI cs)
3442 // TODO: pull up to controller method
3443 ColourMenuHelper.setColourSelected(colourMenu, cs);
3445 viewport.setGlobalColourScheme(cs);
3447 alignPanel.paintAlignment(true);
3451 * Show the PID threshold slider panel
3454 protected void modifyPID_actionPerformed()
3456 SliderPanel.setPIDSliderSource(alignPanel,
3457 viewport.getResidueShading(), alignPanel.getViewName());
3458 SliderPanel.showPIDSlider();
3462 * Show the Conservation slider panel
3465 protected void modifyConservation_actionPerformed()
3467 SliderPanel.setConservationSlider(alignPanel,
3468 viewport.getResidueShading(), alignPanel.getViewName());
3469 SliderPanel.showConservationSlider();
3473 * Action on selecting or deselecting (Colour) By Conservation
3476 public void conservationMenuItem_actionPerformed(boolean selected)
3478 modifyConservation.setEnabled(selected);
3479 viewport.setConservationSelected(selected);
3480 viewport.getResidueShading().setConservationApplied(selected);
3482 changeColour(viewport.getGlobalColourScheme());
3485 modifyConservation_actionPerformed();
3489 SliderPanel.hideConservationSlider();
3494 * Action on selecting or deselecting (Colour) Above PID Threshold
3497 public void abovePIDThreshold_actionPerformed(boolean selected)
3499 modifyPID.setEnabled(selected);
3500 viewport.setAbovePIDThreshold(selected);
3503 viewport.getResidueShading().setThreshold(0,
3504 viewport.isIgnoreGapsConsensus());
3507 changeColour(viewport.getGlobalColourScheme());
3510 modifyPID_actionPerformed();
3514 SliderPanel.hidePIDSlider();
3525 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3527 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3528 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3529 .getAlignment().getSequenceAt(0));
3530 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3531 viewport.getAlignment()));
3532 alignPanel.paintAlignment(true);
3542 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3544 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3545 AlignmentSorter.sortByID(viewport.getAlignment());
3546 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3547 viewport.getAlignment()));
3548 alignPanel.paintAlignment(true);
3558 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3560 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3561 AlignmentSorter.sortByLength(viewport.getAlignment());
3562 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3563 viewport.getAlignment()));
3564 alignPanel.paintAlignment(true);
3574 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3576 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3577 AlignmentSorter.sortByGroup(viewport.getAlignment());
3578 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3579 viewport.getAlignment()));
3581 alignPanel.paintAlignment(true);
3591 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3593 new RedundancyPanel(alignPanel, this);
3603 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3605 if ((viewport.getSelectionGroup() == null)
3606 || (viewport.getSelectionGroup().getSize() < 2))
3608 JvOptionPane.showInternalMessageDialog(this, MessageManager
3609 .getString("label.you_must_select_least_two_sequences"),
3610 MessageManager.getString("label.invalid_selection"),
3611 JvOptionPane.WARNING_MESSAGE);
3615 JInternalFrame frame = new JInternalFrame();
3616 frame.setContentPane(new PairwiseAlignPanel(viewport));
3617 Desktop.addInternalFrame(frame,
3618 MessageManager.getString("action.pairwise_alignment"), 600,
3624 public void autoCalculate_actionPerformed(ActionEvent e)
3626 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3627 if (viewport.autoCalculateConsensus)
3629 viewport.firePropertyChange("alignment", null, viewport
3630 .getAlignment().getSequences());
3635 public void sortByTreeOption_actionPerformed(ActionEvent e)
3637 viewport.sortByTree = sortByTree.isSelected();
3641 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3643 viewport.followSelection = listenToViewSelections.isSelected();
3647 * Constructs a tree panel and adds it to the desktop
3650 * tree type (NJ or AV)
3652 * name of score model used to compute the tree
3654 * parameters for the distance or similarity calculation
3656 void newTreePanel(String type, String modelName, SimilarityParamsI options)
3658 String frameTitle = "";
3661 boolean onSelection = false;
3662 if (viewport.getSelectionGroup() != null
3663 && viewport.getSelectionGroup().getSize() > 0)
3665 SequenceGroup sg = viewport.getSelectionGroup();
3667 /* Decide if the selection is a column region */
3668 for (SequenceI _s : sg.getSequences())
3670 if (_s.getLength() < sg.getEndRes())
3676 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3678 .getString("label.sequences_selection_not_aligned"),
3679 JvOptionPane.WARNING_MESSAGE);
3688 if (viewport.getAlignment().getHeight() < 2)
3694 tp = new TreePanel(alignPanel, type, modelName, options);
3695 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3697 frameTitle += " from ";
3699 if (viewport.viewName != null)
3701 frameTitle += viewport.viewName + " of ";
3704 frameTitle += this.title;
3706 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3717 public void addSortByOrderMenuItem(String title,
3718 final AlignmentOrder order)
3720 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3721 "action.by_title_param", new Object[] { title }));
3723 item.addActionListener(new java.awt.event.ActionListener()
3726 public void actionPerformed(ActionEvent e)
3728 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3730 // TODO: JBPNote - have to map order entries to curent SequenceI
3732 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3734 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3737 alignPanel.paintAlignment(true);
3743 * Add a new sort by annotation score menu item
3746 * the menu to add the option to
3748 * the label used to retrieve scores for each sequence on the
3751 public void addSortByAnnotScoreMenuItem(JMenu sort,
3752 final String scoreLabel)
3754 final JMenuItem item = new JMenuItem(scoreLabel);
3756 item.addActionListener(new java.awt.event.ActionListener()
3759 public void actionPerformed(ActionEvent e)
3761 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3762 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3763 viewport.getAlignment());// ,viewport.getSelectionGroup());
3764 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3765 viewport.getAlignment()));
3766 alignPanel.paintAlignment(true);
3772 * last hash for alignment's annotation array - used to minimise cost of
3775 protected int _annotationScoreVectorHash;
3778 * search the alignment and rebuild the sort by annotation score submenu the
3779 * last alignment annotation vector hash is stored to minimize cost of
3780 * rebuilding in subsequence calls.
3784 public void buildSortByAnnotationScoresMenu()
3786 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3791 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3793 sortByAnnotScore.removeAll();
3794 // almost certainly a quicker way to do this - but we keep it simple
3795 Hashtable scoreSorts = new Hashtable();
3796 AlignmentAnnotation aann[];
3797 for (SequenceI sqa : viewport.getAlignment().getSequences())
3799 aann = sqa.getAnnotation();
3800 for (int i = 0; aann != null && i < aann.length; i++)
3802 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3804 scoreSorts.put(aann[i].label, aann[i].label);
3808 Enumeration labels = scoreSorts.keys();
3809 while (labels.hasMoreElements())
3811 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3812 (String) labels.nextElement());
3814 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3817 _annotationScoreVectorHash = viewport.getAlignment()
3818 .getAlignmentAnnotation().hashCode();
3823 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3824 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3825 * call. Listeners are added to remove the menu item when the treePanel is
3826 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3830 public void buildTreeSortMenu()
3832 sortByTreeMenu.removeAll();
3834 List<Component> comps = PaintRefresher.components.get(viewport
3835 .getSequenceSetId());
3836 List<TreePanel> treePanels = new ArrayList<>();
3837 for (Component comp : comps)
3839 if (comp instanceof TreePanel)
3841 treePanels.add((TreePanel) comp);
3845 if (treePanels.size() < 1)
3847 sortByTreeMenu.setVisible(false);
3851 sortByTreeMenu.setVisible(true);
3853 for (final TreePanel tp : treePanels)
3855 final JMenuItem item = new JMenuItem(tp.getTitle());
3856 item.addActionListener(new java.awt.event.ActionListener()
3859 public void actionPerformed(ActionEvent e)
3861 tp.sortByTree_actionPerformed();
3862 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3867 sortByTreeMenu.add(item);
3871 public boolean sortBy(AlignmentOrder alorder, String undoname)
3873 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3874 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3875 if (undoname != null)
3877 addHistoryItem(new OrderCommand(undoname, oldOrder,
3878 viewport.getAlignment()));
3880 alignPanel.paintAlignment(true);
3885 * Work out whether the whole set of sequences or just the selected set will
3886 * be submitted for multiple alignment.
3889 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3891 // Now, check we have enough sequences
3892 AlignmentView msa = null;
3894 if ((viewport.getSelectionGroup() != null)
3895 && (viewport.getSelectionGroup().getSize() > 1))
3897 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3898 // some common interface!
3900 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3901 * SequenceI[sz = seqs.getSize(false)];
3903 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3904 * seqs.getSequenceAt(i); }
3906 msa = viewport.getAlignmentView(true);
3908 else if (viewport.getSelectionGroup() != null
3909 && viewport.getSelectionGroup().getSize() == 1)
3911 int option = JvOptionPane.showConfirmDialog(this,
3912 MessageManager.getString("warn.oneseq_msainput_selection"),
3913 MessageManager.getString("label.invalid_selection"),
3914 JvOptionPane.OK_CANCEL_OPTION);
3915 if (option == JvOptionPane.OK_OPTION)
3917 msa = viewport.getAlignmentView(false);
3922 msa = viewport.getAlignmentView(false);
3928 * Decides what is submitted to a secondary structure prediction service: the
3929 * first sequence in the alignment, or in the current selection, or, if the
3930 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3931 * region or the whole alignment. (where the first sequence in the set is the
3932 * one that the prediction will be for).
3934 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3936 AlignmentView seqs = null;
3938 if ((viewport.getSelectionGroup() != null)
3939 && (viewport.getSelectionGroup().getSize() > 0))
3941 seqs = viewport.getAlignmentView(true);
3945 seqs = viewport.getAlignmentView(false);
3947 // limit sequences - JBPNote in future - could spawn multiple prediction
3949 // TODO: viewport.getAlignment().isAligned is a global state - the local
3950 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3951 if (!viewport.getAlignment().isAligned(false))
3953 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3954 // TODO: if seqs.getSequences().length>1 then should really have warned
3968 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3970 // Pick the tree file
3971 JalviewFileChooser chooser = new JalviewFileChooser(
3972 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3973 chooser.setFileView(new JalviewFileView());
3974 chooser.setDialogTitle(MessageManager
3975 .getString("label.select_newick_like_tree_file"));
3976 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3978 int value = chooser.showOpenDialog(null);
3980 if (value == JalviewFileChooser.APPROVE_OPTION)
3982 String filePath = chooser.getSelectedFile().getPath();
3983 Cache.setProperty("LAST_DIRECTORY", filePath);
3984 NewickFile fin = null;
3987 fin = new NewickFile(filePath, DataSourceType.FILE);
3988 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3989 } catch (Exception ex)
3996 .getString("label.problem_reading_tree_file"),
3997 JvOptionPane.WARNING_MESSAGE);
3998 ex.printStackTrace();
4000 if (fin != null && fin.hasWarningMessage())
4002 JvOptionPane.showMessageDialog(Desktop.desktop, fin
4003 .getWarningMessage(), MessageManager
4004 .getString("label.possible_problem_with_tree_file"),
4005 JvOptionPane.WARNING_MESSAGE);
4010 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4012 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4015 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4016 int h, int x, int y)
4018 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4022 * Add a treeviewer for the tree extracted from a Newick file object to the
4023 * current alignment view
4030 * Associated alignment input data (or null)
4039 * @return TreePanel handle
4041 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4042 AlignmentView input, int w, int h, int x, int y)
4044 TreePanel tp = null;
4050 if (nf.getTree() != null)
4052 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4058 tp.setLocation(x, y);
4061 Desktop.addInternalFrame(tp, treeTitle, w, h);
4063 } catch (Exception ex)
4065 ex.printStackTrace();
4071 private boolean buildingMenu = false;
4074 * Generates menu items and listener event actions for web service clients
4077 public void BuildWebServiceMenu()
4079 while (buildingMenu)
4083 System.err.println("Waiting for building menu to finish.");
4085 } catch (Exception e)
4089 final AlignFrame me = this;
4090 buildingMenu = true;
4091 new Thread(new Runnable()
4096 final List<JMenuItem> legacyItems = new ArrayList<>();
4099 // System.err.println("Building ws menu again "
4100 // + Thread.currentThread());
4101 // TODO: add support for context dependent disabling of services based
4103 // alignment and current selection
4104 // TODO: add additional serviceHandle parameter to specify abstract
4106 // class independently of AbstractName
4107 // TODO: add in rediscovery GUI function to restart discoverer
4108 // TODO: group services by location as well as function and/or
4110 // object broker mechanism.
4111 final Vector<JMenu> wsmenu = new Vector<>();
4112 final IProgressIndicator af = me;
4115 * do not i18n these strings - they are hard-coded in class
4116 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4117 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4119 final JMenu msawsmenu = new JMenu("Alignment");
4120 final JMenu secstrmenu = new JMenu(
4121 "Secondary Structure Prediction");
4122 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4123 final JMenu analymenu = new JMenu("Analysis");
4124 final JMenu dismenu = new JMenu("Protein Disorder");
4125 // JAL-940 - only show secondary structure prediction services from
4126 // the legacy server
4127 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4129 Discoverer.services != null && (Discoverer.services.size() > 0))
4131 // TODO: refactor to allow list of AbstractName/Handler bindings to
4133 // stored or retrieved from elsewhere
4134 // No MSAWS used any more:
4135 // Vector msaws = null; // (Vector)
4136 // Discoverer.services.get("MsaWS");
4137 Vector secstrpr = (Vector) Discoverer.services
4139 if (secstrpr != null)
4141 // Add any secondary structure prediction services
4142 for (int i = 0, j = secstrpr.size(); i < j; i++)
4144 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4146 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4147 .getServiceClient(sh);
4148 int p = secstrmenu.getItemCount();
4149 impl.attachWSMenuEntry(secstrmenu, me);
4150 int q = secstrmenu.getItemCount();
4151 for (int litm = p; litm < q; litm++)
4153 legacyItems.add(secstrmenu.getItem(litm));
4159 // Add all submenus in the order they should appear on the web
4161 wsmenu.add(msawsmenu);
4162 wsmenu.add(secstrmenu);
4163 wsmenu.add(dismenu);
4164 wsmenu.add(analymenu);
4165 // No search services yet
4166 // wsmenu.add(seqsrchmenu);
4168 javax.swing.SwingUtilities.invokeLater(new Runnable()
4175 webService.removeAll();
4176 // first, add discovered services onto the webservices menu
4177 if (wsmenu.size() > 0)
4179 for (int i = 0, j = wsmenu.size(); i < j; i++)
4181 webService.add(wsmenu.get(i));
4186 webService.add(me.webServiceNoServices);
4188 // TODO: move into separate menu builder class.
4189 boolean new_sspred = false;
4190 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4192 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4193 if (jws2servs != null)
4195 if (jws2servs.hasServices())
4197 jws2servs.attachWSMenuEntry(webService, me);
4198 for (Jws2Instance sv : jws2servs.getServices())
4200 if (sv.description.toLowerCase().contains("jpred"))
4202 for (JMenuItem jmi : legacyItems)
4204 jmi.setVisible(false);
4210 if (jws2servs.isRunning())
4212 JMenuItem tm = new JMenuItem(
4213 "Still discovering JABA Services");
4214 tm.setEnabled(false);
4219 build_urlServiceMenu(me.webService);
4220 build_fetchdbmenu(webService);
4221 for (JMenu item : wsmenu)
4223 if (item.getItemCount() == 0)
4225 item.setEnabled(false);
4229 item.setEnabled(true);
4232 } catch (Exception e)
4235 .debug("Exception during web service menu building process.",
4240 } catch (Exception e)
4243 buildingMenu = false;
4250 * construct any groupURL type service menu entries.
4254 private void build_urlServiceMenu(JMenu webService)
4256 // TODO: remove this code when 2.7 is released
4257 // DEBUG - alignmentView
4259 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4260 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4262 * @Override public void actionPerformed(ActionEvent e) {
4263 * jalview.datamodel.AlignmentView
4264 * .testSelectionViews(af.viewport.getAlignment(),
4265 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4267 * }); webService.add(testAlView);
4269 // TODO: refactor to RestClient discoverer and merge menu entries for
4270 // rest-style services with other types of analysis/calculation service
4271 // SHmmr test client - still being implemented.
4272 // DEBUG - alignmentView
4274 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4277 client.attachWSMenuEntry(
4278 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4284 * Searches the alignment sequences for xRefs and builds the Show
4285 * Cross-References menu (formerly called Show Products), with database
4286 * sources for which cross-references are found (protein sources for a
4287 * nucleotide alignment and vice versa)
4289 * @return true if Show Cross-references menu should be enabled
4291 public boolean canShowProducts()
4293 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4294 AlignmentI dataset = viewport.getAlignment().getDataset();
4296 showProducts.removeAll();
4297 final boolean dna = viewport.getAlignment().isNucleotide();
4299 if (seqs == null || seqs.length == 0)
4301 // nothing to see here.
4305 boolean showp = false;
4308 List<String> ptypes = new CrossRef(seqs, dataset)
4309 .findXrefSourcesForSequences(dna);
4311 for (final String source : ptypes)
4314 final AlignFrame af = this;
4315 JMenuItem xtype = new JMenuItem(source);
4316 xtype.addActionListener(new ActionListener()
4319 public void actionPerformed(ActionEvent e)
4321 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4324 showProducts.add(xtype);
4326 showProducts.setVisible(showp);
4327 showProducts.setEnabled(showp);
4328 } catch (Exception e)
4331 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4339 * Finds and displays cross-references for the selected sequences (protein
4340 * products for nucleotide sequences, dna coding sequences for peptides).
4343 * the sequences to show cross-references for
4345 * true if from a nucleotide alignment (so showing proteins)
4347 * the database to show cross-references for
4349 protected void showProductsFor(final SequenceI[] sel,
4350 final boolean _odna, final String source)
4352 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4357 * Construct and display a new frame containing the translation of this
4358 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4361 public void showTranslation_actionPerformed(ActionEvent e)
4363 AlignmentI al = null;
4366 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4368 al = dna.translateCdna();
4369 } catch (Exception ex)
4371 jalview.bin.Cache.log.error(
4372 "Exception during translation. Please report this !", ex);
4373 final String msg = MessageManager
4374 .getString("label.error_when_translating_sequences_submit_bug_report");
4375 final String errorTitle = MessageManager
4376 .getString("label.implementation_error")
4377 + MessageManager.getString("label.translation_failed");
4378 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4379 JvOptionPane.ERROR_MESSAGE);
4382 if (al == null || al.getHeight() == 0)
4384 final String msg = MessageManager
4385 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4386 final String errorTitle = MessageManager
4387 .getString("label.translation_failed");
4388 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4389 JvOptionPane.WARNING_MESSAGE);
4393 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4394 af.setFileFormat(this.currentFileFormat);
4395 final String newTitle = MessageManager.formatMessage(
4396 "label.translation_of_params",
4397 new Object[] { this.getTitle() });
4398 af.setTitle(newTitle);
4399 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4401 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4402 viewport.openSplitFrame(af, new Alignment(seqs));
4406 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4413 * Set the file format
4417 public void setFileFormat(FileFormatI format)
4419 this.currentFileFormat = format;
4423 * Try to load a features file onto the alignment.
4426 * contents or path to retrieve file
4428 * access mode of file (see jalview.io.AlignFile)
4429 * @return true if features file was parsed correctly.
4431 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4433 return avc.parseFeaturesFile(file, sourceType,
4434 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4439 public void refreshFeatureUI(boolean enableIfNecessary)
4441 // note - currently this is only still here rather than in the controller
4442 // because of the featureSettings hard reference that is yet to be
4444 if (enableIfNecessary)
4446 viewport.setShowSequenceFeatures(true);
4447 showSeqFeatures.setSelected(true);
4453 public void dragEnter(DropTargetDragEvent evt)
4458 public void dragExit(DropTargetEvent evt)
4463 public void dragOver(DropTargetDragEvent evt)
4468 public void dropActionChanged(DropTargetDragEvent evt)
4473 public void drop(DropTargetDropEvent evt)
4475 // JAL-1552 - acceptDrop required before getTransferable call for
4476 // Java's Transferable for native dnd
4477 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4478 Transferable t = evt.getTransferable();
4479 List<String> files = new ArrayList<>();
4480 List<DataSourceType> protocols = new ArrayList<>();
4484 Desktop.transferFromDropTarget(files, protocols, evt, t);
4485 } catch (Exception e)
4487 e.printStackTrace();
4493 // check to see if any of these files have names matching sequences in
4495 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4496 .getAlignment().getSequencesArray());
4498 * Object[] { String,SequenceI}
4500 ArrayList<Object[]> filesmatched = new ArrayList<>();
4501 ArrayList<String> filesnotmatched = new ArrayList<>();
4502 for (int i = 0; i < files.size(); i++)
4504 String file = files.get(i).toString();
4506 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4507 if (protocol == DataSourceType.FILE)
4509 File fl = new File(file);
4510 pdbfn = fl.getName();
4512 else if (protocol == DataSourceType.URL)
4514 URL url = new URL(file);
4515 pdbfn = url.getFile();
4517 if (pdbfn.length() > 0)
4519 // attempt to find a match in the alignment
4520 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4521 int l = 0, c = pdbfn.indexOf(".");
4522 while (mtch == null && c != -1)
4527 } while ((c = pdbfn.indexOf(".", l)) > l);
4530 pdbfn = pdbfn.substring(0, l);
4532 mtch = idm.findAllIdMatches(pdbfn);
4536 FileFormatI type = null;
4539 type = new IdentifyFile().identify(file, protocol);
4540 } catch (Exception ex)
4544 if (type != null && type.isStructureFile())
4546 filesmatched.add(new Object[] { file, protocol, mtch });
4550 // File wasn't named like one of the sequences or wasn't a PDB file.
4551 filesnotmatched.add(file);
4555 if (filesmatched.size() > 0)
4557 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4563 "label.automatically_associate_structure_files_with_sequences_same_name",
4564 new Object[] { Integer
4570 .getString("label.automatically_associate_structure_files_by_name"),
4571 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4574 for (Object[] fm : filesmatched)
4576 // try and associate
4577 // TODO: may want to set a standard ID naming formalism for
4578 // associating PDB files which have no IDs.
4579 for (SequenceI toassoc : (SequenceI[]) fm[2])
4581 PDBEntry pe = new AssociatePdbFileWithSeq()
4582 .associatePdbWithSeq((String) fm[0],
4583 (DataSourceType) fm[1], toassoc, false,
4587 System.err.println("Associated file : "
4588 + ((String) fm[0]) + " with "
4589 + toassoc.getDisplayId(true));
4593 alignPanel.paintAlignment(true);
4597 if (filesnotmatched.size() > 0)
4600 && (Cache.getDefault(
4601 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4607 "label.ignore_unmatched_dropped_files_info",
4608 new Object[] { Integer
4615 .getString("label.ignore_unmatched_dropped_files"),
4616 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4620 for (String fn : filesnotmatched)
4622 loadJalviewDataFile(fn, null, null, null);
4626 } catch (Exception ex)
4628 ex.printStackTrace();
4634 * Attempt to load a "dropped" file or URL string, by testing in turn for
4636 * <li>an Annotation file</li>
4637 * <li>a JNet file</li>
4638 * <li>a features file</li>
4639 * <li>else try to interpret as an alignment file</li>
4643 * either a filename or a URL string.
4644 * @throws InterruptedException
4645 * @throws IOException
4647 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4648 FileFormatI format, SequenceI assocSeq)
4649 throws IOException, InterruptedException
4653 if (sourceType == null)
4655 sourceType = FormatAdapter.checkProtocol(file);
4657 // if the file isn't identified, or not positively identified as some
4658 // other filetype (PFAM is default unidentified alignment file type) then
4659 // try to parse as annotation.
4660 boolean isAnnotation = (format == null || FileFormat.Pfam
4661 .equals(format)) ? new AnnotationFile()
4662 .annotateAlignmentView(viewport, file, sourceType) : false;
4666 // first see if its a T-COFFEE score file
4667 TCoffeeScoreFile tcf = null;
4670 tcf = new TCoffeeScoreFile(file, sourceType);
4673 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4676 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4677 isAnnotation = true;
4679 .setText(MessageManager
4680 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4684 // some problem - if no warning its probable that the ID matching
4685 // process didn't work
4689 tcf.getWarningMessage() == null ? MessageManager
4690 .getString("label.check_file_matches_sequence_ids_alignment")
4691 : tcf.getWarningMessage(),
4693 .getString("label.problem_reading_tcoffee_score_file"),
4694 JvOptionPane.WARNING_MESSAGE);
4701 } catch (Exception x)
4704 .debug("Exception when processing data source as T-COFFEE score file",
4710 // try to see if its a JNet 'concise' style annotation file *before*
4712 // try to parse it as a features file
4715 format = new IdentifyFile().identify(file, sourceType);
4717 if (FileFormat.ScoreMatrix == format)
4719 ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4722 // todo: i18n this message
4724 .setText(MessageManager.formatMessage(
4725 "label.successfully_loaded_matrix",
4726 sm.getMatrixName()));
4728 else if (FileFormat.HMMER3.equals(format))
4730 HMMFile hmmFile = new HMMFile(new FileParse(file, sourceType)); // TODO
4737 HiddenMarkovModel hmm = hmmFile.getHMM();
4738 SequenceI hmmSeq = hmm.initHMMSequence(this, 0);
4739 getViewport().initInformation(hmmSeq);
4740 new Thread(new InformationThread(getViewport(),
4741 getViewport().getAlignPanel())
4745 isAnnotation = true;
4748 else if (FileFormat.Jnet.equals(format))
4750 JPredFile predictions = new JPredFile(file, sourceType);
4751 new JnetAnnotationMaker();
4752 JnetAnnotationMaker.add_annotation(predictions,
4753 viewport.getAlignment(), 0, false);
4754 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4755 viewport.getAlignment().setSeqrep(repseq);
4756 HiddenColumns cs = new HiddenColumns();
4757 cs.hideInsertionsFor(repseq);
4758 viewport.getAlignment().setHiddenColumns(cs);
4759 isAnnotation = true;
4761 // else if (IdentifyFile.FeaturesFile.equals(format))
4762 else if (FileFormat.Features.equals(format))
4764 if (parseFeaturesFile(file, sourceType))
4766 alignPanel.paintAlignment(true);
4771 new FileLoader().LoadFile(viewport, file, sourceType, format);
4777 alignPanel.adjustAnnotationHeight();
4778 viewport.updateSequenceIdColours();
4779 buildSortByAnnotationScoresMenu();
4780 alignPanel.paintAlignment(true);
4782 } catch (Exception ex)
4784 ex.printStackTrace();
4785 } catch (OutOfMemoryError oom)
4790 } catch (Exception x)
4795 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4796 : "using " + sourceType + " from " + file)
4798 + (format != null ? "(parsing as '" + format
4799 + "' file)" : ""), oom, Desktop.desktop);
4801 if (autoAlignNewSequences && !recurring)
4804 HiddenMarkovModel hmm = getViewport().getAlignment()
4805 .getHMMConsensusSequences(false).get(0).getHMM();
4806 HMMERCommands.hmmAlign(this, false, hmm);
4812 * Method invoked by the ChangeListener on the tabbed pane, in other words
4813 * when a different tabbed pane is selected by the user or programmatically.
4816 public void tabSelectionChanged(int index)
4820 alignPanel = alignPanels.get(index);
4821 viewport = alignPanel.av;
4822 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4823 setMenusFromViewport(viewport);
4827 * 'focus' any colour slider that is open to the selected viewport
4829 if (viewport.getConservationSelected())
4831 SliderPanel.setConservationSlider(alignPanel,
4832 viewport.getResidueShading(), alignPanel.getViewName());
4836 SliderPanel.hideConservationSlider();
4838 if (viewport.getAbovePIDThreshold())
4840 SliderPanel.setPIDSliderSource(alignPanel,
4841 viewport.getResidueShading(), alignPanel.getViewName());
4845 SliderPanel.hidePIDSlider();
4849 * If there is a frame linked to this one in a SplitPane, switch it to the
4850 * same view tab index. No infinite recursion of calls should happen, since
4851 * tabSelectionChanged() should not get invoked on setting the selected
4852 * index to an unchanged value. Guard against setting an invalid index
4853 * before the new view peer tab has been created.
4855 final AlignViewportI peer = viewport.getCodingComplement();
4858 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4859 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4861 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4867 * On right mouse click on view tab, prompt for and set new view name.
4870 public void tabbedPane_mousePressed(MouseEvent e)
4872 if (e.isPopupTrigger())
4874 String msg = MessageManager.getString("label.enter_view_name");
4875 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4876 JvOptionPane.QUESTION_MESSAGE);
4880 viewport.viewName = reply;
4881 // TODO warn if reply is in getExistingViewNames()?
4882 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4887 public AlignViewport getCurrentView()
4893 * Open the dialog for regex description parsing.
4896 protected void extractScores_actionPerformed(ActionEvent e)
4898 ParseProperties pp = new jalview.analysis.ParseProperties(
4899 viewport.getAlignment());
4900 // TODO: verify regex and introduce GUI dialog for version 2.5
4901 // if (pp.getScoresFromDescription("col", "score column ",
4902 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4904 if (pp.getScoresFromDescription("description column",
4905 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4907 buildSortByAnnotationScoresMenu();
4915 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4919 protected void showDbRefs_actionPerformed(ActionEvent e)
4921 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4927 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4931 protected void showNpFeats_actionPerformed(ActionEvent e)
4933 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4937 * find the viewport amongst the tabs in this alignment frame and close that
4942 public boolean closeView(AlignViewportI av)
4946 this.closeMenuItem_actionPerformed(false);
4949 Component[] comp = tabbedPane.getComponents();
4950 for (int i = 0; comp != null && i < comp.length; i++)
4952 if (comp[i] instanceof AlignmentPanel)
4954 if (((AlignmentPanel) comp[i]).av == av)
4957 closeView((AlignmentPanel) comp[i]);
4965 protected void build_fetchdbmenu(JMenu webService)
4967 // Temporary hack - DBRef Fetcher always top level ws entry.
4968 // TODO We probably want to store a sequence database checklist in
4969 // preferences and have checkboxes.. rather than individual sources selected
4971 final JMenu rfetch = new JMenu(
4972 MessageManager.getString("action.fetch_db_references"));
4973 rfetch.setToolTipText(MessageManager
4974 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4975 webService.add(rfetch);
4977 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4978 MessageManager.getString("option.trim_retrieved_seqs"));
4979 trimrs.setToolTipText(MessageManager
4980 .getString("label.trim_retrieved_sequences"));
4981 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4982 trimrs.addActionListener(new ActionListener()
4985 public void actionPerformed(ActionEvent e)
4987 trimrs.setSelected(trimrs.isSelected());
4988 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4989 Boolean.valueOf(trimrs.isSelected()).toString());
4993 JMenuItem fetchr = new JMenuItem(
4994 MessageManager.getString("label.standard_databases"));
4995 fetchr.setToolTipText(MessageManager
4996 .getString("label.fetch_embl_uniprot"));
4997 fetchr.addActionListener(new ActionListener()
5001 public void actionPerformed(ActionEvent e)
5003 new Thread(new Runnable()
5008 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5009 .getAlignment().isNucleotide();
5010 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5011 .getSequenceSelection(), alignPanel.alignFrame, null,
5012 alignPanel.alignFrame.featureSettings, isNucleotide);
5013 dbRefFetcher.addListener(new FetchFinishedListenerI()
5016 public void finished()
5018 AlignFrame.this.setMenusForViewport();
5021 dbRefFetcher.fetchDBRefs(false);
5029 final AlignFrame me = this;
5030 new Thread(new Runnable()
5035 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5036 .getSequenceFetcherSingleton(me);
5037 javax.swing.SwingUtilities.invokeLater(new Runnable()
5042 String[] dbclasses = sf.getOrderedSupportedSources();
5043 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5044 // jalview.util.QuickSort.sort(otherdb, otherdb);
5045 List<DbSourceProxy> otherdb;
5046 JMenu dfetch = new JMenu();
5047 JMenu ifetch = new JMenu();
5048 JMenuItem fetchr = null;
5049 int comp = 0, icomp = 0, mcomp = 15;
5050 String mname = null;
5052 for (String dbclass : dbclasses)
5054 otherdb = sf.getSourceProxy(dbclass);
5055 // add a single entry for this class, or submenu allowing 'fetch
5057 if (otherdb == null || otherdb.size() < 1)
5061 // List<DbSourceProxy> dbs=otherdb;
5062 // otherdb=new ArrayList<DbSourceProxy>();
5063 // for (DbSourceProxy db:dbs)
5065 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5069 mname = "From " + dbclass;
5071 if (otherdb.size() == 1)
5073 final DbSourceProxy[] dassource = otherdb
5074 .toArray(new DbSourceProxy[0]);
5075 DbSourceProxy src = otherdb.get(0);
5076 fetchr = new JMenuItem(src.getDbSource());
5077 fetchr.addActionListener(new ActionListener()
5081 public void actionPerformed(ActionEvent e)
5083 new Thread(new Runnable()
5089 boolean isNucleotide = alignPanel.alignFrame
5090 .getViewport().getAlignment()
5092 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5093 alignPanel.av.getSequenceSelection(),
5094 alignPanel.alignFrame, dassource,
5095 alignPanel.alignFrame.featureSettings,
5098 .addListener(new FetchFinishedListenerI()
5101 public void finished()
5103 AlignFrame.this.setMenusForViewport();
5106 dbRefFetcher.fetchDBRefs(false);
5112 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5113 MessageManager.formatMessage(
5114 "label.fetch_retrieve_from",
5115 new Object[] { src.getDbName() })));
5121 final DbSourceProxy[] dassource = otherdb
5122 .toArray(new DbSourceProxy[0]);
5124 DbSourceProxy src = otherdb.get(0);
5125 fetchr = new JMenuItem(MessageManager.formatMessage(
5126 "label.fetch_all_param",
5127 new Object[] { src.getDbSource() }));
5128 fetchr.addActionListener(new ActionListener()
5131 public void actionPerformed(ActionEvent e)
5133 new Thread(new Runnable()
5139 boolean isNucleotide = alignPanel.alignFrame
5140 .getViewport().getAlignment()
5142 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5143 alignPanel.av.getSequenceSelection(),
5144 alignPanel.alignFrame, dassource,
5145 alignPanel.alignFrame.featureSettings,
5148 .addListener(new FetchFinishedListenerI()
5151 public void finished()
5153 AlignFrame.this.setMenusForViewport();
5156 dbRefFetcher.fetchDBRefs(false);
5162 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5163 MessageManager.formatMessage(
5164 "label.fetch_retrieve_from_all_sources",
5166 Integer.valueOf(otherdb.size())
5167 .toString(), src.getDbSource(),
5168 src.getDbName() })));
5171 // and then build the rest of the individual menus
5172 ifetch = new JMenu(MessageManager.formatMessage(
5173 "label.source_from_db_source",
5174 new Object[] { src.getDbSource() }));
5176 String imname = null;
5178 for (DbSourceProxy sproxy : otherdb)
5180 String dbname = sproxy.getDbName();
5181 String sname = dbname.length() > 5 ? dbname.substring(0,
5182 5) + "..." : dbname;
5183 String msname = dbname.length() > 10 ? dbname.substring(
5184 0, 10) + "..." : dbname;
5187 imname = MessageManager.formatMessage(
5188 "label.from_msname", new Object[] { sname });
5190 fetchr = new JMenuItem(msname);
5191 final DbSourceProxy[] dassrc = { sproxy };
5192 fetchr.addActionListener(new ActionListener()
5196 public void actionPerformed(ActionEvent e)
5198 new Thread(new Runnable()
5204 boolean isNucleotide = alignPanel.alignFrame
5205 .getViewport().getAlignment()
5207 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5208 alignPanel.av.getSequenceSelection(),
5209 alignPanel.alignFrame, dassrc,
5210 alignPanel.alignFrame.featureSettings,
5213 .addListener(new FetchFinishedListenerI()
5216 public void finished()
5218 AlignFrame.this.setMenusForViewport();
5221 dbRefFetcher.fetchDBRefs(false);
5227 fetchr.setToolTipText("<html>"
5228 + MessageManager.formatMessage(
5229 "label.fetch_retrieve_from", new Object[]
5233 if (++icomp >= mcomp || i == (otherdb.size()))
5235 ifetch.setText(MessageManager.formatMessage(
5236 "label.source_to_target", imname, sname));
5238 ifetch = new JMenu();
5246 if (comp >= mcomp || dbi >= (dbclasses.length))
5248 dfetch.setText(MessageManager.formatMessage(
5249 "label.source_to_target", mname, dbclass));
5251 dfetch = new JMenu();
5264 * Left justify the whole alignment.
5267 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5269 AlignmentI al = viewport.getAlignment();
5271 viewport.firePropertyChange("alignment", null, al);
5275 * Right justify the whole alignment.
5278 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5280 AlignmentI al = viewport.getAlignment();
5282 viewport.firePropertyChange("alignment", null, al);
5286 public void setShowSeqFeatures(boolean b)
5288 showSeqFeatures.setSelected(b);
5289 viewport.setShowSequenceFeatures(b);
5296 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5297 * awt.event.ActionEvent)
5300 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5302 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5303 alignPanel.paintAlignment(true);
5310 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5314 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5316 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5317 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5325 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5326 * .event.ActionEvent)
5329 protected void showGroupConservation_actionPerformed(ActionEvent e)
5331 viewport.setShowGroupConservation(showGroupConservation.getState());
5332 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5339 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5340 * .event.ActionEvent)
5343 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5345 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5346 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5353 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5354 * .event.ActionEvent)
5357 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5359 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5360 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5364 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5366 showSequenceLogo.setState(true);
5367 viewport.setShowSequenceLogo(true);
5368 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5369 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5373 protected void showInformationHistogram_actionPerformed(ActionEvent e)
5375 viewport.setShowInformationHistogram(
5376 showInformationHistogram.getState());
5377 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5381 protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
5383 viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState());
5384 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5388 protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
5390 showHMMSequenceLogo.setState(true);
5391 viewport.setShowHMMSequenceLogo(true);
5392 viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState());
5393 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5397 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5399 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5406 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5407 * .event.ActionEvent)
5410 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5412 if (avc.makeGroupsFromSelection())
5414 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5415 alignPanel.updateAnnotation();
5416 alignPanel.paintAlignment(true);
5420 public void clearAlignmentSeqRep()
5422 // TODO refactor alignmentseqrep to controller
5423 if (viewport.getAlignment().hasSeqrep())
5425 viewport.getAlignment().setSeqrep(null);
5426 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5427 alignPanel.updateAnnotation();
5428 alignPanel.paintAlignment(true);
5433 protected void createGroup_actionPerformed(ActionEvent e)
5435 if (avc.createGroup())
5437 alignPanel.alignmentChanged();
5442 protected void unGroup_actionPerformed(ActionEvent e)
5446 alignPanel.alignmentChanged();
5451 * make the given alignmentPanel the currently selected tab
5453 * @param alignmentPanel
5455 public void setDisplayedView(AlignmentPanel alignmentPanel)
5457 if (!viewport.getSequenceSetId().equals(
5458 alignmentPanel.av.getSequenceSetId()))
5462 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5464 if (tabbedPane != null
5465 && tabbedPane.getTabCount() > 0
5466 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5467 .getSelectedIndex())
5469 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5474 * Action on selection of menu options to Show or Hide annotations.
5477 * @param forSequences
5478 * update sequence-related annotations
5479 * @param forAlignment
5480 * update non-sequence-related annotations
5483 protected void setAnnotationsVisibility(boolean visible,
5484 boolean forSequences, boolean forAlignment)
5486 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5487 .getAlignmentAnnotation();
5492 for (AlignmentAnnotation aa : anns)
5495 * don't display non-positional annotations on an alignment
5497 if (aa.annotations == null)
5501 boolean apply = (aa.sequenceRef == null && forAlignment)
5502 || (aa.sequenceRef != null && forSequences);
5505 aa.visible = visible;
5508 alignPanel.validateAnnotationDimensions(true);
5509 alignPanel.alignmentChanged();
5513 * Store selected annotation sort order for the view and repaint.
5516 protected void sortAnnotations_actionPerformed()
5518 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5520 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5521 alignPanel.paintAlignment(true);
5526 * @return alignment panels in this alignment frame
5528 public List<? extends AlignmentViewPanel> getAlignPanels()
5530 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5534 * Open a new alignment window, with the cDNA associated with this (protein)
5535 * alignment, aligned as is the protein.
5537 protected void viewAsCdna_actionPerformed()
5539 // TODO no longer a menu action - refactor as required
5540 final AlignmentI alignment = getViewport().getAlignment();
5541 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5542 if (mappings == null)
5546 List<SequenceI> cdnaSeqs = new ArrayList<>();
5547 for (SequenceI aaSeq : alignment.getSequences())
5549 for (AlignedCodonFrame acf : mappings)
5551 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5555 * There is a cDNA mapping for this protein sequence - add to new
5556 * alignment. It will share the same dataset sequence as other mapped
5557 * cDNA (no new mappings need to be created).
5559 final Sequence newSeq = new Sequence(dnaSeq);
5560 newSeq.setDatasetSequence(dnaSeq);
5561 cdnaSeqs.add(newSeq);
5565 if (cdnaSeqs.size() == 0)
5567 // show a warning dialog no mapped cDNA
5570 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5572 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5573 AlignFrame.DEFAULT_HEIGHT);
5574 cdna.alignAs(alignment);
5575 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5577 Desktop.addInternalFrame(alignFrame, newtitle,
5578 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5582 * Set visibility of dna/protein complement view (available when shown in a
5588 protected void showComplement_actionPerformed(boolean show)
5590 SplitContainerI sf = getSplitViewContainer();
5593 sf.setComplementVisible(this, show);
5598 * Generate the reverse (optionally complemented) of the selected sequences,
5599 * and add them to the alignment
5602 protected void showReverse_actionPerformed(boolean complement)
5604 AlignmentI al = null;
5607 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5608 al = dna.reverseCdna(complement);
5609 viewport.addAlignment(al, "");
5610 addHistoryItem(new EditCommand(
5611 MessageManager.getString("label.add_sequences"),
5612 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5613 viewport.getAlignment()));
5614 } catch (Exception ex)
5616 System.err.println(ex.getMessage());
5622 * Try to run a script in the Groovy console, having first ensured that this
5623 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5624 * be targeted at this alignment.
5627 protected void runGroovy_actionPerformed()
5629 Jalview.setCurrentAlignFrame(this);
5630 groovy.ui.Console console = Desktop.getGroovyConsole();
5631 if (console != null)
5635 console.runScript();
5636 } catch (Exception ex)
5638 System.err.println((ex.toString()));
5640 .showInternalMessageDialog(Desktop.desktop, MessageManager
5641 .getString("label.couldnt_run_groovy_script"),
5643 .getString("label.groovy_support_failed"),
5644 JvOptionPane.ERROR_MESSAGE);
5649 System.err.println("Can't run Groovy script as console not found");
5654 * Hides columns containing (or not containing) a specified feature, provided
5655 * that would not leave all columns hidden
5657 * @param featureType
5658 * @param columnsContaining
5661 public boolean hideFeatureColumns(String featureType,
5662 boolean columnsContaining)
5664 boolean notForHiding = avc.markColumnsContainingFeatures(
5665 columnsContaining, false, false, featureType);
5668 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5669 false, featureType))
5671 getViewport().hideSelectedColumns();
5679 protected void selectHighlightedColumns_actionPerformed(
5680 ActionEvent actionEvent)
5682 // include key modifier check in case user selects from menu
5683 avc.markHighlightedColumns(
5684 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5686 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5690 * Rebuilds the Colour menu, including any user-defined colours which have
5691 * been loaded either on startup or during the session
5693 public void buildColourMenu()
5695 colourMenu.removeAll();
5697 colourMenu.add(applyToAllGroups);
5698 colourMenu.add(textColour);
5699 colourMenu.addSeparator();
5701 ColourMenuHelper.addMenuItems(colourMenu, this,
5702 viewport.getAlignment(), false);
5704 colourMenu.addSeparator();
5705 colourMenu.add(conservationMenuItem);
5706 colourMenu.add(modifyConservation);
5707 colourMenu.add(abovePIDThreshold);
5708 colourMenu.add(modifyPID);
5709 colourMenu.add(annotationColour);
5711 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5712 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5716 * Open a dialog (if not already open) that allows the user to select and
5717 * calculate PCA or Tree analysis
5719 protected void openTreePcaDialog()
5721 if (alignPanel.getCalculationDialog() == null)
5723 new CalculationChooser(AlignFrame.this);
5728 class PrintThread extends Thread
5732 public PrintThread(AlignmentPanel ap)
5737 static PageFormat pf;
5742 PrinterJob printJob = PrinterJob.getPrinterJob();
5746 printJob.setPrintable(ap, pf);
5750 printJob.setPrintable(ap);
5753 if (printJob.printDialog())
5758 } catch (Exception PrintException)
5760 PrintException.printStackTrace();