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.HMMAlignThread;
67 import jalview.hmmer.HMMBuildThread;
68 import jalview.io.AlignmentProperties;
69 import jalview.io.AnnotationFile;
70 import jalview.io.BioJsHTMLOutput;
71 import jalview.io.DataSourceType;
72 import jalview.io.FileFormat;
73 import jalview.io.FileFormatI;
74 import jalview.io.FileFormats;
75 import jalview.io.FileLoader;
76 import jalview.io.FileParse;
77 import jalview.io.FormatAdapter;
78 import jalview.io.HMMFile;
79 import jalview.io.HtmlSvgOutput;
80 import jalview.io.IdentifyFile;
81 import jalview.io.JPredFile;
82 import jalview.io.JalviewFileChooser;
83 import jalview.io.JalviewFileView;
84 import jalview.io.JnetAnnotationMaker;
85 import jalview.io.NewickFile;
86 import jalview.io.ScoreMatrixFile;
87 import jalview.io.TCoffeeScoreFile;
88 import jalview.jbgui.GAlignFrame;
89 import jalview.schemes.ColourSchemeI;
90 import jalview.schemes.ColourSchemes;
91 import jalview.schemes.ResidueColourScheme;
92 import jalview.schemes.TCoffeeColourScheme;
93 import jalview.util.MessageManager;
94 import jalview.viewmodel.AlignmentViewport;
95 import jalview.viewmodel.ViewportRanges;
96 import jalview.ws.DBRefFetcher;
97 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
98 import jalview.ws.jws1.Discoverer;
99 import jalview.ws.jws2.Jws2Discoverer;
100 import jalview.ws.jws2.jabaws2.Jws2Instance;
101 import jalview.ws.seqfetcher.DbSourceProxy;
103 import java.awt.BorderLayout;
104 import java.awt.Component;
105 import java.awt.Rectangle;
106 import java.awt.Toolkit;
107 import java.awt.datatransfer.Clipboard;
108 import java.awt.datatransfer.DataFlavor;
109 import java.awt.datatransfer.StringSelection;
110 import java.awt.datatransfer.Transferable;
111 import java.awt.dnd.DnDConstants;
112 import java.awt.dnd.DropTargetDragEvent;
113 import java.awt.dnd.DropTargetDropEvent;
114 import java.awt.dnd.DropTargetEvent;
115 import java.awt.dnd.DropTargetListener;
116 import java.awt.event.ActionEvent;
117 import java.awt.event.ActionListener;
118 import java.awt.event.FocusAdapter;
119 import java.awt.event.FocusEvent;
120 import java.awt.event.ItemEvent;
121 import java.awt.event.ItemListener;
122 import java.awt.event.KeyAdapter;
123 import java.awt.event.KeyEvent;
124 import java.awt.event.MouseEvent;
125 import java.awt.print.PageFormat;
126 import java.awt.print.PrinterJob;
127 import java.beans.PropertyChangeEvent;
129 import java.io.FileWriter;
130 import java.io.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.JOptionPane;
150 import javax.swing.JScrollPane;
151 import javax.swing.SwingUtilities;
157 * @version $Revision$
159 public class AlignFrame extends GAlignFrame implements DropTargetListener,
160 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
163 Map<String, Float> distribution = new HashMap<>(); // temporary
165 public static final int DEFAULT_WIDTH = 700;
167 public static final int DEFAULT_HEIGHT = 500;
169 boolean autoAlignNewSequences;
174 * The currently displayed panel (selected tabbed view if more than one)
176 public AlignmentPanel alignPanel;
178 AlignViewport viewport;
180 ViewportRanges vpRanges;
182 public AlignViewControllerI avc;
184 List<AlignmentPanel> alignPanels = new ArrayList<>();
187 * Last format used to load or save alignments in this window
189 FileFormatI currentFileFormat = null;
192 * Current filename for this alignment
194 String fileName = null;
198 * Creates a new AlignFrame object with specific width and height.
204 public AlignFrame(AlignmentI al, int width, int height)
206 this(al, null, width, height);
210 * Creates a new AlignFrame object with specific width, height and
216 * @param sequenceSetId
218 public AlignFrame(AlignmentI al, int width, int height,
219 String sequenceSetId)
221 this(al, null, width, height, sequenceSetId);
225 * Creates a new AlignFrame object with specific width, height and
231 * @param sequenceSetId
234 public AlignFrame(AlignmentI al, int width, int height,
235 String sequenceSetId, String viewId)
237 this(al, null, width, height, sequenceSetId, viewId);
241 * new alignment window with hidden columns
245 * @param hiddenColumns
246 * ColumnSelection or null
248 * Width of alignment frame
252 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
253 int width, int height)
255 this(al, hiddenColumns, width, height, null);
259 * Create alignment frame for al with hiddenColumns, a specific width and
260 * height, and specific sequenceId
263 * @param hiddenColumns
266 * @param sequenceSetId
269 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
270 int width, int height, String sequenceSetId)
272 this(al, hiddenColumns, width, height, sequenceSetId, null);
276 * Create alignment frame for al with hiddenColumns, a specific width and
277 * height, and specific sequenceId
280 * @param hiddenColumns
283 * @param sequenceSetId
288 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
289 int width, int height, String sequenceSetId, String viewId)
291 setSize(width, height);
293 if (al.getDataset() == null)
298 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
300 alignPanel = new AlignmentPanel(this, viewport);
302 addAlignmentPanel(alignPanel, true);
306 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
307 HiddenColumns hiddenColumns, int width, int height)
309 setSize(width, height);
311 if (al.getDataset() == null)
316 viewport = new AlignViewport(al, hiddenColumns);
318 if (hiddenSeqs != null && hiddenSeqs.length > 0)
320 viewport.hideSequence(hiddenSeqs);
322 alignPanel = new AlignmentPanel(this, viewport);
323 addAlignmentPanel(alignPanel, true);
328 * Make a new AlignFrame from existing alignmentPanels
335 public AlignFrame(AlignmentPanel ap)
339 addAlignmentPanel(ap, false);
343 public void setIsRecurring(boolean status)
349 * initalise the alignframe from the underlying viewport data and the
354 if (!Jalview.isHeadlessMode())
356 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
359 vpRanges = viewport.getRanges();
360 avc = new jalview.controller.AlignViewController(this, viewport,
362 if (viewport.getAlignmentConservationAnnotation() == null)
364 // BLOSUM62Colour.setEnabled(false);
365 conservationMenuItem.setEnabled(false);
366 modifyConservation.setEnabled(false);
367 // PIDColour.setEnabled(false);
368 // abovePIDThreshold.setEnabled(false);
369 // modifyPID.setEnabled(false);
372 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
375 if (sortby.equals("Id"))
377 sortIDMenuItem_actionPerformed(null);
379 else if (sortby.equals("Pairwise Identity"))
381 sortPairwiseMenuItem_actionPerformed(null);
385 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
387 setMenusFromViewport(viewport);
388 buildSortByAnnotationScoresMenu();
389 calculateTree.addActionListener(new ActionListener()
393 public void actionPerformed(ActionEvent e)
401 if (Desktop.desktop != null)
403 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
404 addServiceListeners();
408 if (viewport.getWrapAlignment())
410 wrapMenuItem_actionPerformed(null);
413 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
415 this.overviewMenuItem_actionPerformed(null);
420 final List<AlignmentPanel> selviews = new ArrayList<>();
421 final List<AlignmentPanel> origview = new ArrayList<>();
422 final String menuLabel = MessageManager
423 .getString("label.copy_format_from");
424 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
425 new ViewSetProvider()
429 public AlignmentPanel[] getAllAlignmentPanels()
432 origview.add(alignPanel);
433 // make an array of all alignment panels except for this one
434 List<AlignmentPanel> aps = new ArrayList<>(
435 Arrays.asList(Desktop.getAlignmentPanels(null)));
436 aps.remove(AlignFrame.this.alignPanel);
437 return aps.toArray(new AlignmentPanel[aps.size()]);
439 }, selviews, new ItemListener()
443 public void itemStateChanged(ItemEvent e)
445 if (origview.size() > 0)
447 final AlignmentPanel ap = origview.get(0);
450 * Copy the ViewStyle of the selected panel to 'this one'.
451 * Don't change value of 'scaleProteinAsCdna' unless copying
454 ViewStyleI vs = selviews.get(0).getAlignViewport()
456 boolean fromSplitFrame = selviews.get(0)
457 .getAlignViewport().getCodingComplement() != null;
460 vs.setScaleProteinAsCdna(ap.getAlignViewport()
461 .getViewStyle().isScaleProteinAsCdna());
463 ap.getAlignViewport().setViewStyle(vs);
466 * Also rescale ViewStyle of SplitFrame complement if there is
467 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
468 * the whole ViewStyle (allow cDNA protein to have different
471 AlignViewportI complement = ap.getAlignViewport()
472 .getCodingComplement();
473 if (complement != null && vs.isScaleProteinAsCdna())
475 AlignFrame af = Desktop.getAlignFrameFor(complement);
476 ((SplitFrame) af.getSplitViewContainer())
478 af.setMenusForViewport();
482 ap.setSelected(true);
483 ap.alignFrame.setMenusForViewport();
488 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
489 .indexOf("devel") > -1
490 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
491 .indexOf("test") > -1)
493 formatMenu.add(vsel);
495 addFocusListener(new FocusAdapter()
498 public void focusGained(FocusEvent e)
500 Jalview.setCurrentAlignFrame(AlignFrame.this);
506 private void buildHMMERMenu()
508 hmmerMenu.removeAll();
510 hmmerMenu.add(changeHMMERLocation);
511 hmmerMenu.addSeparator();
513 hmmerMenu.add(autoAlignSeqs);
514 hmmerMenu.addSeparator();
516 hmmerMenu.add(hmmAlign);
517 hmmerMenu.add(hmmBuild);
518 hmmerMenu.add(hmmSearch);
523 * Change the filename and format for the alignment, and enable the 'reload'
524 * button functionality.
531 public void setFileName(String file, FileFormatI format)
534 setFileFormat(format);
535 reload.setEnabled(true);
539 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
542 void addKeyListener()
544 addKeyListener(new KeyAdapter()
547 public void keyPressed(KeyEvent evt)
549 if (viewport.cursorMode
550 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
551 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
552 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
553 && Character.isDigit(evt.getKeyChar()))
555 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
558 switch (evt.getKeyCode())
561 case 27: // escape key
562 deselectAllSequenceMenuItem_actionPerformed(null);
566 case KeyEvent.VK_DOWN:
567 if (evt.isAltDown() || !viewport.cursorMode)
569 moveSelectedSequences(false);
571 if (viewport.cursorMode)
573 alignPanel.getSeqPanel().moveCursor(0, 1);
578 if (evt.isAltDown() || !viewport.cursorMode)
580 moveSelectedSequences(true);
582 if (viewport.cursorMode)
584 alignPanel.getSeqPanel().moveCursor(0, -1);
589 case KeyEvent.VK_LEFT:
590 if (evt.isAltDown() || !viewport.cursorMode)
592 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
596 alignPanel.getSeqPanel().moveCursor(-1, 0);
601 case KeyEvent.VK_RIGHT:
602 if (evt.isAltDown() || !viewport.cursorMode)
604 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
608 alignPanel.getSeqPanel().moveCursor(1, 0);
612 case KeyEvent.VK_SPACE:
613 if (viewport.cursorMode)
615 alignPanel.getSeqPanel().insertGapAtCursor(
616 evt.isControlDown() || evt.isShiftDown()
621 // case KeyEvent.VK_A:
622 // if (viewport.cursorMode)
624 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
625 // //System.out.println("A");
629 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
630 * System.out.println("closing bracket"); } break;
632 case KeyEvent.VK_DELETE:
633 case KeyEvent.VK_BACK_SPACE:
634 if (!viewport.cursorMode)
636 cut_actionPerformed(null);
640 alignPanel.getSeqPanel().deleteGapAtCursor(
641 evt.isControlDown() || evt.isShiftDown()
648 if (viewport.cursorMode)
650 alignPanel.getSeqPanel().setCursorRow();
654 if (viewport.cursorMode && !evt.isControlDown())
656 alignPanel.getSeqPanel().setCursorColumn();
660 if (viewport.cursorMode)
662 alignPanel.getSeqPanel().setCursorPosition();
666 case KeyEvent.VK_ENTER:
667 case KeyEvent.VK_COMMA:
668 if (viewport.cursorMode)
670 alignPanel.getSeqPanel().setCursorRowAndColumn();
675 if (viewport.cursorMode)
677 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
681 if (viewport.cursorMode)
683 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
688 viewport.cursorMode = !viewport.cursorMode;
689 statusBar.setText(MessageManager.formatMessage(
690 "label.keyboard_editing_mode",
691 new String[] { (viewport.cursorMode ? "on" : "off") }));
692 if (viewport.cursorMode)
694 alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
696 alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
699 alignPanel.getSeqPanel().seqCanvas.repaint();
705 Help.showHelpWindow();
706 } catch (Exception ex)
708 ex.printStackTrace();
713 boolean toggleSeqs = !evt.isControlDown();
714 boolean toggleCols = !evt.isShiftDown();
715 toggleHiddenRegions(toggleSeqs, toggleCols);
720 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
721 boolean modifyExisting = true; // always modify, don't clear
722 // evt.isShiftDown();
723 boolean invertHighlighted = evt.isAltDown();
724 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
728 case KeyEvent.VK_PAGE_UP:
729 if (viewport.getWrapAlignment())
731 vpRanges.scrollUp(true);
738 case KeyEvent.VK_PAGE_DOWN:
739 if (viewport.getWrapAlignment())
741 vpRanges.scrollUp(false);
752 public void keyReleased(KeyEvent evt)
754 switch (evt.getKeyCode())
756 case KeyEvent.VK_LEFT:
757 if (evt.isAltDown() || !viewport.cursorMode)
759 viewport.firePropertyChange("alignment", null, viewport
760 .getAlignment().getSequences());
764 case KeyEvent.VK_RIGHT:
765 if (evt.isAltDown() || !viewport.cursorMode)
767 viewport.firePropertyChange("alignment", null, viewport
768 .getAlignment().getSequences());
776 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
778 ap.alignFrame = this;
779 avc = new jalview.controller.AlignViewController(this, viewport,
784 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
786 int aSize = alignPanels.size();
788 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
790 if (aSize == 1 && ap.av.viewName == null)
792 this.getContentPane().add(ap, BorderLayout.CENTER);
798 setInitialTabVisible();
801 expandViews.setEnabled(true);
802 gatherViews.setEnabled(true);
803 tabbedPane.addTab(ap.av.viewName, ap);
805 ap.setVisible(false);
810 if (ap.av.isPadGaps())
812 ap.av.getAlignment().padGaps();
814 ap.av.updateConservation(ap);
815 ap.av.updateConsensus(ap);
816 ap.av.updateStrucConsensus(ap);
817 ap.av.updateInformation(ap);
821 public void setInitialTabVisible()
823 expandViews.setEnabled(true);
824 gatherViews.setEnabled(true);
825 tabbedPane.setVisible(true);
826 AlignmentPanel first = alignPanels.get(0);
827 tabbedPane.addTab(first.av.viewName, first);
828 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
831 public AlignViewport getViewport()
836 /* Set up intrinsic listeners for dynamically generated GUI bits. */
837 private void addServiceListeners()
839 final java.beans.PropertyChangeListener thisListener;
840 Desktop.instance.addJalviewPropertyChangeListener("services",
841 thisListener = new java.beans.PropertyChangeListener()
844 public void propertyChange(PropertyChangeEvent evt)
846 // // System.out.println("Discoverer property change.");
847 // if (evt.getPropertyName().equals("services"))
849 SwingUtilities.invokeLater(new Runnable()
856 .println("Rebuild WS Menu for service change");
857 BuildWebServiceMenu();
864 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
867 public void internalFrameClosed(
868 javax.swing.event.InternalFrameEvent evt)
870 // System.out.println("deregistering discoverer listener");
871 Desktop.instance.removeJalviewPropertyChangeListener("services",
873 closeMenuItem_actionPerformed(true);
876 // Finally, build the menu once to get current service state
877 new Thread(new Runnable()
882 BuildWebServiceMenu();
888 * Configure menu items that vary according to whether the alignment is
889 * nucleotide or protein
891 public void setGUINucleotide()
893 AlignmentI al = getViewport().getAlignment();
894 boolean nucleotide = al.isNucleotide();
896 showTranslation.setVisible(nucleotide);
897 showReverse.setVisible(nucleotide);
898 showReverseComplement.setVisible(nucleotide);
899 conservationMenuItem.setEnabled(!nucleotide);
900 modifyConservation.setEnabled(!nucleotide
901 && conservationMenuItem.isSelected());
902 showGroupConservation.setEnabled(!nucleotide);
904 showComplementMenuItem.setText(nucleotide ? MessageManager
905 .getString("label.protein") : MessageManager
906 .getString("label.nucleotide"));
910 * set up menus for the current viewport. This may be called after any
911 * operation that affects the data in the current view (selection changed,
912 * etc) to update the menus to reflect the new state.
915 public void setMenusForViewport()
917 setMenusFromViewport(viewport);
921 * Need to call this method when tabs are selected for multiple views, or when
922 * loading from Jalview2XML.java
927 void setMenusFromViewport(AlignViewport av)
929 padGapsMenuitem.setSelected(av.isPadGaps());
930 colourTextMenuItem.setSelected(av.isShowColourText());
931 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
932 modifyPID.setEnabled(abovePIDThreshold.isSelected());
933 conservationMenuItem.setSelected(av.getConservationSelected());
934 modifyConservation.setEnabled(conservationMenuItem.isSelected());
935 seqLimits.setSelected(av.getShowJVSuffix());
936 idRightAlign.setSelected(av.isRightAlignIds());
937 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
938 renderGapsMenuItem.setSelected(av.isRenderGaps());
939 wrapMenuItem.setSelected(av.getWrapAlignment());
940 scaleAbove.setVisible(av.getWrapAlignment());
941 scaleLeft.setVisible(av.getWrapAlignment());
942 scaleRight.setVisible(av.getWrapAlignment());
943 annotationPanelMenuItem.setState(av.isShowAnnotation());
945 * Show/hide annotations only enabled if annotation panel is shown
947 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
948 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
949 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
950 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
951 viewBoxesMenuItem.setSelected(av.getShowBoxes());
952 viewTextMenuItem.setSelected(av.getShowText());
953 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
954 showGroupConsensus.setSelected(av.isShowGroupConsensus());
955 showGroupConservation.setSelected(av.isShowGroupConservation());
956 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
957 showSequenceLogo.setSelected(av.isShowSequenceLogo());
958 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
959 showInformationHistogram.setSelected(av.isShowInformationHistogram());
960 showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
961 normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
963 ColourMenuHelper.setColourSelected(colourMenu,
964 av.getGlobalColourScheme());
966 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
967 hiddenMarkers.setState(av.getShowHiddenMarkers());
968 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
969 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
970 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
971 autoCalculate.setSelected(av.autoCalculateConsensus);
972 sortByTree.setSelected(av.sortByTree);
973 listenToViewSelections.setSelected(av.followSelection);
975 showProducts.setEnabled(canShowProducts());
976 setGroovyEnabled(Desktop.getGroovyConsole() != null);
982 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
986 public void setGroovyEnabled(boolean b)
988 runGroovy.setEnabled(b);
991 private IProgressIndicator progressBar;
996 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
999 public void setProgressBar(String message, long id)
1001 progressBar.setProgressBar(message, id);
1005 public void registerHandler(final long id,
1006 final IProgressIndicatorHandler handler)
1008 progressBar.registerHandler(id, handler);
1013 * @return true if any progress bars are still active
1016 public boolean operationInProgress()
1018 return progressBar.operationInProgress();
1022 public void setStatus(String text)
1024 statusBar.setText(text);
1028 * Added so Castor Mapping file can obtain Jalview Version
1030 public String getVersion()
1032 return jalview.bin.Cache.getProperty("VERSION");
1035 public FeatureRenderer getFeatureRenderer()
1037 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1041 public void fetchSequence_actionPerformed(ActionEvent e)
1043 new jalview.gui.SequenceFetcher(this);
1047 public void addFromFile_actionPerformed(ActionEvent e)
1049 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1053 public void hmmBuild_actionPerformed(ActionEvent e)
1054 throws IOException, InterruptedException
1056 new Thread(new HMMBuildThread(this)).start();
1057 alignPanel.repaint();
1062 public void hmmAlign_actionPerformed(ActionEvent e)
1063 throws IOException, InterruptedException
1065 new Thread(new HMMAlignThread(this, true)).start();
1066 alignPanel.repaint();
1070 public void changeHMMERLocation_actionPerformed(ActionEvent e)
1072 String location = JOptionPane.showInputDialog(
1073 MessageManager.getString("label.enter_location"));
1074 Cache.setProperty(Preferences.HMMER_PATH, location);
1078 public void autoAlignSeqs_actionPerformed(boolean autoAlignSeqs)
1080 autoAlignNewSequences = autoAlignSeqs;
1081 alignPanel.repaint();
1085 public void hmmSearch_actionPerformed(ActionEvent e)
1087 alignPanel.repaint();
1091 public void reload_actionPerformed(ActionEvent e)
1093 if (fileName != null)
1095 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1096 // originating file's format
1097 // TODO: work out how to recover feature settings for correct view(s) when
1098 // file is reloaded.
1099 if (FileFormat.Jalview.equals(currentFileFormat))
1101 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1102 for (int i = 0; i < frames.length; i++)
1104 if (frames[i] instanceof AlignFrame && frames[i] != this
1105 && ((AlignFrame) frames[i]).fileName != null
1106 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1110 frames[i].setSelected(true);
1111 Desktop.instance.closeAssociatedWindows();
1112 } catch (java.beans.PropertyVetoException ex)
1118 Desktop.instance.closeAssociatedWindows();
1120 FileLoader loader = new FileLoader();
1121 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1122 : DataSourceType.FILE;
1123 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1127 Rectangle bounds = this.getBounds();
1129 FileLoader loader = new FileLoader();
1130 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1131 : DataSourceType.FILE;
1132 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1133 protocol, currentFileFormat);
1135 newframe.setBounds(bounds);
1136 if (featureSettings != null && featureSettings.isShowing())
1138 final Rectangle fspos = featureSettings.frame.getBounds();
1139 // TODO: need a 'show feature settings' function that takes bounds -
1140 // need to refactor Desktop.addFrame
1141 newframe.featureSettings_actionPerformed(null);
1142 final FeatureSettings nfs = newframe.featureSettings;
1143 SwingUtilities.invokeLater(new Runnable()
1148 nfs.frame.setBounds(fspos);
1151 this.featureSettings.close();
1152 this.featureSettings = null;
1154 this.closeMenuItem_actionPerformed(true);
1160 public void addFromText_actionPerformed(ActionEvent e)
1162 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1167 public void addFromURL_actionPerformed(ActionEvent e)
1169 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1173 public void save_actionPerformed(ActionEvent e)
1175 if (fileName == null || (currentFileFormat == null)
1176 || fileName.startsWith("http"))
1178 saveAs_actionPerformed(null);
1182 saveAlignment(fileName, currentFileFormat);
1193 public void saveAs_actionPerformed(ActionEvent e)
1195 String format = currentFileFormat == null ? null : currentFileFormat
1197 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1198 Cache.getProperty("LAST_DIRECTORY"), format);
1200 chooser.setFileView(new JalviewFileView());
1201 chooser.setDialogTitle(MessageManager
1202 .getString("label.save_alignment_to_file"));
1203 chooser.setToolTipText(MessageManager.getString("action.save"));
1205 int value = chooser.showSaveDialog(this);
1207 if (value == JalviewFileChooser.APPROVE_OPTION)
1209 currentFileFormat = chooser.getSelectedFormat();
1210 while (currentFileFormat == null)
1213 .showInternalMessageDialog(
1216 .getString("label.select_file_format_before_saving"),
1218 .getString("label.file_format_not_specified"),
1219 JvOptionPane.WARNING_MESSAGE);
1220 currentFileFormat = chooser.getSelectedFormat();
1221 value = chooser.showSaveDialog(this);
1222 if (value != JalviewFileChooser.APPROVE_OPTION)
1228 fileName = chooser.getSelectedFile().getPath();
1230 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1232 Cache.setProperty("LAST_DIRECTORY", fileName);
1233 saveAlignment(fileName, currentFileFormat);
1237 public boolean saveAlignment(String file, FileFormatI format)
1239 boolean success = true;
1241 if (FileFormat.Jalview.equals(format))
1243 String shortName = title;
1245 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1247 shortName = shortName.substring(shortName
1248 .lastIndexOf(java.io.File.separatorChar) + 1);
1251 success = new Jalview2XML().saveAlignment(this, file, shortName);
1253 statusBar.setText(MessageManager.formatMessage(
1254 "label.successfully_saved_to_file_in_format", new Object[] {
1255 fileName, format }));
1260 AlignmentExportData exportData = getAlignmentForExport(format,
1262 if (exportData.getSettings().isCancelled())
1266 FormatAdapter f = new FormatAdapter(alignPanel,
1267 exportData.getSettings());
1268 String output = f.formatSequences(
1270 exportData.getAlignment(), // class cast exceptions will
1271 // occur in the distant future
1272 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1273 f.getCacheSuffixDefault(format), viewport.getAlignment()
1274 .getHiddenColumns());
1284 PrintWriter out = new PrintWriter(new FileWriter(file));
1288 this.setTitle(file);
1289 statusBar.setText(MessageManager.formatMessage(
1290 "label.successfully_saved_to_file_in_format",
1291 new Object[] { fileName, format.getName() }));
1292 } catch (Exception ex)
1295 ex.printStackTrace();
1302 JvOptionPane.showInternalMessageDialog(this, MessageManager
1303 .formatMessage("label.couldnt_save_file",
1304 new Object[] { fileName }), MessageManager
1305 .getString("label.error_saving_file"),
1306 JvOptionPane.WARNING_MESSAGE);
1312 private void warningMessage(String warning, String title)
1314 if (new jalview.util.Platform().isHeadless())
1316 System.err.println("Warning: " + title + "\nWarning: " + warning);
1321 JvOptionPane.showInternalMessageDialog(this, warning, title,
1322 JvOptionPane.WARNING_MESSAGE);
1334 protected void outputText_actionPerformed(ActionEvent e)
1336 FileFormatI fileFormat = FileFormats.getInstance().forName(
1337 e.getActionCommand());
1338 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1340 if (exportData.getSettings().isCancelled())
1344 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1345 cap.setForInput(null);
1348 FileFormatI format = fileFormat;
1349 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1350 .formatSequences(format, exportData.getAlignment(),
1351 exportData.getOmitHidden(),
1353 .getStartEndPostions(), viewport
1354 .getAlignment().getHiddenColumns()));
1355 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1356 "label.alignment_output_command",
1357 new Object[] { e.getActionCommand() }), 600, 500);
1358 } catch (OutOfMemoryError oom)
1360 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1366 public static AlignmentExportData getAlignmentForExport(
1367 FileFormatI format, AlignViewportI viewport,
1368 AlignExportSettingI exportSettings)
1370 AlignmentI alignmentToExport = null;
1371 AlignExportSettingI settings = exportSettings;
1372 String[] omitHidden = null;
1374 HiddenSequences hiddenSeqs = viewport.getAlignment()
1375 .getHiddenSequences();
1377 alignmentToExport = viewport.getAlignment();
1379 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1380 if (settings == null)
1382 settings = new AlignExportSettings(hasHiddenSeqs,
1383 viewport.hasHiddenColumns(), format);
1385 // settings.isExportAnnotations();
1387 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1389 omitHidden = viewport.getViewAsString(false,
1390 settings.isExportHiddenSequences());
1393 int[] alignmentStartEnd = new int[2];
1394 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1396 alignmentToExport = hiddenSeqs.getFullAlignment();
1400 alignmentToExport = viewport.getAlignment();
1402 alignmentStartEnd = alignmentToExport
1403 .getVisibleStartAndEndIndex(viewport.getAlignment()
1405 .getHiddenRegions());
1406 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1407 omitHidden, alignmentStartEnd, settings);
1418 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1420 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1421 htmlSVG.exportHTML(null);
1425 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1427 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1428 bjs.exportHTML(null);
1431 public void createImageMap(File file, String image)
1433 alignPanel.makePNGImageMap(file, image);
1443 public void createPNG(File f)
1445 alignPanel.makePNG(f);
1455 public void createEPS(File f)
1457 alignPanel.makeEPS(f);
1461 public void createSVG(File f)
1463 alignPanel.makeSVG(f);
1467 public void pageSetup_actionPerformed(ActionEvent e)
1469 PrinterJob printJob = PrinterJob.getPrinterJob();
1470 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1480 public void printMenuItem_actionPerformed(ActionEvent e)
1482 // Putting in a thread avoids Swing painting problems
1483 PrintThread thread = new PrintThread(alignPanel);
1488 public void exportFeatures_actionPerformed(ActionEvent e)
1490 new AnnotationExporter().exportFeatures(alignPanel);
1494 public void exportAnnotations_actionPerformed(ActionEvent e)
1496 new AnnotationExporter().exportAnnotations(alignPanel);
1500 public void associatedData_actionPerformed(ActionEvent e)
1501 throws IOException, InterruptedException
1503 // Pick the tree file
1504 JalviewFileChooser chooser = new JalviewFileChooser(
1505 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1506 chooser.setFileView(new JalviewFileView());
1507 chooser.setDialogTitle(MessageManager
1508 .getString("label.load_jalview_annotations"));
1509 chooser.setToolTipText(MessageManager
1510 .getString("label.load_jalview_annotations"));
1512 int value = chooser.showOpenDialog(null);
1514 if (value == JalviewFileChooser.APPROVE_OPTION)
1516 String choice = chooser.getSelectedFile().getPath();
1517 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1518 loadJalviewDataFile(choice, null, null, null);
1524 * Close the current view or all views in the alignment frame. If the frame
1525 * only contains one view then the alignment will be removed from memory.
1527 * @param closeAllTabs
1530 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1532 if (alignPanels != null && alignPanels.size() < 2)
1534 closeAllTabs = true;
1539 if (alignPanels != null)
1543 if (this.isClosed())
1545 // really close all the windows - otherwise wait till
1546 // setClosed(true) is called
1547 for (int i = 0; i < alignPanels.size(); i++)
1549 AlignmentPanel ap = alignPanels.get(i);
1556 closeView(alignPanel);
1563 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1564 * be called recursively, with the frame now in 'closed' state
1566 this.setClosed(true);
1568 } catch (Exception ex)
1570 ex.printStackTrace();
1575 * Close the specified panel and close up tabs appropriately.
1577 * @param panelToClose
1579 public void closeView(AlignmentPanel panelToClose)
1581 int index = tabbedPane.getSelectedIndex();
1582 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1583 alignPanels.remove(panelToClose);
1584 panelToClose.closePanel();
1585 panelToClose = null;
1587 tabbedPane.removeTabAt(closedindex);
1588 tabbedPane.validate();
1590 if (index > closedindex || index == tabbedPane.getTabCount())
1592 // modify currently selected tab index if necessary.
1596 this.tabSelectionChanged(index);
1602 void updateEditMenuBar()
1605 if (viewport.getHistoryList().size() > 0)
1607 undoMenuItem.setEnabled(true);
1608 CommandI command = viewport.getHistoryList().peek();
1609 undoMenuItem.setText(MessageManager.formatMessage(
1610 "label.undo_command",
1611 new Object[] { command.getDescription() }));
1615 undoMenuItem.setEnabled(false);
1616 undoMenuItem.setText(MessageManager.getString("action.undo"));
1619 if (viewport.getRedoList().size() > 0)
1621 redoMenuItem.setEnabled(true);
1623 CommandI command = viewport.getRedoList().peek();
1624 redoMenuItem.setText(MessageManager.formatMessage(
1625 "label.redo_command",
1626 new Object[] { command.getDescription() }));
1630 redoMenuItem.setEnabled(false);
1631 redoMenuItem.setText(MessageManager.getString("action.redo"));
1636 public void addHistoryItem(CommandI command)
1638 if (command.getSize() > 0)
1640 viewport.addToHistoryList(command);
1641 viewport.clearRedoList();
1642 updateEditMenuBar();
1643 viewport.updateHiddenColumns();
1644 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1645 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1646 // viewport.getColumnSelection()
1647 // .getHiddenColumns().size() > 0);
1653 * @return alignment objects for all views
1655 AlignmentI[] getViewAlignments()
1657 if (alignPanels != null)
1659 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1661 for (AlignmentPanel ap : alignPanels)
1663 als[i++] = ap.av.getAlignment();
1667 if (viewport != null)
1669 return new AlignmentI[] { viewport.getAlignment() };
1681 protected void undoMenuItem_actionPerformed(ActionEvent e)
1683 if (viewport.getHistoryList().isEmpty())
1687 CommandI command = viewport.getHistoryList().pop();
1688 viewport.addToRedoList(command);
1689 command.undoCommand(getViewAlignments());
1691 AlignmentViewport originalSource = getOriginatingSource(command);
1692 updateEditMenuBar();
1694 if (originalSource != null)
1696 if (originalSource != viewport)
1699 .warn("Implementation worry: mismatch of viewport origin for undo");
1701 originalSource.updateHiddenColumns();
1702 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1704 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1705 // viewport.getColumnSelection()
1706 // .getHiddenColumns().size() > 0);
1707 originalSource.firePropertyChange("alignment", null, originalSource
1708 .getAlignment().getSequences());
1719 protected void redoMenuItem_actionPerformed(ActionEvent e)
1721 if (viewport.getRedoList().size() < 1)
1726 CommandI command = viewport.getRedoList().pop();
1727 viewport.addToHistoryList(command);
1728 command.doCommand(getViewAlignments());
1730 AlignmentViewport originalSource = getOriginatingSource(command);
1731 updateEditMenuBar();
1733 if (originalSource != null)
1736 if (originalSource != viewport)
1739 .warn("Implementation worry: mismatch of viewport origin for redo");
1741 originalSource.updateHiddenColumns();
1742 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1744 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1745 // viewport.getColumnSelection()
1746 // .getHiddenColumns().size() > 0);
1747 originalSource.firePropertyChange("alignment", null, originalSource
1748 .getAlignment().getSequences());
1752 AlignmentViewport getOriginatingSource(CommandI command)
1754 AlignmentViewport originalSource = null;
1755 // For sequence removal and addition, we need to fire
1756 // the property change event FROM the viewport where the
1757 // original alignment was altered
1758 AlignmentI al = null;
1759 if (command instanceof EditCommand)
1761 EditCommand editCommand = (EditCommand) command;
1762 al = editCommand.getAlignment();
1763 List<Component> comps = PaintRefresher.components.get(viewport
1764 .getSequenceSetId());
1766 for (Component comp : comps)
1768 if (comp instanceof AlignmentPanel)
1770 if (al == ((AlignmentPanel) comp).av.getAlignment())
1772 originalSource = ((AlignmentPanel) comp).av;
1779 if (originalSource == null)
1781 // The original view is closed, we must validate
1782 // the current view against the closed view first
1785 PaintRefresher.validateSequences(al, viewport.getAlignment());
1788 originalSource = viewport;
1791 return originalSource;
1800 public void moveSelectedSequences(boolean up)
1802 SequenceGroup sg = viewport.getSelectionGroup();
1808 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1809 viewport.getHiddenRepSequences(), up);
1810 alignPanel.paintAlignment(true);
1813 synchronized void slideSequences(boolean right, int size)
1815 List<SequenceI> sg = new ArrayList<>();
1816 if (viewport.cursorMode)
1818 sg.add(viewport.getAlignment().getSequenceAt(
1819 alignPanel.getSeqPanel().seqCanvas.cursorY));
1821 else if (viewport.getSelectionGroup() != null
1822 && viewport.getSelectionGroup().getSize() != viewport
1823 .getAlignment().getHeight())
1825 sg = viewport.getSelectionGroup().getSequences(
1826 viewport.getHiddenRepSequences());
1834 List<SequenceI> invertGroup = new ArrayList<>();
1836 for (SequenceI seq : viewport.getAlignment().getSequences())
1838 if (!sg.contains(seq))
1840 invertGroup.add(seq);
1844 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1846 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1847 for (int i = 0; i < invertGroup.size(); i++)
1849 seqs2[i] = invertGroup.get(i);
1852 SlideSequencesCommand ssc;
1855 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1856 size, viewport.getGapCharacter());
1860 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1861 size, viewport.getGapCharacter());
1864 int groupAdjustment = 0;
1865 if (ssc.getGapsInsertedBegin() && right)
1867 if (viewport.cursorMode)
1869 alignPanel.getSeqPanel().moveCursor(size, 0);
1873 groupAdjustment = size;
1876 else if (!ssc.getGapsInsertedBegin() && !right)
1878 if (viewport.cursorMode)
1880 alignPanel.getSeqPanel().moveCursor(-size, 0);
1884 groupAdjustment = -size;
1888 if (groupAdjustment != 0)
1890 viewport.getSelectionGroup().setStartRes(
1891 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1892 viewport.getSelectionGroup().setEndRes(
1893 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1897 * just extend the last slide command if compatible; but not if in
1898 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1900 boolean appendHistoryItem = false;
1901 Deque<CommandI> historyList = viewport.getHistoryList();
1902 boolean inSplitFrame = getSplitViewContainer() != null;
1903 if (!inSplitFrame && historyList != null && historyList.size() > 0
1904 && historyList.peek() instanceof SlideSequencesCommand)
1906 appendHistoryItem = ssc
1907 .appendSlideCommand((SlideSequencesCommand) historyList
1911 if (!appendHistoryItem)
1913 addHistoryItem(ssc);
1926 protected void copy_actionPerformed(ActionEvent e)
1929 if (viewport.getSelectionGroup() == null)
1933 // TODO: preserve the ordering of displayed alignment annotation in any
1934 // internal paste (particularly sequence associated annotation)
1935 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1936 String[] omitHidden = null;
1938 if (viewport.hasHiddenColumns())
1940 omitHidden = viewport.getViewAsString(true);
1943 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1944 seqs, omitHidden, null);
1946 StringSelection ss = new StringSelection(output);
1950 jalview.gui.Desktop.internalCopy = true;
1951 // Its really worth setting the clipboard contents
1952 // to empty before setting the large StringSelection!!
1953 Toolkit.getDefaultToolkit().getSystemClipboard()
1954 .setContents(new StringSelection(""), null);
1956 Toolkit.getDefaultToolkit().getSystemClipboard()
1957 .setContents(ss, Desktop.instance);
1958 } catch (OutOfMemoryError er)
1960 new OOMWarning("copying region", er);
1964 ArrayList<int[]> hiddenColumns = null;
1965 if (viewport.hasHiddenColumns())
1967 hiddenColumns = new ArrayList<>();
1968 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1969 .getSelectionGroup().getEndRes();
1970 for (int[] region : viewport.getAlignment().getHiddenColumns()
1971 .getHiddenRegions())
1973 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1975 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1976 region[1] - hiddenOffset });
1981 Desktop.jalviewClipboard = new Object[] { seqs,
1982 viewport.getAlignment().getDataset(), hiddenColumns };
1983 statusBar.setText(MessageManager.formatMessage(
1984 "label.copied_sequences_to_clipboard", new Object[] { Integer
1985 .valueOf(seqs.length).toString() }));
1993 * @throws InterruptedException
1994 * @throws IOException
1997 protected void pasteNew_actionPerformed(ActionEvent e)
1998 throws IOException, InterruptedException
2008 * @throws InterruptedException
2009 * @throws IOException
2012 protected void pasteThis_actionPerformed(ActionEvent e)
2013 throws IOException, InterruptedException
2019 * Paste contents of Jalview clipboard
2021 * @param newAlignment
2022 * true to paste to a new alignment, otherwise add to this.
2023 * @throws InterruptedException
2024 * @throws IOException
2026 void paste(boolean newAlignment) throws IOException, InterruptedException
2028 boolean externalPaste = true;
2031 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2032 Transferable contents = c.getContents(this);
2034 if (contents == null)
2043 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2044 if (str.length() < 1)
2049 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2051 } catch (OutOfMemoryError er)
2053 new OOMWarning("Out of memory pasting sequences!!", er);
2057 SequenceI[] sequences;
2058 boolean annotationAdded = false;
2059 AlignmentI alignment = null;
2061 if (Desktop.jalviewClipboard != null)
2063 // The clipboard was filled from within Jalview, we must use the
2065 // And dataset from the copied alignment
2066 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2067 // be doubly sure that we create *new* sequence objects.
2068 sequences = new SequenceI[newseq.length];
2069 for (int i = 0; i < newseq.length; i++)
2071 sequences[i] = new Sequence(newseq[i]);
2073 alignment = new Alignment(sequences);
2074 externalPaste = false;
2078 // parse the clipboard as an alignment.
2079 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2081 sequences = alignment.getSequencesArray();
2085 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2091 if (Desktop.jalviewClipboard != null)
2093 // dataset is inherited
2094 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2098 // new dataset is constructed
2099 alignment.setDataset(null);
2101 alwidth = alignment.getWidth() + 1;
2105 AlignmentI pastedal = alignment; // preserve pasted alignment object
2106 // Add pasted sequences and dataset into existing alignment.
2107 alignment = viewport.getAlignment();
2108 alwidth = alignment.getWidth() + 1;
2109 // decide if we need to import sequences from an existing dataset
2110 boolean importDs = Desktop.jalviewClipboard != null
2111 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2112 // importDs==true instructs us to copy over new dataset sequences from
2113 // an existing alignment
2114 Vector newDs = (importDs) ? new Vector() : null; // used to create
2115 // minimum dataset set
2117 for (int i = 0; i < sequences.length; i++)
2121 newDs.addElement(null);
2123 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2125 if (importDs && ds != null)
2127 if (!newDs.contains(ds))
2129 newDs.setElementAt(ds, i);
2130 ds = new Sequence(ds);
2131 // update with new dataset sequence
2132 sequences[i].setDatasetSequence(ds);
2136 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2141 // copy and derive new dataset sequence
2142 sequences[i] = sequences[i].deriveSequence();
2143 alignment.getDataset().addSequence(
2144 sequences[i].getDatasetSequence());
2145 // TODO: avoid creation of duplicate dataset sequences with a
2146 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2148 alignment.addSequence(sequences[i]); // merges dataset
2152 newDs.clear(); // tidy up
2154 if (alignment.getAlignmentAnnotation() != null)
2156 for (AlignmentAnnotation alan : alignment
2157 .getAlignmentAnnotation())
2159 if (alan.graphGroup > fgroup)
2161 fgroup = alan.graphGroup;
2165 if (pastedal.getAlignmentAnnotation() != null)
2167 // Add any annotation attached to alignment.
2168 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2169 for (int i = 0; i < alann.length; i++)
2171 annotationAdded = true;
2172 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2174 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2175 if (newann.graphGroup > -1)
2177 if (newGraphGroups.size() <= newann.graphGroup
2178 || newGraphGroups.get(newann.graphGroup) == null)
2180 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2182 newGraphGroups.add(q, null);
2184 newGraphGroups.set(newann.graphGroup, new Integer(
2187 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2191 newann.padAnnotation(alwidth);
2192 alignment.addAnnotation(newann);
2202 addHistoryItem(new EditCommand(
2203 MessageManager.getString("label.add_sequences"),
2204 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2206 // Add any annotations attached to sequences
2207 for (int i = 0; i < sequences.length; i++)
2209 if (sequences[i].getAnnotation() != null)
2211 AlignmentAnnotation newann;
2212 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2214 annotationAdded = true;
2215 newann = sequences[i].getAnnotation()[a];
2216 newann.adjustForAlignment();
2217 newann.padAnnotation(alwidth);
2218 if (newann.graphGroup > -1)
2220 if (newann.graphGroup > -1)
2222 if (newGraphGroups.size() <= newann.graphGroup
2223 || newGraphGroups.get(newann.graphGroup) == null)
2225 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2227 newGraphGroups.add(q, null);
2229 newGraphGroups.set(newann.graphGroup, new Integer(
2232 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2236 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2241 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2248 // propagate alignment changed.
2249 vpRanges.setEndSeq(alignment.getHeight());
2250 if (annotationAdded)
2252 // Duplicate sequence annotation in all views.
2253 AlignmentI[] alview = this.getViewAlignments();
2254 for (int i = 0; i < sequences.length; i++)
2256 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2261 for (int avnum = 0; avnum < alview.length; avnum++)
2263 if (alview[avnum] != alignment)
2265 // duplicate in a view other than the one with input focus
2266 int avwidth = alview[avnum].getWidth() + 1;
2267 // this relies on sann being preserved after we
2268 // modify the sequence's annotation array for each duplication
2269 for (int a = 0; a < sann.length; a++)
2271 AlignmentAnnotation newann = new AlignmentAnnotation(
2273 sequences[i].addAlignmentAnnotation(newann);
2274 newann.padAnnotation(avwidth);
2275 alview[avnum].addAnnotation(newann); // annotation was
2276 // duplicated earlier
2277 // TODO JAL-1145 graphGroups are not updated for sequence
2278 // annotation added to several views. This may cause
2280 alview[avnum].setAnnotationIndex(newann, a);
2285 buildSortByAnnotationScoresMenu();
2287 viewport.firePropertyChange("alignment", null,
2288 alignment.getSequences());
2289 if (alignPanels != null)
2291 for (AlignmentPanel ap : alignPanels)
2293 ap.validateAnnotationDimensions(false);
2298 alignPanel.validateAnnotationDimensions(false);
2304 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2306 String newtitle = new String("Copied sequences");
2308 if (Desktop.jalviewClipboard != null
2309 && Desktop.jalviewClipboard[2] != null)
2311 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2312 for (int[] region : hc)
2314 af.viewport.hideColumns(region[0], region[1]);
2318 // >>>This is a fix for the moment, until a better solution is
2320 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2322 alignPanel.getSeqPanel().seqCanvas
2323 .getFeatureRenderer());
2325 // TODO: maintain provenance of an alignment, rather than just make the
2326 // title a concatenation of operations.
2329 if (title.startsWith("Copied sequences"))
2335 newtitle = newtitle.concat("- from " + title);
2340 newtitle = new String("Pasted sequences");
2343 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2348 } catch (Exception ex)
2350 ex.printStackTrace();
2351 System.out.println("Exception whilst pasting: " + ex);
2352 // could be anything being pasted in here
2357 protected void expand_newalign(ActionEvent e)
2361 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2362 .getAlignment(), -1);
2363 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2365 String newtitle = new String("Flanking alignment");
2367 if (Desktop.jalviewClipboard != null
2368 && Desktop.jalviewClipboard[2] != null)
2370 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2371 for (int region[] : hc)
2373 af.viewport.hideColumns(region[0], region[1]);
2377 // >>>This is a fix for the moment, until a better solution is
2379 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2381 alignPanel.getSeqPanel().seqCanvas
2382 .getFeatureRenderer());
2384 // TODO: maintain provenance of an alignment, rather than just make the
2385 // title a concatenation of operations.
2387 if (title.startsWith("Copied sequences"))
2393 newtitle = newtitle.concat("- from " + title);
2397 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2399 } catch (Exception ex)
2401 ex.printStackTrace();
2402 System.out.println("Exception whilst pasting: " + ex);
2403 // could be anything being pasted in here
2404 } catch (OutOfMemoryError oom)
2406 new OOMWarning("Viewing flanking region of alignment", oom);
2417 protected void cut_actionPerformed(ActionEvent e)
2419 copy_actionPerformed(null);
2420 delete_actionPerformed(null);
2430 protected void delete_actionPerformed(ActionEvent evt)
2433 SequenceGroup sg = viewport.getSelectionGroup();
2440 * If the cut affects all sequences, warn, remove highlighted columns
2442 if (sg.getSize() == viewport.getAlignment().getHeight())
2444 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2445 .getAlignment().getWidth()) ? true : false;
2446 if (isEntireAlignWidth)
2448 int confirm = JvOptionPane.showConfirmDialog(this,
2449 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2450 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2451 JvOptionPane.OK_CANCEL_OPTION);
2453 if (confirm == JvOptionPane.CANCEL_OPTION
2454 || confirm == JvOptionPane.CLOSED_OPTION)
2459 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2460 sg.getEndRes() + 1);
2462 SequenceI[] cut = sg.getSequences()
2463 .toArray(new SequenceI[sg.getSize()]);
2465 addHistoryItem(new EditCommand(
2466 MessageManager.getString("label.cut_sequences"), Action.CUT,
2467 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2468 viewport.getAlignment()));
2470 viewport.setSelectionGroup(null);
2471 viewport.sendSelection();
2472 viewport.getAlignment().deleteGroup(sg);
2474 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2476 if (viewport.getAlignment().getHeight() < 1)
2480 this.setClosed(true);
2481 } catch (Exception ex)
2494 protected void deleteGroups_actionPerformed(ActionEvent e)
2496 if (avc.deleteGroups())
2498 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2499 alignPanel.updateAnnotation();
2500 alignPanel.paintAlignment(true);
2511 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2513 SequenceGroup sg = new SequenceGroup();
2515 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2517 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2520 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2521 viewport.setSelectionGroup(sg);
2522 viewport.sendSelection();
2523 // JAL-2034 - should delegate to
2524 // alignPanel to decide if overview needs
2526 alignPanel.paintAlignment(false);
2527 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2537 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2539 if (viewport.cursorMode)
2541 alignPanel.getSeqPanel().keyboardNo1 = null;
2542 alignPanel.getSeqPanel().keyboardNo2 = null;
2544 viewport.setSelectionGroup(null);
2545 viewport.getColumnSelection().clear();
2546 viewport.setSelectionGroup(null);
2547 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2548 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2549 // JAL-2034 - should delegate to
2550 // alignPanel to decide if overview needs
2552 alignPanel.paintAlignment(false);
2553 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2554 viewport.sendSelection();
2564 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2566 SequenceGroup sg = viewport.getSelectionGroup();
2570 selectAllSequenceMenuItem_actionPerformed(null);
2575 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2577 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2579 // JAL-2034 - should delegate to
2580 // alignPanel to decide if overview needs
2583 alignPanel.paintAlignment(true);
2584 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2585 viewport.sendSelection();
2589 public void invertColSel_actionPerformed(ActionEvent e)
2591 viewport.invertColumnSelection();
2592 alignPanel.paintAlignment(true);
2593 viewport.sendSelection();
2603 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2605 trimAlignment(true);
2615 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2617 trimAlignment(false);
2620 void trimAlignment(boolean trimLeft)
2622 ColumnSelection colSel = viewport.getColumnSelection();
2625 if (!colSel.isEmpty())
2629 column = colSel.getMin();
2633 column = colSel.getMax();
2637 if (viewport.getSelectionGroup() != null)
2639 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2640 viewport.getHiddenRepSequences());
2644 seqs = viewport.getAlignment().getSequencesArray();
2647 TrimRegionCommand trimRegion;
2650 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2651 column, viewport.getAlignment());
2652 vpRanges.setStartRes(0);
2656 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2657 column, viewport.getAlignment());
2660 statusBar.setText(MessageManager.formatMessage(
2661 "label.removed_columns",
2662 new String[] { Integer.valueOf(trimRegion.getSize())
2665 addHistoryItem(trimRegion);
2667 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2669 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2670 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2672 viewport.getAlignment().deleteGroup(sg);
2676 viewport.firePropertyChange("alignment", null, viewport
2677 .getAlignment().getSequences());
2688 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2690 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2693 if (viewport.getSelectionGroup() != null)
2695 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2696 viewport.getHiddenRepSequences());
2697 start = viewport.getSelectionGroup().getStartRes();
2698 end = viewport.getSelectionGroup().getEndRes();
2702 seqs = viewport.getAlignment().getSequencesArray();
2705 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2706 "Remove Gapped Columns", seqs, start, end,
2707 viewport.getAlignment());
2709 addHistoryItem(removeGapCols);
2711 statusBar.setText(MessageManager.formatMessage(
2712 "label.removed_empty_columns",
2713 new Object[] { Integer.valueOf(removeGapCols.getSize())
2716 // This is to maintain viewport position on first residue
2717 // of first sequence
2718 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2719 int startRes = seq.findPosition(vpRanges.getStartRes());
2720 // ShiftList shifts;
2721 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2722 // edit.alColumnChanges=shifts.getInverse();
2723 // if (viewport.hasHiddenColumns)
2724 // viewport.getColumnSelection().compensateForEdits(shifts);
2725 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2726 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2738 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2740 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2743 if (viewport.getSelectionGroup() != null)
2745 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2746 viewport.getHiddenRepSequences());
2747 start = viewport.getSelectionGroup().getStartRes();
2748 end = viewport.getSelectionGroup().getEndRes();
2752 seqs = viewport.getAlignment().getSequencesArray();
2755 // This is to maintain viewport position on first residue
2756 // of first sequence
2757 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2758 int startRes = seq.findPosition(vpRanges.getStartRes());
2760 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2761 viewport.getAlignment()));
2763 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2765 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2777 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2779 viewport.setPadGaps(padGapsMenuitem.isSelected());
2780 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2791 public void findMenuItem_actionPerformed(ActionEvent e)
2797 * Create a new view of the current alignment.
2800 public void newView_actionPerformed(ActionEvent e)
2802 newView(null, true);
2806 * Creates and shows a new view of the current alignment.
2809 * title of newly created view; if null, one will be generated
2810 * @param copyAnnotation
2811 * if true then duplicate all annnotation, groups and settings
2812 * @return new alignment panel, already displayed.
2814 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2817 * Create a new AlignmentPanel (with its own, new Viewport)
2819 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2821 if (!copyAnnotation)
2824 * remove all groups and annotation except for the automatic stuff
2826 newap.av.getAlignment().deleteAllGroups();
2827 newap.av.getAlignment().deleteAllAnnotations(false);
2830 newap.av.setGatherViewsHere(false);
2832 if (viewport.viewName == null)
2834 viewport.viewName = MessageManager
2835 .getString("label.view_name_original");
2839 * Views share the same edits undo and redo stacks
2841 newap.av.setHistoryList(viewport.getHistoryList());
2842 newap.av.setRedoList(viewport.getRedoList());
2845 * Views share the same mappings; need to deregister any new mappings
2846 * created by copyAlignPanel, and register the new reference to the shared
2849 newap.av.replaceMappings(viewport.getAlignment());
2852 * start up cDNA consensus (if applicable) now mappings are in place
2854 if (newap.av.initComplementConsensus())
2856 newap.refresh(true); // adjust layout of annotations
2859 newap.av.viewName = getNewViewName(viewTitle);
2861 addAlignmentPanel(newap, true);
2862 newap.alignmentChanged();
2864 if (alignPanels.size() == 2)
2866 viewport.setGatherViewsHere(true);
2868 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2873 * Make a new name for the view, ensuring it is unique within the current
2874 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2875 * these now use viewId. Unique view names are still desirable for usability.)
2880 protected String getNewViewName(String viewTitle)
2882 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2883 boolean addFirstIndex = false;
2884 if (viewTitle == null || viewTitle.trim().length() == 0)
2886 viewTitle = MessageManager.getString("action.view");
2887 addFirstIndex = true;
2891 index = 1;// we count from 1 if given a specific name
2893 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2895 List<Component> comps = PaintRefresher.components.get(viewport
2896 .getSequenceSetId());
2898 List<String> existingNames = getExistingViewNames(comps);
2900 while (existingNames.contains(newViewName))
2902 newViewName = viewTitle + " " + (++index);
2908 * Returns a list of distinct view names found in the given list of
2909 * components. View names are held on the viewport of an AlignmentPanel.
2914 protected List<String> getExistingViewNames(List<Component> comps)
2916 List<String> existingNames = new ArrayList<>();
2917 for (Component comp : comps)
2919 if (comp instanceof AlignmentPanel)
2921 AlignmentPanel ap = (AlignmentPanel) comp;
2922 if (!existingNames.contains(ap.av.viewName))
2924 existingNames.add(ap.av.viewName);
2928 return existingNames;
2932 * Explode tabbed views into separate windows.
2935 public void expandViews_actionPerformed(ActionEvent e)
2937 Desktop.explodeViews(this);
2941 * Gather views in separate windows back into a tabbed presentation.
2944 public void gatherViews_actionPerformed(ActionEvent e)
2946 Desktop.instance.gatherViews(this);
2956 public void font_actionPerformed(ActionEvent e)
2958 new FontChooser(alignPanel);
2968 protected void seqLimit_actionPerformed(ActionEvent e)
2970 viewport.setShowJVSuffix(seqLimits.isSelected());
2972 alignPanel.getIdPanel().getIdCanvas()
2973 .setPreferredSize(alignPanel.calculateIdWidth());
2974 alignPanel.paintAlignment(true);
2978 public void idRightAlign_actionPerformed(ActionEvent e)
2980 viewport.setRightAlignIds(idRightAlign.isSelected());
2981 alignPanel.paintAlignment(true);
2985 public void centreColumnLabels_actionPerformed(ActionEvent e)
2987 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2988 alignPanel.paintAlignment(true);
2994 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2997 protected void followHighlight_actionPerformed()
3000 * Set the 'follow' flag on the Viewport (and scroll to position if now
3003 final boolean state = this.followHighlightMenuItem.getState();
3004 viewport.setFollowHighlight(state);
3007 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
3018 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3020 viewport.setColourText(colourTextMenuItem.isSelected());
3021 alignPanel.paintAlignment(true);
3031 public void wrapMenuItem_actionPerformed(ActionEvent e)
3033 scaleAbove.setVisible(wrapMenuItem.isSelected());
3034 scaleLeft.setVisible(wrapMenuItem.isSelected());
3035 scaleRight.setVisible(wrapMenuItem.isSelected());
3036 viewport.setWrapAlignment(wrapMenuItem.isSelected());
3037 alignPanel.updateLayout();
3041 public void showAllSeqs_actionPerformed(ActionEvent e)
3043 viewport.showAllHiddenSeqs();
3047 public void showAllColumns_actionPerformed(ActionEvent e)
3049 viewport.showAllHiddenColumns();
3051 viewport.sendSelection();
3055 public void hideSelSequences_actionPerformed(ActionEvent e)
3057 viewport.hideAllSelectedSeqs();
3058 // alignPanel.paintAlignment(true);
3062 * called by key handler and the hide all/show all menu items
3067 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3070 boolean hide = false;
3071 SequenceGroup sg = viewport.getSelectionGroup();
3072 if (!toggleSeqs && !toggleCols)
3074 // Hide everything by the current selection - this is a hack - we do the
3075 // invert and then hide
3076 // first check that there will be visible columns after the invert.
3077 if (viewport.hasSelectedColumns()
3078 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3081 // now invert the sequence set, if required - empty selection implies
3082 // that no hiding is required.
3085 invertSequenceMenuItem_actionPerformed(null);
3086 sg = viewport.getSelectionGroup();
3090 viewport.expandColSelection(sg, true);
3091 // finally invert the column selection and get the new sequence
3093 invertColSel_actionPerformed(null);
3100 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3102 hideSelSequences_actionPerformed(null);
3105 else if (!(toggleCols && viewport.hasSelectedColumns()))
3107 showAllSeqs_actionPerformed(null);
3113 if (viewport.hasSelectedColumns())
3115 hideSelColumns_actionPerformed(null);
3118 viewport.setSelectionGroup(sg);
3123 showAllColumns_actionPerformed(null);
3132 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3133 * event.ActionEvent)
3136 public void hideAllButSelection_actionPerformed(ActionEvent e)
3138 toggleHiddenRegions(false, false);
3139 viewport.sendSelection();
3146 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3150 public void hideAllSelection_actionPerformed(ActionEvent e)
3152 SequenceGroup sg = viewport.getSelectionGroup();
3153 viewport.expandColSelection(sg, false);
3154 viewport.hideAllSelectedSeqs();
3155 viewport.hideSelectedColumns();
3156 alignPanel.paintAlignment(true);
3157 viewport.sendSelection();
3164 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3168 public void showAllhidden_actionPerformed(ActionEvent e)
3170 viewport.showAllHiddenColumns();
3171 viewport.showAllHiddenSeqs();
3172 alignPanel.paintAlignment(true);
3173 viewport.sendSelection();
3177 public void hideSelColumns_actionPerformed(ActionEvent e)
3179 viewport.hideSelectedColumns();
3180 alignPanel.paintAlignment(true);
3181 viewport.sendSelection();
3185 public void hiddenMarkers_actionPerformed(ActionEvent e)
3187 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3198 protected void scaleAbove_actionPerformed(ActionEvent e)
3200 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3201 alignPanel.paintAlignment(true);
3211 protected void scaleLeft_actionPerformed(ActionEvent e)
3213 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3214 alignPanel.paintAlignment(true);
3224 protected void scaleRight_actionPerformed(ActionEvent e)
3226 viewport.setScaleRightWrapped(scaleRight.isSelected());
3227 alignPanel.paintAlignment(true);
3237 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3239 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3240 alignPanel.paintAlignment(true);
3250 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3252 viewport.setShowText(viewTextMenuItem.isSelected());
3253 alignPanel.paintAlignment(true);
3263 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3265 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3266 alignPanel.paintAlignment(true);
3269 public FeatureSettings featureSettings;
3272 public FeatureSettingsControllerI getFeatureSettingsUI()
3274 return featureSettings;
3278 public void featureSettings_actionPerformed(ActionEvent e)
3280 if (featureSettings != null)
3282 featureSettings.close();
3283 featureSettings = null;
3285 if (!showSeqFeatures.isSelected())
3287 // make sure features are actually displayed
3288 showSeqFeatures.setSelected(true);
3289 showSeqFeatures_actionPerformed(null);
3291 featureSettings = new FeatureSettings(this);
3295 * Set or clear 'Show Sequence Features'
3301 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3303 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3304 alignPanel.paintAlignment(true);
3305 if (alignPanel.getOverviewPanel() != null)
3307 alignPanel.getOverviewPanel().updateOverviewImage();
3312 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3313 * the annotations panel as a whole.
3315 * The options to show/hide all annotations should be enabled when the panel
3316 * is shown, and disabled when the panel is hidden.
3321 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3323 final boolean setVisible = annotationPanelMenuItem.isSelected();
3324 viewport.setShowAnnotation(setVisible);
3325 this.showAllSeqAnnotations.setEnabled(setVisible);
3326 this.hideAllSeqAnnotations.setEnabled(setVisible);
3327 this.showAllAlAnnotations.setEnabled(setVisible);
3328 this.hideAllAlAnnotations.setEnabled(setVisible);
3329 alignPanel.updateLayout();
3333 public void alignmentProperties()
3335 JEditorPane editPane = new JEditorPane("text/html", "");
3336 editPane.setEditable(false);
3337 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3339 editPane.setText(MessageManager.formatMessage("label.html_content",
3340 new Object[] { contents.toString() }));
3341 JInternalFrame frame = new JInternalFrame();
3342 frame.getContentPane().add(new JScrollPane(editPane));
3344 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3345 "label.alignment_properties", new Object[] { getTitle() }),
3356 public void overviewMenuItem_actionPerformed(ActionEvent e)
3358 if (alignPanel.overviewPanel != null)
3363 JInternalFrame frame = new JInternalFrame();
3364 OverviewPanel overview = new OverviewPanel(alignPanel);
3365 frame.setContentPane(overview);
3366 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3367 "label.overview_params", new Object[] { this.getTitle() }),
3368 true, frame.getWidth(), frame.getHeight(), true, true);
3370 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3371 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3374 public void internalFrameClosed(
3375 javax.swing.event.InternalFrameEvent evt)
3377 alignPanel.setOverviewPanel(null);
3381 alignPanel.setOverviewPanel(overview);
3385 public void textColour_actionPerformed()
3387 new TextColourChooser().chooseColour(alignPanel, null);
3391 * public void covariationColour_actionPerformed() {
3393 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3397 public void annotationColour_actionPerformed()
3399 new AnnotationColourChooser(viewport, alignPanel);
3403 public void annotationColumn_actionPerformed(ActionEvent e)
3405 new AnnotationColumnChooser(viewport, alignPanel);
3409 * Action on the user checking or unchecking the option to apply the selected
3410 * colour scheme to all groups. If unchecked, groups may have their own
3411 * independent colour schemes.
3416 public void applyToAllGroups_actionPerformed(boolean selected)
3418 viewport.setColourAppliesToAllGroups(selected);
3422 * Action on user selecting a colour from the colour menu
3425 * the name (not the menu item label!) of the colour scheme
3428 public void changeColour_actionPerformed(String name)
3431 * 'User Defined' opens a panel to configure or load a
3432 * user-defined colour scheme
3434 if (ResidueColourScheme.USER_DEFINED.equals(name))
3436 new UserDefinedColours(alignPanel);
3441 * otherwise set the chosen colour scheme (or null for 'None')
3443 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3444 viewport.getAlignment(), viewport.getHiddenRepSequences());
3449 * Actions on setting or changing the alignment colour scheme
3454 public void changeColour(ColourSchemeI cs)
3456 // TODO: pull up to controller method
3457 ColourMenuHelper.setColourSelected(colourMenu, cs);
3459 viewport.setGlobalColourScheme(cs);
3461 alignPanel.paintAlignment(true);
3465 * Show the PID threshold slider panel
3468 protected void modifyPID_actionPerformed()
3470 SliderPanel.setPIDSliderSource(alignPanel,
3471 viewport.getResidueShading(), alignPanel.getViewName());
3472 SliderPanel.showPIDSlider();
3476 * Show the Conservation slider panel
3479 protected void modifyConservation_actionPerformed()
3481 SliderPanel.setConservationSlider(alignPanel,
3482 viewport.getResidueShading(), alignPanel.getViewName());
3483 SliderPanel.showConservationSlider();
3487 * Action on selecting or deselecting (Colour) By Conservation
3490 public void conservationMenuItem_actionPerformed(boolean selected)
3492 modifyConservation.setEnabled(selected);
3493 viewport.setConservationSelected(selected);
3494 viewport.getResidueShading().setConservationApplied(selected);
3496 changeColour(viewport.getGlobalColourScheme());
3499 modifyConservation_actionPerformed();
3503 SliderPanel.hideConservationSlider();
3508 * Action on selecting or deselecting (Colour) Above PID Threshold
3511 public void abovePIDThreshold_actionPerformed(boolean selected)
3513 modifyPID.setEnabled(selected);
3514 viewport.setAbovePIDThreshold(selected);
3517 viewport.getResidueShading().setThreshold(0,
3518 viewport.isIgnoreGapsConsensus());
3521 changeColour(viewport.getGlobalColourScheme());
3524 modifyPID_actionPerformed();
3528 SliderPanel.hidePIDSlider();
3539 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3541 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3542 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3543 .getAlignment().getSequenceAt(0));
3544 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3545 viewport.getAlignment()));
3546 alignPanel.paintAlignment(true);
3556 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3558 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3559 AlignmentSorter.sortByID(viewport.getAlignment());
3560 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3561 viewport.getAlignment()));
3562 alignPanel.paintAlignment(true);
3572 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3574 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3575 AlignmentSorter.sortByLength(viewport.getAlignment());
3576 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3577 viewport.getAlignment()));
3578 alignPanel.paintAlignment(true);
3588 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3590 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3591 AlignmentSorter.sortByGroup(viewport.getAlignment());
3592 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3593 viewport.getAlignment()));
3595 alignPanel.paintAlignment(true);
3605 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3607 new RedundancyPanel(alignPanel, this);
3617 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3619 if ((viewport.getSelectionGroup() == null)
3620 || (viewport.getSelectionGroup().getSize() < 2))
3622 JvOptionPane.showInternalMessageDialog(this, MessageManager
3623 .getString("label.you_must_select_least_two_sequences"),
3624 MessageManager.getString("label.invalid_selection"),
3625 JvOptionPane.WARNING_MESSAGE);
3629 JInternalFrame frame = new JInternalFrame();
3630 frame.setContentPane(new PairwiseAlignPanel(viewport));
3631 Desktop.addInternalFrame(frame,
3632 MessageManager.getString("action.pairwise_alignment"), 600,
3638 public void autoCalculate_actionPerformed(ActionEvent e)
3640 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3641 if (viewport.autoCalculateConsensus)
3643 viewport.firePropertyChange("alignment", null, viewport
3644 .getAlignment().getSequences());
3649 public void sortByTreeOption_actionPerformed(ActionEvent e)
3651 viewport.sortByTree = sortByTree.isSelected();
3655 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3657 viewport.followSelection = listenToViewSelections.isSelected();
3661 * Constructs a tree panel and adds it to the desktop
3664 * tree type (NJ or AV)
3666 * name of score model used to compute the tree
3668 * parameters for the distance or similarity calculation
3670 void newTreePanel(String type, String modelName, SimilarityParamsI options)
3672 String frameTitle = "";
3675 boolean onSelection = false;
3676 if (viewport.getSelectionGroup() != null
3677 && viewport.getSelectionGroup().getSize() > 0)
3679 SequenceGroup sg = viewport.getSelectionGroup();
3681 /* Decide if the selection is a column region */
3682 for (SequenceI _s : sg.getSequences())
3684 if (_s.getLength() < sg.getEndRes())
3690 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3692 .getString("label.sequences_selection_not_aligned"),
3693 JvOptionPane.WARNING_MESSAGE);
3702 if (viewport.getAlignment().getHeight() < 2)
3708 tp = new TreePanel(alignPanel, type, modelName, options);
3709 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3711 frameTitle += " from ";
3713 if (viewport.viewName != null)
3715 frameTitle += viewport.viewName + " of ";
3718 frameTitle += this.title;
3720 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3731 public void addSortByOrderMenuItem(String title,
3732 final AlignmentOrder order)
3734 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3735 "action.by_title_param", new Object[] { title }));
3737 item.addActionListener(new java.awt.event.ActionListener()
3740 public void actionPerformed(ActionEvent e)
3742 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3744 // TODO: JBPNote - have to map order entries to curent SequenceI
3746 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3748 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3751 alignPanel.paintAlignment(true);
3757 * Add a new sort by annotation score menu item
3760 * the menu to add the option to
3762 * the label used to retrieve scores for each sequence on the
3765 public void addSortByAnnotScoreMenuItem(JMenu sort,
3766 final String scoreLabel)
3768 final JMenuItem item = new JMenuItem(scoreLabel);
3770 item.addActionListener(new java.awt.event.ActionListener()
3773 public void actionPerformed(ActionEvent e)
3775 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3776 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3777 viewport.getAlignment());// ,viewport.getSelectionGroup());
3778 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3779 viewport.getAlignment()));
3780 alignPanel.paintAlignment(true);
3786 * last hash for alignment's annotation array - used to minimise cost of
3789 protected int _annotationScoreVectorHash;
3792 * search the alignment and rebuild the sort by annotation score submenu the
3793 * last alignment annotation vector hash is stored to minimize cost of
3794 * rebuilding in subsequence calls.
3798 public void buildSortByAnnotationScoresMenu()
3800 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3805 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3807 sortByAnnotScore.removeAll();
3808 // almost certainly a quicker way to do this - but we keep it simple
3809 Hashtable scoreSorts = new Hashtable();
3810 AlignmentAnnotation aann[];
3811 for (SequenceI sqa : viewport.getAlignment().getSequences())
3813 aann = sqa.getAnnotation();
3814 for (int i = 0; aann != null && i < aann.length; i++)
3816 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3818 scoreSorts.put(aann[i].label, aann[i].label);
3822 Enumeration labels = scoreSorts.keys();
3823 while (labels.hasMoreElements())
3825 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3826 (String) labels.nextElement());
3828 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3831 _annotationScoreVectorHash = viewport.getAlignment()
3832 .getAlignmentAnnotation().hashCode();
3837 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3838 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3839 * call. Listeners are added to remove the menu item when the treePanel is
3840 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3844 public void buildTreeSortMenu()
3846 sortByTreeMenu.removeAll();
3848 List<Component> comps = PaintRefresher.components.get(viewport
3849 .getSequenceSetId());
3850 List<TreePanel> treePanels = new ArrayList<>();
3851 for (Component comp : comps)
3853 if (comp instanceof TreePanel)
3855 treePanels.add((TreePanel) comp);
3859 if (treePanels.size() < 1)
3861 sortByTreeMenu.setVisible(false);
3865 sortByTreeMenu.setVisible(true);
3867 for (final TreePanel tp : treePanels)
3869 final JMenuItem item = new JMenuItem(tp.getTitle());
3870 item.addActionListener(new java.awt.event.ActionListener()
3873 public void actionPerformed(ActionEvent e)
3875 tp.sortByTree_actionPerformed();
3876 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3881 sortByTreeMenu.add(item);
3885 public boolean sortBy(AlignmentOrder alorder, String undoname)
3887 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3888 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3889 if (undoname != null)
3891 addHistoryItem(new OrderCommand(undoname, oldOrder,
3892 viewport.getAlignment()));
3894 alignPanel.paintAlignment(true);
3899 * Work out whether the whole set of sequences or just the selected set will
3900 * be submitted for multiple alignment.
3903 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3905 // Now, check we have enough sequences
3906 AlignmentView msa = null;
3908 if ((viewport.getSelectionGroup() != null)
3909 && (viewport.getSelectionGroup().getSize() > 1))
3911 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3912 // some common interface!
3914 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3915 * SequenceI[sz = seqs.getSize(false)];
3917 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3918 * seqs.getSequenceAt(i); }
3920 msa = viewport.getAlignmentView(true);
3922 else if (viewport.getSelectionGroup() != null
3923 && viewport.getSelectionGroup().getSize() == 1)
3925 int option = JvOptionPane.showConfirmDialog(this,
3926 MessageManager.getString("warn.oneseq_msainput_selection"),
3927 MessageManager.getString("label.invalid_selection"),
3928 JvOptionPane.OK_CANCEL_OPTION);
3929 if (option == JvOptionPane.OK_OPTION)
3931 msa = viewport.getAlignmentView(false);
3936 msa = viewport.getAlignmentView(false);
3942 * Decides what is submitted to a secondary structure prediction service: the
3943 * first sequence in the alignment, or in the current selection, or, if the
3944 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3945 * region or the whole alignment. (where the first sequence in the set is the
3946 * one that the prediction will be for).
3948 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3950 AlignmentView seqs = null;
3952 if ((viewport.getSelectionGroup() != null)
3953 && (viewport.getSelectionGroup().getSize() > 0))
3955 seqs = viewport.getAlignmentView(true);
3959 seqs = viewport.getAlignmentView(false);
3961 // limit sequences - JBPNote in future - could spawn multiple prediction
3963 // TODO: viewport.getAlignment().isAligned is a global state - the local
3964 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3965 if (!viewport.getAlignment().isAligned(false))
3967 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3968 // TODO: if seqs.getSequences().length>1 then should really have warned
3982 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3984 // Pick the tree file
3985 JalviewFileChooser chooser = new JalviewFileChooser(
3986 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3987 chooser.setFileView(new JalviewFileView());
3988 chooser.setDialogTitle(MessageManager
3989 .getString("label.select_newick_like_tree_file"));
3990 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3992 int value = chooser.showOpenDialog(null);
3994 if (value == JalviewFileChooser.APPROVE_OPTION)
3996 String filePath = chooser.getSelectedFile().getPath();
3997 Cache.setProperty("LAST_DIRECTORY", filePath);
3998 NewickFile fin = null;
4001 fin = new NewickFile(filePath, DataSourceType.FILE);
4002 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4003 } catch (Exception ex)
4010 .getString("label.problem_reading_tree_file"),
4011 JvOptionPane.WARNING_MESSAGE);
4012 ex.printStackTrace();
4014 if (fin != null && fin.hasWarningMessage())
4016 JvOptionPane.showMessageDialog(Desktop.desktop, fin
4017 .getWarningMessage(), MessageManager
4018 .getString("label.possible_problem_with_tree_file"),
4019 JvOptionPane.WARNING_MESSAGE);
4024 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4026 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4029 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4030 int h, int x, int y)
4032 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4036 * Add a treeviewer for the tree extracted from a Newick file object to the
4037 * current alignment view
4044 * Associated alignment input data (or null)
4053 * @return TreePanel handle
4055 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4056 AlignmentView input, int w, int h, int x, int y)
4058 TreePanel tp = null;
4064 if (nf.getTree() != null)
4066 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4072 tp.setLocation(x, y);
4075 Desktop.addInternalFrame(tp, treeTitle, w, h);
4077 } catch (Exception ex)
4079 ex.printStackTrace();
4085 private boolean buildingMenu = false;
4088 * Generates menu items and listener event actions for web service clients
4091 public void BuildWebServiceMenu()
4093 while (buildingMenu)
4097 System.err.println("Waiting for building menu to finish.");
4099 } catch (Exception e)
4103 final AlignFrame me = this;
4104 buildingMenu = true;
4105 new Thread(new Runnable()
4110 final List<JMenuItem> legacyItems = new ArrayList<>();
4113 // System.err.println("Building ws menu again "
4114 // + Thread.currentThread());
4115 // TODO: add support for context dependent disabling of services based
4117 // alignment and current selection
4118 // TODO: add additional serviceHandle parameter to specify abstract
4120 // class independently of AbstractName
4121 // TODO: add in rediscovery GUI function to restart discoverer
4122 // TODO: group services by location as well as function and/or
4124 // object broker mechanism.
4125 final Vector<JMenu> wsmenu = new Vector<>();
4126 final IProgressIndicator af = me;
4129 * do not i18n these strings - they are hard-coded in class
4130 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4131 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4133 final JMenu msawsmenu = new JMenu("Alignment");
4134 final JMenu secstrmenu = new JMenu(
4135 "Secondary Structure Prediction");
4136 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4137 final JMenu analymenu = new JMenu("Analysis");
4138 final JMenu dismenu = new JMenu("Protein Disorder");
4139 // JAL-940 - only show secondary structure prediction services from
4140 // the legacy server
4141 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4143 Discoverer.services != null && (Discoverer.services.size() > 0))
4145 // TODO: refactor to allow list of AbstractName/Handler bindings to
4147 // stored or retrieved from elsewhere
4148 // No MSAWS used any more:
4149 // Vector msaws = null; // (Vector)
4150 // Discoverer.services.get("MsaWS");
4151 Vector secstrpr = (Vector) Discoverer.services
4153 if (secstrpr != null)
4155 // Add any secondary structure prediction services
4156 for (int i = 0, j = secstrpr.size(); i < j; i++)
4158 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4160 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4161 .getServiceClient(sh);
4162 int p = secstrmenu.getItemCount();
4163 impl.attachWSMenuEntry(secstrmenu, me);
4164 int q = secstrmenu.getItemCount();
4165 for (int litm = p; litm < q; litm++)
4167 legacyItems.add(secstrmenu.getItem(litm));
4173 // Add all submenus in the order they should appear on the web
4175 wsmenu.add(msawsmenu);
4176 wsmenu.add(secstrmenu);
4177 wsmenu.add(dismenu);
4178 wsmenu.add(analymenu);
4179 // No search services yet
4180 // wsmenu.add(seqsrchmenu);
4182 javax.swing.SwingUtilities.invokeLater(new Runnable()
4189 webService.removeAll();
4190 // first, add discovered services onto the webservices menu
4191 if (wsmenu.size() > 0)
4193 for (int i = 0, j = wsmenu.size(); i < j; i++)
4195 webService.add(wsmenu.get(i));
4200 webService.add(me.webServiceNoServices);
4202 // TODO: move into separate menu builder class.
4203 boolean new_sspred = false;
4204 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4206 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4207 if (jws2servs != null)
4209 if (jws2servs.hasServices())
4211 jws2servs.attachWSMenuEntry(webService, me);
4212 for (Jws2Instance sv : jws2servs.getServices())
4214 if (sv.description.toLowerCase().contains("jpred"))
4216 for (JMenuItem jmi : legacyItems)
4218 jmi.setVisible(false);
4224 if (jws2servs.isRunning())
4226 JMenuItem tm = new JMenuItem(
4227 "Still discovering JABA Services");
4228 tm.setEnabled(false);
4233 build_urlServiceMenu(me.webService);
4234 build_fetchdbmenu(webService);
4235 for (JMenu item : wsmenu)
4237 if (item.getItemCount() == 0)
4239 item.setEnabled(false);
4243 item.setEnabled(true);
4246 } catch (Exception e)
4249 .debug("Exception during web service menu building process.",
4254 } catch (Exception e)
4257 buildingMenu = false;
4264 * construct any groupURL type service menu entries.
4268 private void build_urlServiceMenu(JMenu webService)
4270 // TODO: remove this code when 2.7 is released
4271 // DEBUG - alignmentView
4273 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4274 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4276 * @Override public void actionPerformed(ActionEvent e) {
4277 * jalview.datamodel.AlignmentView
4278 * .testSelectionViews(af.viewport.getAlignment(),
4279 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4281 * }); webService.add(testAlView);
4283 // TODO: refactor to RestClient discoverer and merge menu entries for
4284 // rest-style services with other types of analysis/calculation service
4285 // SHmmr test client - still being implemented.
4286 // DEBUG - alignmentView
4288 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4291 client.attachWSMenuEntry(
4292 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4298 * Searches the alignment sequences for xRefs and builds the Show
4299 * Cross-References menu (formerly called Show Products), with database
4300 * sources for which cross-references are found (protein sources for a
4301 * nucleotide alignment and vice versa)
4303 * @return true if Show Cross-references menu should be enabled
4305 public boolean canShowProducts()
4307 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4308 AlignmentI dataset = viewport.getAlignment().getDataset();
4310 showProducts.removeAll();
4311 final boolean dna = viewport.getAlignment().isNucleotide();
4313 if (seqs == null || seqs.length == 0)
4315 // nothing to see here.
4319 boolean showp = false;
4322 List<String> ptypes = new CrossRef(seqs, dataset)
4323 .findXrefSourcesForSequences(dna);
4325 for (final String source : ptypes)
4328 final AlignFrame af = this;
4329 JMenuItem xtype = new JMenuItem(source);
4330 xtype.addActionListener(new ActionListener()
4333 public void actionPerformed(ActionEvent e)
4335 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4338 showProducts.add(xtype);
4340 showProducts.setVisible(showp);
4341 showProducts.setEnabled(showp);
4342 } catch (Exception e)
4345 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4353 * Finds and displays cross-references for the selected sequences (protein
4354 * products for nucleotide sequences, dna coding sequences for peptides).
4357 * the sequences to show cross-references for
4359 * true if from a nucleotide alignment (so showing proteins)
4361 * the database to show cross-references for
4363 protected void showProductsFor(final SequenceI[] sel,
4364 final boolean _odna, final String source)
4366 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4371 * Construct and display a new frame containing the translation of this
4372 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4375 public void showTranslation_actionPerformed(ActionEvent e)
4377 AlignmentI al = null;
4380 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4382 al = dna.translateCdna();
4383 } catch (Exception ex)
4385 jalview.bin.Cache.log.error(
4386 "Exception during translation. Please report this !", ex);
4387 final String msg = MessageManager
4388 .getString("label.error_when_translating_sequences_submit_bug_report");
4389 final String errorTitle = MessageManager
4390 .getString("label.implementation_error")
4391 + MessageManager.getString("label.translation_failed");
4392 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4393 JvOptionPane.ERROR_MESSAGE);
4396 if (al == null || al.getHeight() == 0)
4398 final String msg = MessageManager
4399 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4400 final String errorTitle = MessageManager
4401 .getString("label.translation_failed");
4402 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4403 JvOptionPane.WARNING_MESSAGE);
4407 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4408 af.setFileFormat(this.currentFileFormat);
4409 final String newTitle = MessageManager.formatMessage(
4410 "label.translation_of_params",
4411 new Object[] { this.getTitle() });
4412 af.setTitle(newTitle);
4413 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4415 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4416 viewport.openSplitFrame(af, new Alignment(seqs));
4420 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4427 * Set the file format
4431 public void setFileFormat(FileFormatI format)
4433 this.currentFileFormat = format;
4437 * Try to load a features file onto the alignment.
4440 * contents or path to retrieve file
4442 * access mode of file (see jalview.io.AlignFile)
4443 * @return true if features file was parsed correctly.
4445 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4447 return avc.parseFeaturesFile(file, sourceType,
4448 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4453 public void refreshFeatureUI(boolean enableIfNecessary)
4455 // note - currently this is only still here rather than in the controller
4456 // because of the featureSettings hard reference that is yet to be
4458 if (enableIfNecessary)
4460 viewport.setShowSequenceFeatures(true);
4461 showSeqFeatures.setSelected(true);
4467 public void dragEnter(DropTargetDragEvent evt)
4472 public void dragExit(DropTargetEvent evt)
4477 public void dragOver(DropTargetDragEvent evt)
4482 public void dropActionChanged(DropTargetDragEvent evt)
4487 public void drop(DropTargetDropEvent evt)
4489 // JAL-1552 - acceptDrop required before getTransferable call for
4490 // Java's Transferable for native dnd
4491 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4492 Transferable t = evt.getTransferable();
4493 List<String> files = new ArrayList<>();
4494 List<DataSourceType> protocols = new ArrayList<>();
4498 Desktop.transferFromDropTarget(files, protocols, evt, t);
4499 } catch (Exception e)
4501 e.printStackTrace();
4507 // check to see if any of these files have names matching sequences in
4509 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4510 .getAlignment().getSequencesArray());
4512 * Object[] { String,SequenceI}
4514 ArrayList<Object[]> filesmatched = new ArrayList<>();
4515 ArrayList<String> filesnotmatched = new ArrayList<>();
4516 for (int i = 0; i < files.size(); i++)
4518 String file = files.get(i).toString();
4520 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4521 if (protocol == DataSourceType.FILE)
4523 File fl = new File(file);
4524 pdbfn = fl.getName();
4526 else if (protocol == DataSourceType.URL)
4528 URL url = new URL(file);
4529 pdbfn = url.getFile();
4531 if (pdbfn.length() > 0)
4533 // attempt to find a match in the alignment
4534 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4535 int l = 0, c = pdbfn.indexOf(".");
4536 while (mtch == null && c != -1)
4541 } while ((c = pdbfn.indexOf(".", l)) > l);
4544 pdbfn = pdbfn.substring(0, l);
4546 mtch = idm.findAllIdMatches(pdbfn);
4550 FileFormatI type = null;
4553 type = new IdentifyFile().identify(file, protocol);
4554 } catch (Exception ex)
4558 if (type != null && type.isStructureFile())
4560 filesmatched.add(new Object[] { file, protocol, mtch });
4564 // File wasn't named like one of the sequences or wasn't a PDB file.
4565 filesnotmatched.add(file);
4569 if (filesmatched.size() > 0)
4571 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4577 "label.automatically_associate_structure_files_with_sequences_same_name",
4578 new Object[] { Integer
4584 .getString("label.automatically_associate_structure_files_by_name"),
4585 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4588 for (Object[] fm : filesmatched)
4590 // try and associate
4591 // TODO: may want to set a standard ID naming formalism for
4592 // associating PDB files which have no IDs.
4593 for (SequenceI toassoc : (SequenceI[]) fm[2])
4595 PDBEntry pe = new AssociatePdbFileWithSeq()
4596 .associatePdbWithSeq((String) fm[0],
4597 (DataSourceType) fm[1], toassoc, false,
4601 System.err.println("Associated file : "
4602 + ((String) fm[0]) + " with "
4603 + toassoc.getDisplayId(true));
4607 alignPanel.paintAlignment(true);
4611 if (filesnotmatched.size() > 0)
4614 && (Cache.getDefault(
4615 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4621 "label.ignore_unmatched_dropped_files_info",
4622 new Object[] { Integer
4629 .getString("label.ignore_unmatched_dropped_files"),
4630 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4634 for (String fn : filesnotmatched)
4636 loadJalviewDataFile(fn, null, null, null);
4640 } catch (Exception ex)
4642 ex.printStackTrace();
4648 * Attempt to load a "dropped" file or URL string, by testing in turn for
4650 * <li>an Annotation file</li>
4651 * <li>a JNet file</li>
4652 * <li>a features file</li>
4653 * <li>else try to interpret as an alignment file</li>
4657 * either a filename or a URL string.
4658 * @throws InterruptedException
4659 * @throws IOException
4661 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4662 FileFormatI format, SequenceI assocSeq)
4666 if (sourceType == null)
4668 sourceType = FormatAdapter.checkProtocol(file);
4670 // if the file isn't identified, or not positively identified as some
4671 // other filetype (PFAM is default unidentified alignment file type) then
4672 // try to parse as annotation.
4673 boolean isAnnotation = (format == null || FileFormat.Pfam
4674 .equals(format)) ? new AnnotationFile()
4675 .annotateAlignmentView(viewport, file, sourceType) : false;
4679 // first see if its a T-COFFEE score file
4680 TCoffeeScoreFile tcf = null;
4683 tcf = new TCoffeeScoreFile(file, sourceType);
4686 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4689 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4690 isAnnotation = true;
4692 .setText(MessageManager
4693 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4697 // some problem - if no warning its probable that the ID matching
4698 // process didn't work
4702 tcf.getWarningMessage() == null ? MessageManager
4703 .getString("label.check_file_matches_sequence_ids_alignment")
4704 : tcf.getWarningMessage(),
4706 .getString("label.problem_reading_tcoffee_score_file"),
4707 JvOptionPane.WARNING_MESSAGE);
4714 } catch (Exception x)
4717 .debug("Exception when processing data source as T-COFFEE score file",
4723 // try to see if its a JNet 'concise' style annotation file *before*
4725 // try to parse it as a features file
4728 format = new IdentifyFile().identify(file, sourceType);
4730 if (FileFormat.ScoreMatrix == format)
4732 ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4735 // todo: i18n this message
4737 .setText(MessageManager.formatMessage(
4738 "label.successfully_loaded_matrix",
4739 sm.getMatrixName()));
4741 else if (FileFormat.HMMER3.equals(format))
4743 HMMFile hmmFile = new HMMFile(new FileParse(file, sourceType));
4744 HiddenMarkovModel hmm = hmmFile.getHMM();
4745 SequenceI hmmSeq = hmm.initHMMSequence(this, 0);
4746 getViewport().initInformation(hmmSeq);
4747 getViewport().updateInformation(alignPanel);
4748 getViewport().alignmentChanged(alignPanel);
4749 isAnnotation = true;
4752 else if (FileFormat.Jnet.equals(format))
4754 JPredFile predictions = new JPredFile(file, sourceType);
4755 new JnetAnnotationMaker();
4756 JnetAnnotationMaker.add_annotation(predictions,
4757 viewport.getAlignment(), 0, false);
4758 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4759 viewport.getAlignment().setSeqrep(repseq);
4760 HiddenColumns cs = new HiddenColumns();
4761 cs.hideInsertionsFor(repseq);
4762 viewport.getAlignment().setHiddenColumns(cs);
4763 isAnnotation = true;
4765 // else if (IdentifyFile.FeaturesFile.equals(format))
4766 else if (FileFormat.Features.equals(format))
4768 if (parseFeaturesFile(file, sourceType))
4770 alignPanel.paintAlignment(true);
4775 new FileLoader().LoadFile(viewport, file, sourceType, format);
4776 if (autoAlignNewSequences && !recurring)
4778 new Thread(new HMMAlignThread(this, false)).start();
4785 alignPanel.adjustAnnotationHeight();
4786 viewport.updateSequenceIdColours();
4787 buildSortByAnnotationScoresMenu();
4788 alignPanel.paintAlignment(true);
4790 } catch (Exception ex)
4792 ex.printStackTrace();
4793 } catch (OutOfMemoryError oom)
4798 } catch (Exception x)
4803 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4804 : "using " + sourceType + " from " + file)
4806 + (format != null ? "(parsing as '" + format
4807 + "' file)" : ""), oom, Desktop.desktop);
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();