2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.GeneticCodeI;
28 import jalview.analysis.ParseProperties;
29 import jalview.analysis.SequenceIdMatcher;
30 import jalview.api.AlignExportSettingI;
31 import jalview.api.AlignViewControllerGuiI;
32 import jalview.api.AlignViewControllerI;
33 import jalview.api.AlignViewportI;
34 import jalview.api.AlignmentViewPanel;
35 import jalview.api.FeatureSettingsControllerI;
36 import jalview.api.FeatureSettingsModelI;
37 import jalview.api.SplitContainerI;
38 import jalview.api.ViewStyleI;
39 import jalview.api.analysis.SimilarityParamsI;
40 import jalview.bin.Cache;
41 import jalview.bin.Jalview;
42 import jalview.commands.CommandI;
43 import jalview.commands.EditCommand;
44 import jalview.commands.EditCommand.Action;
45 import jalview.commands.OrderCommand;
46 import jalview.commands.RemoveGapColCommand;
47 import jalview.commands.RemoveGapsCommand;
48 import jalview.commands.SlideSequencesCommand;
49 import jalview.commands.TrimRegionCommand;
50 import jalview.datamodel.AlignedCodonFrame;
51 import jalview.datamodel.Alignment;
52 import jalview.datamodel.AlignmentAnnotation;
53 import jalview.datamodel.AlignmentExportData;
54 import jalview.datamodel.AlignmentI;
55 import jalview.datamodel.AlignmentOrder;
56 import jalview.datamodel.AlignmentView;
57 import jalview.datamodel.ColumnSelection;
58 import jalview.datamodel.HiddenColumns;
59 import jalview.datamodel.HiddenSequences;
60 import jalview.datamodel.PDBEntry;
61 import jalview.datamodel.SeqCigar;
62 import jalview.datamodel.Sequence;
63 import jalview.datamodel.SequenceGroup;
64 import jalview.datamodel.SequenceI;
65 import jalview.gui.ColourMenuHelper.ColourChangeListener;
66 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
67 import jalview.io.AlignmentProperties;
68 import jalview.io.AnnotationFile;
69 import jalview.io.BackupFiles;
70 import jalview.io.BioJsHTMLOutput;
71 import jalview.io.DataSourceType;
72 import jalview.io.FileFormat;
73 import jalview.io.FileFormatI;
74 import jalview.io.FileFormats;
75 import jalview.io.FileLoader;
76 import jalview.io.FileParse;
77 import jalview.io.FormatAdapter;
78 import jalview.io.HtmlSvgOutput;
79 import jalview.io.IdentifyFile;
80 import jalview.io.JPredFile;
81 import jalview.io.JalviewFileChooser;
82 import jalview.io.JalviewFileView;
83 import jalview.io.JnetAnnotationMaker;
84 import jalview.io.NewickFile;
85 import jalview.io.ScoreMatrixFile;
86 import jalview.io.TCoffeeScoreFile;
87 import jalview.io.vcf.VCFLoader;
88 import jalview.jbgui.GAlignFrame;
89 import jalview.schemes.ColourSchemeI;
90 import jalview.schemes.ColourSchemes;
91 import jalview.schemes.ResidueColourScheme;
92 import jalview.schemes.TCoffeeColourScheme;
93 import jalview.util.MessageManager;
94 import jalview.viewmodel.AlignmentViewport;
95 import jalview.viewmodel.ViewportRanges;
96 import jalview.ws.DBRefFetcher;
97 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
98 import jalview.ws.jws1.Discoverer;
99 import jalview.ws.jws2.Jws2Discoverer;
100 import jalview.ws.jws2.jabaws2.Jws2Instance;
101 import jalview.ws.seqfetcher.DbSourceProxy;
103 import java.awt.BorderLayout;
104 import java.awt.Component;
105 import java.awt.Rectangle;
106 import java.awt.Toolkit;
107 import java.awt.datatransfer.Clipboard;
108 import java.awt.datatransfer.DataFlavor;
109 import java.awt.datatransfer.StringSelection;
110 import java.awt.datatransfer.Transferable;
111 import java.awt.dnd.DnDConstants;
112 import java.awt.dnd.DropTargetDragEvent;
113 import java.awt.dnd.DropTargetDropEvent;
114 import java.awt.dnd.DropTargetEvent;
115 import java.awt.dnd.DropTargetListener;
116 import java.awt.event.ActionEvent;
117 import java.awt.event.ActionListener;
118 import java.awt.event.FocusAdapter;
119 import java.awt.event.FocusEvent;
120 import java.awt.event.ItemEvent;
121 import java.awt.event.ItemListener;
122 import java.awt.event.KeyAdapter;
123 import java.awt.event.KeyEvent;
124 import java.awt.event.MouseEvent;
125 import java.awt.print.PageFormat;
126 import java.awt.print.PrinterJob;
127 import java.beans.PropertyChangeEvent;
129 import java.io.FileWriter;
130 import java.io.PrintWriter;
132 import java.util.ArrayList;
133 import java.util.Arrays;
134 import java.util.Deque;
135 import java.util.Enumeration;
136 import java.util.Hashtable;
137 import java.util.List;
138 import java.util.Vector;
140 import javax.swing.ButtonGroup;
141 import javax.swing.JCheckBoxMenuItem;
142 import javax.swing.JEditorPane;
143 import javax.swing.JInternalFrame;
144 import javax.swing.JLayeredPane;
145 import javax.swing.JMenu;
146 import javax.swing.JMenuItem;
147 import javax.swing.JScrollPane;
148 import javax.swing.SwingUtilities;
154 * @version $Revision$
156 public class AlignFrame extends GAlignFrame implements DropTargetListener,
157 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
160 public static final int DEFAULT_WIDTH = 700;
162 public static final int DEFAULT_HEIGHT = 500;
165 * The currently displayed panel (selected tabbed view if more than one)
167 public AlignmentPanel alignPanel;
169 AlignViewport viewport;
171 public AlignViewControllerI avc;
173 List<AlignmentPanel> alignPanels = new ArrayList<>();
176 * Last format used to load or save alignments in this window
178 FileFormatI currentFileFormat = null;
181 * Current filename for this alignment
183 String fileName = null;
186 * Creates a new AlignFrame object with specific width and height.
192 public AlignFrame(AlignmentI al, int width, int height)
194 this(al, null, width, height);
198 * Creates a new AlignFrame object with specific width, height and
204 * @param sequenceSetId
206 public AlignFrame(AlignmentI al, int width, int height,
207 String sequenceSetId)
209 this(al, null, width, height, sequenceSetId);
213 * Creates a new AlignFrame object with specific width, height and
219 * @param sequenceSetId
222 public AlignFrame(AlignmentI al, int width, int height,
223 String sequenceSetId, String viewId)
225 this(al, null, width, height, sequenceSetId, viewId);
229 * new alignment window with hidden columns
233 * @param hiddenColumns
234 * ColumnSelection or null
236 * Width of alignment frame
240 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
243 this(al, hiddenColumns, width, height, null);
247 * Create alignment frame for al with hiddenColumns, a specific width and
248 * height, and specific sequenceId
251 * @param hiddenColumns
254 * @param sequenceSetId
257 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
258 int height, String sequenceSetId)
260 this(al, hiddenColumns, width, height, sequenceSetId, null);
264 * Create alignment frame for al with hiddenColumns, a specific width and
265 * height, and specific sequenceId
268 * @param hiddenColumns
271 * @param sequenceSetId
276 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
277 int height, String sequenceSetId, String viewId)
279 setSize(width, height);
281 if (al.getDataset() == null)
286 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
288 alignPanel = new AlignmentPanel(this, viewport);
290 addAlignmentPanel(alignPanel, true);
294 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
295 HiddenColumns hiddenColumns, int width, int height)
297 setSize(width, height);
299 if (al.getDataset() == null)
304 viewport = new AlignViewport(al, hiddenColumns);
306 if (hiddenSeqs != null && hiddenSeqs.length > 0)
308 viewport.hideSequence(hiddenSeqs);
310 alignPanel = new AlignmentPanel(this, viewport);
311 addAlignmentPanel(alignPanel, true);
316 * Make a new AlignFrame from existing alignmentPanels
323 public AlignFrame(AlignmentPanel ap)
327 addAlignmentPanel(ap, false);
332 * initalise the alignframe from the underlying viewport data and the
337 if (!Jalview.isHeadlessMode())
339 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
342 avc = new jalview.controller.AlignViewController(this, viewport,
344 if (viewport.getAlignmentConservationAnnotation() == null)
346 // BLOSUM62Colour.setEnabled(false);
347 conservationMenuItem.setEnabled(false);
348 modifyConservation.setEnabled(false);
349 // PIDColour.setEnabled(false);
350 // abovePIDThreshold.setEnabled(false);
351 // modifyPID.setEnabled(false);
354 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
357 if (sortby.equals("Id"))
359 sortIDMenuItem_actionPerformed(null);
361 else if (sortby.equals("Pairwise Identity"))
363 sortPairwiseMenuItem_actionPerformed(null);
367 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
369 setMenusFromViewport(viewport);
370 buildSortByAnnotationScoresMenu();
371 calculateTree.addActionListener(new ActionListener()
375 public void actionPerformed(ActionEvent e)
382 if (Desktop.desktop != null)
384 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
385 addServiceListeners();
389 if (viewport.getWrapAlignment())
391 wrapMenuItem_actionPerformed(null);
394 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
396 this.overviewMenuItem_actionPerformed(null);
401 final List<AlignmentPanel> selviews = new ArrayList<>();
402 final List<AlignmentPanel> origview = new ArrayList<>();
403 final String menuLabel = MessageManager
404 .getString("label.copy_format_from");
405 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
406 new ViewSetProvider()
410 public AlignmentPanel[] getAllAlignmentPanels()
413 origview.add(alignPanel);
414 // make an array of all alignment panels except for this one
415 List<AlignmentPanel> aps = new ArrayList<>(
416 Arrays.asList(Desktop.getAlignmentPanels(null)));
417 aps.remove(AlignFrame.this.alignPanel);
418 return aps.toArray(new AlignmentPanel[aps.size()]);
420 }, selviews, new ItemListener()
424 public void itemStateChanged(ItemEvent e)
426 if (origview.size() > 0)
428 final AlignmentPanel ap = origview.get(0);
431 * Copy the ViewStyle of the selected panel to 'this one'.
432 * Don't change value of 'scaleProteinAsCdna' unless copying
435 ViewStyleI vs = selviews.get(0).getAlignViewport()
437 boolean fromSplitFrame = selviews.get(0)
438 .getAlignViewport().getCodingComplement() != null;
441 vs.setScaleProteinAsCdna(ap.getAlignViewport()
442 .getViewStyle().isScaleProteinAsCdna());
444 ap.getAlignViewport().setViewStyle(vs);
447 * Also rescale ViewStyle of SplitFrame complement if there is
448 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
449 * the whole ViewStyle (allow cDNA protein to have different
452 AlignViewportI complement = ap.getAlignViewport()
453 .getCodingComplement();
454 if (complement != null && vs.isScaleProteinAsCdna())
456 AlignFrame af = Desktop.getAlignFrameFor(complement);
457 ((SplitFrame) af.getSplitViewContainer())
459 af.setMenusForViewport();
463 ap.setSelected(true);
464 ap.alignFrame.setMenusForViewport();
469 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
470 .indexOf("devel") > -1
471 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
472 .indexOf("test") > -1)
474 formatMenu.add(vsel);
476 addFocusListener(new FocusAdapter()
479 public void focusGained(FocusEvent e)
481 Jalview.setCurrentAlignFrame(AlignFrame.this);
488 * Change the filename and format for the alignment, and enable the 'reload'
489 * button functionality.
496 public void setFileName(String file, FileFormatI format)
499 setFileFormat(format);
500 reload.setEnabled(true);
504 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
507 void addKeyListener()
509 addKeyListener(new KeyAdapter()
512 public void keyPressed(KeyEvent evt)
514 if (viewport.cursorMode
515 && ((evt.getKeyCode() >= KeyEvent.VK_0
516 && evt.getKeyCode() <= KeyEvent.VK_9)
517 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
518 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
519 && Character.isDigit(evt.getKeyChar()))
521 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
524 switch (evt.getKeyCode())
527 case 27: // escape key
528 deselectAllSequenceMenuItem_actionPerformed(null);
532 case KeyEvent.VK_DOWN:
533 if (evt.isAltDown() || !viewport.cursorMode)
535 moveSelectedSequences(false);
537 if (viewport.cursorMode)
539 alignPanel.getSeqPanel().moveCursor(0, 1,
540 evt.isShiftDown() && !evt.isAltDown());
545 if (evt.isAltDown() || !viewport.cursorMode)
547 moveSelectedSequences(true);
549 if (viewport.cursorMode)
551 alignPanel.getSeqPanel().moveCursor(0, -1,
552 evt.isShiftDown() && !evt.isAltDown());
556 case KeyEvent.VK_LEFT:
557 if (evt.isAltDown() || !viewport.cursorMode)
559 slideSequences(false,
560 alignPanel.getSeqPanel().getKeyboardNo1());
564 alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
569 case KeyEvent.VK_RIGHT:
570 if (evt.isAltDown() || !viewport.cursorMode)
572 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
576 alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
580 case KeyEvent.VK_SPACE:
581 if (viewport.cursorMode)
583 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
584 || evt.isShiftDown() || evt.isAltDown());
588 // case KeyEvent.VK_A:
589 // if (viewport.cursorMode)
591 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
592 // //System.out.println("A");
596 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
597 * System.out.println("closing bracket"); } break;
599 case KeyEvent.VK_DELETE:
600 case KeyEvent.VK_BACK_SPACE:
601 if (!viewport.cursorMode)
603 cut_actionPerformed(null);
607 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
608 || evt.isShiftDown() || evt.isAltDown());
614 if (viewport.cursorMode)
616 alignPanel.getSeqPanel().setCursorRow();
620 if (viewport.cursorMode && !evt.isControlDown())
622 alignPanel.getSeqPanel().setCursorColumn();
626 if (viewport.cursorMode)
628 alignPanel.getSeqPanel().setCursorPosition();
632 case KeyEvent.VK_ENTER:
633 case KeyEvent.VK_COMMA:
634 if (viewport.cursorMode)
636 alignPanel.getSeqPanel().setCursorRowAndColumn();
641 if (viewport.cursorMode)
643 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
647 if (viewport.cursorMode)
649 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
654 viewport.cursorMode = !viewport.cursorMode;
655 statusBar.setText(MessageManager
656 .formatMessage("label.keyboard_editing_mode", new String[]
657 { (viewport.cursorMode ? "on" : "off") }));
658 if (viewport.cursorMode)
660 ViewportRanges ranges = viewport.getRanges();
661 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
663 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
666 alignPanel.getSeqPanel().seqCanvas.repaint();
672 Help.showHelpWindow();
673 } catch (Exception ex)
675 ex.printStackTrace();
680 boolean toggleSeqs = !evt.isControlDown();
681 boolean toggleCols = !evt.isShiftDown();
682 toggleHiddenRegions(toggleSeqs, toggleCols);
687 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
688 boolean modifyExisting = true; // always modify, don't clear
689 // evt.isShiftDown();
690 boolean invertHighlighted = evt.isAltDown();
691 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
695 case KeyEvent.VK_PAGE_UP:
696 viewport.getRanges().pageUp();
698 case KeyEvent.VK_PAGE_DOWN:
699 viewport.getRanges().pageDown();
705 public void keyReleased(KeyEvent evt)
707 switch (evt.getKeyCode())
709 case KeyEvent.VK_LEFT:
710 if (evt.isAltDown() || !viewport.cursorMode)
712 viewport.firePropertyChange("alignment", null,
713 viewport.getAlignment().getSequences());
717 case KeyEvent.VK_RIGHT:
718 if (evt.isAltDown() || !viewport.cursorMode)
720 viewport.firePropertyChange("alignment", null,
721 viewport.getAlignment().getSequences());
729 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
731 ap.alignFrame = this;
732 avc = new jalview.controller.AlignViewController(this, viewport,
737 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
739 int aSize = alignPanels.size();
741 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
743 if (aSize == 1 && ap.av.getViewName() == null)
745 this.getContentPane().add(ap, BorderLayout.CENTER);
751 setInitialTabVisible();
754 expandViews.setEnabled(true);
755 gatherViews.setEnabled(true);
756 tabbedPane.addTab(ap.av.getViewName(), ap);
758 ap.setVisible(false);
763 if (ap.av.isPadGaps())
765 ap.av.getAlignment().padGaps();
767 ap.av.updateConservation(ap);
768 ap.av.updateConsensus(ap);
769 ap.av.updateStrucConsensus(ap);
773 public void setInitialTabVisible()
775 expandViews.setEnabled(true);
776 gatherViews.setEnabled(true);
777 tabbedPane.setVisible(true);
778 AlignmentPanel first = alignPanels.get(0);
779 tabbedPane.addTab(first.av.getViewName(), first);
780 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
783 public AlignViewport getViewport()
788 /* Set up intrinsic listeners for dynamically generated GUI bits. */
789 private void addServiceListeners()
791 final java.beans.PropertyChangeListener thisListener;
792 Desktop.instance.addJalviewPropertyChangeListener("services",
793 thisListener = new java.beans.PropertyChangeListener()
796 public void propertyChange(PropertyChangeEvent evt)
798 // // System.out.println("Discoverer property change.");
799 // if (evt.getPropertyName().equals("services"))
801 SwingUtilities.invokeLater(new Runnable()
808 "Rebuild WS Menu for service change");
809 BuildWebServiceMenu();
816 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
819 public void internalFrameClosed(
820 javax.swing.event.InternalFrameEvent evt)
822 // System.out.println("deregistering discoverer listener");
823 Desktop.instance.removeJalviewPropertyChangeListener("services",
825 closeMenuItem_actionPerformed(true);
828 // Finally, build the menu once to get current service state
829 new Thread(new Runnable()
834 BuildWebServiceMenu();
840 * Configure menu items that vary according to whether the alignment is
841 * nucleotide or protein
843 public void setGUINucleotide()
845 AlignmentI al = getViewport().getAlignment();
846 boolean nucleotide = al.isNucleotide();
848 loadVcf.setVisible(nucleotide);
849 showTranslation.setVisible(nucleotide);
850 showReverse.setVisible(nucleotide);
851 showReverseComplement.setVisible(nucleotide);
852 conservationMenuItem.setEnabled(!nucleotide);
854 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
855 showGroupConservation.setEnabled(!nucleotide);
857 showComplementMenuItem
858 .setText(nucleotide ? MessageManager.getString("label.protein")
859 : MessageManager.getString("label.nucleotide"));
863 * set up menus for the current viewport. This may be called after any
864 * operation that affects the data in the current view (selection changed,
865 * etc) to update the menus to reflect the new state.
868 public void setMenusForViewport()
870 setMenusFromViewport(viewport);
874 * Need to call this method when tabs are selected for multiple views, or when
875 * loading from Jalview2XML.java
880 public void setMenusFromViewport(AlignViewport av)
882 padGapsMenuitem.setSelected(av.isPadGaps());
883 colourTextMenuItem.setSelected(av.isShowColourText());
884 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
885 modifyPID.setEnabled(abovePIDThreshold.isSelected());
886 conservationMenuItem.setSelected(av.getConservationSelected());
887 modifyConservation.setEnabled(conservationMenuItem.isSelected());
888 seqLimits.setSelected(av.getShowJVSuffix());
889 idRightAlign.setSelected(av.isRightAlignIds());
890 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
891 renderGapsMenuItem.setSelected(av.isRenderGaps());
892 wrapMenuItem.setSelected(av.getWrapAlignment());
893 scaleAbove.setVisible(av.getWrapAlignment());
894 scaleLeft.setVisible(av.getWrapAlignment());
895 scaleRight.setVisible(av.getWrapAlignment());
896 annotationPanelMenuItem.setState(av.isShowAnnotation());
898 * Show/hide annotations only enabled if annotation panel is shown
900 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
901 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
902 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
903 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
904 viewBoxesMenuItem.setSelected(av.getShowBoxes());
905 viewTextMenuItem.setSelected(av.getShowText());
906 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
907 showGroupConsensus.setSelected(av.isShowGroupConsensus());
908 showGroupConservation.setSelected(av.isShowGroupConservation());
909 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
910 showSequenceLogo.setSelected(av.isShowSequenceLogo());
911 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
913 ColourMenuHelper.setColourSelected(colourMenu,
914 av.getGlobalColourScheme());
916 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
917 hiddenMarkers.setState(av.getShowHiddenMarkers());
918 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
919 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
920 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
921 autoCalculate.setSelected(av.autoCalculateConsensus);
922 sortByTree.setSelected(av.sortByTree);
923 listenToViewSelections.setSelected(av.followSelection);
925 showProducts.setEnabled(canShowProducts());
926 setGroovyEnabled(Desktop.getGroovyConsole() != null);
932 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
936 public void setGroovyEnabled(boolean b)
938 runGroovy.setEnabled(b);
941 private IProgressIndicator progressBar;
946 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
949 public void setProgressBar(String message, long id)
951 progressBar.setProgressBar(message, id);
955 public void registerHandler(final long id,
956 final IProgressIndicatorHandler handler)
958 progressBar.registerHandler(id, handler);
963 * @return true if any progress bars are still active
966 public boolean operationInProgress()
968 return progressBar.operationInProgress();
972 * Sets the text of the status bar. Note that setting a null or empty value
973 * will cause the status bar to be hidden, with possibly undesirable flicker
974 * of the screen layout.
977 public void setStatus(String text)
979 statusBar.setText(text == null || text.isEmpty() ? " " : text);
983 * Added so Castor Mapping file can obtain Jalview Version
985 public String getVersion()
987 return jalview.bin.Cache.getProperty("VERSION");
990 public FeatureRenderer getFeatureRenderer()
992 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
996 public void fetchSequence_actionPerformed(ActionEvent e)
998 new jalview.gui.SequenceFetcher(this);
1002 public void addFromFile_actionPerformed(ActionEvent e)
1004 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1008 public void reload_actionPerformed(ActionEvent e)
1010 if (fileName != null)
1012 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1013 // originating file's format
1014 // TODO: work out how to recover feature settings for correct view(s) when
1015 // file is reloaded.
1016 if (FileFormat.Jalview.equals(currentFileFormat))
1018 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1019 for (int i = 0; i < frames.length; i++)
1021 if (frames[i] instanceof AlignFrame && frames[i] != this
1022 && ((AlignFrame) frames[i]).fileName != null
1023 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1027 frames[i].setSelected(true);
1028 Desktop.instance.closeAssociatedWindows();
1029 } catch (java.beans.PropertyVetoException ex)
1035 Desktop.instance.closeAssociatedWindows();
1037 FileLoader loader = new FileLoader();
1038 DataSourceType protocol = fileName.startsWith("http:")
1039 ? DataSourceType.URL
1040 : DataSourceType.FILE;
1041 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1045 Rectangle bounds = this.getBounds();
1047 FileLoader loader = new FileLoader();
1048 DataSourceType protocol = fileName.startsWith("http:")
1049 ? DataSourceType.URL
1050 : DataSourceType.FILE;
1051 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1052 protocol, currentFileFormat);
1054 newframe.setBounds(bounds);
1055 if (featureSettings != null && featureSettings.isShowing())
1057 final Rectangle fspos = featureSettings.frame.getBounds();
1058 // TODO: need a 'show feature settings' function that takes bounds -
1059 // need to refactor Desktop.addFrame
1060 newframe.featureSettings_actionPerformed(null);
1061 final FeatureSettings nfs = newframe.featureSettings;
1062 SwingUtilities.invokeLater(new Runnable()
1067 nfs.frame.setBounds(fspos);
1070 this.featureSettings.close();
1071 this.featureSettings = null;
1073 this.closeMenuItem_actionPerformed(true);
1079 public void addFromText_actionPerformed(ActionEvent e)
1082 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1086 public void addFromURL_actionPerformed(ActionEvent e)
1088 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1092 public void save_actionPerformed(ActionEvent e)
1094 if (fileName == null || (currentFileFormat == null)
1095 || fileName.startsWith("http"))
1097 saveAs_actionPerformed(null);
1101 saveAlignment(fileName, currentFileFormat);
1112 public void saveAs_actionPerformed(ActionEvent e)
1114 String format = currentFileFormat == null ? null
1115 : currentFileFormat.getName();
1116 JalviewFileChooser chooser = JalviewFileChooser
1117 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1119 chooser.setFileView(new JalviewFileView());
1120 chooser.setDialogTitle(
1121 MessageManager.getString("label.save_alignment_to_file"));
1122 chooser.setToolTipText(MessageManager.getString("action.save"));
1124 int value = chooser.showSaveDialog(this);
1126 if (value == JalviewFileChooser.APPROVE_OPTION)
1128 currentFileFormat = chooser.getSelectedFormat();
1129 while (currentFileFormat == null)
1131 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1132 MessageManager.getString(
1133 "label.select_file_format_before_saving"),
1134 MessageManager.getString("label.file_format_not_specified"),
1135 JvOptionPane.WARNING_MESSAGE);
1136 currentFileFormat = chooser.getSelectedFormat();
1137 value = chooser.showSaveDialog(this);
1138 if (value != JalviewFileChooser.APPROVE_OPTION)
1144 fileName = chooser.getSelectedFile().getPath();
1146 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1148 Cache.setProperty("LAST_DIRECTORY", fileName);
1149 saveAlignment(fileName, currentFileFormat);
1153 public boolean saveAlignment(String file, FileFormatI format)
1155 boolean success = true;
1157 if (FileFormat.Jalview.equals(format))
1159 String shortName = title;
1161 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1163 shortName = shortName.substring(
1164 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1167 success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1170 statusBar.setText(MessageManager.formatMessage(
1171 "label.successfully_saved_to_file_in_format", new Object[]
1172 { fileName, format }));
1177 AlignmentExportData exportData = getAlignmentForExport(format,
1179 if (exportData.getSettings().isCancelled())
1183 FormatAdapter f = new FormatAdapter(alignPanel,
1184 exportData.getSettings());
1185 String output = f.formatSequences(format, exportData.getAlignment(), // class
1189 // occur in the distant future
1190 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1191 f.getCacheSuffixDefault(format),
1192 viewport.getAlignment().getHiddenColumns());
1200 // create backupfiles object and get new temp filename destination
1201 BackupFiles backupfiles = new BackupFiles(file);
1205 PrintWriter out = new PrintWriter(
1206 new FileWriter(backupfiles.getTempFilePath()));
1210 this.setTitle(file);
1211 statusBar.setText(MessageManager.formatMessage(
1212 "label.successfully_saved_to_file_in_format", new Object[]
1213 { fileName, format.getName() }));
1214 } catch (Exception ex)
1217 ex.printStackTrace();
1220 backupfiles.setWriteSuccess(success);
1221 // do the backup file roll and rename the temp file to actual file
1222 success = backupfiles.rollBackupsAndRenameTempFile();
1229 JvOptionPane.showInternalMessageDialog(this, MessageManager
1230 .formatMessage("label.couldnt_save_file", new Object[]
1232 MessageManager.getString("label.error_saving_file"),
1233 JvOptionPane.WARNING_MESSAGE);
1239 private void warningMessage(String warning, String title)
1241 if (new jalview.util.Platform().isHeadless())
1243 System.err.println("Warning: " + title + "\nWarning: " + warning);
1248 JvOptionPane.showInternalMessageDialog(this, warning, title,
1249 JvOptionPane.WARNING_MESSAGE);
1261 protected void outputText_actionPerformed(ActionEvent e)
1263 FileFormatI fileFormat = FileFormats.getInstance()
1264 .forName(e.getActionCommand());
1265 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1267 if (exportData.getSettings().isCancelled())
1271 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1272 cap.setForInput(null);
1275 FileFormatI format = fileFormat;
1276 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1277 .formatSequences(format, exportData.getAlignment(),
1278 exportData.getOmitHidden(),
1279 exportData.getStartEndPostions(),
1280 viewport.getAlignment().getHiddenColumns()));
1281 Desktop.addInternalFrame(cap, MessageManager
1282 .formatMessage("label.alignment_output_command", new Object[]
1283 { e.getActionCommand() }), 600, 500);
1284 } catch (OutOfMemoryError oom)
1286 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1293 public static AlignmentExportData getAlignmentForExport(
1294 FileFormatI format, AlignViewportI viewport,
1295 AlignExportSettingI exportSettings)
1297 AlignmentI alignmentToExport = null;
1298 AlignExportSettingI settings = exportSettings;
1299 String[] omitHidden = null;
1301 HiddenSequences hiddenSeqs = viewport.getAlignment()
1302 .getHiddenSequences();
1304 alignmentToExport = viewport.getAlignment();
1306 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1307 if (settings == null)
1309 settings = new AlignExportSettings(hasHiddenSeqs,
1310 viewport.hasHiddenColumns(), format);
1312 // settings.isExportAnnotations();
1314 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1316 omitHidden = viewport.getViewAsString(false,
1317 settings.isExportHiddenSequences());
1320 int[] alignmentStartEnd = new int[2];
1321 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1323 alignmentToExport = hiddenSeqs.getFullAlignment();
1327 alignmentToExport = viewport.getAlignment();
1329 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1330 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1331 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1332 omitHidden, alignmentStartEnd, settings);
1343 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1345 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1346 htmlSVG.exportHTML(null);
1350 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1352 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1353 bjs.exportHTML(null);
1356 public void createImageMap(File file, String image)
1358 alignPanel.makePNGImageMap(file, image);
1368 public void createPNG(File f)
1370 alignPanel.makePNG(f);
1380 public void createEPS(File f)
1382 alignPanel.makeEPS(f);
1386 public void createSVG(File f)
1388 alignPanel.makeSVG(f);
1392 public void pageSetup_actionPerformed(ActionEvent e)
1394 PrinterJob printJob = PrinterJob.getPrinterJob();
1395 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1405 public void printMenuItem_actionPerformed(ActionEvent e)
1407 // Putting in a thread avoids Swing painting problems
1408 PrintThread thread = new PrintThread(alignPanel);
1413 public void exportFeatures_actionPerformed(ActionEvent e)
1415 new AnnotationExporter(alignPanel).exportFeatures();
1419 public void exportAnnotations_actionPerformed(ActionEvent e)
1421 new AnnotationExporter(alignPanel).exportAnnotations();
1425 public void associatedData_actionPerformed(ActionEvent e)
1427 // Pick the tree file
1428 JalviewFileChooser chooser = new JalviewFileChooser(
1429 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1430 chooser.setFileView(new JalviewFileView());
1431 chooser.setDialogTitle(
1432 MessageManager.getString("label.load_jalview_annotations"));
1433 chooser.setToolTipText(
1434 MessageManager.getString("label.load_jalview_annotations"));
1436 int value = chooser.showOpenDialog(null);
1438 if (value == JalviewFileChooser.APPROVE_OPTION)
1440 String choice = chooser.getSelectedFile().getPath();
1441 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1442 loadJalviewDataFile(choice, null, null, null);
1448 * Close the current view or all views in the alignment frame. If the frame
1449 * only contains one view then the alignment will be removed from memory.
1451 * @param closeAllTabs
1454 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1456 if (alignPanels != null && alignPanels.size() < 2)
1458 closeAllTabs = true;
1463 if (alignPanels != null)
1467 if (this.isClosed())
1469 // really close all the windows - otherwise wait till
1470 // setClosed(true) is called
1471 for (int i = 0; i < alignPanels.size(); i++)
1473 AlignmentPanel ap = alignPanels.get(i);
1480 closeView(alignPanel);
1485 if (featureSettings != null && featureSettings.isOpen())
1487 featureSettings.close();
1488 featureSettings = null;
1491 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1492 * be called recursively, with the frame now in 'closed' state
1494 this.setClosed(true);
1496 } catch (Exception ex)
1498 ex.printStackTrace();
1503 * Close the specified panel and close up tabs appropriately.
1505 * @param panelToClose
1507 public void closeView(AlignmentPanel panelToClose)
1509 int index = tabbedPane.getSelectedIndex();
1510 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1511 alignPanels.remove(panelToClose);
1512 panelToClose.closePanel();
1513 panelToClose = null;
1515 tabbedPane.removeTabAt(closedindex);
1516 tabbedPane.validate();
1518 if (index > closedindex || index == tabbedPane.getTabCount())
1520 // modify currently selected tab index if necessary.
1524 this.tabSelectionChanged(index);
1530 void updateEditMenuBar()
1533 if (viewport.getHistoryList().size() > 0)
1535 undoMenuItem.setEnabled(true);
1536 CommandI command = viewport.getHistoryList().peek();
1537 undoMenuItem.setText(MessageManager
1538 .formatMessage("label.undo_command", new Object[]
1539 { command.getDescription() }));
1543 undoMenuItem.setEnabled(false);
1544 undoMenuItem.setText(MessageManager.getString("action.undo"));
1547 if (viewport.getRedoList().size() > 0)
1549 redoMenuItem.setEnabled(true);
1551 CommandI command = viewport.getRedoList().peek();
1552 redoMenuItem.setText(MessageManager
1553 .formatMessage("label.redo_command", new Object[]
1554 { command.getDescription() }));
1558 redoMenuItem.setEnabled(false);
1559 redoMenuItem.setText(MessageManager.getString("action.redo"));
1564 public void addHistoryItem(CommandI command)
1566 if (command.getSize() > 0)
1568 viewport.addToHistoryList(command);
1569 viewport.clearRedoList();
1570 updateEditMenuBar();
1571 viewport.updateHiddenColumns();
1572 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1573 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1574 // viewport.getColumnSelection()
1575 // .getHiddenColumns().size() > 0);
1581 * @return alignment objects for all views
1583 AlignmentI[] getViewAlignments()
1585 if (alignPanels != null)
1587 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1589 for (AlignmentPanel ap : alignPanels)
1591 als[i++] = ap.av.getAlignment();
1595 if (viewport != null)
1597 return new AlignmentI[] { viewport.getAlignment() };
1609 protected void undoMenuItem_actionPerformed(ActionEvent e)
1611 if (viewport.getHistoryList().isEmpty())
1615 CommandI command = viewport.getHistoryList().pop();
1616 viewport.addToRedoList(command);
1617 command.undoCommand(getViewAlignments());
1619 AlignmentViewport originalSource = getOriginatingSource(command);
1620 updateEditMenuBar();
1622 if (originalSource != null)
1624 if (originalSource != viewport)
1627 "Implementation worry: mismatch of viewport origin for undo");
1629 originalSource.updateHiddenColumns();
1630 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1632 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1633 // viewport.getColumnSelection()
1634 // .getHiddenColumns().size() > 0);
1635 originalSource.firePropertyChange("alignment", null,
1636 originalSource.getAlignment().getSequences());
1647 protected void redoMenuItem_actionPerformed(ActionEvent e)
1649 if (viewport.getRedoList().size() < 1)
1654 CommandI command = viewport.getRedoList().pop();
1655 viewport.addToHistoryList(command);
1656 command.doCommand(getViewAlignments());
1658 AlignmentViewport originalSource = getOriginatingSource(command);
1659 updateEditMenuBar();
1661 if (originalSource != null)
1664 if (originalSource != viewport)
1667 "Implementation worry: mismatch of viewport origin for redo");
1669 originalSource.updateHiddenColumns();
1670 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1672 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1673 // viewport.getColumnSelection()
1674 // .getHiddenColumns().size() > 0);
1675 originalSource.firePropertyChange("alignment", null,
1676 originalSource.getAlignment().getSequences());
1680 AlignmentViewport getOriginatingSource(CommandI command)
1682 AlignmentViewport originalSource = null;
1683 // For sequence removal and addition, we need to fire
1684 // the property change event FROM the viewport where the
1685 // original alignment was altered
1686 AlignmentI al = null;
1687 if (command instanceof EditCommand)
1689 EditCommand editCommand = (EditCommand) command;
1690 al = editCommand.getAlignment();
1691 List<Component> comps = PaintRefresher.components
1692 .get(viewport.getSequenceSetId());
1694 for (Component comp : comps)
1696 if (comp instanceof AlignmentPanel)
1698 if (al == ((AlignmentPanel) comp).av.getAlignment())
1700 originalSource = ((AlignmentPanel) comp).av;
1707 if (originalSource == null)
1709 // The original view is closed, we must validate
1710 // the current view against the closed view first
1713 PaintRefresher.validateSequences(al, viewport.getAlignment());
1716 originalSource = viewport;
1719 return originalSource;
1728 public void moveSelectedSequences(boolean up)
1730 SequenceGroup sg = viewport.getSelectionGroup();
1736 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1737 viewport.getHiddenRepSequences(), up);
1738 alignPanel.paintAlignment(true, false);
1741 synchronized void slideSequences(boolean right, int size)
1743 List<SequenceI> sg = new ArrayList<>();
1744 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup()
1745 .getSize() != viewport.getAlignment().getHeight())
1747 sg = viewport.getSelectionGroup()
1748 .getSequences(viewport.getHiddenRepSequences());
1751 if (sg.size() == 0 && viewport.cursorMode)
1753 sg.add(viewport.getAlignment()
1754 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1762 List<SequenceI> invertGroup = new ArrayList<>();
1764 for (SequenceI seq : viewport.getAlignment().getSequences())
1766 if (!sg.contains(seq))
1768 invertGroup.add(seq);
1772 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1774 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1775 for (int i = 0; i < invertGroup.size(); i++)
1777 seqs2[i] = invertGroup.get(i);
1780 SlideSequencesCommand ssc;
1783 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1784 viewport.getGapCharacter());
1788 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1789 viewport.getGapCharacter());
1792 int groupAdjustment = 0;
1793 if (ssc.getGapsInsertedBegin() && right)
1795 if (viewport.cursorMode)
1797 alignPanel.getSeqPanel().moveCursor(size, 0);
1801 groupAdjustment = size;
1804 else if (!ssc.getGapsInsertedBegin() && !right)
1806 if (viewport.cursorMode)
1808 alignPanel.getSeqPanel().moveCursor(-size, 0);
1812 groupAdjustment = -size;
1816 if (groupAdjustment != 0)
1818 viewport.getSelectionGroup().setStartRes(
1819 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1820 viewport.getSelectionGroup().setEndRes(
1821 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1825 * just extend the last slide command if compatible; but not if in
1826 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1828 boolean appendHistoryItem = false;
1829 Deque<CommandI> historyList = viewport.getHistoryList();
1830 boolean inSplitFrame = getSplitViewContainer() != null;
1831 if (!inSplitFrame && historyList != null && historyList.size() > 0
1832 && historyList.peek() instanceof SlideSequencesCommand)
1834 appendHistoryItem = ssc.appendSlideCommand(
1835 (SlideSequencesCommand) historyList.peek());
1838 if (!appendHistoryItem)
1840 addHistoryItem(ssc);
1853 protected void copy_actionPerformed(ActionEvent e)
1855 if (viewport.getSelectionGroup() == null)
1859 // TODO: preserve the ordering of displayed alignment annotation in any
1860 // internal paste (particularly sequence associated annotation)
1861 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1862 String[] omitHidden = null;
1864 if (viewport.hasHiddenColumns())
1866 omitHidden = viewport.getViewAsString(true);
1869 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1870 seqs, omitHidden, null);
1872 StringSelection ss = new StringSelection(output);
1876 jalview.gui.Desktop.internalCopy = true;
1877 // Its really worth setting the clipboard contents
1878 // to empty before setting the large StringSelection!!
1879 Toolkit.getDefaultToolkit().getSystemClipboard()
1880 .setContents(new StringSelection(""), null);
1882 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1884 } catch (OutOfMemoryError er)
1886 new OOMWarning("copying region", er);
1890 HiddenColumns hiddenColumns = null;
1891 if (viewport.hasHiddenColumns())
1893 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1894 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1896 // create new HiddenColumns object with copy of hidden regions
1897 // between startRes and endRes, offset by startRes
1898 hiddenColumns = new HiddenColumns(
1899 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1900 hiddenCutoff, hiddenOffset);
1903 Desktop.jalviewClipboard = new Object[] { seqs,
1904 viewport.getAlignment().getDataset(), hiddenColumns };
1905 statusBar.setText(MessageManager.formatMessage(
1906 "label.copied_sequences_to_clipboard", new Object[]
1907 { Integer.valueOf(seqs.length).toString() }));
1917 protected void pasteNew_actionPerformed(ActionEvent e)
1929 protected void pasteThis_actionPerformed(ActionEvent e)
1935 * Paste contents of Jalview clipboard
1937 * @param newAlignment
1938 * true to paste to a new alignment, otherwise add to this.
1940 void paste(boolean newAlignment)
1942 boolean externalPaste = true;
1945 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1946 Transferable contents = c.getContents(this);
1948 if (contents == null)
1957 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1958 if (str.length() < 1)
1963 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1965 } catch (OutOfMemoryError er)
1967 new OOMWarning("Out of memory pasting sequences!!", er);
1971 SequenceI[] sequences;
1972 boolean annotationAdded = false;
1973 AlignmentI alignment = null;
1975 if (Desktop.jalviewClipboard != null)
1977 // The clipboard was filled from within Jalview, we must use the
1979 // And dataset from the copied alignment
1980 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1981 // be doubly sure that we create *new* sequence objects.
1982 sequences = new SequenceI[newseq.length];
1983 for (int i = 0; i < newseq.length; i++)
1985 sequences[i] = new Sequence(newseq[i]);
1987 alignment = new Alignment(sequences);
1988 externalPaste = false;
1992 // parse the clipboard as an alignment.
1993 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1995 sequences = alignment.getSequencesArray();
1999 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2005 if (Desktop.jalviewClipboard != null)
2007 // dataset is inherited
2008 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2012 // new dataset is constructed
2013 alignment.setDataset(null);
2015 alwidth = alignment.getWidth() + 1;
2019 AlignmentI pastedal = alignment; // preserve pasted alignment object
2020 // Add pasted sequences and dataset into existing alignment.
2021 alignment = viewport.getAlignment();
2022 alwidth = alignment.getWidth() + 1;
2023 // decide if we need to import sequences from an existing dataset
2024 boolean importDs = Desktop.jalviewClipboard != null
2025 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2026 // importDs==true instructs us to copy over new dataset sequences from
2027 // an existing alignment
2028 Vector newDs = (importDs) ? new Vector() : null; // used to create
2029 // minimum dataset set
2031 for (int i = 0; i < sequences.length; i++)
2035 newDs.addElement(null);
2037 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2039 if (importDs && ds != null)
2041 if (!newDs.contains(ds))
2043 newDs.setElementAt(ds, i);
2044 ds = new Sequence(ds);
2045 // update with new dataset sequence
2046 sequences[i].setDatasetSequence(ds);
2050 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2055 // copy and derive new dataset sequence
2056 sequences[i] = sequences[i].deriveSequence();
2057 alignment.getDataset()
2058 .addSequence(sequences[i].getDatasetSequence());
2059 // TODO: avoid creation of duplicate dataset sequences with a
2060 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2062 alignment.addSequence(sequences[i]); // merges dataset
2066 newDs.clear(); // tidy up
2068 if (alignment.getAlignmentAnnotation() != null)
2070 for (AlignmentAnnotation alan : alignment
2071 .getAlignmentAnnotation())
2073 if (alan.graphGroup > fgroup)
2075 fgroup = alan.graphGroup;
2079 if (pastedal.getAlignmentAnnotation() != null)
2081 // Add any annotation attached to alignment.
2082 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2083 for (int i = 0; i < alann.length; i++)
2085 annotationAdded = true;
2086 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2088 AlignmentAnnotation newann = new AlignmentAnnotation(
2090 if (newann.graphGroup > -1)
2092 if (newGraphGroups.size() <= newann.graphGroup
2093 || newGraphGroups.get(newann.graphGroup) == null)
2095 for (int q = newGraphGroups
2096 .size(); q <= newann.graphGroup; q++)
2098 newGraphGroups.add(q, null);
2100 newGraphGroups.set(newann.graphGroup,
2101 Integer.valueOf(++fgroup));
2103 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2107 newann.padAnnotation(alwidth);
2108 alignment.addAnnotation(newann);
2118 addHistoryItem(new EditCommand(
2119 MessageManager.getString("label.add_sequences"),
2120 Action.PASTE, sequences, 0, alignment.getWidth(),
2123 // Add any annotations attached to sequences
2124 for (int i = 0; i < sequences.length; i++)
2126 if (sequences[i].getAnnotation() != null)
2128 AlignmentAnnotation newann;
2129 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2131 annotationAdded = true;
2132 newann = sequences[i].getAnnotation()[a];
2133 newann.adjustForAlignment();
2134 newann.padAnnotation(alwidth);
2135 if (newann.graphGroup > -1)
2137 if (newann.graphGroup > -1)
2139 if (newGraphGroups.size() <= newann.graphGroup
2140 || newGraphGroups.get(newann.graphGroup) == null)
2142 for (int q = newGraphGroups
2143 .size(); q <= newann.graphGroup; q++)
2145 newGraphGroups.add(q, null);
2147 newGraphGroups.set(newann.graphGroup,
2148 Integer.valueOf(++fgroup));
2150 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2154 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2158 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2166 // propagate alignment changed.
2167 viewport.getRanges().setEndSeq(alignment.getHeight());
2168 if (annotationAdded)
2170 // Duplicate sequence annotation in all views.
2171 AlignmentI[] alview = this.getViewAlignments();
2172 for (int i = 0; i < sequences.length; i++)
2174 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2179 for (int avnum = 0; avnum < alview.length; avnum++)
2181 if (alview[avnum] != alignment)
2183 // duplicate in a view other than the one with input focus
2184 int avwidth = alview[avnum].getWidth() + 1;
2185 // this relies on sann being preserved after we
2186 // modify the sequence's annotation array for each duplication
2187 for (int a = 0; a < sann.length; a++)
2189 AlignmentAnnotation newann = new AlignmentAnnotation(
2191 sequences[i].addAlignmentAnnotation(newann);
2192 newann.padAnnotation(avwidth);
2193 alview[avnum].addAnnotation(newann); // annotation was
2194 // duplicated earlier
2195 // TODO JAL-1145 graphGroups are not updated for sequence
2196 // annotation added to several views. This may cause
2198 alview[avnum].setAnnotationIndex(newann, a);
2203 buildSortByAnnotationScoresMenu();
2205 viewport.firePropertyChange("alignment", null,
2206 alignment.getSequences());
2207 if (alignPanels != null)
2209 for (AlignmentPanel ap : alignPanels)
2211 ap.validateAnnotationDimensions(false);
2216 alignPanel.validateAnnotationDimensions(false);
2222 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2224 String newtitle = new String("Copied sequences");
2226 if (Desktop.jalviewClipboard != null
2227 && Desktop.jalviewClipboard[2] != null)
2229 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2230 af.viewport.setHiddenColumns(hc);
2233 // >>>This is a fix for the moment, until a better solution is
2235 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2236 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2237 .getFeatureRenderer());
2239 // TODO: maintain provenance of an alignment, rather than just make the
2240 // title a concatenation of operations.
2243 if (title.startsWith("Copied sequences"))
2249 newtitle = newtitle.concat("- from " + title);
2254 newtitle = new String("Pasted sequences");
2257 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2262 } catch (Exception ex)
2264 ex.printStackTrace();
2265 System.out.println("Exception whilst pasting: " + ex);
2266 // could be anything being pasted in here
2272 protected void expand_newalign(ActionEvent e)
2276 AlignmentI alignment = AlignmentUtils
2277 .expandContext(getViewport().getAlignment(), -1);
2278 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2280 String newtitle = new String("Flanking alignment");
2282 if (Desktop.jalviewClipboard != null
2283 && Desktop.jalviewClipboard[2] != null)
2285 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2286 af.viewport.setHiddenColumns(hc);
2289 // >>>This is a fix for the moment, until a better solution is
2291 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2292 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2293 .getFeatureRenderer());
2295 // TODO: maintain provenance of an alignment, rather than just make the
2296 // title a concatenation of operations.
2298 if (title.startsWith("Copied sequences"))
2304 newtitle = newtitle.concat("- from " + title);
2308 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2310 } catch (Exception ex)
2312 ex.printStackTrace();
2313 System.out.println("Exception whilst pasting: " + ex);
2314 // could be anything being pasted in here
2315 } catch (OutOfMemoryError oom)
2317 new OOMWarning("Viewing flanking region of alignment", oom);
2328 protected void cut_actionPerformed(ActionEvent e)
2330 copy_actionPerformed(null);
2331 delete_actionPerformed(null);
2341 protected void delete_actionPerformed(ActionEvent evt)
2344 SequenceGroup sg = viewport.getSelectionGroup();
2351 * If the cut affects all sequences, warn, remove highlighted columns
2353 if (sg.getSize() == viewport.getAlignment().getHeight())
2355 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2356 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2357 if (isEntireAlignWidth)
2359 int confirm = JvOptionPane.showConfirmDialog(this,
2360 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2361 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2362 JvOptionPane.OK_CANCEL_OPTION);
2364 if (confirm == JvOptionPane.CANCEL_OPTION
2365 || confirm == JvOptionPane.CLOSED_OPTION)
2370 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2371 sg.getEndRes() + 1);
2373 SequenceI[] cut = sg.getSequences()
2374 .toArray(new SequenceI[sg.getSize()]);
2376 addHistoryItem(new EditCommand(
2377 MessageManager.getString("label.cut_sequences"), Action.CUT,
2378 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2379 viewport.getAlignment()));
2381 viewport.setSelectionGroup(null);
2382 viewport.sendSelection();
2383 viewport.getAlignment().deleteGroup(sg);
2385 viewport.firePropertyChange("alignment", null,
2386 viewport.getAlignment().getSequences());
2387 if (viewport.getAlignment().getHeight() < 1)
2391 this.setClosed(true);
2392 } catch (Exception ex)
2405 protected void deleteGroups_actionPerformed(ActionEvent e)
2407 if (avc.deleteGroups())
2409 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2410 alignPanel.updateAnnotation();
2411 alignPanel.paintAlignment(true, true);
2422 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2424 SequenceGroup sg = new SequenceGroup(
2425 viewport.getAlignment().getSequences());
2427 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2428 viewport.setSelectionGroup(sg);
2429 viewport.isSelectionGroupChanged(true);
2430 viewport.sendSelection();
2431 // JAL-2034 - should delegate to
2432 // alignPanel to decide if overview needs
2434 alignPanel.paintAlignment(false, false);
2435 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2445 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2447 if (viewport.cursorMode)
2449 alignPanel.getSeqPanel().keyboardNo1 = null;
2450 alignPanel.getSeqPanel().keyboardNo2 = null;
2452 viewport.setSelectionGroup(null);
2453 viewport.getColumnSelection().clear();
2454 viewport.setSearchResults(null);
2455 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2456 // JAL-2034 - should delegate to
2457 // alignPanel to decide if overview needs
2459 alignPanel.paintAlignment(false, false);
2460 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2461 viewport.sendSelection();
2471 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2473 SequenceGroup sg = viewport.getSelectionGroup();
2477 selectAllSequenceMenuItem_actionPerformed(null);
2482 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2484 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2486 // JAL-2034 - should delegate to
2487 // alignPanel to decide if overview needs
2490 alignPanel.paintAlignment(true, false);
2491 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2492 viewport.sendSelection();
2496 public void invertColSel_actionPerformed(ActionEvent e)
2498 viewport.invertColumnSelection();
2499 alignPanel.paintAlignment(true, false);
2500 viewport.sendSelection();
2510 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2512 trimAlignment(true);
2522 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2524 trimAlignment(false);
2527 void trimAlignment(boolean trimLeft)
2529 ColumnSelection colSel = viewport.getColumnSelection();
2532 if (!colSel.isEmpty())
2536 column = colSel.getMin();
2540 column = colSel.getMax();
2544 if (viewport.getSelectionGroup() != null)
2546 seqs = viewport.getSelectionGroup()
2547 .getSequencesAsArray(viewport.getHiddenRepSequences());
2551 seqs = viewport.getAlignment().getSequencesArray();
2554 TrimRegionCommand trimRegion;
2557 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2558 column, viewport.getAlignment());
2559 viewport.getRanges().setStartRes(0);
2563 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2564 column, viewport.getAlignment());
2567 statusBar.setText(MessageManager
2568 .formatMessage("label.removed_columns", new String[]
2569 { Integer.valueOf(trimRegion.getSize()).toString() }));
2571 addHistoryItem(trimRegion);
2573 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2575 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2576 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2578 viewport.getAlignment().deleteGroup(sg);
2582 viewport.firePropertyChange("alignment", null,
2583 viewport.getAlignment().getSequences());
2594 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2596 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2599 if (viewport.getSelectionGroup() != null)
2601 seqs = viewport.getSelectionGroup()
2602 .getSequencesAsArray(viewport.getHiddenRepSequences());
2603 start = viewport.getSelectionGroup().getStartRes();
2604 end = viewport.getSelectionGroup().getEndRes();
2608 seqs = viewport.getAlignment().getSequencesArray();
2611 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2612 "Remove Gapped Columns", seqs, start, end,
2613 viewport.getAlignment());
2615 addHistoryItem(removeGapCols);
2617 statusBar.setText(MessageManager
2618 .formatMessage("label.removed_empty_columns", new Object[]
2619 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2621 // This is to maintain viewport position on first residue
2622 // of first sequence
2623 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2624 ViewportRanges ranges = viewport.getRanges();
2625 int startRes = seq.findPosition(ranges.getStartRes());
2626 // ShiftList shifts;
2627 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2628 // edit.alColumnChanges=shifts.getInverse();
2629 // if (viewport.hasHiddenColumns)
2630 // viewport.getColumnSelection().compensateForEdits(shifts);
2631 ranges.setStartRes(seq.findIndex(startRes) - 1);
2632 viewport.firePropertyChange("alignment", null,
2633 viewport.getAlignment().getSequences());
2644 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2646 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2649 if (viewport.getSelectionGroup() != null)
2651 seqs = viewport.getSelectionGroup()
2652 .getSequencesAsArray(viewport.getHiddenRepSequences());
2653 start = viewport.getSelectionGroup().getStartRes();
2654 end = viewport.getSelectionGroup().getEndRes();
2658 seqs = viewport.getAlignment().getSequencesArray();
2661 // This is to maintain viewport position on first residue
2662 // of first sequence
2663 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2664 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2666 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2667 viewport.getAlignment()));
2669 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2671 viewport.firePropertyChange("alignment", null,
2672 viewport.getAlignment().getSequences());
2683 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2685 viewport.setPadGaps(padGapsMenuitem.isSelected());
2686 viewport.firePropertyChange("alignment", null,
2687 viewport.getAlignment().getSequences());
2697 public void findMenuItem_actionPerformed(ActionEvent e)
2703 * Create a new view of the current alignment.
2706 public void newView_actionPerformed(ActionEvent e)
2708 newView(null, true);
2712 * Creates and shows a new view of the current alignment.
2715 * title of newly created view; if null, one will be generated
2716 * @param copyAnnotation
2717 * if true then duplicate all annnotation, groups and settings
2718 * @return new alignment panel, already displayed.
2720 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2723 * Create a new AlignmentPanel (with its own, new Viewport)
2725 AlignmentPanel newap = new jalview.project.Jalview2XML()
2726 .copyAlignPanel(alignPanel);
2727 if (!copyAnnotation)
2730 * remove all groups and annotation except for the automatic stuff
2732 newap.av.getAlignment().deleteAllGroups();
2733 newap.av.getAlignment().deleteAllAnnotations(false);
2736 newap.av.setGatherViewsHere(false);
2738 if (viewport.getViewName() == null)
2740 viewport.setViewName(MessageManager
2741 .getString("label.view_name_original"));
2745 * Views share the same edits undo and redo stacks
2747 newap.av.setHistoryList(viewport.getHistoryList());
2748 newap.av.setRedoList(viewport.getRedoList());
2751 * copy any visualisation settings that are not saved in the project
2753 newap.av.setColourAppliesToAllGroups(
2754 viewport.getColourAppliesToAllGroups());
2757 * Views share the same mappings; need to deregister any new mappings
2758 * created by copyAlignPanel, and register the new reference to the shared
2761 newap.av.replaceMappings(viewport.getAlignment());
2764 * start up cDNA consensus (if applicable) now mappings are in place
2766 if (newap.av.initComplementConsensus())
2768 newap.refresh(true); // adjust layout of annotations
2771 newap.av.setViewName(getNewViewName(viewTitle));
2773 addAlignmentPanel(newap, true);
2774 newap.alignmentChanged();
2776 if (alignPanels.size() == 2)
2778 viewport.setGatherViewsHere(true);
2780 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2785 * Make a new name for the view, ensuring it is unique within the current
2786 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2787 * these now use viewId. Unique view names are still desirable for usability.)
2792 protected String getNewViewName(String viewTitle)
2794 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2795 boolean addFirstIndex = false;
2796 if (viewTitle == null || viewTitle.trim().length() == 0)
2798 viewTitle = MessageManager.getString("action.view");
2799 addFirstIndex = true;
2803 index = 1;// we count from 1 if given a specific name
2805 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2807 List<Component> comps = PaintRefresher.components
2808 .get(viewport.getSequenceSetId());
2810 List<String> existingNames = getExistingViewNames(comps);
2812 while (existingNames.contains(newViewName))
2814 newViewName = viewTitle + " " + (++index);
2820 * Returns a list of distinct view names found in the given list of
2821 * components. View names are held on the viewport of an AlignmentPanel.
2826 protected List<String> getExistingViewNames(List<Component> comps)
2828 List<String> existingNames = new ArrayList<>();
2829 for (Component comp : comps)
2831 if (comp instanceof AlignmentPanel)
2833 AlignmentPanel ap = (AlignmentPanel) comp;
2834 if (!existingNames.contains(ap.av.getViewName()))
2836 existingNames.add(ap.av.getViewName());
2840 return existingNames;
2844 * Explode tabbed views into separate windows.
2847 public void expandViews_actionPerformed(ActionEvent e)
2849 Desktop.explodeViews(this);
2853 * Gather views in separate windows back into a tabbed presentation.
2856 public void gatherViews_actionPerformed(ActionEvent e)
2858 Desktop.instance.gatherViews(this);
2868 public void font_actionPerformed(ActionEvent e)
2870 new FontChooser(alignPanel);
2880 protected void seqLimit_actionPerformed(ActionEvent e)
2882 viewport.setShowJVSuffix(seqLimits.isSelected());
2884 alignPanel.getIdPanel().getIdCanvas()
2885 .setPreferredSize(alignPanel.calculateIdWidth());
2886 alignPanel.paintAlignment(true, false);
2890 public void idRightAlign_actionPerformed(ActionEvent e)
2892 viewport.setRightAlignIds(idRightAlign.isSelected());
2893 alignPanel.paintAlignment(false, false);
2897 public void centreColumnLabels_actionPerformed(ActionEvent e)
2899 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2900 alignPanel.paintAlignment(false, false);
2906 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2909 protected void followHighlight_actionPerformed()
2912 * Set the 'follow' flag on the Viewport (and scroll to position if now
2915 final boolean state = this.followHighlightMenuItem.getState();
2916 viewport.setFollowHighlight(state);
2919 alignPanel.scrollToPosition(viewport.getSearchResults());
2930 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2932 viewport.setColourText(colourTextMenuItem.isSelected());
2933 alignPanel.paintAlignment(false, false);
2943 public void wrapMenuItem_actionPerformed(ActionEvent e)
2945 scaleAbove.setVisible(wrapMenuItem.isSelected());
2946 scaleLeft.setVisible(wrapMenuItem.isSelected());
2947 scaleRight.setVisible(wrapMenuItem.isSelected());
2948 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2949 alignPanel.updateLayout();
2953 public void showAllSeqs_actionPerformed(ActionEvent e)
2955 viewport.showAllHiddenSeqs();
2959 public void showAllColumns_actionPerformed(ActionEvent e)
2961 viewport.showAllHiddenColumns();
2962 alignPanel.paintAlignment(true, true);
2963 viewport.sendSelection();
2967 public void hideSelSequences_actionPerformed(ActionEvent e)
2969 viewport.hideAllSelectedSeqs();
2973 * called by key handler and the hide all/show all menu items
2978 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2981 boolean hide = false;
2982 SequenceGroup sg = viewport.getSelectionGroup();
2983 if (!toggleSeqs && !toggleCols)
2985 // Hide everything by the current selection - this is a hack - we do the
2986 // invert and then hide
2987 // first check that there will be visible columns after the invert.
2988 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2989 && sg.getStartRes() <= sg.getEndRes()))
2991 // now invert the sequence set, if required - empty selection implies
2992 // that no hiding is required.
2995 invertSequenceMenuItem_actionPerformed(null);
2996 sg = viewport.getSelectionGroup();
3000 viewport.expandColSelection(sg, true);
3001 // finally invert the column selection and get the new sequence
3003 invertColSel_actionPerformed(null);
3010 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3012 hideSelSequences_actionPerformed(null);
3015 else if (!(toggleCols && viewport.hasSelectedColumns()))
3017 showAllSeqs_actionPerformed(null);
3023 if (viewport.hasSelectedColumns())
3025 hideSelColumns_actionPerformed(null);
3028 viewport.setSelectionGroup(sg);
3033 showAllColumns_actionPerformed(null);
3042 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3043 * event.ActionEvent)
3046 public void hideAllButSelection_actionPerformed(ActionEvent e)
3048 toggleHiddenRegions(false, false);
3049 viewport.sendSelection();
3056 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3060 public void hideAllSelection_actionPerformed(ActionEvent e)
3062 SequenceGroup sg = viewport.getSelectionGroup();
3063 viewport.expandColSelection(sg, false);
3064 viewport.hideAllSelectedSeqs();
3065 viewport.hideSelectedColumns();
3066 alignPanel.updateLayout();
3067 alignPanel.paintAlignment(true, true);
3068 viewport.sendSelection();
3075 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3079 public void showAllhidden_actionPerformed(ActionEvent e)
3081 viewport.showAllHiddenColumns();
3082 viewport.showAllHiddenSeqs();
3083 alignPanel.paintAlignment(true, true);
3084 viewport.sendSelection();
3088 public void hideSelColumns_actionPerformed(ActionEvent e)
3090 viewport.hideSelectedColumns();
3091 alignPanel.updateLayout();
3092 alignPanel.paintAlignment(true, true);
3093 viewport.sendSelection();
3097 public void hiddenMarkers_actionPerformed(ActionEvent e)
3099 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3110 protected void scaleAbove_actionPerformed(ActionEvent e)
3112 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3113 alignPanel.updateLayout();
3114 alignPanel.paintAlignment(true, false);
3124 protected void scaleLeft_actionPerformed(ActionEvent e)
3126 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3127 alignPanel.updateLayout();
3128 alignPanel.paintAlignment(true, false);
3138 protected void scaleRight_actionPerformed(ActionEvent e)
3140 viewport.setScaleRightWrapped(scaleRight.isSelected());
3141 alignPanel.updateLayout();
3142 alignPanel.paintAlignment(true, false);
3152 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3154 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3155 alignPanel.paintAlignment(false, false);
3165 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3167 viewport.setShowText(viewTextMenuItem.isSelected());
3168 alignPanel.paintAlignment(false, false);
3178 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3180 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3181 alignPanel.paintAlignment(false, false);
3184 public FeatureSettings featureSettings;
3187 public FeatureSettingsControllerI getFeatureSettingsUI()
3189 return featureSettings;
3193 public void featureSettings_actionPerformed(ActionEvent e)
3195 showFeatureSettingsUI();
3199 public FeatureSettingsControllerI showFeatureSettingsUI()
3201 if (featureSettings != null)
3203 featureSettings.closeOldSettings();
3204 featureSettings = null;
3206 if (!showSeqFeatures.isSelected())
3208 // make sure features are actually displayed
3209 showSeqFeatures.setSelected(true);
3210 showSeqFeatures_actionPerformed(null);
3212 featureSettings = new FeatureSettings(this);
3213 return featureSettings;
3217 * Set or clear 'Show Sequence Features'
3223 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3225 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3226 alignPanel.paintAlignment(true, true);
3230 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3231 * the annotations panel as a whole.
3233 * The options to show/hide all annotations should be enabled when the panel
3234 * is shown, and disabled when the panel is hidden.
3239 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3241 final boolean setVisible = annotationPanelMenuItem.isSelected();
3242 viewport.setShowAnnotation(setVisible);
3243 this.showAllSeqAnnotations.setEnabled(setVisible);
3244 this.hideAllSeqAnnotations.setEnabled(setVisible);
3245 this.showAllAlAnnotations.setEnabled(setVisible);
3246 this.hideAllAlAnnotations.setEnabled(setVisible);
3247 alignPanel.updateLayout();
3251 public void alignmentProperties()
3253 JEditorPane editPane = new JEditorPane("text/html", "");
3254 editPane.setEditable(false);
3255 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3258 MessageManager.formatMessage("label.html_content", new Object[]
3259 { contents.toString() }));
3260 JInternalFrame frame = new JInternalFrame();
3261 frame.getContentPane().add(new JScrollPane(editPane));
3263 Desktop.addInternalFrame(frame, MessageManager
3264 .formatMessage("label.alignment_properties", new Object[]
3265 { getTitle() }), 500, 400);
3275 public void overviewMenuItem_actionPerformed(ActionEvent e)
3277 if (alignPanel.overviewPanel != null)
3282 JInternalFrame frame = new JInternalFrame();
3283 final OverviewPanel overview = new OverviewPanel(alignPanel);
3284 frame.setContentPane(overview);
3285 Desktop.addInternalFrame(frame, MessageManager
3286 .formatMessage("label.overview_params", new Object[]
3287 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3290 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3291 frame.addInternalFrameListener(
3292 new javax.swing.event.InternalFrameAdapter()
3295 public void internalFrameClosed(
3296 javax.swing.event.InternalFrameEvent evt)
3299 alignPanel.setOverviewPanel(null);
3302 if (getKeyListeners().length > 0)
3304 frame.addKeyListener(getKeyListeners()[0]);
3307 alignPanel.setOverviewPanel(overview);
3311 public void textColour_actionPerformed()
3313 new TextColourChooser().chooseColour(alignPanel, null);
3317 * public void covariationColour_actionPerformed() {
3319 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3323 public void annotationColour_actionPerformed()
3325 new AnnotationColourChooser(viewport, alignPanel);
3329 public void annotationColumn_actionPerformed(ActionEvent e)
3331 new AnnotationColumnChooser(viewport, alignPanel);
3335 * Action on the user checking or unchecking the option to apply the selected
3336 * colour scheme to all groups. If unchecked, groups may have their own
3337 * independent colour schemes.
3342 public void applyToAllGroups_actionPerformed(boolean selected)
3344 viewport.setColourAppliesToAllGroups(selected);
3348 * Action on user selecting a colour from the colour menu
3351 * the name (not the menu item label!) of the colour scheme
3354 public void changeColour_actionPerformed(String name)
3357 * 'User Defined' opens a panel to configure or load a
3358 * user-defined colour scheme
3360 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3362 new UserDefinedColours(alignPanel);
3367 * otherwise set the chosen colour scheme (or null for 'None')
3369 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3371 viewport.getAlignment(), viewport.getHiddenRepSequences());
3376 * Actions on setting or changing the alignment colour scheme
3381 public void changeColour(ColourSchemeI cs)
3383 // TODO: pull up to controller method
3384 ColourMenuHelper.setColourSelected(colourMenu, cs);
3386 viewport.setGlobalColourScheme(cs);
3388 alignPanel.paintAlignment(true, true);
3392 * Show the PID threshold slider panel
3395 protected void modifyPID_actionPerformed()
3397 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3398 alignPanel.getViewName());
3399 SliderPanel.showPIDSlider();
3403 * Show the Conservation slider panel
3406 protected void modifyConservation_actionPerformed()
3408 SliderPanel.setConservationSlider(alignPanel,
3409 viewport.getResidueShading(), alignPanel.getViewName());
3410 SliderPanel.showConservationSlider();
3414 * Action on selecting or deselecting (Colour) By Conservation
3417 public void conservationMenuItem_actionPerformed(boolean selected)
3419 modifyConservation.setEnabled(selected);
3420 viewport.setConservationSelected(selected);
3421 viewport.getResidueShading().setConservationApplied(selected);
3423 changeColour(viewport.getGlobalColourScheme());
3426 modifyConservation_actionPerformed();
3430 SliderPanel.hideConservationSlider();
3435 * Action on selecting or deselecting (Colour) Above PID Threshold
3438 public void abovePIDThreshold_actionPerformed(boolean selected)
3440 modifyPID.setEnabled(selected);
3441 viewport.setAbovePIDThreshold(selected);
3444 viewport.getResidueShading().setThreshold(0,
3445 viewport.isIgnoreGapsConsensus());
3448 changeColour(viewport.getGlobalColourScheme());
3451 modifyPID_actionPerformed();
3455 SliderPanel.hidePIDSlider();
3466 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3468 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3469 AlignmentSorter.sortByPID(viewport.getAlignment(),
3470 viewport.getAlignment().getSequenceAt(0));
3471 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3472 viewport.getAlignment()));
3473 alignPanel.paintAlignment(true, false);
3483 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3485 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3486 AlignmentSorter.sortByID(viewport.getAlignment());
3488 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3489 alignPanel.paintAlignment(true, false);
3499 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3501 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3502 AlignmentSorter.sortByLength(viewport.getAlignment());
3503 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3504 viewport.getAlignment()));
3505 alignPanel.paintAlignment(true, false);
3515 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3517 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3518 AlignmentSorter.sortByGroup(viewport.getAlignment());
3519 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3520 viewport.getAlignment()));
3522 alignPanel.paintAlignment(true, false);
3532 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3534 new RedundancyPanel(alignPanel, this);
3544 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3546 if ((viewport.getSelectionGroup() == null)
3547 || (viewport.getSelectionGroup().getSize() < 2))
3549 JvOptionPane.showInternalMessageDialog(this,
3550 MessageManager.getString(
3551 "label.you_must_select_least_two_sequences"),
3552 MessageManager.getString("label.invalid_selection"),
3553 JvOptionPane.WARNING_MESSAGE);
3557 JInternalFrame frame = new JInternalFrame();
3558 frame.setContentPane(new PairwiseAlignPanel(viewport));
3559 Desktop.addInternalFrame(frame,
3560 MessageManager.getString("action.pairwise_alignment"), 600,
3566 public void autoCalculate_actionPerformed(ActionEvent e)
3568 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3569 if (viewport.autoCalculateConsensus)
3571 viewport.firePropertyChange("alignment", null,
3572 viewport.getAlignment().getSequences());
3577 public void sortByTreeOption_actionPerformed(ActionEvent e)
3579 viewport.sortByTree = sortByTree.isSelected();
3583 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3585 viewport.followSelection = listenToViewSelections.isSelected();
3589 * Constructs a tree panel and adds it to the desktop
3592 * tree type (NJ or AV)
3594 * name of score model used to compute the tree
3596 * parameters for the distance or similarity calculation
3598 void newTreePanel(String type, String modelName,
3599 SimilarityParamsI options)
3601 String frameTitle = "";
3604 boolean onSelection = false;
3605 if (viewport.getSelectionGroup() != null
3606 && viewport.getSelectionGroup().getSize() > 0)
3608 SequenceGroup sg = viewport.getSelectionGroup();
3610 /* Decide if the selection is a column region */
3611 for (SequenceI _s : sg.getSequences())
3613 if (_s.getLength() < sg.getEndRes())
3615 JvOptionPane.showMessageDialog(Desktop.desktop,
3616 MessageManager.getString(
3617 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3618 MessageManager.getString(
3619 "label.sequences_selection_not_aligned"),
3620 JvOptionPane.WARNING_MESSAGE);
3629 if (viewport.getAlignment().getHeight() < 2)
3635 tp = new TreePanel(alignPanel, type, modelName, options);
3636 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3638 frameTitle += " from ";
3640 if (viewport.getViewName() != null)
3642 frameTitle += viewport.getViewName() + " of ";
3645 frameTitle += this.title;
3647 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3658 public void addSortByOrderMenuItem(String title,
3659 final AlignmentOrder order)
3661 final JMenuItem item = new JMenuItem(MessageManager
3662 .formatMessage("action.by_title_param", new Object[]
3665 item.addActionListener(new java.awt.event.ActionListener()
3668 public void actionPerformed(ActionEvent e)
3670 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3672 // TODO: JBPNote - have to map order entries to curent SequenceI
3674 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3676 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3677 viewport.getAlignment()));
3679 alignPanel.paintAlignment(true, false);
3685 * Add a new sort by annotation score menu item
3688 * the menu to add the option to
3690 * the label used to retrieve scores for each sequence on the
3693 public void addSortByAnnotScoreMenuItem(JMenu sort,
3694 final String scoreLabel)
3696 final JMenuItem item = new JMenuItem(scoreLabel);
3698 item.addActionListener(new java.awt.event.ActionListener()
3701 public void actionPerformed(ActionEvent e)
3703 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3704 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3705 viewport.getAlignment());// ,viewport.getSelectionGroup());
3706 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3707 viewport.getAlignment()));
3708 alignPanel.paintAlignment(true, false);
3714 * last hash for alignment's annotation array - used to minimise cost of
3717 protected int _annotationScoreVectorHash;
3720 * search the alignment and rebuild the sort by annotation score submenu the
3721 * last alignment annotation vector hash is stored to minimize cost of
3722 * rebuilding in subsequence calls.
3726 public void buildSortByAnnotationScoresMenu()
3728 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3733 if (viewport.getAlignment().getAlignmentAnnotation()
3734 .hashCode() != _annotationScoreVectorHash)
3736 sortByAnnotScore.removeAll();
3737 // almost certainly a quicker way to do this - but we keep it simple
3738 Hashtable scoreSorts = new Hashtable();
3739 AlignmentAnnotation aann[];
3740 for (SequenceI sqa : viewport.getAlignment().getSequences())
3742 aann = sqa.getAnnotation();
3743 for (int i = 0; aann != null && i < aann.length; i++)
3745 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3747 scoreSorts.put(aann[i].label, aann[i].label);
3751 Enumeration labels = scoreSorts.keys();
3752 while (labels.hasMoreElements())
3754 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3755 (String) labels.nextElement());
3757 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3760 _annotationScoreVectorHash = viewport.getAlignment()
3761 .getAlignmentAnnotation().hashCode();
3766 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3767 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3768 * call. Listeners are added to remove the menu item when the treePanel is
3769 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3773 public void buildTreeSortMenu()
3775 sortByTreeMenu.removeAll();
3777 List<Component> comps = PaintRefresher.components
3778 .get(viewport.getSequenceSetId());
3779 List<TreePanel> treePanels = new ArrayList<>();
3780 for (Component comp : comps)
3782 if (comp instanceof TreePanel)
3784 treePanels.add((TreePanel) comp);
3788 if (treePanels.size() < 1)
3790 sortByTreeMenu.setVisible(false);
3794 sortByTreeMenu.setVisible(true);
3796 for (final TreePanel tp : treePanels)
3798 final JMenuItem item = new JMenuItem(tp.getTitle());
3799 item.addActionListener(new java.awt.event.ActionListener()
3802 public void actionPerformed(ActionEvent e)
3804 tp.sortByTree_actionPerformed();
3805 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3810 sortByTreeMenu.add(item);
3814 public boolean sortBy(AlignmentOrder alorder, String undoname)
3816 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3817 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3818 if (undoname != null)
3820 addHistoryItem(new OrderCommand(undoname, oldOrder,
3821 viewport.getAlignment()));
3823 alignPanel.paintAlignment(true, false);
3828 * Work out whether the whole set of sequences or just the selected set will
3829 * be submitted for multiple alignment.
3832 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3834 // Now, check we have enough sequences
3835 AlignmentView msa = null;
3837 if ((viewport.getSelectionGroup() != null)
3838 && (viewport.getSelectionGroup().getSize() > 1))
3840 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3841 // some common interface!
3843 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3844 * SequenceI[sz = seqs.getSize(false)];
3846 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3847 * seqs.getSequenceAt(i); }
3849 msa = viewport.getAlignmentView(true);
3851 else if (viewport.getSelectionGroup() != null
3852 && viewport.getSelectionGroup().getSize() == 1)
3854 int option = JvOptionPane.showConfirmDialog(this,
3855 MessageManager.getString("warn.oneseq_msainput_selection"),
3856 MessageManager.getString("label.invalid_selection"),
3857 JvOptionPane.OK_CANCEL_OPTION);
3858 if (option == JvOptionPane.OK_OPTION)
3860 msa = viewport.getAlignmentView(false);
3865 msa = viewport.getAlignmentView(false);
3871 * Decides what is submitted to a secondary structure prediction service: the
3872 * first sequence in the alignment, or in the current selection, or, if the
3873 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3874 * region or the whole alignment. (where the first sequence in the set is the
3875 * one that the prediction will be for).
3877 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3879 AlignmentView seqs = null;
3881 if ((viewport.getSelectionGroup() != null)
3882 && (viewport.getSelectionGroup().getSize() > 0))
3884 seqs = viewport.getAlignmentView(true);
3888 seqs = viewport.getAlignmentView(false);
3890 // limit sequences - JBPNote in future - could spawn multiple prediction
3892 // TODO: viewport.getAlignment().isAligned is a global state - the local
3893 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3894 if (!viewport.getAlignment().isAligned(false))
3896 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3897 // TODO: if seqs.getSequences().length>1 then should really have warned
3911 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3913 // Pick the tree file
3914 JalviewFileChooser chooser = new JalviewFileChooser(
3915 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3916 chooser.setFileView(new JalviewFileView());
3917 chooser.setDialogTitle(
3918 MessageManager.getString("label.select_newick_like_tree_file"));
3919 chooser.setToolTipText(
3920 MessageManager.getString("label.load_tree_file"));
3922 int value = chooser.showOpenDialog(null);
3924 if (value == JalviewFileChooser.APPROVE_OPTION)
3926 String filePath = chooser.getSelectedFile().getPath();
3927 Cache.setProperty("LAST_DIRECTORY", filePath);
3928 NewickFile fin = null;
3931 fin = new NewickFile(filePath, DataSourceType.FILE);
3932 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3933 } catch (Exception ex)
3935 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3936 MessageManager.getString("label.problem_reading_tree_file"),
3937 JvOptionPane.WARNING_MESSAGE);
3938 ex.printStackTrace();
3940 if (fin != null && fin.hasWarningMessage())
3942 JvOptionPane.showMessageDialog(Desktop.desktop,
3943 fin.getWarningMessage(),
3945 .getString("label.possible_problem_with_tree_file"),
3946 JvOptionPane.WARNING_MESSAGE);
3951 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3953 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3956 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3957 int h, int x, int y)
3959 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3963 * Add a treeviewer for the tree extracted from a Newick file object to the
3964 * current alignment view
3971 * Associated alignment input data (or null)
3980 * @return TreePanel handle
3982 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3983 AlignmentView input, int w, int h, int x, int y)
3985 TreePanel tp = null;
3991 if (nf.getTree() != null)
3993 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3999 tp.setLocation(x, y);
4002 Desktop.addInternalFrame(tp, treeTitle, w, h);
4004 } catch (Exception ex)
4006 ex.printStackTrace();
4012 private boolean buildingMenu = false;
4015 * Generates menu items and listener event actions for web service clients
4018 public void BuildWebServiceMenu()
4020 while (buildingMenu)
4024 System.err.println("Waiting for building menu to finish.");
4026 } catch (Exception e)
4030 final AlignFrame me = this;
4031 buildingMenu = true;
4032 new Thread(new Runnable()
4037 final List<JMenuItem> legacyItems = new ArrayList<>();
4040 // System.err.println("Building ws menu again "
4041 // + Thread.currentThread());
4042 // TODO: add support for context dependent disabling of services based
4044 // alignment and current selection
4045 // TODO: add additional serviceHandle parameter to specify abstract
4047 // class independently of AbstractName
4048 // TODO: add in rediscovery GUI function to restart discoverer
4049 // TODO: group services by location as well as function and/or
4051 // object broker mechanism.
4052 final Vector<JMenu> wsmenu = new Vector<>();
4053 final IProgressIndicator af = me;
4056 * do not i18n these strings - they are hard-coded in class
4057 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4058 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4060 final JMenu msawsmenu = new JMenu("Alignment");
4061 final JMenu secstrmenu = new JMenu(
4062 "Secondary Structure Prediction");
4063 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4064 final JMenu analymenu = new JMenu("Analysis");
4065 final JMenu dismenu = new JMenu("Protein Disorder");
4066 // JAL-940 - only show secondary structure prediction services from
4067 // the legacy server
4068 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4070 Discoverer.services != null && (Discoverer.services.size() > 0))
4072 // TODO: refactor to allow list of AbstractName/Handler bindings to
4074 // stored or retrieved from elsewhere
4075 // No MSAWS used any more:
4076 // Vector msaws = null; // (Vector)
4077 // Discoverer.services.get("MsaWS");
4078 Vector secstrpr = (Vector) Discoverer.services
4080 if (secstrpr != null)
4082 // Add any secondary structure prediction services
4083 for (int i = 0, j = secstrpr.size(); i < j; i++)
4085 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4087 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4088 .getServiceClient(sh);
4089 int p = secstrmenu.getItemCount();
4090 impl.attachWSMenuEntry(secstrmenu, me);
4091 int q = secstrmenu.getItemCount();
4092 for (int litm = p; litm < q; litm++)
4094 legacyItems.add(secstrmenu.getItem(litm));
4100 // Add all submenus in the order they should appear on the web
4102 wsmenu.add(msawsmenu);
4103 wsmenu.add(secstrmenu);
4104 wsmenu.add(dismenu);
4105 wsmenu.add(analymenu);
4106 // No search services yet
4107 // wsmenu.add(seqsrchmenu);
4109 javax.swing.SwingUtilities.invokeLater(new Runnable()
4116 webService.removeAll();
4117 // first, add discovered services onto the webservices menu
4118 if (wsmenu.size() > 0)
4120 for (int i = 0, j = wsmenu.size(); i < j; i++)
4122 webService.add(wsmenu.get(i));
4127 webService.add(me.webServiceNoServices);
4129 // TODO: move into separate menu builder class.
4130 boolean new_sspred = false;
4131 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4133 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4134 if (jws2servs != null)
4136 if (jws2servs.hasServices())
4138 jws2servs.attachWSMenuEntry(webService, me);
4139 for (Jws2Instance sv : jws2servs.getServices())
4141 if (sv.description.toLowerCase().contains("jpred"))
4143 for (JMenuItem jmi : legacyItems)
4145 jmi.setVisible(false);
4151 if (jws2servs.isRunning())
4153 JMenuItem tm = new JMenuItem(
4154 "Still discovering JABA Services");
4155 tm.setEnabled(false);
4160 build_urlServiceMenu(me.webService);
4161 build_fetchdbmenu(webService);
4162 for (JMenu item : wsmenu)
4164 if (item.getItemCount() == 0)
4166 item.setEnabled(false);
4170 item.setEnabled(true);
4173 } catch (Exception e)
4176 "Exception during web service menu building process.",
4181 } catch (Exception e)
4184 buildingMenu = false;
4191 * construct any groupURL type service menu entries.
4195 private void build_urlServiceMenu(JMenu webService)
4197 // TODO: remove this code when 2.7 is released
4198 // DEBUG - alignmentView
4200 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4201 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4203 * @Override public void actionPerformed(ActionEvent e) {
4204 * jalview.datamodel.AlignmentView
4205 * .testSelectionViews(af.viewport.getAlignment(),
4206 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4208 * }); webService.add(testAlView);
4210 // TODO: refactor to RestClient discoverer and merge menu entries for
4211 // rest-style services with other types of analysis/calculation service
4212 // SHmmr test client - still being implemented.
4213 // DEBUG - alignmentView
4215 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4218 client.attachWSMenuEntry(
4219 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4225 * Searches the alignment sequences for xRefs and builds the Show
4226 * Cross-References menu (formerly called Show Products), with database
4227 * sources for which cross-references are found (protein sources for a
4228 * nucleotide alignment and vice versa)
4230 * @return true if Show Cross-references menu should be enabled
4232 public boolean canShowProducts()
4234 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4235 AlignmentI dataset = viewport.getAlignment().getDataset();
4237 showProducts.removeAll();
4238 final boolean dna = viewport.getAlignment().isNucleotide();
4240 if (seqs == null || seqs.length == 0)
4242 // nothing to see here.
4246 boolean showp = false;
4249 List<String> ptypes = new CrossRef(seqs, dataset)
4250 .findXrefSourcesForSequences(dna);
4252 for (final String source : ptypes)
4255 final AlignFrame af = this;
4256 JMenuItem xtype = new JMenuItem(source);
4257 xtype.addActionListener(new ActionListener()
4260 public void actionPerformed(ActionEvent e)
4262 showProductsFor(af.viewport.getSequenceSelection(), dna,
4266 showProducts.add(xtype);
4268 showProducts.setVisible(showp);
4269 showProducts.setEnabled(showp);
4270 } catch (Exception e)
4273 "canShowProducts threw an exception - please report to help@jalview.org",
4281 * Finds and displays cross-references for the selected sequences (protein
4282 * products for nucleotide sequences, dna coding sequences for peptides).
4285 * the sequences to show cross-references for
4287 * true if from a nucleotide alignment (so showing proteins)
4289 * the database to show cross-references for
4291 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4292 final String source)
4294 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4299 * Construct and display a new frame containing the translation of this
4300 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4303 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4305 AlignmentI al = null;
4308 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4310 al = dna.translateCdna(codeTable);
4311 } catch (Exception ex)
4313 jalview.bin.Cache.log.error(
4314 "Exception during translation. Please report this !", ex);
4315 final String msg = MessageManager.getString(
4316 "label.error_when_translating_sequences_submit_bug_report");
4317 final String errorTitle = MessageManager
4318 .getString("label.implementation_error")
4319 + MessageManager.getString("label.translation_failed");
4320 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4321 JvOptionPane.ERROR_MESSAGE);
4324 if (al == null || al.getHeight() == 0)
4326 final String msg = MessageManager.getString(
4327 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4328 final String errorTitle = MessageManager
4329 .getString("label.translation_failed");
4330 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4331 JvOptionPane.WARNING_MESSAGE);
4335 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4336 af.setFileFormat(this.currentFileFormat);
4337 final String newTitle = MessageManager
4338 .formatMessage("label.translation_of_params", new Object[]
4339 { this.getTitle(), codeTable.getId() });
4340 af.setTitle(newTitle);
4341 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4343 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4344 viewport.openSplitFrame(af, new Alignment(seqs));
4348 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4355 * Set the file format
4359 public void setFileFormat(FileFormatI format)
4361 this.currentFileFormat = format;
4365 * Try to load a features file onto the alignment.
4368 * contents or path to retrieve file
4370 * access mode of file (see jalview.io.AlignFile)
4371 * @return true if features file was parsed correctly.
4373 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4375 return avc.parseFeaturesFile(file, sourceType,
4376 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4381 public void refreshFeatureUI(boolean enableIfNecessary)
4383 // note - currently this is only still here rather than in the controller
4384 // because of the featureSettings hard reference that is yet to be
4386 if (enableIfNecessary)
4388 viewport.setShowSequenceFeatures(true);
4389 showSeqFeatures.setSelected(true);
4395 public void dragEnter(DropTargetDragEvent evt)
4400 public void dragExit(DropTargetEvent evt)
4405 public void dragOver(DropTargetDragEvent evt)
4410 public void dropActionChanged(DropTargetDragEvent evt)
4415 public void drop(DropTargetDropEvent evt)
4417 // JAL-1552 - acceptDrop required before getTransferable call for
4418 // Java's Transferable for native dnd
4419 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4420 Transferable t = evt.getTransferable();
4421 final AlignFrame thisaf = this;
4422 final List<String> files = new ArrayList<>();
4423 List<DataSourceType> protocols = new ArrayList<>();
4427 Desktop.transferFromDropTarget(files, protocols, evt, t);
4428 } catch (Exception e)
4430 e.printStackTrace();
4434 new Thread(new Runnable()
4441 // check to see if any of these files have names matching sequences
4444 SequenceIdMatcher idm = new SequenceIdMatcher(
4445 viewport.getAlignment().getSequencesArray());
4447 * Object[] { String,SequenceI}
4449 ArrayList<Object[]> filesmatched = new ArrayList<>();
4450 ArrayList<String> filesnotmatched = new ArrayList<>();
4451 for (int i = 0; i < files.size(); i++)
4453 String file = files.get(i).toString();
4455 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4456 if (protocol == DataSourceType.FILE)
4458 File fl = new File(file);
4459 pdbfn = fl.getName();
4461 else if (protocol == DataSourceType.URL)
4463 URL url = new URL(file);
4464 pdbfn = url.getFile();
4466 if (pdbfn.length() > 0)
4468 // attempt to find a match in the alignment
4469 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4470 int l = 0, c = pdbfn.indexOf(".");
4471 while (mtch == null && c != -1)
4476 } while ((c = pdbfn.indexOf(".", l)) > l);
4479 pdbfn = pdbfn.substring(0, l);
4481 mtch = idm.findAllIdMatches(pdbfn);
4485 FileFormatI type = null;
4488 type = new IdentifyFile().identify(file, protocol);
4489 } catch (Exception ex)
4493 if (type != null && type.isStructureFile())
4495 filesmatched.add(new Object[] { file, protocol, mtch });
4499 // File wasn't named like one of the sequences or wasn't a PDB
4501 filesnotmatched.add(file);
4505 if (filesmatched.size() > 0)
4507 boolean autoAssociate = Cache
4508 .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4511 String msg = MessageManager.formatMessage(
4512 "label.automatically_associate_structure_files_with_sequences_same_name",
4514 { Integer.valueOf(filesmatched.size())
4516 String ttl = MessageManager.getString(
4517 "label.automatically_associate_structure_files_by_name");
4518 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4519 ttl, JvOptionPane.YES_NO_OPTION);
4520 autoAssociate = choice == JvOptionPane.YES_OPTION;
4524 for (Object[] fm : filesmatched)
4526 // try and associate
4527 // TODO: may want to set a standard ID naming formalism for
4528 // associating PDB files which have no IDs.
4529 for (SequenceI toassoc : (SequenceI[]) fm[2])
4531 PDBEntry pe = new AssociatePdbFileWithSeq()
4532 .associatePdbWithSeq((String) fm[0],
4533 (DataSourceType) fm[1], toassoc, false,
4537 System.err.println("Associated file : "
4538 + ((String) fm[0]) + " with "
4539 + toassoc.getDisplayId(true));
4543 // TODO: do we need to update overview ? only if features are
4545 alignPanel.paintAlignment(true, false);
4551 * add declined structures as sequences
4553 for (Object[] o : filesmatched)
4555 filesnotmatched.add((String) o[0]);
4559 if (filesnotmatched.size() > 0)
4561 if (assocfiles > 0 && (Cache.getDefault(
4562 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4563 || JvOptionPane.showConfirmDialog(thisaf,
4564 "<html>" + MessageManager.formatMessage(
4565 "label.ignore_unmatched_dropped_files_info",
4568 filesnotmatched.size())
4571 MessageManager.getString(
4572 "label.ignore_unmatched_dropped_files"),
4573 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4577 for (String fn : filesnotmatched)
4579 loadJalviewDataFile(fn, null, null, null);
4583 } catch (Exception ex)
4585 ex.printStackTrace();
4593 * Attempt to load a "dropped" file or URL string, by testing in turn for
4595 * <li>an Annotation file</li>
4596 * <li>a JNet file</li>
4597 * <li>a features file</li>
4598 * <li>else try to interpret as an alignment file</li>
4602 * either a filename or a URL string.
4604 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4605 FileFormatI format, SequenceI assocSeq)
4609 if (sourceType == null)
4611 sourceType = FormatAdapter.checkProtocol(file);
4613 // if the file isn't identified, or not positively identified as some
4614 // other filetype (PFAM is default unidentified alignment file type) then
4615 // try to parse as annotation.
4616 boolean isAnnotation = (format == null
4617 || FileFormat.Pfam.equals(format))
4618 ? new AnnotationFile().annotateAlignmentView(viewport,
4624 // first see if its a T-COFFEE score file
4625 TCoffeeScoreFile tcf = null;
4628 tcf = new TCoffeeScoreFile(file, sourceType);
4631 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4635 new TCoffeeColourScheme(viewport.getAlignment()));
4636 isAnnotation = true;
4637 statusBar.setText(MessageManager.getString(
4638 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4642 // some problem - if no warning its probable that the ID matching
4643 // process didn't work
4644 JvOptionPane.showMessageDialog(Desktop.desktop,
4645 tcf.getWarningMessage() == null
4646 ? MessageManager.getString(
4647 "label.check_file_matches_sequence_ids_alignment")
4648 : tcf.getWarningMessage(),
4649 MessageManager.getString(
4650 "label.problem_reading_tcoffee_score_file"),
4651 JvOptionPane.WARNING_MESSAGE);
4658 } catch (Exception x)
4661 "Exception when processing data source as T-COFFEE score file",
4667 // try to see if its a JNet 'concise' style annotation file *before*
4669 // try to parse it as a features file
4672 format = new IdentifyFile().identify(file, sourceType);
4674 if (FileFormat.ScoreMatrix == format)
4676 ScoreMatrixFile sm = new ScoreMatrixFile(
4677 new FileParse(file, sourceType));
4679 // todo: i18n this message
4680 statusBar.setText(MessageManager.formatMessage(
4681 "label.successfully_loaded_matrix",
4682 sm.getMatrixName()));
4684 else if (FileFormat.Jnet.equals(format))
4686 JPredFile predictions = new JPredFile(file, sourceType);
4687 new JnetAnnotationMaker();
4688 JnetAnnotationMaker.add_annotation(predictions,
4689 viewport.getAlignment(), 0, false);
4690 viewport.getAlignment().setupJPredAlignment();
4691 isAnnotation = true;
4693 // else if (IdentifyFile.FeaturesFile.equals(format))
4694 else if (FileFormat.Features.equals(format))
4696 if (parseFeaturesFile(file, sourceType))
4698 SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4699 if (splitFrame != null)
4701 splitFrame.repaint();
4705 alignPanel.paintAlignment(true, true);
4711 new FileLoader().LoadFile(viewport, file, sourceType, format);
4718 alignPanel.adjustAnnotationHeight();
4719 viewport.updateSequenceIdColours();
4720 buildSortByAnnotationScoresMenu();
4721 alignPanel.paintAlignment(true, true);
4723 } catch (Exception ex)
4725 ex.printStackTrace();
4726 } catch (OutOfMemoryError oom)
4731 } catch (Exception x)
4736 + (sourceType != null
4737 ? (sourceType == DataSourceType.PASTE
4739 : "using " + sourceType + " from "
4743 ? "(parsing as '" + format + "' file)"
4745 oom, Desktop.desktop);
4750 * Method invoked by the ChangeListener on the tabbed pane, in other words
4751 * when a different tabbed pane is selected by the user or programmatically.
4754 public void tabSelectionChanged(int index)
4758 alignPanel = alignPanels.get(index);
4759 viewport = alignPanel.av;
4760 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4761 setMenusFromViewport(viewport);
4762 if (featureSettings != null && featureSettings.isOpen()
4763 && featureSettings.fr.getViewport() != viewport)
4765 if (viewport.isShowSequenceFeatures())
4767 // refresh the featureSettings to reflect UI change
4768 showFeatureSettingsUI();
4772 // close feature settings for this view.
4773 featureSettings.close();
4780 * 'focus' any colour slider that is open to the selected viewport
4782 if (viewport.getConservationSelected())
4784 SliderPanel.setConservationSlider(alignPanel,
4785 viewport.getResidueShading(), alignPanel.getViewName());
4789 SliderPanel.hideConservationSlider();
4791 if (viewport.getAbovePIDThreshold())
4793 SliderPanel.setPIDSliderSource(alignPanel,
4794 viewport.getResidueShading(), alignPanel.getViewName());
4798 SliderPanel.hidePIDSlider();
4802 * If there is a frame linked to this one in a SplitPane, switch it to the
4803 * same view tab index. No infinite recursion of calls should happen, since
4804 * tabSelectionChanged() should not get invoked on setting the selected
4805 * index to an unchanged value. Guard against setting an invalid index
4806 * before the new view peer tab has been created.
4808 final AlignViewportI peer = viewport.getCodingComplement();
4811 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4812 .getAlignPanel().alignFrame;
4813 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4815 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4821 * On right mouse click on view tab, prompt for and set new view name.
4824 public void tabbedPane_mousePressed(MouseEvent e)
4826 if (e.isPopupTrigger())
4828 String msg = MessageManager.getString("label.enter_view_name");
4829 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4830 JvOptionPane.QUESTION_MESSAGE);
4834 viewport.setViewName(reply);
4835 // TODO warn if reply is in getExistingViewNames()?
4836 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4841 public AlignViewport getCurrentView()
4847 * Open the dialog for regex description parsing.
4850 protected void extractScores_actionPerformed(ActionEvent e)
4852 ParseProperties pp = new jalview.analysis.ParseProperties(
4853 viewport.getAlignment());
4854 // TODO: verify regex and introduce GUI dialog for version 2.5
4855 // if (pp.getScoresFromDescription("col", "score column ",
4856 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4858 if (pp.getScoresFromDescription("description column",
4859 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4861 buildSortByAnnotationScoresMenu();
4869 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4873 protected void showDbRefs_actionPerformed(ActionEvent e)
4875 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4881 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4885 protected void showNpFeats_actionPerformed(ActionEvent e)
4887 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4891 * find the viewport amongst the tabs in this alignment frame and close that
4896 public boolean closeView(AlignViewportI av)
4900 this.closeMenuItem_actionPerformed(false);
4903 Component[] comp = tabbedPane.getComponents();
4904 for (int i = 0; comp != null && i < comp.length; i++)
4906 if (comp[i] instanceof AlignmentPanel)
4908 if (((AlignmentPanel) comp[i]).av == av)
4911 closeView((AlignmentPanel) comp[i]);
4919 protected void build_fetchdbmenu(JMenu webService)
4921 // Temporary hack - DBRef Fetcher always top level ws entry.
4922 // TODO We probably want to store a sequence database checklist in
4923 // preferences and have checkboxes.. rather than individual sources selected
4925 final JMenu rfetch = new JMenu(
4926 MessageManager.getString("action.fetch_db_references"));
4927 rfetch.setToolTipText(MessageManager.getString(
4928 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4929 webService.add(rfetch);
4931 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4932 MessageManager.getString("option.trim_retrieved_seqs"));
4933 trimrs.setToolTipText(
4934 MessageManager.getString("label.trim_retrieved_sequences"));
4936 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4937 trimrs.addActionListener(new ActionListener()
4940 public void actionPerformed(ActionEvent e)
4942 trimrs.setSelected(trimrs.isSelected());
4943 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4944 Boolean.valueOf(trimrs.isSelected()).toString());
4948 JMenuItem fetchr = new JMenuItem(
4949 MessageManager.getString("label.standard_databases"));
4950 fetchr.setToolTipText(
4951 MessageManager.getString("label.fetch_embl_uniprot"));
4952 fetchr.addActionListener(new ActionListener()
4956 public void actionPerformed(ActionEvent e)
4958 new Thread(new Runnable()
4963 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4964 .getAlignment().isNucleotide();
4965 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4966 alignPanel.av.getSequenceSelection(),
4967 alignPanel.alignFrame, null,
4968 alignPanel.alignFrame.featureSettings, isNucleotide);
4969 dbRefFetcher.addListener(new FetchFinishedListenerI()
4972 public void finished()
4975 for (FeatureSettingsModelI srcSettings : dbRefFetcher
4976 .getFeatureSettingsModels())
4979 alignPanel.av.mergeFeaturesStyle(srcSettings);
4981 AlignFrame.this.setMenusForViewport();
4984 dbRefFetcher.fetchDBRefs(false);
4992 final AlignFrame me = this;
4993 new Thread(new Runnable()
4998 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4999 .getSequenceFetcherSingleton(me);
5000 javax.swing.SwingUtilities.invokeLater(new Runnable()
5005 String[] dbclasses = sf.getOrderedSupportedSources();
5006 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5007 // jalview.util.QuickSort.sort(otherdb, otherdb);
5008 List<DbSourceProxy> otherdb;
5009 JMenu dfetch = new JMenu();
5010 JMenu ifetch = new JMenu();
5011 JMenuItem fetchr = null;
5012 int comp = 0, icomp = 0, mcomp = 15;
5013 String mname = null;
5015 for (String dbclass : dbclasses)
5017 otherdb = sf.getSourceProxy(dbclass);
5018 // add a single entry for this class, or submenu allowing 'fetch
5020 if (otherdb == null || otherdb.size() < 1)
5024 // List<DbSourceProxy> dbs=otherdb;
5025 // otherdb=new ArrayList<DbSourceProxy>();
5026 // for (DbSourceProxy db:dbs)
5028 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5032 mname = "From " + dbclass;
5034 if (otherdb.size() == 1)
5036 final DbSourceProxy[] dassource = otherdb
5037 .toArray(new DbSourceProxy[0]);
5038 DbSourceProxy src = otherdb.get(0);
5039 fetchr = new JMenuItem(src.getDbSource());
5040 fetchr.addActionListener(new ActionListener()
5044 public void actionPerformed(ActionEvent e)
5046 new Thread(new Runnable()
5052 boolean isNucleotide = alignPanel.alignFrame
5053 .getViewport().getAlignment()
5055 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5056 alignPanel.av.getSequenceSelection(),
5057 alignPanel.alignFrame, dassource,
5058 alignPanel.alignFrame.featureSettings,
5061 .addListener(new FetchFinishedListenerI()
5064 public void finished()
5066 FeatureSettingsModelI srcSettings = dassource[0]
5067 .getFeatureColourScheme();
5068 alignPanel.av.mergeFeaturesStyle(
5070 AlignFrame.this.setMenusForViewport();
5073 dbRefFetcher.fetchDBRefs(false);
5079 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5080 MessageManager.formatMessage(
5081 "label.fetch_retrieve_from", new Object[]
5082 { src.getDbName() })));
5088 final DbSourceProxy[] dassource = otherdb
5089 .toArray(new DbSourceProxy[0]);
5091 DbSourceProxy src = otherdb.get(0);
5092 fetchr = new JMenuItem(MessageManager
5093 .formatMessage("label.fetch_all_param", new Object[]
5094 { src.getDbSource() }));
5095 fetchr.addActionListener(new ActionListener()
5098 public void actionPerformed(ActionEvent e)
5100 new Thread(new Runnable()
5106 boolean isNucleotide = alignPanel.alignFrame
5107 .getViewport().getAlignment()
5109 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5110 alignPanel.av.getSequenceSelection(),
5111 alignPanel.alignFrame, dassource,
5112 alignPanel.alignFrame.featureSettings,
5115 .addListener(new FetchFinishedListenerI()
5118 public void finished()
5120 AlignFrame.this.setMenusForViewport();
5123 dbRefFetcher.fetchDBRefs(false);
5129 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5130 MessageManager.formatMessage(
5131 "label.fetch_retrieve_from_all_sources",
5133 { Integer.valueOf(otherdb.size())
5135 src.getDbSource(), src.getDbName() })));
5138 // and then build the rest of the individual menus
5139 ifetch = new JMenu(MessageManager.formatMessage(
5140 "label.source_from_db_source", new Object[]
5141 { src.getDbSource() }));
5143 String imname = null;
5145 for (DbSourceProxy sproxy : otherdb)
5147 String dbname = sproxy.getDbName();
5148 String sname = dbname.length() > 5
5149 ? dbname.substring(0, 5) + "..."
5151 String msname = dbname.length() > 10
5152 ? dbname.substring(0, 10) + "..."
5156 imname = MessageManager
5157 .formatMessage("label.from_msname", new Object[]
5160 fetchr = new JMenuItem(msname);
5161 final DbSourceProxy[] dassrc = { sproxy };
5162 fetchr.addActionListener(new ActionListener()
5166 public void actionPerformed(ActionEvent e)
5168 new Thread(new Runnable()
5174 boolean isNucleotide = alignPanel.alignFrame
5175 .getViewport().getAlignment()
5177 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5178 alignPanel.av.getSequenceSelection(),
5179 alignPanel.alignFrame, dassrc,
5180 alignPanel.alignFrame.featureSettings,
5183 .addListener(new FetchFinishedListenerI()
5186 public void finished()
5188 AlignFrame.this.setMenusForViewport();
5191 dbRefFetcher.fetchDBRefs(false);
5197 fetchr.setToolTipText(
5198 "<html>" + MessageManager.formatMessage(
5199 "label.fetch_retrieve_from", new Object[]
5203 if (++icomp >= mcomp || i == (otherdb.size()))
5205 ifetch.setText(MessageManager.formatMessage(
5206 "label.source_to_target", imname, sname));
5208 ifetch = new JMenu();
5216 if (comp >= mcomp || dbi >= (dbclasses.length))
5218 dfetch.setText(MessageManager.formatMessage(
5219 "label.source_to_target", mname, dbclass));
5221 dfetch = new JMenu();
5234 * Left justify the whole alignment.
5237 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5239 AlignmentI al = viewport.getAlignment();
5241 viewport.firePropertyChange("alignment", null, al);
5245 * Right justify the whole alignment.
5248 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5250 AlignmentI al = viewport.getAlignment();
5252 viewport.firePropertyChange("alignment", null, al);
5256 public void setShowSeqFeatures(boolean b)
5258 showSeqFeatures.setSelected(b);
5259 viewport.setShowSequenceFeatures(b);
5266 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5267 * awt.event.ActionEvent)
5270 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5272 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5273 alignPanel.paintAlignment(false, false);
5280 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5284 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5286 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5287 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5295 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5296 * .event.ActionEvent)
5299 protected void showGroupConservation_actionPerformed(ActionEvent e)
5301 viewport.setShowGroupConservation(showGroupConservation.getState());
5302 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5309 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5310 * .event.ActionEvent)
5313 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5315 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5316 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5323 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5324 * .event.ActionEvent)
5327 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5329 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5330 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5334 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5336 showSequenceLogo.setState(true);
5337 viewport.setShowSequenceLogo(true);
5338 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5339 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5343 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5345 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5352 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5353 * .event.ActionEvent)
5356 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5358 if (avc.makeGroupsFromSelection())
5360 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5361 alignPanel.updateAnnotation();
5362 alignPanel.paintAlignment(true,
5363 viewport.needToUpdateStructureViews());
5367 public void clearAlignmentSeqRep()
5369 // TODO refactor alignmentseqrep to controller
5370 if (viewport.getAlignment().hasSeqrep())
5372 viewport.getAlignment().setSeqrep(null);
5373 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5374 alignPanel.updateAnnotation();
5375 alignPanel.paintAlignment(true, true);
5380 protected void createGroup_actionPerformed(ActionEvent e)
5382 if (avc.createGroup())
5384 if (applyAutoAnnotationSettings.isSelected())
5386 alignPanel.updateAnnotation(true, false);
5388 alignPanel.alignmentChanged();
5393 protected void unGroup_actionPerformed(ActionEvent e)
5397 alignPanel.alignmentChanged();
5402 * make the given alignmentPanel the currently selected tab
5404 * @param alignmentPanel
5406 public void setDisplayedView(AlignmentPanel alignmentPanel)
5408 if (!viewport.getSequenceSetId()
5409 .equals(alignmentPanel.av.getSequenceSetId()))
5411 throw new Error(MessageManager.getString(
5412 "error.implementation_error_cannot_show_view_alignment_frame"));
5414 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5415 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5417 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5422 * Action on selection of menu options to Show or Hide annotations.
5425 * @param forSequences
5426 * update sequence-related annotations
5427 * @param forAlignment
5428 * update non-sequence-related annotations
5431 protected void setAnnotationsVisibility(boolean visible,
5432 boolean forSequences, boolean forAlignment)
5434 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5435 .getAlignmentAnnotation();
5440 for (AlignmentAnnotation aa : anns)
5443 * don't display non-positional annotations on an alignment
5445 if (aa.annotations == null)
5449 boolean apply = (aa.sequenceRef == null && forAlignment)
5450 || (aa.sequenceRef != null && forSequences);
5453 aa.visible = visible;
5456 alignPanel.validateAnnotationDimensions(true);
5457 alignPanel.alignmentChanged();
5461 * Store selected annotation sort order for the view and repaint.
5464 protected void sortAnnotations_actionPerformed()
5466 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5468 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5469 alignPanel.paintAlignment(false, false);
5474 * @return alignment panels in this alignment frame
5476 public List<? extends AlignmentViewPanel> getAlignPanels()
5478 // alignPanels is never null
5479 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5484 * Open a new alignment window, with the cDNA associated with this (protein)
5485 * alignment, aligned as is the protein.
5487 protected void viewAsCdna_actionPerformed()
5489 // TODO no longer a menu action - refactor as required
5490 final AlignmentI alignment = getViewport().getAlignment();
5491 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5492 if (mappings == null)
5496 List<SequenceI> cdnaSeqs = new ArrayList<>();
5497 for (SequenceI aaSeq : alignment.getSequences())
5499 for (AlignedCodonFrame acf : mappings)
5501 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5505 * There is a cDNA mapping for this protein sequence - add to new
5506 * alignment. It will share the same dataset sequence as other mapped
5507 * cDNA (no new mappings need to be created).
5509 final Sequence newSeq = new Sequence(dnaSeq);
5510 newSeq.setDatasetSequence(dnaSeq);
5511 cdnaSeqs.add(newSeq);
5515 if (cdnaSeqs.size() == 0)
5517 // show a warning dialog no mapped cDNA
5520 AlignmentI cdna = new Alignment(
5521 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5522 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5523 AlignFrame.DEFAULT_HEIGHT);
5524 cdna.alignAs(alignment);
5525 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5527 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5528 AlignFrame.DEFAULT_HEIGHT);
5532 * Set visibility of dna/protein complement view (available when shown in a
5538 protected void showComplement_actionPerformed(boolean show)
5540 SplitContainerI sf = getSplitViewContainer();
5543 sf.setComplementVisible(this, show);
5548 * Generate the reverse (optionally complemented) of the selected sequences,
5549 * and add them to the alignment
5552 protected void showReverse_actionPerformed(boolean complement)
5554 AlignmentI al = null;
5557 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5558 al = dna.reverseCdna(complement);
5559 viewport.addAlignment(al, "");
5560 addHistoryItem(new EditCommand(
5561 MessageManager.getString("label.add_sequences"), Action.PASTE,
5562 al.getSequencesArray(), 0, al.getWidth(),
5563 viewport.getAlignment()));
5564 } catch (Exception ex)
5566 System.err.println(ex.getMessage());
5572 * Try to run a script in the Groovy console, having first ensured that this
5573 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5574 * be targeted at this alignment.
5577 protected void runGroovy_actionPerformed()
5579 Jalview.setCurrentAlignFrame(this);
5580 groovy.ui.Console console = Desktop.getGroovyConsole();
5581 if (console != null)
5585 console.runScript();
5586 } catch (Exception ex)
5588 System.err.println((ex.toString()));
5589 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5590 MessageManager.getString("label.couldnt_run_groovy_script"),
5591 MessageManager.getString("label.groovy_support_failed"),
5592 JvOptionPane.ERROR_MESSAGE);
5597 System.err.println("Can't run Groovy script as console not found");
5602 * Hides columns containing (or not containing) a specified feature, provided
5603 * that would not leave all columns hidden
5605 * @param featureType
5606 * @param columnsContaining
5609 public boolean hideFeatureColumns(String featureType,
5610 boolean columnsContaining)
5612 boolean notForHiding = avc.markColumnsContainingFeatures(
5613 columnsContaining, false, false, featureType);
5616 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5617 false, featureType))
5619 getViewport().hideSelectedColumns();
5627 protected void selectHighlightedColumns_actionPerformed(
5628 ActionEvent actionEvent)
5630 // include key modifier check in case user selects from menu
5631 avc.markHighlightedColumns(
5632 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5633 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5634 | ActionEvent.CTRL_MASK)) != 0);
5638 * Rebuilds the Colour menu, including any user-defined colours which have
5639 * been loaded either on startup or during the session
5641 public void buildColourMenu()
5643 colourMenu.removeAll();
5645 colourMenu.add(applyToAllGroups);
5646 colourMenu.add(textColour);
5647 colourMenu.addSeparator();
5649 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5650 viewport.getAlignment(), false);
5652 colourMenu.add(annotationColour);
5653 bg.add(annotationColour);
5654 colourMenu.addSeparator();
5655 colourMenu.add(conservationMenuItem);
5656 colourMenu.add(modifyConservation);
5657 colourMenu.add(abovePIDThreshold);
5658 colourMenu.add(modifyPID);
5660 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5661 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5665 * Open a dialog (if not already open) that allows the user to select and
5666 * calculate PCA or Tree analysis
5668 protected void openTreePcaDialog()
5670 if (alignPanel.getCalculationDialog() == null)
5672 new CalculationChooser(AlignFrame.this);
5677 protected void loadVcf_actionPerformed()
5679 JalviewFileChooser chooser = new JalviewFileChooser(
5680 Cache.getProperty("LAST_DIRECTORY"));
5681 chooser.setFileView(new JalviewFileView());
5682 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5683 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5685 int value = chooser.showOpenDialog(null);
5687 if (value == JalviewFileChooser.APPROVE_OPTION)
5689 String choice = chooser.getSelectedFile().getPath();
5690 Cache.setProperty("LAST_DIRECTORY", choice);
5691 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5692 new VCFLoader(choice).loadVCF(seqs, this);
5697 private Rectangle lastFeatureSettingsBounds = null;
5699 public void setFeatureSettingsGeometry(Rectangle bounds)
5701 lastFeatureSettingsBounds = bounds;
5705 public Rectangle getFeatureSettingsGeometry()
5707 return lastFeatureSettingsBounds;
5711 class PrintThread extends Thread
5715 public PrintThread(AlignmentPanel ap)
5720 static PageFormat pf;
5725 PrinterJob printJob = PrinterJob.getPrinterJob();
5729 printJob.setPrintable(ap, pf);
5733 printJob.setPrintable(ap);
5736 if (printJob.printDialog())
5741 } catch (Exception PrintException)
5743 PrintException.printStackTrace();