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 java.awt.BorderLayout;
24 import java.awt.Component;
25 import java.awt.Rectangle;
26 import java.awt.Toolkit;
27 import java.awt.datatransfer.Clipboard;
28 import java.awt.datatransfer.DataFlavor;
29 import java.awt.datatransfer.StringSelection;
30 import java.awt.datatransfer.Transferable;
31 import java.awt.dnd.DnDConstants;
32 import java.awt.dnd.DropTargetDragEvent;
33 import java.awt.dnd.DropTargetDropEvent;
34 import java.awt.dnd.DropTargetEvent;
35 import java.awt.dnd.DropTargetListener;
36 import java.awt.event.ActionEvent;
37 import java.awt.event.ActionListener;
38 import java.awt.event.FocusAdapter;
39 import java.awt.event.FocusEvent;
40 import java.awt.event.ItemEvent;
41 import java.awt.event.ItemListener;
42 import java.awt.event.KeyAdapter;
43 import java.awt.event.KeyEvent;
44 import java.awt.event.MouseEvent;
45 import java.awt.print.PageFormat;
46 import java.awt.print.PrinterJob;
47 import java.beans.PropertyChangeEvent;
49 import java.io.FileWriter;
50 import java.io.PrintWriter;
52 import java.util.ArrayList;
53 import java.util.Arrays;
54 import java.util.Deque;
55 import java.util.Enumeration;
56 import java.util.Hashtable;
57 import java.util.List;
58 import java.util.Vector;
60 import javax.swing.ButtonGroup;
61 import javax.swing.JCheckBoxMenuItem;
62 import javax.swing.JEditorPane;
63 import javax.swing.JInternalFrame;
64 import javax.swing.JLayeredPane;
65 import javax.swing.JMenu;
66 import javax.swing.JMenuItem;
67 import javax.swing.JScrollPane;
68 import javax.swing.SwingUtilities;
70 import jalview.analysis.AlignmentSorter;
71 import jalview.analysis.AlignmentUtils;
72 import jalview.analysis.CrossRef;
73 import jalview.analysis.Dna;
74 import jalview.analysis.GeneticCodeI;
75 import jalview.analysis.ParseProperties;
76 import jalview.analysis.SequenceIdMatcher;
77 import jalview.api.AlignExportSettingI;
78 import jalview.api.AlignViewControllerGuiI;
79 import jalview.api.AlignViewControllerI;
80 import jalview.api.AlignViewportI;
81 import jalview.api.AlignmentViewPanel;
82 import jalview.api.FeatureSettingsControllerI;
83 import jalview.api.FeatureSettingsModelI;
84 import jalview.api.SplitContainerI;
85 import jalview.api.ViewStyleI;
86 import jalview.api.analysis.SimilarityParamsI;
87 import jalview.bin.Cache;
88 import jalview.bin.Jalview;
89 import jalview.commands.CommandI;
90 import jalview.commands.EditCommand;
91 import jalview.commands.EditCommand.Action;
92 import jalview.commands.OrderCommand;
93 import jalview.commands.RemoveGapColCommand;
94 import jalview.commands.RemoveGapsCommand;
95 import jalview.commands.SlideSequencesCommand;
96 import jalview.commands.TrimRegionCommand;
97 import jalview.datamodel.AlignedCodonFrame;
98 import jalview.datamodel.Alignment;
99 import jalview.datamodel.AlignmentAnnotation;
100 import jalview.datamodel.AlignmentExportData;
101 import jalview.datamodel.AlignmentI;
102 import jalview.datamodel.AlignmentOrder;
103 import jalview.datamodel.AlignmentView;
104 import jalview.datamodel.ColumnSelection;
105 import jalview.datamodel.HiddenColumns;
106 import jalview.datamodel.HiddenSequences;
107 import jalview.datamodel.PDBEntry;
108 import jalview.datamodel.SeqCigar;
109 import jalview.datamodel.Sequence;
110 import jalview.datamodel.SequenceGroup;
111 import jalview.datamodel.SequenceI;
112 import jalview.gui.ColourMenuHelper.ColourChangeListener;
113 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
114 import jalview.io.AlignmentProperties;
115 import jalview.io.AnnotationFile;
116 import jalview.io.BackupFiles;
117 import jalview.io.BioJsHTMLOutput;
118 import jalview.io.DataSourceType;
119 import jalview.io.FileFormat;
120 import jalview.io.FileFormatI;
121 import jalview.io.FileFormats;
122 import jalview.io.FileLoader;
123 import jalview.io.FileParse;
124 import jalview.io.FormatAdapter;
125 import jalview.io.HtmlSvgOutput;
126 import jalview.io.IdentifyFile;
127 import jalview.io.JPredFile;
128 import jalview.io.JalviewFileChooser;
129 import jalview.io.JalviewFileView;
130 import jalview.io.JnetAnnotationMaker;
131 import jalview.io.NewickFile;
132 import jalview.io.ScoreMatrixFile;
133 import jalview.io.TCoffeeScoreFile;
134 import jalview.io.vcf.VCFLoader;
135 import jalview.jbgui.GAlignFrame;
136 import jalview.schemes.ColourSchemeI;
137 import jalview.schemes.ColourSchemes;
138 import jalview.schemes.ResidueColourScheme;
139 import jalview.schemes.TCoffeeColourScheme;
140 import jalview.util.HttpUtils;
141 import jalview.util.MessageManager;
142 import jalview.viewmodel.AlignmentViewport;
143 import jalview.viewmodel.ViewportRanges;
144 import jalview.ws.DBRefFetcher;
145 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
146 import jalview.ws.jws1.Discoverer;
147 import jalview.ws.jws2.Jws2Discoverer;
148 import jalview.ws.jws2.jabaws2.Jws2Instance;
149 import jalview.ws.seqfetcher.DbSourceProxy;
155 * @version $Revision$
157 public class AlignFrame extends GAlignFrame implements DropTargetListener,
158 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
161 public static final int DEFAULT_WIDTH = 700;
163 public static final int DEFAULT_HEIGHT = 500;
166 * The currently displayed panel (selected tabbed view if more than one)
168 public AlignmentPanel alignPanel;
170 AlignViewport viewport;
172 public AlignViewControllerI avc;
174 List<AlignmentPanel> alignPanels = new ArrayList<>();
177 * Last format used to load or save alignments in this window
179 FileFormatI currentFileFormat = null;
182 * Current filename for this alignment
184 String fileName = null;
187 * Creates a new AlignFrame object with specific width and height.
193 public AlignFrame(AlignmentI al, int width, int height)
195 this(al, null, width, height);
199 * Creates a new AlignFrame object with specific width, height and
205 * @param sequenceSetId
207 public AlignFrame(AlignmentI al, int width, int height,
208 String sequenceSetId)
210 this(al, null, width, height, sequenceSetId);
214 * Creates a new AlignFrame object with specific width, height and
220 * @param sequenceSetId
223 public AlignFrame(AlignmentI al, int width, int height,
224 String sequenceSetId, String viewId)
226 this(al, null, width, height, sequenceSetId, viewId);
230 * new alignment window with hidden columns
234 * @param hiddenColumns
235 * ColumnSelection or null
237 * Width of alignment frame
241 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
244 this(al, hiddenColumns, width, height, null);
248 * Create alignment frame for al with hiddenColumns, a specific width and
249 * height, and specific sequenceId
252 * @param hiddenColumns
255 * @param sequenceSetId
258 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
259 int height, String sequenceSetId)
261 this(al, hiddenColumns, width, height, sequenceSetId, null);
265 * Create alignment frame for al with hiddenColumns, a specific width and
266 * height, and specific sequenceId
269 * @param hiddenColumns
272 * @param sequenceSetId
277 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
278 int height, String sequenceSetId, String viewId)
280 setSize(width, height);
282 if (al.getDataset() == null)
287 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
289 alignPanel = new AlignmentPanel(this, viewport);
291 addAlignmentPanel(alignPanel, true);
295 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
296 HiddenColumns hiddenColumns, int width, int height)
298 setSize(width, height);
300 if (al.getDataset() == null)
305 viewport = new AlignViewport(al, hiddenColumns);
307 if (hiddenSeqs != null && hiddenSeqs.length > 0)
309 viewport.hideSequence(hiddenSeqs);
311 alignPanel = new AlignmentPanel(this, viewport);
312 addAlignmentPanel(alignPanel, true);
317 * Make a new AlignFrame from existing alignmentPanels
324 public AlignFrame(AlignmentPanel ap)
328 addAlignmentPanel(ap, false);
333 * initalise the alignframe from the underlying viewport data and the
338 if (!Jalview.isHeadlessMode())
340 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
343 avc = new jalview.controller.AlignViewController(this, viewport,
345 if (viewport.getAlignmentConservationAnnotation() == null)
347 // BLOSUM62Colour.setEnabled(false);
348 conservationMenuItem.setEnabled(false);
349 modifyConservation.setEnabled(false);
350 // PIDColour.setEnabled(false);
351 // abovePIDThreshold.setEnabled(false);
352 // modifyPID.setEnabled(false);
355 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
358 if (sortby.equals("Id"))
360 sortIDMenuItem_actionPerformed(null);
362 else if (sortby.equals("Pairwise Identity"))
364 sortPairwiseMenuItem_actionPerformed(null);
368 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
370 setMenusFromViewport(viewport);
371 buildSortByAnnotationScoresMenu();
372 calculateTree.addActionListener(new ActionListener()
376 public void actionPerformed(ActionEvent e)
383 if (Desktop.desktop != null)
385 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
386 addServiceListeners();
390 if (viewport.getWrapAlignment())
392 wrapMenuItem_actionPerformed(null);
395 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
397 this.overviewMenuItem_actionPerformed(null);
402 final List<AlignmentPanel> selviews = new ArrayList<>();
403 final List<AlignmentPanel> origview = new ArrayList<>();
404 final String menuLabel = MessageManager
405 .getString("label.copy_format_from");
406 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
407 new ViewSetProvider()
411 public AlignmentPanel[] getAllAlignmentPanels()
414 origview.add(alignPanel);
415 // make an array of all alignment panels except for this one
416 List<AlignmentPanel> aps = new ArrayList<>(
417 Arrays.asList(Desktop.getAlignmentPanels(null)));
418 aps.remove(AlignFrame.this.alignPanel);
419 return aps.toArray(new AlignmentPanel[aps.size()]);
421 }, selviews, new ItemListener()
425 public void itemStateChanged(ItemEvent e)
427 if (origview.size() > 0)
429 final AlignmentPanel ap = origview.get(0);
432 * Copy the ViewStyle of the selected panel to 'this one'.
433 * Don't change value of 'scaleProteinAsCdna' unless copying
436 ViewStyleI vs = selviews.get(0).getAlignViewport()
438 boolean fromSplitFrame = selviews.get(0)
439 .getAlignViewport().getCodingComplement() != null;
442 vs.setScaleProteinAsCdna(ap.getAlignViewport()
443 .getViewStyle().isScaleProteinAsCdna());
445 ap.getAlignViewport().setViewStyle(vs);
448 * Also rescale ViewStyle of SplitFrame complement if there is
449 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
450 * the whole ViewStyle (allow cDNA protein to have different
453 AlignViewportI complement = ap.getAlignViewport()
454 .getCodingComplement();
455 if (complement != null && vs.isScaleProteinAsCdna())
457 AlignFrame af = Desktop.getAlignFrameFor(complement);
458 ((SplitFrame) af.getSplitViewContainer())
460 af.setMenusForViewport();
464 ap.setSelected(true);
465 ap.alignFrame.setMenusForViewport();
470 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
471 .indexOf("devel") > -1
472 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
473 .indexOf("test") > -1)
475 formatMenu.add(vsel);
477 addFocusListener(new FocusAdapter()
480 public void focusGained(FocusEvent e)
482 Jalview.setCurrentAlignFrame(AlignFrame.this);
489 * Change the filename and format for the alignment, and enable the 'reload'
490 * button functionality.
497 public void setFileName(String file, FileFormatI format)
500 setFileFormat(format);
501 reload.setEnabled(true);
505 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
508 void addKeyListener()
510 addKeyListener(new KeyAdapter()
513 public void keyPressed(KeyEvent evt)
515 if (viewport.cursorMode
516 && ((evt.getKeyCode() >= KeyEvent.VK_0
517 && evt.getKeyCode() <= KeyEvent.VK_9)
518 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
519 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
520 && Character.isDigit(evt.getKeyChar()))
522 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
525 switch (evt.getKeyCode())
528 case 27: // escape key
529 deselectAllSequenceMenuItem_actionPerformed(null);
533 case KeyEvent.VK_DOWN:
534 if (evt.isAltDown() || !viewport.cursorMode)
536 moveSelectedSequences(false);
538 if (viewport.cursorMode)
540 alignPanel.getSeqPanel().moveCursor(0, 1,
541 evt.isShiftDown() && !evt.isAltDown());
546 if (evt.isAltDown() || !viewport.cursorMode)
548 moveSelectedSequences(true);
550 if (viewport.cursorMode)
552 alignPanel.getSeqPanel().moveCursor(0, -1,
553 evt.isShiftDown() && !evt.isAltDown());
557 case KeyEvent.VK_LEFT:
558 if (evt.isAltDown() || !viewport.cursorMode)
560 slideSequences(false,
561 alignPanel.getSeqPanel().getKeyboardNo1());
565 alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
570 case KeyEvent.VK_RIGHT:
571 if (evt.isAltDown() || !viewport.cursorMode)
573 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
577 alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
581 case KeyEvent.VK_SPACE:
582 if (viewport.cursorMode)
584 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
585 || evt.isShiftDown() || evt.isAltDown());
589 // case KeyEvent.VK_A:
590 // if (viewport.cursorMode)
592 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
593 // //System.out.println("A");
597 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
598 * System.out.println("closing bracket"); } break;
600 case KeyEvent.VK_DELETE:
601 case KeyEvent.VK_BACK_SPACE:
602 if (!viewport.cursorMode)
604 cut_actionPerformed(null);
608 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
609 || evt.isShiftDown() || evt.isAltDown());
615 if (viewport.cursorMode)
617 alignPanel.getSeqPanel().setCursorRow();
621 if (viewport.cursorMode && !evt.isControlDown())
623 alignPanel.getSeqPanel().setCursorColumn();
627 if (viewport.cursorMode)
629 alignPanel.getSeqPanel().setCursorPosition();
633 case KeyEvent.VK_ENTER:
634 case KeyEvent.VK_COMMA:
635 if (viewport.cursorMode)
637 alignPanel.getSeqPanel().setCursorRowAndColumn();
642 if (viewport.cursorMode)
644 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
648 if (viewport.cursorMode)
650 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
655 viewport.cursorMode = !viewport.cursorMode;
656 statusBar.setText(MessageManager
657 .formatMessage("label.keyboard_editing_mode", new String[]
658 { (viewport.cursorMode ? "on" : "off") }));
659 if (viewport.cursorMode)
661 ViewportRanges ranges = viewport.getRanges();
662 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
664 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
667 alignPanel.getSeqPanel().seqCanvas.repaint();
673 Help.showHelpWindow();
674 } catch (Exception ex)
676 ex.printStackTrace();
681 boolean toggleSeqs = !evt.isControlDown();
682 boolean toggleCols = !evt.isShiftDown();
683 toggleHiddenRegions(toggleSeqs, toggleCols);
688 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
689 boolean modifyExisting = true; // always modify, don't clear
690 // evt.isShiftDown();
691 boolean invertHighlighted = evt.isAltDown();
692 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
696 case KeyEvent.VK_PAGE_UP:
697 viewport.getRanges().pageUp();
699 case KeyEvent.VK_PAGE_DOWN:
700 viewport.getRanges().pageDown();
706 public void keyReleased(KeyEvent evt)
708 switch (evt.getKeyCode())
710 case KeyEvent.VK_LEFT:
711 if (evt.isAltDown() || !viewport.cursorMode)
713 viewport.firePropertyChange("alignment", null,
714 viewport.getAlignment().getSequences());
718 case KeyEvent.VK_RIGHT:
719 if (evt.isAltDown() || !viewport.cursorMode)
721 viewport.firePropertyChange("alignment", null,
722 viewport.getAlignment().getSequences());
730 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
732 ap.alignFrame = this;
733 avc = new jalview.controller.AlignViewController(this, viewport,
738 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
740 int aSize = alignPanels.size();
742 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
744 if (aSize == 1 && ap.av.getViewName() == null)
746 this.getContentPane().add(ap, BorderLayout.CENTER);
752 setInitialTabVisible();
755 expandViews.setEnabled(true);
756 gatherViews.setEnabled(true);
757 tabbedPane.addTab(ap.av.getViewName(), ap);
759 ap.setVisible(false);
764 if (ap.av.isPadGaps())
766 ap.av.getAlignment().padGaps();
768 ap.av.updateConservation(ap);
769 ap.av.updateConsensus(ap);
770 ap.av.updateStrucConsensus(ap);
774 public void setInitialTabVisible()
776 expandViews.setEnabled(true);
777 gatherViews.setEnabled(true);
778 tabbedPane.setVisible(true);
779 AlignmentPanel first = alignPanels.get(0);
780 tabbedPane.addTab(first.av.getViewName(), first);
781 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
784 public AlignViewport getViewport()
789 /* Set up intrinsic listeners for dynamically generated GUI bits. */
790 private void addServiceListeners()
792 final java.beans.PropertyChangeListener thisListener;
793 Desktop.instance.addJalviewPropertyChangeListener("services",
794 thisListener = new java.beans.PropertyChangeListener()
797 public void propertyChange(PropertyChangeEvent evt)
799 // // System.out.println("Discoverer property change.");
800 // if (evt.getPropertyName().equals("services"))
802 SwingUtilities.invokeLater(new Runnable()
809 "Rebuild WS Menu for service change");
810 BuildWebServiceMenu();
817 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
820 public void internalFrameClosed(
821 javax.swing.event.InternalFrameEvent evt)
823 // System.out.println("deregistering discoverer listener");
824 Desktop.instance.removeJalviewPropertyChangeListener("services",
826 closeMenuItem_actionPerformed(true);
829 // Finally, build the menu once to get current service state
830 new Thread(new Runnable()
835 BuildWebServiceMenu();
841 * Configure menu items that vary according to whether the alignment is
842 * nucleotide or protein
844 public void setGUINucleotide()
846 AlignmentI al = getViewport().getAlignment();
847 boolean nucleotide = al.isNucleotide();
849 loadVcf.setVisible(nucleotide);
850 showTranslation.setVisible(nucleotide);
851 showReverse.setVisible(nucleotide);
852 showReverseComplement.setVisible(nucleotide);
853 conservationMenuItem.setEnabled(!nucleotide);
855 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
856 showGroupConservation.setEnabled(!nucleotide);
858 showComplementMenuItem
859 .setText(nucleotide ? MessageManager.getString("label.protein")
860 : MessageManager.getString("label.nucleotide"));
864 * set up menus for the current viewport. This may be called after any
865 * operation that affects the data in the current view (selection changed,
866 * etc) to update the menus to reflect the new state.
869 public void setMenusForViewport()
871 setMenusFromViewport(viewport);
875 * Need to call this method when tabs are selected for multiple views, or when
876 * loading from Jalview2XML.java
881 public void setMenusFromViewport(AlignViewport av)
883 padGapsMenuitem.setSelected(av.isPadGaps());
884 colourTextMenuItem.setSelected(av.isShowColourText());
885 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
886 modifyPID.setEnabled(abovePIDThreshold.isSelected());
887 conservationMenuItem.setSelected(av.getConservationSelected());
888 modifyConservation.setEnabled(conservationMenuItem.isSelected());
889 seqLimits.setSelected(av.getShowJVSuffix());
890 idRightAlign.setSelected(av.isRightAlignIds());
891 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
892 renderGapsMenuItem.setSelected(av.isRenderGaps());
893 wrapMenuItem.setSelected(av.getWrapAlignment());
894 scaleAbove.setVisible(av.getWrapAlignment());
895 scaleLeft.setVisible(av.getWrapAlignment());
896 scaleRight.setVisible(av.getWrapAlignment());
897 annotationPanelMenuItem.setState(av.isShowAnnotation());
899 * Show/hide annotations only enabled if annotation panel is shown
901 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
902 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
903 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
904 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
905 viewBoxesMenuItem.setSelected(av.getShowBoxes());
906 viewTextMenuItem.setSelected(av.getShowText());
907 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
908 showGroupConsensus.setSelected(av.isShowGroupConsensus());
909 showGroupConservation.setSelected(av.isShowGroupConservation());
910 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
911 showSequenceLogo.setSelected(av.isShowSequenceLogo());
912 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
914 ColourMenuHelper.setColourSelected(colourMenu,
915 av.getGlobalColourScheme());
917 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
918 hiddenMarkers.setState(av.getShowHiddenMarkers());
919 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
920 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
921 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
922 autoCalculate.setSelected(av.autoCalculateConsensus);
923 sortByTree.setSelected(av.sortByTree);
924 listenToViewSelections.setSelected(av.followSelection);
926 showProducts.setEnabled(canShowProducts());
927 setGroovyEnabled(Desktop.getGroovyConsole() != null);
933 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
937 public void setGroovyEnabled(boolean b)
939 runGroovy.setEnabled(b);
942 private IProgressIndicator progressBar;
947 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
950 public void setProgressBar(String message, long id)
952 progressBar.setProgressBar(message, id);
956 public void registerHandler(final long id,
957 final IProgressIndicatorHandler handler)
959 progressBar.registerHandler(id, handler);
964 * @return true if any progress bars are still active
967 public boolean operationInProgress()
969 return progressBar.operationInProgress();
973 * Sets the text of the status bar. Note that setting a null or empty value
974 * will cause the status bar to be hidden, with possibly undesirable flicker
975 * of the screen layout.
978 public void setStatus(String text)
980 statusBar.setText(text == null || text.isEmpty() ? " " : text);
984 * Added so Castor Mapping file can obtain Jalview Version
986 public String getVersion()
988 return jalview.bin.Cache.getProperty("VERSION");
991 public FeatureRenderer getFeatureRenderer()
993 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
997 public void fetchSequence_actionPerformed(ActionEvent e)
999 new jalview.gui.SequenceFetcher(this);
1003 public void addFromFile_actionPerformed(ActionEvent e)
1005 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1009 public void reload_actionPerformed(ActionEvent e)
1011 if (fileName != null)
1013 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1014 // originating file's format
1015 // TODO: work out how to recover feature settings for correct view(s) when
1016 // file is reloaded.
1017 if (FileFormat.Jalview.equals(currentFileFormat))
1019 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1020 for (int i = 0; i < frames.length; i++)
1022 if (frames[i] instanceof AlignFrame && frames[i] != this
1023 && ((AlignFrame) frames[i]).fileName != null
1024 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1028 frames[i].setSelected(true);
1029 Desktop.instance.closeAssociatedWindows();
1030 } catch (java.beans.PropertyVetoException ex)
1036 Desktop.instance.closeAssociatedWindows();
1038 FileLoader loader = new FileLoader();
1039 DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
1040 ? DataSourceType.URL
1041 : DataSourceType.FILE;
1042 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1046 Rectangle bounds = this.getBounds();
1048 FileLoader loader = new FileLoader();
1049 DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
1050 ? DataSourceType.URL
1051 : DataSourceType.FILE;
1052 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1053 protocol, currentFileFormat);
1055 newframe.setBounds(bounds);
1056 if (featureSettings != null && featureSettings.isShowing())
1058 final Rectangle fspos = featureSettings.frame.getBounds();
1059 // TODO: need a 'show feature settings' function that takes bounds -
1060 // need to refactor Desktop.addFrame
1061 newframe.featureSettings_actionPerformed(null);
1062 final FeatureSettings nfs = newframe.featureSettings;
1063 SwingUtilities.invokeLater(new Runnable()
1068 nfs.frame.setBounds(fspos);
1071 this.featureSettings.close();
1072 this.featureSettings = null;
1074 this.closeMenuItem_actionPerformed(true);
1080 public void addFromText_actionPerformed(ActionEvent e)
1083 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1087 public void addFromURL_actionPerformed(ActionEvent e)
1089 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1093 public void save_actionPerformed(ActionEvent e)
1095 if (fileName == null || (currentFileFormat == null)
1096 || HttpUtils.startsWithHttpOrHttps(fileName))
1098 saveAs_actionPerformed(null);
1102 saveAlignment(fileName, currentFileFormat);
1113 public void saveAs_actionPerformed(ActionEvent e)
1115 String format = currentFileFormat == null ? null
1116 : currentFileFormat.getName();
1117 JalviewFileChooser chooser = JalviewFileChooser
1118 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1120 chooser.setFileView(new JalviewFileView());
1121 chooser.setDialogTitle(
1122 MessageManager.getString("label.save_alignment_to_file"));
1123 chooser.setToolTipText(MessageManager.getString("action.save"));
1125 int value = chooser.showSaveDialog(this);
1127 if (value == JalviewFileChooser.APPROVE_OPTION)
1129 currentFileFormat = chooser.getSelectedFormat();
1130 while (currentFileFormat == null)
1132 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1133 MessageManager.getString(
1134 "label.select_file_format_before_saving"),
1135 MessageManager.getString("label.file_format_not_specified"),
1136 JvOptionPane.WARNING_MESSAGE);
1137 currentFileFormat = chooser.getSelectedFormat();
1138 value = chooser.showSaveDialog(this);
1139 if (value != JalviewFileChooser.APPROVE_OPTION)
1145 fileName = chooser.getSelectedFile().getPath();
1147 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1149 Cache.setProperty("LAST_DIRECTORY", fileName);
1150 saveAlignment(fileName, currentFileFormat);
1154 public boolean saveAlignment(String file, FileFormatI format)
1156 boolean success = true;
1158 if (FileFormat.Jalview.equals(format))
1160 String shortName = title;
1162 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1164 shortName = shortName.substring(
1165 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1168 success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1171 statusBar.setText(MessageManager.formatMessage(
1172 "label.successfully_saved_to_file_in_format", new Object[]
1173 { fileName, format }));
1178 AlignmentExportData exportData = getAlignmentForExport(format,
1180 if (exportData.getSettings().isCancelled())
1184 FormatAdapter f = new FormatAdapter(alignPanel,
1185 exportData.getSettings());
1186 String output = f.formatSequences(format, exportData.getAlignment(), // class
1190 // occur in the distant future
1191 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1192 f.getCacheSuffixDefault(format),
1193 viewport.getAlignment().getHiddenColumns());
1201 // create backupfiles object and get new temp filename destination
1202 BackupFiles backupfiles = new BackupFiles(file);
1206 PrintWriter out = new PrintWriter(
1207 new FileWriter(backupfiles.getTempFilePath()));
1211 this.setTitle(file);
1212 statusBar.setText(MessageManager.formatMessage(
1213 "label.successfully_saved_to_file_in_format", new Object[]
1214 { fileName, format.getName() }));
1215 } catch (Exception ex)
1218 ex.printStackTrace();
1221 backupfiles.setWriteSuccess(success);
1222 // do the backup file roll and rename the temp file to actual file
1223 success = backupfiles.rollBackupsAndRenameTempFile();
1230 JvOptionPane.showInternalMessageDialog(this, MessageManager
1231 .formatMessage("label.couldnt_save_file", new Object[]
1233 MessageManager.getString("label.error_saving_file"),
1234 JvOptionPane.WARNING_MESSAGE);
1240 private void warningMessage(String warning, String title)
1242 if (new jalview.util.Platform().isHeadless())
1244 System.err.println("Warning: " + title + "\nWarning: " + warning);
1249 JvOptionPane.showInternalMessageDialog(this, warning, title,
1250 JvOptionPane.WARNING_MESSAGE);
1262 protected void outputText_actionPerformed(ActionEvent e)
1264 FileFormatI fileFormat = FileFormats.getInstance()
1265 .forName(e.getActionCommand());
1266 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1268 if (exportData.getSettings().isCancelled())
1272 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1273 cap.setForInput(null);
1276 FileFormatI format = fileFormat;
1277 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1278 .formatSequences(format, exportData.getAlignment(),
1279 exportData.getOmitHidden(),
1280 exportData.getStartEndPostions(),
1281 viewport.getAlignment().getHiddenColumns()));
1282 Desktop.addInternalFrame(cap, MessageManager
1283 .formatMessage("label.alignment_output_command", new Object[]
1284 { e.getActionCommand() }), 600, 500);
1285 } catch (OutOfMemoryError oom)
1287 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1294 public static AlignmentExportData getAlignmentForExport(
1295 FileFormatI format, AlignViewportI viewport,
1296 AlignExportSettingI exportSettings)
1298 AlignmentI alignmentToExport = null;
1299 AlignExportSettingI settings = exportSettings;
1300 String[] omitHidden = null;
1302 HiddenSequences hiddenSeqs = viewport.getAlignment()
1303 .getHiddenSequences();
1305 alignmentToExport = viewport.getAlignment();
1307 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1308 if (settings == null)
1310 settings = new AlignExportSettings(hasHiddenSeqs,
1311 viewport.hasHiddenColumns(), format);
1313 // settings.isExportAnnotations();
1315 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1317 omitHidden = viewport.getViewAsString(false,
1318 settings.isExportHiddenSequences());
1321 int[] alignmentStartEnd = new int[2];
1322 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1324 alignmentToExport = hiddenSeqs.getFullAlignment();
1328 alignmentToExport = viewport.getAlignment();
1330 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1331 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1332 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1333 omitHidden, alignmentStartEnd, settings);
1344 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1346 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1347 htmlSVG.exportHTML(null);
1351 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1353 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1354 bjs.exportHTML(null);
1357 public void createImageMap(File file, String image)
1359 alignPanel.makePNGImageMap(file, image);
1369 public void createPNG(File f)
1371 alignPanel.makePNG(f);
1381 public void createEPS(File f)
1383 alignPanel.makeEPS(f);
1387 public void createSVG(File f)
1389 alignPanel.makeSVG(f);
1393 public void pageSetup_actionPerformed(ActionEvent e)
1395 PrinterJob printJob = PrinterJob.getPrinterJob();
1396 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1406 public void printMenuItem_actionPerformed(ActionEvent e)
1408 // Putting in a thread avoids Swing painting problems
1409 PrintThread thread = new PrintThread(alignPanel);
1414 public void exportFeatures_actionPerformed(ActionEvent e)
1416 new AnnotationExporter(alignPanel).exportFeatures();
1420 public void exportAnnotations_actionPerformed(ActionEvent e)
1422 new AnnotationExporter(alignPanel).exportAnnotations();
1426 public void associatedData_actionPerformed(ActionEvent e)
1428 // Pick the tree file
1429 JalviewFileChooser chooser = new JalviewFileChooser(
1430 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1431 chooser.setFileView(new JalviewFileView());
1432 chooser.setDialogTitle(
1433 MessageManager.getString("label.load_jalview_annotations"));
1434 chooser.setToolTipText(
1435 MessageManager.getString("label.load_jalview_annotations"));
1437 int value = chooser.showOpenDialog(null);
1439 if (value == JalviewFileChooser.APPROVE_OPTION)
1441 String choice = chooser.getSelectedFile().getPath();
1442 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1443 loadJalviewDataFile(choice, null, null, null);
1449 * Close the current view or all views in the alignment frame. If the frame
1450 * only contains one view then the alignment will be removed from memory.
1452 * @param closeAllTabs
1455 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1457 if (alignPanels != null && alignPanels.size() < 2)
1459 closeAllTabs = true;
1464 if (alignPanels != null)
1468 if (this.isClosed())
1470 // really close all the windows - otherwise wait till
1471 // setClosed(true) is called
1472 for (int i = 0; i < alignPanels.size(); i++)
1474 AlignmentPanel ap = alignPanels.get(i);
1481 closeView(alignPanel);
1486 if (featureSettings != null && featureSettings.isOpen())
1488 featureSettings.close();
1489 featureSettings = null;
1492 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1493 * be called recursively, with the frame now in 'closed' state
1495 this.setClosed(true);
1497 } catch (Exception ex)
1499 ex.printStackTrace();
1504 * Close the specified panel and close up tabs appropriately.
1506 * @param panelToClose
1508 public void closeView(AlignmentPanel panelToClose)
1510 int index = tabbedPane.getSelectedIndex();
1511 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1512 alignPanels.remove(panelToClose);
1513 panelToClose.closePanel();
1514 panelToClose = null;
1516 tabbedPane.removeTabAt(closedindex);
1517 tabbedPane.validate();
1519 if (index > closedindex || index == tabbedPane.getTabCount())
1521 // modify currently selected tab index if necessary.
1525 this.tabSelectionChanged(index);
1531 void updateEditMenuBar()
1534 if (viewport.getHistoryList().size() > 0)
1536 undoMenuItem.setEnabled(true);
1537 CommandI command = viewport.getHistoryList().peek();
1538 undoMenuItem.setText(MessageManager
1539 .formatMessage("label.undo_command", new Object[]
1540 { command.getDescription() }));
1544 undoMenuItem.setEnabled(false);
1545 undoMenuItem.setText(MessageManager.getString("action.undo"));
1548 if (viewport.getRedoList().size() > 0)
1550 redoMenuItem.setEnabled(true);
1552 CommandI command = viewport.getRedoList().peek();
1553 redoMenuItem.setText(MessageManager
1554 .formatMessage("label.redo_command", new Object[]
1555 { command.getDescription() }));
1559 redoMenuItem.setEnabled(false);
1560 redoMenuItem.setText(MessageManager.getString("action.redo"));
1565 public void addHistoryItem(CommandI command)
1567 if (command.getSize() > 0)
1569 viewport.addToHistoryList(command);
1570 viewport.clearRedoList();
1571 updateEditMenuBar();
1572 viewport.updateHiddenColumns();
1573 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1574 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1575 // viewport.getColumnSelection()
1576 // .getHiddenColumns().size() > 0);
1582 * @return alignment objects for all views
1584 AlignmentI[] getViewAlignments()
1586 if (alignPanels != null)
1588 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1590 for (AlignmentPanel ap : alignPanels)
1592 als[i++] = ap.av.getAlignment();
1596 if (viewport != null)
1598 return new AlignmentI[] { viewport.getAlignment() };
1610 protected void undoMenuItem_actionPerformed(ActionEvent e)
1612 if (viewport.getHistoryList().isEmpty())
1616 CommandI command = viewport.getHistoryList().pop();
1617 viewport.addToRedoList(command);
1618 command.undoCommand(getViewAlignments());
1620 AlignmentViewport originalSource = getOriginatingSource(command);
1621 updateEditMenuBar();
1623 if (originalSource != null)
1625 if (originalSource != viewport)
1628 "Implementation worry: mismatch of viewport origin for undo");
1630 originalSource.updateHiddenColumns();
1631 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1633 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1634 // viewport.getColumnSelection()
1635 // .getHiddenColumns().size() > 0);
1636 originalSource.firePropertyChange("alignment", null,
1637 originalSource.getAlignment().getSequences());
1648 protected void redoMenuItem_actionPerformed(ActionEvent e)
1650 if (viewport.getRedoList().size() < 1)
1655 CommandI command = viewport.getRedoList().pop();
1656 viewport.addToHistoryList(command);
1657 command.doCommand(getViewAlignments());
1659 AlignmentViewport originalSource = getOriginatingSource(command);
1660 updateEditMenuBar();
1662 if (originalSource != null)
1665 if (originalSource != viewport)
1668 "Implementation worry: mismatch of viewport origin for redo");
1670 originalSource.updateHiddenColumns();
1671 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1673 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1674 // viewport.getColumnSelection()
1675 // .getHiddenColumns().size() > 0);
1676 originalSource.firePropertyChange("alignment", null,
1677 originalSource.getAlignment().getSequences());
1681 AlignmentViewport getOriginatingSource(CommandI command)
1683 AlignmentViewport originalSource = null;
1684 // For sequence removal and addition, we need to fire
1685 // the property change event FROM the viewport where the
1686 // original alignment was altered
1687 AlignmentI al = null;
1688 if (command instanceof EditCommand)
1690 EditCommand editCommand = (EditCommand) command;
1691 al = editCommand.getAlignment();
1692 List<Component> comps = PaintRefresher.components
1693 .get(viewport.getSequenceSetId());
1695 for (Component comp : comps)
1697 if (comp instanceof AlignmentPanel)
1699 if (al == ((AlignmentPanel) comp).av.getAlignment())
1701 originalSource = ((AlignmentPanel) comp).av;
1708 if (originalSource == null)
1710 // The original view is closed, we must validate
1711 // the current view against the closed view first
1714 PaintRefresher.validateSequences(al, viewport.getAlignment());
1717 originalSource = viewport;
1720 return originalSource;
1729 public void moveSelectedSequences(boolean up)
1731 SequenceGroup sg = viewport.getSelectionGroup();
1737 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1738 viewport.getHiddenRepSequences(), up);
1739 alignPanel.paintAlignment(true, false);
1742 synchronized void slideSequences(boolean right, int size)
1744 List<SequenceI> sg = new ArrayList<>();
1745 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup()
1746 .getSize() != viewport.getAlignment().getHeight())
1748 sg = viewport.getSelectionGroup()
1749 .getSequences(viewport.getHiddenRepSequences());
1752 if (sg.size() == 0 && viewport.cursorMode)
1754 sg.add(viewport.getAlignment()
1755 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1763 List<SequenceI> invertGroup = new ArrayList<>();
1765 for (SequenceI seq : viewport.getAlignment().getSequences())
1767 if (!sg.contains(seq))
1769 invertGroup.add(seq);
1773 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1775 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1776 for (int i = 0; i < invertGroup.size(); i++)
1778 seqs2[i] = invertGroup.get(i);
1781 SlideSequencesCommand ssc;
1784 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1785 viewport.getGapCharacter());
1789 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1790 viewport.getGapCharacter());
1793 int groupAdjustment = 0;
1794 if (ssc.getGapsInsertedBegin() && right)
1796 if (viewport.cursorMode)
1798 alignPanel.getSeqPanel().moveCursor(size, 0);
1802 groupAdjustment = size;
1805 else if (!ssc.getGapsInsertedBegin() && !right)
1807 if (viewport.cursorMode)
1809 alignPanel.getSeqPanel().moveCursor(-size, 0);
1813 groupAdjustment = -size;
1817 if (groupAdjustment != 0)
1819 viewport.getSelectionGroup().setStartRes(
1820 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1821 viewport.getSelectionGroup().setEndRes(
1822 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1826 * just extend the last slide command if compatible; but not if in
1827 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1829 boolean appendHistoryItem = false;
1830 Deque<CommandI> historyList = viewport.getHistoryList();
1831 boolean inSplitFrame = getSplitViewContainer() != null;
1832 if (!inSplitFrame && historyList != null && historyList.size() > 0
1833 && historyList.peek() instanceof SlideSequencesCommand)
1835 appendHistoryItem = ssc.appendSlideCommand(
1836 (SlideSequencesCommand) historyList.peek());
1839 if (!appendHistoryItem)
1841 addHistoryItem(ssc);
1854 protected void copy_actionPerformed(ActionEvent e)
1856 if (viewport.getSelectionGroup() == null)
1860 // TODO: preserve the ordering of displayed alignment annotation in any
1861 // internal paste (particularly sequence associated annotation)
1862 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1863 String[] omitHidden = null;
1865 if (viewport.hasHiddenColumns())
1867 omitHidden = viewport.getViewAsString(true);
1870 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1871 seqs, omitHidden, null);
1873 StringSelection ss = new StringSelection(output);
1877 jalview.gui.Desktop.internalCopy = true;
1878 // Its really worth setting the clipboard contents
1879 // to empty before setting the large StringSelection!!
1880 Toolkit.getDefaultToolkit().getSystemClipboard()
1881 .setContents(new StringSelection(""), null);
1883 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1885 } catch (OutOfMemoryError er)
1887 new OOMWarning("copying region", er);
1891 HiddenColumns hiddenColumns = null;
1892 if (viewport.hasHiddenColumns())
1894 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1895 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1897 // create new HiddenColumns object with copy of hidden regions
1898 // between startRes and endRes, offset by startRes
1899 hiddenColumns = new HiddenColumns(
1900 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1901 hiddenCutoff, hiddenOffset);
1904 Desktop.jalviewClipboard = new Object[] { seqs,
1905 viewport.getAlignment().getDataset(), hiddenColumns };
1906 statusBar.setText(MessageManager.formatMessage(
1907 "label.copied_sequences_to_clipboard", new Object[]
1908 { Integer.valueOf(seqs.length).toString() }));
1918 protected void pasteNew_actionPerformed(ActionEvent e)
1930 protected void pasteThis_actionPerformed(ActionEvent e)
1936 * Paste contents of Jalview clipboard
1938 * @param newAlignment
1939 * true to paste to a new alignment, otherwise add to this.
1941 void paste(boolean newAlignment)
1943 boolean externalPaste = true;
1946 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1947 Transferable contents = c.getContents(this);
1949 if (contents == null)
1958 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1959 if (str.length() < 1)
1964 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1966 } catch (OutOfMemoryError er)
1968 new OOMWarning("Out of memory pasting sequences!!", er);
1972 SequenceI[] sequences;
1973 boolean annotationAdded = false;
1974 AlignmentI alignment = null;
1976 if (Desktop.jalviewClipboard != null)
1978 // The clipboard was filled from within Jalview, we must use the
1980 // And dataset from the copied alignment
1981 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1982 // be doubly sure that we create *new* sequence objects.
1983 sequences = new SequenceI[newseq.length];
1984 for (int i = 0; i < newseq.length; i++)
1986 sequences[i] = new Sequence(newseq[i]);
1988 alignment = new Alignment(sequences);
1989 externalPaste = false;
1993 // parse the clipboard as an alignment.
1994 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1996 sequences = alignment.getSequencesArray();
2000 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2006 if (Desktop.jalviewClipboard != null)
2008 // dataset is inherited
2009 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2013 // new dataset is constructed
2014 alignment.setDataset(null);
2016 alwidth = alignment.getWidth() + 1;
2020 AlignmentI pastedal = alignment; // preserve pasted alignment object
2021 // Add pasted sequences and dataset into existing alignment.
2022 alignment = viewport.getAlignment();
2023 alwidth = alignment.getWidth() + 1;
2024 // decide if we need to import sequences from an existing dataset
2025 boolean importDs = Desktop.jalviewClipboard != null
2026 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2027 // importDs==true instructs us to copy over new dataset sequences from
2028 // an existing alignment
2029 Vector newDs = (importDs) ? new Vector() : null; // used to create
2030 // minimum dataset set
2032 for (int i = 0; i < sequences.length; i++)
2036 newDs.addElement(null);
2038 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2040 if (importDs && ds != null)
2042 if (!newDs.contains(ds))
2044 newDs.setElementAt(ds, i);
2045 ds = new Sequence(ds);
2046 // update with new dataset sequence
2047 sequences[i].setDatasetSequence(ds);
2051 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2056 // copy and derive new dataset sequence
2057 sequences[i] = sequences[i].deriveSequence();
2058 alignment.getDataset()
2059 .addSequence(sequences[i].getDatasetSequence());
2060 // TODO: avoid creation of duplicate dataset sequences with a
2061 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2063 alignment.addSequence(sequences[i]); // merges dataset
2067 newDs.clear(); // tidy up
2069 if (alignment.getAlignmentAnnotation() != null)
2071 for (AlignmentAnnotation alan : alignment
2072 .getAlignmentAnnotation())
2074 if (alan.graphGroup > fgroup)
2076 fgroup = alan.graphGroup;
2080 if (pastedal.getAlignmentAnnotation() != null)
2082 // Add any annotation attached to alignment.
2083 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2084 for (int i = 0; i < alann.length; i++)
2086 annotationAdded = true;
2087 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2089 AlignmentAnnotation newann = new AlignmentAnnotation(
2091 if (newann.graphGroup > -1)
2093 if (newGraphGroups.size() <= newann.graphGroup
2094 || newGraphGroups.get(newann.graphGroup) == null)
2096 for (int q = newGraphGroups
2097 .size(); q <= newann.graphGroup; q++)
2099 newGraphGroups.add(q, null);
2101 newGraphGroups.set(newann.graphGroup,
2102 Integer.valueOf(++fgroup));
2104 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2108 newann.padAnnotation(alwidth);
2109 alignment.addAnnotation(newann);
2119 addHistoryItem(new EditCommand(
2120 MessageManager.getString("label.add_sequences"),
2121 Action.PASTE, sequences, 0, alignment.getWidth(),
2124 // Add any annotations attached to sequences
2125 for (int i = 0; i < sequences.length; i++)
2127 if (sequences[i].getAnnotation() != null)
2129 AlignmentAnnotation newann;
2130 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2132 annotationAdded = true;
2133 newann = sequences[i].getAnnotation()[a];
2134 newann.adjustForAlignment();
2135 newann.padAnnotation(alwidth);
2136 if (newann.graphGroup > -1)
2138 if (newann.graphGroup > -1)
2140 if (newGraphGroups.size() <= newann.graphGroup
2141 || newGraphGroups.get(newann.graphGroup) == null)
2143 for (int q = newGraphGroups
2144 .size(); q <= newann.graphGroup; q++)
2146 newGraphGroups.add(q, null);
2148 newGraphGroups.set(newann.graphGroup,
2149 Integer.valueOf(++fgroup));
2151 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2155 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2159 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2167 // propagate alignment changed.
2168 viewport.getRanges().setEndSeq(alignment.getHeight());
2169 if (annotationAdded)
2171 // Duplicate sequence annotation in all views.
2172 AlignmentI[] alview = this.getViewAlignments();
2173 for (int i = 0; i < sequences.length; i++)
2175 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2180 for (int avnum = 0; avnum < alview.length; avnum++)
2182 if (alview[avnum] != alignment)
2184 // duplicate in a view other than the one with input focus
2185 int avwidth = alview[avnum].getWidth() + 1;
2186 // this relies on sann being preserved after we
2187 // modify the sequence's annotation array for each duplication
2188 for (int a = 0; a < sann.length; a++)
2190 AlignmentAnnotation newann = new AlignmentAnnotation(
2192 sequences[i].addAlignmentAnnotation(newann);
2193 newann.padAnnotation(avwidth);
2194 alview[avnum].addAnnotation(newann); // annotation was
2195 // duplicated earlier
2196 // TODO JAL-1145 graphGroups are not updated for sequence
2197 // annotation added to several views. This may cause
2199 alview[avnum].setAnnotationIndex(newann, a);
2204 buildSortByAnnotationScoresMenu();
2206 viewport.firePropertyChange("alignment", null,
2207 alignment.getSequences());
2208 if (alignPanels != null)
2210 for (AlignmentPanel ap : alignPanels)
2212 ap.validateAnnotationDimensions(false);
2217 alignPanel.validateAnnotationDimensions(false);
2223 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2225 String newtitle = new String("Copied sequences");
2227 if (Desktop.jalviewClipboard != null
2228 && Desktop.jalviewClipboard[2] != null)
2230 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2231 af.viewport.setHiddenColumns(hc);
2234 // >>>This is a fix for the moment, until a better solution is
2236 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2237 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2238 .getFeatureRenderer());
2240 // TODO: maintain provenance of an alignment, rather than just make the
2241 // title a concatenation of operations.
2244 if (title.startsWith("Copied sequences"))
2250 newtitle = newtitle.concat("- from " + title);
2255 newtitle = new String("Pasted sequences");
2258 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2263 } catch (Exception ex)
2265 ex.printStackTrace();
2266 System.out.println("Exception whilst pasting: " + ex);
2267 // could be anything being pasted in here
2273 protected void expand_newalign(ActionEvent e)
2277 AlignmentI alignment = AlignmentUtils
2278 .expandContext(getViewport().getAlignment(), -1);
2279 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2281 String newtitle = new String("Flanking alignment");
2283 if (Desktop.jalviewClipboard != null
2284 && Desktop.jalviewClipboard[2] != null)
2286 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2287 af.viewport.setHiddenColumns(hc);
2290 // >>>This is a fix for the moment, until a better solution is
2292 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2293 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2294 .getFeatureRenderer());
2296 // TODO: maintain provenance of an alignment, rather than just make the
2297 // title a concatenation of operations.
2299 if (title.startsWith("Copied sequences"))
2305 newtitle = newtitle.concat("- from " + title);
2309 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2311 } catch (Exception ex)
2313 ex.printStackTrace();
2314 System.out.println("Exception whilst pasting: " + ex);
2315 // could be anything being pasted in here
2316 } catch (OutOfMemoryError oom)
2318 new OOMWarning("Viewing flanking region of alignment", oom);
2329 protected void cut_actionPerformed(ActionEvent e)
2331 copy_actionPerformed(null);
2332 delete_actionPerformed(null);
2342 protected void delete_actionPerformed(ActionEvent evt)
2345 SequenceGroup sg = viewport.getSelectionGroup();
2352 * If the cut affects all sequences, warn, remove highlighted columns
2354 if (sg.getSize() == viewport.getAlignment().getHeight())
2356 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2357 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2358 if (isEntireAlignWidth)
2360 int confirm = JvOptionPane.showConfirmDialog(this,
2361 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2362 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2363 JvOptionPane.OK_CANCEL_OPTION);
2365 if (confirm == JvOptionPane.CANCEL_OPTION
2366 || confirm == JvOptionPane.CLOSED_OPTION)
2371 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2372 sg.getEndRes() + 1);
2374 SequenceI[] cut = sg.getSequences()
2375 .toArray(new SequenceI[sg.getSize()]);
2377 addHistoryItem(new EditCommand(
2378 MessageManager.getString("label.cut_sequences"), Action.CUT,
2379 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2380 viewport.getAlignment()));
2382 viewport.setSelectionGroup(null);
2383 viewport.sendSelection();
2384 viewport.getAlignment().deleteGroup(sg);
2386 viewport.firePropertyChange("alignment", null,
2387 viewport.getAlignment().getSequences());
2388 if (viewport.getAlignment().getHeight() < 1)
2392 this.setClosed(true);
2393 } catch (Exception ex)
2406 protected void deleteGroups_actionPerformed(ActionEvent e)
2408 if (avc.deleteGroups())
2410 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2411 alignPanel.updateAnnotation();
2412 alignPanel.paintAlignment(true, true);
2423 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2425 SequenceGroup sg = new SequenceGroup(
2426 viewport.getAlignment().getSequences());
2428 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2429 viewport.setSelectionGroup(sg);
2430 viewport.isSelectionGroupChanged(true);
2431 viewport.sendSelection();
2432 // JAL-2034 - should delegate to
2433 // alignPanel to decide if overview needs
2435 alignPanel.paintAlignment(false, false);
2436 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2446 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2448 if (viewport.cursorMode)
2450 alignPanel.getSeqPanel().keyboardNo1 = null;
2451 alignPanel.getSeqPanel().keyboardNo2 = null;
2453 viewport.setSelectionGroup(null);
2454 viewport.getColumnSelection().clear();
2455 viewport.setSearchResults(null);
2456 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2457 // JAL-2034 - should delegate to
2458 // alignPanel to decide if overview needs
2460 alignPanel.paintAlignment(false, false);
2461 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2462 viewport.sendSelection();
2472 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2474 SequenceGroup sg = viewport.getSelectionGroup();
2478 selectAllSequenceMenuItem_actionPerformed(null);
2483 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2485 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2487 // JAL-2034 - should delegate to
2488 // alignPanel to decide if overview needs
2491 alignPanel.paintAlignment(true, false);
2492 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2493 viewport.sendSelection();
2497 public void invertColSel_actionPerformed(ActionEvent e)
2499 viewport.invertColumnSelection();
2500 alignPanel.paintAlignment(true, false);
2501 viewport.sendSelection();
2511 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2513 trimAlignment(true);
2523 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2525 trimAlignment(false);
2528 void trimAlignment(boolean trimLeft)
2530 ColumnSelection colSel = viewport.getColumnSelection();
2533 if (!colSel.isEmpty())
2537 column = colSel.getMin();
2541 column = colSel.getMax();
2545 if (viewport.getSelectionGroup() != null)
2547 seqs = viewport.getSelectionGroup()
2548 .getSequencesAsArray(viewport.getHiddenRepSequences());
2552 seqs = viewport.getAlignment().getSequencesArray();
2555 TrimRegionCommand trimRegion;
2558 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2559 column, viewport.getAlignment());
2560 viewport.getRanges().setStartRes(0);
2564 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2565 column, viewport.getAlignment());
2568 statusBar.setText(MessageManager
2569 .formatMessage("label.removed_columns", new String[]
2570 { Integer.valueOf(trimRegion.getSize()).toString() }));
2572 addHistoryItem(trimRegion);
2574 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2576 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2577 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2579 viewport.getAlignment().deleteGroup(sg);
2583 viewport.firePropertyChange("alignment", null,
2584 viewport.getAlignment().getSequences());
2595 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2597 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2600 if (viewport.getSelectionGroup() != null)
2602 seqs = viewport.getSelectionGroup()
2603 .getSequencesAsArray(viewport.getHiddenRepSequences());
2604 start = viewport.getSelectionGroup().getStartRes();
2605 end = viewport.getSelectionGroup().getEndRes();
2609 seqs = viewport.getAlignment().getSequencesArray();
2612 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2613 "Remove Gapped Columns", seqs, start, end,
2614 viewport.getAlignment());
2616 addHistoryItem(removeGapCols);
2618 statusBar.setText(MessageManager
2619 .formatMessage("label.removed_empty_columns", new Object[]
2620 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2622 // This is to maintain viewport position on first residue
2623 // of first sequence
2624 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2625 ViewportRanges ranges = viewport.getRanges();
2626 int startRes = seq.findPosition(ranges.getStartRes());
2627 // ShiftList shifts;
2628 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2629 // edit.alColumnChanges=shifts.getInverse();
2630 // if (viewport.hasHiddenColumns)
2631 // viewport.getColumnSelection().compensateForEdits(shifts);
2632 ranges.setStartRes(seq.findIndex(startRes) - 1);
2633 viewport.firePropertyChange("alignment", null,
2634 viewport.getAlignment().getSequences());
2645 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2647 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2650 if (viewport.getSelectionGroup() != null)
2652 seqs = viewport.getSelectionGroup()
2653 .getSequencesAsArray(viewport.getHiddenRepSequences());
2654 start = viewport.getSelectionGroup().getStartRes();
2655 end = viewport.getSelectionGroup().getEndRes();
2659 seqs = viewport.getAlignment().getSequencesArray();
2662 // This is to maintain viewport position on first residue
2663 // of first sequence
2664 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2665 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2667 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2668 viewport.getAlignment()));
2670 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2672 viewport.firePropertyChange("alignment", null,
2673 viewport.getAlignment().getSequences());
2684 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2686 viewport.setPadGaps(padGapsMenuitem.isSelected());
2687 viewport.firePropertyChange("alignment", null,
2688 viewport.getAlignment().getSequences());
2698 public void findMenuItem_actionPerformed(ActionEvent e)
2704 * Create a new view of the current alignment.
2707 public void newView_actionPerformed(ActionEvent e)
2709 newView(null, true);
2713 * Creates and shows a new view of the current alignment.
2716 * title of newly created view; if null, one will be generated
2717 * @param copyAnnotation
2718 * if true then duplicate all annnotation, groups and settings
2719 * @return new alignment panel, already displayed.
2721 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2724 * Create a new AlignmentPanel (with its own, new Viewport)
2726 AlignmentPanel newap = new jalview.project.Jalview2XML()
2727 .copyAlignPanel(alignPanel);
2728 if (!copyAnnotation)
2731 * remove all groups and annotation except for the automatic stuff
2733 newap.av.getAlignment().deleteAllGroups();
2734 newap.av.getAlignment().deleteAllAnnotations(false);
2737 newap.av.setGatherViewsHere(false);
2739 if (viewport.getViewName() == null)
2741 viewport.setViewName(
2742 MessageManager.getString("label.view_name_original"));
2746 * Views share the same edits undo and redo stacks
2748 newap.av.setHistoryList(viewport.getHistoryList());
2749 newap.av.setRedoList(viewport.getRedoList());
2752 * copy any visualisation settings that are not saved in the project
2754 newap.av.setColourAppliesToAllGroups(
2755 viewport.getColourAppliesToAllGroups());
2758 * Views share the same mappings; need to deregister any new mappings
2759 * created by copyAlignPanel, and register the new reference to the shared
2762 newap.av.replaceMappings(viewport.getAlignment());
2765 * start up cDNA consensus (if applicable) now mappings are in place
2767 if (newap.av.initComplementConsensus())
2769 newap.refresh(true); // adjust layout of annotations
2772 newap.av.setViewName(getNewViewName(viewTitle));
2774 addAlignmentPanel(newap, true);
2775 newap.alignmentChanged();
2777 if (alignPanels.size() == 2)
2779 viewport.setGatherViewsHere(true);
2781 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2786 * Make a new name for the view, ensuring it is unique within the current
2787 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2788 * these now use viewId. Unique view names are still desirable for usability.)
2793 protected String getNewViewName(String viewTitle)
2795 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2796 boolean addFirstIndex = false;
2797 if (viewTitle == null || viewTitle.trim().length() == 0)
2799 viewTitle = MessageManager.getString("action.view");
2800 addFirstIndex = true;
2804 index = 1;// we count from 1 if given a specific name
2806 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2808 List<Component> comps = PaintRefresher.components
2809 .get(viewport.getSequenceSetId());
2811 List<String> existingNames = getExistingViewNames(comps);
2813 while (existingNames.contains(newViewName))
2815 newViewName = viewTitle + " " + (++index);
2821 * Returns a list of distinct view names found in the given list of
2822 * components. View names are held on the viewport of an AlignmentPanel.
2827 protected List<String> getExistingViewNames(List<Component> comps)
2829 List<String> existingNames = new ArrayList<>();
2830 for (Component comp : comps)
2832 if (comp instanceof AlignmentPanel)
2834 AlignmentPanel ap = (AlignmentPanel) comp;
2835 if (!existingNames.contains(ap.av.getViewName()))
2837 existingNames.add(ap.av.getViewName());
2841 return existingNames;
2845 * Explode tabbed views into separate windows.
2848 public void expandViews_actionPerformed(ActionEvent e)
2850 Desktop.explodeViews(this);
2854 * Gather views in separate windows back into a tabbed presentation.
2857 public void gatherViews_actionPerformed(ActionEvent e)
2859 Desktop.instance.gatherViews(this);
2869 public void font_actionPerformed(ActionEvent e)
2871 new FontChooser(alignPanel);
2881 protected void seqLimit_actionPerformed(ActionEvent e)
2883 viewport.setShowJVSuffix(seqLimits.isSelected());
2885 alignPanel.getIdPanel().getIdCanvas()
2886 .setPreferredSize(alignPanel.calculateIdWidth());
2887 alignPanel.paintAlignment(true, false);
2891 public void idRightAlign_actionPerformed(ActionEvent e)
2893 viewport.setRightAlignIds(idRightAlign.isSelected());
2894 alignPanel.paintAlignment(false, false);
2898 public void centreColumnLabels_actionPerformed(ActionEvent e)
2900 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2901 alignPanel.paintAlignment(false, false);
2907 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2910 protected void followHighlight_actionPerformed()
2913 * Set the 'follow' flag on the Viewport (and scroll to position if now
2916 final boolean state = this.followHighlightMenuItem.getState();
2917 viewport.setFollowHighlight(state);
2920 alignPanel.scrollToPosition(viewport.getSearchResults());
2931 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2933 viewport.setColourText(colourTextMenuItem.isSelected());
2934 alignPanel.paintAlignment(false, false);
2944 public void wrapMenuItem_actionPerformed(ActionEvent e)
2946 scaleAbove.setVisible(wrapMenuItem.isSelected());
2947 scaleLeft.setVisible(wrapMenuItem.isSelected());
2948 scaleRight.setVisible(wrapMenuItem.isSelected());
2949 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2950 alignPanel.updateLayout();
2954 public void showAllSeqs_actionPerformed(ActionEvent e)
2956 viewport.showAllHiddenSeqs();
2960 public void showAllColumns_actionPerformed(ActionEvent e)
2962 viewport.showAllHiddenColumns();
2963 alignPanel.paintAlignment(true, true);
2964 viewport.sendSelection();
2968 public void hideSelSequences_actionPerformed(ActionEvent e)
2970 viewport.hideAllSelectedSeqs();
2974 * called by key handler and the hide all/show all menu items
2979 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2982 boolean hide = false;
2983 SequenceGroup sg = viewport.getSelectionGroup();
2984 if (!toggleSeqs && !toggleCols)
2986 // Hide everything by the current selection - this is a hack - we do the
2987 // invert and then hide
2988 // first check that there will be visible columns after the invert.
2989 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2990 && sg.getStartRes() <= sg.getEndRes()))
2992 // now invert the sequence set, if required - empty selection implies
2993 // that no hiding is required.
2996 invertSequenceMenuItem_actionPerformed(null);
2997 sg = viewport.getSelectionGroup();
3001 viewport.expandColSelection(sg, true);
3002 // finally invert the column selection and get the new sequence
3004 invertColSel_actionPerformed(null);
3011 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3013 hideSelSequences_actionPerformed(null);
3016 else if (!(toggleCols && viewport.hasSelectedColumns()))
3018 showAllSeqs_actionPerformed(null);
3024 if (viewport.hasSelectedColumns())
3026 hideSelColumns_actionPerformed(null);
3029 viewport.setSelectionGroup(sg);
3034 showAllColumns_actionPerformed(null);
3043 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3044 * event.ActionEvent)
3047 public void hideAllButSelection_actionPerformed(ActionEvent e)
3049 toggleHiddenRegions(false, false);
3050 viewport.sendSelection();
3057 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3061 public void hideAllSelection_actionPerformed(ActionEvent e)
3063 SequenceGroup sg = viewport.getSelectionGroup();
3064 viewport.expandColSelection(sg, false);
3065 viewport.hideAllSelectedSeqs();
3066 viewport.hideSelectedColumns();
3067 alignPanel.updateLayout();
3068 alignPanel.paintAlignment(true, true);
3069 viewport.sendSelection();
3076 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3080 public void showAllhidden_actionPerformed(ActionEvent e)
3082 viewport.showAllHiddenColumns();
3083 viewport.showAllHiddenSeqs();
3084 alignPanel.paintAlignment(true, true);
3085 viewport.sendSelection();
3089 public void hideSelColumns_actionPerformed(ActionEvent e)
3091 viewport.hideSelectedColumns();
3092 alignPanel.updateLayout();
3093 alignPanel.paintAlignment(true, true);
3094 viewport.sendSelection();
3098 public void hiddenMarkers_actionPerformed(ActionEvent e)
3100 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3111 protected void scaleAbove_actionPerformed(ActionEvent e)
3113 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3114 alignPanel.updateLayout();
3115 alignPanel.paintAlignment(true, false);
3125 protected void scaleLeft_actionPerformed(ActionEvent e)
3127 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3128 alignPanel.updateLayout();
3129 alignPanel.paintAlignment(true, false);
3139 protected void scaleRight_actionPerformed(ActionEvent e)
3141 viewport.setScaleRightWrapped(scaleRight.isSelected());
3142 alignPanel.updateLayout();
3143 alignPanel.paintAlignment(true, false);
3153 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3155 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3156 alignPanel.paintAlignment(false, false);
3166 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3168 viewport.setShowText(viewTextMenuItem.isSelected());
3169 alignPanel.paintAlignment(false, false);
3179 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3181 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3182 alignPanel.paintAlignment(false, false);
3185 public FeatureSettings featureSettings;
3188 public FeatureSettingsControllerI getFeatureSettingsUI()
3190 return featureSettings;
3194 public void featureSettings_actionPerformed(ActionEvent e)
3196 showFeatureSettingsUI();
3200 public FeatureSettingsControllerI showFeatureSettingsUI()
3202 if (featureSettings != null)
3204 featureSettings.closeOldSettings();
3205 featureSettings = null;
3207 if (!showSeqFeatures.isSelected())
3209 // make sure features are actually displayed
3210 showSeqFeatures.setSelected(true);
3211 showSeqFeatures_actionPerformed(null);
3213 featureSettings = new FeatureSettings(this);
3214 return featureSettings;
3218 * Set or clear 'Show Sequence Features'
3224 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3226 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3227 alignPanel.paintAlignment(true, true);
3231 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3232 * the annotations panel as a whole.
3234 * The options to show/hide all annotations should be enabled when the panel
3235 * is shown, and disabled when the panel is hidden.
3240 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3242 final boolean setVisible = annotationPanelMenuItem.isSelected();
3243 viewport.setShowAnnotation(setVisible);
3244 this.showAllSeqAnnotations.setEnabled(setVisible);
3245 this.hideAllSeqAnnotations.setEnabled(setVisible);
3246 this.showAllAlAnnotations.setEnabled(setVisible);
3247 this.hideAllAlAnnotations.setEnabled(setVisible);
3248 alignPanel.updateLayout();
3252 public void alignmentProperties()
3254 JEditorPane editPane = new JEditorPane("text/html", "");
3255 editPane.setEditable(false);
3256 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3259 MessageManager.formatMessage("label.html_content", new Object[]
3260 { contents.toString() }));
3261 JInternalFrame frame = new JInternalFrame();
3262 frame.getContentPane().add(new JScrollPane(editPane));
3264 Desktop.addInternalFrame(frame, MessageManager
3265 .formatMessage("label.alignment_properties", new Object[]
3266 { getTitle() }), 500, 400);
3276 public void overviewMenuItem_actionPerformed(ActionEvent e)
3278 if (alignPanel.overviewPanel != null)
3283 JInternalFrame frame = new JInternalFrame();
3284 final OverviewPanel overview = new OverviewPanel(alignPanel);
3285 frame.setContentPane(overview);
3286 Desktop.addInternalFrame(frame, MessageManager
3287 .formatMessage("label.overview_params", new Object[]
3288 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3291 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3292 frame.addInternalFrameListener(
3293 new javax.swing.event.InternalFrameAdapter()
3296 public void internalFrameClosed(
3297 javax.swing.event.InternalFrameEvent evt)
3300 alignPanel.setOverviewPanel(null);
3303 if (getKeyListeners().length > 0)
3305 frame.addKeyListener(getKeyListeners()[0]);
3308 alignPanel.setOverviewPanel(overview);
3312 public void textColour_actionPerformed()
3314 new TextColourChooser().chooseColour(alignPanel, null);
3318 * public void covariationColour_actionPerformed() {
3320 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3324 public void annotationColour_actionPerformed()
3326 new AnnotationColourChooser(viewport, alignPanel);
3330 public void annotationColumn_actionPerformed(ActionEvent e)
3332 new AnnotationColumnChooser(viewport, alignPanel);
3336 * Action on the user checking or unchecking the option to apply the selected
3337 * colour scheme to all groups. If unchecked, groups may have their own
3338 * independent colour schemes.
3343 public void applyToAllGroups_actionPerformed(boolean selected)
3345 viewport.setColourAppliesToAllGroups(selected);
3349 * Action on user selecting a colour from the colour menu
3352 * the name (not the menu item label!) of the colour scheme
3355 public void changeColour_actionPerformed(String name)
3358 * 'User Defined' opens a panel to configure or load a
3359 * user-defined colour scheme
3361 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3363 new UserDefinedColours(alignPanel);
3368 * otherwise set the chosen colour scheme (or null for 'None')
3370 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3371 viewport, viewport.getAlignment(),
3372 viewport.getHiddenRepSequences());
3377 * Actions on setting or changing the alignment colour scheme
3382 public void changeColour(ColourSchemeI cs)
3384 // TODO: pull up to controller method
3385 ColourMenuHelper.setColourSelected(colourMenu, cs);
3387 viewport.setGlobalColourScheme(cs);
3389 alignPanel.paintAlignment(true, true);
3393 * Show the PID threshold slider panel
3396 protected void modifyPID_actionPerformed()
3398 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3399 alignPanel.getViewName());
3400 SliderPanel.showPIDSlider();
3404 * Show the Conservation slider panel
3407 protected void modifyConservation_actionPerformed()
3409 SliderPanel.setConservationSlider(alignPanel,
3410 viewport.getResidueShading(), alignPanel.getViewName());
3411 SliderPanel.showConservationSlider();
3415 * Action on selecting or deselecting (Colour) By Conservation
3418 public void conservationMenuItem_actionPerformed(boolean selected)
3420 modifyConservation.setEnabled(selected);
3421 viewport.setConservationSelected(selected);
3422 viewport.getResidueShading().setConservationApplied(selected);
3424 changeColour(viewport.getGlobalColourScheme());
3427 modifyConservation_actionPerformed();
3431 SliderPanel.hideConservationSlider();
3436 * Action on selecting or deselecting (Colour) Above PID Threshold
3439 public void abovePIDThreshold_actionPerformed(boolean selected)
3441 modifyPID.setEnabled(selected);
3442 viewport.setAbovePIDThreshold(selected);
3445 viewport.getResidueShading().setThreshold(0,
3446 viewport.isIgnoreGapsConsensus());
3449 changeColour(viewport.getGlobalColourScheme());
3452 modifyPID_actionPerformed();
3456 SliderPanel.hidePIDSlider();
3467 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3469 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3470 AlignmentSorter.sortByPID(viewport.getAlignment(),
3471 viewport.getAlignment().getSequenceAt(0));
3472 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3473 viewport.getAlignment()));
3474 alignPanel.paintAlignment(true, false);
3484 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3486 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3487 AlignmentSorter.sortByID(viewport.getAlignment());
3489 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3490 alignPanel.paintAlignment(true, false);
3500 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3502 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3503 AlignmentSorter.sortByLength(viewport.getAlignment());
3504 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3505 viewport.getAlignment()));
3506 alignPanel.paintAlignment(true, false);
3516 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3518 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3519 AlignmentSorter.sortByGroup(viewport.getAlignment());
3520 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3521 viewport.getAlignment()));
3523 alignPanel.paintAlignment(true, false);
3533 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3535 new RedundancyPanel(alignPanel, this);
3545 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3547 if ((viewport.getSelectionGroup() == null)
3548 || (viewport.getSelectionGroup().getSize() < 2))
3550 JvOptionPane.showInternalMessageDialog(this,
3551 MessageManager.getString(
3552 "label.you_must_select_least_two_sequences"),
3553 MessageManager.getString("label.invalid_selection"),
3554 JvOptionPane.WARNING_MESSAGE);
3558 JInternalFrame frame = new JInternalFrame();
3559 frame.setContentPane(new PairwiseAlignPanel(viewport));
3560 Desktop.addInternalFrame(frame,
3561 MessageManager.getString("action.pairwise_alignment"), 600,
3567 public void autoCalculate_actionPerformed(ActionEvent e)
3569 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3570 if (viewport.autoCalculateConsensus)
3572 viewport.firePropertyChange("alignment", null,
3573 viewport.getAlignment().getSequences());
3578 public void sortByTreeOption_actionPerformed(ActionEvent e)
3580 viewport.sortByTree = sortByTree.isSelected();
3584 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3586 viewport.followSelection = listenToViewSelections.isSelected();
3590 * Constructs a tree panel and adds it to the desktop
3593 * tree type (NJ or AV)
3595 * name of score model used to compute the tree
3597 * parameters for the distance or similarity calculation
3599 void newTreePanel(String type, String modelName,
3600 SimilarityParamsI options)
3602 String frameTitle = "";
3605 boolean onSelection = false;
3606 if (viewport.getSelectionGroup() != null
3607 && viewport.getSelectionGroup().getSize() > 0)
3609 SequenceGroup sg = viewport.getSelectionGroup();
3611 /* Decide if the selection is a column region */
3612 for (SequenceI _s : sg.getSequences())
3614 if (_s.getLength() < sg.getEndRes())
3616 JvOptionPane.showMessageDialog(Desktop.desktop,
3617 MessageManager.getString(
3618 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3619 MessageManager.getString(
3620 "label.sequences_selection_not_aligned"),
3621 JvOptionPane.WARNING_MESSAGE);
3630 if (viewport.getAlignment().getHeight() < 2)
3636 tp = new TreePanel(alignPanel, type, modelName, options);
3637 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3639 frameTitle += " from ";
3641 if (viewport.getViewName() != null)
3643 frameTitle += viewport.getViewName() + " of ";
3646 frameTitle += this.title;
3648 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3659 public void addSortByOrderMenuItem(String title,
3660 final AlignmentOrder order)
3662 final JMenuItem item = new JMenuItem(MessageManager
3663 .formatMessage("action.by_title_param", new Object[]
3666 item.addActionListener(new java.awt.event.ActionListener()
3669 public void actionPerformed(ActionEvent e)
3671 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3673 // TODO: JBPNote - have to map order entries to curent SequenceI
3675 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3677 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3678 viewport.getAlignment()));
3680 alignPanel.paintAlignment(true, false);
3686 * Add a new sort by annotation score menu item
3689 * the menu to add the option to
3691 * the label used to retrieve scores for each sequence on the
3694 public void addSortByAnnotScoreMenuItem(JMenu sort,
3695 final String scoreLabel)
3697 final JMenuItem item = new JMenuItem(scoreLabel);
3699 item.addActionListener(new java.awt.event.ActionListener()
3702 public void actionPerformed(ActionEvent e)
3704 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3705 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3706 viewport.getAlignment());// ,viewport.getSelectionGroup());
3707 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3708 viewport.getAlignment()));
3709 alignPanel.paintAlignment(true, false);
3715 * last hash for alignment's annotation array - used to minimise cost of
3718 protected int _annotationScoreVectorHash;
3721 * search the alignment and rebuild the sort by annotation score submenu the
3722 * last alignment annotation vector hash is stored to minimize cost of
3723 * rebuilding in subsequence calls.
3727 public void buildSortByAnnotationScoresMenu()
3729 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3734 if (viewport.getAlignment().getAlignmentAnnotation()
3735 .hashCode() != _annotationScoreVectorHash)
3737 sortByAnnotScore.removeAll();
3738 // almost certainly a quicker way to do this - but we keep it simple
3739 Hashtable scoreSorts = new Hashtable();
3740 AlignmentAnnotation aann[];
3741 for (SequenceI sqa : viewport.getAlignment().getSequences())
3743 aann = sqa.getAnnotation();
3744 for (int i = 0; aann != null && i < aann.length; i++)
3746 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3748 scoreSorts.put(aann[i].label, aann[i].label);
3752 Enumeration labels = scoreSorts.keys();
3753 while (labels.hasMoreElements())
3755 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3756 (String) labels.nextElement());
3758 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3761 _annotationScoreVectorHash = viewport.getAlignment()
3762 .getAlignmentAnnotation().hashCode();
3767 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3768 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3769 * call. Listeners are added to remove the menu item when the treePanel is
3770 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3774 public void buildTreeSortMenu()
3776 sortByTreeMenu.removeAll();
3778 List<Component> comps = PaintRefresher.components
3779 .get(viewport.getSequenceSetId());
3780 List<TreePanel> treePanels = new ArrayList<>();
3781 for (Component comp : comps)
3783 if (comp instanceof TreePanel)
3785 treePanels.add((TreePanel) comp);
3789 if (treePanels.size() < 1)
3791 sortByTreeMenu.setVisible(false);
3795 sortByTreeMenu.setVisible(true);
3797 for (final TreePanel tp : treePanels)
3799 final JMenuItem item = new JMenuItem(tp.getTitle());
3800 item.addActionListener(new java.awt.event.ActionListener()
3803 public void actionPerformed(ActionEvent e)
3805 tp.sortByTree_actionPerformed();
3806 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3811 sortByTreeMenu.add(item);
3815 public boolean sortBy(AlignmentOrder alorder, String undoname)
3817 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3818 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3819 if (undoname != null)
3821 addHistoryItem(new OrderCommand(undoname, oldOrder,
3822 viewport.getAlignment()));
3824 alignPanel.paintAlignment(true, false);
3829 * Work out whether the whole set of sequences or just the selected set will
3830 * be submitted for multiple alignment.
3833 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3835 // Now, check we have enough sequences
3836 AlignmentView msa = null;
3838 if ((viewport.getSelectionGroup() != null)
3839 && (viewport.getSelectionGroup().getSize() > 1))
3841 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3842 // some common interface!
3844 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3845 * SequenceI[sz = seqs.getSize(false)];
3847 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3848 * seqs.getSequenceAt(i); }
3850 msa = viewport.getAlignmentView(true);
3852 else if (viewport.getSelectionGroup() != null
3853 && viewport.getSelectionGroup().getSize() == 1)
3855 int option = JvOptionPane.showConfirmDialog(this,
3856 MessageManager.getString("warn.oneseq_msainput_selection"),
3857 MessageManager.getString("label.invalid_selection"),
3858 JvOptionPane.OK_CANCEL_OPTION);
3859 if (option == JvOptionPane.OK_OPTION)
3861 msa = viewport.getAlignmentView(false);
3866 msa = viewport.getAlignmentView(false);
3872 * Decides what is submitted to a secondary structure prediction service: the
3873 * first sequence in the alignment, or in the current selection, or, if the
3874 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3875 * region or the whole alignment. (where the first sequence in the set is the
3876 * one that the prediction will be for).
3878 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3880 AlignmentView seqs = null;
3882 if ((viewport.getSelectionGroup() != null)
3883 && (viewport.getSelectionGroup().getSize() > 0))
3885 seqs = viewport.getAlignmentView(true);
3889 seqs = viewport.getAlignmentView(false);
3891 // limit sequences - JBPNote in future - could spawn multiple prediction
3893 // TODO: viewport.getAlignment().isAligned is a global state - the local
3894 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3895 if (!viewport.getAlignment().isAligned(false))
3897 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3898 // TODO: if seqs.getSequences().length>1 then should really have warned
3912 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3914 // Pick the tree file
3915 JalviewFileChooser chooser = new JalviewFileChooser(
3916 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3917 chooser.setFileView(new JalviewFileView());
3918 chooser.setDialogTitle(
3919 MessageManager.getString("label.select_newick_like_tree_file"));
3920 chooser.setToolTipText(
3921 MessageManager.getString("label.load_tree_file"));
3923 int value = chooser.showOpenDialog(null);
3925 if (value == JalviewFileChooser.APPROVE_OPTION)
3927 String filePath = chooser.getSelectedFile().getPath();
3928 Cache.setProperty("LAST_DIRECTORY", filePath);
3929 NewickFile fin = null;
3932 fin = new NewickFile(filePath, DataSourceType.FILE);
3933 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3934 } catch (Exception ex)
3936 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3937 MessageManager.getString("label.problem_reading_tree_file"),
3938 JvOptionPane.WARNING_MESSAGE);
3939 ex.printStackTrace();
3941 if (fin != null && fin.hasWarningMessage())
3943 JvOptionPane.showMessageDialog(Desktop.desktop,
3944 fin.getWarningMessage(),
3946 .getString("label.possible_problem_with_tree_file"),
3947 JvOptionPane.WARNING_MESSAGE);
3952 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3954 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3957 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3958 int h, int x, int y)
3960 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3964 * Add a treeviewer for the tree extracted from a Newick file object to the
3965 * current alignment view
3972 * Associated alignment input data (or null)
3981 * @return TreePanel handle
3983 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3984 AlignmentView input, int w, int h, int x, int y)
3986 TreePanel tp = null;
3992 if (nf.getTree() != null)
3994 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4000 tp.setLocation(x, y);
4003 Desktop.addInternalFrame(tp, treeTitle, w, h);
4005 } catch (Exception ex)
4007 ex.printStackTrace();
4013 private boolean buildingMenu = false;
4016 * Generates menu items and listener event actions for web service clients
4019 public void BuildWebServiceMenu()
4021 while (buildingMenu)
4025 System.err.println("Waiting for building menu to finish.");
4027 } catch (Exception e)
4031 final AlignFrame me = this;
4032 buildingMenu = true;
4033 new Thread(new Runnable()
4038 final List<JMenuItem> legacyItems = new ArrayList<>();
4041 // System.err.println("Building ws menu again "
4042 // + Thread.currentThread());
4043 // TODO: add support for context dependent disabling of services based
4045 // alignment and current selection
4046 // TODO: add additional serviceHandle parameter to specify abstract
4048 // class independently of AbstractName
4049 // TODO: add in rediscovery GUI function to restart discoverer
4050 // TODO: group services by location as well as function and/or
4052 // object broker mechanism.
4053 final Vector<JMenu> wsmenu = new Vector<>();
4054 final IProgressIndicator af = me;
4057 * do not i18n these strings - they are hard-coded in class
4058 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4059 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4061 final JMenu msawsmenu = new JMenu("Alignment");
4062 final JMenu secstrmenu = new JMenu(
4063 "Secondary Structure Prediction");
4064 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4065 final JMenu analymenu = new JMenu("Analysis");
4066 final JMenu dismenu = new JMenu("Protein Disorder");
4067 // JAL-940 - only show secondary structure prediction services from
4068 // the legacy server
4069 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4071 Discoverer.services != null && (Discoverer.services.size() > 0))
4073 // TODO: refactor to allow list of AbstractName/Handler bindings to
4075 // stored or retrieved from elsewhere
4076 // No MSAWS used any more:
4077 // Vector msaws = null; // (Vector)
4078 // Discoverer.services.get("MsaWS");
4079 Vector secstrpr = (Vector) Discoverer.services
4081 if (secstrpr != null)
4083 // Add any secondary structure prediction services
4084 for (int i = 0, j = secstrpr.size(); i < j; i++)
4086 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4088 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4089 .getServiceClient(sh);
4090 int p = secstrmenu.getItemCount();
4091 impl.attachWSMenuEntry(secstrmenu, me);
4092 int q = secstrmenu.getItemCount();
4093 for (int litm = p; litm < q; litm++)
4095 legacyItems.add(secstrmenu.getItem(litm));
4101 // Add all submenus in the order they should appear on the web
4103 wsmenu.add(msawsmenu);
4104 wsmenu.add(secstrmenu);
4105 wsmenu.add(dismenu);
4106 wsmenu.add(analymenu);
4107 // No search services yet
4108 // wsmenu.add(seqsrchmenu);
4110 javax.swing.SwingUtilities.invokeLater(new Runnable()
4117 webService.removeAll();
4118 // first, add discovered services onto the webservices menu
4119 if (wsmenu.size() > 0)
4121 for (int i = 0, j = wsmenu.size(); i < j; i++)
4123 webService.add(wsmenu.get(i));
4128 webService.add(me.webServiceNoServices);
4130 // TODO: move into separate menu builder class.
4131 boolean new_sspred = false;
4132 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4134 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4135 if (jws2servs != null)
4137 if (jws2servs.hasServices())
4139 jws2servs.attachWSMenuEntry(webService, me);
4140 for (Jws2Instance sv : jws2servs.getServices())
4142 if (sv.description.toLowerCase().contains("jpred"))
4144 for (JMenuItem jmi : legacyItems)
4146 jmi.setVisible(false);
4152 if (jws2servs.isRunning())
4154 JMenuItem tm = new JMenuItem(
4155 "Still discovering JABA Services");
4156 tm.setEnabled(false);
4161 build_urlServiceMenu(me.webService);
4162 build_fetchdbmenu(webService);
4163 for (JMenu item : wsmenu)
4165 if (item.getItemCount() == 0)
4167 item.setEnabled(false);
4171 item.setEnabled(true);
4174 } catch (Exception e)
4177 "Exception during web service menu building process.",
4182 } catch (Exception e)
4185 buildingMenu = false;
4192 * construct any groupURL type service menu entries.
4196 private void build_urlServiceMenu(JMenu webService)
4198 // TODO: remove this code when 2.7 is released
4199 // DEBUG - alignmentView
4201 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4202 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4204 * @Override public void actionPerformed(ActionEvent e) {
4205 * jalview.datamodel.AlignmentView
4206 * .testSelectionViews(af.viewport.getAlignment(),
4207 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4209 * }); webService.add(testAlView);
4211 // TODO: refactor to RestClient discoverer and merge menu entries for
4212 // rest-style services with other types of analysis/calculation service
4213 // SHmmr test client - still being implemented.
4214 // DEBUG - alignmentView
4216 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4219 client.attachWSMenuEntry(
4220 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4226 * Searches the alignment sequences for xRefs and builds the Show
4227 * Cross-References menu (formerly called Show Products), with database
4228 * sources for which cross-references are found (protein sources for a
4229 * nucleotide alignment and vice versa)
4231 * @return true if Show Cross-references menu should be enabled
4233 public boolean canShowProducts()
4235 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4236 AlignmentI dataset = viewport.getAlignment().getDataset();
4238 showProducts.removeAll();
4239 final boolean dna = viewport.getAlignment().isNucleotide();
4241 if (seqs == null || seqs.length == 0)
4243 // nothing to see here.
4247 boolean showp = false;
4250 List<String> ptypes = new CrossRef(seqs, dataset)
4251 .findXrefSourcesForSequences(dna);
4253 for (final String source : ptypes)
4256 final AlignFrame af = this;
4257 JMenuItem xtype = new JMenuItem(source);
4258 xtype.addActionListener(new ActionListener()
4261 public void actionPerformed(ActionEvent e)
4263 showProductsFor(af.viewport.getSequenceSelection(), dna,
4267 showProducts.add(xtype);
4269 showProducts.setVisible(showp);
4270 showProducts.setEnabled(showp);
4271 } catch (Exception e)
4274 "canShowProducts threw an exception - please report to help@jalview.org",
4282 * Finds and displays cross-references for the selected sequences (protein
4283 * products for nucleotide sequences, dna coding sequences for peptides).
4286 * the sequences to show cross-references for
4288 * true if from a nucleotide alignment (so showing proteins)
4290 * the database to show cross-references for
4292 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4293 final String source)
4295 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4300 * Construct and display a new frame containing the translation of this
4301 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4304 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4306 AlignmentI al = null;
4309 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4311 al = dna.translateCdna(codeTable);
4312 } catch (Exception ex)
4314 jalview.bin.Cache.log.error(
4315 "Exception during translation. Please report this !", ex);
4316 final String msg = MessageManager.getString(
4317 "label.error_when_translating_sequences_submit_bug_report");
4318 final String errorTitle = MessageManager
4319 .getString("label.implementation_error")
4320 + MessageManager.getString("label.translation_failed");
4321 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4322 JvOptionPane.ERROR_MESSAGE);
4325 if (al == null || al.getHeight() == 0)
4327 final String msg = MessageManager.getString(
4328 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4329 final String errorTitle = MessageManager
4330 .getString("label.translation_failed");
4331 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4332 JvOptionPane.WARNING_MESSAGE);
4336 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4337 af.setFileFormat(this.currentFileFormat);
4338 final String newTitle = MessageManager
4339 .formatMessage("label.translation_of_params", new Object[]
4340 { this.getTitle(), codeTable.getId() });
4341 af.setTitle(newTitle);
4342 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4344 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4345 viewport.openSplitFrame(af, new Alignment(seqs));
4349 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4356 * Set the file format
4360 public void setFileFormat(FileFormatI format)
4362 this.currentFileFormat = format;
4366 * Try to load a features file onto the alignment.
4369 * contents or path to retrieve file
4371 * access mode of file (see jalview.io.AlignFile)
4372 * @return true if features file was parsed correctly.
4374 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4376 return avc.parseFeaturesFile(file, sourceType,
4377 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4382 public void refreshFeatureUI(boolean enableIfNecessary)
4384 // note - currently this is only still here rather than in the controller
4385 // because of the featureSettings hard reference that is yet to be
4387 if (enableIfNecessary)
4389 viewport.setShowSequenceFeatures(true);
4390 showSeqFeatures.setSelected(true);
4396 public void dragEnter(DropTargetDragEvent evt)
4401 public void dragExit(DropTargetEvent evt)
4406 public void dragOver(DropTargetDragEvent evt)
4411 public void dropActionChanged(DropTargetDragEvent evt)
4416 public void drop(DropTargetDropEvent evt)
4418 // JAL-1552 - acceptDrop required before getTransferable call for
4419 // Java's Transferable for native dnd
4420 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4421 Transferable t = evt.getTransferable();
4422 final AlignFrame thisaf = this;
4423 final List<String> files = new ArrayList<>();
4424 List<DataSourceType> protocols = new ArrayList<>();
4428 Desktop.transferFromDropTarget(files, protocols, evt, t);
4429 } catch (Exception e)
4431 e.printStackTrace();
4435 new Thread(new Runnable()
4442 // check to see if any of these files have names matching sequences
4445 SequenceIdMatcher idm = new SequenceIdMatcher(
4446 viewport.getAlignment().getSequencesArray());
4448 * Object[] { String,SequenceI}
4450 ArrayList<Object[]> filesmatched = new ArrayList<>();
4451 ArrayList<String> filesnotmatched = new ArrayList<>();
4452 for (int i = 0; i < files.size(); i++)
4454 String file = files.get(i).toString();
4456 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4457 if (protocol == DataSourceType.FILE)
4459 File fl = new File(file);
4460 pdbfn = fl.getName();
4462 else if (protocol == DataSourceType.URL)
4464 URL url = new URL(file);
4465 pdbfn = url.getFile();
4467 if (pdbfn.length() > 0)
4469 // attempt to find a match in the alignment
4470 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4471 int l = 0, c = pdbfn.indexOf(".");
4472 while (mtch == null && c != -1)
4477 } while ((c = pdbfn.indexOf(".", l)) > l);
4480 pdbfn = pdbfn.substring(0, l);
4482 mtch = idm.findAllIdMatches(pdbfn);
4486 FileFormatI type = null;
4489 type = new IdentifyFile().identify(file, protocol);
4490 } catch (Exception ex)
4494 if (type != null && type.isStructureFile())
4496 filesmatched.add(new Object[] { file, protocol, mtch });
4500 // File wasn't named like one of the sequences or wasn't a PDB
4502 filesnotmatched.add(file);
4506 if (filesmatched.size() > 0)
4508 boolean autoAssociate = Cache
4509 .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4512 String msg = MessageManager.formatMessage(
4513 "label.automatically_associate_structure_files_with_sequences_same_name",
4515 { Integer.valueOf(filesmatched.size())
4517 String ttl = MessageManager.getString(
4518 "label.automatically_associate_structure_files_by_name");
4519 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4520 ttl, JvOptionPane.YES_NO_OPTION);
4521 autoAssociate = choice == JvOptionPane.YES_OPTION;
4525 for (Object[] fm : filesmatched)
4527 // try and associate
4528 // TODO: may want to set a standard ID naming formalism for
4529 // associating PDB files which have no IDs.
4530 for (SequenceI toassoc : (SequenceI[]) fm[2])
4532 PDBEntry pe = new AssociatePdbFileWithSeq()
4533 .associatePdbWithSeq((String) fm[0],
4534 (DataSourceType) fm[1], toassoc, false,
4538 System.err.println("Associated file : "
4539 + ((String) fm[0]) + " with "
4540 + toassoc.getDisplayId(true));
4544 // TODO: do we need to update overview ? only if features are
4546 alignPanel.paintAlignment(true, false);
4552 * add declined structures as sequences
4554 for (Object[] o : filesmatched)
4556 filesnotmatched.add((String) o[0]);
4560 if (filesnotmatched.size() > 0)
4562 if (assocfiles > 0 && (Cache.getDefault(
4563 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4564 || JvOptionPane.showConfirmDialog(thisaf,
4565 "<html>" + MessageManager.formatMessage(
4566 "label.ignore_unmatched_dropped_files_info",
4569 filesnotmatched.size())
4572 MessageManager.getString(
4573 "label.ignore_unmatched_dropped_files"),
4574 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4578 for (String fn : filesnotmatched)
4580 loadJalviewDataFile(fn, null, null, null);
4584 } catch (Exception ex)
4586 ex.printStackTrace();
4594 * Attempt to load a "dropped" file or URL string, by testing in turn for
4596 * <li>an Annotation file</li>
4597 * <li>a JNet file</li>
4598 * <li>a features file</li>
4599 * <li>else try to interpret as an alignment file</li>
4603 * either a filename or a URL string.
4605 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4606 FileFormatI format, SequenceI assocSeq)
4610 if (sourceType == null)
4612 sourceType = FormatAdapter.checkProtocol(file);
4614 // if the file isn't identified, or not positively identified as some
4615 // other filetype (PFAM is default unidentified alignment file type) then
4616 // try to parse as annotation.
4617 boolean isAnnotation = (format == null
4618 || FileFormat.Pfam.equals(format))
4619 ? new AnnotationFile().annotateAlignmentView(viewport,
4625 // first see if its a T-COFFEE score file
4626 TCoffeeScoreFile tcf = null;
4629 tcf = new TCoffeeScoreFile(file, sourceType);
4632 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4636 new TCoffeeColourScheme(viewport.getAlignment()));
4637 isAnnotation = true;
4638 statusBar.setText(MessageManager.getString(
4639 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4643 // some problem - if no warning its probable that the ID matching
4644 // process didn't work
4645 JvOptionPane.showMessageDialog(Desktop.desktop,
4646 tcf.getWarningMessage() == null
4647 ? MessageManager.getString(
4648 "label.check_file_matches_sequence_ids_alignment")
4649 : tcf.getWarningMessage(),
4650 MessageManager.getString(
4651 "label.problem_reading_tcoffee_score_file"),
4652 JvOptionPane.WARNING_MESSAGE);
4659 } catch (Exception x)
4662 "Exception when processing data source as T-COFFEE score file",
4668 // try to see if its a JNet 'concise' style annotation file *before*
4670 // try to parse it as a features file
4673 format = new IdentifyFile().identify(file, sourceType);
4675 if (FileFormat.ScoreMatrix == format)
4677 ScoreMatrixFile sm = new ScoreMatrixFile(
4678 new FileParse(file, sourceType));
4680 // todo: i18n this message
4681 statusBar.setText(MessageManager.formatMessage(
4682 "label.successfully_loaded_matrix",
4683 sm.getMatrixName()));
4685 else if (FileFormat.Jnet.equals(format))
4687 JPredFile predictions = new JPredFile(file, sourceType);
4688 new JnetAnnotationMaker();
4689 JnetAnnotationMaker.add_annotation(predictions,
4690 viewport.getAlignment(), 0, false);
4691 viewport.getAlignment().setupJPredAlignment();
4692 isAnnotation = true;
4694 // else if (IdentifyFile.FeaturesFile.equals(format))
4695 else if (FileFormat.Features.equals(format))
4697 if (parseFeaturesFile(file, sourceType))
4699 SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4700 if (splitFrame != null)
4702 splitFrame.repaint();
4706 alignPanel.paintAlignment(true, true);
4712 new FileLoader().LoadFile(viewport, file, sourceType, format);
4719 alignPanel.adjustAnnotationHeight();
4720 viewport.updateSequenceIdColours();
4721 buildSortByAnnotationScoresMenu();
4722 alignPanel.paintAlignment(true, true);
4724 } catch (Exception ex)
4726 ex.printStackTrace();
4727 } catch (OutOfMemoryError oom)
4732 } catch (Exception x)
4737 + (sourceType != null
4738 ? (sourceType == DataSourceType.PASTE
4740 : "using " + sourceType + " from "
4744 ? "(parsing as '" + format + "' file)"
4746 oom, Desktop.desktop);
4751 * Method invoked by the ChangeListener on the tabbed pane, in other words
4752 * when a different tabbed pane is selected by the user or programmatically.
4755 public void tabSelectionChanged(int index)
4759 alignPanel = alignPanels.get(index);
4760 viewport = alignPanel.av;
4761 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4762 setMenusFromViewport(viewport);
4763 if (featureSettings != null && featureSettings.isOpen()
4764 && featureSettings.fr.getViewport() != viewport)
4766 if (viewport.isShowSequenceFeatures())
4768 // refresh the featureSettings to reflect UI change
4769 showFeatureSettingsUI();
4773 // close feature settings for this view.
4774 featureSettings.close();
4781 * 'focus' any colour slider that is open to the selected viewport
4783 if (viewport.getConservationSelected())
4785 SliderPanel.setConservationSlider(alignPanel,
4786 viewport.getResidueShading(), alignPanel.getViewName());
4790 SliderPanel.hideConservationSlider();
4792 if (viewport.getAbovePIDThreshold())
4794 SliderPanel.setPIDSliderSource(alignPanel,
4795 viewport.getResidueShading(), alignPanel.getViewName());
4799 SliderPanel.hidePIDSlider();
4803 * If there is a frame linked to this one in a SplitPane, switch it to the
4804 * same view tab index. No infinite recursion of calls should happen, since
4805 * tabSelectionChanged() should not get invoked on setting the selected
4806 * index to an unchanged value. Guard against setting an invalid index
4807 * before the new view peer tab has been created.
4809 final AlignViewportI peer = viewport.getCodingComplement();
4812 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4813 .getAlignPanel().alignFrame;
4814 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4816 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4822 * On right mouse click on view tab, prompt for and set new view name.
4825 public void tabbedPane_mousePressed(MouseEvent e)
4827 if (e.isPopupTrigger())
4829 String msg = MessageManager.getString("label.enter_view_name");
4830 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4831 JvOptionPane.QUESTION_MESSAGE);
4835 viewport.setViewName(reply);
4836 // TODO warn if reply is in getExistingViewNames()?
4837 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4842 public AlignViewport getCurrentView()
4848 * Open the dialog for regex description parsing.
4851 protected void extractScores_actionPerformed(ActionEvent e)
4853 ParseProperties pp = new jalview.analysis.ParseProperties(
4854 viewport.getAlignment());
4855 // TODO: verify regex and introduce GUI dialog for version 2.5
4856 // if (pp.getScoresFromDescription("col", "score column ",
4857 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4859 if (pp.getScoresFromDescription("description column",
4860 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4862 buildSortByAnnotationScoresMenu();
4870 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4874 protected void showDbRefs_actionPerformed(ActionEvent e)
4876 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4882 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4886 protected void showNpFeats_actionPerformed(ActionEvent e)
4888 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4892 * find the viewport amongst the tabs in this alignment frame and close that
4897 public boolean closeView(AlignViewportI av)
4901 this.closeMenuItem_actionPerformed(false);
4904 Component[] comp = tabbedPane.getComponents();
4905 for (int i = 0; comp != null && i < comp.length; i++)
4907 if (comp[i] instanceof AlignmentPanel)
4909 if (((AlignmentPanel) comp[i]).av == av)
4912 closeView((AlignmentPanel) comp[i]);
4920 protected void build_fetchdbmenu(JMenu webService)
4922 // Temporary hack - DBRef Fetcher always top level ws entry.
4923 // TODO We probably want to store a sequence database checklist in
4924 // preferences and have checkboxes.. rather than individual sources selected
4926 final JMenu rfetch = new JMenu(
4927 MessageManager.getString("action.fetch_db_references"));
4928 rfetch.setToolTipText(MessageManager.getString(
4929 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4930 webService.add(rfetch);
4932 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4933 MessageManager.getString("option.trim_retrieved_seqs"));
4934 trimrs.setToolTipText(
4935 MessageManager.getString("label.trim_retrieved_sequences"));
4937 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4938 trimrs.addActionListener(new ActionListener()
4941 public void actionPerformed(ActionEvent e)
4943 trimrs.setSelected(trimrs.isSelected());
4944 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4945 Boolean.valueOf(trimrs.isSelected()).toString());
4949 JMenuItem fetchr = new JMenuItem(
4950 MessageManager.getString("label.standard_databases"));
4951 fetchr.setToolTipText(
4952 MessageManager.getString("label.fetch_embl_uniprot"));
4953 fetchr.addActionListener(new ActionListener()
4957 public void actionPerformed(ActionEvent e)
4959 new Thread(new Runnable()
4964 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4965 .getAlignment().isNucleotide();
4966 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4967 alignPanel.av.getSequenceSelection(),
4968 alignPanel.alignFrame, null,
4969 alignPanel.alignFrame.featureSettings, isNucleotide);
4970 dbRefFetcher.addListener(new FetchFinishedListenerI()
4973 public void finished()
4976 for (FeatureSettingsModelI srcSettings : dbRefFetcher
4977 .getFeatureSettingsModels())
4980 alignPanel.av.mergeFeaturesStyle(srcSettings);
4982 AlignFrame.this.setMenusForViewport();
4985 dbRefFetcher.fetchDBRefs(false);
4993 final AlignFrame me = this;
4994 new Thread(new Runnable()
4999 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5000 .getSequenceFetcherSingleton(me);
5001 javax.swing.SwingUtilities.invokeLater(new Runnable()
5006 String[] dbclasses = sf.getOrderedSupportedSources();
5007 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5008 // jalview.util.QuickSort.sort(otherdb, otherdb);
5009 List<DbSourceProxy> otherdb;
5010 JMenu dfetch = new JMenu();
5011 JMenu ifetch = new JMenu();
5012 JMenuItem fetchr = null;
5013 int comp = 0, icomp = 0, mcomp = 15;
5014 String mname = null;
5016 for (String dbclass : dbclasses)
5018 otherdb = sf.getSourceProxy(dbclass);
5019 // add a single entry for this class, or submenu allowing 'fetch
5021 if (otherdb == null || otherdb.size() < 1)
5025 // List<DbSourceProxy> dbs=otherdb;
5026 // otherdb=new ArrayList<DbSourceProxy>();
5027 // for (DbSourceProxy db:dbs)
5029 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5033 mname = "From " + dbclass;
5035 if (otherdb.size() == 1)
5037 final DbSourceProxy[] dassource = otherdb
5038 .toArray(new DbSourceProxy[0]);
5039 DbSourceProxy src = otherdb.get(0);
5040 fetchr = new JMenuItem(src.getDbSource());
5041 fetchr.addActionListener(new ActionListener()
5045 public void actionPerformed(ActionEvent e)
5047 new Thread(new Runnable()
5053 boolean isNucleotide = alignPanel.alignFrame
5054 .getViewport().getAlignment()
5056 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5057 alignPanel.av.getSequenceSelection(),
5058 alignPanel.alignFrame, dassource,
5059 alignPanel.alignFrame.featureSettings,
5062 .addListener(new FetchFinishedListenerI()
5065 public void finished()
5067 FeatureSettingsModelI srcSettings = dassource[0]
5068 .getFeatureColourScheme();
5069 alignPanel.av.mergeFeaturesStyle(
5071 AlignFrame.this.setMenusForViewport();
5074 dbRefFetcher.fetchDBRefs(false);
5080 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5081 MessageManager.formatMessage(
5082 "label.fetch_retrieve_from", new Object[]
5083 { src.getDbName() })));
5089 final DbSourceProxy[] dassource = otherdb
5090 .toArray(new DbSourceProxy[0]);
5092 DbSourceProxy src = otherdb.get(0);
5093 fetchr = new JMenuItem(MessageManager
5094 .formatMessage("label.fetch_all_param", new Object[]
5095 { src.getDbSource() }));
5096 fetchr.addActionListener(new ActionListener()
5099 public void actionPerformed(ActionEvent e)
5101 new Thread(new Runnable()
5107 boolean isNucleotide = alignPanel.alignFrame
5108 .getViewport().getAlignment()
5110 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5111 alignPanel.av.getSequenceSelection(),
5112 alignPanel.alignFrame, dassource,
5113 alignPanel.alignFrame.featureSettings,
5116 .addListener(new FetchFinishedListenerI()
5119 public void finished()
5121 AlignFrame.this.setMenusForViewport();
5124 dbRefFetcher.fetchDBRefs(false);
5130 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5131 MessageManager.formatMessage(
5132 "label.fetch_retrieve_from_all_sources",
5134 { Integer.valueOf(otherdb.size())
5136 src.getDbSource(), src.getDbName() })));
5139 // and then build the rest of the individual menus
5140 ifetch = new JMenu(MessageManager.formatMessage(
5141 "label.source_from_db_source", new Object[]
5142 { src.getDbSource() }));
5144 String imname = null;
5146 for (DbSourceProxy sproxy : otherdb)
5148 String dbname = sproxy.getDbName();
5149 String sname = dbname.length() > 5
5150 ? dbname.substring(0, 5) + "..."
5152 String msname = dbname.length() > 10
5153 ? dbname.substring(0, 10) + "..."
5157 imname = MessageManager
5158 .formatMessage("label.from_msname", new Object[]
5161 fetchr = new JMenuItem(msname);
5162 final DbSourceProxy[] dassrc = { sproxy };
5163 fetchr.addActionListener(new ActionListener()
5167 public void actionPerformed(ActionEvent e)
5169 new Thread(new Runnable()
5175 boolean isNucleotide = alignPanel.alignFrame
5176 .getViewport().getAlignment()
5178 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5179 alignPanel.av.getSequenceSelection(),
5180 alignPanel.alignFrame, dassrc,
5181 alignPanel.alignFrame.featureSettings,
5184 .addListener(new FetchFinishedListenerI()
5187 public void finished()
5189 AlignFrame.this.setMenusForViewport();
5192 dbRefFetcher.fetchDBRefs(false);
5198 fetchr.setToolTipText(
5199 "<html>" + MessageManager.formatMessage(
5200 "label.fetch_retrieve_from", new Object[]
5204 if (++icomp >= mcomp || i == (otherdb.size()))
5206 ifetch.setText(MessageManager.formatMessage(
5207 "label.source_to_target", imname, sname));
5209 ifetch = new JMenu();
5217 if (comp >= mcomp || dbi >= (dbclasses.length))
5219 dfetch.setText(MessageManager.formatMessage(
5220 "label.source_to_target", mname, dbclass));
5222 dfetch = new JMenu();
5235 * Left justify the whole alignment.
5238 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5240 AlignmentI al = viewport.getAlignment();
5242 viewport.firePropertyChange("alignment", null, al);
5246 * Right justify the whole alignment.
5249 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5251 AlignmentI al = viewport.getAlignment();
5253 viewport.firePropertyChange("alignment", null, al);
5257 public void setShowSeqFeatures(boolean b)
5259 showSeqFeatures.setSelected(b);
5260 viewport.setShowSequenceFeatures(b);
5267 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5268 * awt.event.ActionEvent)
5271 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5273 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5274 alignPanel.paintAlignment(false, false);
5281 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5285 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5287 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5288 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5296 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5297 * .event.ActionEvent)
5300 protected void showGroupConservation_actionPerformed(ActionEvent e)
5302 viewport.setShowGroupConservation(showGroupConservation.getState());
5303 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5310 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5311 * .event.ActionEvent)
5314 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5316 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5317 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5324 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5325 * .event.ActionEvent)
5328 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5330 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5331 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5335 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5337 showSequenceLogo.setState(true);
5338 viewport.setShowSequenceLogo(true);
5339 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5340 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5344 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5346 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5353 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5354 * .event.ActionEvent)
5357 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5359 if (avc.makeGroupsFromSelection())
5361 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5362 alignPanel.updateAnnotation();
5363 alignPanel.paintAlignment(true,
5364 viewport.needToUpdateStructureViews());
5368 public void clearAlignmentSeqRep()
5370 // TODO refactor alignmentseqrep to controller
5371 if (viewport.getAlignment().hasSeqrep())
5373 viewport.getAlignment().setSeqrep(null);
5374 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5375 alignPanel.updateAnnotation();
5376 alignPanel.paintAlignment(true, true);
5381 protected void createGroup_actionPerformed(ActionEvent e)
5383 if (avc.createGroup())
5385 if (applyAutoAnnotationSettings.isSelected())
5387 alignPanel.updateAnnotation(true, false);
5389 alignPanel.alignmentChanged();
5394 protected void unGroup_actionPerformed(ActionEvent e)
5398 alignPanel.alignmentChanged();
5403 * make the given alignmentPanel the currently selected tab
5405 * @param alignmentPanel
5407 public void setDisplayedView(AlignmentPanel alignmentPanel)
5409 if (!viewport.getSequenceSetId()
5410 .equals(alignmentPanel.av.getSequenceSetId()))
5412 throw new Error(MessageManager.getString(
5413 "error.implementation_error_cannot_show_view_alignment_frame"));
5415 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5416 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5418 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5423 * Action on selection of menu options to Show or Hide annotations.
5426 * @param forSequences
5427 * update sequence-related annotations
5428 * @param forAlignment
5429 * update non-sequence-related annotations
5432 protected void setAnnotationsVisibility(boolean visible,
5433 boolean forSequences, boolean forAlignment)
5435 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5436 .getAlignmentAnnotation();
5441 for (AlignmentAnnotation aa : anns)
5444 * don't display non-positional annotations on an alignment
5446 if (aa.annotations == null)
5450 boolean apply = (aa.sequenceRef == null && forAlignment)
5451 || (aa.sequenceRef != null && forSequences);
5454 aa.visible = visible;
5457 alignPanel.validateAnnotationDimensions(true);
5458 alignPanel.alignmentChanged();
5462 * Store selected annotation sort order for the view and repaint.
5465 protected void sortAnnotations_actionPerformed()
5467 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5469 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5470 alignPanel.paintAlignment(false, false);
5475 * @return alignment panels in this alignment frame
5477 public List<? extends AlignmentViewPanel> getAlignPanels()
5479 // alignPanels is never null
5480 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5485 * Open a new alignment window, with the cDNA associated with this (protein)
5486 * alignment, aligned as is the protein.
5488 protected void viewAsCdna_actionPerformed()
5490 // TODO no longer a menu action - refactor as required
5491 final AlignmentI alignment = getViewport().getAlignment();
5492 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5493 if (mappings == null)
5497 List<SequenceI> cdnaSeqs = new ArrayList<>();
5498 for (SequenceI aaSeq : alignment.getSequences())
5500 for (AlignedCodonFrame acf : mappings)
5502 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5506 * There is a cDNA mapping for this protein sequence - add to new
5507 * alignment. It will share the same dataset sequence as other mapped
5508 * cDNA (no new mappings need to be created).
5510 final Sequence newSeq = new Sequence(dnaSeq);
5511 newSeq.setDatasetSequence(dnaSeq);
5512 cdnaSeqs.add(newSeq);
5516 if (cdnaSeqs.size() == 0)
5518 // show a warning dialog no mapped cDNA
5521 AlignmentI cdna = new Alignment(
5522 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5523 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5524 AlignFrame.DEFAULT_HEIGHT);
5525 cdna.alignAs(alignment);
5526 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5528 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5529 AlignFrame.DEFAULT_HEIGHT);
5533 * Set visibility of dna/protein complement view (available when shown in a
5539 protected void showComplement_actionPerformed(boolean show)
5541 SplitContainerI sf = getSplitViewContainer();
5544 sf.setComplementVisible(this, show);
5549 * Generate the reverse (optionally complemented) of the selected sequences,
5550 * and add them to the alignment
5553 protected void showReverse_actionPerformed(boolean complement)
5555 AlignmentI al = null;
5558 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5559 al = dna.reverseCdna(complement);
5560 viewport.addAlignment(al, "");
5561 addHistoryItem(new EditCommand(
5562 MessageManager.getString("label.add_sequences"), Action.PASTE,
5563 al.getSequencesArray(), 0, al.getWidth(),
5564 viewport.getAlignment()));
5565 } catch (Exception ex)
5567 System.err.println(ex.getMessage());
5573 * Try to run a script in the Groovy console, having first ensured that this
5574 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5575 * be targeted at this alignment.
5578 protected void runGroovy_actionPerformed()
5580 Jalview.setCurrentAlignFrame(this);
5581 groovy.ui.Console console = Desktop.getGroovyConsole();
5582 if (console != null)
5586 console.runScript();
5587 } catch (Exception ex)
5589 System.err.println((ex.toString()));
5590 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5591 MessageManager.getString("label.couldnt_run_groovy_script"),
5592 MessageManager.getString("label.groovy_support_failed"),
5593 JvOptionPane.ERROR_MESSAGE);
5598 System.err.println("Can't run Groovy script as console not found");
5603 * Hides columns containing (or not containing) a specified feature, provided
5604 * that would not leave all columns hidden
5606 * @param featureType
5607 * @param columnsContaining
5610 public boolean hideFeatureColumns(String featureType,
5611 boolean columnsContaining)
5613 boolean notForHiding = avc.markColumnsContainingFeatures(
5614 columnsContaining, false, false, featureType);
5617 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5618 false, featureType))
5620 getViewport().hideSelectedColumns();
5628 protected void selectHighlightedColumns_actionPerformed(
5629 ActionEvent actionEvent)
5631 // include key modifier check in case user selects from menu
5632 avc.markHighlightedColumns(
5633 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5634 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5635 | ActionEvent.CTRL_MASK)) != 0);
5639 * Rebuilds the Colour menu, including any user-defined colours which have
5640 * been loaded either on startup or during the session
5642 public void buildColourMenu()
5644 colourMenu.removeAll();
5646 colourMenu.add(applyToAllGroups);
5647 colourMenu.add(textColour);
5648 colourMenu.addSeparator();
5650 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5651 viewport.getAlignment(), false);
5653 colourMenu.add(annotationColour);
5654 bg.add(annotationColour);
5655 colourMenu.addSeparator();
5656 colourMenu.add(conservationMenuItem);
5657 colourMenu.add(modifyConservation);
5658 colourMenu.add(abovePIDThreshold);
5659 colourMenu.add(modifyPID);
5661 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5662 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5666 * Open a dialog (if not already open) that allows the user to select and
5667 * calculate PCA or Tree analysis
5669 protected void openTreePcaDialog()
5671 if (alignPanel.getCalculationDialog() == null)
5673 new CalculationChooser(AlignFrame.this);
5678 protected void loadVcf_actionPerformed()
5680 JalviewFileChooser chooser = new JalviewFileChooser(
5681 Cache.getProperty("LAST_DIRECTORY"));
5682 chooser.setFileView(new JalviewFileView());
5683 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5684 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5686 int value = chooser.showOpenDialog(null);
5688 if (value == JalviewFileChooser.APPROVE_OPTION)
5690 String choice = chooser.getSelectedFile().getPath();
5691 Cache.setProperty("LAST_DIRECTORY", choice);
5692 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5693 new VCFLoader(choice).loadVCF(seqs, this);
5698 private Rectangle lastFeatureSettingsBounds = null;
5701 public void setFeatureSettingsGeometry(Rectangle bounds)
5703 lastFeatureSettingsBounds = bounds;
5707 public Rectangle getFeatureSettingsGeometry()
5709 return lastFeatureSettingsBounds;
5713 class PrintThread extends Thread
5717 public PrintThread(AlignmentPanel ap)
5722 static PageFormat pf;
5727 PrinterJob printJob = PrinterJob.getPrinterJob();
5731 printJob.setPrintable(ap, pf);
5735 printJob.setPrintable(ap);
5738 if (printJob.printDialog())
5743 } catch (Exception PrintException)
5745 PrintException.printStackTrace();