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.Color;
25 import java.awt.Component;
26 import java.awt.Rectangle;
27 import java.awt.Toolkit;
28 import java.awt.datatransfer.Clipboard;
29 import java.awt.datatransfer.DataFlavor;
30 import java.awt.datatransfer.StringSelection;
31 import java.awt.datatransfer.Transferable;
32 import java.awt.dnd.DnDConstants;
33 import java.awt.dnd.DropTargetDragEvent;
34 import java.awt.dnd.DropTargetDropEvent;
35 import java.awt.dnd.DropTargetEvent;
36 import java.awt.dnd.DropTargetListener;
37 import java.awt.event.ActionEvent;
38 import java.awt.event.ActionListener;
39 import java.awt.event.FocusAdapter;
40 import java.awt.event.FocusEvent;
41 import java.awt.event.ItemEvent;
42 import java.awt.event.ItemListener;
43 import java.awt.event.KeyAdapter;
44 import java.awt.event.KeyEvent;
45 import java.awt.event.MouseEvent;
46 import java.awt.print.PageFormat;
47 import java.awt.print.PrinterJob;
48 import java.beans.PropertyChangeEvent;
50 import java.io.FileWriter;
51 import java.io.PrintWriter;
53 import java.util.ArrayList;
54 import java.util.Arrays;
55 import java.util.Deque;
56 import java.util.Enumeration;
57 import java.util.Hashtable;
58 import java.util.List;
59 import java.util.Vector;
61 import javax.swing.ButtonGroup;
62 import javax.swing.JCheckBoxMenuItem;
63 import javax.swing.JComponent;
64 import javax.swing.JEditorPane;
65 import javax.swing.JInternalFrame;
66 import javax.swing.JLabel;
67 import javax.swing.JLayeredPane;
68 import javax.swing.JMenu;
69 import javax.swing.JMenuItem;
70 import javax.swing.JPanel;
71 import javax.swing.JScrollPane;
72 import javax.swing.SwingUtilities;
74 import ext.vamsas.ServiceHandle;
75 import jalview.analysis.AlignmentSorter;
76 import jalview.analysis.AlignmentUtils;
77 import jalview.analysis.CrossRef;
78 import jalview.analysis.Dna;
79 import jalview.analysis.GeneticCodeI;
80 import jalview.analysis.ParseProperties;
81 import jalview.analysis.SequenceIdMatcher;
82 import jalview.api.AlignExportSettingsI;
83 import jalview.api.AlignViewControllerGuiI;
84 import jalview.api.AlignViewControllerI;
85 import jalview.api.AlignViewportI;
86 import jalview.api.AlignmentViewPanel;
87 import jalview.api.FeatureSettingsControllerI;
88 import jalview.api.FeatureSettingsModelI;
89 import jalview.api.SplitContainerI;
90 import jalview.api.ViewStyleI;
91 import jalview.api.analysis.SimilarityParamsI;
92 import jalview.bin.Cache;
93 import jalview.bin.Jalview;
94 import jalview.commands.CommandI;
95 import jalview.commands.EditCommand;
96 import jalview.commands.EditCommand.Action;
97 import jalview.commands.OrderCommand;
98 import jalview.commands.RemoveGapColCommand;
99 import jalview.commands.RemoveGapsCommand;
100 import jalview.commands.SlideSequencesCommand;
101 import jalview.commands.TrimRegionCommand;
102 import jalview.datamodel.AlignExportSettingsAdapter;
103 import jalview.datamodel.AlignedCodonFrame;
104 import jalview.datamodel.Alignment;
105 import jalview.datamodel.AlignmentAnnotation;
106 import jalview.datamodel.AlignmentExportData;
107 import jalview.datamodel.AlignmentI;
108 import jalview.datamodel.AlignmentOrder;
109 import jalview.datamodel.AlignmentView;
110 import jalview.datamodel.ColumnSelection;
111 import jalview.datamodel.HiddenColumns;
112 import jalview.datamodel.PDBEntry;
113 import jalview.datamodel.SeqCigar;
114 import jalview.datamodel.Sequence;
115 import jalview.datamodel.SequenceGroup;
116 import jalview.datamodel.SequenceI;
117 import jalview.gui.ColourMenuHelper.ColourChangeListener;
118 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
119 import jalview.io.AlignmentProperties;
120 import jalview.io.AnnotationFile;
121 import jalview.io.BackupFiles;
122 import jalview.io.BioJsHTMLOutput;
123 import jalview.io.DataSourceType;
124 import jalview.io.FileFormat;
125 import jalview.io.FileFormatI;
126 import jalview.io.FileFormats;
127 import jalview.io.FileLoader;
128 import jalview.io.FileParse;
129 import jalview.io.FormatAdapter;
130 import jalview.io.HtmlSvgOutput;
131 import jalview.io.IdentifyFile;
132 import jalview.io.JPredFile;
133 import jalview.io.JalviewFileChooser;
134 import jalview.io.JalviewFileView;
135 import jalview.io.JnetAnnotationMaker;
136 import jalview.io.NewickFile;
137 import jalview.io.ScoreMatrixFile;
138 import jalview.io.TCoffeeScoreFile;
139 import jalview.io.vcf.VCFLoader;
140 import jalview.jbgui.GAlignFrame;
141 import jalview.project.Jalview2XML;
142 import jalview.schemes.ColourSchemeI;
143 import jalview.schemes.ColourSchemes;
144 import jalview.schemes.ResidueColourScheme;
145 import jalview.schemes.TCoffeeColourScheme;
146 import jalview.util.ImageMaker.TYPE;
147 import jalview.util.MessageManager;
148 import jalview.util.Platform;
149 import jalview.viewmodel.AlignmentViewport;
150 import jalview.viewmodel.ViewportRanges;
151 import jalview.ws.DBRefFetcher;
152 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
153 import jalview.ws.jws1.Discoverer;
154 import jalview.ws.jws2.Jws2Discoverer;
155 import jalview.ws.jws2.jabaws2.Jws2Instance;
156 import jalview.ws.seqfetcher.DbSourceProxy;
162 * @version $Revision$
164 @SuppressWarnings("serial")
165 public class AlignFrame extends GAlignFrame implements DropTargetListener,
166 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
169 public static final int DEFAULT_WIDTH = 700;
171 public static final int DEFAULT_HEIGHT = 500;
174 * The currently displayed panel (selected tabbed view if more than one)
176 public AlignmentPanel alignPanel;
178 AlignViewport viewport;
180 public AlignViewControllerI avc;
182 List<AlignmentPanel> alignPanels = new ArrayList<>();
185 * Last format used to load or save alignments in this window
187 FileFormatI currentFileFormat = null;
190 * Current filename for this alignment
192 String fileName = null;
197 * Creates a new AlignFrame object with specific width and height.
203 public AlignFrame(AlignmentI al, int width, int height)
205 this(al, null, width, height);
209 * Creates a new AlignFrame object with specific width, height and
215 * @param sequenceSetId
217 public AlignFrame(AlignmentI al, int width, int height,
218 String sequenceSetId)
220 this(al, null, width, height, sequenceSetId);
224 * Creates a new AlignFrame object with specific width, height and
230 * @param sequenceSetId
233 public AlignFrame(AlignmentI al, int width, int height,
234 String sequenceSetId, String viewId)
236 this(al, null, width, height, sequenceSetId, viewId);
240 * new alignment window with hidden columns
244 * @param hiddenColumns
245 * ColumnSelection or null
247 * Width of alignment frame
251 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
254 this(al, hiddenColumns, width, height, null);
258 * Create alignment frame for al with hiddenColumns, a specific width and
259 * height, and specific sequenceId
262 * @param hiddenColumns
265 * @param sequenceSetId
268 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
269 int height, String sequenceSetId)
271 this(al, hiddenColumns, width, height, sequenceSetId, null);
275 * Create alignment frame for al with hiddenColumns, a specific width and
276 * height, and specific sequenceId
279 * @param hiddenColumns
282 * @param sequenceSetId
287 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
288 int height, String sequenceSetId, String viewId)
290 setSize(width, height);
292 if (al.getDataset() == null)
297 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
299 alignPanel = new AlignmentPanel(this, viewport);
301 addAlignmentPanel(alignPanel, true);
305 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
306 HiddenColumns hiddenColumns, int width, int height)
308 setSize(width, height);
310 if (al.getDataset() == null)
315 viewport = new AlignViewport(al, hiddenColumns);
317 if (hiddenSeqs != null && hiddenSeqs.length > 0)
319 viewport.hideSequence(hiddenSeqs);
321 alignPanel = new AlignmentPanel(this, viewport);
322 addAlignmentPanel(alignPanel, true);
327 * Make a new AlignFrame from existing alignmentPanels
334 public AlignFrame(AlignmentPanel ap)
338 addAlignmentPanel(ap, false);
343 * initalise the alignframe from the underlying viewport data and the
348 // setBackground(Color.white); // BH 2019
350 if (!Jalview.isHeadlessMode())
352 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
355 avc = new jalview.controller.AlignViewController(this, viewport,
357 if (viewport.getAlignmentConservationAnnotation() == null)
359 // BLOSUM62Colour.setEnabled(false);
360 conservationMenuItem.setEnabled(false);
361 modifyConservation.setEnabled(false);
362 // PIDColour.setEnabled(false);
363 // abovePIDThreshold.setEnabled(false);
364 // modifyPID.setEnabled(false);
367 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
370 if (sortby.equals("Id"))
372 sortIDMenuItem_actionPerformed(null);
374 else if (sortby.equals("Pairwise Identity"))
376 sortPairwiseMenuItem_actionPerformed(null);
380 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
382 setMenusFromViewport(viewport);
383 buildSortByAnnotationScoresMenu();
384 calculateTree.addActionListener(new ActionListener()
388 public void actionPerformed(ActionEvent e)
395 if (Desktop.desktop != null)
397 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
398 if (!Platform.isJS())
400 addServiceListeners();
405 if (viewport.getWrapAlignment())
407 wrapMenuItem_actionPerformed(null);
410 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
412 this.overviewMenuItem_actionPerformed(null);
417 final List<AlignmentViewPanel> selviews = new ArrayList<>();
418 final List<AlignmentPanel> origview = new ArrayList<>();
419 final String menuLabel = MessageManager
420 .getString("label.copy_format_from");
421 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
422 new ViewSetProvider()
426 public AlignmentPanel[] getAllAlignmentPanels()
429 origview.add(alignPanel);
430 // make an array of all alignment panels except for this one
431 List<AlignmentPanel> aps = new ArrayList<>(
432 Arrays.asList(Desktop.getAlignmentPanels(null)));
433 aps.remove(AlignFrame.this.alignPanel);
434 return aps.toArray(new AlignmentPanel[aps.size()]);
436 }, selviews, new ItemListener()
440 public void itemStateChanged(ItemEvent e)
442 if (origview.size() > 0)
444 final AlignmentPanel ap = origview.get(0);
447 * Copy the ViewStyle of the selected panel to 'this one'.
448 * Don't change value of 'scaleProteinAsCdna' unless copying
451 ViewStyleI vs = selviews.get(0).getAlignViewport()
453 boolean fromSplitFrame = selviews.get(0)
454 .getAlignViewport().getCodingComplement() != null;
457 vs.setScaleProteinAsCdna(ap.getAlignViewport()
458 .getViewStyle().isScaleProteinAsCdna());
460 ap.getAlignViewport().setViewStyle(vs);
463 * Also rescale ViewStyle of SplitFrame complement if there is
464 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
465 * the whole ViewStyle (allow cDNA protein to have different
468 AlignViewportI complement = ap.getAlignViewport()
469 .getCodingComplement();
470 if (complement != null && vs.isScaleProteinAsCdna())
472 AlignFrame af = Desktop.getAlignFrameFor(complement);
473 ((SplitFrame) af.getSplitViewContainer())
475 af.setMenusForViewport();
479 ap.setSelected(true);
480 ap.alignFrame.setMenusForViewport();
485 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
486 .indexOf("devel") > -1
487 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
488 .indexOf("test") > -1)
490 formatMenu.add(vsel);
492 addFocusListener(new FocusAdapter()
495 public void focusGained(FocusEvent e)
497 Jalview.setCurrentAlignFrame(AlignFrame.this);
504 * Change the filename and format for the alignment, and enable the 'reload'
505 * button functionality.
512 public void setFileName(String file, FileFormatI format)
515 setFileFormat(format);
516 reload.setEnabled(true);
520 * JavaScript will have this, maybe others. More dependable than a file name
521 * and maintains a reference to the actual bytes loaded.
525 public void setFileObject(File file)
527 this.fileObject = file;
531 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
534 void addKeyListener()
536 addKeyListener(new KeyAdapter()
539 public void keyPressed(KeyEvent evt)
541 if (viewport.cursorMode
542 && ((evt.getKeyCode() >= KeyEvent.VK_0
543 && evt.getKeyCode() <= KeyEvent.VK_9)
544 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
545 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
546 && Character.isDigit(evt.getKeyChar()))
548 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
551 switch (evt.getKeyCode())
554 case 27: // escape key
555 deselectAllSequenceMenuItem_actionPerformed(null);
559 case KeyEvent.VK_DOWN:
560 if (evt.isAltDown() || !viewport.cursorMode)
562 moveSelectedSequences(false);
564 if (viewport.cursorMode)
566 alignPanel.getSeqPanel().moveCursor(0, 1);
571 if (evt.isAltDown() || !viewport.cursorMode)
573 moveSelectedSequences(true);
575 if (viewport.cursorMode)
577 alignPanel.getSeqPanel().moveCursor(0, -1);
582 case KeyEvent.VK_LEFT:
583 if (evt.isAltDown() || !viewport.cursorMode)
585 slideSequences(false,
586 alignPanel.getSeqPanel().getKeyboardNo1());
590 alignPanel.getSeqPanel().moveCursor(-1, 0);
595 case KeyEvent.VK_RIGHT:
596 if (evt.isAltDown() || !viewport.cursorMode)
598 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
602 alignPanel.getSeqPanel().moveCursor(1, 0);
606 case KeyEvent.VK_SPACE:
607 if (viewport.cursorMode)
609 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
610 || evt.isShiftDown() || evt.isAltDown());
614 // case KeyEvent.VK_A:
615 // if (viewport.cursorMode)
617 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
618 // //System.out.println("A");
622 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
623 * System.out.println("closing bracket"); } break;
625 case KeyEvent.VK_DELETE:
626 case KeyEvent.VK_BACK_SPACE:
627 if (!viewport.cursorMode)
629 cut_actionPerformed();
633 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
634 || evt.isShiftDown() || evt.isAltDown());
640 if (viewport.cursorMode)
642 alignPanel.getSeqPanel().setCursorRow();
646 if (viewport.cursorMode && !evt.isControlDown())
648 alignPanel.getSeqPanel().setCursorColumn();
652 if (viewport.cursorMode)
654 alignPanel.getSeqPanel().setCursorPosition();
658 case KeyEvent.VK_ENTER:
659 case KeyEvent.VK_COMMA:
660 if (viewport.cursorMode)
662 alignPanel.getSeqPanel().setCursorRowAndColumn();
667 if (viewport.cursorMode)
669 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
673 if (viewport.cursorMode)
675 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
680 viewport.cursorMode = !viewport.cursorMode;
681 setStatus(MessageManager
682 .formatMessage("label.keyboard_editing_mode", new String[]
683 { (viewport.cursorMode ? "on" : "off") }));
684 if (viewport.cursorMode)
686 ViewportRanges ranges = viewport.getRanges();
687 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
689 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
692 alignPanel.getSeqPanel().seqCanvas.repaint();
698 Help.showHelpWindow();
699 } catch (Exception ex)
701 ex.printStackTrace();
706 boolean toggleSeqs = !evt.isControlDown();
707 boolean toggleCols = !evt.isShiftDown();
708 toggleHiddenRegions(toggleSeqs, toggleCols);
713 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
714 boolean modifyExisting = true; // always modify, don't clear
715 // evt.isShiftDown();
716 boolean invertHighlighted = evt.isAltDown();
717 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
721 case KeyEvent.VK_PAGE_UP:
722 viewport.getRanges().pageUp();
724 case KeyEvent.VK_PAGE_DOWN:
725 viewport.getRanges().pageDown();
731 public void keyReleased(KeyEvent evt)
733 switch (evt.getKeyCode())
735 case KeyEvent.VK_LEFT:
736 if (evt.isAltDown() || !viewport.cursorMode)
738 viewport.firePropertyChange("alignment", null,
739 viewport.getAlignment().getSequences());
743 case KeyEvent.VK_RIGHT:
744 if (evt.isAltDown() || !viewport.cursorMode)
746 viewport.firePropertyChange("alignment", null,
747 viewport.getAlignment().getSequences());
755 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
757 ap.alignFrame = this;
758 avc = new jalview.controller.AlignViewController(this, viewport,
763 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
765 int aSize = alignPanels.size();
767 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
769 if (aSize == 1 && ap.av.getViewName() == null)
771 this.getContentPane().add(ap, BorderLayout.CENTER);
777 setInitialTabVisible();
780 expandViews.setEnabled(true);
781 gatherViews.setEnabled(true);
782 tabbedPane.addTab(ap.av.getViewName(), ap);
784 ap.setVisible(false);
789 if (ap.av.isPadGaps())
791 ap.av.getAlignment().padGaps();
793 ap.av.updateConservation(ap);
794 ap.av.updateConsensus(ap);
795 ap.av.updateStrucConsensus(ap);
799 public void setInitialTabVisible()
801 expandViews.setEnabled(true);
802 gatherViews.setEnabled(true);
803 tabbedPane.setVisible(true);
804 AlignmentPanel first = alignPanels.get(0);
805 tabbedPane.addTab(first.av.getViewName(), first);
806 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
809 public AlignViewport getViewport()
814 /* Set up intrinsic listeners for dynamically generated GUI bits. */
815 private void addServiceListeners()
817 final java.beans.PropertyChangeListener thisListener;
818 Desktop.instance.addJalviewPropertyChangeListener("services",
819 thisListener = new java.beans.PropertyChangeListener()
822 public void propertyChange(PropertyChangeEvent evt)
824 // // System.out.println("Discoverer property change.");
825 // if (evt.getPropertyName().equals("services"))
827 SwingUtilities.invokeLater(new Runnable()
834 "Rebuild WS Menu for service change");
835 BuildWebServiceMenu();
842 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
845 public void internalFrameClosed(
846 javax.swing.event.InternalFrameEvent evt)
848 // System.out.println("deregistering discoverer listener");
849 Desktop.instance.removeJalviewPropertyChangeListener("services",
851 closeMenuItem_actionPerformed(true);
854 // Finally, build the menu once to get current service state
855 new Thread(new Runnable()
860 BuildWebServiceMenu();
866 * Configure menu items that vary according to whether the alignment is
867 * nucleotide or protein
869 public void setGUINucleotide()
871 AlignmentI al = getViewport().getAlignment();
872 boolean nucleotide = al.isNucleotide();
874 loadVcf.setVisible(nucleotide);
875 showTranslation.setVisible(nucleotide);
876 showReverse.setVisible(nucleotide);
877 showReverseComplement.setVisible(nucleotide);
878 conservationMenuItem.setEnabled(!nucleotide);
880 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
881 showGroupConservation.setEnabled(!nucleotide);
883 showComplementMenuItem
884 .setText(nucleotide ? MessageManager.getString("label.protein")
885 : MessageManager.getString("label.nucleotide"));
889 * set up menus for the current viewport. This may be called after any
890 * operation that affects the data in the current view (selection changed,
891 * etc) to update the menus to reflect the new state.
894 public void setMenusForViewport()
896 setMenusFromViewport(viewport);
900 * Need to call this method when tabs are selected for multiple views, or when
901 * loading from Jalview2XML.java
906 public void setMenusFromViewport(AlignViewport av)
908 padGapsMenuitem.setSelected(av.isPadGaps());
909 colourTextMenuItem.setSelected(av.isShowColourText());
910 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
911 modifyPID.setEnabled(abovePIDThreshold.isSelected());
912 conservationMenuItem.setSelected(av.getConservationSelected());
913 modifyConservation.setEnabled(conservationMenuItem.isSelected());
914 seqLimits.setSelected(av.getShowJVSuffix());
915 idRightAlign.setSelected(av.isRightAlignIds());
916 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
917 renderGapsMenuItem.setSelected(av.isRenderGaps());
918 wrapMenuItem.setSelected(av.getWrapAlignment());
919 scaleAbove.setVisible(av.getWrapAlignment());
920 scaleLeft.setVisible(av.getWrapAlignment());
921 scaleRight.setVisible(av.getWrapAlignment());
922 annotationPanelMenuItem.setState(av.isShowAnnotation());
924 * Show/hide annotations only enabled if annotation panel is shown
926 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
927 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
928 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
929 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
930 viewBoxesMenuItem.setSelected(av.getShowBoxes());
931 viewTextMenuItem.setSelected(av.getShowText());
932 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
933 showGroupConsensus.setSelected(av.isShowGroupConsensus());
934 showGroupConservation.setSelected(av.isShowGroupConservation());
935 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
936 showSequenceLogo.setSelected(av.isShowSequenceLogo());
937 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
939 ColourMenuHelper.setColourSelected(colourMenu,
940 av.getGlobalColourScheme());
942 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
943 hiddenMarkers.setState(av.getShowHiddenMarkers());
944 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
945 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
946 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
947 autoCalculate.setSelected(av.autoCalculateConsensus);
948 sortByTree.setSelected(av.sortByTree);
949 listenToViewSelections.setSelected(av.followSelection);
951 showProducts.setEnabled(canShowProducts());
952 setGroovyEnabled(Desktop.getGroovyConsole() != null);
958 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
962 public void setGroovyEnabled(boolean b)
964 runGroovy.setEnabled(b);
967 private IProgressIndicator progressBar;
972 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
975 public void setProgressBar(String message, long id)
977 progressBar.setProgressBar(message, id);
981 public void registerHandler(final long id,
982 final IProgressIndicatorHandler handler)
984 progressBar.registerHandler(id, handler);
989 * @return true if any progress bars are still active
992 public boolean operationInProgress()
994 return progressBar.operationInProgress();
998 * Sets the text of the status bar. Note that setting a null or empty value
999 * will cause the status bar to be hidden, with possibly undesirable flicker
1000 * of the screen layout.
1003 public void setStatus(String text)
1005 statusBar.setText(text == null || text.isEmpty() ? " " : text);
1009 * Added so Castor Mapping file can obtain Jalview Version
1011 public String getVersion()
1013 return jalview.bin.Cache.getProperty("VERSION");
1016 public FeatureRenderer getFeatureRenderer()
1018 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1022 public void fetchSequence_actionPerformed()
1024 new SequenceFetcher(this);
1028 public void addFromFile_actionPerformed(ActionEvent e)
1030 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1034 public void reload_actionPerformed(ActionEvent e)
1036 if (fileName != null)
1038 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1039 // originating file's format
1040 // TODO: work out how to recover feature settings for correct view(s) when
1041 // file is reloaded.
1042 if (FileFormat.Jalview.equals(currentFileFormat))
1044 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1045 for (int i = 0; i < frames.length; i++)
1047 if (frames[i] instanceof AlignFrame && frames[i] != this
1048 && ((AlignFrame) frames[i]).fileName != null
1049 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1053 frames[i].setSelected(true);
1054 Desktop.instance.closeAssociatedWindows();
1055 } catch (java.beans.PropertyVetoException ex)
1061 Desktop.instance.closeAssociatedWindows();
1063 FileLoader loader = new FileLoader();
1064 DataSourceType protocol = fileName.startsWith("http:")
1065 ? DataSourceType.URL
1066 : DataSourceType.FILE;
1067 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1071 Rectangle bounds = this.getBounds();
1073 FileLoader loader = new FileLoader();
1075 AlignFrame newframe = null;
1077 if (fileObject == null)
1080 DataSourceType protocol = (fileName.startsWith("http:")
1081 ? DataSourceType.URL
1082 : DataSourceType.FILE);
1083 newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1088 newframe = loader.LoadFileWaitTillLoaded(fileObject,
1089 DataSourceType.FILE, currentFileFormat);
1092 newframe.setBounds(bounds);
1093 if (featureSettings != null && featureSettings.isShowing())
1095 final Rectangle fspos = featureSettings.frame.getBounds();
1096 // TODO: need a 'show feature settings' function that takes bounds -
1097 // need to refactor Desktop.addFrame
1098 newframe.featureSettings_actionPerformed(null);
1099 final FeatureSettings nfs = newframe.featureSettings;
1100 SwingUtilities.invokeLater(new Runnable()
1105 nfs.frame.setBounds(fspos);
1108 this.featureSettings.close();
1109 this.featureSettings = null;
1111 this.closeMenuItem_actionPerformed(true);
1117 public void addFromText_actionPerformed(ActionEvent e)
1120 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1124 public void addFromURL_actionPerformed(ActionEvent e)
1126 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1130 public void save_actionPerformed(ActionEvent e)
1132 if (fileName == null || (currentFileFormat == null)
1133 || fileName.startsWith("http"))
1135 saveAs_actionPerformed();
1139 saveAlignment(fileName, currentFileFormat);
1144 * Saves the alignment to a file with a name chosen by the user, if necessary
1145 * warning if a file would be overwritten
1148 public void saveAs_actionPerformed()
1150 String format = currentFileFormat == null ? null
1151 : currentFileFormat.getName();
1152 JalviewFileChooser chooser = JalviewFileChooser
1153 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1155 chooser.setFileView(new JalviewFileView());
1156 chooser.setDialogTitle(
1157 MessageManager.getString("label.save_alignment_to_file"));
1158 chooser.setToolTipText(MessageManager.getString("action.save"));
1160 int value = chooser.showSaveDialog(this);
1162 if (value != JalviewFileChooser.APPROVE_OPTION)
1166 currentFileFormat = chooser.getSelectedFormat();
1167 // todo is this (2005) test now obsolete - value is never null?
1168 while (currentFileFormat == null)
1170 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1172 .getString("label.select_file_format_before_saving"),
1173 MessageManager.getString("label.file_format_not_specified"),
1174 JvOptionPane.WARNING_MESSAGE);
1175 currentFileFormat = chooser.getSelectedFormat();
1176 value = chooser.showSaveDialog(this);
1177 if (value != JalviewFileChooser.APPROVE_OPTION)
1183 fileName = chooser.getSelectedFile().getPath();
1185 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1186 Cache.setProperty("LAST_DIRECTORY", fileName);
1187 saveAlignment(fileName, currentFileFormat);
1190 boolean lastSaveSuccessful = false;
1192 FileFormatI lastFormatSaved;
1194 String lastFilenameSaved;
1197 * Raise a dialog or status message for the last call to saveAlignment.
1199 * @return true if last call to saveAlignment(file, format) was successful.
1201 public boolean isSaveAlignmentSuccessful()
1204 if (!lastSaveSuccessful)
1206 JvOptionPane.showInternalMessageDialog(this, MessageManager
1207 .formatMessage("label.couldnt_save_file", new Object[]
1208 { lastFilenameSaved }),
1209 MessageManager.getString("label.error_saving_file"),
1210 JvOptionPane.WARNING_MESSAGE);
1215 setStatus(MessageManager.formatMessage(
1216 "label.successfully_saved_to_file_in_format", new Object[]
1217 { lastFilenameSaved, lastFormatSaved }));
1220 return lastSaveSuccessful;
1224 * Saves the alignment to the specified file path, in the specified format,
1225 * which may be an alignment format, or Jalview project format. If the
1226 * alignment has hidden regions, or the format is one capable of including
1227 * non-sequence data (features, annotations, groups), then the user may be
1228 * prompted to specify what to include in the output.
1233 public void saveAlignment(String file, FileFormatI format)
1235 lastSaveSuccessful = true;
1236 lastFilenameSaved = file;
1237 lastFormatSaved = format;
1239 if (FileFormat.Jalview.equals(format))
1241 String shortName = title;
1242 if (shortName.indexOf(File.separatorChar) > -1)
1244 shortName = shortName.substring(
1245 shortName.lastIndexOf(File.separatorChar) + 1);
1247 lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName);
1249 statusBar.setText(MessageManager.formatMessage(
1250 "label.successfully_saved_to_file_in_format", new Object[]
1251 { fileName, format }));
1256 AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1257 Runnable cancelAction = new Runnable()
1262 lastSaveSuccessful = false;
1265 Runnable outputAction = new Runnable()
1270 // todo defer this to inside formatSequences (or later)
1271 AlignmentExportData exportData = viewport
1272 .getAlignExportData(options);
1273 String output = new FormatAdapter(alignPanel, options)
1274 .formatSequences(format, exportData.getAlignment(),
1275 exportData.getOmitHidden(),
1276 exportData.getStartEndPostions(),
1277 viewport.getAlignment().getHiddenColumns());
1280 lastSaveSuccessful = false;
1284 // create backupfiles object and get new temp filename destination
1285 boolean doBackup = BackupFiles.getEnabled();
1286 BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
1289 String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
1290 PrintWriter out = new PrintWriter(
1291 new FileWriter(tempFilePath));
1295 AlignFrame.this.setTitle(file);
1296 statusBar.setText(MessageManager.formatMessage(
1297 "label.successfully_saved_to_file_in_format", new Object[]
1298 { fileName, format.getName() }));
1299 lastSaveSuccessful = true;
1300 } catch (Exception ex)
1302 lastSaveSuccessful = false;
1303 ex.printStackTrace();
1308 backupfiles.setWriteSuccess(lastSaveSuccessful);
1309 // do the backup file roll and rename the temp file to actual file
1310 lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1317 * show dialog with export options if applicable; else just do it
1319 if (AlignExportOptions.isNeeded(viewport, format))
1321 AlignExportOptions choices = new AlignExportOptions(
1322 alignPanel.getAlignViewport(), format, options);
1323 choices.setResponseAction(0, outputAction);
1324 choices.setResponseAction(1, cancelAction);
1325 choices.showDialog();
1334 * Outputs the alignment to textbox in the requested format, if necessary
1335 * first prompting the user for whether to include hidden regions or
1338 * @param fileFormatName
1341 protected void outputText_actionPerformed(String fileFormatName)
1343 FileFormatI fileFormat = FileFormats.getInstance()
1344 .forName(fileFormatName);
1345 AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1346 Runnable outputAction = new Runnable()
1351 // todo defer this to inside formatSequences (or later)
1352 AlignmentExportData exportData = viewport
1353 .getAlignExportData(options);
1354 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1355 cap.setForInput(null);
1358 FileFormatI format = fileFormat;
1359 cap.setText(new FormatAdapter(alignPanel, options)
1360 .formatSequences(format, exportData.getAlignment(),
1361 exportData.getOmitHidden(),
1362 exportData.getStartEndPostions(),
1363 viewport.getAlignment().getHiddenColumns()));
1364 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1365 "label.alignment_output_command", new Object[]
1366 { fileFormat.getName() }), 600, 500);
1367 } catch (OutOfMemoryError oom)
1369 new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1377 * show dialog with export options if applicable; else just do it
1379 if (AlignExportOptions.isNeeded(viewport, fileFormat))
1381 AlignExportOptions choices = new AlignExportOptions(
1382 alignPanel.getAlignViewport(), fileFormat, options);
1383 choices.setResponseAction(0, outputAction);
1384 choices.showDialog();
1399 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1401 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1402 htmlSVG.exportHTML(null);
1406 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1408 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1409 bjs.exportHTML(null);
1412 public void createImageMap(File file, String image)
1414 alignPanel.makePNGImageMap(file, image);
1418 * Creates a PNG image of the alignment and writes it to the given file. If
1419 * the file is null, the user is prompted to choose a file.
1424 public void createPNG(File f)
1426 alignPanel.makeAlignmentImage(TYPE.PNG, f);
1430 * Creates an EPS image of the alignment and writes it to the given file. If
1431 * the file is null, the user is prompted to choose a file.
1436 public void createEPS(File f)
1438 alignPanel.makeAlignmentImage(TYPE.EPS, f);
1442 * Creates an SVG image of the alignment and writes it to the given file. If
1443 * the file is null, the user is prompted to choose a file.
1448 public void createSVG(File f)
1450 alignPanel.makeAlignmentImage(TYPE.SVG, f);
1454 public void pageSetup_actionPerformed(ActionEvent e)
1456 PrinterJob printJob = PrinterJob.getPrinterJob();
1457 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1467 public void printMenuItem_actionPerformed(ActionEvent e)
1469 // Putting in a thread avoids Swing painting problems
1470 PrintThread thread = new PrintThread(alignPanel);
1475 public void exportFeatures_actionPerformed(ActionEvent e)
1477 new AnnotationExporter(alignPanel).exportFeatures();
1481 public void exportAnnotations_actionPerformed(ActionEvent e)
1483 new AnnotationExporter(alignPanel).exportAnnotations();
1487 public void associatedData_actionPerformed(ActionEvent e)
1489 final JalviewFileChooser chooser = new JalviewFileChooser(
1490 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1491 chooser.setFileView(new JalviewFileView());
1492 String tooltip = MessageManager.getString("label.load_jalview_annotations");
1493 chooser.setDialogTitle(tooltip);
1494 chooser.setToolTipText(tooltip);
1495 chooser.setResponseHandler(0, new Runnable()
1500 String choice = chooser.getSelectedFile().getPath();
1501 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1502 loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1506 chooser.showOpenDialog(this);
1510 * Close the current view or all views in the alignment frame. If the frame
1511 * only contains one view then the alignment will be removed from memory.
1513 * @param closeAllTabs
1516 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1518 if (alignPanels != null && alignPanels.size() < 2)
1520 closeAllTabs = true;
1525 if (alignPanels != null)
1529 if (this.isClosed())
1531 // really close all the windows - otherwise wait till
1532 // setClosed(true) is called
1533 for (int i = 0; i < alignPanels.size(); i++)
1535 AlignmentPanel ap = alignPanels.get(i);
1542 closeView(alignPanel);
1547 if (featureSettings != null && featureSettings.isOpen())
1549 featureSettings.close();
1550 featureSettings = null;
1553 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1554 * be called recursively, with the frame now in 'closed' state
1556 this.setClosed(true);
1558 } catch (Exception ex)
1560 ex.printStackTrace();
1565 * Close the specified panel and close up tabs appropriately.
1567 * @param panelToClose
1569 public void closeView(AlignmentPanel panelToClose)
1571 int index = tabbedPane.getSelectedIndex();
1572 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1573 alignPanels.remove(panelToClose);
1574 panelToClose.closePanel();
1575 panelToClose = null;
1577 tabbedPane.removeTabAt(closedindex);
1578 tabbedPane.validate();
1580 if (index > closedindex || index == tabbedPane.getTabCount())
1582 // modify currently selected tab index if necessary.
1586 this.tabSelectionChanged(index);
1592 void updateEditMenuBar()
1595 if (viewport.getHistoryList().size() > 0)
1597 undoMenuItem.setEnabled(true);
1598 CommandI command = viewport.getHistoryList().peek();
1599 undoMenuItem.setText(MessageManager
1600 .formatMessage("label.undo_command", new Object[]
1601 { command.getDescription() }));
1605 undoMenuItem.setEnabled(false);
1606 undoMenuItem.setText(MessageManager.getString("action.undo"));
1609 if (viewport.getRedoList().size() > 0)
1611 redoMenuItem.setEnabled(true);
1613 CommandI command = viewport.getRedoList().peek();
1614 redoMenuItem.setText(MessageManager
1615 .formatMessage("label.redo_command", new Object[]
1616 { command.getDescription() }));
1620 redoMenuItem.setEnabled(false);
1621 redoMenuItem.setText(MessageManager.getString("action.redo"));
1626 public void addHistoryItem(CommandI command)
1628 if (command.getSize() > 0)
1630 viewport.addToHistoryList(command);
1631 viewport.clearRedoList();
1632 updateEditMenuBar();
1633 viewport.updateHiddenColumns();
1634 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1635 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1636 // viewport.getColumnSelection()
1637 // .getHiddenColumns().size() > 0);
1643 * @return alignment objects for all views
1645 AlignmentI[] getViewAlignments()
1647 if (alignPanels != null)
1649 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1651 for (AlignmentPanel ap : alignPanels)
1653 als[i++] = ap.av.getAlignment();
1657 if (viewport != null)
1659 return new AlignmentI[] { viewport.getAlignment() };
1671 protected void undoMenuItem_actionPerformed(ActionEvent e)
1673 if (viewport.getHistoryList().isEmpty())
1677 CommandI command = viewport.getHistoryList().pop();
1678 viewport.addToRedoList(command);
1679 command.undoCommand(getViewAlignments());
1681 AlignmentViewport originalSource = getOriginatingSource(command);
1682 updateEditMenuBar();
1684 if (originalSource != null)
1686 if (originalSource != viewport)
1689 "Implementation worry: mismatch of viewport origin for undo");
1691 originalSource.updateHiddenColumns();
1692 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1694 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1695 // viewport.getColumnSelection()
1696 // .getHiddenColumns().size() > 0);
1697 originalSource.firePropertyChange("alignment", null,
1698 originalSource.getAlignment().getSequences());
1709 protected void redoMenuItem_actionPerformed(ActionEvent e)
1711 if (viewport.getRedoList().size() < 1)
1716 CommandI command = viewport.getRedoList().pop();
1717 viewport.addToHistoryList(command);
1718 command.doCommand(getViewAlignments());
1720 AlignmentViewport originalSource = getOriginatingSource(command);
1721 updateEditMenuBar();
1723 if (originalSource != null)
1726 if (originalSource != viewport)
1729 "Implementation worry: mismatch of viewport origin for redo");
1731 originalSource.updateHiddenColumns();
1732 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1734 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1735 // viewport.getColumnSelection()
1736 // .getHiddenColumns().size() > 0);
1737 originalSource.firePropertyChange("alignment", null,
1738 originalSource.getAlignment().getSequences());
1742 AlignmentViewport getOriginatingSource(CommandI command)
1744 AlignmentViewport originalSource = null;
1745 // For sequence removal and addition, we need to fire
1746 // the property change event FROM the viewport where the
1747 // original alignment was altered
1748 AlignmentI al = null;
1749 if (command instanceof EditCommand)
1751 EditCommand editCommand = (EditCommand) command;
1752 al = editCommand.getAlignment();
1753 List<Component> comps = PaintRefresher.components
1754 .get(viewport.getSequenceSetId());
1756 for (Component comp : comps)
1758 if (comp instanceof AlignmentPanel)
1760 if (al == ((AlignmentPanel) comp).av.getAlignment())
1762 originalSource = ((AlignmentPanel) comp).av;
1769 if (originalSource == null)
1771 // The original view is closed, we must validate
1772 // the current view against the closed view first
1775 PaintRefresher.validateSequences(al, viewport.getAlignment());
1778 originalSource = viewport;
1781 return originalSource;
1785 * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection or the sequence under cursor in keyboard mode
1790 public void moveSelectedSequences(boolean up)
1792 SequenceGroup sg = viewport.getSelectionGroup();
1796 if (viewport.cursorMode)
1798 sg = new SequenceGroup();
1799 sg.addSequence(viewport.getAlignment()
1800 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY),false);
1806 if (sg.getSize() < 1)
1811 // TODO: JAL-3733 - add an event to the undo buffer for this !
1813 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1814 viewport.getHiddenRepSequences(), up);
1815 alignPanel.paintAlignment(true, false);
1818 synchronized void slideSequences(boolean right, int size)
1820 List<SequenceI> sg = new ArrayList<>();
1821 if (viewport.cursorMode)
1823 sg.add(viewport.getAlignment()
1824 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1826 else if (viewport.getSelectionGroup() != null
1827 && viewport.getSelectionGroup().getSize() != viewport
1828 .getAlignment().getHeight())
1830 sg = viewport.getSelectionGroup()
1831 .getSequences(viewport.getHiddenRepSequences());
1839 List<SequenceI> invertGroup = new ArrayList<>();
1841 for (SequenceI seq : viewport.getAlignment().getSequences())
1843 if (!sg.contains(seq))
1845 invertGroup.add(seq);
1849 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1851 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1852 for (int i = 0; i < invertGroup.size(); i++)
1854 seqs2[i] = invertGroup.get(i);
1857 SlideSequencesCommand ssc;
1860 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1861 viewport.getGapCharacter());
1865 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1866 viewport.getGapCharacter());
1869 int groupAdjustment = 0;
1870 if (ssc.getGapsInsertedBegin() && right)
1872 if (viewport.cursorMode)
1874 alignPanel.getSeqPanel().moveCursor(size, 0);
1878 groupAdjustment = size;
1881 else if (!ssc.getGapsInsertedBegin() && !right)
1883 if (viewport.cursorMode)
1885 alignPanel.getSeqPanel().moveCursor(-size, 0);
1889 groupAdjustment = -size;
1893 if (groupAdjustment != 0)
1895 viewport.getSelectionGroup().setStartRes(
1896 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1897 viewport.getSelectionGroup().setEndRes(
1898 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1902 * just extend the last slide command if compatible; but not if in
1903 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1905 boolean appendHistoryItem = false;
1906 Deque<CommandI> historyList = viewport.getHistoryList();
1907 boolean inSplitFrame = getSplitViewContainer() != null;
1908 if (!inSplitFrame && historyList != null && historyList.size() > 0
1909 && historyList.peek() instanceof SlideSequencesCommand)
1911 appendHistoryItem = ssc.appendSlideCommand(
1912 (SlideSequencesCommand) historyList.peek());
1915 if (!appendHistoryItem)
1917 addHistoryItem(ssc);
1930 protected void copy_actionPerformed()
1932 if (viewport.getSelectionGroup() == null)
1936 // TODO: preserve the ordering of displayed alignment annotation in any
1937 // internal paste (particularly sequence associated annotation)
1938 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1939 String[] omitHidden = null;
1941 if (viewport.hasHiddenColumns())
1943 omitHidden = viewport.getViewAsString(true);
1946 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1947 seqs, omitHidden, null);
1949 StringSelection ss = new StringSelection(output);
1953 jalview.gui.Desktop.internalCopy = true;
1954 // Its really worth setting the clipboard contents
1955 // to empty before setting the large StringSelection!!
1956 Toolkit.getDefaultToolkit().getSystemClipboard()
1957 .setContents(new StringSelection(""), null);
1959 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1961 } catch (OutOfMemoryError er)
1963 new OOMWarning("copying region", er);
1967 HiddenColumns hiddenColumns = null;
1968 if (viewport.hasHiddenColumns())
1970 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1971 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1973 // create new HiddenColumns object with copy of hidden regions
1974 // between startRes and endRes, offset by startRes
1975 hiddenColumns = new HiddenColumns(
1976 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1977 hiddenCutoff, hiddenOffset);
1980 Desktop.jalviewClipboard = new Object[] { seqs,
1981 viewport.getAlignment().getDataset(), hiddenColumns };
1982 setStatus(MessageManager.formatMessage(
1983 "label.copied_sequences_to_clipboard", new Object[]
1984 { Integer.valueOf(seqs.length).toString() }));
1994 protected void pasteNew_actionPerformed(ActionEvent e)
2006 protected void pasteThis_actionPerformed(ActionEvent e)
2012 * Paste contents of Jalview clipboard
2014 * @param newAlignment
2015 * true to paste to a new alignment, otherwise add to this.
2017 void paste(boolean newAlignment)
2019 boolean externalPaste = true;
2022 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2023 Transferable contents = c.getContents(this);
2025 if (contents == null)
2034 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2035 if (str.length() < 1)
2040 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2042 } catch (OutOfMemoryError er)
2044 new OOMWarning("Out of memory pasting sequences!!", er);
2048 SequenceI[] sequences;
2049 boolean annotationAdded = false;
2050 AlignmentI alignment = null;
2052 if (Desktop.jalviewClipboard != null)
2054 // The clipboard was filled from within Jalview, we must use the
2056 // And dataset from the copied alignment
2057 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2058 // be doubly sure that we create *new* sequence objects.
2059 sequences = new SequenceI[newseq.length];
2060 for (int i = 0; i < newseq.length; i++)
2062 sequences[i] = new Sequence(newseq[i]);
2064 alignment = new Alignment(sequences);
2065 externalPaste = false;
2069 // parse the clipboard as an alignment.
2070 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2072 sequences = alignment.getSequencesArray();
2076 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2082 if (Desktop.jalviewClipboard != null)
2084 // dataset is inherited
2085 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2089 // new dataset is constructed
2090 alignment.setDataset(null);
2092 alwidth = alignment.getWidth() + 1;
2096 AlignmentI pastedal = alignment; // preserve pasted alignment object
2097 // Add pasted sequences and dataset into existing alignment.
2098 alignment = viewport.getAlignment();
2099 alwidth = alignment.getWidth() + 1;
2100 // decide if we need to import sequences from an existing dataset
2101 boolean importDs = Desktop.jalviewClipboard != null
2102 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2103 // importDs==true instructs us to copy over new dataset sequences from
2104 // an existing alignment
2105 Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
2107 // minimum dataset set
2109 for (int i = 0; i < sequences.length; i++)
2113 newDs.addElement(null);
2115 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2117 if (importDs && ds != null)
2119 if (!newDs.contains(ds))
2121 newDs.setElementAt(ds, i);
2122 ds = new Sequence(ds);
2123 // update with new dataset sequence
2124 sequences[i].setDatasetSequence(ds);
2128 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2133 // copy and derive new dataset sequence
2134 sequences[i] = sequences[i].deriveSequence();
2135 alignment.getDataset()
2136 .addSequence(sequences[i].getDatasetSequence());
2137 // TODO: avoid creation of duplicate dataset sequences with a
2138 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2140 alignment.addSequence(sequences[i]); // merges dataset
2144 newDs.clear(); // tidy up
2146 if (alignment.getAlignmentAnnotation() != null)
2148 for (AlignmentAnnotation alan : alignment
2149 .getAlignmentAnnotation())
2151 if (alan.graphGroup > fgroup)
2153 fgroup = alan.graphGroup;
2157 if (pastedal.getAlignmentAnnotation() != null)
2159 // Add any annotation attached to alignment.
2160 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2161 for (int i = 0; i < alann.length; i++)
2163 annotationAdded = true;
2164 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2166 AlignmentAnnotation newann = new AlignmentAnnotation(
2168 if (newann.graphGroup > -1)
2170 if (newGraphGroups.size() <= newann.graphGroup
2171 || newGraphGroups.get(newann.graphGroup) == null)
2173 for (int q = newGraphGroups
2174 .size(); q <= newann.graphGroup; q++)
2176 newGraphGroups.add(q, null);
2178 newGraphGroups.set(newann.graphGroup,
2179 Integer.valueOf(++fgroup));
2181 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2185 newann.padAnnotation(alwidth);
2186 alignment.addAnnotation(newann);
2196 addHistoryItem(new EditCommand(
2197 MessageManager.getString("label.add_sequences"),
2198 Action.PASTE, sequences, 0, alignment.getWidth(),
2201 // Add any annotations attached to sequences
2202 for (int i = 0; i < sequences.length; i++)
2204 if (sequences[i].getAnnotation() != null)
2206 AlignmentAnnotation newann;
2207 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2209 annotationAdded = true;
2210 newann = sequences[i].getAnnotation()[a];
2211 newann.adjustForAlignment();
2212 newann.padAnnotation(alwidth);
2213 if (newann.graphGroup > -1)
2215 if (newann.graphGroup > -1)
2217 if (newGraphGroups.size() <= newann.graphGroup
2218 || newGraphGroups.get(newann.graphGroup) == null)
2220 for (int q = newGraphGroups
2221 .size(); q <= newann.graphGroup; q++)
2223 newGraphGroups.add(q, null);
2225 newGraphGroups.set(newann.graphGroup,
2226 Integer.valueOf(++fgroup));
2228 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2232 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2236 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2244 // propagate alignment changed.
2245 viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
2246 if (annotationAdded)
2248 // Duplicate sequence annotation in all views.
2249 AlignmentI[] alview = this.getViewAlignments();
2250 for (int i = 0; i < sequences.length; i++)
2252 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2257 for (int avnum = 0; avnum < alview.length; avnum++)
2259 if (alview[avnum] != alignment)
2261 // duplicate in a view other than the one with input focus
2262 int avwidth = alview[avnum].getWidth() + 1;
2263 // this relies on sann being preserved after we
2264 // modify the sequence's annotation array for each duplication
2265 for (int a = 0; a < sann.length; a++)
2267 AlignmentAnnotation newann = new AlignmentAnnotation(
2269 sequences[i].addAlignmentAnnotation(newann);
2270 newann.padAnnotation(avwidth);
2271 alview[avnum].addAnnotation(newann); // annotation was
2272 // duplicated earlier
2273 // TODO JAL-1145 graphGroups are not updated for sequence
2274 // annotation added to several views. This may cause
2276 alview[avnum].setAnnotationIndex(newann, a);
2281 buildSortByAnnotationScoresMenu();
2283 viewport.firePropertyChange("alignment", null,
2284 alignment.getSequences());
2285 if (alignPanels != null)
2287 for (AlignmentPanel ap : alignPanels)
2289 ap.validateAnnotationDimensions(false);
2294 alignPanel.validateAnnotationDimensions(false);
2300 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2302 String newtitle = new String("Copied sequences");
2304 if (Desktop.jalviewClipboard != null
2305 && Desktop.jalviewClipboard[2] != null)
2307 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2308 af.viewport.setHiddenColumns(hc);
2311 // >>>This is a fix for the moment, until a better solution is
2313 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2314 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2315 .getFeatureRenderer());
2317 // TODO: maintain provenance of an alignment, rather than just make the
2318 // title a concatenation of operations.
2321 if (title.startsWith("Copied sequences"))
2327 newtitle = newtitle.concat("- from " + title);
2332 newtitle = new String("Pasted sequences");
2335 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2340 } catch (Exception ex)
2342 ex.printStackTrace();
2343 System.out.println("Exception whilst pasting: " + ex);
2344 // could be anything being pasted in here
2350 protected void expand_newalign(ActionEvent e)
2354 AlignmentI alignment = AlignmentUtils
2355 .expandContext(getViewport().getAlignment(), -1);
2356 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2358 String newtitle = new String("Flanking alignment");
2360 if (Desktop.jalviewClipboard != null
2361 && Desktop.jalviewClipboard[2] != null)
2363 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2364 af.viewport.setHiddenColumns(hc);
2367 // >>>This is a fix for the moment, until a better solution is
2369 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2370 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2371 .getFeatureRenderer());
2373 // TODO: maintain provenance of an alignment, rather than just make the
2374 // title a concatenation of operations.
2376 if (title.startsWith("Copied sequences"))
2382 newtitle = newtitle.concat("- from " + title);
2386 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2388 } catch (Exception ex)
2390 ex.printStackTrace();
2391 System.out.println("Exception whilst pasting: " + ex);
2392 // could be anything being pasted in here
2393 } catch (OutOfMemoryError oom)
2395 new OOMWarning("Viewing flanking region of alignment", oom);
2400 * Action Cut (delete and copy) the selected region
2403 protected void cut_actionPerformed()
2405 copy_actionPerformed();
2406 delete_actionPerformed();
2410 * Performs menu option to Delete the currently selected region
2413 protected void delete_actionPerformed()
2416 SequenceGroup sg = viewport.getSelectionGroup();
2422 Runnable okAction = new Runnable()
2427 SequenceI[] cut = sg.getSequences()
2428 .toArray(new SequenceI[sg.getSize()]);
2430 addHistoryItem(new EditCommand(
2431 MessageManager.getString("label.cut_sequences"), Action.CUT,
2432 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2433 viewport.getAlignment()));
2435 viewport.setSelectionGroup(null);
2436 viewport.sendSelection();
2437 viewport.getAlignment().deleteGroup(sg);
2439 viewport.firePropertyChange("alignment", null,
2440 viewport.getAlignment().getSequences());
2441 if (viewport.getAlignment().getHeight() < 1)
2445 AlignFrame.this.setClosed(true);
2446 } catch (Exception ex)
2453 * If the cut affects all sequences, prompt for confirmation
2455 boolean wholeHeight = sg.getSize() == viewport.getAlignment().getHeight();
2456 boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2457 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2458 if (wholeHeight && wholeWidth)
2460 JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2461 dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2462 Object[] options = new Object[] { MessageManager.getString("action.ok"),
2463 MessageManager.getString("action.cancel") };
2464 dialog.showDialog(MessageManager.getString("warn.delete_all"),
2465 MessageManager.getString("label.delete_all"),
2466 JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2467 options, options[0]);
2481 protected void deleteGroups_actionPerformed(ActionEvent e)
2483 if (avc.deleteGroups())
2485 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2486 alignPanel.updateAnnotation();
2487 alignPanel.paintAlignment(true, true);
2498 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2500 SequenceGroup sg = new SequenceGroup(
2501 viewport.getAlignment().getSequences());
2503 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2504 viewport.setSelectionGroup(sg);
2505 viewport.isSelectionGroupChanged(true);
2506 viewport.sendSelection();
2507 // JAL-2034 - should delegate to
2508 // alignPanel to decide if overview needs
2510 alignPanel.paintAlignment(false, false);
2511 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2521 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2523 if (viewport.cursorMode)
2525 alignPanel.getSeqPanel().keyboardNo1 = null;
2526 alignPanel.getSeqPanel().keyboardNo2 = null;
2528 viewport.setSelectionGroup(null);
2529 viewport.getColumnSelection().clear();
2530 viewport.setSearchResults(null);
2531 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2532 // JAL-2034 - should delegate to
2533 // alignPanel to decide if overview needs
2535 alignPanel.paintAlignment(false, false);
2536 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2537 viewport.sendSelection();
2547 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2549 SequenceGroup sg = viewport.getSelectionGroup();
2553 selectAllSequenceMenuItem_actionPerformed(null);
2558 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2560 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2562 // JAL-2034 - should delegate to
2563 // alignPanel to decide if overview needs
2566 alignPanel.paintAlignment(true, false);
2567 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2568 viewport.sendSelection();
2572 public void invertColSel_actionPerformed(ActionEvent e)
2574 viewport.invertColumnSelection();
2575 alignPanel.paintAlignment(true, false);
2576 viewport.sendSelection();
2586 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2588 trimAlignment(true);
2598 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2600 trimAlignment(false);
2603 void trimAlignment(boolean trimLeft)
2605 ColumnSelection colSel = viewport.getColumnSelection();
2608 if (!colSel.isEmpty())
2612 column = colSel.getMin();
2616 column = colSel.getMax();
2620 if (viewport.getSelectionGroup() != null)
2622 seqs = viewport.getSelectionGroup()
2623 .getSequencesAsArray(viewport.getHiddenRepSequences());
2627 seqs = viewport.getAlignment().getSequencesArray();
2630 TrimRegionCommand trimRegion;
2633 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2634 column, viewport.getAlignment());
2635 viewport.getRanges().setStartRes(0);
2639 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2640 column, viewport.getAlignment());
2643 setStatus(MessageManager
2644 .formatMessage("label.removed_columns", new String[]
2645 { Integer.valueOf(trimRegion.getSize()).toString() }));
2647 addHistoryItem(trimRegion);
2649 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2651 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2652 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2654 viewport.getAlignment().deleteGroup(sg);
2658 viewport.firePropertyChange("alignment", null,
2659 viewport.getAlignment().getSequences());
2670 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2672 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2675 if (viewport.getSelectionGroup() != null)
2677 seqs = viewport.getSelectionGroup()
2678 .getSequencesAsArray(viewport.getHiddenRepSequences());
2679 start = viewport.getSelectionGroup().getStartRes();
2680 end = viewport.getSelectionGroup().getEndRes();
2684 seqs = viewport.getAlignment().getSequencesArray();
2687 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2688 "Remove Gapped Columns", seqs, start, end,
2689 viewport.getAlignment());
2691 addHistoryItem(removeGapCols);
2693 setStatus(MessageManager
2694 .formatMessage("label.removed_empty_columns", new Object[]
2695 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2697 // This is to maintain viewport position on first residue
2698 // of first sequence
2699 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2700 ViewportRanges ranges = viewport.getRanges();
2701 int startRes = seq.findPosition(ranges.getStartRes());
2702 // ShiftList shifts;
2703 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2704 // edit.alColumnChanges=shifts.getInverse();
2705 // if (viewport.hasHiddenColumns)
2706 // viewport.getColumnSelection().compensateForEdits(shifts);
2707 ranges.setStartRes(seq.findIndex(startRes) - 1);
2708 viewport.firePropertyChange("alignment", null,
2709 viewport.getAlignment().getSequences());
2720 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2722 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2725 if (viewport.getSelectionGroup() != null)
2727 seqs = viewport.getSelectionGroup()
2728 .getSequencesAsArray(viewport.getHiddenRepSequences());
2729 start = viewport.getSelectionGroup().getStartRes();
2730 end = viewport.getSelectionGroup().getEndRes();
2734 seqs = viewport.getAlignment().getSequencesArray();
2737 // This is to maintain viewport position on first residue
2738 // of first sequence
2739 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2740 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2742 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2743 viewport.getAlignment()));
2745 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2747 viewport.firePropertyChange("alignment", null,
2748 viewport.getAlignment().getSequences());
2759 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2761 viewport.setPadGaps(padGapsMenuitem.isSelected());
2762 viewport.firePropertyChange("alignment", null,
2763 viewport.getAlignment().getSequences());
2767 * Opens a Finder dialog
2772 public void findMenuItem_actionPerformed(ActionEvent e)
2774 new Finder(alignPanel);
2778 * Create a new view of the current alignment.
2781 public void newView_actionPerformed(ActionEvent e)
2783 newView(null, true);
2787 * Creates and shows a new view of the current alignment.
2790 * title of newly created view; if null, one will be generated
2791 * @param copyAnnotation
2792 * if true then duplicate all annnotation, groups and settings
2793 * @return new alignment panel, already displayed.
2795 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2798 * Create a new AlignmentPanel (with its own, new Viewport)
2800 AlignmentPanel newap = new jalview.project.Jalview2XML()
2801 .copyAlignPanel(alignPanel);
2802 if (!copyAnnotation)
2805 * remove all groups and annotation except for the automatic stuff
2807 newap.av.getAlignment().deleteAllGroups();
2808 newap.av.getAlignment().deleteAllAnnotations(false);
2811 newap.av.setGatherViewsHere(false);
2813 if (viewport.getViewName() == null)
2815 viewport.setViewName(MessageManager
2816 .getString("label.view_name_original"));
2820 * Views share the same edits undo and redo stacks
2822 newap.av.setHistoryList(viewport.getHistoryList());
2823 newap.av.setRedoList(viewport.getRedoList());
2826 * copy any visualisation settings that are not saved in the project
2828 newap.av.setColourAppliesToAllGroups(
2829 viewport.getColourAppliesToAllGroups());
2832 * Views share the same mappings; need to deregister any new mappings
2833 * created by copyAlignPanel, and register the new reference to the shared
2836 newap.av.replaceMappings(viewport.getAlignment());
2839 * start up cDNA consensus (if applicable) now mappings are in place
2841 if (newap.av.initComplementConsensus())
2843 newap.refresh(true); // adjust layout of annotations
2846 newap.av.setViewName(getNewViewName(viewTitle));
2848 addAlignmentPanel(newap, true);
2849 newap.alignmentChanged();
2851 if (alignPanels.size() == 2)
2853 viewport.setGatherViewsHere(true);
2855 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2860 * Make a new name for the view, ensuring it is unique within the current
2861 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2862 * these now use viewId. Unique view names are still desirable for usability.)
2867 protected String getNewViewName(String viewTitle)
2869 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2870 boolean addFirstIndex = false;
2871 if (viewTitle == null || viewTitle.trim().length() == 0)
2873 viewTitle = MessageManager.getString("action.view");
2874 addFirstIndex = true;
2878 index = 1;// we count from 1 if given a specific name
2880 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2882 List<Component> comps = PaintRefresher.components
2883 .get(viewport.getSequenceSetId());
2885 List<String> existingNames = getExistingViewNames(comps);
2887 while (existingNames.contains(newViewName))
2889 newViewName = viewTitle + " " + (++index);
2895 * Returns a list of distinct view names found in the given list of
2896 * components. View names are held on the viewport of an AlignmentPanel.
2901 protected List<String> getExistingViewNames(List<Component> comps)
2903 List<String> existingNames = new ArrayList<>();
2904 for (Component comp : comps)
2906 if (comp instanceof AlignmentPanel)
2908 AlignmentPanel ap = (AlignmentPanel) comp;
2909 if (!existingNames.contains(ap.av.getViewName()))
2911 existingNames.add(ap.av.getViewName());
2915 return existingNames;
2919 * Explode tabbed views into separate windows.
2922 public void expandViews_actionPerformed(ActionEvent e)
2924 Desktop.explodeViews(this);
2928 * Gather views in separate windows back into a tabbed presentation.
2931 public void gatherViews_actionPerformed(ActionEvent e)
2933 Desktop.instance.gatherViews(this);
2943 public void font_actionPerformed(ActionEvent e)
2945 new FontChooser(alignPanel);
2955 protected void seqLimit_actionPerformed(ActionEvent e)
2957 viewport.setShowJVSuffix(seqLimits.isSelected());
2959 alignPanel.getIdPanel().getIdCanvas()
2960 .setPreferredSize(alignPanel.calculateIdWidth());
2961 alignPanel.paintAlignment(true, false);
2965 public void idRightAlign_actionPerformed(ActionEvent e)
2967 viewport.setRightAlignIds(idRightAlign.isSelected());
2968 alignPanel.paintAlignment(false, false);
2972 public void centreColumnLabels_actionPerformed(ActionEvent e)
2974 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2975 alignPanel.paintAlignment(false, false);
2981 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2984 protected void followHighlight_actionPerformed()
2987 * Set the 'follow' flag on the Viewport (and scroll to position if now
2990 final boolean state = this.followHighlightMenuItem.getState();
2991 viewport.setFollowHighlight(state);
2994 alignPanel.scrollToPosition(viewport.getSearchResults());
3005 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3007 viewport.setColourText(colourTextMenuItem.isSelected());
3008 alignPanel.paintAlignment(false, false);
3018 public void wrapMenuItem_actionPerformed(ActionEvent e)
3020 scaleAbove.setVisible(wrapMenuItem.isSelected());
3021 scaleLeft.setVisible(wrapMenuItem.isSelected());
3022 scaleRight.setVisible(wrapMenuItem.isSelected());
3023 viewport.setWrapAlignment(wrapMenuItem.isSelected());
3024 alignPanel.updateLayout();
3028 public void showAllSeqs_actionPerformed(ActionEvent e)
3030 viewport.showAllHiddenSeqs();
3034 public void showAllColumns_actionPerformed(ActionEvent e)
3036 viewport.showAllHiddenColumns();
3037 alignPanel.paintAlignment(true, true);
3038 viewport.sendSelection();
3042 public void hideSelSequences_actionPerformed(ActionEvent e)
3044 viewport.hideAllSelectedSeqs();
3048 * called by key handler and the hide all/show all menu items
3053 protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3056 boolean hide = false;
3057 SequenceGroup sg = viewport.getSelectionGroup();
3058 if (!toggleSeqs && !toggleCols)
3060 // Hide everything by the current selection - this is a hack - we do the
3061 // invert and then hide
3062 // first check that there will be visible columns after the invert.
3063 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3064 && sg.getStartRes() <= sg.getEndRes()))
3066 // now invert the sequence set, if required - empty selection implies
3067 // that no hiding is required.
3070 invertSequenceMenuItem_actionPerformed(null);
3071 sg = viewport.getSelectionGroup();
3075 viewport.expandColSelection(sg, true);
3076 // finally invert the column selection and get the new sequence
3078 invertColSel_actionPerformed(null);
3085 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3087 hideSelSequences_actionPerformed(null);
3090 else if (!(toggleCols && viewport.hasSelectedColumns()))
3092 showAllSeqs_actionPerformed(null);
3098 if (viewport.hasSelectedColumns())
3100 hideSelColumns_actionPerformed(null);
3103 viewport.setSelectionGroup(sg);
3108 showAllColumns_actionPerformed(null);
3117 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3118 * event.ActionEvent)
3121 public void hideAllButSelection_actionPerformed(ActionEvent e)
3123 toggleHiddenRegions(false, false);
3124 viewport.sendSelection();
3131 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3135 public void hideAllSelection_actionPerformed(ActionEvent e)
3137 SequenceGroup sg = viewport.getSelectionGroup();
3138 viewport.expandColSelection(sg, false);
3139 viewport.hideAllSelectedSeqs();
3140 viewport.hideSelectedColumns();
3141 alignPanel.updateLayout();
3142 alignPanel.paintAlignment(true, true);
3143 viewport.sendSelection();
3150 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3154 public void showAllhidden_actionPerformed(ActionEvent e)
3156 viewport.showAllHiddenColumns();
3157 viewport.showAllHiddenSeqs();
3158 alignPanel.paintAlignment(true, true);
3159 viewport.sendSelection();
3163 public void hideSelColumns_actionPerformed(ActionEvent e)
3165 viewport.hideSelectedColumns();
3166 alignPanel.updateLayout();
3167 alignPanel.paintAlignment(true, true);
3168 viewport.sendSelection();
3172 public void hiddenMarkers_actionPerformed(ActionEvent e)
3174 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3185 protected void scaleAbove_actionPerformed(ActionEvent e)
3187 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3188 alignPanel.updateLayout();
3189 alignPanel.paintAlignment(true, false);
3199 protected void scaleLeft_actionPerformed(ActionEvent e)
3201 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3202 alignPanel.updateLayout();
3203 alignPanel.paintAlignment(true, false);
3213 protected void scaleRight_actionPerformed(ActionEvent e)
3215 viewport.setScaleRightWrapped(scaleRight.isSelected());
3216 alignPanel.updateLayout();
3217 alignPanel.paintAlignment(true, false);
3227 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3229 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3230 alignPanel.paintAlignment(false, false);
3240 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3242 viewport.setShowText(viewTextMenuItem.isSelected());
3243 alignPanel.paintAlignment(false, false);
3253 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3255 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3256 alignPanel.paintAlignment(false, false);
3259 public FeatureSettings featureSettings;
3262 public FeatureSettingsControllerI getFeatureSettingsUI()
3264 return featureSettings;
3268 public void featureSettings_actionPerformed(ActionEvent e)
3270 showFeatureSettingsUI();
3274 public FeatureSettingsControllerI showFeatureSettingsUI()
3276 if (featureSettings != null)
3278 featureSettings.closeOldSettings();
3279 featureSettings = null;
3281 if (!showSeqFeatures.isSelected())
3283 // make sure features are actually displayed
3284 showSeqFeatures.setSelected(true);
3285 showSeqFeatures_actionPerformed(null);
3287 featureSettings = new FeatureSettings(this);
3288 return featureSettings;
3292 * Set or clear 'Show Sequence Features'
3298 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3300 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3301 alignPanel.paintAlignment(true, true);
3305 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3306 * the annotations panel as a whole.
3308 * The options to show/hide all annotations should be enabled when the panel
3309 * is shown, and disabled when the panel is hidden.
3314 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3316 final boolean setVisible = annotationPanelMenuItem.isSelected();
3317 viewport.setShowAnnotation(setVisible);
3318 this.showAllSeqAnnotations.setEnabled(setVisible);
3319 this.hideAllSeqAnnotations.setEnabled(setVisible);
3320 this.showAllAlAnnotations.setEnabled(setVisible);
3321 this.hideAllAlAnnotations.setEnabled(setVisible);
3322 alignPanel.updateLayout();
3326 public void alignmentProperties()
3329 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3332 String content = MessageManager.formatMessage("label.html_content",
3334 { contents.toString() });
3337 if (Platform.isJS())
3339 JLabel textLabel = new JLabel();
3340 textLabel.setText(content);
3341 textLabel.setBackground(Color.WHITE);
3343 pane = new JPanel(new BorderLayout());
3344 ((JPanel) pane).setOpaque(true);
3345 pane.setBackground(Color.WHITE);
3346 ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3355 JEditorPane editPane = new JEditorPane("text/html", "");
3356 editPane.setEditable(false);
3357 editPane.setText(content);
3361 JInternalFrame frame = new JInternalFrame();
3363 frame.getContentPane().add(new JScrollPane(pane));
3365 Desktop.addInternalFrame(frame, MessageManager
3366 .formatMessage("label.alignment_properties", new Object[]
3367 { getTitle() }), 500, 400);
3371 * Opens an Overview panel for the alignment, unless one is open already
3376 public void overviewMenuItem_actionPerformed(ActionEvent e)
3378 if (alignPanel.overviewPanel != null)
3383 boolean showHiddenRegions = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
3385 openOverviewPanel(showHiddenRegions);
3388 public OverviewPanel openOverviewPanel(boolean showHidden)
3390 JInternalFrame frame = new JInternalFrame();
3391 final OverviewPanel overview = new OverviewPanel(alignPanel, showHidden);
3392 frame.setContentPane(overview);
3393 Desktop.addInternalFrame(frame, MessageManager
3394 .formatMessage("label.overview_params", new Object[]
3395 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3398 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3399 frame.addInternalFrameListener(
3400 new javax.swing.event.InternalFrameAdapter()
3403 public void internalFrameClosed(
3404 javax.swing.event.InternalFrameEvent evt)
3407 alignPanel.setOverviewPanel(null);
3410 if (getKeyListeners().length > 0)
3412 frame.addKeyListener(getKeyListeners()[0]);
3415 alignPanel.setOverviewPanel(overview);
3421 public void textColour_actionPerformed()
3423 new TextColourChooser().chooseColour(alignPanel, null);
3427 * public void covariationColour_actionPerformed() {
3429 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3433 public void annotationColour_actionPerformed()
3435 new AnnotationColourChooser(viewport, alignPanel);
3439 public void annotationColumn_actionPerformed(ActionEvent e)
3441 new AnnotationColumnChooser(viewport, alignPanel);
3445 * Action on the user checking or unchecking the option to apply the selected
3446 * colour scheme to all groups. If unchecked, groups may have their own
3447 * independent colour schemes.
3452 public void applyToAllGroups_actionPerformed(boolean selected)
3454 viewport.setColourAppliesToAllGroups(selected);
3458 * Action on user selecting a colour from the colour menu
3461 * the name (not the menu item label!) of the colour scheme
3464 public void changeColour_actionPerformed(String name)
3467 * 'User Defined' opens a panel to configure or load a
3468 * user-defined colour scheme
3470 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3472 new UserDefinedColours(alignPanel);
3477 * otherwise set the chosen colour scheme (or null for 'None')
3479 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3481 viewport.getAlignment(), viewport.getHiddenRepSequences());
3486 * Actions on setting or changing the alignment colour scheme
3491 public void changeColour(ColourSchemeI cs)
3493 // TODO: pull up to controller method
3494 ColourMenuHelper.setColourSelected(colourMenu, cs);
3496 viewport.setGlobalColourScheme(cs);
3498 alignPanel.paintAlignment(true, true);
3502 * Show the PID threshold slider panel
3505 protected void modifyPID_actionPerformed()
3507 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3508 alignPanel.getViewName());
3509 SliderPanel.showPIDSlider();
3513 * Show the Conservation slider panel
3516 protected void modifyConservation_actionPerformed()
3518 SliderPanel.setConservationSlider(alignPanel,
3519 viewport.getResidueShading(), alignPanel.getViewName());
3520 SliderPanel.showConservationSlider();
3524 * Action on selecting or deselecting (Colour) By Conservation
3527 public void conservationMenuItem_actionPerformed(boolean selected)
3529 modifyConservation.setEnabled(selected);
3530 viewport.setConservationSelected(selected);
3531 viewport.getResidueShading().setConservationApplied(selected);
3533 changeColour(viewport.getGlobalColourScheme());
3536 modifyConservation_actionPerformed();
3540 SliderPanel.hideConservationSlider();
3545 * Action on selecting or deselecting (Colour) Above PID Threshold
3548 public void abovePIDThreshold_actionPerformed(boolean selected)
3550 modifyPID.setEnabled(selected);
3551 viewport.setAbovePIDThreshold(selected);
3554 viewport.getResidueShading().setThreshold(0,
3555 viewport.isIgnoreGapsConsensus());
3558 changeColour(viewport.getGlobalColourScheme());
3561 modifyPID_actionPerformed();
3565 SliderPanel.hidePIDSlider();
3576 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3578 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3579 AlignmentSorter.sortByPID(viewport.getAlignment(),
3580 viewport.getAlignment().getSequenceAt(0));
3581 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3582 viewport.getAlignment()));
3583 alignPanel.paintAlignment(true, false);
3593 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3595 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3596 AlignmentSorter.sortByID(viewport.getAlignment());
3598 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3599 alignPanel.paintAlignment(true, false);
3609 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3611 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3612 AlignmentSorter.sortByLength(viewport.getAlignment());
3613 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3614 viewport.getAlignment()));
3615 alignPanel.paintAlignment(true, false);
3625 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3627 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3628 AlignmentSorter.sortByGroup(viewport.getAlignment());
3629 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3630 viewport.getAlignment()));
3632 alignPanel.paintAlignment(true, false);
3642 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3644 new RedundancyPanel(alignPanel, this);
3654 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3656 if ((viewport.getSelectionGroup() == null)
3657 || (viewport.getSelectionGroup().getSize() < 2))
3659 JvOptionPane.showInternalMessageDialog(this,
3660 MessageManager.getString(
3661 "label.you_must_select_least_two_sequences"),
3662 MessageManager.getString("label.invalid_selection"),
3663 JvOptionPane.WARNING_MESSAGE);
3667 JInternalFrame frame = new JInternalFrame();
3668 frame.setContentPane(new PairwiseAlignPanel(viewport));
3669 Desktop.addInternalFrame(frame,
3670 MessageManager.getString("action.pairwise_alignment"), 600,
3676 public void autoCalculate_actionPerformed(ActionEvent e)
3678 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3679 if (viewport.autoCalculateConsensus)
3681 viewport.firePropertyChange("alignment", null,
3682 viewport.getAlignment().getSequences());
3687 public void sortByTreeOption_actionPerformed(ActionEvent e)
3689 viewport.sortByTree = sortByTree.isSelected();
3693 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3695 viewport.followSelection = listenToViewSelections.isSelected();
3699 * Constructs a tree panel and adds it to the desktop
3702 * tree type (NJ or AV)
3704 * name of score model used to compute the tree
3706 * parameters for the distance or similarity calculation
3708 void newTreePanel(String type, String modelName,
3709 SimilarityParamsI options)
3711 String frameTitle = "";
3714 boolean onSelection = false;
3715 if (viewport.getSelectionGroup() != null
3716 && viewport.getSelectionGroup().getSize() > 0)
3718 SequenceGroup sg = viewport.getSelectionGroup();
3720 /* Decide if the selection is a column region */
3721 for (SequenceI _s : sg.getSequences())
3723 if (_s.getLength() < sg.getEndRes())
3725 JvOptionPane.showMessageDialog(Desktop.desktop,
3726 MessageManager.getString(
3727 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3728 MessageManager.getString(
3729 "label.sequences_selection_not_aligned"),
3730 JvOptionPane.WARNING_MESSAGE);
3739 if (viewport.getAlignment().getHeight() < 2)
3745 tp = new TreePanel(alignPanel, type, modelName, options);
3746 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3748 frameTitle += " from ";
3750 if (viewport.getViewName() != null)
3752 frameTitle += viewport.getViewName() + " of ";
3755 frameTitle += this.title;
3757 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3768 public void addSortByOrderMenuItem(String title,
3769 final AlignmentOrder order)
3771 final JMenuItem item = new JMenuItem(MessageManager
3772 .formatMessage("action.by_title_param", new Object[]
3775 item.addActionListener(new java.awt.event.ActionListener()
3778 public void actionPerformed(ActionEvent e)
3780 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3782 // TODO: JBPNote - have to map order entries to curent SequenceI
3784 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3786 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3787 viewport.getAlignment()));
3789 alignPanel.paintAlignment(true, false);
3795 * Add a new sort by annotation score menu item
3798 * the menu to add the option to
3800 * the label used to retrieve scores for each sequence on the
3803 public void addSortByAnnotScoreMenuItem(JMenu sort,
3804 final String scoreLabel)
3806 final JMenuItem item = new JMenuItem(scoreLabel);
3808 item.addActionListener(new java.awt.event.ActionListener()
3811 public void actionPerformed(ActionEvent e)
3813 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3814 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3815 viewport.getAlignment());// ,viewport.getSelectionGroup());
3816 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3817 viewport.getAlignment()));
3818 alignPanel.paintAlignment(true, false);
3824 * last hash for alignment's annotation array - used to minimise cost of
3827 protected int _annotationScoreVectorHash;
3830 * search the alignment and rebuild the sort by annotation score submenu the
3831 * last alignment annotation vector hash is stored to minimize cost of
3832 * rebuilding in subsequence calls.
3836 public void buildSortByAnnotationScoresMenu()
3838 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3843 if (viewport.getAlignment().getAlignmentAnnotation()
3844 .hashCode() != _annotationScoreVectorHash)
3846 sortByAnnotScore.removeAll();
3847 // almost certainly a quicker way to do this - but we keep it simple
3848 Hashtable<String, String> scoreSorts = new Hashtable<>();
3849 AlignmentAnnotation aann[];
3850 for (SequenceI sqa : viewport.getAlignment().getSequences())
3852 aann = sqa.getAnnotation();
3853 for (int i = 0; aann != null && i < aann.length; i++)
3855 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3857 scoreSorts.put(aann[i].label, aann[i].label);
3861 Enumeration<String> labels = scoreSorts.keys();
3862 while (labels.hasMoreElements())
3864 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3865 labels.nextElement());
3867 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3870 _annotationScoreVectorHash = viewport.getAlignment()
3871 .getAlignmentAnnotation().hashCode();
3876 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3877 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3878 * call. Listeners are added to remove the menu item when the treePanel is
3879 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3883 public void buildTreeSortMenu()
3885 sortByTreeMenu.removeAll();
3887 List<Component> comps = PaintRefresher.components
3888 .get(viewport.getSequenceSetId());
3889 List<TreePanel> treePanels = new ArrayList<>();
3890 for (Component comp : comps)
3892 if (comp instanceof TreePanel)
3894 treePanels.add((TreePanel) comp);
3898 if (treePanels.size() < 1)
3900 sortByTreeMenu.setVisible(false);
3904 sortByTreeMenu.setVisible(true);
3906 for (final TreePanel tp : treePanels)
3908 final JMenuItem item = new JMenuItem(tp.getTitle());
3909 item.addActionListener(new java.awt.event.ActionListener()
3912 public void actionPerformed(ActionEvent e)
3914 tp.sortByTree_actionPerformed();
3915 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3920 sortByTreeMenu.add(item);
3924 public boolean sortBy(AlignmentOrder alorder, String undoname)
3926 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3927 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3928 if (undoname != null)
3930 addHistoryItem(new OrderCommand(undoname, oldOrder,
3931 viewport.getAlignment()));
3933 alignPanel.paintAlignment(true, false);
3938 * Work out whether the whole set of sequences or just the selected set will
3939 * be submitted for multiple alignment.
3942 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3944 // Now, check we have enough sequences
3945 AlignmentView msa = null;
3947 if ((viewport.getSelectionGroup() != null)
3948 && (viewport.getSelectionGroup().getSize() > 1))
3950 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3951 // some common interface!
3953 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3954 * SequenceI[sz = seqs.getSize(false)];
3956 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3957 * seqs.getSequenceAt(i); }
3959 msa = viewport.getAlignmentView(true);
3961 else if (viewport.getSelectionGroup() != null
3962 && viewport.getSelectionGroup().getSize() == 1)
3964 int option = JvOptionPane.showConfirmDialog(this,
3965 MessageManager.getString("warn.oneseq_msainput_selection"),
3966 MessageManager.getString("label.invalid_selection"),
3967 JvOptionPane.OK_CANCEL_OPTION);
3968 if (option == JvOptionPane.OK_OPTION)
3970 msa = viewport.getAlignmentView(false);
3975 msa = viewport.getAlignmentView(false);
3981 * Decides what is submitted to a secondary structure prediction service: the
3982 * first sequence in the alignment, or in the current selection, or, if the
3983 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3984 * region or the whole alignment. (where the first sequence in the set is the
3985 * one that the prediction will be for).
3987 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3989 AlignmentView seqs = null;
3991 if ((viewport.getSelectionGroup() != null)
3992 && (viewport.getSelectionGroup().getSize() > 0))
3994 seqs = viewport.getAlignmentView(true);
3998 seqs = viewport.getAlignmentView(false);
4000 // limit sequences - JBPNote in future - could spawn multiple prediction
4002 // TODO: viewport.getAlignment().isAligned is a global state - the local
4003 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4004 if (!viewport.getAlignment().isAligned(false))
4006 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4007 // TODO: if seqs.getSequences().length>1 then should really have warned
4021 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4023 // Pick the tree file
4024 JalviewFileChooser chooser = new JalviewFileChooser(
4025 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4026 chooser.setFileView(new JalviewFileView());
4027 chooser.setDialogTitle(
4028 MessageManager.getString("label.select_newick_like_tree_file"));
4029 chooser.setToolTipText(
4030 MessageManager.getString("label.load_tree_file"));
4032 chooser.setResponseHandler(0,new Runnable()
4037 String filePath = chooser.getSelectedFile().getPath();
4038 Cache.setProperty("LAST_DIRECTORY", filePath);
4039 NewickFile fin = null;
4042 fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4043 DataSourceType.FILE));
4044 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4045 } catch (Exception ex)
4047 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4049 .getString("label.problem_reading_tree_file"),
4050 JvOptionPane.WARNING_MESSAGE);
4051 ex.printStackTrace();
4053 if (fin != null && fin.hasWarningMessage())
4055 JvOptionPane.showMessageDialog(Desktop.desktop,
4056 fin.getWarningMessage(),
4057 MessageManager.getString(
4058 "label.possible_problem_with_tree_file"),
4059 JvOptionPane.WARNING_MESSAGE);
4063 chooser.showOpenDialog(this);
4066 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4068 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4071 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4072 int h, int x, int y)
4074 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4078 * Add a treeviewer for the tree extracted from a Newick file object to the
4079 * current alignment view
4086 * Associated alignment input data (or null)
4095 * @return TreePanel handle
4097 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4098 AlignmentView input, int w, int h, int x, int y)
4100 TreePanel tp = null;
4106 if (nf.getTree() != null)
4108 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4114 tp.setLocation(x, y);
4117 Desktop.addInternalFrame(tp, treeTitle, w, h);
4119 } catch (Exception ex)
4121 ex.printStackTrace();
4127 private boolean buildingMenu = false;
4130 * Generates menu items and listener event actions for web service clients
4133 public void BuildWebServiceMenu()
4135 while (buildingMenu)
4139 System.err.println("Waiting for building menu to finish.");
4141 } catch (Exception e)
4145 final AlignFrame me = this;
4146 buildingMenu = true;
4147 new Thread(new Runnable()
4152 final List<JMenuItem> legacyItems = new ArrayList<>();
4155 // System.err.println("Building ws menu again "
4156 // + Thread.currentThread());
4157 // TODO: add support for context dependent disabling of services based
4159 // alignment and current selection
4160 // TODO: add additional serviceHandle parameter to specify abstract
4162 // class independently of AbstractName
4163 // TODO: add in rediscovery GUI function to restart discoverer
4164 // TODO: group services by location as well as function and/or
4166 // object broker mechanism.
4167 final Vector<JMenu> wsmenu = new Vector<>();
4168 final IProgressIndicator af = me;
4171 * do not i18n these strings - they are hard-coded in class
4172 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4173 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4175 final JMenu msawsmenu = new JMenu("Alignment");
4176 final JMenu secstrmenu = new JMenu(
4177 "Secondary Structure Prediction");
4178 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4179 final JMenu analymenu = new JMenu("Analysis");
4180 final JMenu dismenu = new JMenu("Protein Disorder");
4181 // JAL-940 - only show secondary structure prediction services from
4182 // the legacy server
4183 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4185 Discoverer.services != null && (Discoverer.services.size() > 0))
4187 // TODO: refactor to allow list of AbstractName/Handler bindings to
4189 // stored or retrieved from elsewhere
4190 // No MSAWS used any more:
4191 // Vector msaws = null; // (Vector)
4192 // Discoverer.services.get("MsaWS");
4193 Vector<ServiceHandle> secstrpr = Discoverer.services
4195 if (secstrpr != null)
4197 // Add any secondary structure prediction services
4198 for (int i = 0, j = secstrpr.size(); i < j; i++)
4200 final ext.vamsas.ServiceHandle sh = secstrpr
4202 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4203 .getServiceClient(sh);
4204 int p = secstrmenu.getItemCount();
4205 impl.attachWSMenuEntry(secstrmenu, me);
4206 int q = secstrmenu.getItemCount();
4207 for (int litm = p; litm < q; litm++)
4209 legacyItems.add(secstrmenu.getItem(litm));
4215 // Add all submenus in the order they should appear on the web
4217 wsmenu.add(msawsmenu);
4218 wsmenu.add(secstrmenu);
4219 wsmenu.add(dismenu);
4220 wsmenu.add(analymenu);
4221 // No search services yet
4222 // wsmenu.add(seqsrchmenu);
4224 javax.swing.SwingUtilities.invokeLater(new Runnable()
4231 webService.removeAll();
4232 // first, add discovered services onto the webservices menu
4233 if (wsmenu.size() > 0)
4235 for (int i = 0, j = wsmenu.size(); i < j; i++)
4237 webService.add(wsmenu.get(i));
4242 webService.add(me.webServiceNoServices);
4244 // TODO: move into separate menu builder class.
4245 boolean new_sspred = false;
4246 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4248 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4249 if (jws2servs != null)
4251 if (jws2servs.hasServices())
4253 jws2servs.attachWSMenuEntry(webService, me);
4254 for (Jws2Instance sv : jws2servs.getServices())
4256 if (sv.description.toLowerCase().contains("jpred"))
4258 for (JMenuItem jmi : legacyItems)
4260 jmi.setVisible(false);
4266 if (jws2servs.isRunning())
4268 JMenuItem tm = new JMenuItem(
4269 "Still discovering JABA Services");
4270 tm.setEnabled(false);
4275 build_urlServiceMenu(me.webService);
4276 build_fetchdbmenu(webService);
4277 for (JMenu item : wsmenu)
4279 if (item.getItemCount() == 0)
4281 item.setEnabled(false);
4285 item.setEnabled(true);
4288 } catch (Exception e)
4291 "Exception during web service menu building process.",
4296 } catch (Exception e)
4299 buildingMenu = false;
4306 * construct any groupURL type service menu entries.
4310 protected void build_urlServiceMenu(JMenu webService)
4312 // TODO: remove this code when 2.7 is released
4313 // DEBUG - alignmentView
4315 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4316 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4318 * @Override public void actionPerformed(ActionEvent e) {
4319 * jalview.datamodel.AlignmentView
4320 * .testSelectionViews(af.viewport.getAlignment(),
4321 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4323 * }); webService.add(testAlView);
4325 // TODO: refactor to RestClient discoverer and merge menu entries for
4326 // rest-style services with other types of analysis/calculation service
4327 // SHmmr test client - still being implemented.
4328 // DEBUG - alignmentView
4330 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4333 client.attachWSMenuEntry(
4334 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4340 * Searches the alignment sequences for xRefs and builds the Show
4341 * Cross-References menu (formerly called Show Products), with database
4342 * sources for which cross-references are found (protein sources for a
4343 * nucleotide alignment and vice versa)
4345 * @return true if Show Cross-references menu should be enabled
4347 public boolean canShowProducts()
4349 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4350 AlignmentI dataset = viewport.getAlignment().getDataset();
4352 showProducts.removeAll();
4353 final boolean dna = viewport.getAlignment().isNucleotide();
4355 if (seqs == null || seqs.length == 0)
4357 // nothing to see here.
4361 boolean showp = false;
4364 List<String> ptypes = new CrossRef(seqs, dataset)
4365 .findXrefSourcesForSequences(dna);
4367 for (final String source : ptypes)
4370 final AlignFrame af = this;
4371 JMenuItem xtype = new JMenuItem(source);
4372 xtype.addActionListener(new ActionListener()
4375 public void actionPerformed(ActionEvent e)
4377 showProductsFor(af.viewport.getSequenceSelection(), dna,
4381 showProducts.add(xtype);
4383 showProducts.setVisible(showp);
4384 showProducts.setEnabled(showp);
4385 } catch (Exception e)
4388 "canShowProducts threw an exception - please report to help@jalview.org",
4396 * Finds and displays cross-references for the selected sequences (protein
4397 * products for nucleotide sequences, dna coding sequences for peptides).
4400 * the sequences to show cross-references for
4402 * true if from a nucleotide alignment (so showing proteins)
4404 * the database to show cross-references for
4406 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4407 final String source)
4409 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4414 * Construct and display a new frame containing the translation of this
4415 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4418 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4420 AlignmentI al = null;
4423 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4425 al = dna.translateCdna(codeTable);
4426 } catch (Exception ex)
4428 jalview.bin.Cache.log.error(
4429 "Exception during translation. Please report this !", ex);
4430 final String msg = MessageManager.getString(
4431 "label.error_when_translating_sequences_submit_bug_report");
4432 final String errorTitle = MessageManager
4433 .getString("label.implementation_error")
4434 + MessageManager.getString("label.translation_failed");
4435 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4436 JvOptionPane.ERROR_MESSAGE);
4439 if (al == null || al.getHeight() == 0)
4441 final String msg = MessageManager.getString(
4442 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4443 final String errorTitle = MessageManager
4444 .getString("label.translation_failed");
4445 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4446 JvOptionPane.WARNING_MESSAGE);
4450 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4451 af.setFileFormat(this.currentFileFormat);
4452 final String newTitle = MessageManager
4453 .formatMessage("label.translation_of_params", new Object[]
4454 { this.getTitle(), codeTable.getId() });
4455 af.setTitle(newTitle);
4456 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4458 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4459 viewport.openSplitFrame(af, new Alignment(seqs));
4463 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4470 * Set the file format
4474 public void setFileFormat(FileFormatI format)
4476 this.currentFileFormat = format;
4480 * Try to load a features file onto the alignment.
4483 * contents or path to retrieve file or a File object
4485 * access mode of file (see jalview.io.AlignFile)
4486 * @return true if features file was parsed correctly.
4488 public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4491 return avc.parseFeaturesFile(file, sourceType,
4492 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4497 public void refreshFeatureUI(boolean enableIfNecessary)
4499 // note - currently this is only still here rather than in the controller
4500 // because of the featureSettings hard reference that is yet to be
4502 if (enableIfNecessary)
4504 viewport.setShowSequenceFeatures(true);
4505 showSeqFeatures.setSelected(true);
4511 public void dragEnter(DropTargetDragEvent evt)
4516 public void dragExit(DropTargetEvent evt)
4521 public void dragOver(DropTargetDragEvent evt)
4526 public void dropActionChanged(DropTargetDragEvent evt)
4531 public void drop(DropTargetDropEvent evt)
4533 // JAL-1552 - acceptDrop required before getTransferable call for
4534 // Java's Transferable for native dnd
4535 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4536 Transferable t = evt.getTransferable();
4538 final AlignFrame thisaf = this;
4539 final List<Object> files = new ArrayList<>();
4540 List<DataSourceType> protocols = new ArrayList<>();
4544 Desktop.transferFromDropTarget(files, protocols, evt, t);
4545 } catch (Exception e)
4547 e.printStackTrace();
4551 new Thread(new Runnable()
4558 // check to see if any of these files have names matching sequences
4561 SequenceIdMatcher idm = new SequenceIdMatcher(
4562 viewport.getAlignment().getSequencesArray());
4564 * Object[] { String,SequenceI}
4566 ArrayList<Object[]> filesmatched = new ArrayList<>();
4567 ArrayList<Object> filesnotmatched = new ArrayList<>();
4568 for (int i = 0; i < files.size(); i++)
4571 Object file = files.get(i);
4572 String fileName = file.toString();
4574 DataSourceType protocol = (file instanceof File
4575 ? DataSourceType.FILE
4576 : FormatAdapter.checkProtocol(fileName));
4577 if (protocol == DataSourceType.FILE)
4580 if (file instanceof File) {
4582 Platform.cacheFileData(fl);
4584 fl = new File(fileName);
4586 pdbfn = fl.getName();
4588 else if (protocol == DataSourceType.URL)
4590 URL url = new URL(fileName);
4591 pdbfn = url.getFile();
4593 if (pdbfn.length() > 0)
4595 // attempt to find a match in the alignment
4596 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4597 int l = 0, c = pdbfn.indexOf(".");
4598 while (mtch == null && c != -1)
4603 } while ((c = pdbfn.indexOf(".", l)) > l);
4606 pdbfn = pdbfn.substring(0, l);
4608 mtch = idm.findAllIdMatches(pdbfn);
4615 type = new IdentifyFile().identify(file, protocol);
4616 } catch (Exception ex)
4620 if (type != null && type.isStructureFile())
4622 filesmatched.add(new Object[] { file, protocol, mtch });
4626 // File wasn't named like one of the sequences or wasn't a PDB
4628 filesnotmatched.add(file);
4632 if (filesmatched.size() > 0)
4634 boolean autoAssociate = Cache
4635 .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4638 String msg = MessageManager.formatMessage(
4639 "label.automatically_associate_structure_files_with_sequences_same_name",
4641 { Integer.valueOf(filesmatched.size())
4643 String ttl = MessageManager.getString(
4644 "label.automatically_associate_structure_files_by_name");
4645 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4646 ttl, JvOptionPane.YES_NO_OPTION);
4647 autoAssociate = choice == JvOptionPane.YES_OPTION;
4651 for (Object[] fm : filesmatched)
4653 // try and associate
4654 // TODO: may want to set a standard ID naming formalism for
4655 // associating PDB files which have no IDs.
4656 for (SequenceI toassoc : (SequenceI[]) fm[2])
4658 PDBEntry pe = new AssociatePdbFileWithSeq()
4659 .associatePdbWithSeq(fm[0].toString(),
4660 (DataSourceType) fm[1], toassoc, false,
4664 System.err.println("Associated file : "
4665 + (fm[0].toString()) + " with "
4666 + toassoc.getDisplayId(true));
4670 // TODO: do we need to update overview ? only if features are
4672 alignPanel.paintAlignment(true, false);
4678 * add declined structures as sequences
4680 for (Object[] o : filesmatched)
4682 filesnotmatched.add(o[0]);
4686 if (filesnotmatched.size() > 0)
4688 if (assocfiles > 0 && (Cache.getDefault(
4689 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4690 || JvOptionPane.showConfirmDialog(thisaf,
4691 "<html>" + MessageManager.formatMessage(
4692 "label.ignore_unmatched_dropped_files_info",
4695 filesnotmatched.size())
4698 MessageManager.getString(
4699 "label.ignore_unmatched_dropped_files"),
4700 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4704 for (Object fn : filesnotmatched)
4706 loadJalviewDataFile(fn, null, null, null);
4710 } catch (Exception ex)
4712 ex.printStackTrace();
4720 * Attempt to load a "dropped" file or URL string, by testing in turn for
4722 * <li>an Annotation file</li>
4723 * <li>a JNet file</li>
4724 * <li>a features file</li>
4725 * <li>else try to interpret as an alignment file</li>
4729 * either a filename or a URL string.
4731 public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4732 FileFormatI format, SequenceI assocSeq)
4734 // BH 2018 was String file
4737 if (sourceType == null)
4739 sourceType = FormatAdapter.checkProtocol(file);
4741 // if the file isn't identified, or not positively identified as some
4742 // other filetype (PFAM is default unidentified alignment file type) then
4743 // try to parse as annotation.
4744 boolean isAnnotation = (format == null
4745 || FileFormat.Pfam.equals(format))
4746 ? new AnnotationFile().annotateAlignmentView(viewport,
4752 // first see if its a T-COFFEE score file
4753 TCoffeeScoreFile tcf = null;
4756 tcf = new TCoffeeScoreFile(file, sourceType);
4759 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4763 new TCoffeeColourScheme(viewport.getAlignment()));
4764 isAnnotation = true;
4765 setStatus(MessageManager.getString(
4766 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4770 // some problem - if no warning its probable that the ID matching
4771 // process didn't work
4772 JvOptionPane.showMessageDialog(Desktop.desktop,
4773 tcf.getWarningMessage() == null
4774 ? MessageManager.getString(
4775 "label.check_file_matches_sequence_ids_alignment")
4776 : tcf.getWarningMessage(),
4777 MessageManager.getString(
4778 "label.problem_reading_tcoffee_score_file"),
4779 JvOptionPane.WARNING_MESSAGE);
4786 } catch (Exception x)
4789 "Exception when processing data source as T-COFFEE score file",
4795 // try to see if its a JNet 'concise' style annotation file *before*
4797 // try to parse it as a features file
4800 format = new IdentifyFile().identify(file, sourceType);
4802 if (FileFormat.ScoreMatrix == format)
4804 ScoreMatrixFile sm = new ScoreMatrixFile(
4805 new FileParse(file, sourceType));
4807 // todo: i18n this message
4808 setStatus(MessageManager.formatMessage(
4809 "label.successfully_loaded_matrix",
4810 sm.getMatrixName()));
4812 else if (FileFormat.Jnet.equals(format))
4814 JPredFile predictions = new JPredFile(file, sourceType);
4815 new JnetAnnotationMaker();
4816 JnetAnnotationMaker.add_annotation(predictions,
4817 viewport.getAlignment(), 0, false);
4818 viewport.getAlignment().setupJPredAlignment();
4819 isAnnotation = true;
4821 // else if (IdentifyFile.FeaturesFile.equals(format))
4822 else if (FileFormat.Features.equals(format))
4824 if (parseFeaturesFile(file, sourceType))
4826 SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4827 if (splitFrame != null)
4829 splitFrame.repaint();
4833 alignPanel.paintAlignment(true, true);
4839 new FileLoader().LoadFile(viewport, file, sourceType, format);
4846 alignPanel.adjustAnnotationHeight();
4847 viewport.updateSequenceIdColours();
4848 buildSortByAnnotationScoresMenu();
4849 alignPanel.paintAlignment(true, true);
4851 } catch (Exception ex)
4853 ex.printStackTrace();
4854 } catch (OutOfMemoryError oom)
4859 } catch (Exception x)
4864 + (sourceType != null
4865 ? (sourceType == DataSourceType.PASTE
4867 : "using " + sourceType + " from "
4871 ? "(parsing as '" + format + "' file)"
4873 oom, Desktop.desktop);
4878 * Method invoked by the ChangeListener on the tabbed pane, in other words
4879 * when a different tabbed pane is selected by the user or programmatically.
4882 public void tabSelectionChanged(int index)
4886 alignPanel = alignPanels.get(index);
4887 viewport = alignPanel.av;
4888 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4889 setMenusFromViewport(viewport);
4890 if (featureSettings != null && featureSettings.isOpen()
4891 && featureSettings.fr.getViewport() != viewport)
4893 if (viewport.isShowSequenceFeatures())
4895 // refresh the featureSettings to reflect UI change
4896 showFeatureSettingsUI();
4900 // close feature settings for this view.
4901 featureSettings.close();
4908 * 'focus' any colour slider that is open to the selected viewport
4910 if (viewport.getConservationSelected())
4912 SliderPanel.setConservationSlider(alignPanel,
4913 viewport.getResidueShading(), alignPanel.getViewName());
4917 SliderPanel.hideConservationSlider();
4919 if (viewport.getAbovePIDThreshold())
4921 SliderPanel.setPIDSliderSource(alignPanel,
4922 viewport.getResidueShading(), alignPanel.getViewName());
4926 SliderPanel.hidePIDSlider();
4930 * If there is a frame linked to this one in a SplitPane, switch it to the
4931 * same view tab index. No infinite recursion of calls should happen, since
4932 * tabSelectionChanged() should not get invoked on setting the selected
4933 * index to an unchanged value. Guard against setting an invalid index
4934 * before the new view peer tab has been created.
4936 final AlignViewportI peer = viewport.getCodingComplement();
4939 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4940 .getAlignPanel().alignFrame;
4941 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4943 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4949 * On right mouse click on view tab, prompt for and set new view name.
4952 public void tabbedPane_mousePressed(MouseEvent e)
4954 if (e.isPopupTrigger())
4956 String msg = MessageManager.getString("label.enter_view_name");
4957 String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
4958 String reply = JvOptionPane.showInputDialog(msg, ttl);
4962 viewport.setViewName(reply);
4963 // TODO warn if reply is in getExistingViewNames()?
4964 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4969 public AlignViewport getCurrentView()
4975 * Open the dialog for regex description parsing.
4978 protected void extractScores_actionPerformed(ActionEvent e)
4980 ParseProperties pp = new jalview.analysis.ParseProperties(
4981 viewport.getAlignment());
4982 // TODO: verify regex and introduce GUI dialog for version 2.5
4983 // if (pp.getScoresFromDescription("col", "score column ",
4984 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4986 if (pp.getScoresFromDescription("description column",
4987 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4989 buildSortByAnnotationScoresMenu();
4997 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5001 protected void showDbRefs_actionPerformed(ActionEvent e)
5003 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5009 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5013 protected void showNpFeats_actionPerformed(ActionEvent e)
5015 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5019 * find the viewport amongst the tabs in this alignment frame and close that
5024 public boolean closeView(AlignViewportI av)
5028 this.closeMenuItem_actionPerformed(false);
5031 Component[] comp = tabbedPane.getComponents();
5032 for (int i = 0; comp != null && i < comp.length; i++)
5034 if (comp[i] instanceof AlignmentPanel)
5036 if (((AlignmentPanel) comp[i]).av == av)
5039 closeView((AlignmentPanel) comp[i]);
5047 protected void build_fetchdbmenu(JMenu webService)
5049 // Temporary hack - DBRef Fetcher always top level ws entry.
5050 // TODO We probably want to store a sequence database checklist in
5051 // preferences and have checkboxes.. rather than individual sources selected
5053 final JMenu rfetch = new JMenu(
5054 MessageManager.getString("action.fetch_db_references"));
5055 rfetch.setToolTipText(MessageManager.getString(
5056 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5057 webService.add(rfetch);
5059 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5060 MessageManager.getString("option.trim_retrieved_seqs"));
5061 trimrs.setToolTipText(
5062 MessageManager.getString("label.trim_retrieved_sequences"));
5064 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5065 trimrs.addActionListener(new ActionListener()
5068 public void actionPerformed(ActionEvent e)
5070 trimrs.setSelected(trimrs.isSelected());
5071 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5072 Boolean.valueOf(trimrs.isSelected()).toString());
5076 JMenuItem fetchr = new JMenuItem(
5077 MessageManager.getString("label.standard_databases"));
5078 fetchr.setToolTipText(
5079 MessageManager.getString("label.fetch_embl_uniprot"));
5080 fetchr.addActionListener(new ActionListener()
5084 public void actionPerformed(ActionEvent e)
5086 new Thread(new Runnable()
5091 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5092 .getAlignment().isNucleotide();
5093 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5094 alignPanel.av.getSequenceSelection(),
5095 alignPanel.alignFrame, null,
5096 alignPanel.alignFrame.featureSettings, isNucleotide);
5097 dbRefFetcher.addListener(new FetchFinishedListenerI()
5100 public void finished()
5103 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5104 .getFeatureSettingsModels())
5107 alignPanel.av.mergeFeaturesStyle(srcSettings);
5109 AlignFrame.this.setMenusForViewport();
5112 dbRefFetcher.fetchDBRefs(false);
5120 new Thread(new Runnable()
5125 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5126 .getSequenceFetcherSingleton();
5127 javax.swing.SwingUtilities.invokeLater(new Runnable()
5132 String[] dbclasses = sf.getNonAlignmentSources();
5133 List<DbSourceProxy> otherdb;
5134 JMenu dfetch = new JMenu();
5135 JMenu ifetch = new JMenu();
5136 JMenuItem fetchr = null;
5137 int comp = 0, icomp = 0, mcomp = 15;
5138 String mname = null;
5140 for (String dbclass : dbclasses)
5142 otherdb = sf.getSourceProxy(dbclass);
5143 // add a single entry for this class, or submenu allowing 'fetch
5145 if (otherdb == null || otherdb.size() < 1)
5151 mname = "From " + dbclass;
5153 if (otherdb.size() == 1)
5155 final DbSourceProxy[] dassource = otherdb
5156 .toArray(new DbSourceProxy[0]);
5157 DbSourceProxy src = otherdb.get(0);
5158 fetchr = new JMenuItem(src.getDbSource());
5159 fetchr.addActionListener(new ActionListener()
5163 public void actionPerformed(ActionEvent e)
5165 new Thread(new Runnable()
5171 boolean isNucleotide = alignPanel.alignFrame
5172 .getViewport().getAlignment()
5174 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5175 alignPanel.av.getSequenceSelection(),
5176 alignPanel.alignFrame, dassource,
5177 alignPanel.alignFrame.featureSettings,
5180 .addListener(new FetchFinishedListenerI()
5183 public void finished()
5185 FeatureSettingsModelI srcSettings = dassource[0]
5186 .getFeatureColourScheme();
5187 alignPanel.av.mergeFeaturesStyle(
5189 AlignFrame.this.setMenusForViewport();
5192 dbRefFetcher.fetchDBRefs(false);
5198 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5199 MessageManager.formatMessage(
5200 "label.fetch_retrieve_from", new Object[]
5201 { src.getDbName() })));
5207 final DbSourceProxy[] dassource = otherdb
5208 .toArray(new DbSourceProxy[0]);
5210 DbSourceProxy src = otherdb.get(0);
5211 fetchr = new JMenuItem(MessageManager
5212 .formatMessage("label.fetch_all_param", new Object[]
5213 { src.getDbSource() }));
5214 fetchr.addActionListener(new ActionListener()
5217 public void actionPerformed(ActionEvent e)
5219 new Thread(new Runnable()
5225 boolean isNucleotide = alignPanel.alignFrame
5226 .getViewport().getAlignment()
5228 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5229 alignPanel.av.getSequenceSelection(),
5230 alignPanel.alignFrame, dassource,
5231 alignPanel.alignFrame.featureSettings,
5234 .addListener(new FetchFinishedListenerI()
5237 public void finished()
5239 AlignFrame.this.setMenusForViewport();
5242 dbRefFetcher.fetchDBRefs(false);
5248 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5249 MessageManager.formatMessage(
5250 "label.fetch_retrieve_from_all_sources",
5252 { Integer.valueOf(otherdb.size())
5254 src.getDbSource(), src.getDbName() })));
5257 // and then build the rest of the individual menus
5258 ifetch = new JMenu(MessageManager.formatMessage(
5259 "label.source_from_db_source", new Object[]
5260 { src.getDbSource() }));
5262 String imname = null;
5264 for (DbSourceProxy sproxy : otherdb)
5266 String dbname = sproxy.getDbName();
5267 String sname = dbname.length() > 5
5268 ? dbname.substring(0, 5) + "..."
5270 String msname = dbname.length() > 10
5271 ? dbname.substring(0, 10) + "..."
5275 imname = MessageManager
5276 .formatMessage("label.from_msname", new Object[]
5279 fetchr = new JMenuItem(msname);
5280 final DbSourceProxy[] dassrc = { sproxy };
5281 fetchr.addActionListener(new ActionListener()
5285 public void actionPerformed(ActionEvent e)
5287 new Thread(new Runnable()
5293 boolean isNucleotide = alignPanel.alignFrame
5294 .getViewport().getAlignment()
5296 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5297 alignPanel.av.getSequenceSelection(),
5298 alignPanel.alignFrame, dassrc,
5299 alignPanel.alignFrame.featureSettings,
5302 .addListener(new FetchFinishedListenerI()
5305 public void finished()
5307 AlignFrame.this.setMenusForViewport();
5310 dbRefFetcher.fetchDBRefs(false);
5316 fetchr.setToolTipText(
5317 "<html>" + MessageManager.formatMessage(
5318 "label.fetch_retrieve_from", new Object[]
5322 if (++icomp >= mcomp || i == (otherdb.size()))
5324 ifetch.setText(MessageManager.formatMessage(
5325 "label.source_to_target", imname, sname));
5327 ifetch = new JMenu();
5335 if (comp >= mcomp || dbi >= (dbclasses.length))
5337 dfetch.setText(MessageManager.formatMessage(
5338 "label.source_to_target", mname, dbclass));
5340 dfetch = new JMenu();
5353 * Left justify the whole alignment.
5356 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5358 AlignmentI al = viewport.getAlignment();
5360 viewport.firePropertyChange("alignment", null, al);
5364 * Right justify the whole alignment.
5367 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5369 AlignmentI al = viewport.getAlignment();
5371 viewport.firePropertyChange("alignment", null, al);
5375 public void setShowSeqFeatures(boolean b)
5377 showSeqFeatures.setSelected(b);
5378 viewport.setShowSequenceFeatures(b);
5385 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5386 * awt.event.ActionEvent)
5389 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5391 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5392 alignPanel.paintAlignment(false, false);
5399 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5403 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5405 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5406 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5414 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5415 * .event.ActionEvent)
5418 protected void showGroupConservation_actionPerformed(ActionEvent e)
5420 viewport.setShowGroupConservation(showGroupConservation.getState());
5421 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5428 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5429 * .event.ActionEvent)
5432 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5434 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5435 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5442 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5443 * .event.ActionEvent)
5446 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5448 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5449 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5453 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5455 showSequenceLogo.setState(true);
5456 viewport.setShowSequenceLogo(true);
5457 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5458 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5462 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5464 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5471 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5472 * .event.ActionEvent)
5475 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5477 if (avc.makeGroupsFromSelection())
5479 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5480 alignPanel.updateAnnotation();
5481 alignPanel.paintAlignment(true,
5482 viewport.needToUpdateStructureViews());
5486 public void clearAlignmentSeqRep()
5488 // TODO refactor alignmentseqrep to controller
5489 if (viewport.getAlignment().hasSeqrep())
5491 viewport.getAlignment().setSeqrep(null);
5492 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5493 alignPanel.updateAnnotation();
5494 alignPanel.paintAlignment(true, true);
5499 protected void createGroup_actionPerformed(ActionEvent e)
5501 if (avc.createGroup())
5503 if (applyAutoAnnotationSettings.isSelected())
5505 alignPanel.updateAnnotation(true, false);
5507 alignPanel.alignmentChanged();
5512 protected void unGroup_actionPerformed(ActionEvent e)
5516 alignPanel.alignmentChanged();
5521 * make the given alignmentPanel the currently selected tab
5523 * @param alignmentPanel
5525 public void setDisplayedView(AlignmentPanel alignmentPanel)
5527 if (!viewport.getSequenceSetId()
5528 .equals(alignmentPanel.av.getSequenceSetId()))
5530 throw new Error(MessageManager.getString(
5531 "error.implementation_error_cannot_show_view_alignment_frame"));
5533 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5534 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5536 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5541 * Action on selection of menu options to Show or Hide annotations.
5544 * @param forSequences
5545 * update sequence-related annotations
5546 * @param forAlignment
5547 * update non-sequence-related annotations
5550 protected void setAnnotationsVisibility(boolean visible,
5551 boolean forSequences, boolean forAlignment)
5553 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5554 .getAlignmentAnnotation();
5559 for (AlignmentAnnotation aa : anns)
5562 * don't display non-positional annotations on an alignment
5564 if (aa.annotations == null)
5568 boolean apply = (aa.sequenceRef == null && forAlignment)
5569 || (aa.sequenceRef != null && forSequences);
5572 aa.visible = visible;
5575 alignPanel.validateAnnotationDimensions(true);
5576 alignPanel.alignmentChanged();
5580 * Store selected annotation sort order for the view and repaint.
5583 protected void sortAnnotations_actionPerformed()
5585 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5587 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5588 alignPanel.paintAlignment(false, false);
5593 * @return alignment panels in this alignment frame
5595 public List<? extends AlignmentViewPanel> getAlignPanels()
5597 // alignPanels is never null
5598 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5603 * Open a new alignment window, with the cDNA associated with this (protein)
5604 * alignment, aligned as is the protein.
5606 protected void viewAsCdna_actionPerformed()
5608 // TODO no longer a menu action - refactor as required
5609 final AlignmentI alignment = getViewport().getAlignment();
5610 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5611 if (mappings == null)
5615 List<SequenceI> cdnaSeqs = new ArrayList<>();
5616 for (SequenceI aaSeq : alignment.getSequences())
5618 for (AlignedCodonFrame acf : mappings)
5620 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5624 * There is a cDNA mapping for this protein sequence - add to new
5625 * alignment. It will share the same dataset sequence as other mapped
5626 * cDNA (no new mappings need to be created).
5628 final Sequence newSeq = new Sequence(dnaSeq);
5629 newSeq.setDatasetSequence(dnaSeq);
5630 cdnaSeqs.add(newSeq);
5634 if (cdnaSeqs.size() == 0)
5636 // show a warning dialog no mapped cDNA
5639 AlignmentI cdna = new Alignment(
5640 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5641 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5642 AlignFrame.DEFAULT_HEIGHT);
5643 cdna.alignAs(alignment);
5644 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5646 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5647 AlignFrame.DEFAULT_HEIGHT);
5651 * Set visibility of dna/protein complement view (available when shown in a
5657 protected void showComplement_actionPerformed(boolean show)
5659 SplitContainerI sf = getSplitViewContainer();
5662 sf.setComplementVisible(this, show);
5667 * Generate the reverse (optionally complemented) of the selected sequences,
5668 * and add them to the alignment
5671 protected void showReverse_actionPerformed(boolean complement)
5673 AlignmentI al = null;
5676 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5677 al = dna.reverseCdna(complement);
5678 viewport.addAlignment(al, "");
5679 addHistoryItem(new EditCommand(
5680 MessageManager.getString("label.add_sequences"), Action.PASTE,
5681 al.getSequencesArray(), 0, al.getWidth(),
5682 viewport.getAlignment()));
5683 } catch (Exception ex)
5685 System.err.println(ex.getMessage());
5691 * Try to run a script in the Groovy console, having first ensured that this
5692 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5693 * be targeted at this alignment.
5696 protected void runGroovy_actionPerformed()
5698 Jalview.setCurrentAlignFrame(this);
5699 groovy.ui.Console console = Desktop.getGroovyConsole();
5700 if (console != null)
5704 console.runScript();
5705 } catch (Exception ex)
5707 System.err.println((ex.toString()));
5708 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5709 MessageManager.getString("label.couldnt_run_groovy_script"),
5710 MessageManager.getString("label.groovy_support_failed"),
5711 JvOptionPane.ERROR_MESSAGE);
5716 System.err.println("Can't run Groovy script as console not found");
5721 * Hides columns containing (or not containing) a specified feature, provided
5722 * that would not leave all columns hidden
5724 * @param featureType
5725 * @param columnsContaining
5728 public boolean hideFeatureColumns(String featureType,
5729 boolean columnsContaining)
5731 boolean notForHiding = avc.markColumnsContainingFeatures(
5732 columnsContaining, false, false, featureType);
5735 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5736 false, featureType))
5738 getViewport().hideSelectedColumns();
5746 protected void selectHighlightedColumns_actionPerformed(
5747 ActionEvent actionEvent)
5749 // include key modifier check in case user selects from menu
5750 avc.markHighlightedColumns(
5751 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5752 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5753 | ActionEvent.CTRL_MASK)) != 0);
5757 * Rebuilds the Colour menu, including any user-defined colours which have
5758 * been loaded either on startup or during the session
5760 public void buildColourMenu()
5762 colourMenu.removeAll();
5764 colourMenu.add(applyToAllGroups);
5765 colourMenu.add(textColour);
5766 colourMenu.addSeparator();
5768 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5769 viewport.getAlignment(), false);
5771 colourMenu.add(annotationColour);
5772 bg.add(annotationColour);
5773 colourMenu.addSeparator();
5774 colourMenu.add(conservationMenuItem);
5775 colourMenu.add(modifyConservation);
5776 colourMenu.add(abovePIDThreshold);
5777 colourMenu.add(modifyPID);
5779 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5780 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5784 * Open a dialog (if not already open) that allows the user to select and
5785 * calculate PCA or Tree analysis
5787 protected void openTreePcaDialog()
5789 if (alignPanel.getCalculationDialog() == null)
5791 new CalculationChooser(AlignFrame.this);
5796 protected void loadVcf_actionPerformed()
5798 JalviewFileChooser chooser = new JalviewFileChooser(
5799 Cache.getProperty("LAST_DIRECTORY"));
5800 chooser.setFileView(new JalviewFileView());
5801 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5802 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5803 final AlignFrame us = this;
5804 chooser.setResponseHandler(0, new Runnable()
5809 String choice = chooser.getSelectedFile().getPath();
5810 Cache.setProperty("LAST_DIRECTORY", choice);
5811 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5812 new VCFLoader(choice).loadVCF(seqs, us);
5815 chooser.showOpenDialog(null);
5819 private Rectangle lastFeatureSettingsBounds = null;
5821 public void setFeatureSettingsGeometry(Rectangle bounds)
5823 lastFeatureSettingsBounds = bounds;
5827 public Rectangle getFeatureSettingsGeometry()
5829 return lastFeatureSettingsBounds;
5833 class PrintThread extends Thread
5837 public PrintThread(AlignmentPanel ap)
5842 static PageFormat pf;
5847 PrinterJob printJob = PrinterJob.getPrinterJob();
5851 printJob.setPrintable(ap, pf);
5855 printJob.setPrintable(ap);
5858 if (printJob.printDialog())
5863 } catch (Exception PrintException)
5865 PrintException.printStackTrace();