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.IOException;
52 import java.io.PrintWriter;
54 import java.util.ArrayList;
55 import java.util.Arrays;
56 import java.util.Deque;
57 import java.util.Enumeration;
58 import java.util.Hashtable;
59 import java.util.List;
60 import java.util.Vector;
62 import javax.swing.ButtonGroup;
63 import javax.swing.JCheckBoxMenuItem;
64 import javax.swing.JComponent;
65 import javax.swing.JEditorPane;
66 import javax.swing.JInternalFrame;
67 import javax.swing.JLabel;
68 import javax.swing.JLayeredPane;
69 import javax.swing.JMenu;
70 import javax.swing.JMenuItem;
71 import javax.swing.JPanel;
72 import javax.swing.JScrollPane;
73 import javax.swing.SwingUtilities;
75 import ext.vamsas.ServiceHandle;
76 import jalview.analysis.AlignmentSorter;
77 import jalview.analysis.AlignmentUtils;
78 import jalview.analysis.CrossRef;
79 import jalview.analysis.Dna;
80 import jalview.analysis.GeneticCodeI;
81 import jalview.analysis.ParseProperties;
82 import jalview.analysis.SequenceIdMatcher;
83 import jalview.api.AlignExportSettingsI;
84 import jalview.api.AlignViewControllerGuiI;
85 import jalview.api.AlignViewControllerI;
86 import jalview.api.AlignViewportI;
87 import jalview.api.AlignmentViewPanel;
88 import jalview.api.FeatureSettingsControllerI;
89 import jalview.api.FeatureSettingsModelI;
90 import jalview.api.SplitContainerI;
91 import jalview.api.ViewStyleI;
92 import jalview.api.analysis.SimilarityParamsI;
93 import jalview.bin.Cache;
94 import jalview.bin.Jalview;
95 import jalview.commands.CommandI;
96 import jalview.commands.EditCommand;
97 import jalview.commands.EditCommand.Action;
98 import jalview.commands.OrderCommand;
99 import jalview.commands.RemoveGapColCommand;
100 import jalview.commands.RemoveGapsCommand;
101 import jalview.commands.SlideSequencesCommand;
102 import jalview.commands.TrimRegionCommand;
103 import jalview.datamodel.AlignExportSettingsAdapter;
104 import jalview.datamodel.AlignedCodonFrame;
105 import jalview.datamodel.Alignment;
106 import jalview.datamodel.AlignmentAnnotation;
107 import jalview.datamodel.AlignmentExportData;
108 import jalview.datamodel.AlignmentI;
109 import jalview.datamodel.AlignmentOrder;
110 import jalview.datamodel.AlignmentView;
111 import jalview.datamodel.ColumnSelection;
112 import jalview.datamodel.HiddenColumns;
113 import jalview.datamodel.PDBEntry;
114 import jalview.datamodel.SeqCigar;
115 import jalview.datamodel.Sequence;
116 import jalview.datamodel.SequenceGroup;
117 import jalview.datamodel.SequenceI;
118 import jalview.gui.ColourMenuHelper.ColourChangeListener;
119 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
120 import jalview.io.AlignmentProperties;
121 import jalview.io.AnnotationFile;
122 import jalview.io.BackupFiles;
123 import jalview.io.BioJsHTMLOutput;
124 import jalview.io.DataSourceType;
125 import jalview.io.FileFormat;
126 import jalview.io.FileFormatI;
127 import jalview.io.FileFormats;
128 import jalview.io.FileLoader;
129 import jalview.io.FileParse;
130 import jalview.io.FormatAdapter;
131 import jalview.io.HtmlSvgOutput;
132 import jalview.io.IdentifyFile;
133 import jalview.io.JPredFile;
134 import jalview.io.JalviewFileChooser;
135 import jalview.io.JalviewFileView;
136 import jalview.io.JnetAnnotationMaker;
137 import jalview.io.NewickFile;
138 import jalview.io.ScoreMatrixFile;
139 import jalview.io.TCoffeeScoreFile;
140 import jalview.io.vcf.VCFLoader;
141 import jalview.jbgui.GAlignFrame;
142 import jalview.project.Jalview2XML;
143 import jalview.schemes.ColourSchemeI;
144 import jalview.schemes.ColourSchemes;
145 import jalview.schemes.ResidueColourScheme;
146 import jalview.schemes.TCoffeeColourScheme;
147 import jalview.util.ImageMaker.TYPE;
148 import jalview.util.MessageManager;
149 import jalview.util.Platform;
150 import jalview.viewmodel.AlignmentViewport;
151 import jalview.viewmodel.ViewportRanges;
152 import jalview.ws.DBRefFetcher;
153 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
154 import jalview.ws.jws1.Discoverer;
155 import jalview.ws.jws2.Jws2Discoverer;
156 import jalview.ws.jws2.jabaws2.Jws2Instance;
157 import jalview.ws.seqfetcher.DbSourceProxy;
163 * @version $Revision$
165 @SuppressWarnings("serial")
166 public class AlignFrame extends GAlignFrame implements DropTargetListener,
167 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
170 public static final int DEFAULT_WIDTH = 700;
172 public static final int DEFAULT_HEIGHT = 500;
175 * The currently displayed panel (selected tabbed view if more than one)
177 public AlignmentPanel alignPanel;
179 AlignViewport viewport;
181 public AlignViewControllerI avc;
183 List<AlignmentPanel> alignPanels = new ArrayList<>();
186 * Last format used to load or save alignments in this window
188 FileFormatI currentFileFormat = null;
191 * Current filename for this alignment
193 String fileName = null;
198 * Creates a new AlignFrame object with specific width and height.
204 public AlignFrame(AlignmentI al, int width, int height)
206 this(al, null, width, height);
210 * Creates a new AlignFrame object with specific width, height and
216 * @param sequenceSetId
218 public AlignFrame(AlignmentI al, int width, int height,
219 String sequenceSetId)
221 this(al, null, width, height, sequenceSetId);
225 * Creates a new AlignFrame object with specific width, height and
231 * @param sequenceSetId
234 public AlignFrame(AlignmentI al, int width, int height,
235 String sequenceSetId, String viewId)
237 this(al, null, width, height, sequenceSetId, viewId);
241 * new alignment window with hidden columns
245 * @param hiddenColumns
246 * ColumnSelection or null
248 * Width of alignment frame
252 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
255 this(al, hiddenColumns, width, height, null);
259 * Create alignment frame for al with hiddenColumns, a specific width and
260 * height, and specific sequenceId
263 * @param hiddenColumns
266 * @param sequenceSetId
269 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
270 int height, String sequenceSetId)
272 this(al, hiddenColumns, width, height, sequenceSetId, null);
276 * Create alignment frame for al with hiddenColumns, a specific width and
277 * height, and specific sequenceId
280 * @param hiddenColumns
283 * @param sequenceSetId
288 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
289 int height, String sequenceSetId, String viewId)
291 setSize(width, height);
293 if (al.getDataset() == null)
298 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
300 alignPanel = new AlignmentPanel(this, viewport);
302 addAlignmentPanel(alignPanel, true);
306 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
307 HiddenColumns hiddenColumns, int width, int height)
309 setSize(width, height);
311 if (al.getDataset() == null)
316 viewport = new AlignViewport(al, hiddenColumns);
318 if (hiddenSeqs != null && hiddenSeqs.length > 0)
320 viewport.hideSequence(hiddenSeqs);
322 alignPanel = new AlignmentPanel(this, viewport);
323 addAlignmentPanel(alignPanel, true);
328 * Make a new AlignFrame from existing alignmentPanels
335 public AlignFrame(AlignmentPanel ap)
339 addAlignmentPanel(ap, false);
344 * initalise the alignframe from the underlying viewport data and the
349 // setBackground(Color.white); // BH 2019
351 if (!Jalview.isHeadlessMode())
353 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
356 avc = new jalview.controller.AlignViewController(this, viewport,
358 if (viewport.getAlignmentConservationAnnotation() == null)
360 // BLOSUM62Colour.setEnabled(false);
361 conservationMenuItem.setEnabled(false);
362 modifyConservation.setEnabled(false);
363 // PIDColour.setEnabled(false);
364 // abovePIDThreshold.setEnabled(false);
365 // modifyPID.setEnabled(false);
368 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
371 if (sortby.equals("Id"))
373 sortIDMenuItem_actionPerformed(null);
375 else if (sortby.equals("Pairwise Identity"))
377 sortPairwiseMenuItem_actionPerformed(null);
381 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
383 setMenusFromViewport(viewport);
384 buildSortByAnnotationScoresMenu();
385 calculateTree.addActionListener(new ActionListener()
389 public void actionPerformed(ActionEvent e)
396 if (Desktop.desktop != null)
398 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
399 if (!Platform.isJS())
401 addServiceListeners();
406 if (viewport.getWrapAlignment())
408 wrapMenuItem_actionPerformed(null);
411 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
413 this.overviewMenuItem_actionPerformed(null);
418 final List<AlignmentViewPanel> selviews = new ArrayList<>();
419 final List<AlignmentPanel> origview = new ArrayList<>();
420 final String menuLabel = MessageManager
421 .getString("label.copy_format_from");
422 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
423 new ViewSetProvider()
427 public AlignmentPanel[] getAllAlignmentPanels()
430 origview.add(alignPanel);
431 // make an array of all alignment panels except for this one
432 List<AlignmentPanel> aps = new ArrayList<>(
433 Arrays.asList(Desktop.getAlignmentPanels(null)));
434 aps.remove(AlignFrame.this.alignPanel);
435 return aps.toArray(new AlignmentPanel[aps.size()]);
437 }, selviews, new ItemListener()
441 public void itemStateChanged(ItemEvent e)
443 if (origview.size() > 0)
445 final AlignmentPanel ap = origview.get(0);
448 * Copy the ViewStyle of the selected panel to 'this one'.
449 * Don't change value of 'scaleProteinAsCdna' unless copying
452 ViewStyleI vs = selviews.get(0).getAlignViewport()
454 boolean fromSplitFrame = selviews.get(0)
455 .getAlignViewport().getCodingComplement() != null;
458 vs.setScaleProteinAsCdna(ap.getAlignViewport()
459 .getViewStyle().isScaleProteinAsCdna());
461 ap.getAlignViewport().setViewStyle(vs);
464 * Also rescale ViewStyle of SplitFrame complement if there is
465 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
466 * the whole ViewStyle (allow cDNA protein to have different
469 AlignViewportI complement = ap.getAlignViewport()
470 .getCodingComplement();
471 if (complement != null && vs.isScaleProteinAsCdna())
473 AlignFrame af = Desktop.getAlignFrameFor(complement);
474 ((SplitFrame) af.getSplitViewContainer())
476 af.setMenusForViewport();
480 ap.setSelected(true);
481 ap.alignFrame.setMenusForViewport();
486 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
487 .indexOf("devel") > -1
488 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
489 .indexOf("test") > -1)
491 formatMenu.add(vsel);
493 addFocusListener(new FocusAdapter()
496 public void focusGained(FocusEvent e)
498 Jalview.setCurrentAlignFrame(AlignFrame.this);
505 * Change the filename and format for the alignment, and enable the 'reload'
506 * button functionality.
513 public void setFileName(String file, FileFormatI format)
516 setFileFormat(format);
517 reload.setEnabled(true);
521 * JavaScript will have this, maybe others. More dependable than a file name
522 * and maintains a reference to the actual bytes loaded.
526 public void setFileObject(File file)
528 this.fileObject = file;
532 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
535 void addKeyListener()
537 addKeyListener(new KeyAdapter()
540 public void keyPressed(KeyEvent evt)
542 if (viewport.cursorMode
543 && ((evt.getKeyCode() >= KeyEvent.VK_0
544 && evt.getKeyCode() <= KeyEvent.VK_9)
545 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
546 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
547 && Character.isDigit(evt.getKeyChar()))
549 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
552 switch (evt.getKeyCode())
555 case 27: // escape key
556 deselectAllSequenceMenuItem_actionPerformed(null);
560 case KeyEvent.VK_DOWN:
561 if (evt.isAltDown() || !viewport.cursorMode)
563 moveSelectedSequences(false);
565 if (viewport.cursorMode)
567 alignPanel.getSeqPanel().moveCursor(0, 1);
572 if (evt.isAltDown() || !viewport.cursorMode)
574 moveSelectedSequences(true);
576 if (viewport.cursorMode)
578 alignPanel.getSeqPanel().moveCursor(0, -1);
583 case KeyEvent.VK_LEFT:
584 if (evt.isAltDown() || !viewport.cursorMode)
586 slideSequences(false,
587 alignPanel.getSeqPanel().getKeyboardNo1());
591 alignPanel.getSeqPanel().moveCursor(-1, 0);
596 case KeyEvent.VK_RIGHT:
597 if (evt.isAltDown() || !viewport.cursorMode)
599 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
603 alignPanel.getSeqPanel().moveCursor(1, 0);
607 case KeyEvent.VK_SPACE:
608 if (viewport.cursorMode)
610 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
611 || evt.isShiftDown() || evt.isAltDown());
615 // case KeyEvent.VK_A:
616 // if (viewport.cursorMode)
618 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
619 // //System.out.println("A");
623 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
624 * System.out.println("closing bracket"); } break;
626 case KeyEvent.VK_DELETE:
627 case KeyEvent.VK_BACK_SPACE:
628 if (!viewport.cursorMode)
630 cut_actionPerformed();
634 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
635 || evt.isShiftDown() || evt.isAltDown());
641 if (viewport.cursorMode)
643 alignPanel.getSeqPanel().setCursorRow();
647 if (viewport.cursorMode && !evt.isControlDown())
649 alignPanel.getSeqPanel().setCursorColumn();
653 if (viewport.cursorMode)
655 alignPanel.getSeqPanel().setCursorPosition();
659 case KeyEvent.VK_ENTER:
660 case KeyEvent.VK_COMMA:
661 if (viewport.cursorMode)
663 alignPanel.getSeqPanel().setCursorRowAndColumn();
668 if (viewport.cursorMode)
670 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
674 if (viewport.cursorMode)
676 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
681 viewport.cursorMode = !viewport.cursorMode;
682 setStatus(MessageManager
683 .formatMessage("label.keyboard_editing_mode", new String[]
684 { (viewport.cursorMode ? "on" : "off") }));
685 if (viewport.cursorMode)
687 ViewportRanges ranges = viewport.getRanges();
688 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
690 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
693 alignPanel.getSeqPanel().seqCanvas.repaint();
699 Help.showHelpWindow();
700 } catch (Exception ex)
702 ex.printStackTrace();
707 boolean toggleSeqs = !evt.isControlDown();
708 boolean toggleCols = !evt.isShiftDown();
709 toggleHiddenRegions(toggleSeqs, toggleCols);
714 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
715 boolean modifyExisting = true; // always modify, don't clear
716 // evt.isShiftDown();
717 boolean invertHighlighted = evt.isAltDown();
718 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
722 case KeyEvent.VK_PAGE_UP:
723 viewport.getRanges().pageUp();
725 case KeyEvent.VK_PAGE_DOWN:
726 viewport.getRanges().pageDown();
732 public void keyReleased(KeyEvent evt)
734 switch (evt.getKeyCode())
736 case KeyEvent.VK_LEFT:
737 if (evt.isAltDown() || !viewport.cursorMode)
739 viewport.firePropertyChange("alignment", null,
740 viewport.getAlignment().getSequences());
744 case KeyEvent.VK_RIGHT:
745 if (evt.isAltDown() || !viewport.cursorMode)
747 viewport.firePropertyChange("alignment", null,
748 viewport.getAlignment().getSequences());
756 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
758 ap.alignFrame = this;
759 avc = new jalview.controller.AlignViewController(this, viewport,
764 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
766 int aSize = alignPanels.size();
768 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
770 if (aSize == 1 && ap.av.getViewName() == null)
772 this.getContentPane().add(ap, BorderLayout.CENTER);
778 setInitialTabVisible();
781 expandViews.setEnabled(true);
782 gatherViews.setEnabled(true);
783 tabbedPane.addTab(ap.av.getViewName(), ap);
785 ap.setVisible(false);
790 if (ap.av.isPadGaps())
792 ap.av.getAlignment().padGaps();
794 ap.av.updateConservation(ap);
795 ap.av.updateConsensus(ap);
796 ap.av.updateStrucConsensus(ap);
800 public void setInitialTabVisible()
802 expandViews.setEnabled(true);
803 gatherViews.setEnabled(true);
804 tabbedPane.setVisible(true);
805 AlignmentPanel first = alignPanels.get(0);
806 tabbedPane.addTab(first.av.getViewName(), first);
807 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
810 public AlignViewport getViewport()
815 /* Set up intrinsic listeners for dynamically generated GUI bits. */
816 private void addServiceListeners()
818 final java.beans.PropertyChangeListener thisListener;
819 Desktop.instance.addJalviewPropertyChangeListener("services",
820 thisListener = new java.beans.PropertyChangeListener()
823 public void propertyChange(PropertyChangeEvent evt)
825 // // System.out.println("Discoverer property change.");
826 // if (evt.getPropertyName().equals("services"))
828 SwingUtilities.invokeLater(new Runnable()
835 "Rebuild WS Menu for service change");
836 BuildWebServiceMenu();
843 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
846 public void internalFrameClosed(
847 javax.swing.event.InternalFrameEvent evt)
849 // System.out.println("deregistering discoverer listener");
850 Desktop.instance.removeJalviewPropertyChangeListener("services",
852 closeMenuItem_actionPerformed(true);
855 // Finally, build the menu once to get current service state
856 new Thread(new Runnable()
861 BuildWebServiceMenu();
867 * Configure menu items that vary according to whether the alignment is
868 * nucleotide or protein
870 public void setGUINucleotide()
872 AlignmentI al = getViewport().getAlignment();
873 boolean nucleotide = al.isNucleotide();
875 loadVcf.setVisible(nucleotide);
876 showTranslation.setVisible(nucleotide);
877 showReverse.setVisible(nucleotide);
878 showReverseComplement.setVisible(nucleotide);
879 conservationMenuItem.setEnabled(!nucleotide);
881 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
882 showGroupConservation.setEnabled(!nucleotide);
884 showComplementMenuItem
885 .setText(nucleotide ? MessageManager.getString("label.protein")
886 : MessageManager.getString("label.nucleotide"));
890 * set up menus for the current viewport. This may be called after any
891 * operation that affects the data in the current view (selection changed,
892 * etc) to update the menus to reflect the new state.
895 public void setMenusForViewport()
897 setMenusFromViewport(viewport);
901 * Need to call this method when tabs are selected for multiple views, or when
902 * loading from Jalview2XML.java
907 public void setMenusFromViewport(AlignViewport av)
909 padGapsMenuitem.setSelected(av.isPadGaps());
910 colourTextMenuItem.setSelected(av.isShowColourText());
911 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
912 modifyPID.setEnabled(abovePIDThreshold.isSelected());
913 conservationMenuItem.setSelected(av.getConservationSelected());
914 modifyConservation.setEnabled(conservationMenuItem.isSelected());
915 seqLimits.setSelected(av.getShowJVSuffix());
916 idRightAlign.setSelected(av.isRightAlignIds());
917 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
918 renderGapsMenuItem.setSelected(av.isRenderGaps());
919 wrapMenuItem.setSelected(av.getWrapAlignment());
920 scaleAbove.setVisible(av.getWrapAlignment());
921 scaleLeft.setVisible(av.getWrapAlignment());
922 scaleRight.setVisible(av.getWrapAlignment());
923 annotationPanelMenuItem.setState(av.isShowAnnotation());
925 * Show/hide annotations only enabled if annotation panel is shown
927 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
928 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
929 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
930 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
931 viewBoxesMenuItem.setSelected(av.getShowBoxes());
932 viewTextMenuItem.setSelected(av.getShowText());
933 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
934 showGroupConsensus.setSelected(av.isShowGroupConsensus());
935 showGroupConservation.setSelected(av.isShowGroupConservation());
936 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
937 showSequenceLogo.setSelected(av.isShowSequenceLogo());
938 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
940 ColourMenuHelper.setColourSelected(colourMenu,
941 av.getGlobalColourScheme());
943 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
944 hiddenMarkers.setState(av.getShowHiddenMarkers());
945 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
946 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
947 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
948 autoCalculate.setSelected(av.autoCalculateConsensus);
949 sortByTree.setSelected(av.sortByTree);
950 listenToViewSelections.setSelected(av.followSelection);
952 showProducts.setEnabled(canShowProducts());
953 setGroovyEnabled(Desktop.getGroovyConsole() != null);
959 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
963 public void setGroovyEnabled(boolean b)
965 runGroovy.setEnabled(b);
968 private IProgressIndicator progressBar;
973 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
976 public void setProgressBar(String message, long id)
978 progressBar.setProgressBar(message, id);
982 public void registerHandler(final long id,
983 final IProgressIndicatorHandler handler)
985 progressBar.registerHandler(id, handler);
990 * @return true if any progress bars are still active
993 public boolean operationInProgress()
995 return progressBar.operationInProgress();
999 * Sets the text of the status bar. Note that setting a null or empty value
1000 * will cause the status bar to be hidden, with possibly undesirable flicker
1001 * of the screen layout.
1004 public void setStatus(String text)
1006 statusBar.setText(text == null || text.isEmpty() ? " " : text);
1010 * Added so Castor Mapping file can obtain Jalview Version
1012 public String getVersion()
1014 return jalview.bin.Cache.getProperty("VERSION");
1017 public FeatureRenderer getFeatureRenderer()
1019 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1023 public void fetchSequence_actionPerformed()
1025 new SequenceFetcher(this);
1029 public void addFromFile_actionPerformed(ActionEvent e)
1031 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1035 public void reload_actionPerformed(ActionEvent e)
1037 if (fileName != null)
1039 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1040 // originating file's format
1041 // TODO: work out how to recover feature settings for correct view(s) when
1042 // file is reloaded.
1043 if (FileFormat.Jalview.equals(currentFileFormat))
1045 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1046 for (int i = 0; i < frames.length; i++)
1048 if (frames[i] instanceof AlignFrame && frames[i] != this
1049 && ((AlignFrame) frames[i]).fileName != null
1050 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1054 frames[i].setSelected(true);
1055 Desktop.instance.closeAssociatedWindows();
1056 } catch (java.beans.PropertyVetoException ex)
1062 Desktop.instance.closeAssociatedWindows();
1064 FileLoader loader = new FileLoader();
1065 DataSourceType protocol = fileName.startsWith("http:")
1066 ? DataSourceType.URL
1067 : DataSourceType.FILE;
1068 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1072 Rectangle bounds = this.getBounds();
1074 FileLoader loader = new FileLoader();
1076 AlignFrame newframe = null;
1078 if (fileObject == null)
1081 DataSourceType protocol = (fileName.startsWith("http:")
1082 ? DataSourceType.URL
1083 : DataSourceType.FILE);
1084 newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1089 newframe = loader.LoadFileWaitTillLoaded(fileObject,
1090 DataSourceType.FILE, currentFileFormat);
1093 newframe.setBounds(bounds);
1094 if (featureSettings != null && featureSettings.isShowing())
1096 final Rectangle fspos = featureSettings.frame.getBounds();
1097 // TODO: need a 'show feature settings' function that takes bounds -
1098 // need to refactor Desktop.addFrame
1099 newframe.featureSettings_actionPerformed(null);
1100 final FeatureSettings nfs = newframe.featureSettings;
1101 SwingUtilities.invokeLater(new Runnable()
1106 nfs.frame.setBounds(fspos);
1109 this.featureSettings.close();
1110 this.featureSettings = null;
1112 this.closeMenuItem_actionPerformed(true);
1118 public void addFromText_actionPerformed(ActionEvent e)
1121 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1125 public void addFromURL_actionPerformed(ActionEvent e)
1127 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1131 public void save_actionPerformed(ActionEvent e)
1133 if (fileName == null || (currentFileFormat == null)
1134 || fileName.startsWith("http"))
1136 saveAs_actionPerformed();
1140 saveAlignment(fileName, currentFileFormat);
1145 * Saves the alignment to a file with a name chosen by the user, if necessary
1146 * warning if a file would be overwritten
1149 public void saveAs_actionPerformed()
1151 String format = currentFileFormat == null ? null
1152 : currentFileFormat.getName();
1153 JalviewFileChooser chooser = JalviewFileChooser
1154 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1156 chooser.setFileView(new JalviewFileView());
1157 chooser.setDialogTitle(
1158 MessageManager.getString("label.save_alignment_to_file"));
1159 chooser.setToolTipText(MessageManager.getString("action.save"));
1161 int value = chooser.showSaveDialog(this);
1163 if (value != JalviewFileChooser.APPROVE_OPTION)
1167 currentFileFormat = chooser.getSelectedFormat();
1168 // todo is this (2005) test now obsolete - value is never null?
1169 while (currentFileFormat == null)
1171 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1173 .getString("label.select_file_format_before_saving"),
1174 MessageManager.getString("label.file_format_not_specified"),
1175 JvOptionPane.WARNING_MESSAGE);
1176 currentFileFormat = chooser.getSelectedFormat();
1177 value = chooser.showSaveDialog(this);
1178 if (value != JalviewFileChooser.APPROVE_OPTION)
1184 fileName = chooser.getSelectedFile().getPath();
1186 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1187 Cache.setProperty("LAST_DIRECTORY", fileName);
1188 saveAlignment(fileName, currentFileFormat);
1191 boolean lastSaveSuccessful = false;
1193 FileFormatI lastFormatSaved;
1195 String lastFilenameSaved;
1198 * Raise a dialog or status message for the last call to saveAlignment.
1200 * @return true if last call to saveAlignment(file, format) was successful.
1202 public boolean isSaveAlignmentSuccessful()
1205 if (!lastSaveSuccessful)
1207 JvOptionPane.showInternalMessageDialog(this, MessageManager
1208 .formatMessage("label.couldnt_save_file", new Object[]
1209 { lastFilenameSaved }),
1210 MessageManager.getString("label.error_saving_file"),
1211 JvOptionPane.WARNING_MESSAGE);
1216 setStatus(MessageManager.formatMessage(
1217 "label.successfully_saved_to_file_in_format", new Object[]
1218 { lastFilenameSaved, lastFormatSaved }));
1221 return lastSaveSuccessful;
1225 * Saves the alignment to the specified file path, in the specified format,
1226 * which may be an alignment format, or Jalview project format. If the
1227 * alignment has hidden regions, or the format is one capable of including
1228 * non-sequence data (features, annotations, groups), then the user may be
1229 * prompted to specify what to include in the output.
1234 public void saveAlignment(String file, FileFormatI format)
1236 lastSaveSuccessful = true;
1237 lastFilenameSaved = file;
1238 lastFormatSaved = format;
1240 if (FileFormat.Jalview.equals(format))
1242 String shortName = title;
1243 if (shortName.indexOf(File.separatorChar) > -1)
1245 shortName = shortName
1246 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
1248 lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
1251 statusBar.setText(MessageManager.formatMessage(
1252 "label.successfully_saved_to_file_in_format", new Object[]
1258 AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1259 Runnable cancelAction = new Runnable()
1264 lastSaveSuccessful = false;
1267 Runnable outputAction = new Runnable()
1272 // todo defer this to inside formatSequences (or later)
1273 AlignmentExportData exportData = viewport
1274 .getAlignExportData(options);
1275 String output = new FormatAdapter(alignPanel, options)
1276 .formatSequences(format, exportData.getAlignment(),
1277 exportData.getOmitHidden(),
1278 exportData.getStartEndPostions(),
1279 viewport.getAlignment().getHiddenColumns());
1282 lastSaveSuccessful = false;
1286 // create backupfiles object and get new temp filename destination
1287 boolean doBackup = BackupFiles.getEnabled();
1288 BackupFiles backupfiles = null;
1292 "ALIGNFRAME making backupfiles object for " + file);
1293 backupfiles = new BackupFiles(file);
1297 String tempFilePath = doBackup ? backupfiles.getTempFilePath()
1299 Cache.log.trace("ALIGNFRAME setting PrintWriter");
1300 PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
1302 if (backupfiles != null)
1304 Cache.log.trace("ALIGNFRAME about to write to temp file "
1305 + backupfiles.getTempFilePath());
1309 Cache.log.trace("ALIGNFRAME about to close file");
1311 Cache.log.trace("ALIGNFRAME closed file");
1312 AlignFrame.this.setTitle(file);
1313 statusBar.setText(MessageManager.formatMessage(
1314 "label.successfully_saved_to_file_in_format",
1316 { fileName, format.getName() }));
1317 lastSaveSuccessful = true;
1318 } catch (IOException e)
1320 lastSaveSuccessful = false;
1322 "ALIGNFRAME Something happened writing the temp file");
1323 Cache.log.error(e.getMessage());
1324 Cache.log.debug(Cache.getStackTraceString(e));
1325 } catch (Exception ex)
1327 lastSaveSuccessful = false;
1329 "ALIGNFRAME Something unexpected happened writing the temp file");
1330 Cache.log.error(ex.getMessage());
1331 Cache.log.debug(Cache.getStackTraceString(ex));
1336 backupfiles.setWriteSuccess(lastSaveSuccessful);
1337 Cache.log.debug("ALIGNFRAME writing temp file was "
1338 + (lastSaveSuccessful ? "" : "NOT ") + "successful");
1339 // do the backup file roll and rename the temp file to actual file
1341 "ALIGNFRAME about to rollBackupsAndRenameTempFile");
1342 lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1344 "ALIGNFRAME performed rollBackupsAndRenameTempFile "
1345 + (lastSaveSuccessful ? "" : "un")
1349 if (!lastSaveSuccessful)
1351 if (!Platform.isHeadless())
1353 JvOptionPane.showInternalMessageDialog(AlignFrame.this,
1354 MessageManager.formatMessage(
1355 "label.couldnt_save_file", new Object[]
1357 MessageManager.getString("label.error_saving_file"),
1358 JvOptionPane.WARNING_MESSAGE);
1366 * show dialog with export options if applicable; else just do it
1368 if (AlignExportOptions.isNeeded(viewport, format))
1370 AlignExportOptions choices = new AlignExportOptions(
1371 alignPanel.getAlignViewport(), format, options);
1372 choices.setResponseAction(0, outputAction);
1373 choices.setResponseAction(1, cancelAction);
1374 choices.showDialog();
1383 * Outputs the alignment to textbox in the requested format, if necessary
1384 * first prompting the user for whether to include hidden regions or
1387 * @param fileFormatName
1390 protected void outputText_actionPerformed(String fileFormatName)
1392 FileFormatI fileFormat = FileFormats.getInstance()
1393 .forName(fileFormatName);
1394 AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1395 Runnable outputAction = new Runnable()
1400 // todo defer this to inside formatSequences (or later)
1401 AlignmentExportData exportData = viewport
1402 .getAlignExportData(options);
1403 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1404 cap.setForInput(null);
1407 FileFormatI format = fileFormat;
1408 cap.setText(new FormatAdapter(alignPanel, options)
1409 .formatSequences(format, exportData.getAlignment(),
1410 exportData.getOmitHidden(),
1411 exportData.getStartEndPostions(),
1412 viewport.getAlignment().getHiddenColumns()));
1413 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1414 "label.alignment_output_command", new Object[]
1415 { fileFormat.getName() }), 600, 500);
1416 } catch (OutOfMemoryError oom)
1418 new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1426 * show dialog with export options if applicable; else just do it
1428 if (AlignExportOptions.isNeeded(viewport, fileFormat))
1430 AlignExportOptions choices = new AlignExportOptions(
1431 alignPanel.getAlignViewport(), fileFormat, options);
1432 choices.setResponseAction(0, outputAction);
1433 choices.showDialog();
1448 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1450 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1451 htmlSVG.exportHTML(null);
1455 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1457 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1458 bjs.exportHTML(null);
1461 public void createImageMap(File file, String image)
1463 alignPanel.makePNGImageMap(file, image);
1467 * Creates a PNG image of the alignment and writes it to the given file. If
1468 * the file is null, the user is prompted to choose a file.
1473 public void createPNG(File f)
1475 alignPanel.makeAlignmentImage(TYPE.PNG, f);
1479 * Creates an EPS image of the alignment and writes it to the given file. If
1480 * the file is null, the user is prompted to choose a file.
1485 public void createEPS(File f)
1487 alignPanel.makeAlignmentImage(TYPE.EPS, f);
1491 * Creates an SVG image of the alignment and writes it to the given file. If
1492 * the file is null, the user is prompted to choose a file.
1497 public void createSVG(File f)
1499 alignPanel.makeAlignmentImage(TYPE.SVG, f);
1503 public void pageSetup_actionPerformed(ActionEvent e)
1505 PrinterJob printJob = PrinterJob.getPrinterJob();
1506 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1516 public void printMenuItem_actionPerformed(ActionEvent e)
1518 // Putting in a thread avoids Swing painting problems
1519 PrintThread thread = new PrintThread(alignPanel);
1524 public void exportFeatures_actionPerformed(ActionEvent e)
1526 new AnnotationExporter(alignPanel).exportFeatures();
1530 public void exportAnnotations_actionPerformed(ActionEvent e)
1532 new AnnotationExporter(alignPanel).exportAnnotations();
1536 public void associatedData_actionPerformed(ActionEvent e)
1538 final JalviewFileChooser chooser = new JalviewFileChooser(
1539 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1540 chooser.setFileView(new JalviewFileView());
1541 String tooltip = MessageManager
1542 .getString("label.load_jalview_annotations");
1543 chooser.setDialogTitle(tooltip);
1544 chooser.setToolTipText(tooltip);
1545 chooser.setResponseHandler(0, new Runnable()
1550 String choice = chooser.getSelectedFile().getPath();
1551 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1552 loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1556 chooser.showOpenDialog(this);
1560 * Close the current view or all views in the alignment frame. If the frame
1561 * only contains one view then the alignment will be removed from memory.
1563 * @param closeAllTabs
1566 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1568 if (alignPanels != null && alignPanels.size() < 2)
1570 closeAllTabs = true;
1575 if (alignPanels != null)
1579 if (this.isClosed())
1581 // really close all the windows - otherwise wait till
1582 // setClosed(true) is called
1583 for (int i = 0; i < alignPanels.size(); i++)
1585 AlignmentPanel ap = alignPanels.get(i);
1592 closeView(alignPanel);
1597 if (featureSettings != null && featureSettings.isOpen())
1599 featureSettings.close();
1600 featureSettings = null;
1603 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1604 * be called recursively, with the frame now in 'closed' state
1606 this.setClosed(true);
1608 } catch (Exception ex)
1610 ex.printStackTrace();
1615 * Close the specified panel and close up tabs appropriately.
1617 * @param panelToClose
1619 public void closeView(AlignmentPanel panelToClose)
1621 int index = tabbedPane.getSelectedIndex();
1622 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1623 alignPanels.remove(panelToClose);
1624 panelToClose.closePanel();
1625 panelToClose = null;
1627 tabbedPane.removeTabAt(closedindex);
1628 tabbedPane.validate();
1630 if (index > closedindex || index == tabbedPane.getTabCount())
1632 // modify currently selected tab index if necessary.
1636 this.tabSelectionChanged(index);
1642 void updateEditMenuBar()
1645 if (viewport.getHistoryList().size() > 0)
1647 undoMenuItem.setEnabled(true);
1648 CommandI command = viewport.getHistoryList().peek();
1649 undoMenuItem.setText(MessageManager
1650 .formatMessage("label.undo_command", new Object[]
1651 { command.getDescription() }));
1655 undoMenuItem.setEnabled(false);
1656 undoMenuItem.setText(MessageManager.getString("action.undo"));
1659 if (viewport.getRedoList().size() > 0)
1661 redoMenuItem.setEnabled(true);
1663 CommandI command = viewport.getRedoList().peek();
1664 redoMenuItem.setText(MessageManager
1665 .formatMessage("label.redo_command", new Object[]
1666 { command.getDescription() }));
1670 redoMenuItem.setEnabled(false);
1671 redoMenuItem.setText(MessageManager.getString("action.redo"));
1676 public void addHistoryItem(CommandI command)
1678 if (command.getSize() > 0)
1680 viewport.addToHistoryList(command);
1681 viewport.clearRedoList();
1682 updateEditMenuBar();
1683 viewport.updateHiddenColumns();
1684 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1685 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1686 // viewport.getColumnSelection()
1687 // .getHiddenColumns().size() > 0);
1693 * @return alignment objects for all views
1695 AlignmentI[] getViewAlignments()
1697 if (alignPanels != null)
1699 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1701 for (AlignmentPanel ap : alignPanels)
1703 als[i++] = ap.av.getAlignment();
1707 if (viewport != null)
1709 return new AlignmentI[] { viewport.getAlignment() };
1721 protected void undoMenuItem_actionPerformed(ActionEvent e)
1723 if (viewport.getHistoryList().isEmpty())
1727 CommandI command = viewport.getHistoryList().pop();
1728 viewport.addToRedoList(command);
1729 command.undoCommand(getViewAlignments());
1731 AlignmentViewport originalSource = getOriginatingSource(command);
1732 updateEditMenuBar();
1734 if (originalSource != null)
1736 if (originalSource != viewport)
1739 "Implementation worry: mismatch of viewport origin for undo");
1741 originalSource.updateHiddenColumns();
1742 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1744 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1745 // viewport.getColumnSelection()
1746 // .getHiddenColumns().size() > 0);
1747 originalSource.firePropertyChange("alignment", null,
1748 originalSource.getAlignment().getSequences());
1759 protected void redoMenuItem_actionPerformed(ActionEvent e)
1761 if (viewport.getRedoList().size() < 1)
1766 CommandI command = viewport.getRedoList().pop();
1767 viewport.addToHistoryList(command);
1768 command.doCommand(getViewAlignments());
1770 AlignmentViewport originalSource = getOriginatingSource(command);
1771 updateEditMenuBar();
1773 if (originalSource != null)
1776 if (originalSource != viewport)
1779 "Implementation worry: mismatch of viewport origin for redo");
1781 originalSource.updateHiddenColumns();
1782 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1784 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1785 // viewport.getColumnSelection()
1786 // .getHiddenColumns().size() > 0);
1787 originalSource.firePropertyChange("alignment", null,
1788 originalSource.getAlignment().getSequences());
1792 AlignmentViewport getOriginatingSource(CommandI command)
1794 AlignmentViewport originalSource = null;
1795 // For sequence removal and addition, we need to fire
1796 // the property change event FROM the viewport where the
1797 // original alignment was altered
1798 AlignmentI al = null;
1799 if (command instanceof EditCommand)
1801 EditCommand editCommand = (EditCommand) command;
1802 al = editCommand.getAlignment();
1803 List<Component> comps = PaintRefresher.components
1804 .get(viewport.getSequenceSetId());
1806 for (Component comp : comps)
1808 if (comp instanceof AlignmentPanel)
1810 if (al == ((AlignmentPanel) comp).av.getAlignment())
1812 originalSource = ((AlignmentPanel) comp).av;
1819 if (originalSource == null)
1821 // The original view is closed, we must validate
1822 // the current view against the closed view first
1825 PaintRefresher.validateSequences(al, viewport.getAlignment());
1828 originalSource = viewport;
1831 return originalSource;
1835 * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
1836 * or the sequence under cursor in keyboard mode
1841 public void moveSelectedSequences(boolean up)
1843 SequenceGroup sg = viewport.getSelectionGroup();
1847 if (viewport.cursorMode)
1849 sg = new SequenceGroup();
1850 sg.addSequence(viewport.getAlignment().getSequenceAt(
1851 alignPanel.getSeqPanel().seqCanvas.cursorY), false);
1859 if (sg.getSize() < 1)
1864 // TODO: JAL-3733 - add an event to the undo buffer for this !
1866 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1867 viewport.getHiddenRepSequences(), up);
1868 alignPanel.paintAlignment(true, false);
1871 synchronized void slideSequences(boolean right, int size)
1873 List<SequenceI> sg = new ArrayList<>();
1874 if (viewport.cursorMode)
1876 sg.add(viewport.getAlignment()
1877 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1879 else if (viewport.getSelectionGroup() != null
1880 && viewport.getSelectionGroup().getSize() != viewport
1881 .getAlignment().getHeight())
1883 sg = viewport.getSelectionGroup()
1884 .getSequences(viewport.getHiddenRepSequences());
1892 List<SequenceI> invertGroup = new ArrayList<>();
1894 for (SequenceI seq : viewport.getAlignment().getSequences())
1896 if (!sg.contains(seq))
1898 invertGroup.add(seq);
1902 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1904 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1905 for (int i = 0; i < invertGroup.size(); i++)
1907 seqs2[i] = invertGroup.get(i);
1910 SlideSequencesCommand ssc;
1913 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1914 viewport.getGapCharacter());
1918 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1919 viewport.getGapCharacter());
1922 int groupAdjustment = 0;
1923 if (ssc.getGapsInsertedBegin() && right)
1925 if (viewport.cursorMode)
1927 alignPanel.getSeqPanel().moveCursor(size, 0);
1931 groupAdjustment = size;
1934 else if (!ssc.getGapsInsertedBegin() && !right)
1936 if (viewport.cursorMode)
1938 alignPanel.getSeqPanel().moveCursor(-size, 0);
1942 groupAdjustment = -size;
1946 if (groupAdjustment != 0)
1948 viewport.getSelectionGroup().setStartRes(
1949 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1950 viewport.getSelectionGroup().setEndRes(
1951 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1955 * just extend the last slide command if compatible; but not if in
1956 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1958 boolean appendHistoryItem = false;
1959 Deque<CommandI> historyList = viewport.getHistoryList();
1960 boolean inSplitFrame = getSplitViewContainer() != null;
1961 if (!inSplitFrame && historyList != null && historyList.size() > 0
1962 && historyList.peek() instanceof SlideSequencesCommand)
1964 appendHistoryItem = ssc.appendSlideCommand(
1965 (SlideSequencesCommand) historyList.peek());
1968 if (!appendHistoryItem)
1970 addHistoryItem(ssc);
1983 protected void copy_actionPerformed()
1985 if (viewport.getSelectionGroup() == null)
1989 // TODO: preserve the ordering of displayed alignment annotation in any
1990 // internal paste (particularly sequence associated annotation)
1991 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1992 String[] omitHidden = null;
1994 if (viewport.hasHiddenColumns())
1996 omitHidden = viewport.getViewAsString(true);
1999 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2000 seqs, omitHidden, null);
2002 StringSelection ss = new StringSelection(output);
2006 jalview.gui.Desktop.internalCopy = true;
2007 // Its really worth setting the clipboard contents
2008 // to empty before setting the large StringSelection!!
2009 Toolkit.getDefaultToolkit().getSystemClipboard()
2010 .setContents(new StringSelection(""), null);
2012 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2014 } catch (OutOfMemoryError er)
2016 new OOMWarning("copying region", er);
2020 HiddenColumns hiddenColumns = null;
2021 if (viewport.hasHiddenColumns())
2023 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2024 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2026 // create new HiddenColumns object with copy of hidden regions
2027 // between startRes and endRes, offset by startRes
2028 hiddenColumns = new HiddenColumns(
2029 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
2030 hiddenCutoff, hiddenOffset);
2033 Desktop.jalviewClipboard = new Object[] { seqs,
2034 viewport.getAlignment().getDataset(), hiddenColumns };
2035 setStatus(MessageManager.formatMessage(
2036 "label.copied_sequences_to_clipboard", new Object[]
2037 { Integer.valueOf(seqs.length).toString() }));
2047 protected void pasteNew_actionPerformed(ActionEvent e)
2059 protected void pasteThis_actionPerformed(ActionEvent e)
2065 * Paste contents of Jalview clipboard
2067 * @param newAlignment
2068 * true to paste to a new alignment, otherwise add to this.
2070 void paste(boolean newAlignment)
2072 boolean externalPaste = true;
2075 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2076 Transferable contents = c.getContents(this);
2078 if (contents == null)
2087 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2088 if (str.length() < 1)
2093 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2095 } catch (OutOfMemoryError er)
2097 new OOMWarning("Out of memory pasting sequences!!", er);
2101 SequenceI[] sequences;
2102 boolean annotationAdded = false;
2103 AlignmentI alignment = null;
2105 if (Desktop.jalviewClipboard != null)
2107 // The clipboard was filled from within Jalview, we must use the
2109 // And dataset from the copied alignment
2110 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2111 // be doubly sure that we create *new* sequence objects.
2112 sequences = new SequenceI[newseq.length];
2113 for (int i = 0; i < newseq.length; i++)
2115 sequences[i] = new Sequence(newseq[i]);
2117 alignment = new Alignment(sequences);
2118 externalPaste = false;
2122 // parse the clipboard as an alignment.
2123 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2125 sequences = alignment.getSequencesArray();
2129 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2135 if (Desktop.jalviewClipboard != null)
2137 // dataset is inherited
2138 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2142 // new dataset is constructed
2143 alignment.setDataset(null);
2145 alwidth = alignment.getWidth() + 1;
2149 AlignmentI pastedal = alignment; // preserve pasted alignment object
2150 // Add pasted sequences and dataset into existing alignment.
2151 alignment = viewport.getAlignment();
2152 alwidth = alignment.getWidth() + 1;
2153 // decide if we need to import sequences from an existing dataset
2154 boolean importDs = Desktop.jalviewClipboard != null
2155 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2156 // importDs==true instructs us to copy over new dataset sequences from
2157 // an existing alignment
2158 Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
2160 // minimum dataset set
2162 for (int i = 0; i < sequences.length; i++)
2166 newDs.addElement(null);
2168 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2170 if (importDs && ds != null)
2172 if (!newDs.contains(ds))
2174 newDs.setElementAt(ds, i);
2175 ds = new Sequence(ds);
2176 // update with new dataset sequence
2177 sequences[i].setDatasetSequence(ds);
2181 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2186 // copy and derive new dataset sequence
2187 sequences[i] = sequences[i].deriveSequence();
2188 alignment.getDataset()
2189 .addSequence(sequences[i].getDatasetSequence());
2190 // TODO: avoid creation of duplicate dataset sequences with a
2191 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2193 alignment.addSequence(sequences[i]); // merges dataset
2197 newDs.clear(); // tidy up
2199 if (alignment.getAlignmentAnnotation() != null)
2201 for (AlignmentAnnotation alan : alignment
2202 .getAlignmentAnnotation())
2204 if (alan.graphGroup > fgroup)
2206 fgroup = alan.graphGroup;
2210 if (pastedal.getAlignmentAnnotation() != null)
2212 // Add any annotation attached to alignment.
2213 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2214 for (int i = 0; i < alann.length; i++)
2216 annotationAdded = true;
2217 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2219 AlignmentAnnotation newann = new AlignmentAnnotation(
2221 if (newann.graphGroup > -1)
2223 if (newGraphGroups.size() <= newann.graphGroup
2224 || newGraphGroups.get(newann.graphGroup) == null)
2226 for (int q = newGraphGroups
2227 .size(); q <= newann.graphGroup; q++)
2229 newGraphGroups.add(q, null);
2231 newGraphGroups.set(newann.graphGroup,
2232 Integer.valueOf(++fgroup));
2234 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2238 newann.padAnnotation(alwidth);
2239 alignment.addAnnotation(newann);
2249 addHistoryItem(new EditCommand(
2250 MessageManager.getString("label.add_sequences"),
2251 Action.PASTE, sequences, 0, alignment.getWidth(),
2254 // Add any annotations attached to sequences
2255 for (int i = 0; i < sequences.length; i++)
2257 if (sequences[i].getAnnotation() != null)
2259 AlignmentAnnotation newann;
2260 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2262 annotationAdded = true;
2263 newann = sequences[i].getAnnotation()[a];
2264 newann.adjustForAlignment();
2265 newann.padAnnotation(alwidth);
2266 if (newann.graphGroup > -1)
2268 if (newann.graphGroup > -1)
2270 if (newGraphGroups.size() <= newann.graphGroup
2271 || newGraphGroups.get(newann.graphGroup) == null)
2273 for (int q = newGraphGroups
2274 .size(); q <= newann.graphGroup; q++)
2276 newGraphGroups.add(q, null);
2278 newGraphGroups.set(newann.graphGroup,
2279 Integer.valueOf(++fgroup));
2281 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2285 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2289 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2297 // propagate alignment changed.
2298 viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
2299 if (annotationAdded)
2301 // Duplicate sequence annotation in all views.
2302 AlignmentI[] alview = this.getViewAlignments();
2303 for (int i = 0; i < sequences.length; i++)
2305 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2310 for (int avnum = 0; avnum < alview.length; avnum++)
2312 if (alview[avnum] != alignment)
2314 // duplicate in a view other than the one with input focus
2315 int avwidth = alview[avnum].getWidth() + 1;
2316 // this relies on sann being preserved after we
2317 // modify the sequence's annotation array for each duplication
2318 for (int a = 0; a < sann.length; a++)
2320 AlignmentAnnotation newann = new AlignmentAnnotation(
2322 sequences[i].addAlignmentAnnotation(newann);
2323 newann.padAnnotation(avwidth);
2324 alview[avnum].addAnnotation(newann); // annotation was
2325 // duplicated earlier
2326 // TODO JAL-1145 graphGroups are not updated for sequence
2327 // annotation added to several views. This may cause
2329 alview[avnum].setAnnotationIndex(newann, a);
2334 buildSortByAnnotationScoresMenu();
2336 viewport.firePropertyChange("alignment", null,
2337 alignment.getSequences());
2338 if (alignPanels != null)
2340 for (AlignmentPanel ap : alignPanels)
2342 ap.validateAnnotationDimensions(false);
2347 alignPanel.validateAnnotationDimensions(false);
2353 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2355 String newtitle = new String("Copied sequences");
2357 if (Desktop.jalviewClipboard != null
2358 && Desktop.jalviewClipboard[2] != null)
2360 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2361 af.viewport.setHiddenColumns(hc);
2364 // >>>This is a fix for the moment, until a better solution is
2366 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2367 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2368 .getFeatureRenderer());
2370 // TODO: maintain provenance of an alignment, rather than just make the
2371 // title a concatenation of operations.
2374 if (title.startsWith("Copied sequences"))
2380 newtitle = newtitle.concat("- from " + title);
2385 newtitle = new String("Pasted sequences");
2388 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2393 } catch (Exception ex)
2395 ex.printStackTrace();
2396 System.out.println("Exception whilst pasting: " + ex);
2397 // could be anything being pasted in here
2403 protected void expand_newalign(ActionEvent e)
2407 AlignmentI alignment = AlignmentUtils
2408 .expandContext(getViewport().getAlignment(), -1);
2409 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2411 String newtitle = new String("Flanking alignment");
2413 if (Desktop.jalviewClipboard != null
2414 && Desktop.jalviewClipboard[2] != null)
2416 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2417 af.viewport.setHiddenColumns(hc);
2420 // >>>This is a fix for the moment, until a better solution is
2422 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2423 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2424 .getFeatureRenderer());
2426 // TODO: maintain provenance of an alignment, rather than just make the
2427 // title a concatenation of operations.
2429 if (title.startsWith("Copied sequences"))
2435 newtitle = newtitle.concat("- from " + title);
2439 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2441 } catch (Exception ex)
2443 ex.printStackTrace();
2444 System.out.println("Exception whilst pasting: " + ex);
2445 // could be anything being pasted in here
2446 } catch (OutOfMemoryError oom)
2448 new OOMWarning("Viewing flanking region of alignment", oom);
2453 * Action Cut (delete and copy) the selected region
2456 protected void cut_actionPerformed()
2458 copy_actionPerformed();
2459 delete_actionPerformed();
2463 * Performs menu option to Delete the currently selected region
2466 protected void delete_actionPerformed()
2469 SequenceGroup sg = viewport.getSelectionGroup();
2475 Runnable okAction = new Runnable()
2480 SequenceI[] cut = sg.getSequences()
2481 .toArray(new SequenceI[sg.getSize()]);
2483 addHistoryItem(new EditCommand(
2484 MessageManager.getString("label.cut_sequences"), Action.CUT,
2485 cut, sg.getStartRes(),
2486 sg.getEndRes() - sg.getStartRes() + 1,
2487 viewport.getAlignment()));
2489 viewport.setSelectionGroup(null);
2490 viewport.sendSelection();
2491 viewport.getAlignment().deleteGroup(sg);
2493 viewport.firePropertyChange("alignment", null,
2494 viewport.getAlignment().getSequences());
2495 if (viewport.getAlignment().getHeight() < 1)
2499 AlignFrame.this.setClosed(true);
2500 } catch (Exception ex)
2508 * If the cut affects all sequences, prompt for confirmation
2510 boolean wholeHeight = sg.getSize() == viewport.getAlignment()
2512 boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2513 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2514 if (wholeHeight && wholeWidth)
2516 JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2517 dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2518 Object[] options = new Object[] {
2519 MessageManager.getString("action.ok"),
2520 MessageManager.getString("action.cancel") };
2521 dialog.showDialog(MessageManager.getString("warn.delete_all"),
2522 MessageManager.getString("label.delete_all"),
2523 JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2524 options, options[0]);
2539 protected void deleteGroups_actionPerformed(ActionEvent e)
2541 if (avc.deleteGroups())
2543 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2544 alignPanel.updateAnnotation();
2545 alignPanel.paintAlignment(true, true);
2556 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2558 SequenceGroup sg = new SequenceGroup(
2559 viewport.getAlignment().getSequences());
2561 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2562 viewport.setSelectionGroup(sg);
2563 viewport.isSelectionGroupChanged(true);
2564 viewport.sendSelection();
2565 // JAL-2034 - should delegate to
2566 // alignPanel to decide if overview needs
2568 alignPanel.paintAlignment(false, false);
2569 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2579 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2581 if (viewport.cursorMode)
2583 alignPanel.getSeqPanel().keyboardNo1 = null;
2584 alignPanel.getSeqPanel().keyboardNo2 = null;
2586 viewport.setSelectionGroup(null);
2587 viewport.getColumnSelection().clear();
2588 viewport.setSearchResults(null);
2589 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2590 // JAL-2034 - should delegate to
2591 // alignPanel to decide if overview needs
2593 alignPanel.paintAlignment(false, false);
2594 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2595 viewport.sendSelection();
2605 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2607 SequenceGroup sg = viewport.getSelectionGroup();
2611 selectAllSequenceMenuItem_actionPerformed(null);
2616 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2618 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2620 // JAL-2034 - should delegate to
2621 // alignPanel to decide if overview needs
2624 alignPanel.paintAlignment(true, false);
2625 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2626 viewport.sendSelection();
2630 public void invertColSel_actionPerformed(ActionEvent e)
2632 viewport.invertColumnSelection();
2633 alignPanel.paintAlignment(true, false);
2634 viewport.sendSelection();
2644 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2646 trimAlignment(true);
2656 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2658 trimAlignment(false);
2661 void trimAlignment(boolean trimLeft)
2663 ColumnSelection colSel = viewport.getColumnSelection();
2666 if (!colSel.isEmpty())
2670 column = colSel.getMin();
2674 column = colSel.getMax();
2678 if (viewport.getSelectionGroup() != null)
2680 seqs = viewport.getSelectionGroup()
2681 .getSequencesAsArray(viewport.getHiddenRepSequences());
2685 seqs = viewport.getAlignment().getSequencesArray();
2688 TrimRegionCommand trimRegion;
2691 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2692 column, viewport.getAlignment());
2693 viewport.getRanges().setStartRes(0);
2697 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2698 column, viewport.getAlignment());
2701 setStatus(MessageManager.formatMessage("label.removed_columns",
2703 { Integer.valueOf(trimRegion.getSize()).toString() }));
2705 addHistoryItem(trimRegion);
2707 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2709 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2710 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2712 viewport.getAlignment().deleteGroup(sg);
2716 viewport.firePropertyChange("alignment", null,
2717 viewport.getAlignment().getSequences());
2728 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2730 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2733 if (viewport.getSelectionGroup() != null)
2735 seqs = viewport.getSelectionGroup()
2736 .getSequencesAsArray(viewport.getHiddenRepSequences());
2737 start = viewport.getSelectionGroup().getStartRes();
2738 end = viewport.getSelectionGroup().getEndRes();
2742 seqs = viewport.getAlignment().getSequencesArray();
2745 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2746 "Remove Gapped Columns", seqs, start, end,
2747 viewport.getAlignment());
2749 addHistoryItem(removeGapCols);
2751 setStatus(MessageManager.formatMessage("label.removed_empty_columns",
2753 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2755 // This is to maintain viewport position on first residue
2756 // of first sequence
2757 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2758 ViewportRanges ranges = viewport.getRanges();
2759 int startRes = seq.findPosition(ranges.getStartRes());
2760 // ShiftList shifts;
2761 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2762 // edit.alColumnChanges=shifts.getInverse();
2763 // if (viewport.hasHiddenColumns)
2764 // viewport.getColumnSelection().compensateForEdits(shifts);
2765 ranges.setStartRes(seq.findIndex(startRes) - 1);
2766 viewport.firePropertyChange("alignment", null,
2767 viewport.getAlignment().getSequences());
2778 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2780 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2783 if (viewport.getSelectionGroup() != null)
2785 seqs = viewport.getSelectionGroup()
2786 .getSequencesAsArray(viewport.getHiddenRepSequences());
2787 start = viewport.getSelectionGroup().getStartRes();
2788 end = viewport.getSelectionGroup().getEndRes();
2792 seqs = viewport.getAlignment().getSequencesArray();
2795 // This is to maintain viewport position on first residue
2796 // of first sequence
2797 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2798 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2800 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2801 viewport.getAlignment()));
2803 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2805 viewport.firePropertyChange("alignment", null,
2806 viewport.getAlignment().getSequences());
2817 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2819 viewport.setPadGaps(padGapsMenuitem.isSelected());
2820 viewport.firePropertyChange("alignment", null,
2821 viewport.getAlignment().getSequences());
2825 * Opens a Finder dialog
2830 public void findMenuItem_actionPerformed(ActionEvent e)
2832 new Finder(alignPanel);
2836 * Create a new view of the current alignment.
2839 public void newView_actionPerformed(ActionEvent e)
2841 newView(null, true);
2845 * Creates and shows a new view of the current alignment.
2848 * title of newly created view; if null, one will be generated
2849 * @param copyAnnotation
2850 * if true then duplicate all annnotation, groups and settings
2851 * @return new alignment panel, already displayed.
2853 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2856 * Create a new AlignmentPanel (with its own, new Viewport)
2858 AlignmentPanel newap = new jalview.project.Jalview2XML()
2859 .copyAlignPanel(alignPanel);
2860 if (!copyAnnotation)
2863 * remove all groups and annotation except for the automatic stuff
2865 newap.av.getAlignment().deleteAllGroups();
2866 newap.av.getAlignment().deleteAllAnnotations(false);
2869 newap.av.setGatherViewsHere(false);
2871 if (viewport.getViewName() == null)
2873 viewport.setViewName(
2874 MessageManager.getString("label.view_name_original"));
2878 * Views share the same edits undo and redo stacks
2880 newap.av.setHistoryList(viewport.getHistoryList());
2881 newap.av.setRedoList(viewport.getRedoList());
2884 * copy any visualisation settings that are not saved in the project
2886 newap.av.setColourAppliesToAllGroups(
2887 viewport.getColourAppliesToAllGroups());
2890 * Views share the same mappings; need to deregister any new mappings
2891 * created by copyAlignPanel, and register the new reference to the shared
2894 newap.av.replaceMappings(viewport.getAlignment());
2897 * start up cDNA consensus (if applicable) now mappings are in place
2899 if (newap.av.initComplementConsensus())
2901 newap.refresh(true); // adjust layout of annotations
2904 newap.av.setViewName(getNewViewName(viewTitle));
2906 addAlignmentPanel(newap, true);
2907 newap.alignmentChanged();
2909 if (alignPanels.size() == 2)
2911 viewport.setGatherViewsHere(true);
2913 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2918 * Make a new name for the view, ensuring it is unique within the current
2919 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2920 * these now use viewId. Unique view names are still desirable for usability.)
2925 protected String getNewViewName(String viewTitle)
2927 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2928 boolean addFirstIndex = false;
2929 if (viewTitle == null || viewTitle.trim().length() == 0)
2931 viewTitle = MessageManager.getString("action.view");
2932 addFirstIndex = true;
2936 index = 1;// we count from 1 if given a specific name
2938 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2940 List<Component> comps = PaintRefresher.components
2941 .get(viewport.getSequenceSetId());
2943 List<String> existingNames = getExistingViewNames(comps);
2945 while (existingNames.contains(newViewName))
2947 newViewName = viewTitle + " " + (++index);
2953 * Returns a list of distinct view names found in the given list of
2954 * components. View names are held on the viewport of an AlignmentPanel.
2959 protected List<String> getExistingViewNames(List<Component> comps)
2961 List<String> existingNames = new ArrayList<>();
2962 for (Component comp : comps)
2964 if (comp instanceof AlignmentPanel)
2966 AlignmentPanel ap = (AlignmentPanel) comp;
2967 if (!existingNames.contains(ap.av.getViewName()))
2969 existingNames.add(ap.av.getViewName());
2973 return existingNames;
2977 * Explode tabbed views into separate windows.
2980 public void expandViews_actionPerformed(ActionEvent e)
2982 Desktop.explodeViews(this);
2986 * Gather views in separate windows back into a tabbed presentation.
2989 public void gatherViews_actionPerformed(ActionEvent e)
2991 Desktop.instance.gatherViews(this);
3001 public void font_actionPerformed(ActionEvent e)
3003 new FontChooser(alignPanel);
3013 protected void seqLimit_actionPerformed(ActionEvent e)
3015 viewport.setShowJVSuffix(seqLimits.isSelected());
3017 alignPanel.getIdPanel().getIdCanvas()
3018 .setPreferredSize(alignPanel.calculateIdWidth());
3019 alignPanel.paintAlignment(true, false);
3023 public void idRightAlign_actionPerformed(ActionEvent e)
3025 viewport.setRightAlignIds(idRightAlign.isSelected());
3026 alignPanel.paintAlignment(false, false);
3030 public void centreColumnLabels_actionPerformed(ActionEvent e)
3032 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3033 alignPanel.paintAlignment(false, false);
3039 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3042 protected void followHighlight_actionPerformed()
3045 * Set the 'follow' flag on the Viewport (and scroll to position if now
3048 final boolean state = this.followHighlightMenuItem.getState();
3049 viewport.setFollowHighlight(state);
3052 alignPanel.scrollToPosition(viewport.getSearchResults());
3063 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3065 viewport.setColourText(colourTextMenuItem.isSelected());
3066 alignPanel.paintAlignment(false, false);
3076 public void wrapMenuItem_actionPerformed(ActionEvent e)
3078 scaleAbove.setVisible(wrapMenuItem.isSelected());
3079 scaleLeft.setVisible(wrapMenuItem.isSelected());
3080 scaleRight.setVisible(wrapMenuItem.isSelected());
3081 viewport.setWrapAlignment(wrapMenuItem.isSelected());
3082 alignPanel.updateLayout();
3086 public void showAllSeqs_actionPerformed(ActionEvent e)
3088 viewport.showAllHiddenSeqs();
3092 public void showAllColumns_actionPerformed(ActionEvent e)
3094 viewport.showAllHiddenColumns();
3095 alignPanel.paintAlignment(true, true);
3096 viewport.sendSelection();
3100 public void hideSelSequences_actionPerformed(ActionEvent e)
3102 viewport.hideAllSelectedSeqs();
3106 * called by key handler and the hide all/show all menu items
3111 protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3114 boolean hide = false;
3115 SequenceGroup sg = viewport.getSelectionGroup();
3116 if (!toggleSeqs && !toggleCols)
3118 // Hide everything by the current selection - this is a hack - we do the
3119 // invert and then hide
3120 // first check that there will be visible columns after the invert.
3121 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3122 && sg.getStartRes() <= sg.getEndRes()))
3124 // now invert the sequence set, if required - empty selection implies
3125 // that no hiding is required.
3128 invertSequenceMenuItem_actionPerformed(null);
3129 sg = viewport.getSelectionGroup();
3133 viewport.expandColSelection(sg, true);
3134 // finally invert the column selection and get the new sequence
3136 invertColSel_actionPerformed(null);
3143 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3145 hideSelSequences_actionPerformed(null);
3148 else if (!(toggleCols && viewport.hasSelectedColumns()))
3150 showAllSeqs_actionPerformed(null);
3156 if (viewport.hasSelectedColumns())
3158 hideSelColumns_actionPerformed(null);
3161 viewport.setSelectionGroup(sg);
3166 showAllColumns_actionPerformed(null);
3175 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3176 * event.ActionEvent)
3179 public void hideAllButSelection_actionPerformed(ActionEvent e)
3181 toggleHiddenRegions(false, false);
3182 viewport.sendSelection();
3189 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3193 public void hideAllSelection_actionPerformed(ActionEvent e)
3195 SequenceGroup sg = viewport.getSelectionGroup();
3196 viewport.expandColSelection(sg, false);
3197 viewport.hideAllSelectedSeqs();
3198 viewport.hideSelectedColumns();
3199 alignPanel.updateLayout();
3200 alignPanel.paintAlignment(true, true);
3201 viewport.sendSelection();
3208 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3212 public void showAllhidden_actionPerformed(ActionEvent e)
3214 viewport.showAllHiddenColumns();
3215 viewport.showAllHiddenSeqs();
3216 alignPanel.paintAlignment(true, true);
3217 viewport.sendSelection();
3221 public void hideSelColumns_actionPerformed(ActionEvent e)
3223 viewport.hideSelectedColumns();
3224 alignPanel.updateLayout();
3225 alignPanel.paintAlignment(true, true);
3226 viewport.sendSelection();
3230 public void hiddenMarkers_actionPerformed(ActionEvent e)
3232 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3243 protected void scaleAbove_actionPerformed(ActionEvent e)
3245 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3246 alignPanel.updateLayout();
3247 alignPanel.paintAlignment(true, false);
3257 protected void scaleLeft_actionPerformed(ActionEvent e)
3259 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3260 alignPanel.updateLayout();
3261 alignPanel.paintAlignment(true, false);
3271 protected void scaleRight_actionPerformed(ActionEvent e)
3273 viewport.setScaleRightWrapped(scaleRight.isSelected());
3274 alignPanel.updateLayout();
3275 alignPanel.paintAlignment(true, false);
3285 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3287 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3288 alignPanel.paintAlignment(false, false);
3298 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3300 viewport.setShowText(viewTextMenuItem.isSelected());
3301 alignPanel.paintAlignment(false, false);
3311 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3313 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3314 alignPanel.paintAlignment(false, false);
3317 public FeatureSettings featureSettings;
3320 public FeatureSettingsControllerI getFeatureSettingsUI()
3322 return featureSettings;
3326 public void featureSettings_actionPerformed(ActionEvent e)
3328 showFeatureSettingsUI();
3332 public FeatureSettingsControllerI showFeatureSettingsUI()
3334 if (featureSettings != null)
3336 featureSettings.closeOldSettings();
3337 featureSettings = null;
3339 if (!showSeqFeatures.isSelected())
3341 // make sure features are actually displayed
3342 showSeqFeatures.setSelected(true);
3343 showSeqFeatures_actionPerformed(null);
3345 featureSettings = new FeatureSettings(this);
3346 return featureSettings;
3350 * Set or clear 'Show Sequence Features'
3356 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3358 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3359 alignPanel.paintAlignment(true, true);
3363 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3364 * the annotations panel as a whole.
3366 * The options to show/hide all annotations should be enabled when the panel
3367 * is shown, and disabled when the panel is hidden.
3372 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3374 final boolean setVisible = annotationPanelMenuItem.isSelected();
3375 viewport.setShowAnnotation(setVisible);
3376 this.showAllSeqAnnotations.setEnabled(setVisible);
3377 this.hideAllSeqAnnotations.setEnabled(setVisible);
3378 this.showAllAlAnnotations.setEnabled(setVisible);
3379 this.hideAllAlAnnotations.setEnabled(setVisible);
3380 alignPanel.updateLayout();
3384 public void alignmentProperties()
3387 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3390 String content = MessageManager.formatMessage("label.html_content",
3392 { contents.toString() });
3395 if (Platform.isJS())
3397 JLabel textLabel = new JLabel();
3398 textLabel.setText(content);
3399 textLabel.setBackground(Color.WHITE);
3401 pane = new JPanel(new BorderLayout());
3402 ((JPanel) pane).setOpaque(true);
3403 pane.setBackground(Color.WHITE);
3404 ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3413 JEditorPane editPane = new JEditorPane("text/html", "");
3414 editPane.setEditable(false);
3415 editPane.setText(content);
3419 JInternalFrame frame = new JInternalFrame();
3421 frame.getContentPane().add(new JScrollPane(pane));
3423 Desktop.addInternalFrame(frame, MessageManager
3424 .formatMessage("label.alignment_properties", new Object[]
3425 { getTitle() }), 500, 400);
3435 public void overviewMenuItem_actionPerformed(ActionEvent e)
3437 if (alignPanel.overviewPanel != null)
3442 JInternalFrame frame = new JInternalFrame();
3443 final OverviewPanel overview = new OverviewPanel(alignPanel);
3444 frame.setContentPane(overview);
3445 Desktop.addInternalFrame(frame, MessageManager
3446 .formatMessage("label.overview_params", new Object[]
3447 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3450 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3451 frame.addInternalFrameListener(
3452 new javax.swing.event.InternalFrameAdapter()
3455 public void internalFrameClosed(
3456 javax.swing.event.InternalFrameEvent evt)
3459 alignPanel.setOverviewPanel(null);
3462 if (getKeyListeners().length > 0)
3464 frame.addKeyListener(getKeyListeners()[0]);
3467 alignPanel.setOverviewPanel(overview);
3471 public void textColour_actionPerformed()
3473 new TextColourChooser().chooseColour(alignPanel, null);
3477 * public void covariationColour_actionPerformed() {
3479 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3483 public void annotationColour_actionPerformed()
3485 new AnnotationColourChooser(viewport, alignPanel);
3489 public void annotationColumn_actionPerformed(ActionEvent e)
3491 new AnnotationColumnChooser(viewport, alignPanel);
3495 * Action on the user checking or unchecking the option to apply the selected
3496 * colour scheme to all groups. If unchecked, groups may have their own
3497 * independent colour schemes.
3502 public void applyToAllGroups_actionPerformed(boolean selected)
3504 viewport.setColourAppliesToAllGroups(selected);
3508 * Action on user selecting a colour from the colour menu
3511 * the name (not the menu item label!) of the colour scheme
3514 public void changeColour_actionPerformed(String name)
3517 * 'User Defined' opens a panel to configure or load a
3518 * user-defined colour scheme
3520 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3522 new UserDefinedColours(alignPanel);
3527 * otherwise set the chosen colour scheme (or null for 'None')
3529 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3530 viewport, viewport.getAlignment(),
3531 viewport.getHiddenRepSequences());
3536 * Actions on setting or changing the alignment colour scheme
3541 public void changeColour(ColourSchemeI cs)
3543 // TODO: pull up to controller method
3544 ColourMenuHelper.setColourSelected(colourMenu, cs);
3546 viewport.setGlobalColourScheme(cs);
3548 alignPanel.paintAlignment(true, true);
3552 * Show the PID threshold slider panel
3555 protected void modifyPID_actionPerformed()
3557 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3558 alignPanel.getViewName());
3559 SliderPanel.showPIDSlider();
3563 * Show the Conservation slider panel
3566 protected void modifyConservation_actionPerformed()
3568 SliderPanel.setConservationSlider(alignPanel,
3569 viewport.getResidueShading(), alignPanel.getViewName());
3570 SliderPanel.showConservationSlider();
3574 * Action on selecting or deselecting (Colour) By Conservation
3577 public void conservationMenuItem_actionPerformed(boolean selected)
3579 modifyConservation.setEnabled(selected);
3580 viewport.setConservationSelected(selected);
3581 viewport.getResidueShading().setConservationApplied(selected);
3583 changeColour(viewport.getGlobalColourScheme());
3586 modifyConservation_actionPerformed();
3590 SliderPanel.hideConservationSlider();
3595 * Action on selecting or deselecting (Colour) Above PID Threshold
3598 public void abovePIDThreshold_actionPerformed(boolean selected)
3600 modifyPID.setEnabled(selected);
3601 viewport.setAbovePIDThreshold(selected);
3604 viewport.getResidueShading().setThreshold(0,
3605 viewport.isIgnoreGapsConsensus());
3608 changeColour(viewport.getGlobalColourScheme());
3611 modifyPID_actionPerformed();
3615 SliderPanel.hidePIDSlider();
3626 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3628 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3629 AlignmentSorter.sortByPID(viewport.getAlignment(),
3630 viewport.getAlignment().getSequenceAt(0));
3631 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3632 viewport.getAlignment()));
3633 alignPanel.paintAlignment(true, false);
3643 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3645 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3646 AlignmentSorter.sortByID(viewport.getAlignment());
3648 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3649 alignPanel.paintAlignment(true, false);
3659 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3661 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3662 AlignmentSorter.sortByLength(viewport.getAlignment());
3663 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3664 viewport.getAlignment()));
3665 alignPanel.paintAlignment(true, false);
3675 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3677 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3678 AlignmentSorter.sortByGroup(viewport.getAlignment());
3679 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3680 viewport.getAlignment()));
3682 alignPanel.paintAlignment(true, false);
3692 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3694 new RedundancyPanel(alignPanel, this);
3704 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3706 if ((viewport.getSelectionGroup() == null)
3707 || (viewport.getSelectionGroup().getSize() < 2))
3709 JvOptionPane.showInternalMessageDialog(this,
3710 MessageManager.getString(
3711 "label.you_must_select_least_two_sequences"),
3712 MessageManager.getString("label.invalid_selection"),
3713 JvOptionPane.WARNING_MESSAGE);
3717 JInternalFrame frame = new JInternalFrame();
3718 frame.setContentPane(new PairwiseAlignPanel(viewport));
3719 Desktop.addInternalFrame(frame,
3720 MessageManager.getString("action.pairwise_alignment"), 600,
3726 public void autoCalculate_actionPerformed(ActionEvent e)
3728 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3729 if (viewport.autoCalculateConsensus)
3731 viewport.firePropertyChange("alignment", null,
3732 viewport.getAlignment().getSequences());
3737 public void sortByTreeOption_actionPerformed(ActionEvent e)
3739 viewport.sortByTree = sortByTree.isSelected();
3743 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3745 viewport.followSelection = listenToViewSelections.isSelected();
3749 * Constructs a tree panel and adds it to the desktop
3752 * tree type (NJ or AV)
3754 * name of score model used to compute the tree
3756 * parameters for the distance or similarity calculation
3758 void newTreePanel(String type, String modelName,
3759 SimilarityParamsI options)
3761 String frameTitle = "";
3764 boolean onSelection = false;
3765 if (viewport.getSelectionGroup() != null
3766 && viewport.getSelectionGroup().getSize() > 0)
3768 SequenceGroup sg = viewport.getSelectionGroup();
3770 /* Decide if the selection is a column region */
3771 for (SequenceI _s : sg.getSequences())
3773 if (_s.getLength() < sg.getEndRes())
3775 JvOptionPane.showMessageDialog(Desktop.desktop,
3776 MessageManager.getString(
3777 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3778 MessageManager.getString(
3779 "label.sequences_selection_not_aligned"),
3780 JvOptionPane.WARNING_MESSAGE);
3789 if (viewport.getAlignment().getHeight() < 2)
3795 tp = new TreePanel(alignPanel, type, modelName, options);
3796 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3798 frameTitle += " from ";
3800 if (viewport.getViewName() != null)
3802 frameTitle += viewport.getViewName() + " of ";
3805 frameTitle += this.title;
3807 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3818 public void addSortByOrderMenuItem(String title,
3819 final AlignmentOrder order)
3821 final JMenuItem item = new JMenuItem(MessageManager
3822 .formatMessage("action.by_title_param", new Object[]
3825 item.addActionListener(new java.awt.event.ActionListener()
3828 public void actionPerformed(ActionEvent e)
3830 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3832 // TODO: JBPNote - have to map order entries to curent SequenceI
3834 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3836 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3837 viewport.getAlignment()));
3839 alignPanel.paintAlignment(true, false);
3845 * Add a new sort by annotation score menu item
3848 * the menu to add the option to
3850 * the label used to retrieve scores for each sequence on the
3853 public void addSortByAnnotScoreMenuItem(JMenu sort,
3854 final String scoreLabel)
3856 final JMenuItem item = new JMenuItem(scoreLabel);
3858 item.addActionListener(new java.awt.event.ActionListener()
3861 public void actionPerformed(ActionEvent e)
3863 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3864 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3865 viewport.getAlignment());// ,viewport.getSelectionGroup());
3866 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3867 viewport.getAlignment()));
3868 alignPanel.paintAlignment(true, false);
3874 * last hash for alignment's annotation array - used to minimise cost of
3877 protected int _annotationScoreVectorHash;
3880 * search the alignment and rebuild the sort by annotation score submenu the
3881 * last alignment annotation vector hash is stored to minimize cost of
3882 * rebuilding in subsequence calls.
3886 public void buildSortByAnnotationScoresMenu()
3888 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3893 if (viewport.getAlignment().getAlignmentAnnotation()
3894 .hashCode() != _annotationScoreVectorHash)
3896 sortByAnnotScore.removeAll();
3897 // almost certainly a quicker way to do this - but we keep it simple
3898 Hashtable<String, String> scoreSorts = new Hashtable<>();
3899 AlignmentAnnotation aann[];
3900 for (SequenceI sqa : viewport.getAlignment().getSequences())
3902 aann = sqa.getAnnotation();
3903 for (int i = 0; aann != null && i < aann.length; i++)
3905 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3907 scoreSorts.put(aann[i].label, aann[i].label);
3911 Enumeration<String> labels = scoreSorts.keys();
3912 while (labels.hasMoreElements())
3914 addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement());
3916 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3919 _annotationScoreVectorHash = viewport.getAlignment()
3920 .getAlignmentAnnotation().hashCode();
3925 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3926 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3927 * call. Listeners are added to remove the menu item when the treePanel is
3928 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3932 public void buildTreeSortMenu()
3934 sortByTreeMenu.removeAll();
3936 List<Component> comps = PaintRefresher.components
3937 .get(viewport.getSequenceSetId());
3938 List<TreePanel> treePanels = new ArrayList<>();
3939 for (Component comp : comps)
3941 if (comp instanceof TreePanel)
3943 treePanels.add((TreePanel) comp);
3947 if (treePanels.size() < 1)
3949 sortByTreeMenu.setVisible(false);
3953 sortByTreeMenu.setVisible(true);
3955 for (final TreePanel tp : treePanels)
3957 final JMenuItem item = new JMenuItem(tp.getTitle());
3958 item.addActionListener(new java.awt.event.ActionListener()
3961 public void actionPerformed(ActionEvent e)
3963 tp.sortByTree_actionPerformed();
3964 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3969 sortByTreeMenu.add(item);
3973 public boolean sortBy(AlignmentOrder alorder, String undoname)
3975 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3976 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3977 if (undoname != null)
3979 addHistoryItem(new OrderCommand(undoname, oldOrder,
3980 viewport.getAlignment()));
3982 alignPanel.paintAlignment(true, false);
3987 * Work out whether the whole set of sequences or just the selected set will
3988 * be submitted for multiple alignment.
3991 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3993 // Now, check we have enough sequences
3994 AlignmentView msa = null;
3996 if ((viewport.getSelectionGroup() != null)
3997 && (viewport.getSelectionGroup().getSize() > 1))
3999 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4000 // some common interface!
4002 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4003 * SequenceI[sz = seqs.getSize(false)];
4005 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4006 * seqs.getSequenceAt(i); }
4008 msa = viewport.getAlignmentView(true);
4010 else if (viewport.getSelectionGroup() != null
4011 && viewport.getSelectionGroup().getSize() == 1)
4013 int option = JvOptionPane.showConfirmDialog(this,
4014 MessageManager.getString("warn.oneseq_msainput_selection"),
4015 MessageManager.getString("label.invalid_selection"),
4016 JvOptionPane.OK_CANCEL_OPTION);
4017 if (option == JvOptionPane.OK_OPTION)
4019 msa = viewport.getAlignmentView(false);
4024 msa = viewport.getAlignmentView(false);
4030 * Decides what is submitted to a secondary structure prediction service: the
4031 * first sequence in the alignment, or in the current selection, or, if the
4032 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4033 * region or the whole alignment. (where the first sequence in the set is the
4034 * one that the prediction will be for).
4036 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4038 AlignmentView seqs = null;
4040 if ((viewport.getSelectionGroup() != null)
4041 && (viewport.getSelectionGroup().getSize() > 0))
4043 seqs = viewport.getAlignmentView(true);
4047 seqs = viewport.getAlignmentView(false);
4049 // limit sequences - JBPNote in future - could spawn multiple prediction
4051 // TODO: viewport.getAlignment().isAligned is a global state - the local
4052 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4053 if (!viewport.getAlignment().isAligned(false))
4055 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4056 // TODO: if seqs.getSequences().length>1 then should really have warned
4070 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4072 // Pick the tree file
4073 JalviewFileChooser chooser = new JalviewFileChooser(
4074 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4075 chooser.setFileView(new JalviewFileView());
4076 chooser.setDialogTitle(
4077 MessageManager.getString("label.select_newick_like_tree_file"));
4078 chooser.setToolTipText(
4079 MessageManager.getString("label.load_tree_file"));
4081 chooser.setResponseHandler(0, new Runnable()
4086 String filePath = chooser.getSelectedFile().getPath();
4087 Cache.setProperty("LAST_DIRECTORY", filePath);
4088 NewickFile fin = null;
4091 fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4092 DataSourceType.FILE));
4093 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4094 } catch (Exception ex)
4096 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4098 .getString("label.problem_reading_tree_file"),
4099 JvOptionPane.WARNING_MESSAGE);
4100 ex.printStackTrace();
4102 if (fin != null && fin.hasWarningMessage())
4104 JvOptionPane.showMessageDialog(Desktop.desktop,
4105 fin.getWarningMessage(),
4106 MessageManager.getString(
4107 "label.possible_problem_with_tree_file"),
4108 JvOptionPane.WARNING_MESSAGE);
4112 chooser.showOpenDialog(this);
4115 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4117 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4120 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4121 int h, int x, int y)
4123 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4127 * Add a treeviewer for the tree extracted from a Newick file object to the
4128 * current alignment view
4135 * Associated alignment input data (or null)
4144 * @return TreePanel handle
4146 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4147 AlignmentView input, int w, int h, int x, int y)
4149 TreePanel tp = null;
4155 if (nf.getTree() != null)
4157 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4163 tp.setLocation(x, y);
4166 Desktop.addInternalFrame(tp, treeTitle, w, h);
4168 } catch (Exception ex)
4170 ex.printStackTrace();
4176 private boolean buildingMenu = false;
4179 * Generates menu items and listener event actions for web service clients
4182 public void BuildWebServiceMenu()
4184 while (buildingMenu)
4188 System.err.println("Waiting for building menu to finish.");
4190 } catch (Exception e)
4194 final AlignFrame me = this;
4195 buildingMenu = true;
4196 new Thread(new Runnable()
4201 final List<JMenuItem> legacyItems = new ArrayList<>();
4204 // System.err.println("Building ws menu again "
4205 // + Thread.currentThread());
4206 // TODO: add support for context dependent disabling of services based
4208 // alignment and current selection
4209 // TODO: add additional serviceHandle parameter to specify abstract
4211 // class independently of AbstractName
4212 // TODO: add in rediscovery GUI function to restart discoverer
4213 // TODO: group services by location as well as function and/or
4215 // object broker mechanism.
4216 final Vector<JMenu> wsmenu = new Vector<>();
4217 final IProgressIndicator af = me;
4220 * do not i18n these strings - they are hard-coded in class
4221 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4222 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4224 final JMenu msawsmenu = new JMenu("Alignment");
4225 final JMenu secstrmenu = new JMenu(
4226 "Secondary Structure Prediction");
4227 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4228 final JMenu analymenu = new JMenu("Analysis");
4229 final JMenu dismenu = new JMenu("Protein Disorder");
4230 // JAL-940 - only show secondary structure prediction services from
4231 // the legacy server
4232 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4234 Discoverer.services != null && (Discoverer.services.size() > 0))
4236 // TODO: refactor to allow list of AbstractName/Handler bindings to
4238 // stored or retrieved from elsewhere
4239 // No MSAWS used any more:
4240 // Vector msaws = null; // (Vector)
4241 // Discoverer.services.get("MsaWS");
4242 Vector<ServiceHandle> secstrpr = Discoverer.services
4244 if (secstrpr != null)
4246 // Add any secondary structure prediction services
4247 for (int i = 0, j = secstrpr.size(); i < j; i++)
4249 final ext.vamsas.ServiceHandle sh = secstrpr.get(i);
4250 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4251 .getServiceClient(sh);
4252 int p = secstrmenu.getItemCount();
4253 impl.attachWSMenuEntry(secstrmenu, me);
4254 int q = secstrmenu.getItemCount();
4255 for (int litm = p; litm < q; litm++)
4257 legacyItems.add(secstrmenu.getItem(litm));
4263 // Add all submenus in the order they should appear on the web
4265 wsmenu.add(msawsmenu);
4266 wsmenu.add(secstrmenu);
4267 wsmenu.add(dismenu);
4268 wsmenu.add(analymenu);
4269 // No search services yet
4270 // wsmenu.add(seqsrchmenu);
4272 javax.swing.SwingUtilities.invokeLater(new Runnable()
4279 webService.removeAll();
4280 // first, add discovered services onto the webservices menu
4281 if (wsmenu.size() > 0)
4283 for (int i = 0, j = wsmenu.size(); i < j; i++)
4285 webService.add(wsmenu.get(i));
4290 webService.add(me.webServiceNoServices);
4292 // TODO: move into separate menu builder class.
4293 boolean new_sspred = false;
4294 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4296 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4297 if (jws2servs != null)
4299 if (jws2servs.hasServices())
4301 jws2servs.attachWSMenuEntry(webService, me);
4302 for (Jws2Instance sv : jws2servs.getServices())
4304 if (sv.description.toLowerCase().contains("jpred"))
4306 for (JMenuItem jmi : legacyItems)
4308 jmi.setVisible(false);
4314 if (jws2servs.isRunning())
4316 JMenuItem tm = new JMenuItem(
4317 "Still discovering JABA Services");
4318 tm.setEnabled(false);
4323 build_urlServiceMenu(me.webService);
4324 build_fetchdbmenu(webService);
4325 for (JMenu item : wsmenu)
4327 if (item.getItemCount() == 0)
4329 item.setEnabled(false);
4333 item.setEnabled(true);
4336 } catch (Exception e)
4339 "Exception during web service menu building process.",
4344 } catch (Exception e)
4347 buildingMenu = false;
4354 * construct any groupURL type service menu entries.
4358 protected void build_urlServiceMenu(JMenu webService)
4360 // TODO: remove this code when 2.7 is released
4361 // DEBUG - alignmentView
4363 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4364 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4366 * @Override public void actionPerformed(ActionEvent e) {
4367 * jalview.datamodel.AlignmentView
4368 * .testSelectionViews(af.viewport.getAlignment(),
4369 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4371 * }); webService.add(testAlView);
4373 // TODO: refactor to RestClient discoverer and merge menu entries for
4374 // rest-style services with other types of analysis/calculation service
4375 // SHmmr test client - still being implemented.
4376 // DEBUG - alignmentView
4378 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4381 client.attachWSMenuEntry(
4382 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4388 * Searches the alignment sequences for xRefs and builds the Show
4389 * Cross-References menu (formerly called Show Products), with database
4390 * sources for which cross-references are found (protein sources for a
4391 * nucleotide alignment and vice versa)
4393 * @return true if Show Cross-references menu should be enabled
4395 public boolean canShowProducts()
4397 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4398 AlignmentI dataset = viewport.getAlignment().getDataset();
4400 showProducts.removeAll();
4401 final boolean dna = viewport.getAlignment().isNucleotide();
4403 if (seqs == null || seqs.length == 0)
4405 // nothing to see here.
4409 boolean showp = false;
4412 List<String> ptypes = new CrossRef(seqs, dataset)
4413 .findXrefSourcesForSequences(dna);
4415 for (final String source : ptypes)
4418 final AlignFrame af = this;
4419 JMenuItem xtype = new JMenuItem(source);
4420 xtype.addActionListener(new ActionListener()
4423 public void actionPerformed(ActionEvent e)
4425 showProductsFor(af.viewport.getSequenceSelection(), dna,
4429 showProducts.add(xtype);
4431 showProducts.setVisible(showp);
4432 showProducts.setEnabled(showp);
4433 } catch (Exception e)
4436 "canShowProducts threw an exception - please report to help@jalview.org",
4444 * Finds and displays cross-references for the selected sequences (protein
4445 * products for nucleotide sequences, dna coding sequences for peptides).
4448 * the sequences to show cross-references for
4450 * true if from a nucleotide alignment (so showing proteins)
4452 * the database to show cross-references for
4454 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4455 final String source)
4457 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4462 * Construct and display a new frame containing the translation of this
4463 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4466 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4468 AlignmentI al = null;
4471 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4473 al = dna.translateCdna(codeTable);
4474 } catch (Exception ex)
4476 jalview.bin.Cache.log.error(
4477 "Exception during translation. Please report this !", ex);
4478 final String msg = MessageManager.getString(
4479 "label.error_when_translating_sequences_submit_bug_report");
4480 final String errorTitle = MessageManager
4481 .getString("label.implementation_error")
4482 + MessageManager.getString("label.translation_failed");
4483 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4484 JvOptionPane.ERROR_MESSAGE);
4487 if (al == null || al.getHeight() == 0)
4489 final String msg = MessageManager.getString(
4490 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4491 final String errorTitle = MessageManager
4492 .getString("label.translation_failed");
4493 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4494 JvOptionPane.WARNING_MESSAGE);
4498 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4499 af.setFileFormat(this.currentFileFormat);
4500 final String newTitle = MessageManager
4501 .formatMessage("label.translation_of_params", new Object[]
4502 { this.getTitle(), codeTable.getId() });
4503 af.setTitle(newTitle);
4504 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4506 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4507 viewport.openSplitFrame(af, new Alignment(seqs));
4511 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4518 * Set the file format
4522 public void setFileFormat(FileFormatI format)
4524 this.currentFileFormat = format;
4528 * Try to load a features file onto the alignment.
4531 * contents or path to retrieve file or a File object
4533 * access mode of file (see jalview.io.AlignFile)
4534 * @return true if features file was parsed correctly.
4536 public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4539 return avc.parseFeaturesFile(file, sourceType,
4540 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4545 public void refreshFeatureUI(boolean enableIfNecessary)
4547 // note - currently this is only still here rather than in the controller
4548 // because of the featureSettings hard reference that is yet to be
4550 if (enableIfNecessary)
4552 viewport.setShowSequenceFeatures(true);
4553 showSeqFeatures.setSelected(true);
4559 public void dragEnter(DropTargetDragEvent evt)
4564 public void dragExit(DropTargetEvent evt)
4569 public void dragOver(DropTargetDragEvent evt)
4574 public void dropActionChanged(DropTargetDragEvent evt)
4579 public void drop(DropTargetDropEvent evt)
4581 // JAL-1552 - acceptDrop required before getTransferable call for
4582 // Java's Transferable for native dnd
4583 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4584 Transferable t = evt.getTransferable();
4586 final AlignFrame thisaf = this;
4587 final List<Object> files = new ArrayList<>();
4588 List<DataSourceType> protocols = new ArrayList<>();
4592 Desktop.transferFromDropTarget(files, protocols, evt, t);
4593 } catch (Exception e)
4595 e.printStackTrace();
4599 new Thread(new Runnable()
4606 // check to see if any of these files have names matching sequences
4609 SequenceIdMatcher idm = new SequenceIdMatcher(
4610 viewport.getAlignment().getSequencesArray());
4612 * Object[] { String,SequenceI}
4614 ArrayList<Object[]> filesmatched = new ArrayList<>();
4615 ArrayList<Object> filesnotmatched = new ArrayList<>();
4616 for (int i = 0; i < files.size(); i++)
4619 Object file = files.get(i);
4620 String fileName = file.toString();
4622 DataSourceType protocol = (file instanceof File
4623 ? DataSourceType.FILE
4624 : FormatAdapter.checkProtocol(fileName));
4625 if (protocol == DataSourceType.FILE)
4628 if (file instanceof File)
4631 Platform.cacheFileData(fl);
4635 fl = new File(fileName);
4637 pdbfn = fl.getName();
4639 else if (protocol == DataSourceType.URL)
4641 URL url = new URL(fileName);
4642 pdbfn = url.getFile();
4644 if (pdbfn.length() > 0)
4646 // attempt to find a match in the alignment
4647 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4648 int l = 0, c = pdbfn.indexOf(".");
4649 while (mtch == null && c != -1)
4654 } while ((c = pdbfn.indexOf(".", l)) > l);
4657 pdbfn = pdbfn.substring(0, l);
4659 mtch = idm.findAllIdMatches(pdbfn);
4666 type = new IdentifyFile().identify(file, protocol);
4667 } catch (Exception ex)
4671 if (type != null && type.isStructureFile())
4673 filesmatched.add(new Object[] { file, protocol, mtch });
4677 // File wasn't named like one of the sequences or wasn't a PDB
4679 filesnotmatched.add(file);
4683 if (filesmatched.size() > 0)
4685 boolean autoAssociate = Cache
4686 .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4689 String msg = MessageManager.formatMessage(
4690 "label.automatically_associate_structure_files_with_sequences_same_name",
4692 { Integer.valueOf(filesmatched.size())
4694 String ttl = MessageManager.getString(
4695 "label.automatically_associate_structure_files_by_name");
4696 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4697 ttl, JvOptionPane.YES_NO_OPTION);
4698 autoAssociate = choice == JvOptionPane.YES_OPTION;
4702 for (Object[] fm : filesmatched)
4704 // try and associate
4705 // TODO: may want to set a standard ID naming formalism for
4706 // associating PDB files which have no IDs.
4707 for (SequenceI toassoc : (SequenceI[]) fm[2])
4709 PDBEntry pe = new AssociatePdbFileWithSeq()
4710 .associatePdbWithSeq(fm[0].toString(),
4711 (DataSourceType) fm[1], toassoc, false,
4715 System.err.println("Associated file : "
4716 + (fm[0].toString()) + " with "
4717 + toassoc.getDisplayId(true));
4721 // TODO: do we need to update overview ? only if features are
4723 alignPanel.paintAlignment(true, false);
4729 * add declined structures as sequences
4731 for (Object[] o : filesmatched)
4733 filesnotmatched.add(o[0]);
4737 if (filesnotmatched.size() > 0)
4739 if (assocfiles > 0 && (Cache.getDefault(
4740 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4741 || JvOptionPane.showConfirmDialog(thisaf,
4742 "<html>" + MessageManager.formatMessage(
4743 "label.ignore_unmatched_dropped_files_info",
4746 filesnotmatched.size())
4749 MessageManager.getString(
4750 "label.ignore_unmatched_dropped_files"),
4751 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4755 for (Object fn : filesnotmatched)
4757 loadJalviewDataFile(fn, null, null, null);
4761 } catch (Exception ex)
4763 ex.printStackTrace();
4771 * Attempt to load a "dropped" file or URL string, by testing in turn for
4773 * <li>an Annotation file</li>
4774 * <li>a JNet file</li>
4775 * <li>a features file</li>
4776 * <li>else try to interpret as an alignment file</li>
4780 * either a filename or a URL string.
4782 public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4783 FileFormatI format, SequenceI assocSeq)
4785 // BH 2018 was String file
4788 if (sourceType == null)
4790 sourceType = FormatAdapter.checkProtocol(file);
4792 // if the file isn't identified, or not positively identified as some
4793 // other filetype (PFAM is default unidentified alignment file type) then
4794 // try to parse as annotation.
4795 boolean isAnnotation = (format == null
4796 || FileFormat.Pfam.equals(format))
4797 ? new AnnotationFile().annotateAlignmentView(viewport,
4803 // first see if its a T-COFFEE score file
4804 TCoffeeScoreFile tcf = null;
4807 tcf = new TCoffeeScoreFile(file, sourceType);
4810 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4814 new TCoffeeColourScheme(viewport.getAlignment()));
4815 isAnnotation = true;
4816 setStatus(MessageManager.getString(
4817 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4821 // some problem - if no warning its probable that the ID matching
4822 // process didn't work
4823 JvOptionPane.showMessageDialog(Desktop.desktop,
4824 tcf.getWarningMessage() == null
4825 ? MessageManager.getString(
4826 "label.check_file_matches_sequence_ids_alignment")
4827 : tcf.getWarningMessage(),
4828 MessageManager.getString(
4829 "label.problem_reading_tcoffee_score_file"),
4830 JvOptionPane.WARNING_MESSAGE);
4837 } catch (Exception x)
4840 "Exception when processing data source as T-COFFEE score file",
4846 // try to see if its a JNet 'concise' style annotation file *before*
4848 // try to parse it as a features file
4851 format = new IdentifyFile().identify(file, sourceType);
4853 if (FileFormat.ScoreMatrix == format)
4855 ScoreMatrixFile sm = new ScoreMatrixFile(
4856 new FileParse(file, sourceType));
4858 // todo: i18n this message
4859 setStatus(MessageManager.formatMessage(
4860 "label.successfully_loaded_matrix",
4861 sm.getMatrixName()));
4863 else if (FileFormat.Jnet.equals(format))
4865 JPredFile predictions = new JPredFile(file, sourceType);
4866 new JnetAnnotationMaker();
4867 JnetAnnotationMaker.add_annotation(predictions,
4868 viewport.getAlignment(), 0, false);
4869 viewport.getAlignment().setupJPredAlignment();
4870 isAnnotation = true;
4872 // else if (IdentifyFile.FeaturesFile.equals(format))
4873 else if (FileFormat.Features.equals(format))
4875 if (parseFeaturesFile(file, sourceType))
4877 SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4878 if (splitFrame != null)
4880 splitFrame.repaint();
4884 alignPanel.paintAlignment(true, true);
4890 new FileLoader().LoadFile(viewport, file, sourceType, format);
4897 alignPanel.adjustAnnotationHeight();
4898 viewport.updateSequenceIdColours();
4899 buildSortByAnnotationScoresMenu();
4900 alignPanel.paintAlignment(true, true);
4902 } catch (Exception ex)
4904 ex.printStackTrace();
4905 } catch (OutOfMemoryError oom)
4910 } catch (Exception x)
4915 + (sourceType != null
4916 ? (sourceType == DataSourceType.PASTE
4918 : "using " + sourceType + " from "
4922 ? "(parsing as '" + format + "' file)"
4924 oom, Desktop.desktop);
4929 * Method invoked by the ChangeListener on the tabbed pane, in other words
4930 * when a different tabbed pane is selected by the user or programmatically.
4933 public void tabSelectionChanged(int index)
4937 alignPanel = alignPanels.get(index);
4938 viewport = alignPanel.av;
4939 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4940 setMenusFromViewport(viewport);
4941 if (featureSettings != null && featureSettings.isOpen()
4942 && featureSettings.fr.getViewport() != viewport)
4944 if (viewport.isShowSequenceFeatures())
4946 // refresh the featureSettings to reflect UI change
4947 showFeatureSettingsUI();
4951 // close feature settings for this view.
4952 featureSettings.close();
4959 * 'focus' any colour slider that is open to the selected viewport
4961 if (viewport.getConservationSelected())
4963 SliderPanel.setConservationSlider(alignPanel,
4964 viewport.getResidueShading(), alignPanel.getViewName());
4968 SliderPanel.hideConservationSlider();
4970 if (viewport.getAbovePIDThreshold())
4972 SliderPanel.setPIDSliderSource(alignPanel,
4973 viewport.getResidueShading(), alignPanel.getViewName());
4977 SliderPanel.hidePIDSlider();
4981 * If there is a frame linked to this one in a SplitPane, switch it to the
4982 * same view tab index. No infinite recursion of calls should happen, since
4983 * tabSelectionChanged() should not get invoked on setting the selected
4984 * index to an unchanged value. Guard against setting an invalid index
4985 * before the new view peer tab has been created.
4987 final AlignViewportI peer = viewport.getCodingComplement();
4990 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4991 .getAlignPanel().alignFrame;
4992 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4994 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5000 * On right mouse click on view tab, prompt for and set new view name.
5003 public void tabbedPane_mousePressed(MouseEvent e)
5005 if (e.isPopupTrigger())
5007 String msg = MessageManager.getString("label.enter_view_name");
5008 String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
5009 String reply = JvOptionPane.showInputDialog(msg, ttl);
5013 viewport.setViewName(reply);
5014 // TODO warn if reply is in getExistingViewNames()?
5015 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5020 public AlignViewport getCurrentView()
5026 * Open the dialog for regex description parsing.
5029 protected void extractScores_actionPerformed(ActionEvent e)
5031 ParseProperties pp = new jalview.analysis.ParseProperties(
5032 viewport.getAlignment());
5033 // TODO: verify regex and introduce GUI dialog for version 2.5
5034 // if (pp.getScoresFromDescription("col", "score column ",
5035 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5037 if (pp.getScoresFromDescription("description column",
5038 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5040 buildSortByAnnotationScoresMenu();
5048 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5052 protected void showDbRefs_actionPerformed(ActionEvent e)
5054 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5060 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5064 protected void showNpFeats_actionPerformed(ActionEvent e)
5066 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5070 * find the viewport amongst the tabs in this alignment frame and close that
5075 public boolean closeView(AlignViewportI av)
5079 this.closeMenuItem_actionPerformed(false);
5082 Component[] comp = tabbedPane.getComponents();
5083 for (int i = 0; comp != null && i < comp.length; i++)
5085 if (comp[i] instanceof AlignmentPanel)
5087 if (((AlignmentPanel) comp[i]).av == av)
5090 closeView((AlignmentPanel) comp[i]);
5098 protected void build_fetchdbmenu(JMenu webService)
5100 // Temporary hack - DBRef Fetcher always top level ws entry.
5101 // TODO We probably want to store a sequence database checklist in
5102 // preferences and have checkboxes.. rather than individual sources selected
5104 final JMenu rfetch = new JMenu(
5105 MessageManager.getString("action.fetch_db_references"));
5106 rfetch.setToolTipText(MessageManager.getString(
5107 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5108 webService.add(rfetch);
5110 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5111 MessageManager.getString("option.trim_retrieved_seqs"));
5112 trimrs.setToolTipText(
5113 MessageManager.getString("label.trim_retrieved_sequences"));
5115 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5116 trimrs.addActionListener(new ActionListener()
5119 public void actionPerformed(ActionEvent e)
5121 trimrs.setSelected(trimrs.isSelected());
5122 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5123 Boolean.valueOf(trimrs.isSelected()).toString());
5127 JMenuItem fetchr = new JMenuItem(
5128 MessageManager.getString("label.standard_databases"));
5129 fetchr.setToolTipText(
5130 MessageManager.getString("label.fetch_embl_uniprot"));
5131 fetchr.addActionListener(new ActionListener()
5135 public void actionPerformed(ActionEvent e)
5137 new Thread(new Runnable()
5142 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5143 .getAlignment().isNucleotide();
5144 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5145 alignPanel.av.getSequenceSelection(),
5146 alignPanel.alignFrame, null,
5147 alignPanel.alignFrame.featureSettings, isNucleotide);
5148 dbRefFetcher.addListener(new FetchFinishedListenerI()
5151 public void finished()
5154 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5155 .getFeatureSettingsModels())
5158 alignPanel.av.mergeFeaturesStyle(srcSettings);
5160 AlignFrame.this.setMenusForViewport();
5163 dbRefFetcher.fetchDBRefs(false);
5171 new Thread(new Runnable()
5176 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5177 .getSequenceFetcherSingleton();
5178 javax.swing.SwingUtilities.invokeLater(new Runnable()
5183 String[] dbclasses = sf.getNonAlignmentSources();
5184 List<DbSourceProxy> otherdb;
5185 JMenu dfetch = new JMenu();
5186 JMenu ifetch = new JMenu();
5187 JMenuItem fetchr = null;
5188 int comp = 0, icomp = 0, mcomp = 15;
5189 String mname = null;
5191 for (String dbclass : dbclasses)
5193 otherdb = sf.getSourceProxy(dbclass);
5194 // add a single entry for this class, or submenu allowing 'fetch
5196 if (otherdb == null || otherdb.size() < 1)
5202 mname = "From " + dbclass;
5204 if (otherdb.size() == 1)
5206 final DbSourceProxy[] dassource = otherdb
5207 .toArray(new DbSourceProxy[0]);
5208 DbSourceProxy src = otherdb.get(0);
5209 fetchr = new JMenuItem(src.getDbSource());
5210 fetchr.addActionListener(new ActionListener()
5214 public void actionPerformed(ActionEvent e)
5216 new Thread(new Runnable()
5222 boolean isNucleotide = alignPanel.alignFrame
5223 .getViewport().getAlignment()
5225 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5226 alignPanel.av.getSequenceSelection(),
5227 alignPanel.alignFrame, dassource,
5228 alignPanel.alignFrame.featureSettings,
5231 .addListener(new FetchFinishedListenerI()
5234 public void finished()
5236 FeatureSettingsModelI srcSettings = dassource[0]
5237 .getFeatureColourScheme();
5238 alignPanel.av.mergeFeaturesStyle(
5240 AlignFrame.this.setMenusForViewport();
5243 dbRefFetcher.fetchDBRefs(false);
5249 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5250 MessageManager.formatMessage(
5251 "label.fetch_retrieve_from", new Object[]
5252 { src.getDbName() })));
5258 final DbSourceProxy[] dassource = otherdb
5259 .toArray(new DbSourceProxy[0]);
5261 DbSourceProxy src = otherdb.get(0);
5262 fetchr = new JMenuItem(MessageManager
5263 .formatMessage("label.fetch_all_param", new Object[]
5264 { src.getDbSource() }));
5265 fetchr.addActionListener(new ActionListener()
5268 public void actionPerformed(ActionEvent e)
5270 new Thread(new Runnable()
5276 boolean isNucleotide = alignPanel.alignFrame
5277 .getViewport().getAlignment()
5279 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5280 alignPanel.av.getSequenceSelection(),
5281 alignPanel.alignFrame, dassource,
5282 alignPanel.alignFrame.featureSettings,
5285 .addListener(new FetchFinishedListenerI()
5288 public void finished()
5290 AlignFrame.this.setMenusForViewport();
5293 dbRefFetcher.fetchDBRefs(false);
5299 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5300 MessageManager.formatMessage(
5301 "label.fetch_retrieve_from_all_sources",
5303 { Integer.valueOf(otherdb.size())
5305 src.getDbSource(), src.getDbName() })));
5308 // and then build the rest of the individual menus
5309 ifetch = new JMenu(MessageManager.formatMessage(
5310 "label.source_from_db_source", new Object[]
5311 { src.getDbSource() }));
5313 String imname = null;
5315 for (DbSourceProxy sproxy : otherdb)
5317 String dbname = sproxy.getDbName();
5318 String sname = dbname.length() > 5
5319 ? dbname.substring(0, 5) + "..."
5321 String msname = dbname.length() > 10
5322 ? dbname.substring(0, 10) + "..."
5326 imname = MessageManager
5327 .formatMessage("label.from_msname", new Object[]
5330 fetchr = new JMenuItem(msname);
5331 final DbSourceProxy[] dassrc = { sproxy };
5332 fetchr.addActionListener(new ActionListener()
5336 public void actionPerformed(ActionEvent e)
5338 new Thread(new Runnable()
5344 boolean isNucleotide = alignPanel.alignFrame
5345 .getViewport().getAlignment()
5347 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5348 alignPanel.av.getSequenceSelection(),
5349 alignPanel.alignFrame, dassrc,
5350 alignPanel.alignFrame.featureSettings,
5353 .addListener(new FetchFinishedListenerI()
5356 public void finished()
5358 AlignFrame.this.setMenusForViewport();
5361 dbRefFetcher.fetchDBRefs(false);
5367 fetchr.setToolTipText(
5368 "<html>" + MessageManager.formatMessage(
5369 "label.fetch_retrieve_from", new Object[]
5373 if (++icomp >= mcomp || i == (otherdb.size()))
5375 ifetch.setText(MessageManager.formatMessage(
5376 "label.source_to_target", imname, sname));
5378 ifetch = new JMenu();
5386 if (comp >= mcomp || dbi >= (dbclasses.length))
5388 dfetch.setText(MessageManager.formatMessage(
5389 "label.source_to_target", mname, dbclass));
5391 dfetch = new JMenu();
5404 * Left justify the whole alignment.
5407 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5409 AlignmentI al = viewport.getAlignment();
5411 viewport.firePropertyChange("alignment", null, al);
5415 * Right justify the whole alignment.
5418 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5420 AlignmentI al = viewport.getAlignment();
5422 viewport.firePropertyChange("alignment", null, al);
5426 public void setShowSeqFeatures(boolean b)
5428 showSeqFeatures.setSelected(b);
5429 viewport.setShowSequenceFeatures(b);
5436 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5437 * awt.event.ActionEvent)
5440 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5442 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5443 alignPanel.paintAlignment(false, false);
5450 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5454 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5456 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5457 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5465 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5466 * .event.ActionEvent)
5469 protected void showGroupConservation_actionPerformed(ActionEvent e)
5471 viewport.setShowGroupConservation(showGroupConservation.getState());
5472 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5479 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5480 * .event.ActionEvent)
5483 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5485 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5486 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5493 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5494 * .event.ActionEvent)
5497 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5499 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5500 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5504 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5506 showSequenceLogo.setState(true);
5507 viewport.setShowSequenceLogo(true);
5508 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5509 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5513 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5515 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5522 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5523 * .event.ActionEvent)
5526 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5528 if (avc.makeGroupsFromSelection())
5530 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5531 alignPanel.updateAnnotation();
5532 alignPanel.paintAlignment(true,
5533 viewport.needToUpdateStructureViews());
5537 public void clearAlignmentSeqRep()
5539 // TODO refactor alignmentseqrep to controller
5540 if (viewport.getAlignment().hasSeqrep())
5542 viewport.getAlignment().setSeqrep(null);
5543 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5544 alignPanel.updateAnnotation();
5545 alignPanel.paintAlignment(true, true);
5550 protected void createGroup_actionPerformed(ActionEvent e)
5552 if (avc.createGroup())
5554 if (applyAutoAnnotationSettings.isSelected())
5556 alignPanel.updateAnnotation(true, false);
5558 alignPanel.alignmentChanged();
5563 protected void unGroup_actionPerformed(ActionEvent e)
5567 alignPanel.alignmentChanged();
5572 * make the given alignmentPanel the currently selected tab
5574 * @param alignmentPanel
5576 public void setDisplayedView(AlignmentPanel alignmentPanel)
5578 if (!viewport.getSequenceSetId()
5579 .equals(alignmentPanel.av.getSequenceSetId()))
5581 throw new Error(MessageManager.getString(
5582 "error.implementation_error_cannot_show_view_alignment_frame"));
5584 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5585 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5587 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5592 * Action on selection of menu options to Show or Hide annotations.
5595 * @param forSequences
5596 * update sequence-related annotations
5597 * @param forAlignment
5598 * update non-sequence-related annotations
5601 protected void setAnnotationsVisibility(boolean visible,
5602 boolean forSequences, boolean forAlignment)
5604 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5605 .getAlignmentAnnotation();
5610 for (AlignmentAnnotation aa : anns)
5613 * don't display non-positional annotations on an alignment
5615 if (aa.annotations == null)
5619 boolean apply = (aa.sequenceRef == null && forAlignment)
5620 || (aa.sequenceRef != null && forSequences);
5623 aa.visible = visible;
5626 alignPanel.validateAnnotationDimensions(true);
5627 alignPanel.alignmentChanged();
5631 * Store selected annotation sort order for the view and repaint.
5634 protected void sortAnnotations_actionPerformed()
5636 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5638 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5639 alignPanel.paintAlignment(false, false);
5644 * @return alignment panels in this alignment frame
5646 public List<? extends AlignmentViewPanel> getAlignPanels()
5648 // alignPanels is never null
5649 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5654 * Open a new alignment window, with the cDNA associated with this (protein)
5655 * alignment, aligned as is the protein.
5657 protected void viewAsCdna_actionPerformed()
5659 // TODO no longer a menu action - refactor as required
5660 final AlignmentI alignment = getViewport().getAlignment();
5661 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5662 if (mappings == null)
5666 List<SequenceI> cdnaSeqs = new ArrayList<>();
5667 for (SequenceI aaSeq : alignment.getSequences())
5669 for (AlignedCodonFrame acf : mappings)
5671 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5675 * There is a cDNA mapping for this protein sequence - add to new
5676 * alignment. It will share the same dataset sequence as other mapped
5677 * cDNA (no new mappings need to be created).
5679 final Sequence newSeq = new Sequence(dnaSeq);
5680 newSeq.setDatasetSequence(dnaSeq);
5681 cdnaSeqs.add(newSeq);
5685 if (cdnaSeqs.size() == 0)
5687 // show a warning dialog no mapped cDNA
5690 AlignmentI cdna = new Alignment(
5691 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5692 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5693 AlignFrame.DEFAULT_HEIGHT);
5694 cdna.alignAs(alignment);
5695 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5697 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5698 AlignFrame.DEFAULT_HEIGHT);
5702 * Set visibility of dna/protein complement view (available when shown in a
5708 protected void showComplement_actionPerformed(boolean show)
5710 SplitContainerI sf = getSplitViewContainer();
5713 sf.setComplementVisible(this, show);
5718 * Generate the reverse (optionally complemented) of the selected sequences,
5719 * and add them to the alignment
5722 protected void showReverse_actionPerformed(boolean complement)
5724 AlignmentI al = null;
5727 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5728 al = dna.reverseCdna(complement);
5729 viewport.addAlignment(al, "");
5730 addHistoryItem(new EditCommand(
5731 MessageManager.getString("label.add_sequences"), Action.PASTE,
5732 al.getSequencesArray(), 0, al.getWidth(),
5733 viewport.getAlignment()));
5734 } catch (Exception ex)
5736 System.err.println(ex.getMessage());
5742 * Try to run a script in the Groovy console, having first ensured that this
5743 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5744 * be targeted at this alignment.
5747 protected void runGroovy_actionPerformed()
5749 Jalview.setCurrentAlignFrame(this);
5750 groovy.ui.Console console = Desktop.getGroovyConsole();
5751 if (console != null)
5755 console.runScript();
5756 } catch (Exception ex)
5758 System.err.println((ex.toString()));
5759 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5760 MessageManager.getString("label.couldnt_run_groovy_script"),
5761 MessageManager.getString("label.groovy_support_failed"),
5762 JvOptionPane.ERROR_MESSAGE);
5767 System.err.println("Can't run Groovy script as console not found");
5772 * Hides columns containing (or not containing) a specified feature, provided
5773 * that would not leave all columns hidden
5775 * @param featureType
5776 * @param columnsContaining
5779 public boolean hideFeatureColumns(String featureType,
5780 boolean columnsContaining)
5782 boolean notForHiding = avc.markColumnsContainingFeatures(
5783 columnsContaining, false, false, featureType);
5786 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5787 false, featureType))
5789 getViewport().hideSelectedColumns();
5797 protected void selectHighlightedColumns_actionPerformed(
5798 ActionEvent actionEvent)
5800 // include key modifier check in case user selects from menu
5801 avc.markHighlightedColumns(
5802 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5803 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5804 | ActionEvent.CTRL_MASK)) != 0);
5808 * Rebuilds the Colour menu, including any user-defined colours which have
5809 * been loaded either on startup or during the session
5811 public void buildColourMenu()
5813 colourMenu.removeAll();
5815 colourMenu.add(applyToAllGroups);
5816 colourMenu.add(textColour);
5817 colourMenu.addSeparator();
5819 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5820 viewport.getAlignment(), false);
5822 colourMenu.add(annotationColour);
5823 bg.add(annotationColour);
5824 colourMenu.addSeparator();
5825 colourMenu.add(conservationMenuItem);
5826 colourMenu.add(modifyConservation);
5827 colourMenu.add(abovePIDThreshold);
5828 colourMenu.add(modifyPID);
5830 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5831 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5835 * Open a dialog (if not already open) that allows the user to select and
5836 * calculate PCA or Tree analysis
5838 protected void openTreePcaDialog()
5840 if (alignPanel.getCalculationDialog() == null)
5842 new CalculationChooser(AlignFrame.this);
5847 protected void loadVcf_actionPerformed()
5849 JalviewFileChooser chooser = new JalviewFileChooser(
5850 Cache.getProperty("LAST_DIRECTORY"));
5851 chooser.setFileView(new JalviewFileView());
5852 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5853 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5854 final AlignFrame us = this;
5855 chooser.setResponseHandler(0, new Runnable()
5860 String choice = chooser.getSelectedFile().getPath();
5861 Cache.setProperty("LAST_DIRECTORY", choice);
5862 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5863 new VCFLoader(choice).loadVCF(seqs, us);
5866 chooser.showOpenDialog(null);
5870 private Rectangle lastFeatureSettingsBounds = null;
5873 public void setFeatureSettingsGeometry(Rectangle bounds)
5875 lastFeatureSettingsBounds = bounds;
5879 public Rectangle getFeatureSettingsGeometry()
5881 return lastFeatureSettingsBounds;
5885 class PrintThread extends Thread
5889 public PrintThread(AlignmentPanel ap)
5894 static PageFormat pf;
5899 PrinterJob printJob = PrinterJob.getPrinterJob();
5903 printJob.setPrintable(ap, pf);
5907 printJob.setPrintable(ap);
5910 if (printJob.printDialog())
5915 } catch (Exception PrintException)
5917 PrintException.printStackTrace();