2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import java.awt.BorderLayout;
24 import java.awt.Color;
25 import java.awt.Component;
26 import java.awt.Rectangle;
27 import java.awt.Toolkit;
28 import java.awt.datatransfer.Clipboard;
29 import java.awt.datatransfer.DataFlavor;
30 import java.awt.datatransfer.StringSelection;
31 import java.awt.datatransfer.Transferable;
32 import java.awt.dnd.DnDConstants;
33 import java.awt.dnd.DropTargetDragEvent;
34 import java.awt.dnd.DropTargetDropEvent;
35 import java.awt.dnd.DropTargetEvent;
36 import java.awt.dnd.DropTargetListener;
37 import java.awt.event.ActionEvent;
38 import java.awt.event.ActionListener;
39 import java.awt.event.FocusAdapter;
40 import java.awt.event.FocusEvent;
41 import java.awt.event.ItemEvent;
42 import java.awt.event.ItemListener;
43 import java.awt.event.KeyAdapter;
44 import java.awt.event.KeyEvent;
45 import java.awt.event.MouseEvent;
46 import java.awt.print.PageFormat;
47 import java.awt.print.PrinterJob;
48 import java.beans.PropertyChangeEvent;
50 import java.io.FileWriter;
51 import java.io.PrintWriter;
53 import java.util.ArrayList;
54 import java.util.Arrays;
55 import java.util.Deque;
56 import java.util.Enumeration;
57 import java.util.Hashtable;
58 import java.util.List;
59 import java.util.Vector;
61 import javax.swing.ButtonGroup;
62 import javax.swing.JCheckBoxMenuItem;
63 import javax.swing.JComponent;
64 import javax.swing.JEditorPane;
65 import javax.swing.JInternalFrame;
66 import javax.swing.JLabel;
67 import javax.swing.JLayeredPane;
68 import javax.swing.JMenu;
69 import javax.swing.JMenuItem;
70 import javax.swing.JPanel;
71 import javax.swing.JScrollPane;
72 import javax.swing.SwingUtilities;
74 import ext.vamsas.ServiceHandle;
75 import jalview.analysis.AlignmentSorter;
76 import jalview.analysis.AlignmentUtils;
77 import jalview.analysis.CrossRef;
78 import jalview.analysis.Dna;
79 import jalview.analysis.GeneticCodeI;
80 import jalview.analysis.ParseProperties;
81 import jalview.analysis.SequenceIdMatcher;
82 import jalview.api.AlignExportSettingsI;
83 import jalview.api.AlignViewControllerGuiI;
84 import jalview.api.AlignViewControllerI;
85 import jalview.api.AlignViewportI;
86 import jalview.api.AlignmentViewPanel;
87 import jalview.api.FeatureSettingsControllerI;
88 import jalview.api.FeatureSettingsModelI;
89 import jalview.api.SplitContainerI;
90 import jalview.api.ViewStyleI;
91 import jalview.api.analysis.SimilarityParamsI;
92 import jalview.bin.Cache;
93 import jalview.bin.Jalview;
94 import jalview.commands.CommandI;
95 import jalview.commands.EditCommand;
96 import jalview.commands.EditCommand.Action;
97 import jalview.commands.OrderCommand;
98 import jalview.commands.RemoveGapColCommand;
99 import jalview.commands.RemoveGapsCommand;
100 import jalview.commands.SlideSequencesCommand;
101 import jalview.commands.TrimRegionCommand;
102 import jalview.datamodel.AlignExportSettingsAdapter;
103 import jalview.datamodel.AlignedCodonFrame;
104 import jalview.datamodel.Alignment;
105 import jalview.datamodel.AlignmentAnnotation;
106 import jalview.datamodel.AlignmentExportData;
107 import jalview.datamodel.AlignmentI;
108 import jalview.datamodel.AlignmentOrder;
109 import jalview.datamodel.AlignmentView;
110 import jalview.datamodel.ColumnSelection;
111 import jalview.datamodel.HiddenColumns;
112 import jalview.datamodel.PDBEntry;
113 import jalview.datamodel.SeqCigar;
114 import jalview.datamodel.Sequence;
115 import jalview.datamodel.SequenceGroup;
116 import jalview.datamodel.SequenceI;
117 import jalview.gui.ColourMenuHelper.ColourChangeListener;
118 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
119 import jalview.io.AlignmentProperties;
120 import jalview.io.AnnotationFile;
121 import jalview.io.BackupFiles;
122 import jalview.io.BioJsHTMLOutput;
123 import jalview.io.DataSourceType;
124 import jalview.io.FileFormat;
125 import jalview.io.FileFormatI;
126 import jalview.io.FileFormats;
127 import jalview.io.FileLoader;
128 import jalview.io.FileParse;
129 import jalview.io.FormatAdapter;
130 import jalview.io.HtmlSvgOutput;
131 import jalview.io.IdentifyFile;
132 import jalview.io.JPredFile;
133 import jalview.io.JalviewFileChooser;
134 import jalview.io.JalviewFileView;
135 import jalview.io.JnetAnnotationMaker;
136 import jalview.io.NewickFile;
137 import jalview.io.ScoreMatrixFile;
138 import jalview.io.TCoffeeScoreFile;
139 import jalview.io.vcf.VCFLoader;
140 import jalview.jbgui.GAlignFrame;
141 import jalview.project.Jalview2XML;
142 import jalview.schemes.ColourSchemeI;
143 import jalview.schemes.ColourSchemes;
144 import jalview.schemes.ResidueColourScheme;
145 import jalview.schemes.TCoffeeColourScheme;
146 import jalview.util.ImageMaker.TYPE;
147 import jalview.util.MessageManager;
148 import jalview.util.Platform;
149 import jalview.viewmodel.AlignmentViewport;
150 import jalview.viewmodel.ViewportRanges;
151 import jalview.ws.DBRefFetcher;
152 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
153 import jalview.ws.jws1.Discoverer;
154 import jalview.ws.jws2.Jws2Discoverer;
155 import jalview.ws.jws2.jabaws2.Jws2Instance;
156 import jalview.ws.seqfetcher.DbSourceProxy;
162 * @version $Revision$
164 @SuppressWarnings("serial")
165 public class AlignFrame extends GAlignFrame implements DropTargetListener,
166 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
169 public static final int DEFAULT_WIDTH = 700;
171 public static final int DEFAULT_HEIGHT = 500;
174 * The currently displayed panel (selected tabbed view if more than one)
176 public AlignmentPanel alignPanel;
178 AlignViewport viewport;
180 public AlignViewControllerI avc;
182 List<AlignmentPanel> alignPanels = new ArrayList<>();
185 * Last format used to load or save alignments in this window
187 FileFormatI currentFileFormat = null;
190 * Current filename for this alignment
192 String fileName = null;
197 * Creates a new AlignFrame object with specific width and height.
203 public AlignFrame(AlignmentI al, int width, int height)
205 this(al, null, width, height);
209 * Creates a new AlignFrame object with specific width, height and
215 * @param sequenceSetId
217 public AlignFrame(AlignmentI al, int width, int height,
218 String sequenceSetId)
220 this(al, null, width, height, sequenceSetId);
224 * Creates a new AlignFrame object with specific width, height and
230 * @param sequenceSetId
233 public AlignFrame(AlignmentI al, int width, int height,
234 String sequenceSetId, String viewId)
236 this(al, null, width, height, sequenceSetId, viewId);
240 * new alignment window with hidden columns
244 * @param hiddenColumns
245 * ColumnSelection or null
247 * Width of alignment frame
251 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
254 this(al, hiddenColumns, width, height, null);
258 * Create alignment frame for al with hiddenColumns, a specific width and
259 * height, and specific sequenceId
262 * @param hiddenColumns
265 * @param sequenceSetId
268 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
269 int height, String sequenceSetId)
271 this(al, hiddenColumns, width, height, sequenceSetId, null);
275 * Create alignment frame for al with hiddenColumns, a specific width and
276 * height, and specific sequenceId
279 * @param hiddenColumns
282 * @param sequenceSetId
287 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
288 int height, String sequenceSetId, String viewId)
290 setSize(width, height);
292 if (al.getDataset() == null)
297 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
299 alignPanel = new AlignmentPanel(this, viewport);
301 addAlignmentPanel(alignPanel, true);
305 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
306 HiddenColumns hiddenColumns, int width, int height)
308 setSize(width, height);
310 if (al.getDataset() == null)
315 viewport = new AlignViewport(al, hiddenColumns);
317 if (hiddenSeqs != null && hiddenSeqs.length > 0)
319 viewport.hideSequence(hiddenSeqs);
321 alignPanel = new AlignmentPanel(this, viewport);
322 addAlignmentPanel(alignPanel, true);
327 * Make a new AlignFrame from existing alignmentPanels
334 public AlignFrame(AlignmentPanel ap)
338 addAlignmentPanel(ap, false);
343 * initalise the alignframe from the underlying viewport data and the
348 // setBackground(Color.white); // BH 2019
350 if (!Jalview.isHeadlessMode())
352 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
355 avc = new jalview.controller.AlignViewController(this, viewport,
357 if (viewport.getAlignmentConservationAnnotation() == null)
359 // BLOSUM62Colour.setEnabled(false);
360 conservationMenuItem.setEnabled(false);
361 modifyConservation.setEnabled(false);
362 // PIDColour.setEnabled(false);
363 // abovePIDThreshold.setEnabled(false);
364 // modifyPID.setEnabled(false);
367 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
370 if (sortby.equals("Id"))
372 sortIDMenuItem_actionPerformed(null);
374 else if (sortby.equals("Pairwise Identity"))
376 sortPairwiseMenuItem_actionPerformed(null);
380 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
382 setMenusFromViewport(viewport);
383 buildSortByAnnotationScoresMenu();
384 calculateTree.addActionListener(new ActionListener()
388 public void actionPerformed(ActionEvent e)
395 if (Desktop.desktop != null)
397 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
398 if (!Platform.isJS())
400 addServiceListeners();
405 if (viewport.getWrapAlignment())
407 wrapMenuItem_actionPerformed(null);
410 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
412 this.overviewMenuItem_actionPerformed(null);
417 final List<AlignmentPanel> selviews = new ArrayList<>();
418 final List<AlignmentPanel> origview = new ArrayList<>();
419 final String menuLabel = MessageManager
420 .getString("label.copy_format_from");
421 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
422 new ViewSetProvider()
426 public AlignmentPanel[] getAllAlignmentPanels()
429 origview.add(alignPanel);
430 // make an array of all alignment panels except for this one
431 List<AlignmentPanel> aps = new ArrayList<>(
432 Arrays.asList(Desktop.getAlignmentPanels(null)));
433 aps.remove(AlignFrame.this.alignPanel);
434 return aps.toArray(new AlignmentPanel[aps.size()]);
436 }, selviews, new ItemListener()
440 public void itemStateChanged(ItemEvent e)
442 if (origview.size() > 0)
444 final AlignmentPanel ap = origview.get(0);
447 * Copy the ViewStyle of the selected panel to 'this one'.
448 * Don't change value of 'scaleProteinAsCdna' unless copying
451 ViewStyleI vs = selviews.get(0).getAlignViewport()
453 boolean fromSplitFrame = selviews.get(0)
454 .getAlignViewport().getCodingComplement() != null;
457 vs.setScaleProteinAsCdna(ap.getAlignViewport()
458 .getViewStyle().isScaleProteinAsCdna());
460 ap.getAlignViewport().setViewStyle(vs);
463 * Also rescale ViewStyle of SplitFrame complement if there is
464 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
465 * the whole ViewStyle (allow cDNA protein to have different
468 AlignViewportI complement = ap.getAlignViewport()
469 .getCodingComplement();
470 if (complement != null && vs.isScaleProteinAsCdna())
472 AlignFrame af = Desktop.getAlignFrameFor(complement);
473 ((SplitFrame) af.getSplitViewContainer())
475 af.setMenusForViewport();
479 ap.setSelected(true);
480 ap.alignFrame.setMenusForViewport();
485 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
486 .indexOf("devel") > -1
487 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
488 .indexOf("test") > -1)
490 formatMenu.add(vsel);
492 addFocusListener(new FocusAdapter()
495 public void focusGained(FocusEvent e)
497 Jalview.setCurrentAlignFrame(AlignFrame.this);
504 * Change the filename and format for the alignment, and enable the 'reload'
505 * button functionality.
512 public void setFileName(String file, FileFormatI format)
515 setFileFormat(format);
516 reload.setEnabled(true);
520 * JavaScript will have this, maybe others. More dependable than a file name
521 * and maintains a reference to the actual bytes loaded.
525 public void setFileObject(File file)
527 this.fileObject = file;
531 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
534 void addKeyListener()
536 addKeyListener(new KeyAdapter()
539 public void keyPressed(KeyEvent evt)
541 if (viewport.cursorMode
542 && ((evt.getKeyCode() >= KeyEvent.VK_0
543 && evt.getKeyCode() <= KeyEvent.VK_9)
544 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
545 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
546 && Character.isDigit(evt.getKeyChar()))
548 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
551 switch (evt.getKeyCode())
554 case 27: // escape key
555 deselectAllSequenceMenuItem_actionPerformed(null);
559 case KeyEvent.VK_DOWN:
560 if (evt.isAltDown() || !viewport.cursorMode)
562 moveSelectedSequences(false);
564 if (viewport.cursorMode)
566 alignPanel.getSeqPanel().moveCursor(0, 1);
571 if (evt.isAltDown() || !viewport.cursorMode)
573 moveSelectedSequences(true);
575 if (viewport.cursorMode)
577 alignPanel.getSeqPanel().moveCursor(0, -1);
582 case KeyEvent.VK_LEFT:
583 if (evt.isAltDown() || !viewport.cursorMode)
585 slideSequences(false,
586 alignPanel.getSeqPanel().getKeyboardNo1());
590 alignPanel.getSeqPanel().moveCursor(-1, 0);
595 case KeyEvent.VK_RIGHT:
596 if (evt.isAltDown() || !viewport.cursorMode)
598 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
602 alignPanel.getSeqPanel().moveCursor(1, 0);
606 case KeyEvent.VK_SPACE:
607 if (viewport.cursorMode)
609 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
610 || evt.isShiftDown() || evt.isAltDown());
614 // case KeyEvent.VK_A:
615 // if (viewport.cursorMode)
617 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
618 // //System.out.println("A");
622 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
623 * System.out.println("closing bracket"); } break;
625 case KeyEvent.VK_DELETE:
626 case KeyEvent.VK_BACK_SPACE:
627 if (!viewport.cursorMode)
629 cut_actionPerformed();
633 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
634 || evt.isShiftDown() || evt.isAltDown());
640 if (viewport.cursorMode)
642 alignPanel.getSeqPanel().setCursorRow();
646 if (viewport.cursorMode && !evt.isControlDown())
648 alignPanel.getSeqPanel().setCursorColumn();
652 if (viewport.cursorMode)
654 alignPanel.getSeqPanel().setCursorPosition();
658 case KeyEvent.VK_ENTER:
659 case KeyEvent.VK_COMMA:
660 if (viewport.cursorMode)
662 alignPanel.getSeqPanel().setCursorRowAndColumn();
667 if (viewport.cursorMode)
669 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
673 if (viewport.cursorMode)
675 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
680 viewport.cursorMode = !viewport.cursorMode;
681 setStatus(MessageManager
682 .formatMessage("label.keyboard_editing_mode", new String[]
683 { (viewport.cursorMode ? "on" : "off") }));
684 if (viewport.cursorMode)
686 ViewportRanges ranges = viewport.getRanges();
687 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
689 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
692 alignPanel.getSeqPanel().seqCanvas.repaint();
698 Help.showHelpWindow();
699 } catch (Exception ex)
701 ex.printStackTrace();
706 boolean toggleSeqs = !evt.isControlDown();
707 boolean toggleCols = !evt.isShiftDown();
708 toggleHiddenRegions(toggleSeqs, toggleCols);
713 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
714 boolean modifyExisting = true; // always modify, don't clear
715 // evt.isShiftDown();
716 boolean invertHighlighted = evt.isAltDown();
717 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
721 case KeyEvent.VK_PAGE_UP:
722 viewport.getRanges().pageUp();
724 case KeyEvent.VK_PAGE_DOWN:
725 viewport.getRanges().pageDown();
731 public void keyReleased(KeyEvent evt)
733 switch (evt.getKeyCode())
735 case KeyEvent.VK_LEFT:
736 if (evt.isAltDown() || !viewport.cursorMode)
738 viewport.firePropertyChange("alignment", null,
739 viewport.getAlignment().getSequences());
743 case KeyEvent.VK_RIGHT:
744 if (evt.isAltDown() || !viewport.cursorMode)
746 viewport.firePropertyChange("alignment", null,
747 viewport.getAlignment().getSequences());
755 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
757 ap.alignFrame = this;
758 avc = new jalview.controller.AlignViewController(this, viewport,
763 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
765 int aSize = alignPanels.size();
767 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
769 if (aSize == 1 && ap.av.getViewName() == null)
771 this.getContentPane().add(ap, BorderLayout.CENTER);
777 setInitialTabVisible();
780 expandViews.setEnabled(true);
781 gatherViews.setEnabled(true);
782 tabbedPane.addTab(ap.av.getViewName(), ap);
784 ap.setVisible(false);
789 if (ap.av.isPadGaps())
791 ap.av.getAlignment().padGaps();
793 ap.av.updateConservation(ap);
794 ap.av.updateConsensus(ap);
795 ap.av.updateStrucConsensus(ap);
799 public void setInitialTabVisible()
801 expandViews.setEnabled(true);
802 gatherViews.setEnabled(true);
803 tabbedPane.setVisible(true);
804 AlignmentPanel first = alignPanels.get(0);
805 tabbedPane.addTab(first.av.getViewName(), first);
806 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
809 public AlignViewport getViewport()
814 /* Set up intrinsic listeners for dynamically generated GUI bits. */
815 private void addServiceListeners()
817 final java.beans.PropertyChangeListener thisListener;
818 Desktop.instance.addJalviewPropertyChangeListener("services",
819 thisListener = new java.beans.PropertyChangeListener()
822 public void propertyChange(PropertyChangeEvent evt)
824 // // System.out.println("Discoverer property change.");
825 // if (evt.getPropertyName().equals("services"))
827 SwingUtilities.invokeLater(new Runnable()
834 "Rebuild WS Menu for service change");
835 BuildWebServiceMenu();
842 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
845 public void internalFrameClosed(
846 javax.swing.event.InternalFrameEvent evt)
848 // System.out.println("deregistering discoverer listener");
849 Desktop.instance.removeJalviewPropertyChangeListener("services",
851 closeMenuItem_actionPerformed(true);
854 // Finally, build the menu once to get current service state
855 new Thread(new Runnable()
860 BuildWebServiceMenu();
866 * Configure menu items that vary according to whether the alignment is
867 * nucleotide or protein
869 public void setGUINucleotide()
871 AlignmentI al = getViewport().getAlignment();
872 boolean nucleotide = al.isNucleotide();
874 loadVcf.setVisible(nucleotide);
875 showTranslation.setVisible(nucleotide);
876 showReverse.setVisible(nucleotide);
877 showReverseComplement.setVisible(nucleotide);
878 conservationMenuItem.setEnabled(!nucleotide);
880 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
881 showGroupConservation.setEnabled(!nucleotide);
883 showComplementMenuItem
884 .setText(nucleotide ? MessageManager.getString("label.protein")
885 : MessageManager.getString("label.nucleotide"));
889 * set up menus for the current viewport. This may be called after any
890 * operation that affects the data in the current view (selection changed,
891 * etc) to update the menus to reflect the new state.
894 public void setMenusForViewport()
896 setMenusFromViewport(viewport);
900 * Need to call this method when tabs are selected for multiple views, or when
901 * loading from Jalview2XML.java
906 public void setMenusFromViewport(AlignViewport av)
908 padGapsMenuitem.setSelected(av.isPadGaps());
909 colourTextMenuItem.setSelected(av.isShowColourText());
910 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
911 modifyPID.setEnabled(abovePIDThreshold.isSelected());
912 conservationMenuItem.setSelected(av.getConservationSelected());
913 modifyConservation.setEnabled(conservationMenuItem.isSelected());
914 seqLimits.setSelected(av.getShowJVSuffix());
915 idRightAlign.setSelected(av.isRightAlignIds());
916 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
917 renderGapsMenuItem.setSelected(av.isRenderGaps());
918 wrapMenuItem.setSelected(av.getWrapAlignment());
919 scaleAbove.setVisible(av.getWrapAlignment());
920 scaleLeft.setVisible(av.getWrapAlignment());
921 scaleRight.setVisible(av.getWrapAlignment());
922 annotationPanelMenuItem.setState(av.isShowAnnotation());
924 * Show/hide annotations only enabled if annotation panel is shown
926 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
927 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
928 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
929 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
930 viewBoxesMenuItem.setSelected(av.getShowBoxes());
931 viewTextMenuItem.setSelected(av.getShowText());
932 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
933 showGroupConsensus.setSelected(av.isShowGroupConsensus());
934 showGroupConservation.setSelected(av.isShowGroupConservation());
935 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
936 showSequenceLogo.setSelected(av.isShowSequenceLogo());
937 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
939 ColourMenuHelper.setColourSelected(colourMenu,
940 av.getGlobalColourScheme());
942 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
943 hiddenMarkers.setState(av.getShowHiddenMarkers());
944 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
945 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
946 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
947 autoCalculate.setSelected(av.autoCalculateConsensus);
948 sortByTree.setSelected(av.sortByTree);
949 listenToViewSelections.setSelected(av.followSelection);
951 showProducts.setEnabled(canShowProducts());
952 setGroovyEnabled(Desktop.getGroovyConsole() != null);
958 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
962 public void setGroovyEnabled(boolean b)
964 runGroovy.setEnabled(b);
967 private IProgressIndicator progressBar;
972 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
975 public void setProgressBar(String message, long id)
977 progressBar.setProgressBar(message, id);
981 public void registerHandler(final long id,
982 final IProgressIndicatorHandler handler)
984 progressBar.registerHandler(id, handler);
989 * @return true if any progress bars are still active
992 public boolean operationInProgress()
994 return progressBar.operationInProgress();
998 * Sets the text of the status bar. Note that setting a null or empty value
999 * will cause the status bar to be hidden, with possibly undesirable flicker
1000 * of the screen layout.
1003 public void setStatus(String text)
1005 statusBar.setText(text == null || text.isEmpty() ? " " : text);
1009 * Added so Castor Mapping file can obtain Jalview Version
1011 public String getVersion()
1013 return jalview.bin.Cache.getProperty("VERSION");
1016 public FeatureRenderer getFeatureRenderer()
1018 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1022 public void fetchSequence_actionPerformed()
1024 new SequenceFetcher(this);
1028 public void addFromFile_actionPerformed(ActionEvent e)
1030 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1034 public void reload_actionPerformed(ActionEvent e)
1036 if (fileName != null)
1038 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1039 // originating file's format
1040 // TODO: work out how to recover feature settings for correct view(s) when
1041 // file is reloaded.
1042 if (FileFormat.Jalview.equals(currentFileFormat))
1044 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1045 for (int i = 0; i < frames.length; i++)
1047 if (frames[i] instanceof AlignFrame && frames[i] != this
1048 && ((AlignFrame) frames[i]).fileName != null
1049 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1053 frames[i].setSelected(true);
1054 Desktop.instance.closeAssociatedWindows();
1055 } catch (java.beans.PropertyVetoException ex)
1061 Desktop.instance.closeAssociatedWindows();
1063 FileLoader loader = new FileLoader();
1064 DataSourceType protocol = fileName.startsWith("http:")
1065 ? DataSourceType.URL
1066 : DataSourceType.FILE;
1067 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1071 Rectangle bounds = this.getBounds();
1073 FileLoader loader = new FileLoader();
1075 AlignFrame newframe = null;
1077 if (fileObject == null)
1080 DataSourceType protocol = (fileName.startsWith("http:")
1081 ? DataSourceType.URL
1082 : DataSourceType.FILE);
1083 newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1088 newframe = loader.LoadFileWaitTillLoaded(fileObject,
1089 DataSourceType.FILE, currentFileFormat);
1092 newframe.setBounds(bounds);
1093 if (featureSettings != null && featureSettings.isShowing())
1095 final Rectangle fspos = featureSettings.frame.getBounds();
1096 // TODO: need a 'show feature settings' function that takes bounds -
1097 // need to refactor Desktop.addFrame
1098 newframe.featureSettings_actionPerformed(null);
1099 final FeatureSettings nfs = newframe.featureSettings;
1100 SwingUtilities.invokeLater(new Runnable()
1105 nfs.frame.setBounds(fspos);
1108 this.featureSettings.close();
1109 this.featureSettings = null;
1111 this.closeMenuItem_actionPerformed(true);
1117 public void addFromText_actionPerformed(ActionEvent e)
1120 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1124 public void addFromURL_actionPerformed(ActionEvent e)
1126 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1130 public void save_actionPerformed(ActionEvent e)
1132 if (fileName == null || (currentFileFormat == null)
1133 || fileName.startsWith("http"))
1135 saveAs_actionPerformed();
1139 saveAlignment(fileName, currentFileFormat);
1144 * Saves the alignment to a file with a name chosen by the user, if necessary
1145 * warning if a file would be overwritten
1148 public void saveAs_actionPerformed()
1150 String format = currentFileFormat == null ? null
1151 : currentFileFormat.getName();
1152 JalviewFileChooser chooser = JalviewFileChooser
1153 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1155 chooser.setFileView(new JalviewFileView());
1156 chooser.setDialogTitle(
1157 MessageManager.getString("label.save_alignment_to_file"));
1158 chooser.setToolTipText(MessageManager.getString("action.save"));
1160 int value = chooser.showSaveDialog(this);
1162 if (value != JalviewFileChooser.APPROVE_OPTION)
1166 currentFileFormat = chooser.getSelectedFormat();
1167 // todo is this (2005) test now obsolete - value is never null?
1168 while (currentFileFormat == null)
1170 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1172 .getString("label.select_file_format_before_saving"),
1173 MessageManager.getString("label.file_format_not_specified"),
1174 JvOptionPane.WARNING_MESSAGE);
1175 currentFileFormat = chooser.getSelectedFormat();
1176 value = chooser.showSaveDialog(this);
1177 if (value != JalviewFileChooser.APPROVE_OPTION)
1183 fileName = chooser.getSelectedFile().getPath();
1185 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1186 Cache.setProperty("LAST_DIRECTORY", fileName);
1187 saveAlignment(fileName, currentFileFormat);
1190 boolean lastSaveSuccessful = false;
1192 FileFormatI lastFormatSaved;
1194 String lastFilenameSaved;
1197 * Raise a dialog or status message for the last call to saveAlignment.
1199 * @return true if last call to saveAlignment(file, format) was successful.
1201 public boolean isSaveAlignmentSuccessful()
1204 if (!lastSaveSuccessful)
1206 JvOptionPane.showInternalMessageDialog(this, MessageManager
1207 .formatMessage("label.couldnt_save_file", new Object[]
1208 { lastFilenameSaved }),
1209 MessageManager.getString("label.error_saving_file"),
1210 JvOptionPane.WARNING_MESSAGE);
1215 setStatus(MessageManager.formatMessage(
1216 "label.successfully_saved_to_file_in_format", new Object[]
1217 { lastFilenameSaved, lastFormatSaved }));
1220 return lastSaveSuccessful;
1224 * Saves the alignment to the specified file path, in the specified format,
1225 * which may be an alignment format, or Jalview project format. If the
1226 * alignment has hidden regions, or the format is one capable of including
1227 * non-sequence data (features, annotations, groups), then the user may be
1228 * prompted to specify what to include in the output.
1233 public void saveAlignment(String file, FileFormatI format)
1235 lastSaveSuccessful = true;
1236 lastFilenameSaved = file;
1237 lastFormatSaved = format;
1239 if (FileFormat.Jalview.equals(format))
1241 String shortName = title;
1242 if (shortName.indexOf(File.separatorChar) > -1)
1244 shortName = shortName.substring(
1245 shortName.lastIndexOf(File.separatorChar) + 1);
1247 lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName);
1249 statusBar.setText(MessageManager.formatMessage(
1250 "label.successfully_saved_to_file_in_format", new Object[]
1251 { fileName, format }));
1256 AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1257 Runnable cancelAction = new Runnable()
1262 lastSaveSuccessful = false;
1265 Runnable outputAction = new Runnable()
1270 // todo defer this to inside formatSequences (or later)
1271 AlignmentExportData exportData = viewport
1272 .getAlignExportData(options);
1273 String output = new FormatAdapter(alignPanel, options)
1274 .formatSequences(format, exportData.getAlignment(),
1275 exportData.getOmitHidden(),
1276 exportData.getStartEndPostions(),
1277 viewport.getAlignment().getHiddenColumns());
1280 lastSaveSuccessful = false;
1284 // create backupfiles object and get new temp filename destination
1285 boolean doBackup = BackupFiles.getEnabled();
1286 BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
1289 String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
1290 PrintWriter out = new PrintWriter(
1291 new FileWriter(tempFilePath));
1295 AlignFrame.this.setTitle(file);
1296 statusBar.setText(MessageManager.formatMessage(
1297 "label.successfully_saved_to_file_in_format", new Object[]
1298 { fileName, format.getName() }));
1299 lastSaveSuccessful = true;
1300 } catch (Exception ex)
1302 lastSaveSuccessful = false;
1303 ex.printStackTrace();
1308 backupfiles.setWriteSuccess(lastSaveSuccessful);
1309 // do the backup file roll and rename the temp file to actual file
1310 lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1317 * show dialog with export options if applicable; else just do it
1319 if (AlignExportOptions.isNeeded(viewport, format))
1321 AlignExportOptions choices = new AlignExportOptions(
1322 alignPanel.getAlignViewport(), format, options);
1323 choices.setResponseAction(0, outputAction);
1324 choices.setResponseAction(1, cancelAction);
1325 choices.showDialog();
1334 * Outputs the alignment to textbox in the requested format, if necessary
1335 * first prompting the user for whether to include hidden regions or
1338 * @param fileFormatName
1341 protected void outputText_actionPerformed(String fileFormatName)
1343 FileFormatI fileFormat = FileFormats.getInstance()
1344 .forName(fileFormatName);
1345 AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1346 Runnable outputAction = new Runnable()
1351 // todo defer this to inside formatSequences (or later)
1352 AlignmentExportData exportData = viewport
1353 .getAlignExportData(options);
1354 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1355 cap.setForInput(null);
1358 FileFormatI format = fileFormat;
1359 cap.setText(new FormatAdapter(alignPanel, options)
1360 .formatSequences(format, exportData.getAlignment(),
1361 exportData.getOmitHidden(),
1362 exportData.getStartEndPostions(),
1363 viewport.getAlignment().getHiddenColumns()));
1364 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1365 "label.alignment_output_command", new Object[]
1366 { fileFormat.getName() }), 600, 500);
1367 } catch (OutOfMemoryError oom)
1369 new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1377 * show dialog with export options if applicable; else just do it
1379 if (AlignExportOptions.isNeeded(viewport, fileFormat))
1381 AlignExportOptions choices = new AlignExportOptions(
1382 alignPanel.getAlignViewport(), fileFormat, options);
1383 choices.setResponseAction(0, outputAction);
1384 choices.showDialog();
1399 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1401 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1402 htmlSVG.exportHTML(null);
1406 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1408 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1409 bjs.exportHTML(null);
1412 public void createImageMap(File file, String image)
1414 alignPanel.makePNGImageMap(file, image);
1418 * Creates a PNG image of the alignment and writes it to the given file. If
1419 * the file is null, the user is prompted to choose a file.
1424 public void createPNG(File f)
1426 alignPanel.makeAlignmentImage(TYPE.PNG, f);
1430 * Creates an EPS image of the alignment and writes it to the given file. If
1431 * the file is null, the user is prompted to choose a file.
1436 public void createEPS(File f)
1438 alignPanel.makeAlignmentImage(TYPE.EPS, f);
1442 * Creates an SVG image of the alignment and writes it to the given file. If
1443 * the file is null, the user is prompted to choose a file.
1448 public void createSVG(File f)
1450 alignPanel.makeAlignmentImage(TYPE.SVG, f);
1454 public void pageSetup_actionPerformed(ActionEvent e)
1456 PrinterJob printJob = PrinterJob.getPrinterJob();
1457 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1467 public void printMenuItem_actionPerformed(ActionEvent e)
1469 // Putting in a thread avoids Swing painting problems
1470 PrintThread thread = new PrintThread(alignPanel);
1475 public void exportFeatures_actionPerformed(ActionEvent e)
1477 new AnnotationExporter(alignPanel).exportFeatures();
1481 public void exportAnnotations_actionPerformed(ActionEvent e)
1483 new AnnotationExporter(alignPanel).exportAnnotations();
1487 public void associatedData_actionPerformed(ActionEvent e)
1489 final JalviewFileChooser chooser = new JalviewFileChooser(
1490 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1491 chooser.setFileView(new JalviewFileView());
1492 chooser.setDialogTitle(
1493 MessageManager.getString("label.load_jalview_annotations"));
1494 chooser.setToolTipText(
1495 MessageManager.getString("label.load_jalview_annotations"));
1496 chooser.setResponseHandler(0, new Runnable()
1501 String choice = chooser.getSelectedFile().getPath();
1502 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1503 loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1507 chooser.showOpenDialog(this);
1511 * Close the current view or all views in the alignment frame. If the frame
1512 * only contains one view then the alignment will be removed from memory.
1514 * @param closeAllTabs
1517 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1519 if (alignPanels != null && alignPanels.size() < 2)
1521 closeAllTabs = true;
1526 if (alignPanels != null)
1530 if (this.isClosed())
1532 // really close all the windows - otherwise wait till
1533 // setClosed(true) is called
1534 for (int i = 0; i < alignPanels.size(); i++)
1536 AlignmentPanel ap = alignPanels.get(i);
1543 closeView(alignPanel);
1548 if (featureSettings != null && featureSettings.isOpen())
1550 featureSettings.close();
1551 featureSettings = null;
1554 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1555 * be called recursively, with the frame now in 'closed' state
1557 this.setClosed(true);
1559 } catch (Exception ex)
1561 ex.printStackTrace();
1566 * Close the specified panel and close up tabs appropriately.
1568 * @param panelToClose
1570 public void closeView(AlignmentPanel panelToClose)
1572 int index = tabbedPane.getSelectedIndex();
1573 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1574 alignPanels.remove(panelToClose);
1575 panelToClose.closePanel();
1576 panelToClose = null;
1578 tabbedPane.removeTabAt(closedindex);
1579 tabbedPane.validate();
1581 if (index > closedindex || index == tabbedPane.getTabCount())
1583 // modify currently selected tab index if necessary.
1587 this.tabSelectionChanged(index);
1593 void updateEditMenuBar()
1596 if (viewport.getHistoryList().size() > 0)
1598 undoMenuItem.setEnabled(true);
1599 CommandI command = viewport.getHistoryList().peek();
1600 undoMenuItem.setText(MessageManager
1601 .formatMessage("label.undo_command", new Object[]
1602 { command.getDescription() }));
1606 undoMenuItem.setEnabled(false);
1607 undoMenuItem.setText(MessageManager.getString("action.undo"));
1610 if (viewport.getRedoList().size() > 0)
1612 redoMenuItem.setEnabled(true);
1614 CommandI command = viewport.getRedoList().peek();
1615 redoMenuItem.setText(MessageManager
1616 .formatMessage("label.redo_command", new Object[]
1617 { command.getDescription() }));
1621 redoMenuItem.setEnabled(false);
1622 redoMenuItem.setText(MessageManager.getString("action.redo"));
1627 public void addHistoryItem(CommandI command)
1629 if (command.getSize() > 0)
1631 viewport.addToHistoryList(command);
1632 viewport.clearRedoList();
1633 updateEditMenuBar();
1634 viewport.updateHiddenColumns();
1635 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1636 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1637 // viewport.getColumnSelection()
1638 // .getHiddenColumns().size() > 0);
1644 * @return alignment objects for all views
1646 AlignmentI[] getViewAlignments()
1648 if (alignPanels != null)
1650 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1652 for (AlignmentPanel ap : alignPanels)
1654 als[i++] = ap.av.getAlignment();
1658 if (viewport != null)
1660 return new AlignmentI[] { viewport.getAlignment() };
1672 protected void undoMenuItem_actionPerformed(ActionEvent e)
1674 if (viewport.getHistoryList().isEmpty())
1678 CommandI command = viewport.getHistoryList().pop();
1679 viewport.addToRedoList(command);
1680 command.undoCommand(getViewAlignments());
1682 AlignmentViewport originalSource = getOriginatingSource(command);
1683 updateEditMenuBar();
1685 if (originalSource != null)
1687 if (originalSource != viewport)
1690 "Implementation worry: mismatch of viewport origin for undo");
1692 originalSource.updateHiddenColumns();
1693 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1695 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1696 // viewport.getColumnSelection()
1697 // .getHiddenColumns().size() > 0);
1698 originalSource.firePropertyChange("alignment", null,
1699 originalSource.getAlignment().getSequences());
1710 protected void redoMenuItem_actionPerformed(ActionEvent e)
1712 if (viewport.getRedoList().size() < 1)
1717 CommandI command = viewport.getRedoList().pop();
1718 viewport.addToHistoryList(command);
1719 command.doCommand(getViewAlignments());
1721 AlignmentViewport originalSource = getOriginatingSource(command);
1722 updateEditMenuBar();
1724 if (originalSource != null)
1727 if (originalSource != viewport)
1730 "Implementation worry: mismatch of viewport origin for redo");
1732 originalSource.updateHiddenColumns();
1733 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1735 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1736 // viewport.getColumnSelection()
1737 // .getHiddenColumns().size() > 0);
1738 originalSource.firePropertyChange("alignment", null,
1739 originalSource.getAlignment().getSequences());
1743 AlignmentViewport getOriginatingSource(CommandI command)
1745 AlignmentViewport originalSource = null;
1746 // For sequence removal and addition, we need to fire
1747 // the property change event FROM the viewport where the
1748 // original alignment was altered
1749 AlignmentI al = null;
1750 if (command instanceof EditCommand)
1752 EditCommand editCommand = (EditCommand) command;
1753 al = editCommand.getAlignment();
1754 List<Component> comps = PaintRefresher.components
1755 .get(viewport.getSequenceSetId());
1757 for (Component comp : comps)
1759 if (comp instanceof AlignmentPanel)
1761 if (al == ((AlignmentPanel) comp).av.getAlignment())
1763 originalSource = ((AlignmentPanel) comp).av;
1770 if (originalSource == null)
1772 // The original view is closed, we must validate
1773 // the current view against the closed view first
1776 PaintRefresher.validateSequences(al, viewport.getAlignment());
1779 originalSource = viewport;
1782 return originalSource;
1791 public void moveSelectedSequences(boolean up)
1793 SequenceGroup sg = viewport.getSelectionGroup();
1799 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1800 viewport.getHiddenRepSequences(), up);
1801 alignPanel.paintAlignment(true, false);
1804 synchronized void slideSequences(boolean right, int size)
1806 List<SequenceI> sg = new ArrayList<>();
1807 if (viewport.cursorMode)
1809 sg.add(viewport.getAlignment()
1810 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1812 else if (viewport.getSelectionGroup() != null
1813 && viewport.getSelectionGroup().getSize() != viewport
1814 .getAlignment().getHeight())
1816 sg = viewport.getSelectionGroup()
1817 .getSequences(viewport.getHiddenRepSequences());
1825 List<SequenceI> invertGroup = new ArrayList<>();
1827 for (SequenceI seq : viewport.getAlignment().getSequences())
1829 if (!sg.contains(seq))
1831 invertGroup.add(seq);
1835 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1837 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1838 for (int i = 0; i < invertGroup.size(); i++)
1840 seqs2[i] = invertGroup.get(i);
1843 SlideSequencesCommand ssc;
1846 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1847 viewport.getGapCharacter());
1851 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1852 viewport.getGapCharacter());
1855 int groupAdjustment = 0;
1856 if (ssc.getGapsInsertedBegin() && right)
1858 if (viewport.cursorMode)
1860 alignPanel.getSeqPanel().moveCursor(size, 0);
1864 groupAdjustment = size;
1867 else if (!ssc.getGapsInsertedBegin() && !right)
1869 if (viewport.cursorMode)
1871 alignPanel.getSeqPanel().moveCursor(-size, 0);
1875 groupAdjustment = -size;
1879 if (groupAdjustment != 0)
1881 viewport.getSelectionGroup().setStartRes(
1882 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1883 viewport.getSelectionGroup().setEndRes(
1884 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1888 * just extend the last slide command if compatible; but not if in
1889 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1891 boolean appendHistoryItem = false;
1892 Deque<CommandI> historyList = viewport.getHistoryList();
1893 boolean inSplitFrame = getSplitViewContainer() != null;
1894 if (!inSplitFrame && historyList != null && historyList.size() > 0
1895 && historyList.peek() instanceof SlideSequencesCommand)
1897 appendHistoryItem = ssc.appendSlideCommand(
1898 (SlideSequencesCommand) historyList.peek());
1901 if (!appendHistoryItem)
1903 addHistoryItem(ssc);
1916 protected void copy_actionPerformed()
1918 if (viewport.getSelectionGroup() == null)
1922 // TODO: preserve the ordering of displayed alignment annotation in any
1923 // internal paste (particularly sequence associated annotation)
1924 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1925 String[] omitHidden = null;
1927 if (viewport.hasHiddenColumns())
1929 omitHidden = viewport.getViewAsString(true);
1932 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1933 seqs, omitHidden, null);
1935 StringSelection ss = new StringSelection(output);
1939 jalview.gui.Desktop.internalCopy = true;
1940 // Its really worth setting the clipboard contents
1941 // to empty before setting the large StringSelection!!
1942 Toolkit.getDefaultToolkit().getSystemClipboard()
1943 .setContents(new StringSelection(""), null);
1945 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1947 } catch (OutOfMemoryError er)
1949 new OOMWarning("copying region", er);
1953 HiddenColumns hiddenColumns = null;
1954 if (viewport.hasHiddenColumns())
1956 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1957 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1959 // create new HiddenColumns object with copy of hidden regions
1960 // between startRes and endRes, offset by startRes
1961 hiddenColumns = new HiddenColumns(
1962 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1963 hiddenCutoff, hiddenOffset);
1966 Desktop.jalviewClipboard = new Object[] { seqs,
1967 viewport.getAlignment().getDataset(), hiddenColumns };
1968 setStatus(MessageManager.formatMessage(
1969 "label.copied_sequences_to_clipboard", new Object[]
1970 { Integer.valueOf(seqs.length).toString() }));
1980 protected void pasteNew_actionPerformed(ActionEvent e)
1992 protected void pasteThis_actionPerformed(ActionEvent e)
1998 * Paste contents of Jalview clipboard
2000 * @param newAlignment
2001 * true to paste to a new alignment, otherwise add to this.
2003 void paste(boolean newAlignment)
2005 boolean externalPaste = true;
2008 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2009 Transferable contents = c.getContents(this);
2011 if (contents == null)
2020 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2021 if (str.length() < 1)
2026 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2028 } catch (OutOfMemoryError er)
2030 new OOMWarning("Out of memory pasting sequences!!", er);
2034 SequenceI[] sequences;
2035 boolean annotationAdded = false;
2036 AlignmentI alignment = null;
2038 if (Desktop.jalviewClipboard != null)
2040 // The clipboard was filled from within Jalview, we must use the
2042 // And dataset from the copied alignment
2043 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2044 // be doubly sure that we create *new* sequence objects.
2045 sequences = new SequenceI[newseq.length];
2046 for (int i = 0; i < newseq.length; i++)
2048 sequences[i] = new Sequence(newseq[i]);
2050 alignment = new Alignment(sequences);
2051 externalPaste = false;
2055 // parse the clipboard as an alignment.
2056 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2058 sequences = alignment.getSequencesArray();
2062 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2068 if (Desktop.jalviewClipboard != null)
2070 // dataset is inherited
2071 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2075 // new dataset is constructed
2076 alignment.setDataset(null);
2078 alwidth = alignment.getWidth() + 1;
2082 AlignmentI pastedal = alignment; // preserve pasted alignment object
2083 // Add pasted sequences and dataset into existing alignment.
2084 alignment = viewport.getAlignment();
2085 alwidth = alignment.getWidth() + 1;
2086 // decide if we need to import sequences from an existing dataset
2087 boolean importDs = Desktop.jalviewClipboard != null
2088 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2089 // importDs==true instructs us to copy over new dataset sequences from
2090 // an existing alignment
2091 Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
2093 // minimum dataset set
2095 for (int i = 0; i < sequences.length; i++)
2099 newDs.addElement(null);
2101 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2103 if (importDs && ds != null)
2105 if (!newDs.contains(ds))
2107 newDs.setElementAt(ds, i);
2108 ds = new Sequence(ds);
2109 // update with new dataset sequence
2110 sequences[i].setDatasetSequence(ds);
2114 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2119 // copy and derive new dataset sequence
2120 sequences[i] = sequences[i].deriveSequence();
2121 alignment.getDataset()
2122 .addSequence(sequences[i].getDatasetSequence());
2123 // TODO: avoid creation of duplicate dataset sequences with a
2124 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2126 alignment.addSequence(sequences[i]); // merges dataset
2130 newDs.clear(); // tidy up
2132 if (alignment.getAlignmentAnnotation() != null)
2134 for (AlignmentAnnotation alan : alignment
2135 .getAlignmentAnnotation())
2137 if (alan.graphGroup > fgroup)
2139 fgroup = alan.graphGroup;
2143 if (pastedal.getAlignmentAnnotation() != null)
2145 // Add any annotation attached to alignment.
2146 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2147 for (int i = 0; i < alann.length; i++)
2149 annotationAdded = true;
2150 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2152 AlignmentAnnotation newann = new AlignmentAnnotation(
2154 if (newann.graphGroup > -1)
2156 if (newGraphGroups.size() <= newann.graphGroup
2157 || newGraphGroups.get(newann.graphGroup) == null)
2159 for (int q = newGraphGroups
2160 .size(); q <= newann.graphGroup; q++)
2162 newGraphGroups.add(q, null);
2164 newGraphGroups.set(newann.graphGroup,
2165 Integer.valueOf(++fgroup));
2167 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2171 newann.padAnnotation(alwidth);
2172 alignment.addAnnotation(newann);
2182 addHistoryItem(new EditCommand(
2183 MessageManager.getString("label.add_sequences"),
2184 Action.PASTE, sequences, 0, alignment.getWidth(),
2187 // Add any annotations attached to sequences
2188 for (int i = 0; i < sequences.length; i++)
2190 if (sequences[i].getAnnotation() != null)
2192 AlignmentAnnotation newann;
2193 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2195 annotationAdded = true;
2196 newann = sequences[i].getAnnotation()[a];
2197 newann.adjustForAlignment();
2198 newann.padAnnotation(alwidth);
2199 if (newann.graphGroup > -1)
2201 if (newann.graphGroup > -1)
2203 if (newGraphGroups.size() <= newann.graphGroup
2204 || newGraphGroups.get(newann.graphGroup) == null)
2206 for (int q = newGraphGroups
2207 .size(); q <= newann.graphGroup; q++)
2209 newGraphGroups.add(q, null);
2211 newGraphGroups.set(newann.graphGroup,
2212 Integer.valueOf(++fgroup));
2214 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2218 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2222 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2230 // propagate alignment changed.
2231 viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
2232 if (annotationAdded)
2234 // Duplicate sequence annotation in all views.
2235 AlignmentI[] alview = this.getViewAlignments();
2236 for (int i = 0; i < sequences.length; i++)
2238 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2243 for (int avnum = 0; avnum < alview.length; avnum++)
2245 if (alview[avnum] != alignment)
2247 // duplicate in a view other than the one with input focus
2248 int avwidth = alview[avnum].getWidth() + 1;
2249 // this relies on sann being preserved after we
2250 // modify the sequence's annotation array for each duplication
2251 for (int a = 0; a < sann.length; a++)
2253 AlignmentAnnotation newann = new AlignmentAnnotation(
2255 sequences[i].addAlignmentAnnotation(newann);
2256 newann.padAnnotation(avwidth);
2257 alview[avnum].addAnnotation(newann); // annotation was
2258 // duplicated earlier
2259 // TODO JAL-1145 graphGroups are not updated for sequence
2260 // annotation added to several views. This may cause
2262 alview[avnum].setAnnotationIndex(newann, a);
2267 buildSortByAnnotationScoresMenu();
2269 viewport.firePropertyChange("alignment", null,
2270 alignment.getSequences());
2271 if (alignPanels != null)
2273 for (AlignmentPanel ap : alignPanels)
2275 ap.validateAnnotationDimensions(false);
2280 alignPanel.validateAnnotationDimensions(false);
2286 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2288 String newtitle = new String("Copied sequences");
2290 if (Desktop.jalviewClipboard != null
2291 && Desktop.jalviewClipboard[2] != null)
2293 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2294 af.viewport.setHiddenColumns(hc);
2297 // >>>This is a fix for the moment, until a better solution is
2299 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2300 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2301 .getFeatureRenderer());
2303 // TODO: maintain provenance of an alignment, rather than just make the
2304 // title a concatenation of operations.
2307 if (title.startsWith("Copied sequences"))
2313 newtitle = newtitle.concat("- from " + title);
2318 newtitle = new String("Pasted sequences");
2321 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2326 } catch (Exception ex)
2328 ex.printStackTrace();
2329 System.out.println("Exception whilst pasting: " + ex);
2330 // could be anything being pasted in here
2336 protected void expand_newalign(ActionEvent e)
2340 AlignmentI alignment = AlignmentUtils
2341 .expandContext(getViewport().getAlignment(), -1);
2342 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2344 String newtitle = new String("Flanking alignment");
2346 if (Desktop.jalviewClipboard != null
2347 && Desktop.jalviewClipboard[2] != null)
2349 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2350 af.viewport.setHiddenColumns(hc);
2353 // >>>This is a fix for the moment, until a better solution is
2355 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2356 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2357 .getFeatureRenderer());
2359 // TODO: maintain provenance of an alignment, rather than just make the
2360 // title a concatenation of operations.
2362 if (title.startsWith("Copied sequences"))
2368 newtitle = newtitle.concat("- from " + title);
2372 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2374 } catch (Exception ex)
2376 ex.printStackTrace();
2377 System.out.println("Exception whilst pasting: " + ex);
2378 // could be anything being pasted in here
2379 } catch (OutOfMemoryError oom)
2381 new OOMWarning("Viewing flanking region of alignment", oom);
2386 * Action Cut (delete and copy) the selected region
2389 protected void cut_actionPerformed()
2391 copy_actionPerformed();
2392 delete_actionPerformed();
2396 * Performs menu option to Delete the currently selected region
2399 protected void delete_actionPerformed()
2402 SequenceGroup sg = viewport.getSelectionGroup();
2408 Runnable okAction = new Runnable()
2413 SequenceI[] cut = sg.getSequences()
2414 .toArray(new SequenceI[sg.getSize()]);
2416 addHistoryItem(new EditCommand(
2417 MessageManager.getString("label.cut_sequences"), Action.CUT,
2418 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2419 viewport.getAlignment()));
2421 viewport.setSelectionGroup(null);
2422 viewport.sendSelection();
2423 viewport.getAlignment().deleteGroup(sg);
2425 viewport.firePropertyChange("alignment", null,
2426 viewport.getAlignment().getSequences());
2427 if (viewport.getAlignment().getHeight() < 1)
2431 AlignFrame.this.setClosed(true);
2432 } catch (Exception ex)
2439 * If the cut affects all sequences, prompt for confirmation
2441 boolean wholeHeight = sg.getSize() == viewport.getAlignment().getHeight();
2442 boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2443 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2444 if (wholeHeight && wholeWidth)
2446 JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2447 dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2448 Object[] options = new Object[] { MessageManager.getString("action.ok"),
2449 MessageManager.getString("action.cancel") };
2450 dialog.showDialog(MessageManager.getString("warn.delete_all"),
2451 MessageManager.getString("label.delete_all"),
2452 JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2453 options, options[0]);
2467 protected void deleteGroups_actionPerformed(ActionEvent e)
2469 if (avc.deleteGroups())
2471 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2472 alignPanel.updateAnnotation();
2473 alignPanel.paintAlignment(true, true);
2484 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2486 SequenceGroup sg = new SequenceGroup(
2487 viewport.getAlignment().getSequences());
2489 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2490 viewport.setSelectionGroup(sg);
2491 viewport.isSelectionGroupChanged(true);
2492 viewport.sendSelection();
2493 // JAL-2034 - should delegate to
2494 // alignPanel to decide if overview needs
2496 alignPanel.paintAlignment(false, false);
2497 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2507 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2509 if (viewport.cursorMode)
2511 alignPanel.getSeqPanel().keyboardNo1 = null;
2512 alignPanel.getSeqPanel().keyboardNo2 = null;
2514 viewport.setSelectionGroup(null);
2515 viewport.getColumnSelection().clear();
2516 viewport.setSelectionGroup(null);
2517 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2518 // JAL-2034 - should delegate to
2519 // alignPanel to decide if overview needs
2521 alignPanel.paintAlignment(false, false);
2522 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2523 viewport.sendSelection();
2533 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2535 SequenceGroup sg = viewport.getSelectionGroup();
2539 selectAllSequenceMenuItem_actionPerformed(null);
2544 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2546 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2548 // JAL-2034 - should delegate to
2549 // alignPanel to decide if overview needs
2552 alignPanel.paintAlignment(true, false);
2553 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2554 viewport.sendSelection();
2558 public void invertColSel_actionPerformed(ActionEvent e)
2560 viewport.invertColumnSelection();
2561 alignPanel.paintAlignment(true, false);
2562 viewport.sendSelection();
2572 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2574 trimAlignment(true);
2584 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2586 trimAlignment(false);
2589 void trimAlignment(boolean trimLeft)
2591 ColumnSelection colSel = viewport.getColumnSelection();
2594 if (!colSel.isEmpty())
2598 column = colSel.getMin();
2602 column = colSel.getMax();
2606 if (viewport.getSelectionGroup() != null)
2608 seqs = viewport.getSelectionGroup()
2609 .getSequencesAsArray(viewport.getHiddenRepSequences());
2613 seqs = viewport.getAlignment().getSequencesArray();
2616 TrimRegionCommand trimRegion;
2619 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2620 column, viewport.getAlignment());
2621 viewport.getRanges().setStartRes(0);
2625 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2626 column, viewport.getAlignment());
2629 setStatus(MessageManager
2630 .formatMessage("label.removed_columns", new String[]
2631 { Integer.valueOf(trimRegion.getSize()).toString() }));
2633 addHistoryItem(trimRegion);
2635 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2637 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2638 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2640 viewport.getAlignment().deleteGroup(sg);
2644 viewport.firePropertyChange("alignment", null,
2645 viewport.getAlignment().getSequences());
2656 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2658 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2661 if (viewport.getSelectionGroup() != null)
2663 seqs = viewport.getSelectionGroup()
2664 .getSequencesAsArray(viewport.getHiddenRepSequences());
2665 start = viewport.getSelectionGroup().getStartRes();
2666 end = viewport.getSelectionGroup().getEndRes();
2670 seqs = viewport.getAlignment().getSequencesArray();
2673 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2674 "Remove Gapped Columns", seqs, start, end,
2675 viewport.getAlignment());
2677 addHistoryItem(removeGapCols);
2679 setStatus(MessageManager
2680 .formatMessage("label.removed_empty_columns", new Object[]
2681 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2683 // This is to maintain viewport position on first residue
2684 // of first sequence
2685 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2686 ViewportRanges ranges = viewport.getRanges();
2687 int startRes = seq.findPosition(ranges.getStartRes());
2688 // ShiftList shifts;
2689 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2690 // edit.alColumnChanges=shifts.getInverse();
2691 // if (viewport.hasHiddenColumns)
2692 // viewport.getColumnSelection().compensateForEdits(shifts);
2693 ranges.setStartRes(seq.findIndex(startRes) - 1);
2694 viewport.firePropertyChange("alignment", null,
2695 viewport.getAlignment().getSequences());
2706 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2708 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2711 if (viewport.getSelectionGroup() != null)
2713 seqs = viewport.getSelectionGroup()
2714 .getSequencesAsArray(viewport.getHiddenRepSequences());
2715 start = viewport.getSelectionGroup().getStartRes();
2716 end = viewport.getSelectionGroup().getEndRes();
2720 seqs = viewport.getAlignment().getSequencesArray();
2723 // This is to maintain viewport position on first residue
2724 // of first sequence
2725 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2726 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2728 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2729 viewport.getAlignment()));
2731 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2733 viewport.firePropertyChange("alignment", null,
2734 viewport.getAlignment().getSequences());
2745 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2747 viewport.setPadGaps(padGapsMenuitem.isSelected());
2748 viewport.firePropertyChange("alignment", null,
2749 viewport.getAlignment().getSequences());
2759 public void findMenuItem_actionPerformed(ActionEvent e)
2765 * Create a new view of the current alignment.
2768 public void newView_actionPerformed(ActionEvent e)
2770 newView(null, true);
2774 * Creates and shows a new view of the current alignment.
2777 * title of newly created view; if null, one will be generated
2778 * @param copyAnnotation
2779 * if true then duplicate all annnotation, groups and settings
2780 * @return new alignment panel, already displayed.
2782 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2785 * Create a new AlignmentPanel (with its own, new Viewport)
2787 AlignmentPanel newap = new jalview.project.Jalview2XML()
2788 .copyAlignPanel(alignPanel);
2789 if (!copyAnnotation)
2792 * remove all groups and annotation except for the automatic stuff
2794 newap.av.getAlignment().deleteAllGroups();
2795 newap.av.getAlignment().deleteAllAnnotations(false);
2798 newap.av.setGatherViewsHere(false);
2800 if (viewport.getViewName() == null)
2802 viewport.setViewName(MessageManager
2803 .getString("label.view_name_original"));
2807 * Views share the same edits undo and redo stacks
2809 newap.av.setHistoryList(viewport.getHistoryList());
2810 newap.av.setRedoList(viewport.getRedoList());
2813 * copy any visualisation settings that are not saved in the project
2815 newap.av.setColourAppliesToAllGroups(
2816 viewport.getColourAppliesToAllGroups());
2819 * Views share the same mappings; need to deregister any new mappings
2820 * created by copyAlignPanel, and register the new reference to the shared
2823 newap.av.replaceMappings(viewport.getAlignment());
2826 * start up cDNA consensus (if applicable) now mappings are in place
2828 if (newap.av.initComplementConsensus())
2830 newap.refresh(true); // adjust layout of annotations
2833 newap.av.setViewName(getNewViewName(viewTitle));
2835 addAlignmentPanel(newap, true);
2836 newap.alignmentChanged();
2838 if (alignPanels.size() == 2)
2840 viewport.setGatherViewsHere(true);
2842 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2847 * Make a new name for the view, ensuring it is unique within the current
2848 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2849 * these now use viewId. Unique view names are still desirable for usability.)
2854 protected String getNewViewName(String viewTitle)
2856 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2857 boolean addFirstIndex = false;
2858 if (viewTitle == null || viewTitle.trim().length() == 0)
2860 viewTitle = MessageManager.getString("action.view");
2861 addFirstIndex = true;
2865 index = 1;// we count from 1 if given a specific name
2867 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2869 List<Component> comps = PaintRefresher.components
2870 .get(viewport.getSequenceSetId());
2872 List<String> existingNames = getExistingViewNames(comps);
2874 while (existingNames.contains(newViewName))
2876 newViewName = viewTitle + " " + (++index);
2882 * Returns a list of distinct view names found in the given list of
2883 * components. View names are held on the viewport of an AlignmentPanel.
2888 protected List<String> getExistingViewNames(List<Component> comps)
2890 List<String> existingNames = new ArrayList<>();
2891 for (Component comp : comps)
2893 if (comp instanceof AlignmentPanel)
2895 AlignmentPanel ap = (AlignmentPanel) comp;
2896 if (!existingNames.contains(ap.av.getViewName()))
2898 existingNames.add(ap.av.getViewName());
2902 return existingNames;
2906 * Explode tabbed views into separate windows.
2909 public void expandViews_actionPerformed(ActionEvent e)
2911 Desktop.explodeViews(this);
2915 * Gather views in separate windows back into a tabbed presentation.
2918 public void gatherViews_actionPerformed(ActionEvent e)
2920 Desktop.instance.gatherViews(this);
2930 public void font_actionPerformed(ActionEvent e)
2932 new FontChooser(alignPanel);
2942 protected void seqLimit_actionPerformed(ActionEvent e)
2944 viewport.setShowJVSuffix(seqLimits.isSelected());
2946 alignPanel.getIdPanel().getIdCanvas()
2947 .setPreferredSize(alignPanel.calculateIdWidth());
2948 alignPanel.paintAlignment(true, false);
2952 public void idRightAlign_actionPerformed(ActionEvent e)
2954 viewport.setRightAlignIds(idRightAlign.isSelected());
2955 alignPanel.paintAlignment(false, false);
2959 public void centreColumnLabels_actionPerformed(ActionEvent e)
2961 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2962 alignPanel.paintAlignment(false, false);
2968 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2971 protected void followHighlight_actionPerformed()
2974 * Set the 'follow' flag on the Viewport (and scroll to position if now
2977 final boolean state = this.followHighlightMenuItem.getState();
2978 viewport.setFollowHighlight(state);
2981 alignPanel.scrollToPosition(viewport.getSearchResults());
2992 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2994 viewport.setColourText(colourTextMenuItem.isSelected());
2995 alignPanel.paintAlignment(false, false);
3005 public void wrapMenuItem_actionPerformed(ActionEvent e)
3007 scaleAbove.setVisible(wrapMenuItem.isSelected());
3008 scaleLeft.setVisible(wrapMenuItem.isSelected());
3009 scaleRight.setVisible(wrapMenuItem.isSelected());
3010 viewport.setWrapAlignment(wrapMenuItem.isSelected());
3011 alignPanel.updateLayout();
3015 public void showAllSeqs_actionPerformed(ActionEvent e)
3017 viewport.showAllHiddenSeqs();
3021 public void showAllColumns_actionPerformed(ActionEvent e)
3023 viewport.showAllHiddenColumns();
3024 alignPanel.paintAlignment(true, true);
3025 viewport.sendSelection();
3029 public void hideSelSequences_actionPerformed(ActionEvent e)
3031 viewport.hideAllSelectedSeqs();
3035 * called by key handler and the hide all/show all menu items
3040 protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3043 boolean hide = false;
3044 SequenceGroup sg = viewport.getSelectionGroup();
3045 if (!toggleSeqs && !toggleCols)
3047 // Hide everything by the current selection - this is a hack - we do the
3048 // invert and then hide
3049 // first check that there will be visible columns after the invert.
3050 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3051 && sg.getStartRes() <= sg.getEndRes()))
3053 // now invert the sequence set, if required - empty selection implies
3054 // that no hiding is required.
3057 invertSequenceMenuItem_actionPerformed(null);
3058 sg = viewport.getSelectionGroup();
3062 viewport.expandColSelection(sg, true);
3063 // finally invert the column selection and get the new sequence
3065 invertColSel_actionPerformed(null);
3072 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3074 hideSelSequences_actionPerformed(null);
3077 else if (!(toggleCols && viewport.hasSelectedColumns()))
3079 showAllSeqs_actionPerformed(null);
3085 if (viewport.hasSelectedColumns())
3087 hideSelColumns_actionPerformed(null);
3090 viewport.setSelectionGroup(sg);
3095 showAllColumns_actionPerformed(null);
3104 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3105 * event.ActionEvent)
3108 public void hideAllButSelection_actionPerformed(ActionEvent e)
3110 toggleHiddenRegions(false, false);
3111 viewport.sendSelection();
3118 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3122 public void hideAllSelection_actionPerformed(ActionEvent e)
3124 SequenceGroup sg = viewport.getSelectionGroup();
3125 viewport.expandColSelection(sg, false);
3126 viewport.hideAllSelectedSeqs();
3127 viewport.hideSelectedColumns();
3128 alignPanel.updateLayout();
3129 alignPanel.paintAlignment(true, true);
3130 viewport.sendSelection();
3137 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3141 public void showAllhidden_actionPerformed(ActionEvent e)
3143 viewport.showAllHiddenColumns();
3144 viewport.showAllHiddenSeqs();
3145 alignPanel.paintAlignment(true, true);
3146 viewport.sendSelection();
3150 public void hideSelColumns_actionPerformed(ActionEvent e)
3152 viewport.hideSelectedColumns();
3153 alignPanel.updateLayout();
3154 alignPanel.paintAlignment(true, true);
3155 viewport.sendSelection();
3159 public void hiddenMarkers_actionPerformed(ActionEvent e)
3161 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3172 protected void scaleAbove_actionPerformed(ActionEvent e)
3174 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3175 alignPanel.updateLayout();
3176 alignPanel.paintAlignment(true, false);
3186 protected void scaleLeft_actionPerformed(ActionEvent e)
3188 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3189 alignPanel.updateLayout();
3190 alignPanel.paintAlignment(true, false);
3200 protected void scaleRight_actionPerformed(ActionEvent e)
3202 viewport.setScaleRightWrapped(scaleRight.isSelected());
3203 alignPanel.updateLayout();
3204 alignPanel.paintAlignment(true, false);
3214 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3216 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3217 alignPanel.paintAlignment(false, false);
3227 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3229 viewport.setShowText(viewTextMenuItem.isSelected());
3230 alignPanel.paintAlignment(false, false);
3240 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3242 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3243 alignPanel.paintAlignment(false, false);
3246 public FeatureSettings featureSettings;
3249 public FeatureSettingsControllerI getFeatureSettingsUI()
3251 return featureSettings;
3255 public void featureSettings_actionPerformed(ActionEvent e)
3257 showFeatureSettingsUI();
3261 public FeatureSettingsControllerI showFeatureSettingsUI()
3263 if (featureSettings != null)
3265 featureSettings.closeOldSettings();
3266 featureSettings = null;
3268 if (!showSeqFeatures.isSelected())
3270 // make sure features are actually displayed
3271 showSeqFeatures.setSelected(true);
3272 showSeqFeatures_actionPerformed(null);
3274 featureSettings = new FeatureSettings(this);
3275 return featureSettings;
3279 * Set or clear 'Show Sequence Features'
3285 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3287 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3288 alignPanel.paintAlignment(true, true);
3292 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3293 * the annotations panel as a whole.
3295 * The options to show/hide all annotations should be enabled when the panel
3296 * is shown, and disabled when the panel is hidden.
3301 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3303 final boolean setVisible = annotationPanelMenuItem.isSelected();
3304 viewport.setShowAnnotation(setVisible);
3305 this.showAllSeqAnnotations.setEnabled(setVisible);
3306 this.hideAllSeqAnnotations.setEnabled(setVisible);
3307 this.showAllAlAnnotations.setEnabled(setVisible);
3308 this.hideAllAlAnnotations.setEnabled(setVisible);
3309 alignPanel.updateLayout();
3313 public void alignmentProperties()
3316 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3319 String content = MessageManager.formatMessage("label.html_content",
3321 { contents.toString() });
3324 if (Platform.isJS())
3326 JLabel textLabel = new JLabel();
3327 textLabel.setText(content);
3328 textLabel.setBackground(Color.WHITE);
3330 pane = new JPanel(new BorderLayout());
3331 ((JPanel) pane).setOpaque(true);
3332 pane.setBackground(Color.WHITE);
3333 ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3342 JEditorPane editPane = new JEditorPane("text/html", "");
3343 editPane.setEditable(false);
3344 editPane.setText(content);
3348 JInternalFrame frame = new JInternalFrame();
3350 frame.getContentPane().add(new JScrollPane(pane));
3352 Desktop.addInternalFrame(frame, MessageManager
3353 .formatMessage("label.alignment_properties", new Object[]
3354 { getTitle() }), 500, 400);
3364 public void overviewMenuItem_actionPerformed(ActionEvent e)
3366 if (alignPanel.overviewPanel != null)
3371 JInternalFrame frame = new JInternalFrame();
3372 final OverviewPanel overview = new OverviewPanel(alignPanel);
3373 frame.setContentPane(overview);
3374 Desktop.addInternalFrame(frame, MessageManager
3375 .formatMessage("label.overview_params", new Object[]
3376 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3379 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3380 frame.addInternalFrameListener(
3381 new javax.swing.event.InternalFrameAdapter()
3384 public void internalFrameClosed(
3385 javax.swing.event.InternalFrameEvent evt)
3388 alignPanel.setOverviewPanel(null);
3391 if (getKeyListeners().length > 0)
3393 frame.addKeyListener(getKeyListeners()[0]);
3396 alignPanel.setOverviewPanel(overview);
3400 public void textColour_actionPerformed()
3402 new TextColourChooser().chooseColour(alignPanel, null);
3406 * public void covariationColour_actionPerformed() {
3408 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3412 public void annotationColour_actionPerformed()
3414 new AnnotationColourChooser(viewport, alignPanel);
3418 public void annotationColumn_actionPerformed(ActionEvent e)
3420 new AnnotationColumnChooser(viewport, alignPanel);
3424 * Action on the user checking or unchecking the option to apply the selected
3425 * colour scheme to all groups. If unchecked, groups may have their own
3426 * independent colour schemes.
3431 public void applyToAllGroups_actionPerformed(boolean selected)
3433 viewport.setColourAppliesToAllGroups(selected);
3437 * Action on user selecting a colour from the colour menu
3440 * the name (not the menu item label!) of the colour scheme
3443 public void changeColour_actionPerformed(String name)
3446 * 'User Defined' opens a panel to configure or load a
3447 * user-defined colour scheme
3449 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3451 new UserDefinedColours(alignPanel);
3456 * otherwise set the chosen colour scheme (or null for 'None')
3458 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3460 viewport.getAlignment(), viewport.getHiddenRepSequences());
3465 * Actions on setting or changing the alignment colour scheme
3470 public void changeColour(ColourSchemeI cs)
3472 // TODO: pull up to controller method
3473 ColourMenuHelper.setColourSelected(colourMenu, cs);
3475 viewport.setGlobalColourScheme(cs);
3477 alignPanel.paintAlignment(true, true);
3481 * Show the PID threshold slider panel
3484 protected void modifyPID_actionPerformed()
3486 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3487 alignPanel.getViewName());
3488 SliderPanel.showPIDSlider();
3492 * Show the Conservation slider panel
3495 protected void modifyConservation_actionPerformed()
3497 SliderPanel.setConservationSlider(alignPanel,
3498 viewport.getResidueShading(), alignPanel.getViewName());
3499 SliderPanel.showConservationSlider();
3503 * Action on selecting or deselecting (Colour) By Conservation
3506 public void conservationMenuItem_actionPerformed(boolean selected)
3508 modifyConservation.setEnabled(selected);
3509 viewport.setConservationSelected(selected);
3510 viewport.getResidueShading().setConservationApplied(selected);
3512 changeColour(viewport.getGlobalColourScheme());
3515 modifyConservation_actionPerformed();
3519 SliderPanel.hideConservationSlider();
3524 * Action on selecting or deselecting (Colour) Above PID Threshold
3527 public void abovePIDThreshold_actionPerformed(boolean selected)
3529 modifyPID.setEnabled(selected);
3530 viewport.setAbovePIDThreshold(selected);
3533 viewport.getResidueShading().setThreshold(0,
3534 viewport.isIgnoreGapsConsensus());
3537 changeColour(viewport.getGlobalColourScheme());
3540 modifyPID_actionPerformed();
3544 SliderPanel.hidePIDSlider();
3555 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3557 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3558 AlignmentSorter.sortByPID(viewport.getAlignment(),
3559 viewport.getAlignment().getSequenceAt(0));
3560 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3561 viewport.getAlignment()));
3562 alignPanel.paintAlignment(true, false);
3572 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3574 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3575 AlignmentSorter.sortByID(viewport.getAlignment());
3577 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3578 alignPanel.paintAlignment(true, false);
3588 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3590 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3591 AlignmentSorter.sortByLength(viewport.getAlignment());
3592 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3593 viewport.getAlignment()));
3594 alignPanel.paintAlignment(true, false);
3604 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3606 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3607 AlignmentSorter.sortByGroup(viewport.getAlignment());
3608 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3609 viewport.getAlignment()));
3611 alignPanel.paintAlignment(true, false);
3621 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3623 new RedundancyPanel(alignPanel, this);
3633 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3635 if ((viewport.getSelectionGroup() == null)
3636 || (viewport.getSelectionGroup().getSize() < 2))
3638 JvOptionPane.showInternalMessageDialog(this,
3639 MessageManager.getString(
3640 "label.you_must_select_least_two_sequences"),
3641 MessageManager.getString("label.invalid_selection"),
3642 JvOptionPane.WARNING_MESSAGE);
3646 JInternalFrame frame = new JInternalFrame();
3647 frame.setContentPane(new PairwiseAlignPanel(viewport));
3648 Desktop.addInternalFrame(frame,
3649 MessageManager.getString("action.pairwise_alignment"), 600,
3655 public void autoCalculate_actionPerformed(ActionEvent e)
3657 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3658 if (viewport.autoCalculateConsensus)
3660 viewport.firePropertyChange("alignment", null,
3661 viewport.getAlignment().getSequences());
3666 public void sortByTreeOption_actionPerformed(ActionEvent e)
3668 viewport.sortByTree = sortByTree.isSelected();
3672 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3674 viewport.followSelection = listenToViewSelections.isSelected();
3678 * Constructs a tree panel and adds it to the desktop
3681 * tree type (NJ or AV)
3683 * name of score model used to compute the tree
3685 * parameters for the distance or similarity calculation
3687 void newTreePanel(String type, String modelName,
3688 SimilarityParamsI options)
3690 String frameTitle = "";
3693 boolean onSelection = false;
3694 if (viewport.getSelectionGroup() != null
3695 && viewport.getSelectionGroup().getSize() > 0)
3697 SequenceGroup sg = viewport.getSelectionGroup();
3699 /* Decide if the selection is a column region */
3700 for (SequenceI _s : sg.getSequences())
3702 if (_s.getLength() < sg.getEndRes())
3704 JvOptionPane.showMessageDialog(Desktop.desktop,
3705 MessageManager.getString(
3706 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3707 MessageManager.getString(
3708 "label.sequences_selection_not_aligned"),
3709 JvOptionPane.WARNING_MESSAGE);
3718 if (viewport.getAlignment().getHeight() < 2)
3724 tp = new TreePanel(alignPanel, type, modelName, options);
3725 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3727 frameTitle += " from ";
3729 if (viewport.getViewName() != null)
3731 frameTitle += viewport.getViewName() + " of ";
3734 frameTitle += this.title;
3736 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3747 public void addSortByOrderMenuItem(String title,
3748 final AlignmentOrder order)
3750 final JMenuItem item = new JMenuItem(MessageManager
3751 .formatMessage("action.by_title_param", new Object[]
3754 item.addActionListener(new java.awt.event.ActionListener()
3757 public void actionPerformed(ActionEvent e)
3759 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3761 // TODO: JBPNote - have to map order entries to curent SequenceI
3763 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3765 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3766 viewport.getAlignment()));
3768 alignPanel.paintAlignment(true, false);
3774 * Add a new sort by annotation score menu item
3777 * the menu to add the option to
3779 * the label used to retrieve scores for each sequence on the
3782 public void addSortByAnnotScoreMenuItem(JMenu sort,
3783 final String scoreLabel)
3785 final JMenuItem item = new JMenuItem(scoreLabel);
3787 item.addActionListener(new java.awt.event.ActionListener()
3790 public void actionPerformed(ActionEvent e)
3792 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3793 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3794 viewport.getAlignment());// ,viewport.getSelectionGroup());
3795 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3796 viewport.getAlignment()));
3797 alignPanel.paintAlignment(true, false);
3803 * last hash for alignment's annotation array - used to minimise cost of
3806 protected int _annotationScoreVectorHash;
3809 * search the alignment and rebuild the sort by annotation score submenu the
3810 * last alignment annotation vector hash is stored to minimize cost of
3811 * rebuilding in subsequence calls.
3815 public void buildSortByAnnotationScoresMenu()
3817 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3822 if (viewport.getAlignment().getAlignmentAnnotation()
3823 .hashCode() != _annotationScoreVectorHash)
3825 sortByAnnotScore.removeAll();
3826 // almost certainly a quicker way to do this - but we keep it simple
3827 Hashtable<String, String> scoreSorts = new Hashtable<>();
3828 AlignmentAnnotation aann[];
3829 for (SequenceI sqa : viewport.getAlignment().getSequences())
3831 aann = sqa.getAnnotation();
3832 for (int i = 0; aann != null && i < aann.length; i++)
3834 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3836 scoreSorts.put(aann[i].label, aann[i].label);
3840 Enumeration<String> labels = scoreSorts.keys();
3841 while (labels.hasMoreElements())
3843 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3844 labels.nextElement());
3846 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3849 _annotationScoreVectorHash = viewport.getAlignment()
3850 .getAlignmentAnnotation().hashCode();
3855 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3856 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3857 * call. Listeners are added to remove the menu item when the treePanel is
3858 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3862 public void buildTreeSortMenu()
3864 sortByTreeMenu.removeAll();
3866 List<Component> comps = PaintRefresher.components
3867 .get(viewport.getSequenceSetId());
3868 List<TreePanel> treePanels = new ArrayList<>();
3869 for (Component comp : comps)
3871 if (comp instanceof TreePanel)
3873 treePanels.add((TreePanel) comp);
3877 if (treePanels.size() < 1)
3879 sortByTreeMenu.setVisible(false);
3883 sortByTreeMenu.setVisible(true);
3885 for (final TreePanel tp : treePanels)
3887 final JMenuItem item = new JMenuItem(tp.getTitle());
3888 item.addActionListener(new java.awt.event.ActionListener()
3891 public void actionPerformed(ActionEvent e)
3893 tp.sortByTree_actionPerformed();
3894 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3899 sortByTreeMenu.add(item);
3903 public boolean sortBy(AlignmentOrder alorder, String undoname)
3905 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3906 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3907 if (undoname != null)
3909 addHistoryItem(new OrderCommand(undoname, oldOrder,
3910 viewport.getAlignment()));
3912 alignPanel.paintAlignment(true, false);
3917 * Work out whether the whole set of sequences or just the selected set will
3918 * be submitted for multiple alignment.
3921 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3923 // Now, check we have enough sequences
3924 AlignmentView msa = null;
3926 if ((viewport.getSelectionGroup() != null)
3927 && (viewport.getSelectionGroup().getSize() > 1))
3929 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3930 // some common interface!
3932 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3933 * SequenceI[sz = seqs.getSize(false)];
3935 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3936 * seqs.getSequenceAt(i); }
3938 msa = viewport.getAlignmentView(true);
3940 else if (viewport.getSelectionGroup() != null
3941 && viewport.getSelectionGroup().getSize() == 1)
3943 int option = JvOptionPane.showConfirmDialog(this,
3944 MessageManager.getString("warn.oneseq_msainput_selection"),
3945 MessageManager.getString("label.invalid_selection"),
3946 JvOptionPane.OK_CANCEL_OPTION);
3947 if (option == JvOptionPane.OK_OPTION)
3949 msa = viewport.getAlignmentView(false);
3954 msa = viewport.getAlignmentView(false);
3960 * Decides what is submitted to a secondary structure prediction service: the
3961 * first sequence in the alignment, or in the current selection, or, if the
3962 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3963 * region or the whole alignment. (where the first sequence in the set is the
3964 * one that the prediction will be for).
3966 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3968 AlignmentView seqs = null;
3970 if ((viewport.getSelectionGroup() != null)
3971 && (viewport.getSelectionGroup().getSize() > 0))
3973 seqs = viewport.getAlignmentView(true);
3977 seqs = viewport.getAlignmentView(false);
3979 // limit sequences - JBPNote in future - could spawn multiple prediction
3981 // TODO: viewport.getAlignment().isAligned is a global state - the local
3982 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3983 if (!viewport.getAlignment().isAligned(false))
3985 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3986 // TODO: if seqs.getSequences().length>1 then should really have warned
4000 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4002 // Pick the tree file
4003 JalviewFileChooser chooser = new JalviewFileChooser(
4004 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4005 chooser.setFileView(new JalviewFileView());
4006 chooser.setDialogTitle(
4007 MessageManager.getString("label.select_newick_like_tree_file"));
4008 chooser.setToolTipText(
4009 MessageManager.getString("label.load_tree_file"));
4011 chooser.setResponseHandler(0,new Runnable()
4016 String filePath = chooser.getSelectedFile().getPath();
4017 Cache.setProperty("LAST_DIRECTORY", filePath);
4018 NewickFile fin = null;
4021 fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4022 DataSourceType.FILE));
4023 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4024 } catch (Exception ex)
4026 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4028 .getString("label.problem_reading_tree_file"),
4029 JvOptionPane.WARNING_MESSAGE);
4030 ex.printStackTrace();
4032 if (fin != null && fin.hasWarningMessage())
4034 JvOptionPane.showMessageDialog(Desktop.desktop,
4035 fin.getWarningMessage(),
4036 MessageManager.getString(
4037 "label.possible_problem_with_tree_file"),
4038 JvOptionPane.WARNING_MESSAGE);
4042 chooser.showOpenDialog(this);
4045 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4047 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4050 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4051 int h, int x, int y)
4053 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4057 * Add a treeviewer for the tree extracted from a Newick file object to the
4058 * current alignment view
4065 * Associated alignment input data (or null)
4074 * @return TreePanel handle
4076 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4077 AlignmentView input, int w, int h, int x, int y)
4079 TreePanel tp = null;
4085 if (nf.getTree() != null)
4087 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4093 tp.setLocation(x, y);
4096 Desktop.addInternalFrame(tp, treeTitle, w, h);
4098 } catch (Exception ex)
4100 ex.printStackTrace();
4106 private boolean buildingMenu = false;
4109 * Generates menu items and listener event actions for web service clients
4112 public void BuildWebServiceMenu()
4114 while (buildingMenu)
4118 System.err.println("Waiting for building menu to finish.");
4120 } catch (Exception e)
4124 final AlignFrame me = this;
4125 buildingMenu = true;
4126 new Thread(new Runnable()
4131 final List<JMenuItem> legacyItems = new ArrayList<>();
4134 // System.err.println("Building ws menu again "
4135 // + Thread.currentThread());
4136 // TODO: add support for context dependent disabling of services based
4138 // alignment and current selection
4139 // TODO: add additional serviceHandle parameter to specify abstract
4141 // class independently of AbstractName
4142 // TODO: add in rediscovery GUI function to restart discoverer
4143 // TODO: group services by location as well as function and/or
4145 // object broker mechanism.
4146 final Vector<JMenu> wsmenu = new Vector<>();
4147 final IProgressIndicator af = me;
4150 * do not i18n these strings - they are hard-coded in class
4151 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4152 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4154 final JMenu msawsmenu = new JMenu("Alignment");
4155 final JMenu secstrmenu = new JMenu(
4156 "Secondary Structure Prediction");
4157 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4158 final JMenu analymenu = new JMenu("Analysis");
4159 final JMenu dismenu = new JMenu("Protein Disorder");
4160 // JAL-940 - only show secondary structure prediction services from
4161 // the legacy server
4162 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4164 Discoverer.services != null && (Discoverer.services.size() > 0))
4166 // TODO: refactor to allow list of AbstractName/Handler bindings to
4168 // stored or retrieved from elsewhere
4169 // No MSAWS used any more:
4170 // Vector msaws = null; // (Vector)
4171 // Discoverer.services.get("MsaWS");
4172 Vector<ServiceHandle> secstrpr = Discoverer.services
4174 if (secstrpr != null)
4176 // Add any secondary structure prediction services
4177 for (int i = 0, j = secstrpr.size(); i < j; i++)
4179 final ext.vamsas.ServiceHandle sh = secstrpr
4181 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4182 .getServiceClient(sh);
4183 int p = secstrmenu.getItemCount();
4184 impl.attachWSMenuEntry(secstrmenu, me);
4185 int q = secstrmenu.getItemCount();
4186 for (int litm = p; litm < q; litm++)
4188 legacyItems.add(secstrmenu.getItem(litm));
4194 // Add all submenus in the order they should appear on the web
4196 wsmenu.add(msawsmenu);
4197 wsmenu.add(secstrmenu);
4198 wsmenu.add(dismenu);
4199 wsmenu.add(analymenu);
4200 // No search services yet
4201 // wsmenu.add(seqsrchmenu);
4203 javax.swing.SwingUtilities.invokeLater(new Runnable()
4210 webService.removeAll();
4211 // first, add discovered services onto the webservices menu
4212 if (wsmenu.size() > 0)
4214 for (int i = 0, j = wsmenu.size(); i < j; i++)
4216 webService.add(wsmenu.get(i));
4221 webService.add(me.webServiceNoServices);
4223 // TODO: move into separate menu builder class.
4224 boolean new_sspred = false;
4225 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4227 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4228 if (jws2servs != null)
4230 if (jws2servs.hasServices())
4232 jws2servs.attachWSMenuEntry(webService, me);
4233 for (Jws2Instance sv : jws2servs.getServices())
4235 if (sv.description.toLowerCase().contains("jpred"))
4237 for (JMenuItem jmi : legacyItems)
4239 jmi.setVisible(false);
4245 if (jws2servs.isRunning())
4247 JMenuItem tm = new JMenuItem(
4248 "Still discovering JABA Services");
4249 tm.setEnabled(false);
4254 build_urlServiceMenu(me.webService);
4255 build_fetchdbmenu(webService);
4256 for (JMenu item : wsmenu)
4258 if (item.getItemCount() == 0)
4260 item.setEnabled(false);
4264 item.setEnabled(true);
4267 } catch (Exception e)
4270 "Exception during web service menu building process.",
4275 } catch (Exception e)
4278 buildingMenu = false;
4285 * construct any groupURL type service menu entries.
4289 protected void build_urlServiceMenu(JMenu webService)
4291 // TODO: remove this code when 2.7 is released
4292 // DEBUG - alignmentView
4294 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4295 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4297 * @Override public void actionPerformed(ActionEvent e) {
4298 * jalview.datamodel.AlignmentView
4299 * .testSelectionViews(af.viewport.getAlignment(),
4300 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4302 * }); webService.add(testAlView);
4304 // TODO: refactor to RestClient discoverer and merge menu entries for
4305 // rest-style services with other types of analysis/calculation service
4306 // SHmmr test client - still being implemented.
4307 // DEBUG - alignmentView
4309 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4312 client.attachWSMenuEntry(
4313 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4319 * Searches the alignment sequences for xRefs and builds the Show
4320 * Cross-References menu (formerly called Show Products), with database
4321 * sources for which cross-references are found (protein sources for a
4322 * nucleotide alignment and vice versa)
4324 * @return true if Show Cross-references menu should be enabled
4326 public boolean canShowProducts()
4328 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4329 AlignmentI dataset = viewport.getAlignment().getDataset();
4331 showProducts.removeAll();
4332 final boolean dna = viewport.getAlignment().isNucleotide();
4334 if (seqs == null || seqs.length == 0)
4336 // nothing to see here.
4340 boolean showp = false;
4343 List<String> ptypes = new CrossRef(seqs, dataset)
4344 .findXrefSourcesForSequences(dna);
4346 for (final String source : ptypes)
4349 final AlignFrame af = this;
4350 JMenuItem xtype = new JMenuItem(source);
4351 xtype.addActionListener(new ActionListener()
4354 public void actionPerformed(ActionEvent e)
4356 showProductsFor(af.viewport.getSequenceSelection(), dna,
4360 showProducts.add(xtype);
4362 showProducts.setVisible(showp);
4363 showProducts.setEnabled(showp);
4364 } catch (Exception e)
4367 "canShowProducts threw an exception - please report to help@jalview.org",
4375 * Finds and displays cross-references for the selected sequences (protein
4376 * products for nucleotide sequences, dna coding sequences for peptides).
4379 * the sequences to show cross-references for
4381 * true if from a nucleotide alignment (so showing proteins)
4383 * the database to show cross-references for
4385 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4386 final String source)
4388 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4393 * Construct and display a new frame containing the translation of this
4394 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4397 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4399 AlignmentI al = null;
4402 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4404 al = dna.translateCdna(codeTable);
4405 } catch (Exception ex)
4407 jalview.bin.Cache.log.error(
4408 "Exception during translation. Please report this !", ex);
4409 final String msg = MessageManager.getString(
4410 "label.error_when_translating_sequences_submit_bug_report");
4411 final String errorTitle = MessageManager
4412 .getString("label.implementation_error")
4413 + MessageManager.getString("label.translation_failed");
4414 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4415 JvOptionPane.ERROR_MESSAGE);
4418 if (al == null || al.getHeight() == 0)
4420 final String msg = MessageManager.getString(
4421 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4422 final String errorTitle = MessageManager
4423 .getString("label.translation_failed");
4424 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4425 JvOptionPane.WARNING_MESSAGE);
4429 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4430 af.setFileFormat(this.currentFileFormat);
4431 final String newTitle = MessageManager
4432 .formatMessage("label.translation_of_params", new Object[]
4433 { this.getTitle(), codeTable.getId() });
4434 af.setTitle(newTitle);
4435 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4437 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4438 viewport.openSplitFrame(af, new Alignment(seqs));
4442 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4449 * Set the file format
4453 public void setFileFormat(FileFormatI format)
4455 this.currentFileFormat = format;
4459 * Try to load a features file onto the alignment.
4462 * contents or path to retrieve file or a File object
4464 * access mode of file (see jalview.io.AlignFile)
4465 * @return true if features file was parsed correctly.
4467 public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4470 return avc.parseFeaturesFile(file, sourceType,
4471 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4476 public void refreshFeatureUI(boolean enableIfNecessary)
4478 // note - currently this is only still here rather than in the controller
4479 // because of the featureSettings hard reference that is yet to be
4481 if (enableIfNecessary)
4483 viewport.setShowSequenceFeatures(true);
4484 showSeqFeatures.setSelected(true);
4490 public void dragEnter(DropTargetDragEvent evt)
4495 public void dragExit(DropTargetEvent evt)
4500 public void dragOver(DropTargetDragEvent evt)
4505 public void dropActionChanged(DropTargetDragEvent evt)
4510 public void drop(DropTargetDropEvent evt)
4512 // JAL-1552 - acceptDrop required before getTransferable call for
4513 // Java's Transferable for native dnd
4514 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4515 Transferable t = evt.getTransferable();
4517 final AlignFrame thisaf = this;
4518 final List<Object> files = new ArrayList<>();
4519 List<DataSourceType> protocols = new ArrayList<>();
4523 Desktop.transferFromDropTarget(files, protocols, evt, t);
4524 } catch (Exception e)
4526 e.printStackTrace();
4530 new Thread(new Runnable()
4537 // check to see if any of these files have names matching sequences
4540 SequenceIdMatcher idm = new SequenceIdMatcher(
4541 viewport.getAlignment().getSequencesArray());
4543 * Object[] { String,SequenceI}
4545 ArrayList<Object[]> filesmatched = new ArrayList<>();
4546 ArrayList<Object> filesnotmatched = new ArrayList<>();
4547 for (int i = 0; i < files.size(); i++)
4550 Object file = files.get(i);
4551 String fileName = file.toString();
4553 DataSourceType protocol = (file instanceof File
4554 ? DataSourceType.FILE
4555 : FormatAdapter.checkProtocol(fileName));
4556 if (protocol == DataSourceType.FILE)
4559 if (file instanceof File) {
4561 Platform.cacheFileData(fl);
4563 fl = new File(fileName);
4565 pdbfn = fl.getName();
4567 else if (protocol == DataSourceType.URL)
4569 URL url = new URL(fileName);
4570 pdbfn = url.getFile();
4572 if (pdbfn.length() > 0)
4574 // attempt to find a match in the alignment
4575 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4576 int l = 0, c = pdbfn.indexOf(".");
4577 while (mtch == null && c != -1)
4582 } while ((c = pdbfn.indexOf(".", l)) > l);
4585 pdbfn = pdbfn.substring(0, l);
4587 mtch = idm.findAllIdMatches(pdbfn);
4594 type = new IdentifyFile().identify(file, protocol);
4595 } catch (Exception ex)
4599 if (type != null && type.isStructureFile())
4601 filesmatched.add(new Object[] { file, protocol, mtch });
4605 // File wasn't named like one of the sequences or wasn't a PDB
4607 filesnotmatched.add(file);
4611 if (filesmatched.size() > 0)
4613 boolean autoAssociate = Cache
4614 .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4617 String msg = MessageManager.formatMessage(
4618 "label.automatically_associate_structure_files_with_sequences_same_name",
4620 { Integer.valueOf(filesmatched.size())
4622 String ttl = MessageManager.getString(
4623 "label.automatically_associate_structure_files_by_name");
4624 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4625 ttl, JvOptionPane.YES_NO_OPTION);
4626 autoAssociate = choice == JvOptionPane.YES_OPTION;
4630 for (Object[] fm : filesmatched)
4632 // try and associate
4633 // TODO: may want to set a standard ID naming formalism for
4634 // associating PDB files which have no IDs.
4635 for (SequenceI toassoc : (SequenceI[]) fm[2])
4637 PDBEntry pe = new AssociatePdbFileWithSeq()
4638 .associatePdbWithSeq(fm[0].toString(),
4639 (DataSourceType) fm[1], toassoc, false,
4643 System.err.println("Associated file : "
4644 + (fm[0].toString()) + " with "
4645 + toassoc.getDisplayId(true));
4649 // TODO: do we need to update overview ? only if features are
4651 alignPanel.paintAlignment(true, false);
4657 * add declined structures as sequences
4659 for (Object[] o : filesmatched)
4661 filesnotmatched.add(o[0]);
4665 if (filesnotmatched.size() > 0)
4667 if (assocfiles > 0 && (Cache.getDefault(
4668 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4669 || JvOptionPane.showConfirmDialog(thisaf,
4670 "<html>" + MessageManager.formatMessage(
4671 "label.ignore_unmatched_dropped_files_info",
4674 filesnotmatched.size())
4677 MessageManager.getString(
4678 "label.ignore_unmatched_dropped_files"),
4679 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4683 for (Object fn : filesnotmatched)
4685 loadJalviewDataFile(fn, null, null, null);
4689 } catch (Exception ex)
4691 ex.printStackTrace();
4699 * Attempt to load a "dropped" file or URL string, by testing in turn for
4701 * <li>an Annotation file</li>
4702 * <li>a JNet file</li>
4703 * <li>a features file</li>
4704 * <li>else try to interpret as an alignment file</li>
4708 * either a filename or a URL string.
4710 public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4711 FileFormatI format, SequenceI assocSeq)
4713 // BH 2018 was String file
4716 if (sourceType == null)
4718 sourceType = FormatAdapter.checkProtocol(file);
4720 // if the file isn't identified, or not positively identified as some
4721 // other filetype (PFAM is default unidentified alignment file type) then
4722 // try to parse as annotation.
4723 boolean isAnnotation = (format == null
4724 || FileFormat.Pfam.equals(format))
4725 ? new AnnotationFile().annotateAlignmentView(viewport,
4731 // first see if its a T-COFFEE score file
4732 TCoffeeScoreFile tcf = null;
4735 tcf = new TCoffeeScoreFile(file, sourceType);
4738 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4742 new TCoffeeColourScheme(viewport.getAlignment()));
4743 isAnnotation = true;
4744 setStatus(MessageManager.getString(
4745 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4749 // some problem - if no warning its probable that the ID matching
4750 // process didn't work
4751 JvOptionPane.showMessageDialog(Desktop.desktop,
4752 tcf.getWarningMessage() == null
4753 ? MessageManager.getString(
4754 "label.check_file_matches_sequence_ids_alignment")
4755 : tcf.getWarningMessage(),
4756 MessageManager.getString(
4757 "label.problem_reading_tcoffee_score_file"),
4758 JvOptionPane.WARNING_MESSAGE);
4765 } catch (Exception x)
4768 "Exception when processing data source as T-COFFEE score file",
4774 // try to see if its a JNet 'concise' style annotation file *before*
4776 // try to parse it as a features file
4779 format = new IdentifyFile().identify(file, sourceType);
4781 if (FileFormat.ScoreMatrix == format)
4783 ScoreMatrixFile sm = new ScoreMatrixFile(
4784 new FileParse(file, sourceType));
4786 // todo: i18n this message
4787 setStatus(MessageManager.formatMessage(
4788 "label.successfully_loaded_matrix",
4789 sm.getMatrixName()));
4791 else if (FileFormat.Jnet.equals(format))
4793 JPredFile predictions = new JPredFile(file, sourceType);
4794 new JnetAnnotationMaker();
4795 JnetAnnotationMaker.add_annotation(predictions,
4796 viewport.getAlignment(), 0, false);
4797 viewport.getAlignment().setupJPredAlignment();
4798 isAnnotation = true;
4800 // else if (IdentifyFile.FeaturesFile.equals(format))
4801 else if (FileFormat.Features.equals(format))
4803 if (parseFeaturesFile(file, sourceType))
4805 SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4806 if (splitFrame != null)
4808 splitFrame.repaint();
4812 alignPanel.paintAlignment(true, true);
4818 new FileLoader().LoadFile(viewport, file, sourceType, format);
4825 alignPanel.adjustAnnotationHeight();
4826 viewport.updateSequenceIdColours();
4827 buildSortByAnnotationScoresMenu();
4828 alignPanel.paintAlignment(true, true);
4830 } catch (Exception ex)
4832 ex.printStackTrace();
4833 } catch (OutOfMemoryError oom)
4838 } catch (Exception x)
4843 + (sourceType != null
4844 ? (sourceType == DataSourceType.PASTE
4846 : "using " + sourceType + " from "
4850 ? "(parsing as '" + format + "' file)"
4852 oom, Desktop.desktop);
4857 * Method invoked by the ChangeListener on the tabbed pane, in other words
4858 * when a different tabbed pane is selected by the user or programmatically.
4861 public void tabSelectionChanged(int index)
4865 alignPanel = alignPanels.get(index);
4866 viewport = alignPanel.av;
4867 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4868 setMenusFromViewport(viewport);
4869 if (featureSettings != null && featureSettings.isOpen()
4870 && featureSettings.fr.getViewport() != viewport)
4872 if (viewport.isShowSequenceFeatures())
4874 // refresh the featureSettings to reflect UI change
4875 showFeatureSettingsUI();
4879 // close feature settings for this view.
4880 featureSettings.close();
4887 * 'focus' any colour slider that is open to the selected viewport
4889 if (viewport.getConservationSelected())
4891 SliderPanel.setConservationSlider(alignPanel,
4892 viewport.getResidueShading(), alignPanel.getViewName());
4896 SliderPanel.hideConservationSlider();
4898 if (viewport.getAbovePIDThreshold())
4900 SliderPanel.setPIDSliderSource(alignPanel,
4901 viewport.getResidueShading(), alignPanel.getViewName());
4905 SliderPanel.hidePIDSlider();
4909 * If there is a frame linked to this one in a SplitPane, switch it to the
4910 * same view tab index. No infinite recursion of calls should happen, since
4911 * tabSelectionChanged() should not get invoked on setting the selected
4912 * index to an unchanged value. Guard against setting an invalid index
4913 * before the new view peer tab has been created.
4915 final AlignViewportI peer = viewport.getCodingComplement();
4918 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4919 .getAlignPanel().alignFrame;
4920 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4922 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4928 * On right mouse click on view tab, prompt for and set new view name.
4931 public void tabbedPane_mousePressed(MouseEvent e)
4933 if (e.isPopupTrigger())
4935 String msg = MessageManager.getString("label.enter_view_name");
4936 String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
4937 String reply = JvOptionPane.showInputDialog(msg, ttl);
4941 viewport.setViewName(reply);
4942 // TODO warn if reply is in getExistingViewNames()?
4943 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4948 public AlignViewport getCurrentView()
4954 * Open the dialog for regex description parsing.
4957 protected void extractScores_actionPerformed(ActionEvent e)
4959 ParseProperties pp = new jalview.analysis.ParseProperties(
4960 viewport.getAlignment());
4961 // TODO: verify regex and introduce GUI dialog for version 2.5
4962 // if (pp.getScoresFromDescription("col", "score column ",
4963 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4965 if (pp.getScoresFromDescription("description column",
4966 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4968 buildSortByAnnotationScoresMenu();
4976 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4980 protected void showDbRefs_actionPerformed(ActionEvent e)
4982 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4988 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4992 protected void showNpFeats_actionPerformed(ActionEvent e)
4994 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4998 * find the viewport amongst the tabs in this alignment frame and close that
5003 public boolean closeView(AlignViewportI av)
5007 this.closeMenuItem_actionPerformed(false);
5010 Component[] comp = tabbedPane.getComponents();
5011 for (int i = 0; comp != null && i < comp.length; i++)
5013 if (comp[i] instanceof AlignmentPanel)
5015 if (((AlignmentPanel) comp[i]).av == av)
5018 closeView((AlignmentPanel) comp[i]);
5026 protected void build_fetchdbmenu(JMenu webService)
5028 // Temporary hack - DBRef Fetcher always top level ws entry.
5029 // TODO We probably want to store a sequence database checklist in
5030 // preferences and have checkboxes.. rather than individual sources selected
5032 final JMenu rfetch = new JMenu(
5033 MessageManager.getString("action.fetch_db_references"));
5034 rfetch.setToolTipText(MessageManager.getString(
5035 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5036 webService.add(rfetch);
5038 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5039 MessageManager.getString("option.trim_retrieved_seqs"));
5040 trimrs.setToolTipText(
5041 MessageManager.getString("label.trim_retrieved_sequences"));
5043 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5044 trimrs.addActionListener(new ActionListener()
5047 public void actionPerformed(ActionEvent e)
5049 trimrs.setSelected(trimrs.isSelected());
5050 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5051 Boolean.valueOf(trimrs.isSelected()).toString());
5055 JMenuItem fetchr = new JMenuItem(
5056 MessageManager.getString("label.standard_databases"));
5057 fetchr.setToolTipText(
5058 MessageManager.getString("label.fetch_embl_uniprot"));
5059 fetchr.addActionListener(new ActionListener()
5063 public void actionPerformed(ActionEvent e)
5065 new Thread(new Runnable()
5070 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5071 .getAlignment().isNucleotide();
5072 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5073 alignPanel.av.getSequenceSelection(),
5074 alignPanel.alignFrame, null,
5075 alignPanel.alignFrame.featureSettings, isNucleotide);
5076 dbRefFetcher.addListener(new FetchFinishedListenerI()
5079 public void finished()
5082 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5083 .getFeatureSettingsModels())
5086 alignPanel.av.mergeFeaturesStyle(srcSettings);
5088 AlignFrame.this.setMenusForViewport();
5091 dbRefFetcher.fetchDBRefs(false);
5099 new Thread(new Runnable()
5104 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5105 .getSequenceFetcherSingleton();
5106 javax.swing.SwingUtilities.invokeLater(new Runnable()
5111 String[] dbclasses = sf.getNonAlignmentSources();
5112 List<DbSourceProxy> otherdb;
5113 JMenu dfetch = new JMenu();
5114 JMenu ifetch = new JMenu();
5115 JMenuItem fetchr = null;
5116 int comp = 0, icomp = 0, mcomp = 15;
5117 String mname = null;
5119 for (String dbclass : dbclasses)
5121 otherdb = sf.getSourceProxy(dbclass);
5122 // add a single entry for this class, or submenu allowing 'fetch
5124 if (otherdb == null || otherdb.size() < 1)
5130 mname = "From " + dbclass;
5132 if (otherdb.size() == 1)
5134 final DbSourceProxy[] dassource = otherdb
5135 .toArray(new DbSourceProxy[0]);
5136 DbSourceProxy src = otherdb.get(0);
5137 fetchr = new JMenuItem(src.getDbSource());
5138 fetchr.addActionListener(new ActionListener()
5142 public void actionPerformed(ActionEvent e)
5144 new Thread(new Runnable()
5150 boolean isNucleotide = alignPanel.alignFrame
5151 .getViewport().getAlignment()
5153 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5154 alignPanel.av.getSequenceSelection(),
5155 alignPanel.alignFrame, dassource,
5156 alignPanel.alignFrame.featureSettings,
5159 .addListener(new FetchFinishedListenerI()
5162 public void finished()
5164 FeatureSettingsModelI srcSettings = dassource[0]
5165 .getFeatureColourScheme();
5166 alignPanel.av.mergeFeaturesStyle(
5168 AlignFrame.this.setMenusForViewport();
5171 dbRefFetcher.fetchDBRefs(false);
5177 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5178 MessageManager.formatMessage(
5179 "label.fetch_retrieve_from", new Object[]
5180 { src.getDbName() })));
5186 final DbSourceProxy[] dassource = otherdb
5187 .toArray(new DbSourceProxy[0]);
5189 DbSourceProxy src = otherdb.get(0);
5190 fetchr = new JMenuItem(MessageManager
5191 .formatMessage("label.fetch_all_param", new Object[]
5192 { src.getDbSource() }));
5193 fetchr.addActionListener(new ActionListener()
5196 public void actionPerformed(ActionEvent e)
5198 new Thread(new Runnable()
5204 boolean isNucleotide = alignPanel.alignFrame
5205 .getViewport().getAlignment()
5207 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5208 alignPanel.av.getSequenceSelection(),
5209 alignPanel.alignFrame, dassource,
5210 alignPanel.alignFrame.featureSettings,
5213 .addListener(new FetchFinishedListenerI()
5216 public void finished()
5218 AlignFrame.this.setMenusForViewport();
5221 dbRefFetcher.fetchDBRefs(false);
5227 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5228 MessageManager.formatMessage(
5229 "label.fetch_retrieve_from_all_sources",
5231 { Integer.valueOf(otherdb.size())
5233 src.getDbSource(), src.getDbName() })));
5236 // and then build the rest of the individual menus
5237 ifetch = new JMenu(MessageManager.formatMessage(
5238 "label.source_from_db_source", new Object[]
5239 { src.getDbSource() }));
5241 String imname = null;
5243 for (DbSourceProxy sproxy : otherdb)
5245 String dbname = sproxy.getDbName();
5246 String sname = dbname.length() > 5
5247 ? dbname.substring(0, 5) + "..."
5249 String msname = dbname.length() > 10
5250 ? dbname.substring(0, 10) + "..."
5254 imname = MessageManager
5255 .formatMessage("label.from_msname", new Object[]
5258 fetchr = new JMenuItem(msname);
5259 final DbSourceProxy[] dassrc = { sproxy };
5260 fetchr.addActionListener(new ActionListener()
5264 public void actionPerformed(ActionEvent e)
5266 new Thread(new Runnable()
5272 boolean isNucleotide = alignPanel.alignFrame
5273 .getViewport().getAlignment()
5275 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5276 alignPanel.av.getSequenceSelection(),
5277 alignPanel.alignFrame, dassrc,
5278 alignPanel.alignFrame.featureSettings,
5281 .addListener(new FetchFinishedListenerI()
5284 public void finished()
5286 AlignFrame.this.setMenusForViewport();
5289 dbRefFetcher.fetchDBRefs(false);
5295 fetchr.setToolTipText(
5296 "<html>" + MessageManager.formatMessage(
5297 "label.fetch_retrieve_from", new Object[]
5301 if (++icomp >= mcomp || i == (otherdb.size()))
5303 ifetch.setText(MessageManager.formatMessage(
5304 "label.source_to_target", imname, sname));
5306 ifetch = new JMenu();
5314 if (comp >= mcomp || dbi >= (dbclasses.length))
5316 dfetch.setText(MessageManager.formatMessage(
5317 "label.source_to_target", mname, dbclass));
5319 dfetch = new JMenu();
5332 * Left justify the whole alignment.
5335 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5337 AlignmentI al = viewport.getAlignment();
5339 viewport.firePropertyChange("alignment", null, al);
5343 * Right justify the whole alignment.
5346 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5348 AlignmentI al = viewport.getAlignment();
5350 viewport.firePropertyChange("alignment", null, al);
5354 public void setShowSeqFeatures(boolean b)
5356 showSeqFeatures.setSelected(b);
5357 viewport.setShowSequenceFeatures(b);
5364 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5365 * awt.event.ActionEvent)
5368 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5370 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5371 alignPanel.paintAlignment(false, false);
5378 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5382 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5384 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5385 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5393 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5394 * .event.ActionEvent)
5397 protected void showGroupConservation_actionPerformed(ActionEvent e)
5399 viewport.setShowGroupConservation(showGroupConservation.getState());
5400 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5407 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5408 * .event.ActionEvent)
5411 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5413 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5414 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5421 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5422 * .event.ActionEvent)
5425 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5427 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5428 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5432 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5434 showSequenceLogo.setState(true);
5435 viewport.setShowSequenceLogo(true);
5436 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5437 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5441 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5443 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5450 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5451 * .event.ActionEvent)
5454 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5456 if (avc.makeGroupsFromSelection())
5458 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5459 alignPanel.updateAnnotation();
5460 alignPanel.paintAlignment(true,
5461 viewport.needToUpdateStructureViews());
5465 public void clearAlignmentSeqRep()
5467 // TODO refactor alignmentseqrep to controller
5468 if (viewport.getAlignment().hasSeqrep())
5470 viewport.getAlignment().setSeqrep(null);
5471 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5472 alignPanel.updateAnnotation();
5473 alignPanel.paintAlignment(true, true);
5478 protected void createGroup_actionPerformed(ActionEvent e)
5480 if (avc.createGroup())
5482 if (applyAutoAnnotationSettings.isSelected())
5484 alignPanel.updateAnnotation(true, false);
5486 alignPanel.alignmentChanged();
5491 protected void unGroup_actionPerformed(ActionEvent e)
5495 alignPanel.alignmentChanged();
5500 * make the given alignmentPanel the currently selected tab
5502 * @param alignmentPanel
5504 public void setDisplayedView(AlignmentPanel alignmentPanel)
5506 if (!viewport.getSequenceSetId()
5507 .equals(alignmentPanel.av.getSequenceSetId()))
5509 throw new Error(MessageManager.getString(
5510 "error.implementation_error_cannot_show_view_alignment_frame"));
5512 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5513 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5515 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5520 * Action on selection of menu options to Show or Hide annotations.
5523 * @param forSequences
5524 * update sequence-related annotations
5525 * @param forAlignment
5526 * update non-sequence-related annotations
5529 protected void setAnnotationsVisibility(boolean visible,
5530 boolean forSequences, boolean forAlignment)
5532 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5533 .getAlignmentAnnotation();
5538 for (AlignmentAnnotation aa : anns)
5541 * don't display non-positional annotations on an alignment
5543 if (aa.annotations == null)
5547 boolean apply = (aa.sequenceRef == null && forAlignment)
5548 || (aa.sequenceRef != null && forSequences);
5551 aa.visible = visible;
5554 alignPanel.validateAnnotationDimensions(true);
5555 alignPanel.alignmentChanged();
5559 * Store selected annotation sort order for the view and repaint.
5562 protected void sortAnnotations_actionPerformed()
5564 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5566 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5567 alignPanel.paintAlignment(false, false);
5572 * @return alignment panels in this alignment frame
5574 public List<? extends AlignmentViewPanel> getAlignPanels()
5576 // alignPanels is never null
5577 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5582 * Open a new alignment window, with the cDNA associated with this (protein)
5583 * alignment, aligned as is the protein.
5585 protected void viewAsCdna_actionPerformed()
5587 // TODO no longer a menu action - refactor as required
5588 final AlignmentI alignment = getViewport().getAlignment();
5589 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5590 if (mappings == null)
5594 List<SequenceI> cdnaSeqs = new ArrayList<>();
5595 for (SequenceI aaSeq : alignment.getSequences())
5597 for (AlignedCodonFrame acf : mappings)
5599 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5603 * There is a cDNA mapping for this protein sequence - add to new
5604 * alignment. It will share the same dataset sequence as other mapped
5605 * cDNA (no new mappings need to be created).
5607 final Sequence newSeq = new Sequence(dnaSeq);
5608 newSeq.setDatasetSequence(dnaSeq);
5609 cdnaSeqs.add(newSeq);
5613 if (cdnaSeqs.size() == 0)
5615 // show a warning dialog no mapped cDNA
5618 AlignmentI cdna = new Alignment(
5619 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5620 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5621 AlignFrame.DEFAULT_HEIGHT);
5622 cdna.alignAs(alignment);
5623 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5625 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5626 AlignFrame.DEFAULT_HEIGHT);
5630 * Set visibility of dna/protein complement view (available when shown in a
5636 protected void showComplement_actionPerformed(boolean show)
5638 SplitContainerI sf = getSplitViewContainer();
5641 sf.setComplementVisible(this, show);
5646 * Generate the reverse (optionally complemented) of the selected sequences,
5647 * and add them to the alignment
5650 protected void showReverse_actionPerformed(boolean complement)
5652 AlignmentI al = null;
5655 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5656 al = dna.reverseCdna(complement);
5657 viewport.addAlignment(al, "");
5658 addHistoryItem(new EditCommand(
5659 MessageManager.getString("label.add_sequences"), Action.PASTE,
5660 al.getSequencesArray(), 0, al.getWidth(),
5661 viewport.getAlignment()));
5662 } catch (Exception ex)
5664 System.err.println(ex.getMessage());
5670 * Try to run a script in the Groovy console, having first ensured that this
5671 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5672 * be targeted at this alignment.
5675 protected void runGroovy_actionPerformed()
5677 Jalview.setCurrentAlignFrame(this);
5678 groovy.ui.Console console = Desktop.getGroovyConsole();
5679 if (console != null)
5683 console.runScript();
5684 } catch (Exception ex)
5686 System.err.println((ex.toString()));
5687 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5688 MessageManager.getString("label.couldnt_run_groovy_script"),
5689 MessageManager.getString("label.groovy_support_failed"),
5690 JvOptionPane.ERROR_MESSAGE);
5695 System.err.println("Can't run Groovy script as console not found");
5700 * Hides columns containing (or not containing) a specified feature, provided
5701 * that would not leave all columns hidden
5703 * @param featureType
5704 * @param columnsContaining
5707 public boolean hideFeatureColumns(String featureType,
5708 boolean columnsContaining)
5710 boolean notForHiding = avc.markColumnsContainingFeatures(
5711 columnsContaining, false, false, featureType);
5714 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5715 false, featureType))
5717 getViewport().hideSelectedColumns();
5725 protected void selectHighlightedColumns_actionPerformed(
5726 ActionEvent actionEvent)
5728 // include key modifier check in case user selects from menu
5729 avc.markHighlightedColumns(
5730 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5731 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5732 | ActionEvent.CTRL_MASK)) != 0);
5736 * Rebuilds the Colour menu, including any user-defined colours which have
5737 * been loaded either on startup or during the session
5739 public void buildColourMenu()
5741 colourMenu.removeAll();
5743 colourMenu.add(applyToAllGroups);
5744 colourMenu.add(textColour);
5745 colourMenu.addSeparator();
5747 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5748 viewport.getAlignment(), false);
5750 colourMenu.add(annotationColour);
5751 bg.add(annotationColour);
5752 colourMenu.addSeparator();
5753 colourMenu.add(conservationMenuItem);
5754 colourMenu.add(modifyConservation);
5755 colourMenu.add(abovePIDThreshold);
5756 colourMenu.add(modifyPID);
5758 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5759 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5763 * Open a dialog (if not already open) that allows the user to select and
5764 * calculate PCA or Tree analysis
5766 protected void openTreePcaDialog()
5768 if (alignPanel.getCalculationDialog() == null)
5770 new CalculationChooser(AlignFrame.this);
5775 protected void loadVcf_actionPerformed()
5777 JalviewFileChooser chooser = new JalviewFileChooser(
5778 Cache.getProperty("LAST_DIRECTORY"));
5779 chooser.setFileView(new JalviewFileView());
5780 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5781 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5782 final AlignFrame us = this;
5783 chooser.setResponseHandler(0, new Runnable()
5788 String choice = chooser.getSelectedFile().getPath();
5789 Cache.setProperty("LAST_DIRECTORY", choice);
5790 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5791 new VCFLoader(choice).loadVCF(seqs, us);
5794 chooser.showOpenDialog(null);
5798 private Rectangle lastFeatureSettingsBounds = null;
5800 public void setFeatureSettingsGeometry(Rectangle bounds)
5802 lastFeatureSettingsBounds = bounds;
5806 public Rectangle getFeatureSettingsGeometry()
5808 return lastFeatureSettingsBounds;
5812 class PrintThread extends Thread
5816 public PrintThread(AlignmentPanel ap)
5821 static PageFormat pf;
5826 PrinterJob printJob = PrinterJob.getPrinterJob();
5830 printJob.setPrintable(ap, pf);
5834 printJob.setPrintable(ap);
5837 if (printJob.printDialog())
5842 } catch (Exception PrintException)
5844 PrintException.printStackTrace();