2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.SimilarityParamsI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenColumns;
57 import jalview.datamodel.HiddenSequences;
58 import jalview.datamodel.PDBEntry;
59 import jalview.datamodel.SeqCigar;
60 import jalview.datamodel.Sequence;
61 import jalview.datamodel.SequenceGroup;
62 import jalview.datamodel.SequenceI;
63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.DataSourceType;
69 import jalview.io.FileFormat;
70 import jalview.io.FileFormatI;
71 import jalview.io.FileFormats;
72 import jalview.io.FileLoader;
73 import jalview.io.FileParse;
74 import jalview.io.FormatAdapter;
75 import jalview.io.HtmlSvgOutput;
76 import jalview.io.IdentifyFile;
77 import jalview.io.JPredFile;
78 import jalview.io.JalviewFileChooser;
79 import jalview.io.JalviewFileView;
80 import jalview.io.JnetAnnotationMaker;
81 import jalview.io.NewickFile;
82 import jalview.io.ScoreMatrixFile;
83 import jalview.io.TCoffeeScoreFile;
84 import jalview.io.vcf.VCFLoader;
85 import jalview.jbgui.GAlignFrame;
86 import jalview.schemes.ColourSchemeI;
87 import jalview.schemes.ColourSchemes;
88 import jalview.schemes.ResidueColourScheme;
89 import jalview.schemes.TCoffeeColourScheme;
90 import jalview.util.MessageManager;
91 import jalview.viewmodel.AlignmentViewport;
92 import jalview.viewmodel.ViewportRanges;
93 import jalview.ws.DBRefFetcher;
94 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
95 import jalview.ws.jws1.Discoverer;
96 import jalview.ws.jws2.Jws2Discoverer;
97 import jalview.ws.jws2.jabaws2.Jws2Instance;
98 import jalview.ws.seqfetcher.DbSourceProxy;
100 import java.awt.BorderLayout;
101 import java.awt.Component;
102 import java.awt.Rectangle;
103 import java.awt.Toolkit;
104 import java.awt.datatransfer.Clipboard;
105 import java.awt.datatransfer.DataFlavor;
106 import java.awt.datatransfer.StringSelection;
107 import java.awt.datatransfer.Transferable;
108 import java.awt.dnd.DnDConstants;
109 import java.awt.dnd.DropTargetDragEvent;
110 import java.awt.dnd.DropTargetDropEvent;
111 import java.awt.dnd.DropTargetEvent;
112 import java.awt.dnd.DropTargetListener;
113 import java.awt.event.ActionEvent;
114 import java.awt.event.ActionListener;
115 import java.awt.event.FocusAdapter;
116 import java.awt.event.FocusEvent;
117 import java.awt.event.ItemEvent;
118 import java.awt.event.ItemListener;
119 import java.awt.event.KeyAdapter;
120 import java.awt.event.KeyEvent;
121 import java.awt.event.MouseEvent;
122 import java.awt.print.PageFormat;
123 import java.awt.print.PrinterJob;
124 import java.beans.PropertyChangeEvent;
125 import java.beans.PropertyChangeListener;
127 import java.io.FileWriter;
128 import java.io.PrintWriter;
130 import java.util.ArrayList;
131 import java.util.Arrays;
132 import java.util.Deque;
133 import java.util.Enumeration;
134 import java.util.Hashtable;
135 import java.util.List;
136 import java.util.Vector;
138 import javax.swing.JCheckBoxMenuItem;
139 import javax.swing.JEditorPane;
140 import javax.swing.JFileChooser;
141 import javax.swing.JInternalFrame;
142 import javax.swing.JLayeredPane;
143 import javax.swing.JMenu;
144 import javax.swing.JMenuItem;
145 import javax.swing.JScrollPane;
146 import javax.swing.SwingUtilities;
152 * @version $Revision$
154 public class AlignFrame extends GAlignFrame implements DropTargetListener,
155 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener,
156 PropertyChangeListener
159 public static final int DEFAULT_WIDTH = 700;
161 public static final int DEFAULT_HEIGHT = 500;
164 * The currently displayed panel (selected tabbed view if more than one)
166 public AlignmentPanel alignPanel;
168 AlignViewport viewport;
170 public AlignViewControllerI avc;
172 List<AlignmentPanel> alignPanels = new ArrayList<>();
175 * Last format used to load or save alignments in this window
177 FileFormatI currentFileFormat = null;
180 * Current filename for this alignment
182 String fileName = null;
185 * Creates a new AlignFrame object with specific width and height.
191 public AlignFrame(AlignmentI al, int width, int height)
193 this(al, null, width, height);
197 * Creates a new AlignFrame object with specific width, height and
203 * @param sequenceSetId
205 public AlignFrame(AlignmentI al, int width, int height,
206 String sequenceSetId)
208 this(al, null, width, height, sequenceSetId);
212 * Creates a new AlignFrame object with specific width, height and
218 * @param sequenceSetId
221 public AlignFrame(AlignmentI al, int width, int height,
222 String sequenceSetId, String viewId)
224 this(al, null, width, height, sequenceSetId, viewId);
228 * new alignment window with hidden columns
232 * @param hiddenColumns
233 * ColumnSelection or null
235 * Width of alignment frame
239 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
242 this(al, hiddenColumns, width, height, null);
246 * Create alignment frame for al with hiddenColumns, a specific width and
247 * height, and specific sequenceId
250 * @param hiddenColumns
253 * @param sequenceSetId
256 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
257 int height, String sequenceSetId)
259 this(al, hiddenColumns, width, height, sequenceSetId, null);
263 * Create alignment frame for al with hiddenColumns, a specific width and
264 * height, and specific sequenceId
267 * @param hiddenColumns
270 * @param sequenceSetId
275 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
276 int height, String sequenceSetId, String viewId)
278 setSize(width, height);
280 if (al.getDataset() == null)
285 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
287 alignPanel = new AlignmentPanel(this, viewport);
289 addAlignmentPanel(alignPanel, true);
293 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
294 HiddenColumns hiddenColumns, int width, int height)
296 setSize(width, height);
298 if (al.getDataset() == null)
303 viewport = new AlignViewport(al, hiddenColumns);
305 if (hiddenSeqs != null && hiddenSeqs.length > 0)
307 viewport.hideSequence(hiddenSeqs);
309 alignPanel = new AlignmentPanel(this, viewport);
310 addAlignmentPanel(alignPanel, true);
315 * Make a new AlignFrame from existing alignmentPanels
322 public AlignFrame(AlignmentPanel ap)
326 addAlignmentPanel(ap, false);
331 public void propertyChange(PropertyChangeEvent evt)
333 Desktop.getDesktop().propertyChange(evt);
337 * initalise the alignframe from the underlying viewport data and the
342 if (!Jalview.isHeadlessMode())
344 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
347 avc = new jalview.controller.AlignViewController(this, viewport,
349 if (viewport.getAlignmentConservationAnnotation() == null)
351 // BLOSUM62Colour.setEnabled(false);
352 conservationMenuItem.setEnabled(false);
353 modifyConservation.setEnabled(false);
354 // PIDColour.setEnabled(false);
355 // abovePIDThreshold.setEnabled(false);
356 // modifyPID.setEnabled(false);
359 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
362 if (sortby.equals("Id"))
364 sortIDMenuItem_actionPerformed(null);
366 else if (sortby.equals("Pairwise Identity"))
368 sortPairwiseMenuItem_actionPerformed(null);
372 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
374 setMenusFromViewport(viewport);
375 buildSortByAnnotationScoresMenu();
376 calculateTree.addActionListener(new ActionListener()
380 public void actionPerformed(ActionEvent e)
387 if (Desktop.desktop != null)
389 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
391 * BH 2018 ignore service listeners
397 addServiceListeners();
402 if (viewport.getWrapAlignment())
404 wrapMenuItem_actionPerformed(null);
407 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
409 this.overviewMenuItem_actionPerformed(null);
414 final List<AlignmentPanel> selviews = new ArrayList<>();
415 final List<AlignmentPanel> origview = new ArrayList<>();
416 final String menuLabel = MessageManager
417 .getString("label.copy_format_from");
418 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
419 new ViewSetProvider()
423 public AlignmentPanel[] getAllAlignmentPanels()
426 origview.add(alignPanel);
427 // make an array of all alignment panels except for this one
428 List<AlignmentPanel> aps = new ArrayList<>(
429 Arrays.asList(Desktop.getAlignmentPanels(null)));
430 aps.remove(AlignFrame.this.alignPanel);
431 return aps.toArray(new AlignmentPanel[aps.size()]);
433 }, selviews, new ItemListener()
437 public void itemStateChanged(ItemEvent e)
439 if (origview.size() > 0)
441 final AlignmentPanel ap = origview.get(0);
444 * Copy the ViewStyle of the selected panel to 'this one'.
445 * Don't change value of 'scaleProteinAsCdna' unless copying
448 ViewStyleI vs = selviews.get(0).getAlignViewport()
450 boolean fromSplitFrame = selviews.get(0)
451 .getAlignViewport().getCodingComplement() != null;
454 vs.setScaleProteinAsCdna(ap.getAlignViewport()
455 .getViewStyle().isScaleProteinAsCdna());
457 ap.getAlignViewport().setViewStyle(vs);
460 * Also rescale ViewStyle of SplitFrame complement if there is
461 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
462 * the whole ViewStyle (allow cDNA protein to have different
465 AlignViewportI complement = ap.getAlignViewport()
466 .getCodingComplement();
467 if (complement != null && vs.isScaleProteinAsCdna())
469 AlignFrame af = Desktop.getAlignFrameFor(complement);
470 ((SplitFrame) af.getSplitViewContainer())
472 af.setMenusForViewport();
476 ap.setSelected(true);
477 ap.alignFrame.setMenusForViewport();
482 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
483 .indexOf("devel") > -1
484 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
485 .indexOf("test") > -1)
487 formatMenu.add(vsel);
489 addFocusListener(new FocusAdapter()
492 public void focusGained(FocusEvent e)
494 Jalview.setCurrentAlignFrame(AlignFrame.this);
501 * Change the filename and format for the alignment, and enable the 'reload'
502 * button functionality.
509 public void setFileName(String file, FileFormatI format)
512 setFileFormat(format);
513 reload.setEnabled(true);
517 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
520 void addKeyListener()
522 addKeyListener(new KeyAdapter()
525 public void keyPressed(KeyEvent evt)
527 if (viewport.cursorMode
528 && ((evt.getKeyCode() >= KeyEvent.VK_0
529 && evt.getKeyCode() <= KeyEvent.VK_9)
530 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
531 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
532 && Character.isDigit(evt.getKeyChar()))
534 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
537 switch (evt.getKeyCode())
540 case 27: // escape key
541 deselectAllSequenceMenuItem_actionPerformed(null);
545 case KeyEvent.VK_DOWN:
546 if (evt.isAltDown() || !viewport.cursorMode)
548 moveSelectedSequences(false);
550 if (viewport.cursorMode)
552 alignPanel.getSeqPanel().moveCursor(0, 1);
557 if (evt.isAltDown() || !viewport.cursorMode)
559 moveSelectedSequences(true);
561 if (viewport.cursorMode)
563 alignPanel.getSeqPanel().moveCursor(0, -1);
568 case KeyEvent.VK_LEFT:
569 if (evt.isAltDown() || !viewport.cursorMode)
571 slideSequences(false,
572 alignPanel.getSeqPanel().getKeyboardNo1());
576 alignPanel.getSeqPanel().moveCursor(-1, 0);
581 case KeyEvent.VK_RIGHT:
582 if (evt.isAltDown() || !viewport.cursorMode)
584 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
588 alignPanel.getSeqPanel().moveCursor(1, 0);
592 case KeyEvent.VK_SPACE:
593 if (viewport.cursorMode)
595 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
596 || evt.isShiftDown() || evt.isAltDown());
600 // case KeyEvent.VK_A:
601 // if (viewport.cursorMode)
603 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
604 // //System.out.println("A");
608 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
609 * System.out.println("closing bracket"); } break;
611 case KeyEvent.VK_DELETE:
612 case KeyEvent.VK_BACK_SPACE:
613 if (!viewport.cursorMode)
615 cut_actionPerformed(null);
619 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
620 || evt.isShiftDown() || evt.isAltDown());
626 if (viewport.cursorMode)
628 alignPanel.getSeqPanel().setCursorRow();
632 if (viewport.cursorMode && !evt.isControlDown())
634 alignPanel.getSeqPanel().setCursorColumn();
638 if (viewport.cursorMode)
640 alignPanel.getSeqPanel().setCursorPosition();
644 case KeyEvent.VK_ENTER:
645 case KeyEvent.VK_COMMA:
646 if (viewport.cursorMode)
648 alignPanel.getSeqPanel().setCursorRowAndColumn();
653 if (viewport.cursorMode)
655 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
659 if (viewport.cursorMode)
661 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
666 viewport.cursorMode = !viewport.cursorMode;
667 statusBar.setText(MessageManager
668 .formatMessage("label.keyboard_editing_mode", new String[]
669 { (viewport.cursorMode ? "on" : "off") }));
670 if (viewport.cursorMode)
672 ViewportRanges ranges = viewport.getRanges();
673 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
675 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
678 alignPanel.getSeqPanel().seqCanvas.repaint();
684 Help.showHelpWindow();
685 } catch (Exception ex)
687 ex.printStackTrace();
692 boolean toggleSeqs = !evt.isControlDown();
693 boolean toggleCols = !evt.isShiftDown();
694 toggleHiddenRegions(toggleSeqs, toggleCols);
699 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
700 boolean modifyExisting = true; // always modify, don't clear
701 // evt.isShiftDown();
702 boolean invertHighlighted = evt.isAltDown();
703 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
707 case KeyEvent.VK_PAGE_UP:
708 viewport.getRanges().pageUp();
710 case KeyEvent.VK_PAGE_DOWN:
711 viewport.getRanges().pageDown();
717 public void keyReleased(KeyEvent evt)
719 switch (evt.getKeyCode())
721 case KeyEvent.VK_LEFT:
722 if (evt.isAltDown() || !viewport.cursorMode)
724 viewport.firePropertyChange("alignment", null,
725 viewport.getAlignment().getSequences());
729 case KeyEvent.VK_RIGHT:
730 if (evt.isAltDown() || !viewport.cursorMode)
732 viewport.firePropertyChange("alignment", null,
733 viewport.getAlignment().getSequences());
741 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
743 ap.alignFrame = this;
744 avc = new jalview.controller.AlignViewController(this, viewport,
749 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
751 int aSize = alignPanels.size();
753 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
755 if (aSize == 1 && ap.av.viewName == null)
757 this.getContentPane().add(ap, BorderLayout.CENTER);
763 setInitialTabVisible();
766 expandViews.setEnabled(true);
767 gatherViews.setEnabled(true);
768 tabbedPane.addTab(ap.av.viewName, ap);
770 ap.setVisible(false);
775 if (ap.av.isPadGaps())
777 ap.av.getAlignment().padGaps();
779 ap.av.updateConservation(ap);
780 ap.av.updateConsensus(ap);
781 ap.av.updateStrucConsensus(ap);
785 public void setInitialTabVisible()
787 expandViews.setEnabled(true);
788 gatherViews.setEnabled(true);
789 tabbedPane.setVisible(true);
790 AlignmentPanel first = alignPanels.get(0);
791 tabbedPane.addTab(first.av.viewName, first);
792 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
795 public AlignViewport getViewport()
800 /* Set up intrinsic listeners for dynamically generated GUI bits. */
801 private void addServiceListeners()
803 final java.beans.PropertyChangeListener thisListener;
804 Desktop.instance.addJalviewPropertyChangeListener("services",
805 thisListener = new java.beans.PropertyChangeListener()
808 public void propertyChange(PropertyChangeEvent evt)
810 // // System.out.println("Discoverer property change.");
811 // if (evt.getPropertyName().equals("services"))
813 SwingUtilities.invokeLater(new Runnable()
820 "Rebuild WS Menu for service change");
821 BuildWebServiceMenu();
828 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
831 public void internalFrameClosed(
832 javax.swing.event.InternalFrameEvent evt)
834 // System.out.println("deregistering discoverer listener");
835 Desktop.instance.removeJalviewPropertyChangeListener("services",
837 closeMenuItem_actionPerformed(true);
840 // Finally, build the menu once to get current service state
841 new Thread(new Runnable()
846 BuildWebServiceMenu();
852 * Configure menu items that vary according to whether the alignment is
853 * nucleotide or protein
855 public void setGUINucleotide()
857 AlignmentI al = getViewport().getAlignment();
858 boolean nucleotide = al.isNucleotide();
860 loadVcf.setVisible(nucleotide);
861 showTranslation.setVisible(nucleotide);
862 showReverse.setVisible(nucleotide);
863 showReverseComplement.setVisible(nucleotide);
864 conservationMenuItem.setEnabled(!nucleotide);
866 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
867 showGroupConservation.setEnabled(!nucleotide);
869 showComplementMenuItem
870 .setText(nucleotide ? MessageManager.getString("label.protein")
871 : MessageManager.getString("label.nucleotide"));
875 * set up menus for the current viewport. This may be called after any
876 * operation that affects the data in the current view (selection changed,
877 * etc) to update the menus to reflect the new state.
880 public void setMenusForViewport()
882 setMenusFromViewport(viewport);
886 * Need to call this method when tabs are selected for multiple views, or when
887 * loading from Jalview2XML.java
892 void setMenusFromViewport(AlignViewport av)
894 padGapsMenuitem.setSelected(av.isPadGaps());
895 colourTextMenuItem.setSelected(av.isShowColourText());
896 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
897 modifyPID.setEnabled(abovePIDThreshold.isSelected());
898 conservationMenuItem.setSelected(av.getConservationSelected());
899 modifyConservation.setEnabled(conservationMenuItem.isSelected());
900 seqLimits.setSelected(av.getShowJVSuffix());
901 idRightAlign.setSelected(av.isRightAlignIds());
902 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
903 renderGapsMenuItem.setSelected(av.isRenderGaps());
904 wrapMenuItem.setSelected(av.getWrapAlignment());
905 scaleAbove.setVisible(av.getWrapAlignment());
906 scaleLeft.setVisible(av.getWrapAlignment());
907 scaleRight.setVisible(av.getWrapAlignment());
908 annotationPanelMenuItem.setState(av.isShowAnnotation());
910 * Show/hide annotations only enabled if annotation panel is shown
912 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
913 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
914 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
915 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
916 viewBoxesMenuItem.setSelected(av.getShowBoxes());
917 viewTextMenuItem.setSelected(av.getShowText());
918 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
919 showGroupConsensus.setSelected(av.isShowGroupConsensus());
920 showGroupConservation.setSelected(av.isShowGroupConservation());
921 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
922 showSequenceLogo.setSelected(av.isShowSequenceLogo());
923 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
925 ColourMenuHelper.setColourSelected(colourMenu,
926 av.getGlobalColourScheme());
928 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
929 hiddenMarkers.setState(av.getShowHiddenMarkers());
930 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
931 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
932 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
933 autoCalculate.setSelected(av.autoCalculateConsensus);
934 sortByTree.setSelected(av.sortByTree);
935 listenToViewSelections.setSelected(av.followSelection);
937 showProducts.setEnabled(canShowProducts());
938 setGroovyEnabled(Desktop.getGroovyConsole() != null);
944 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
948 public void setGroovyEnabled(boolean b)
950 runGroovy.setEnabled(b);
953 private IProgressIndicator progressBar;
958 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
961 public void setProgressBar(String message, long id)
963 progressBar.setProgressBar(message, id);
967 public void registerHandler(final long id,
968 final IProgressIndicatorHandler handler)
970 progressBar.registerHandler(id, handler);
975 * @return true if any progress bars are still active
978 public boolean operationInProgress()
980 return progressBar.operationInProgress();
984 public void setStatus(String text)
986 statusBar.setText(text);
990 * Added so Castor Mapping file can obtain Jalview Version
992 public String getVersion()
994 return jalview.bin.Cache.getProperty("VERSION");
997 public FeatureRenderer getFeatureRenderer()
999 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1003 public void fetchSequence_actionPerformed(ActionEvent e)
1005 new jalview.gui.SequenceFetcher(this);
1009 public void addFromFile_actionPerformed(ActionEvent e)
1011 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1015 public void reload_actionPerformed(ActionEvent e)
1017 if (fileName != null)
1019 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1020 // originating file's format
1021 // TODO: work out how to recover feature settings for correct view(s) when
1022 // file is reloaded.
1023 if (FileFormat.Jalview.equals(currentFileFormat))
1025 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1026 for (int i = 0; i < frames.length; i++)
1028 if (frames[i] instanceof AlignFrame && frames[i] != this
1029 && ((AlignFrame) frames[i]).fileName != null
1030 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1034 frames[i].setSelected(true);
1035 Desktop.instance.closeAssociatedWindows();
1036 } catch (java.beans.PropertyVetoException ex)
1042 Desktop.instance.closeAssociatedWindows();
1044 FileLoader loader = new FileLoader();
1045 DataSourceType protocol = fileName.startsWith("http:")
1046 ? DataSourceType.URL
1047 : DataSourceType.FILE;
1048 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1052 Rectangle bounds = this.getBounds();
1054 FileLoader loader = new FileLoader();
1055 DataSourceType protocol = fileName.startsWith("http:")
1056 ? DataSourceType.URL
1057 : DataSourceType.FILE;
1058 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1059 protocol, currentFileFormat);
1061 newframe.setBounds(bounds);
1062 if (featureSettings != null && featureSettings.isShowing())
1064 final Rectangle fspos = featureSettings.frame.getBounds();
1065 // TODO: need a 'show feature settings' function that takes bounds -
1066 // need to refactor Desktop.addFrame
1067 newframe.featureSettings_actionPerformed(null);
1068 final FeatureSettings nfs = newframe.featureSettings;
1069 SwingUtilities.invokeLater(new Runnable()
1074 nfs.frame.setBounds(fspos);
1077 this.featureSettings.close();
1078 this.featureSettings = null;
1080 this.closeMenuItem_actionPerformed(true);
1086 public void addFromText_actionPerformed(ActionEvent e)
1089 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1093 public void addFromURL_actionPerformed(ActionEvent e)
1095 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1099 public void save_actionPerformed(ActionEvent e)
1101 if (fileName == null || (currentFileFormat == null)
1102 || fileName.startsWith("http"))
1104 saveAs_actionPerformed(null);
1108 saveAlignment(fileName, currentFileFormat);
1119 public void saveAs_actionPerformed(ActionEvent e)
1121 // TODO: JAL-3048 JalviewFileChooser - Save option
1123 String format = currentFileFormat == null ? null
1124 : currentFileFormat.getName();
1125 JalviewFileChooser chooser = JalviewFileChooser
1126 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1128 chooser.setFileView(new JalviewFileView());
1129 chooser.setDialogTitle(
1130 MessageManager.getString("label.save_alignment_to_file"));
1131 chooser.setToolTipText(MessageManager.getString("action.save"));
1133 int value = chooser.showSaveDialog(this);
1136 if (value == JalviewFileChooser.APPROVE_OPTION)
1138 currentFileFormat = chooser.getSelectedFormat();
1139 while (currentFileFormat == null)
1141 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1142 MessageManager.getString(
1143 "label.select_file_format_before_saving"),
1144 MessageManager.getString("label.file_format_not_specified"),
1145 JvOptionPane.WARNING_MESSAGE);
1146 currentFileFormat = chooser.getSelectedFormat();
1147 value = chooser.showSaveDialog(this);
1148 if (value != JalviewFileChooser.APPROVE_OPTION)
1154 fileName = chooser.getSelectedFile().getPath();
1156 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1158 Cache.setProperty("LAST_DIRECTORY", fileName);
1159 saveAlignment(fileName, currentFileFormat);
1163 public boolean saveAlignment(String file, FileFormatI format)
1165 boolean success = true;
1167 if (FileFormat.Jalview.equals(format))
1169 String shortName = title;
1171 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1173 shortName = shortName.substring(
1174 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1177 success = new Jalview2XML().saveAlignment(this, file, shortName);
1179 statusBar.setText(MessageManager.formatMessage(
1180 "label.successfully_saved_to_file_in_format", new Object[]
1181 { fileName, format }));
1186 AlignmentExportData exportData = getAlignmentForExport(format,
1188 if (exportData.getSettings().isCancelled())
1192 FormatAdapter f = new FormatAdapter(alignPanel,
1193 exportData.getSettings());
1194 String output = f.formatSequences(format, exportData.getAlignment(), // class
1198 // occur in the distant future
1199 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1200 f.getCacheSuffixDefault(format),
1201 viewport.getAlignment().getHiddenColumns());
1211 PrintWriter out = new PrintWriter(new FileWriter(file));
1215 this.setTitle(file);
1216 statusBar.setText(MessageManager.formatMessage(
1217 "label.successfully_saved_to_file_in_format", new Object[]
1218 { fileName, format.getName() }));
1219 } catch (Exception ex)
1222 ex.printStackTrace();
1229 JvOptionPane.showInternalMessageDialog(this, MessageManager
1230 .formatMessage("label.couldnt_save_file", new Object[]
1232 MessageManager.getString("label.error_saving_file"),
1233 JvOptionPane.WARNING_MESSAGE);
1239 private void warningMessage(String warning, String title)
1241 if (new jalview.util.Platform().isHeadless())
1243 System.err.println("Warning: " + title + "\nWarning: " + warning);
1248 JvOptionPane.showInternalMessageDialog(this, warning, title,
1249 JvOptionPane.WARNING_MESSAGE);
1261 protected void outputText_actionPerformed(ActionEvent e)
1263 FileFormatI fileFormat = FileFormats.getInstance()
1264 .forName(e.getActionCommand());
1265 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1267 if (exportData.getSettings().isCancelled())
1271 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1272 cap.setForInput(null);
1275 FileFormatI format = fileFormat;
1276 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1277 .formatSequences(format, exportData.getAlignment(),
1278 exportData.getOmitHidden(),
1279 exportData.getStartEndPostions(),
1280 viewport.getAlignment().getHiddenColumns()));
1281 Desktop.addInternalFrame(cap, MessageManager
1282 .formatMessage("label.alignment_output_command", new Object[]
1283 { e.getActionCommand() }), 600, 500);
1284 } catch (OutOfMemoryError oom)
1286 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1293 public static AlignmentExportData getAlignmentForExport(
1294 FileFormatI format, AlignViewportI viewport,
1295 AlignExportSettingI exportSettings)
1297 AlignmentI alignmentToExport = null;
1298 AlignExportSettingI settings = exportSettings;
1299 String[] omitHidden = null;
1301 HiddenSequences hiddenSeqs = viewport.getAlignment()
1302 .getHiddenSequences();
1304 alignmentToExport = viewport.getAlignment();
1306 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1307 if (settings == null)
1309 settings = new AlignExportSettings(hasHiddenSeqs,
1310 viewport.hasHiddenColumns(), format);
1312 // settings.isExportAnnotations();
1314 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1316 omitHidden = viewport.getViewAsString(false,
1317 settings.isExportHiddenSequences());
1320 int[] alignmentStartEnd = new int[2];
1321 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1323 alignmentToExport = hiddenSeqs.getFullAlignment();
1327 alignmentToExport = viewport.getAlignment();
1329 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1330 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1331 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1332 omitHidden, alignmentStartEnd, settings);
1343 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1345 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1346 htmlSVG.exportHTML(null);
1350 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1352 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1353 bjs.exportHTML(null);
1356 public void createImageMap(File file, String image)
1358 alignPanel.makePNGImageMap(file, image);
1368 public void createPNG(File f)
1370 alignPanel.makePNG(f);
1380 public void createEPS(File f)
1382 alignPanel.makeEPS(f);
1386 public void createSVG(File f)
1388 alignPanel.makeSVG(f);
1392 public void pageSetup_actionPerformed(ActionEvent e)
1394 PrinterJob printJob = PrinterJob.getPrinterJob();
1395 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1405 public void printMenuItem_actionPerformed(ActionEvent e)
1407 // Putting in a thread avoids Swing painting problems
1408 PrintThread thread = new PrintThread(alignPanel);
1413 public void exportFeatures_actionPerformed(ActionEvent e)
1415 new AnnotationExporter(alignPanel).exportFeatures();
1419 public void exportAnnotations_actionPerformed(ActionEvent e)
1421 new AnnotationExporter(alignPanel).exportAnnotations();
1425 public void associatedData_actionPerformed(ActionEvent e)
1427 JalviewFileChooser chooser = new JalviewFileChooser(
1428 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1429 chooser.setFileView(new JalviewFileView());
1430 chooser.setDialogTitle(
1431 MessageManager.getString("label.load_jalview_annotations"));
1432 chooser.setToolTipText(
1433 MessageManager.getString("label.load_jalview_annotations"));
1435 Desktop.getDesktop().dialogData = new Object[] { "SelectedFile",
1442 Object[] data = Desktop.getDesktop().dialogData;
1443 int value = ((Integer) data[0]).intValue();
1445 if (value == JFileChooser.APPROVE_OPTION)
1447 JalviewFileChooser chooser = (JalviewFileChooser) data[2];
1448 String choice = chooser.getSelectedFile().getPath();
1449 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1450 loadJalviewDataFile(choice, null, null, null);
1456 chooser.showOpenDialog(null);
1463 * Close the current view or all views in the alignment frame. If the frame
1464 * only contains one view then the alignment will be removed from memory.
1466 * @param closeAllTabs
1469 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1471 if (alignPanels != null && alignPanels.size() < 2)
1473 closeAllTabs = true;
1478 if (alignPanels != null)
1482 if (this.isClosed())
1484 // really close all the windows - otherwise wait till
1485 // setClosed(true) is called
1486 for (int i = 0; i < alignPanels.size(); i++)
1488 AlignmentPanel ap = alignPanels.get(i);
1495 closeView(alignPanel);
1502 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1503 * be called recursively, with the frame now in 'closed' state
1505 this.setClosed(true);
1507 } catch (Exception ex)
1509 ex.printStackTrace();
1514 * Close the specified panel and close up tabs appropriately.
1516 * @param panelToClose
1518 public void closeView(AlignmentPanel panelToClose)
1520 int index = tabbedPane.getSelectedIndex();
1521 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1522 alignPanels.remove(panelToClose);
1523 panelToClose.closePanel();
1524 panelToClose = null;
1526 tabbedPane.removeTabAt(closedindex);
1527 tabbedPane.validate();
1529 if (index > closedindex || index == tabbedPane.getTabCount())
1531 // modify currently selected tab index if necessary.
1535 this.tabSelectionChanged(index);
1541 void updateEditMenuBar()
1544 if (viewport.getHistoryList().size() > 0)
1546 undoMenuItem.setEnabled(true);
1547 CommandI command = viewport.getHistoryList().peek();
1548 undoMenuItem.setText(MessageManager
1549 .formatMessage("label.undo_command", new Object[]
1550 { command.getDescription() }));
1554 undoMenuItem.setEnabled(false);
1555 undoMenuItem.setText(MessageManager.getString("action.undo"));
1558 if (viewport.getRedoList().size() > 0)
1560 redoMenuItem.setEnabled(true);
1562 CommandI command = viewport.getRedoList().peek();
1563 redoMenuItem.setText(MessageManager
1564 .formatMessage("label.redo_command", new Object[]
1565 { command.getDescription() }));
1569 redoMenuItem.setEnabled(false);
1570 redoMenuItem.setText(MessageManager.getString("action.redo"));
1575 public void addHistoryItem(CommandI command)
1577 if (command.getSize() > 0)
1579 viewport.addToHistoryList(command);
1580 viewport.clearRedoList();
1581 updateEditMenuBar();
1582 viewport.updateHiddenColumns();
1583 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1584 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1585 // viewport.getColumnSelection()
1586 // .getHiddenColumns().size() > 0);
1592 * @return alignment objects for all views
1594 AlignmentI[] getViewAlignments()
1596 if (alignPanels != null)
1598 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1600 for (AlignmentPanel ap : alignPanels)
1602 als[i++] = ap.av.getAlignment();
1606 if (viewport != null)
1608 return new AlignmentI[] { viewport.getAlignment() };
1620 protected void undoMenuItem_actionPerformed(ActionEvent e)
1622 if (viewport.getHistoryList().isEmpty())
1626 CommandI command = viewport.getHistoryList().pop();
1627 viewport.addToRedoList(command);
1628 command.undoCommand(getViewAlignments());
1630 AlignmentViewport originalSource = getOriginatingSource(command);
1631 updateEditMenuBar();
1633 if (originalSource != null)
1635 if (originalSource != viewport)
1638 "Implementation worry: mismatch of viewport origin for undo");
1640 originalSource.updateHiddenColumns();
1641 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1643 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1644 // viewport.getColumnSelection()
1645 // .getHiddenColumns().size() > 0);
1646 originalSource.firePropertyChange("alignment", null,
1647 originalSource.getAlignment().getSequences());
1658 protected void redoMenuItem_actionPerformed(ActionEvent e)
1660 if (viewport.getRedoList().size() < 1)
1665 CommandI command = viewport.getRedoList().pop();
1666 viewport.addToHistoryList(command);
1667 command.doCommand(getViewAlignments());
1669 AlignmentViewport originalSource = getOriginatingSource(command);
1670 updateEditMenuBar();
1672 if (originalSource != null)
1675 if (originalSource != viewport)
1678 "Implementation worry: mismatch of viewport origin for redo");
1680 originalSource.updateHiddenColumns();
1681 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1683 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1684 // viewport.getColumnSelection()
1685 // .getHiddenColumns().size() > 0);
1686 originalSource.firePropertyChange("alignment", null,
1687 originalSource.getAlignment().getSequences());
1691 AlignmentViewport getOriginatingSource(CommandI command)
1693 AlignmentViewport originalSource = null;
1694 // For sequence removal and addition, we need to fire
1695 // the property change event FROM the viewport where the
1696 // original alignment was altered
1697 AlignmentI al = null;
1698 if (command instanceof EditCommand)
1700 EditCommand editCommand = (EditCommand) command;
1701 al = editCommand.getAlignment();
1702 List<Component> comps = PaintRefresher.components
1703 .get(viewport.getSequenceSetId());
1705 for (Component comp : comps)
1707 if (comp instanceof AlignmentPanel)
1709 if (al == ((AlignmentPanel) comp).av.getAlignment())
1711 originalSource = ((AlignmentPanel) comp).av;
1718 if (originalSource == null)
1720 // The original view is closed, we must validate
1721 // the current view against the closed view first
1724 PaintRefresher.validateSequences(al, viewport.getAlignment());
1727 originalSource = viewport;
1730 return originalSource;
1739 public void moveSelectedSequences(boolean up)
1741 SequenceGroup sg = viewport.getSelectionGroup();
1747 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1748 viewport.getHiddenRepSequences(), up);
1749 alignPanel.paintAlignment(true, false);
1752 synchronized void slideSequences(boolean right, int size)
1754 List<SequenceI> sg = new ArrayList<>();
1755 if (viewport.cursorMode)
1757 sg.add(viewport.getAlignment()
1758 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1760 else if (viewport.getSelectionGroup() != null
1761 && viewport.getSelectionGroup().getSize() != viewport
1762 .getAlignment().getHeight())
1764 sg = viewport.getSelectionGroup()
1765 .getSequences(viewport.getHiddenRepSequences());
1773 List<SequenceI> invertGroup = new ArrayList<>();
1775 for (SequenceI seq : viewport.getAlignment().getSequences())
1777 if (!sg.contains(seq))
1779 invertGroup.add(seq);
1783 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1785 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1786 for (int i = 0; i < invertGroup.size(); i++)
1788 seqs2[i] = invertGroup.get(i);
1791 SlideSequencesCommand ssc;
1794 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1795 viewport.getGapCharacter());
1799 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1800 viewport.getGapCharacter());
1803 int groupAdjustment = 0;
1804 if (ssc.getGapsInsertedBegin() && right)
1806 if (viewport.cursorMode)
1808 alignPanel.getSeqPanel().moveCursor(size, 0);
1812 groupAdjustment = size;
1815 else if (!ssc.getGapsInsertedBegin() && !right)
1817 if (viewport.cursorMode)
1819 alignPanel.getSeqPanel().moveCursor(-size, 0);
1823 groupAdjustment = -size;
1827 if (groupAdjustment != 0)
1829 viewport.getSelectionGroup().setStartRes(
1830 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1831 viewport.getSelectionGroup().setEndRes(
1832 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1836 * just extend the last slide command if compatible; but not if in
1837 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1839 boolean appendHistoryItem = false;
1840 Deque<CommandI> historyList = viewport.getHistoryList();
1841 boolean inSplitFrame = getSplitViewContainer() != null;
1842 if (!inSplitFrame && historyList != null && historyList.size() > 0
1843 && historyList.peek() instanceof SlideSequencesCommand)
1845 appendHistoryItem = ssc.appendSlideCommand(
1846 (SlideSequencesCommand) historyList.peek());
1849 if (!appendHistoryItem)
1851 addHistoryItem(ssc);
1864 protected void copy_actionPerformed(ActionEvent e)
1866 if (viewport.getSelectionGroup() == null)
1870 // TODO: preserve the ordering of displayed alignment annotation in any
1871 // internal paste (particularly sequence associated annotation)
1872 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1873 String[] omitHidden = null;
1875 if (viewport.hasHiddenColumns())
1877 omitHidden = viewport.getViewAsString(true);
1880 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1881 seqs, omitHidden, null);
1883 StringSelection ss = new StringSelection(output);
1887 jalview.gui.Desktop.internalCopy = true;
1888 // Its really worth setting the clipboard contents
1889 // to empty before setting the large StringSelection!!
1890 Toolkit.getDefaultToolkit().getSystemClipboard()
1891 .setContents(new StringSelection(""), null);
1893 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1895 } catch (OutOfMemoryError er)
1897 new OOMWarning("copying region", er);
1901 HiddenColumns hiddenColumns = null;
1902 if (viewport.hasHiddenColumns())
1904 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1905 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1907 // create new HiddenColumns object with copy of hidden regions
1908 // between startRes and endRes, offset by startRes
1909 hiddenColumns = new HiddenColumns(
1910 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1911 hiddenCutoff, hiddenOffset);
1914 Desktop.jalviewClipboard = new Object[] { seqs,
1915 viewport.getAlignment().getDataset(), hiddenColumns };
1916 statusBar.setText(MessageManager.formatMessage(
1917 "label.copied_sequences_to_clipboard", new Object[]
1918 { Integer.valueOf(seqs.length).toString() }));
1928 protected void pasteNew_actionPerformed(ActionEvent e)
1940 protected void pasteThis_actionPerformed(ActionEvent e)
1946 * Paste contents of Jalview clipboard
1948 * @param newAlignment
1949 * true to paste to a new alignment, otherwise add to this.
1951 void paste(boolean newAlignment)
1953 boolean externalPaste = true;
1956 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1957 Transferable contents = c.getContents(this);
1959 if (contents == null)
1968 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1969 if (str.length() < 1)
1974 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1976 } catch (OutOfMemoryError er)
1978 new OOMWarning("Out of memory pasting sequences!!", er);
1982 SequenceI[] sequences;
1983 boolean annotationAdded = false;
1984 AlignmentI alignment = null;
1986 if (Desktop.jalviewClipboard != null)
1988 // The clipboard was filled from within Jalview, we must use the
1990 // And dataset from the copied alignment
1991 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1992 // be doubly sure that we create *new* sequence objects.
1993 sequences = new SequenceI[newseq.length];
1994 for (int i = 0; i < newseq.length; i++)
1996 sequences[i] = new Sequence(newseq[i]);
1998 alignment = new Alignment(sequences);
1999 externalPaste = false;
2003 // parse the clipboard as an alignment.
2004 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2006 sequences = alignment.getSequencesArray();
2010 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2016 if (Desktop.jalviewClipboard != null)
2018 // dataset is inherited
2019 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2023 // new dataset is constructed
2024 alignment.setDataset(null);
2026 alwidth = alignment.getWidth() + 1;
2030 AlignmentI pastedal = alignment; // preserve pasted alignment object
2031 // Add pasted sequences and dataset into existing alignment.
2032 alignment = viewport.getAlignment();
2033 alwidth = alignment.getWidth() + 1;
2034 // decide if we need to import sequences from an existing dataset
2035 boolean importDs = Desktop.jalviewClipboard != null
2036 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2037 // importDs==true instructs us to copy over new dataset sequences from
2038 // an existing alignment
2039 Vector newDs = (importDs) ? new Vector() : null; // used to create
2040 // minimum dataset set
2042 for (int i = 0; i < sequences.length; i++)
2046 newDs.addElement(null);
2048 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2050 if (importDs && ds != null)
2052 if (!newDs.contains(ds))
2054 newDs.setElementAt(ds, i);
2055 ds = new Sequence(ds);
2056 // update with new dataset sequence
2057 sequences[i].setDatasetSequence(ds);
2061 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2066 // copy and derive new dataset sequence
2067 sequences[i] = sequences[i].deriveSequence();
2068 alignment.getDataset()
2069 .addSequence(sequences[i].getDatasetSequence());
2070 // TODO: avoid creation of duplicate dataset sequences with a
2071 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2073 alignment.addSequence(sequences[i]); // merges dataset
2077 newDs.clear(); // tidy up
2079 if (alignment.getAlignmentAnnotation() != null)
2081 for (AlignmentAnnotation alan : alignment
2082 .getAlignmentAnnotation())
2084 if (alan.graphGroup > fgroup)
2086 fgroup = alan.graphGroup;
2090 if (pastedal.getAlignmentAnnotation() != null)
2092 // Add any annotation attached to alignment.
2093 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2094 for (int i = 0; i < alann.length; i++)
2096 annotationAdded = true;
2097 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2099 AlignmentAnnotation newann = new AlignmentAnnotation(
2101 if (newann.graphGroup > -1)
2103 if (newGraphGroups.size() <= newann.graphGroup
2104 || newGraphGroups.get(newann.graphGroup) == null)
2106 for (int q = newGraphGroups
2107 .size(); q <= newann.graphGroup; q++)
2109 newGraphGroups.add(q, null);
2111 newGraphGroups.set(newann.graphGroup,
2112 new Integer(++fgroup));
2114 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2118 newann.padAnnotation(alwidth);
2119 alignment.addAnnotation(newann);
2129 addHistoryItem(new EditCommand(
2130 MessageManager.getString("label.add_sequences"),
2131 Action.PASTE, sequences, 0, alignment.getWidth(),
2134 // Add any annotations attached to sequences
2135 for (int i = 0; i < sequences.length; i++)
2137 if (sequences[i].getAnnotation() != null)
2139 AlignmentAnnotation newann;
2140 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2142 annotationAdded = true;
2143 newann = sequences[i].getAnnotation()[a];
2144 newann.adjustForAlignment();
2145 newann.padAnnotation(alwidth);
2146 if (newann.graphGroup > -1)
2148 if (newann.graphGroup > -1)
2150 if (newGraphGroups.size() <= newann.graphGroup
2151 || newGraphGroups.get(newann.graphGroup) == null)
2153 for (int q = newGraphGroups
2154 .size(); q <= newann.graphGroup; q++)
2156 newGraphGroups.add(q, null);
2158 newGraphGroups.set(newann.graphGroup,
2159 new Integer(++fgroup));
2161 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2165 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2169 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2177 // propagate alignment changed.
2178 viewport.getRanges().setEndSeq(alignment.getHeight());
2179 if (annotationAdded)
2181 // Duplicate sequence annotation in all views.
2182 AlignmentI[] alview = this.getViewAlignments();
2183 for (int i = 0; i < sequences.length; i++)
2185 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2190 for (int avnum = 0; avnum < alview.length; avnum++)
2192 if (alview[avnum] != alignment)
2194 // duplicate in a view other than the one with input focus
2195 int avwidth = alview[avnum].getWidth() + 1;
2196 // this relies on sann being preserved after we
2197 // modify the sequence's annotation array for each duplication
2198 for (int a = 0; a < sann.length; a++)
2200 AlignmentAnnotation newann = new AlignmentAnnotation(
2202 sequences[i].addAlignmentAnnotation(newann);
2203 newann.padAnnotation(avwidth);
2204 alview[avnum].addAnnotation(newann); // annotation was
2205 // duplicated earlier
2206 // TODO JAL-1145 graphGroups are not updated for sequence
2207 // annotation added to several views. This may cause
2209 alview[avnum].setAnnotationIndex(newann, a);
2214 buildSortByAnnotationScoresMenu();
2216 viewport.firePropertyChange("alignment", null,
2217 alignment.getSequences());
2218 if (alignPanels != null)
2220 for (AlignmentPanel ap : alignPanels)
2222 ap.validateAnnotationDimensions(false);
2227 alignPanel.validateAnnotationDimensions(false);
2233 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2235 String newtitle = new String("Copied sequences");
2237 if (Desktop.jalviewClipboard != null
2238 && Desktop.jalviewClipboard[2] != null)
2240 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2241 af.viewport.setHiddenColumns(hc);
2244 // >>>This is a fix for the moment, until a better solution is
2246 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2247 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2248 .getFeatureRenderer());
2250 // TODO: maintain provenance of an alignment, rather than just make the
2251 // title a concatenation of operations.
2254 if (title.startsWith("Copied sequences"))
2260 newtitle = newtitle.concat("- from " + title);
2265 newtitle = new String("Pasted sequences");
2268 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2273 } catch (Exception ex)
2275 ex.printStackTrace();
2276 System.out.println("Exception whilst pasting: " + ex);
2277 // could be anything being pasted in here
2283 protected void expand_newalign(ActionEvent e)
2287 AlignmentI alignment = AlignmentUtils
2288 .expandContext(getViewport().getAlignment(), -1);
2289 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2291 String newtitle = new String("Flanking alignment");
2293 if (Desktop.jalviewClipboard != null
2294 && Desktop.jalviewClipboard[2] != null)
2296 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2297 af.viewport.setHiddenColumns(hc);
2300 // >>>This is a fix for the moment, until a better solution is
2302 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2303 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2304 .getFeatureRenderer());
2306 // TODO: maintain provenance of an alignment, rather than just make the
2307 // title a concatenation of operations.
2309 if (title.startsWith("Copied sequences"))
2315 newtitle = newtitle.concat("- from " + title);
2319 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2321 } catch (Exception ex)
2323 ex.printStackTrace();
2324 System.out.println("Exception whilst pasting: " + ex);
2325 // could be anything being pasted in here
2326 } catch (OutOfMemoryError oom)
2328 new OOMWarning("Viewing flanking region of alignment", oom);
2339 protected void cut_actionPerformed(ActionEvent e)
2341 copy_actionPerformed(null);
2342 delete_actionPerformed(null);
2352 protected void delete_actionPerformed(ActionEvent evt)
2355 SequenceGroup sg = viewport.getSelectionGroup();
2362 * If the cut affects all sequences, warn, remove highlighted columns
2364 if (sg.getSize() == viewport.getAlignment().getHeight())
2366 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2367 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2368 if (isEntireAlignWidth)
2370 int confirm = JvOptionPane.showConfirmDialog(this,
2371 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2372 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2373 JvOptionPane.OK_CANCEL_OPTION);
2375 if (confirm == JvOptionPane.CANCEL_OPTION
2376 || confirm == JvOptionPane.CLOSED_OPTION)
2381 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2382 sg.getEndRes() + 1);
2384 SequenceI[] cut = sg.getSequences()
2385 .toArray(new SequenceI[sg.getSize()]);
2387 addHistoryItem(new EditCommand(
2388 MessageManager.getString("label.cut_sequences"), Action.CUT,
2389 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2390 viewport.getAlignment()));
2392 viewport.setSelectionGroup(null);
2393 viewport.sendSelection();
2394 viewport.getAlignment().deleteGroup(sg);
2396 viewport.firePropertyChange("alignment", null,
2397 viewport.getAlignment().getSequences());
2398 if (viewport.getAlignment().getHeight() < 1)
2402 this.setClosed(true);
2403 } catch (Exception ex)
2416 protected void deleteGroups_actionPerformed(ActionEvent e)
2418 if (avc.deleteGroups())
2420 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2421 alignPanel.updateAnnotation();
2422 alignPanel.paintAlignment(true, true);
2433 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2435 SequenceGroup sg = new SequenceGroup();
2437 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2439 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2442 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2443 viewport.setSelectionGroup(sg);
2444 viewport.sendSelection();
2445 // JAL-2034 - should delegate to
2446 // alignPanel to decide if overview needs
2448 alignPanel.paintAlignment(false, false);
2449 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2459 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2461 if (viewport.cursorMode)
2463 alignPanel.getSeqPanel().keyboardNo1 = null;
2464 alignPanel.getSeqPanel().keyboardNo2 = null;
2466 viewport.setSelectionGroup(null);
2467 viewport.getColumnSelection().clear();
2468 viewport.setSelectionGroup(null);
2469 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2470 // JAL-2034 - should delegate to
2471 // alignPanel to decide if overview needs
2473 alignPanel.paintAlignment(false, false);
2474 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2475 viewport.sendSelection();
2485 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2487 SequenceGroup sg = viewport.getSelectionGroup();
2491 selectAllSequenceMenuItem_actionPerformed(null);
2496 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2498 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2500 // JAL-2034 - should delegate to
2501 // alignPanel to decide if overview needs
2504 alignPanel.paintAlignment(true, false);
2505 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2506 viewport.sendSelection();
2510 public void invertColSel_actionPerformed(ActionEvent e)
2512 viewport.invertColumnSelection();
2513 alignPanel.paintAlignment(true, false);
2514 viewport.sendSelection();
2524 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2526 trimAlignment(true);
2536 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2538 trimAlignment(false);
2541 void trimAlignment(boolean trimLeft)
2543 ColumnSelection colSel = viewport.getColumnSelection();
2546 if (!colSel.isEmpty())
2550 column = colSel.getMin();
2554 column = colSel.getMax();
2558 if (viewport.getSelectionGroup() != null)
2560 seqs = viewport.getSelectionGroup()
2561 .getSequencesAsArray(viewport.getHiddenRepSequences());
2565 seqs = viewport.getAlignment().getSequencesArray();
2568 TrimRegionCommand trimRegion;
2571 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2572 column, viewport.getAlignment());
2573 viewport.getRanges().setStartRes(0);
2577 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2578 column, viewport.getAlignment());
2581 statusBar.setText(MessageManager
2582 .formatMessage("label.removed_columns", new String[]
2583 { Integer.valueOf(trimRegion.getSize()).toString() }));
2585 addHistoryItem(trimRegion);
2587 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2589 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2590 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2592 viewport.getAlignment().deleteGroup(sg);
2596 viewport.firePropertyChange("alignment", null,
2597 viewport.getAlignment().getSequences());
2608 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2610 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2613 if (viewport.getSelectionGroup() != null)
2615 seqs = viewport.getSelectionGroup()
2616 .getSequencesAsArray(viewport.getHiddenRepSequences());
2617 start = viewport.getSelectionGroup().getStartRes();
2618 end = viewport.getSelectionGroup().getEndRes();
2622 seqs = viewport.getAlignment().getSequencesArray();
2625 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2626 "Remove Gapped Columns", seqs, start, end,
2627 viewport.getAlignment());
2629 addHistoryItem(removeGapCols);
2631 statusBar.setText(MessageManager
2632 .formatMessage("label.removed_empty_columns", new Object[]
2633 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2635 // This is to maintain viewport position on first residue
2636 // of first sequence
2637 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2638 ViewportRanges ranges = viewport.getRanges();
2639 int startRes = seq.findPosition(ranges.getStartRes());
2640 // ShiftList shifts;
2641 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2642 // edit.alColumnChanges=shifts.getInverse();
2643 // if (viewport.hasHiddenColumns)
2644 // viewport.getColumnSelection().compensateForEdits(shifts);
2645 ranges.setStartRes(seq.findIndex(startRes) - 1);
2646 viewport.firePropertyChange("alignment", null,
2647 viewport.getAlignment().getSequences());
2658 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2660 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2663 if (viewport.getSelectionGroup() != null)
2665 seqs = viewport.getSelectionGroup()
2666 .getSequencesAsArray(viewport.getHiddenRepSequences());
2667 start = viewport.getSelectionGroup().getStartRes();
2668 end = viewport.getSelectionGroup().getEndRes();
2672 seqs = viewport.getAlignment().getSequencesArray();
2675 // This is to maintain viewport position on first residue
2676 // of first sequence
2677 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2678 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2680 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2681 viewport.getAlignment()));
2683 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2685 viewport.firePropertyChange("alignment", null,
2686 viewport.getAlignment().getSequences());
2697 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2699 viewport.setPadGaps(padGapsMenuitem.isSelected());
2700 viewport.firePropertyChange("alignment", null,
2701 viewport.getAlignment().getSequences());
2711 public void findMenuItem_actionPerformed(ActionEvent e)
2717 * Create a new view of the current alignment.
2720 public void newView_actionPerformed(ActionEvent e)
2722 newView(null, true);
2726 * Creates and shows a new view of the current alignment.
2729 * title of newly created view; if null, one will be generated
2730 * @param copyAnnotation
2731 * if true then duplicate all annnotation, groups and settings
2732 * @return new alignment panel, already displayed.
2734 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2737 * Create a new AlignmentPanel (with its own, new Viewport)
2739 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2740 if (!copyAnnotation)
2743 * remove all groups and annotation except for the automatic stuff
2745 newap.av.getAlignment().deleteAllGroups();
2746 newap.av.getAlignment().deleteAllAnnotations(false);
2749 newap.av.setGatherViewsHere(false);
2751 if (viewport.viewName == null)
2753 viewport.viewName = MessageManager
2754 .getString("label.view_name_original");
2758 * Views share the same edits undo and redo stacks
2760 newap.av.setHistoryList(viewport.getHistoryList());
2761 newap.av.setRedoList(viewport.getRedoList());
2764 * Views share the same mappings; need to deregister any new mappings
2765 * created by copyAlignPanel, and register the new reference to the shared
2768 newap.av.replaceMappings(viewport.getAlignment());
2771 * start up cDNA consensus (if applicable) now mappings are in place
2773 if (newap.av.initComplementConsensus())
2775 newap.refresh(true); // adjust layout of annotations
2778 newap.av.viewName = getNewViewName(viewTitle);
2780 addAlignmentPanel(newap, true);
2781 newap.alignmentChanged();
2783 if (alignPanels.size() == 2)
2785 viewport.setGatherViewsHere(true);
2787 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2792 * Make a new name for the view, ensuring it is unique within the current
2793 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2794 * these now use viewId. Unique view names are still desirable for usability.)
2799 protected String getNewViewName(String viewTitle)
2801 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2802 boolean addFirstIndex = false;
2803 if (viewTitle == null || viewTitle.trim().length() == 0)
2805 viewTitle = MessageManager.getString("action.view");
2806 addFirstIndex = true;
2810 index = 1;// we count from 1 if given a specific name
2812 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2814 List<Component> comps = PaintRefresher.components
2815 .get(viewport.getSequenceSetId());
2817 List<String> existingNames = getExistingViewNames(comps);
2819 while (existingNames.contains(newViewName))
2821 newViewName = viewTitle + " " + (++index);
2827 * Returns a list of distinct view names found in the given list of
2828 * components. View names are held on the viewport of an AlignmentPanel.
2833 protected List<String> getExistingViewNames(List<Component> comps)
2835 List<String> existingNames = new ArrayList<>();
2836 for (Component comp : comps)
2838 if (comp instanceof AlignmentPanel)
2840 AlignmentPanel ap = (AlignmentPanel) comp;
2841 if (!existingNames.contains(ap.av.viewName))
2843 existingNames.add(ap.av.viewName);
2847 return existingNames;
2851 * Explode tabbed views into separate windows.
2854 public void expandViews_actionPerformed(ActionEvent e)
2856 Desktop.explodeViews(this);
2860 * Gather views in separate windows back into a tabbed presentation.
2863 public void gatherViews_actionPerformed(ActionEvent e)
2865 Desktop.instance.gatherViews(this);
2875 public void font_actionPerformed(ActionEvent e)
2877 new FontChooser(alignPanel);
2887 protected void seqLimit_actionPerformed(ActionEvent e)
2889 viewport.setShowJVSuffix(seqLimits.isSelected());
2891 alignPanel.getIdPanel().getIdCanvas()
2892 .setPreferredSize(alignPanel.calculateIdWidth());
2893 alignPanel.paintAlignment(true, false);
2897 public void idRightAlign_actionPerformed(ActionEvent e)
2899 viewport.setRightAlignIds(idRightAlign.isSelected());
2900 alignPanel.paintAlignment(false, false);
2904 public void centreColumnLabels_actionPerformed(ActionEvent e)
2906 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2907 alignPanel.paintAlignment(false, false);
2913 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2916 protected void followHighlight_actionPerformed()
2919 * Set the 'follow' flag on the Viewport (and scroll to position if now
2922 final boolean state = this.followHighlightMenuItem.getState();
2923 viewport.setFollowHighlight(state);
2926 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2937 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2939 viewport.setColourText(colourTextMenuItem.isSelected());
2940 alignPanel.paintAlignment(false, false);
2950 public void wrapMenuItem_actionPerformed(ActionEvent e)
2952 scaleAbove.setVisible(wrapMenuItem.isSelected());
2953 scaleLeft.setVisible(wrapMenuItem.isSelected());
2954 scaleRight.setVisible(wrapMenuItem.isSelected());
2955 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2956 alignPanel.updateLayout();
2960 public void showAllSeqs_actionPerformed(ActionEvent e)
2962 viewport.showAllHiddenSeqs();
2966 public void showAllColumns_actionPerformed(ActionEvent e)
2968 viewport.showAllHiddenColumns();
2969 alignPanel.paintAlignment(true, true);
2970 viewport.sendSelection();
2974 public void hideSelSequences_actionPerformed(ActionEvent e)
2976 viewport.hideAllSelectedSeqs();
2980 * called by key handler and the hide all/show all menu items
2985 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2988 boolean hide = false;
2989 SequenceGroup sg = viewport.getSelectionGroup();
2990 if (!toggleSeqs && !toggleCols)
2992 // Hide everything by the current selection - this is a hack - we do the
2993 // invert and then hide
2994 // first check that there will be visible columns after the invert.
2995 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2996 && sg.getStartRes() <= sg.getEndRes()))
2998 // now invert the sequence set, if required - empty selection implies
2999 // that no hiding is required.
3002 invertSequenceMenuItem_actionPerformed(null);
3003 sg = viewport.getSelectionGroup();
3007 viewport.expandColSelection(sg, true);
3008 // finally invert the column selection and get the new sequence
3010 invertColSel_actionPerformed(null);
3017 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3019 hideSelSequences_actionPerformed(null);
3022 else if (!(toggleCols && viewport.hasSelectedColumns()))
3024 showAllSeqs_actionPerformed(null);
3030 if (viewport.hasSelectedColumns())
3032 hideSelColumns_actionPerformed(null);
3035 viewport.setSelectionGroup(sg);
3040 showAllColumns_actionPerformed(null);
3049 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3050 * event.ActionEvent)
3053 public void hideAllButSelection_actionPerformed(ActionEvent e)
3055 toggleHiddenRegions(false, false);
3056 viewport.sendSelection();
3063 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3067 public void hideAllSelection_actionPerformed(ActionEvent e)
3069 SequenceGroup sg = viewport.getSelectionGroup();
3070 viewport.expandColSelection(sg, false);
3071 viewport.hideAllSelectedSeqs();
3072 viewport.hideSelectedColumns();
3073 alignPanel.paintAlignment(true, true);
3074 viewport.sendSelection();
3081 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3085 public void showAllhidden_actionPerformed(ActionEvent e)
3087 viewport.showAllHiddenColumns();
3088 viewport.showAllHiddenSeqs();
3089 alignPanel.paintAlignment(true, true);
3090 viewport.sendSelection();
3094 public void hideSelColumns_actionPerformed(ActionEvent e)
3096 viewport.hideSelectedColumns();
3097 alignPanel.paintAlignment(true, true);
3098 viewport.sendSelection();
3102 public void hiddenMarkers_actionPerformed(ActionEvent e)
3104 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3115 protected void scaleAbove_actionPerformed(ActionEvent e)
3117 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3118 // TODO: do we actually need to update overview for scale above change ?
3119 alignPanel.paintAlignment(true, false);
3129 protected void scaleLeft_actionPerformed(ActionEvent e)
3131 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3132 alignPanel.paintAlignment(true, false);
3142 protected void scaleRight_actionPerformed(ActionEvent e)
3144 viewport.setScaleRightWrapped(scaleRight.isSelected());
3145 alignPanel.paintAlignment(true, false);
3155 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3157 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3158 alignPanel.paintAlignment(false, false);
3168 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3170 viewport.setShowText(viewTextMenuItem.isSelected());
3171 alignPanel.paintAlignment(false, false);
3181 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3183 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3184 alignPanel.paintAlignment(false, false);
3187 public FeatureSettings featureSettings;
3190 public FeatureSettingsControllerI getFeatureSettingsUI()
3192 return featureSettings;
3196 public void featureSettings_actionPerformed(ActionEvent e)
3198 if (featureSettings != null)
3200 featureSettings.close();
3201 featureSettings = null;
3203 if (!showSeqFeatures.isSelected())
3205 // make sure features are actually displayed
3206 showSeqFeatures.setSelected(true);
3207 showSeqFeatures_actionPerformed(null);
3209 featureSettings = new FeatureSettings(this);
3213 * Set or clear 'Show Sequence Features'
3219 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3221 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3222 alignPanel.paintAlignment(true, true);
3226 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3227 * the annotations panel as a whole.
3229 * The options to show/hide all annotations should be enabled when the panel
3230 * is shown, and disabled when the panel is hidden.
3235 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3237 final boolean setVisible = annotationPanelMenuItem.isSelected();
3238 viewport.setShowAnnotation(setVisible);
3239 this.showAllSeqAnnotations.setEnabled(setVisible);
3240 this.hideAllSeqAnnotations.setEnabled(setVisible);
3241 this.showAllAlAnnotations.setEnabled(setVisible);
3242 this.hideAllAlAnnotations.setEnabled(setVisible);
3243 alignPanel.updateLayout();
3247 public void alignmentProperties()
3249 JEditorPane editPane = new JEditorPane("text/html", "");
3250 editPane.setEditable(false);
3251 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3254 MessageManager.formatMessage("label.html_content", new Object[]
3255 { contents.toString() }));
3256 JInternalFrame frame = new JInternalFrame();
3257 frame.getContentPane().add(new JScrollPane(editPane));
3259 Desktop.addInternalFrame(frame, MessageManager
3260 .formatMessage("label.alignment_properties", new Object[]
3261 { getTitle() }), 500, 400);
3271 public void overviewMenuItem_actionPerformed(ActionEvent e)
3273 if (alignPanel.overviewPanel != null)
3278 JInternalFrame frame = new JInternalFrame();
3279 final OverviewPanel overview = new OverviewPanel(alignPanel);
3280 frame.setContentPane(overview);
3281 Desktop.addInternalFrame(frame, MessageManager
3282 .formatMessage("label.overview_params", new Object[]
3283 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3286 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3287 frame.addInternalFrameListener(
3288 new javax.swing.event.InternalFrameAdapter()
3291 public void internalFrameClosed(
3292 javax.swing.event.InternalFrameEvent evt)
3295 alignPanel.setOverviewPanel(null);
3298 if (getKeyListeners().length > 0)
3300 frame.addKeyListener(getKeyListeners()[0]);
3303 alignPanel.setOverviewPanel(overview);
3307 public void textColour_actionPerformed()
3309 new TextColourChooser().chooseColour(alignPanel, null);
3313 * public void covariationColour_actionPerformed() {
3315 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3319 public void annotationColour_actionPerformed()
3321 new AnnotationColourChooser(viewport, alignPanel);
3325 public void annotationColumn_actionPerformed(ActionEvent e)
3327 new AnnotationColumnChooser(viewport, alignPanel);
3331 * Action on the user checking or unchecking the option to apply the selected
3332 * colour scheme to all groups. If unchecked, groups may have their own
3333 * independent colour schemes.
3338 public void applyToAllGroups_actionPerformed(boolean selected)
3340 viewport.setColourAppliesToAllGroups(selected);
3344 * Action on user selecting a colour from the colour menu
3347 * the name (not the menu item label!) of the colour scheme
3350 public void changeColour_actionPerformed(String name)
3353 * 'User Defined' opens a panel to configure or load a
3354 * user-defined colour scheme
3356 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3358 new UserDefinedColours(alignPanel);
3363 * otherwise set the chosen colour scheme (or null for 'None')
3365 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3366 viewport.getAlignment(), viewport.getHiddenRepSequences());
3371 * Actions on setting or changing the alignment colour scheme
3376 public void changeColour(ColourSchemeI cs)
3378 // TODO: pull up to controller method
3379 ColourMenuHelper.setColourSelected(colourMenu, cs);
3381 viewport.setGlobalColourScheme(cs);
3383 alignPanel.paintAlignment(true, true);
3387 * Show the PID threshold slider panel
3390 protected void modifyPID_actionPerformed()
3392 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3393 alignPanel.getViewName());
3394 SliderPanel.showPIDSlider();
3398 * Show the Conservation slider panel
3401 protected void modifyConservation_actionPerformed()
3403 SliderPanel.setConservationSlider(alignPanel,
3404 viewport.getResidueShading(), alignPanel.getViewName());
3405 SliderPanel.showConservationSlider();
3409 * Action on selecting or deselecting (Colour) By Conservation
3412 public void conservationMenuItem_actionPerformed(boolean selected)
3414 modifyConservation.setEnabled(selected);
3415 viewport.setConservationSelected(selected);
3416 viewport.getResidueShading().setConservationApplied(selected);
3418 changeColour(viewport.getGlobalColourScheme());
3421 modifyConservation_actionPerformed();
3425 SliderPanel.hideConservationSlider();
3430 * Action on selecting or deselecting (Colour) Above PID Threshold
3433 public void abovePIDThreshold_actionPerformed(boolean selected)
3435 modifyPID.setEnabled(selected);
3436 viewport.setAbovePIDThreshold(selected);
3439 viewport.getResidueShading().setThreshold(0,
3440 viewport.isIgnoreGapsConsensus());
3443 changeColour(viewport.getGlobalColourScheme());
3446 modifyPID_actionPerformed();
3450 SliderPanel.hidePIDSlider();
3461 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3463 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3464 AlignmentSorter.sortByPID(viewport.getAlignment(),
3465 viewport.getAlignment().getSequenceAt(0));
3466 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3467 viewport.getAlignment()));
3468 alignPanel.paintAlignment(true, false);
3478 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3480 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3481 AlignmentSorter.sortByID(viewport.getAlignment());
3483 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3484 alignPanel.paintAlignment(true, false);
3494 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3496 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3497 AlignmentSorter.sortByLength(viewport.getAlignment());
3498 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3499 viewport.getAlignment()));
3500 alignPanel.paintAlignment(true, false);
3510 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3512 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3513 AlignmentSorter.sortByGroup(viewport.getAlignment());
3514 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3515 viewport.getAlignment()));
3517 alignPanel.paintAlignment(true, false);
3527 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3529 new RedundancyPanel(alignPanel, this);
3539 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3541 if ((viewport.getSelectionGroup() == null)
3542 || (viewport.getSelectionGroup().getSize() < 2))
3544 JvOptionPane.showInternalMessageDialog(this,
3545 MessageManager.getString(
3546 "label.you_must_select_least_two_sequences"),
3547 MessageManager.getString("label.invalid_selection"),
3548 JvOptionPane.WARNING_MESSAGE);
3552 JInternalFrame frame = new JInternalFrame();
3553 frame.setContentPane(new PairwiseAlignPanel(viewport));
3554 Desktop.addInternalFrame(frame,
3555 MessageManager.getString("action.pairwise_alignment"), 600,
3561 public void autoCalculate_actionPerformed(ActionEvent e)
3563 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3564 if (viewport.autoCalculateConsensus)
3566 viewport.firePropertyChange("alignment", null,
3567 viewport.getAlignment().getSequences());
3572 public void sortByTreeOption_actionPerformed(ActionEvent e)
3574 viewport.sortByTree = sortByTree.isSelected();
3578 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3580 viewport.followSelection = listenToViewSelections.isSelected();
3584 * Constructs a tree panel and adds it to the desktop
3587 * tree type (NJ or AV)
3589 * name of score model used to compute the tree
3591 * parameters for the distance or similarity calculation
3593 void newTreePanel(String type, String modelName,
3594 SimilarityParamsI options)
3596 String frameTitle = "";
3599 boolean onSelection = false;
3600 if (viewport.getSelectionGroup() != null
3601 && viewport.getSelectionGroup().getSize() > 0)
3603 SequenceGroup sg = viewport.getSelectionGroup();
3605 /* Decide if the selection is a column region */
3606 for (SequenceI _s : sg.getSequences())
3608 if (_s.getLength() < sg.getEndRes())
3610 JvOptionPane.showMessageDialog(Desktop.desktop,
3611 MessageManager.getString(
3612 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3613 MessageManager.getString(
3614 "label.sequences_selection_not_aligned"),
3615 JvOptionPane.WARNING_MESSAGE);
3624 if (viewport.getAlignment().getHeight() < 2)
3630 tp = new TreePanel(alignPanel, type, modelName, options);
3631 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3633 frameTitle += " from ";
3635 if (viewport.viewName != null)
3637 frameTitle += viewport.viewName + " of ";
3640 frameTitle += this.title;
3642 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3653 public void addSortByOrderMenuItem(String title,
3654 final AlignmentOrder order)
3656 final JMenuItem item = new JMenuItem(MessageManager
3657 .formatMessage("action.by_title_param", new Object[]
3660 item.addActionListener(new java.awt.event.ActionListener()
3663 public void actionPerformed(ActionEvent e)
3665 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3667 // TODO: JBPNote - have to map order entries to curent SequenceI
3669 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3671 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3672 viewport.getAlignment()));
3674 alignPanel.paintAlignment(true, false);
3680 * Add a new sort by annotation score menu item
3683 * the menu to add the option to
3685 * the label used to retrieve scores for each sequence on the
3688 public void addSortByAnnotScoreMenuItem(JMenu sort,
3689 final String scoreLabel)
3691 final JMenuItem item = new JMenuItem(scoreLabel);
3693 item.addActionListener(new java.awt.event.ActionListener()
3696 public void actionPerformed(ActionEvent e)
3698 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3699 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3700 viewport.getAlignment());// ,viewport.getSelectionGroup());
3701 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3702 viewport.getAlignment()));
3703 alignPanel.paintAlignment(true, false);
3709 * last hash for alignment's annotation array - used to minimise cost of
3712 protected int _annotationScoreVectorHash;
3715 * search the alignment and rebuild the sort by annotation score submenu the
3716 * last alignment annotation vector hash is stored to minimize cost of
3717 * rebuilding in subsequence calls.
3721 public void buildSortByAnnotationScoresMenu()
3723 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3728 if (viewport.getAlignment().getAlignmentAnnotation()
3729 .hashCode() != _annotationScoreVectorHash)
3731 sortByAnnotScore.removeAll();
3732 // almost certainly a quicker way to do this - but we keep it simple
3733 Hashtable scoreSorts = new Hashtable();
3734 AlignmentAnnotation aann[];
3735 for (SequenceI sqa : viewport.getAlignment().getSequences())
3737 aann = sqa.getAnnotation();
3738 for (int i = 0; aann != null && i < aann.length; i++)
3740 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3742 scoreSorts.put(aann[i].label, aann[i].label);
3746 Enumeration labels = scoreSorts.keys();
3747 while (labels.hasMoreElements())
3749 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3750 (String) labels.nextElement());
3752 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3755 _annotationScoreVectorHash = viewport.getAlignment()
3756 .getAlignmentAnnotation().hashCode();
3761 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3762 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3763 * call. Listeners are added to remove the menu item when the treePanel is
3764 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3768 public void buildTreeSortMenu()
3770 sortByTreeMenu.removeAll();
3772 List<Component> comps = PaintRefresher.components
3773 .get(viewport.getSequenceSetId());
3774 List<TreePanel> treePanels = new ArrayList<>();
3775 for (Component comp : comps)
3777 if (comp instanceof TreePanel)
3779 treePanels.add((TreePanel) comp);
3783 if (treePanels.size() < 1)
3785 sortByTreeMenu.setVisible(false);
3789 sortByTreeMenu.setVisible(true);
3791 for (final TreePanel tp : treePanels)
3793 final JMenuItem item = new JMenuItem(tp.getTitle());
3794 item.addActionListener(new java.awt.event.ActionListener()
3797 public void actionPerformed(ActionEvent e)
3799 tp.sortByTree_actionPerformed();
3800 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3805 sortByTreeMenu.add(item);
3809 public boolean sortBy(AlignmentOrder alorder, String undoname)
3811 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3812 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3813 if (undoname != null)
3815 addHistoryItem(new OrderCommand(undoname, oldOrder,
3816 viewport.getAlignment()));
3818 alignPanel.paintAlignment(true, false);
3823 * Work out whether the whole set of sequences or just the selected set will
3824 * be submitted for multiple alignment.
3827 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3829 // Now, check we have enough sequences
3830 AlignmentView msa = null;
3832 if ((viewport.getSelectionGroup() != null)
3833 && (viewport.getSelectionGroup().getSize() > 1))
3835 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3836 // some common interface!
3838 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3839 * SequenceI[sz = seqs.getSize(false)];
3841 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3842 * seqs.getSequenceAt(i); }
3844 msa = viewport.getAlignmentView(true);
3846 else if (viewport.getSelectionGroup() != null
3847 && viewport.getSelectionGroup().getSize() == 1)
3849 int option = JvOptionPane.showConfirmDialog(this,
3850 MessageManager.getString("warn.oneseq_msainput_selection"),
3851 MessageManager.getString("label.invalid_selection"),
3852 JvOptionPane.OK_CANCEL_OPTION);
3853 if (option == JvOptionPane.OK_OPTION)
3855 msa = viewport.getAlignmentView(false);
3860 msa = viewport.getAlignmentView(false);
3866 * Decides what is submitted to a secondary structure prediction service: the
3867 * first sequence in the alignment, or in the current selection, or, if the
3868 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3869 * region or the whole alignment. (where the first sequence in the set is the
3870 * one that the prediction will be for).
3872 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3874 AlignmentView seqs = null;
3876 if ((viewport.getSelectionGroup() != null)
3877 && (viewport.getSelectionGroup().getSize() > 0))
3879 seqs = viewport.getAlignmentView(true);
3883 seqs = viewport.getAlignmentView(false);
3885 // limit sequences - JBPNote in future - could spawn multiple prediction
3887 // TODO: viewport.getAlignment().isAligned is a global state - the local
3888 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3889 if (!viewport.getAlignment().isAligned(false))
3891 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3892 // TODO: if seqs.getSequences().length>1 then should really have warned
3906 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3908 // TODO: JAL-3048 JalviewFileChooser
3909 // Pick the tree file
3910 JalviewFileChooser chooser = new JalviewFileChooser(
3911 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3912 chooser.setFileView(new JalviewFileView());
3913 chooser.setDialogTitle(
3914 MessageManager.getString("label.select_newick_like_tree_file"));
3915 chooser.setToolTipText(
3916 MessageManager.getString("label.load_tree_file"));
3918 int value = chooser.showOpenDialog(null);
3920 if (value == JalviewFileChooser.APPROVE_OPTION)
3922 String filePath = chooser.getSelectedFile().getPath();
3923 Cache.setProperty("LAST_DIRECTORY", filePath);
3924 NewickFile fin = null;
3927 fin = new NewickFile(filePath, DataSourceType.FILE);
3928 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3929 } catch (Exception ex)
3931 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3932 MessageManager.getString("label.problem_reading_tree_file"),
3933 JvOptionPane.WARNING_MESSAGE);
3934 ex.printStackTrace();
3936 if (fin != null && fin.hasWarningMessage())
3938 JvOptionPane.showMessageDialog(Desktop.desktop,
3939 fin.getWarningMessage(),
3941 .getString("label.possible_problem_with_tree_file"),
3942 JvOptionPane.WARNING_MESSAGE);
3947 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3949 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3952 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3953 int h, int x, int y)
3955 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3959 * Add a treeviewer for the tree extracted from a Newick file object to the
3960 * current alignment view
3967 * Associated alignment input data (or null)
3976 * @return TreePanel handle
3978 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3979 AlignmentView input, int w, int h, int x, int y)
3981 TreePanel tp = null;
3987 if (nf.getTree() != null)
3989 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3995 tp.setLocation(x, y);
3998 Desktop.addInternalFrame(tp, treeTitle, w, h);
4000 } catch (Exception ex)
4002 ex.printStackTrace();
4008 private boolean buildingMenu = false;
4011 * Generates menu items and listener event actions for web service clients
4014 public void BuildWebServiceMenu()
4016 while (buildingMenu)
4020 System.err.println("Waiting for building menu to finish.");
4022 } catch (Exception e)
4026 final AlignFrame me = this;
4027 buildingMenu = true;
4028 new Thread(new Runnable()
4033 final List<JMenuItem> legacyItems = new ArrayList<>();
4036 // System.err.println("Building ws menu again "
4037 // + Thread.currentThread());
4038 // TODO: add support for context dependent disabling of services based
4040 // alignment and current selection
4041 // TODO: add additional serviceHandle parameter to specify abstract
4043 // class independently of AbstractName
4044 // TODO: add in rediscovery GUI function to restart discoverer
4045 // TODO: group services by location as well as function and/or
4047 // object broker mechanism.
4048 final Vector<JMenu> wsmenu = new Vector<>();
4049 final IProgressIndicator af = me;
4052 * do not i18n these strings - they are hard-coded in class
4053 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4054 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4056 final JMenu msawsmenu = new JMenu("Alignment");
4057 final JMenu secstrmenu = new JMenu(
4058 "Secondary Structure Prediction");
4059 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4060 final JMenu analymenu = new JMenu("Analysis");
4061 final JMenu dismenu = new JMenu("Protein Disorder");
4062 // JAL-940 - only show secondary structure prediction services from
4063 // the legacy server
4064 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4066 Discoverer.services != null && (Discoverer.services.size() > 0))
4068 // TODO: refactor to allow list of AbstractName/Handler bindings to
4070 // stored or retrieved from elsewhere
4071 // No MSAWS used any more:
4072 // Vector msaws = null; // (Vector)
4073 // Discoverer.services.get("MsaWS");
4074 Vector secstrpr = (Vector) Discoverer.services
4076 if (secstrpr != null)
4078 // Add any secondary structure prediction services
4079 for (int i = 0, j = secstrpr.size(); i < j; i++)
4081 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4083 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4084 .getServiceClient(sh);
4085 int p = secstrmenu.getItemCount();
4086 impl.attachWSMenuEntry(secstrmenu, me);
4087 int q = secstrmenu.getItemCount();
4088 for (int litm = p; litm < q; litm++)
4090 legacyItems.add(secstrmenu.getItem(litm));
4096 // Add all submenus in the order they should appear on the web
4098 wsmenu.add(msawsmenu);
4099 wsmenu.add(secstrmenu);
4100 wsmenu.add(dismenu);
4101 wsmenu.add(analymenu);
4102 // No search services yet
4103 // wsmenu.add(seqsrchmenu);
4105 javax.swing.SwingUtilities.invokeLater(new Runnable()
4112 webService.removeAll();
4113 // first, add discovered services onto the webservices menu
4114 if (wsmenu.size() > 0)
4116 for (int i = 0, j = wsmenu.size(); i < j; i++)
4118 webService.add(wsmenu.get(i));
4123 webService.add(me.webServiceNoServices);
4125 // TODO: move into separate menu builder class.
4126 boolean new_sspred = false;
4127 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4129 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4130 if (jws2servs != null)
4132 if (jws2servs.hasServices())
4134 jws2servs.attachWSMenuEntry(webService, me);
4135 for (Jws2Instance sv : jws2servs.getServices())
4137 if (sv.description.toLowerCase().contains("jpred"))
4139 for (JMenuItem jmi : legacyItems)
4141 jmi.setVisible(false);
4147 if (jws2servs.isRunning())
4149 JMenuItem tm = new JMenuItem(
4150 "Still discovering JABA Services");
4151 tm.setEnabled(false);
4156 build_urlServiceMenu(me.webService);
4157 build_fetchdbmenu(webService);
4158 for (JMenu item : wsmenu)
4160 if (item.getItemCount() == 0)
4162 item.setEnabled(false);
4166 item.setEnabled(true);
4169 } catch (Exception e)
4172 "Exception during web service menu building process.",
4177 } catch (Exception e)
4180 buildingMenu = false;
4187 * construct any groupURL type service menu entries.
4191 private void build_urlServiceMenu(JMenu webService)
4193 // TODO: remove this code when 2.7 is released
4194 // DEBUG - alignmentView
4196 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4197 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4199 * @Override public void actionPerformed(ActionEvent e) {
4200 * jalview.datamodel.AlignmentView
4201 * .testSelectionViews(af.viewport.getAlignment(),
4202 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4204 * }); webService.add(testAlView);
4206 // TODO: refactor to RestClient discoverer and merge menu entries for
4207 // rest-style services with other types of analysis/calculation service
4208 // SHmmr test client - still being implemented.
4209 // DEBUG - alignmentView
4211 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4214 client.attachWSMenuEntry(
4215 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4221 * Searches the alignment sequences for xRefs and builds the Show
4222 * Cross-References menu (formerly called Show Products), with database
4223 * sources for which cross-references are found (protein sources for a
4224 * nucleotide alignment and vice versa)
4226 * @return true if Show Cross-references menu should be enabled
4228 public boolean canShowProducts()
4230 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4231 AlignmentI dataset = viewport.getAlignment().getDataset();
4233 showProducts.removeAll();
4234 final boolean dna = viewport.getAlignment().isNucleotide();
4236 if (seqs == null || seqs.length == 0)
4238 // nothing to see here.
4242 boolean showp = false;
4245 List<String> ptypes = new CrossRef(seqs, dataset)
4246 .findXrefSourcesForSequences(dna);
4248 for (final String source : ptypes)
4251 final AlignFrame af = this;
4252 JMenuItem xtype = new JMenuItem(source);
4253 xtype.addActionListener(new ActionListener()
4256 public void actionPerformed(ActionEvent e)
4258 showProductsFor(af.viewport.getSequenceSelection(), dna,
4262 showProducts.add(xtype);
4264 showProducts.setVisible(showp);
4265 showProducts.setEnabled(showp);
4266 } catch (Exception e)
4269 "canShowProducts threw an exception - please report to help@jalview.org",
4277 * Finds and displays cross-references for the selected sequences (protein
4278 * products for nucleotide sequences, dna coding sequences for peptides).
4281 * the sequences to show cross-references for
4283 * true if from a nucleotide alignment (so showing proteins)
4285 * the database to show cross-references for
4287 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4288 final String source)
4290 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4295 * Construct and display a new frame containing the translation of this
4296 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4299 public void showTranslation_actionPerformed(ActionEvent e)
4301 AlignmentI al = null;
4304 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4306 al = dna.translateCdna();
4307 } catch (Exception ex)
4309 jalview.bin.Cache.log.error(
4310 "Exception during translation. Please report this !", ex);
4311 final String msg = MessageManager.getString(
4312 "label.error_when_translating_sequences_submit_bug_report");
4313 final String errorTitle = MessageManager
4314 .getString("label.implementation_error")
4315 + MessageManager.getString("label.translation_failed");
4316 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4317 JvOptionPane.ERROR_MESSAGE);
4320 if (al == null || al.getHeight() == 0)
4322 final String msg = MessageManager.getString(
4323 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4324 final String errorTitle = MessageManager
4325 .getString("label.translation_failed");
4326 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4327 JvOptionPane.WARNING_MESSAGE);
4331 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4332 af.setFileFormat(this.currentFileFormat);
4333 final String newTitle = MessageManager
4334 .formatMessage("label.translation_of_params", new Object[]
4335 { this.getTitle() });
4336 af.setTitle(newTitle);
4337 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4339 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4340 viewport.openSplitFrame(af, new Alignment(seqs));
4344 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4351 * Set the file format
4355 public void setFileFormat(FileFormatI format)
4357 this.currentFileFormat = format;
4361 * Try to load a features file onto the alignment.
4364 * contents or path to retrieve file or a File object
4366 * access mode of file (see jalview.io.AlignFile)
4367 * @return true if features file was parsed correctly.
4369 public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4372 return avc.parseFeaturesFile(file, sourceType,
4373 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4378 public void refreshFeatureUI(boolean enableIfNecessary)
4380 // note - currently this is only still here rather than in the controller
4381 // because of the featureSettings hard reference that is yet to be
4383 if (enableIfNecessary)
4385 viewport.setShowSequenceFeatures(true);
4386 showSeqFeatures.setSelected(true);
4392 public void dragEnter(DropTargetDragEvent evt)
4397 public void dragExit(DropTargetEvent evt)
4402 public void dragOver(DropTargetDragEvent evt)
4407 public void dropActionChanged(DropTargetDragEvent evt)
4412 public void drop(DropTargetDropEvent evt)
4414 // JAL-1552 - acceptDrop required before getTransferable call for
4415 // Java's Transferable for native dnd
4416 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4417 Transferable t = evt.getTransferable();
4420 final AlignFrame thisaf = this;
4421 final List<Object> files = new ArrayList<>();
4422 List<DataSourceType> protocols = new ArrayList<>();
4426 Desktop.transferFromDropTarget(files, protocols, evt, t);
4427 } catch (Exception e)
4429 e.printStackTrace();
4433 new Thread(new Runnable()
4440 // check to see if any of these files have names matching sequences
4443 SequenceIdMatcher idm = new SequenceIdMatcher(
4444 viewport.getAlignment().getSequencesArray());
4446 * Object[] { String,SequenceI}
4448 ArrayList<Object[]> filesmatched = new ArrayList<>();
4449 ArrayList<Object> filesnotmatched = new ArrayList<>();
4450 for (int i = 0; i < files.size(); i++)
4453 Object file = files.get(i);
4454 String fileName = file.toString();
4456 DataSourceType protocol = (file instanceof File ? DataSourceType.FILE : FormatAdapter.checkProtocol(fileName));
4457 if (protocol == DataSourceType.FILE)
4459 File fl = (file instanceof File ? (File) file : new File(fileName));
4460 pdbfn = fl.getName();
4462 else if (protocol == DataSourceType.URL)
4464 URL url = new URL(fileName);
4465 pdbfn = url.getFile();
4467 if (pdbfn.length() > 0)
4469 // attempt to find a match in the alignment
4470 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4471 int l = 0, c = pdbfn.indexOf(".");
4472 while (mtch == null && c != -1)
4477 } while ((c = pdbfn.indexOf(".", l)) > l);
4480 pdbfn = pdbfn.substring(0, l);
4482 mtch = idm.findAllIdMatches(pdbfn);
4489 type = new IdentifyFile().identify(file, protocol);
4490 } catch (Exception ex)
4494 if (type != null && type.isStructureFile())
4496 filesmatched.add(new Object[] { file, protocol, mtch });
4500 // File wasn't named like one of the sequences or wasn't a PDB
4502 filesnotmatched.add(file);
4506 if (filesmatched.size() > 0)
4508 boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4511 String msg = MessageManager.formatMessage(
4512 "label.automatically_associate_structure_files_with_sequences_same_name",
4514 { Integer.valueOf(filesmatched.size())
4516 String ttl = MessageManager.getString(
4517 "label.automatically_associate_structure_files_by_name");
4518 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4519 ttl, JvOptionPane.YES_NO_OPTION);
4520 autoAssociate = choice == JvOptionPane.YES_OPTION;
4524 for (Object[] fm : filesmatched)
4526 // try and associate
4527 // TODO: may want to set a standard ID naming formalism for
4528 // associating PDB files which have no IDs.
4529 for (SequenceI toassoc : (SequenceI[]) fm[2])
4531 PDBEntry pe = new AssociatePdbFileWithSeq()
4532 .associatePdbWithSeq((String) fm[0],
4533 (DataSourceType) fm[1], toassoc, false,
4537 System.err.println("Associated file : "
4538 + ((String) fm[0]) + " with "
4539 + toassoc.getDisplayId(true));
4543 // TODO: do we need to update overview ? only if features are
4545 alignPanel.paintAlignment(true, false);
4551 * add declined structures as sequences
4553 for (Object[] o : filesmatched)
4555 filesnotmatched.add(o[0]);
4559 if (filesnotmatched.size() > 0)
4561 if (assocfiles > 0 && (Cache.getDefault(
4562 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4563 || JvOptionPane.showConfirmDialog(thisaf,
4564 "<html>" + MessageManager.formatMessage(
4565 "label.ignore_unmatched_dropped_files_info",
4568 filesnotmatched.size())
4571 MessageManager.getString(
4572 "label.ignore_unmatched_dropped_files"),
4573 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4577 for (Object fn : filesnotmatched)
4579 loadJalviewDataFile(fn, null, null, null);
4583 } catch (Exception ex)
4585 ex.printStackTrace();
4593 * Attempt to load a "dropped" file or URL string, by testing in turn for
4595 * <li>an Annotation file</li>
4596 * <li>a JNet file</li>
4597 * <li>a features file</li>
4598 * <li>else try to interpret as an alignment file</li>
4602 * either a filename or a URL string.
4604 public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4605 FileFormatI format, SequenceI assocSeq)
4607 // BH 2018 was String file
4610 if (sourceType == null)
4612 sourceType = FormatAdapter.checkProtocol(file);
4614 // if the file isn't identified, or not positively identified as some
4615 // other filetype (PFAM is default unidentified alignment file type) then
4616 // try to parse as annotation.
4617 boolean isAnnotation = (format == null
4618 || FileFormat.Pfam.equals(format))
4619 ? new AnnotationFile().annotateAlignmentView(viewport,
4625 // first see if its a T-COFFEE score file
4626 TCoffeeScoreFile tcf = null;
4629 tcf = new TCoffeeScoreFile(file, sourceType);
4632 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4636 new TCoffeeColourScheme(viewport.getAlignment()));
4637 isAnnotation = true;
4638 statusBar.setText(MessageManager.getString(
4639 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4643 // some problem - if no warning its probable that the ID matching
4644 // process didn't work
4645 JvOptionPane.showMessageDialog(Desktop.desktop,
4646 tcf.getWarningMessage() == null
4647 ? MessageManager.getString(
4648 "label.check_file_matches_sequence_ids_alignment")
4649 : tcf.getWarningMessage(),
4650 MessageManager.getString(
4651 "label.problem_reading_tcoffee_score_file"),
4652 JvOptionPane.WARNING_MESSAGE);
4659 } catch (Exception x)
4662 "Exception when processing data source as T-COFFEE score file",
4668 // try to see if its a JNet 'concise' style annotation file *before*
4670 // try to parse it as a features file
4673 format = new IdentifyFile().identify(file, sourceType);
4675 if (FileFormat.ScoreMatrix == format)
4677 ScoreMatrixFile sm = new ScoreMatrixFile(
4678 new FileParse(file, sourceType));
4680 // todo: i18n this message
4681 statusBar.setText(MessageManager.formatMessage(
4682 "label.successfully_loaded_matrix",
4683 sm.getMatrixName()));
4685 else if (FileFormat.Jnet.equals(format))
4687 JPredFile predictions = new JPredFile(file, sourceType);
4688 new JnetAnnotationMaker();
4689 JnetAnnotationMaker.add_annotation(predictions,
4690 viewport.getAlignment(), 0, false);
4691 viewport.getAlignment().setupJPredAlignment();
4692 isAnnotation = true;
4694 // else if (IdentifyFile.FeaturesFile.equals(format))
4695 else if (FileFormat.Features.equals(format))
4697 if (parseFeaturesFile(file, sourceType))
4699 alignPanel.paintAlignment(true, true);
4704 new FileLoader().LoadFile(viewport, file, sourceType, format);
4711 alignPanel.adjustAnnotationHeight();
4712 viewport.updateSequenceIdColours();
4713 buildSortByAnnotationScoresMenu();
4714 alignPanel.paintAlignment(true, true);
4716 } catch (Exception ex)
4718 ex.printStackTrace();
4719 } catch (OutOfMemoryError oom)
4724 } catch (Exception x)
4729 + (sourceType != null
4730 ? (sourceType == DataSourceType.PASTE
4732 : "using " + sourceType + " from "
4736 ? "(parsing as '" + format + "' file)"
4738 oom, Desktop.desktop);
4743 * Method invoked by the ChangeListener on the tabbed pane, in other words
4744 * when a different tabbed pane is selected by the user or programmatically.
4747 public void tabSelectionChanged(int index)
4751 alignPanel = alignPanels.get(index);
4752 viewport = alignPanel.av;
4753 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4754 setMenusFromViewport(viewport);
4758 * 'focus' any colour slider that is open to the selected viewport
4760 if (viewport.getConservationSelected())
4762 SliderPanel.setConservationSlider(alignPanel,
4763 viewport.getResidueShading(), alignPanel.getViewName());
4767 SliderPanel.hideConservationSlider();
4769 if (viewport.getAbovePIDThreshold())
4771 SliderPanel.setPIDSliderSource(alignPanel,
4772 viewport.getResidueShading(), alignPanel.getViewName());
4776 SliderPanel.hidePIDSlider();
4780 * If there is a frame linked to this one in a SplitPane, switch it to the
4781 * same view tab index. No infinite recursion of calls should happen, since
4782 * tabSelectionChanged() should not get invoked on setting the selected
4783 * index to an unchanged value. Guard against setting an invalid index
4784 * before the new view peer tab has been created.
4786 final AlignViewportI peer = viewport.getCodingComplement();
4789 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4790 .getAlignPanel().alignFrame;
4791 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4793 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4799 * On right mouse click on view tab, prompt for and set new view name.
4802 public void tabbedPane_mousePressed(MouseEvent e)
4804 if (e.isPopupTrigger())
4806 String msg = MessageManager.getString("label.enter_view_name");
4807 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4808 JvOptionPane.QUESTION_MESSAGE);
4812 viewport.viewName = reply;
4813 // TODO warn if reply is in getExistingViewNames()?
4814 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4819 public AlignViewport getCurrentView()
4825 * Open the dialog for regex description parsing.
4828 protected void extractScores_actionPerformed(ActionEvent e)
4830 ParseProperties pp = new jalview.analysis.ParseProperties(
4831 viewport.getAlignment());
4832 // TODO: verify regex and introduce GUI dialog for version 2.5
4833 // if (pp.getScoresFromDescription("col", "score column ",
4834 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4836 if (pp.getScoresFromDescription("description column",
4837 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4839 buildSortByAnnotationScoresMenu();
4847 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4851 protected void showDbRefs_actionPerformed(ActionEvent e)
4853 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4859 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4863 protected void showNpFeats_actionPerformed(ActionEvent e)
4865 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4869 * find the viewport amongst the tabs in this alignment frame and close that
4874 public boolean closeView(AlignViewportI av)
4878 this.closeMenuItem_actionPerformed(false);
4881 Component[] comp = tabbedPane.getComponents();
4882 for (int i = 0; comp != null && i < comp.length; i++)
4884 if (comp[i] instanceof AlignmentPanel)
4886 if (((AlignmentPanel) comp[i]).av == av)
4889 closeView((AlignmentPanel) comp[i]);
4897 protected void build_fetchdbmenu(JMenu webService)
4899 // Temporary hack - DBRef Fetcher always top level ws entry.
4900 // TODO We probably want to store a sequence database checklist in
4901 // preferences and have checkboxes.. rather than individual sources selected
4903 final JMenu rfetch = new JMenu(
4904 MessageManager.getString("action.fetch_db_references"));
4905 rfetch.setToolTipText(MessageManager.getString(
4906 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4907 webService.add(rfetch);
4909 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4910 MessageManager.getString("option.trim_retrieved_seqs"));
4911 trimrs.setToolTipText(
4912 MessageManager.getString("label.trim_retrieved_sequences"));
4914 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4915 trimrs.addActionListener(new ActionListener()
4918 public void actionPerformed(ActionEvent e)
4920 trimrs.setSelected(trimrs.isSelected());
4921 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4922 Boolean.valueOf(trimrs.isSelected()).toString());
4926 JMenuItem fetchr = new JMenuItem(
4927 MessageManager.getString("label.standard_databases"));
4928 fetchr.setToolTipText(
4929 MessageManager.getString("label.fetch_embl_uniprot"));
4930 fetchr.addActionListener(new ActionListener()
4934 public void actionPerformed(ActionEvent e)
4936 new Thread(new Runnable()
4941 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4942 .getAlignment().isNucleotide();
4943 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4944 alignPanel.av.getSequenceSelection(),
4945 alignPanel.alignFrame, null,
4946 alignPanel.alignFrame.featureSettings, isNucleotide);
4947 dbRefFetcher.addListener(new FetchFinishedListenerI()
4950 public void finished()
4952 AlignFrame.this.setMenusForViewport();
4955 dbRefFetcher.fetchDBRefs(false);
4963 final AlignFrame me = this;
4964 new Thread(new Runnable()
4969 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4970 .getSequenceFetcherSingleton(me);
4971 javax.swing.SwingUtilities.invokeLater(new Runnable()
4976 String[] dbclasses = sf.getOrderedSupportedSources();
4977 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4978 // jalview.util.QuickSort.sort(otherdb, otherdb);
4979 List<DbSourceProxy> otherdb;
4980 JMenu dfetch = new JMenu();
4981 JMenu ifetch = new JMenu();
4982 JMenuItem fetchr = null;
4983 int comp = 0, icomp = 0, mcomp = 15;
4984 String mname = null;
4986 for (String dbclass : dbclasses)
4988 otherdb = sf.getSourceProxy(dbclass);
4989 // add a single entry for this class, or submenu allowing 'fetch
4991 if (otherdb == null || otherdb.size() < 1)
4995 // List<DbSourceProxy> dbs=otherdb;
4996 // otherdb=new ArrayList<DbSourceProxy>();
4997 // for (DbSourceProxy db:dbs)
4999 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5003 mname = "From " + dbclass;
5005 if (otherdb.size() == 1)
5007 final DbSourceProxy[] dassource = otherdb
5008 .toArray(new DbSourceProxy[0]);
5009 DbSourceProxy src = otherdb.get(0);
5010 fetchr = new JMenuItem(src.getDbSource());
5011 fetchr.addActionListener(new ActionListener()
5015 public void actionPerformed(ActionEvent e)
5017 new Thread(new Runnable()
5023 boolean isNucleotide = alignPanel.alignFrame
5024 .getViewport().getAlignment()
5026 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5027 alignPanel.av.getSequenceSelection(),
5028 alignPanel.alignFrame, dassource,
5029 alignPanel.alignFrame.featureSettings,
5032 .addListener(new FetchFinishedListenerI()
5035 public void finished()
5037 AlignFrame.this.setMenusForViewport();
5040 dbRefFetcher.fetchDBRefs(false);
5046 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5047 MessageManager.formatMessage(
5048 "label.fetch_retrieve_from", new Object[]
5049 { src.getDbName() })));
5055 final DbSourceProxy[] dassource = otherdb
5056 .toArray(new DbSourceProxy[0]);
5058 DbSourceProxy src = otherdb.get(0);
5059 fetchr = new JMenuItem(MessageManager
5060 .formatMessage("label.fetch_all_param", new Object[]
5061 { src.getDbSource() }));
5062 fetchr.addActionListener(new ActionListener()
5065 public void actionPerformed(ActionEvent e)
5067 new Thread(new Runnable()
5073 boolean isNucleotide = alignPanel.alignFrame
5074 .getViewport().getAlignment()
5076 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5077 alignPanel.av.getSequenceSelection(),
5078 alignPanel.alignFrame, dassource,
5079 alignPanel.alignFrame.featureSettings,
5082 .addListener(new FetchFinishedListenerI()
5085 public void finished()
5087 AlignFrame.this.setMenusForViewport();
5090 dbRefFetcher.fetchDBRefs(false);
5096 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5097 MessageManager.formatMessage(
5098 "label.fetch_retrieve_from_all_sources",
5100 { Integer.valueOf(otherdb.size())
5102 src.getDbSource(), src.getDbName() })));
5105 // and then build the rest of the individual menus
5106 ifetch = new JMenu(MessageManager.formatMessage(
5107 "label.source_from_db_source", new Object[]
5108 { src.getDbSource() }));
5110 String imname = null;
5112 for (DbSourceProxy sproxy : otherdb)
5114 String dbname = sproxy.getDbName();
5115 String sname = dbname.length() > 5
5116 ? dbname.substring(0, 5) + "..."
5118 String msname = dbname.length() > 10
5119 ? dbname.substring(0, 10) + "..."
5123 imname = MessageManager
5124 .formatMessage("label.from_msname", new Object[]
5127 fetchr = new JMenuItem(msname);
5128 final DbSourceProxy[] dassrc = { sproxy };
5129 fetchr.addActionListener(new ActionListener()
5133 public void actionPerformed(ActionEvent e)
5135 new Thread(new Runnable()
5141 boolean isNucleotide = alignPanel.alignFrame
5142 .getViewport().getAlignment()
5144 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5145 alignPanel.av.getSequenceSelection(),
5146 alignPanel.alignFrame, dassrc,
5147 alignPanel.alignFrame.featureSettings,
5150 .addListener(new FetchFinishedListenerI()
5153 public void finished()
5155 AlignFrame.this.setMenusForViewport();
5158 dbRefFetcher.fetchDBRefs(false);
5164 fetchr.setToolTipText(
5165 "<html>" + MessageManager.formatMessage(
5166 "label.fetch_retrieve_from", new Object[]
5170 if (++icomp >= mcomp || i == (otherdb.size()))
5172 ifetch.setText(MessageManager.formatMessage(
5173 "label.source_to_target", imname, sname));
5175 ifetch = new JMenu();
5183 if (comp >= mcomp || dbi >= (dbclasses.length))
5185 dfetch.setText(MessageManager.formatMessage(
5186 "label.source_to_target", mname, dbclass));
5188 dfetch = new JMenu();
5201 * Left justify the whole alignment.
5204 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5206 AlignmentI al = viewport.getAlignment();
5208 viewport.firePropertyChange("alignment", null, al);
5212 * Right justify the whole alignment.
5215 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5217 AlignmentI al = viewport.getAlignment();
5219 viewport.firePropertyChange("alignment", null, al);
5223 public void setShowSeqFeatures(boolean b)
5225 showSeqFeatures.setSelected(b);
5226 viewport.setShowSequenceFeatures(b);
5233 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5234 * awt.event.ActionEvent)
5237 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5239 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5240 alignPanel.paintAlignment(false, false);
5247 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5251 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5253 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5254 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5262 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5263 * .event.ActionEvent)
5266 protected void showGroupConservation_actionPerformed(ActionEvent e)
5268 viewport.setShowGroupConservation(showGroupConservation.getState());
5269 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5276 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5277 * .event.ActionEvent)
5280 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5282 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5283 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5290 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5291 * .event.ActionEvent)
5294 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5296 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5297 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5301 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5303 showSequenceLogo.setState(true);
5304 viewport.setShowSequenceLogo(true);
5305 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5306 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5310 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5312 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5319 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5320 * .event.ActionEvent)
5323 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5325 if (avc.makeGroupsFromSelection())
5327 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5328 alignPanel.updateAnnotation();
5329 alignPanel.paintAlignment(true, true);
5333 public void clearAlignmentSeqRep()
5335 // TODO refactor alignmentseqrep to controller
5336 if (viewport.getAlignment().hasSeqrep())
5338 viewport.getAlignment().setSeqrep(null);
5339 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5340 alignPanel.updateAnnotation();
5341 alignPanel.paintAlignment(true, true);
5346 protected void createGroup_actionPerformed(ActionEvent e)
5348 if (avc.createGroup())
5350 alignPanel.alignmentChanged();
5355 protected void unGroup_actionPerformed(ActionEvent e)
5359 alignPanel.alignmentChanged();
5364 * make the given alignmentPanel the currently selected tab
5366 * @param alignmentPanel
5368 public void setDisplayedView(AlignmentPanel alignmentPanel)
5370 if (!viewport.getSequenceSetId()
5371 .equals(alignmentPanel.av.getSequenceSetId()))
5373 throw new Error(MessageManager.getString(
5374 "error.implementation_error_cannot_show_view_alignment_frame"));
5376 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5377 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5379 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5384 * Action on selection of menu options to Show or Hide annotations.
5387 * @param forSequences
5388 * update sequence-related annotations
5389 * @param forAlignment
5390 * update non-sequence-related annotations
5393 protected void setAnnotationsVisibility(boolean visible,
5394 boolean forSequences, boolean forAlignment)
5396 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5397 .getAlignmentAnnotation();
5402 for (AlignmentAnnotation aa : anns)
5405 * don't display non-positional annotations on an alignment
5407 if (aa.annotations == null)
5411 boolean apply = (aa.sequenceRef == null && forAlignment)
5412 || (aa.sequenceRef != null && forSequences);
5415 aa.visible = visible;
5418 alignPanel.validateAnnotationDimensions(true);
5419 alignPanel.alignmentChanged();
5423 * Store selected annotation sort order for the view and repaint.
5426 protected void sortAnnotations_actionPerformed()
5428 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5430 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5431 alignPanel.paintAlignment(false, false);
5436 * @return alignment panels in this alignment frame
5438 public List<? extends AlignmentViewPanel> getAlignPanels()
5440 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5444 * Open a new alignment window, with the cDNA associated with this (protein)
5445 * alignment, aligned as is the protein.
5447 protected void viewAsCdna_actionPerformed()
5449 // TODO no longer a menu action - refactor as required
5450 final AlignmentI alignment = getViewport().getAlignment();
5451 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5452 if (mappings == null)
5456 List<SequenceI> cdnaSeqs = new ArrayList<>();
5457 for (SequenceI aaSeq : alignment.getSequences())
5459 for (AlignedCodonFrame acf : mappings)
5461 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5465 * There is a cDNA mapping for this protein sequence - add to new
5466 * alignment. It will share the same dataset sequence as other mapped
5467 * cDNA (no new mappings need to be created).
5469 final Sequence newSeq = new Sequence(dnaSeq);
5470 newSeq.setDatasetSequence(dnaSeq);
5471 cdnaSeqs.add(newSeq);
5475 if (cdnaSeqs.size() == 0)
5477 // show a warning dialog no mapped cDNA
5480 AlignmentI cdna = new Alignment(
5481 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5482 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5483 AlignFrame.DEFAULT_HEIGHT);
5484 cdna.alignAs(alignment);
5485 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5487 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5488 AlignFrame.DEFAULT_HEIGHT);
5492 * Set visibility of dna/protein complement view (available when shown in a
5498 protected void showComplement_actionPerformed(boolean show)
5500 SplitContainerI sf = getSplitViewContainer();
5503 sf.setComplementVisible(this, show);
5508 * Generate the reverse (optionally complemented) of the selected sequences,
5509 * and add them to the alignment
5512 protected void showReverse_actionPerformed(boolean complement)
5514 AlignmentI al = null;
5517 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5518 al = dna.reverseCdna(complement);
5519 viewport.addAlignment(al, "");
5520 addHistoryItem(new EditCommand(
5521 MessageManager.getString("label.add_sequences"), Action.PASTE,
5522 al.getSequencesArray(), 0, al.getWidth(),
5523 viewport.getAlignment()));
5524 } catch (Exception ex)
5526 System.err.println(ex.getMessage());
5532 * Try to run a script in the Groovy console, having first ensured that this
5533 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5534 * be targeted at this alignment.
5537 protected void runGroovy_actionPerformed()
5539 Jalview.setCurrentAlignFrame(this);
5540 groovy.ui.Console console = Desktop.getGroovyConsole();
5541 if (console != null)
5545 console.runScript();
5546 } catch (Exception ex)
5548 System.err.println((ex.toString()));
5549 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5550 MessageManager.getString("label.couldnt_run_groovy_script"),
5551 MessageManager.getString("label.groovy_support_failed"),
5552 JvOptionPane.ERROR_MESSAGE);
5557 System.err.println("Can't run Groovy script as console not found");
5562 * Hides columns containing (or not containing) a specified feature, provided
5563 * that would not leave all columns hidden
5565 * @param featureType
5566 * @param columnsContaining
5569 public boolean hideFeatureColumns(String featureType,
5570 boolean columnsContaining)
5572 boolean notForHiding = avc.markColumnsContainingFeatures(
5573 columnsContaining, false, false, featureType);
5576 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5577 false, featureType))
5579 getViewport().hideSelectedColumns();
5587 protected void selectHighlightedColumns_actionPerformed(
5588 ActionEvent actionEvent)
5590 // include key modifier check in case user selects from menu
5591 avc.markHighlightedColumns(
5592 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5593 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5594 | ActionEvent.CTRL_MASK)) != 0);
5598 * Rebuilds the Colour menu, including any user-defined colours which have
5599 * been loaded either on startup or during the session
5601 public void buildColourMenu()
5603 colourMenu.removeAll();
5605 colourMenu.add(applyToAllGroups);
5606 colourMenu.add(textColour);
5607 colourMenu.addSeparator();
5609 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5612 colourMenu.addSeparator();
5613 colourMenu.add(conservationMenuItem);
5614 colourMenu.add(modifyConservation);
5615 colourMenu.add(abovePIDThreshold);
5616 colourMenu.add(modifyPID);
5617 colourMenu.add(annotationColour);
5619 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5620 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5624 * Open a dialog (if not already open) that allows the user to select and
5625 * calculate PCA or Tree analysis
5627 protected void openTreePcaDialog()
5629 if (alignPanel.getCalculationDialog() == null)
5631 new CalculationChooser(AlignFrame.this);
5636 protected void loadVcf_actionPerformed()
5638 // TODO: JAL-3048 - No VCF support in JsJalview
5639 JalviewFileChooser chooser = new JalviewFileChooser(
5640 Cache.getProperty("LAST_DIRECTORY"));
5641 chooser.setFileView(new JalviewFileView());
5642 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5643 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5645 int value = chooser.showOpenDialog(null);
5647 if (value == JalviewFileChooser.APPROVE_OPTION)
5649 String choice = chooser.getSelectedFile().getPath();
5650 Cache.setProperty("LAST_DIRECTORY", choice);
5651 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5652 new VCFLoader(choice).loadVCF(seqs, this);
5659 class PrintThread extends Thread
5663 public PrintThread(AlignmentPanel ap)
5668 static PageFormat pf;
5673 PrinterJob printJob = PrinterJob.getPrinterJob();
5677 printJob.setPrintable(ap, pf);
5681 printJob.setPrintable(ap);
5684 if (printJob.printDialog())
5689 } catch (Exception PrintException)
5691 PrintException.printStackTrace();