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;
126 import java.io.FileWriter;
127 import java.io.PrintWriter;
129 import java.util.ArrayList;
130 import java.util.Arrays;
131 import java.util.Deque;
132 import java.util.Enumeration;
133 import java.util.Hashtable;
134 import java.util.List;
135 import java.util.Vector;
137 import javax.swing.ButtonGroup;
138 import javax.swing.JCheckBoxMenuItem;
139 import javax.swing.JEditorPane;
140 import javax.swing.JInternalFrame;
141 import javax.swing.JLayeredPane;
142 import javax.swing.JMenu;
143 import javax.swing.JMenuItem;
144 import javax.swing.JScrollPane;
145 import javax.swing.SwingUtilities;
151 * @version $Revision$
153 public class AlignFrame extends GAlignFrame implements DropTargetListener,
154 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
157 public static final int DEFAULT_WIDTH = 700;
159 public static final int DEFAULT_HEIGHT = 500;
162 * The currently displayed panel (selected tabbed view if more than one)
164 public AlignmentPanel alignPanel;
166 AlignViewport viewport;
168 public AlignViewControllerI avc;
170 List<AlignmentPanel> alignPanels = new ArrayList<>();
173 * Last format used to load or save alignments in this window
175 FileFormatI currentFileFormat = null;
178 * Current filename for this alignment
180 String fileName = null;
183 * Creates a new AlignFrame object with specific width and height.
189 public AlignFrame(AlignmentI al, int width, int height)
191 this(al, null, width, height);
195 * Creates a new AlignFrame object with specific width, height and
201 * @param sequenceSetId
203 public AlignFrame(AlignmentI al, int width, int height,
204 String sequenceSetId)
206 this(al, null, width, height, sequenceSetId);
210 * Creates a new AlignFrame object with specific width, height and
216 * @param sequenceSetId
219 public AlignFrame(AlignmentI al, int width, int height,
220 String sequenceSetId, String viewId)
222 this(al, null, width, height, sequenceSetId, viewId);
226 * new alignment window with hidden columns
230 * @param hiddenColumns
231 * ColumnSelection or null
233 * Width of alignment frame
237 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
240 this(al, hiddenColumns, width, height, null);
244 * Create alignment frame for al with hiddenColumns, a specific width and
245 * height, and specific sequenceId
248 * @param hiddenColumns
251 * @param sequenceSetId
254 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
255 int height, String sequenceSetId)
257 this(al, hiddenColumns, width, height, sequenceSetId, null);
261 * Create alignment frame for al with hiddenColumns, a specific width and
262 * height, and specific sequenceId
265 * @param hiddenColumns
268 * @param sequenceSetId
273 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
274 int height, String sequenceSetId, String viewId)
276 setSize(width, height);
278 if (al.getDataset() == null)
283 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
285 alignPanel = new AlignmentPanel(this, viewport);
287 addAlignmentPanel(alignPanel, true);
291 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
292 HiddenColumns hiddenColumns, int width, int height)
294 setSize(width, height);
296 if (al.getDataset() == null)
301 viewport = new AlignViewport(al, hiddenColumns);
303 if (hiddenSeqs != null && hiddenSeqs.length > 0)
305 viewport.hideSequence(hiddenSeqs);
307 alignPanel = new AlignmentPanel(this, viewport);
308 addAlignmentPanel(alignPanel, true);
313 * Make a new AlignFrame from existing alignmentPanels
320 public AlignFrame(AlignmentPanel ap)
324 addAlignmentPanel(ap, false);
329 * initalise the alignframe from the underlying viewport data and the
334 if (!Jalview.isHeadlessMode())
336 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
339 avc = new jalview.controller.AlignViewController(this, viewport,
341 if (viewport.getAlignmentConservationAnnotation() == null)
343 // BLOSUM62Colour.setEnabled(false);
344 conservationMenuItem.setEnabled(false);
345 modifyConservation.setEnabled(false);
346 // PIDColour.setEnabled(false);
347 // abovePIDThreshold.setEnabled(false);
348 // modifyPID.setEnabled(false);
351 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
354 if (sortby.equals("Id"))
356 sortIDMenuItem_actionPerformed(null);
358 else if (sortby.equals("Pairwise Identity"))
360 sortPairwiseMenuItem_actionPerformed(null);
364 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
366 setMenusFromViewport(viewport);
367 buildSortByAnnotationScoresMenu();
368 calculateTree.addActionListener(new ActionListener()
372 public void actionPerformed(ActionEvent e)
379 if (Desktop.desktop != null)
381 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
382 addServiceListeners();
386 if (viewport.getWrapAlignment())
388 wrapMenuItem_actionPerformed(null);
391 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
393 this.overviewMenuItem_actionPerformed(null);
398 final List<AlignmentPanel> selviews = new ArrayList<>();
399 final List<AlignmentPanel> origview = new ArrayList<>();
400 final String menuLabel = MessageManager
401 .getString("label.copy_format_from");
402 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
403 new ViewSetProvider()
407 public AlignmentPanel[] getAllAlignmentPanels()
410 origview.add(alignPanel);
411 // make an array of all alignment panels except for this one
412 List<AlignmentPanel> aps = new ArrayList<>(
413 Arrays.asList(Desktop.getAlignmentPanels(null)));
414 aps.remove(AlignFrame.this.alignPanel);
415 return aps.toArray(new AlignmentPanel[aps.size()]);
417 }, selviews, new ItemListener()
421 public void itemStateChanged(ItemEvent e)
423 if (origview.size() > 0)
425 final AlignmentPanel ap = origview.get(0);
428 * Copy the ViewStyle of the selected panel to 'this one'.
429 * Don't change value of 'scaleProteinAsCdna' unless copying
432 ViewStyleI vs = selviews.get(0).getAlignViewport()
434 boolean fromSplitFrame = selviews.get(0)
435 .getAlignViewport().getCodingComplement() != null;
438 vs.setScaleProteinAsCdna(ap.getAlignViewport()
439 .getViewStyle().isScaleProteinAsCdna());
441 ap.getAlignViewport().setViewStyle(vs);
444 * Also rescale ViewStyle of SplitFrame complement if there is
445 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
446 * the whole ViewStyle (allow cDNA protein to have different
449 AlignViewportI complement = ap.getAlignViewport()
450 .getCodingComplement();
451 if (complement != null && vs.isScaleProteinAsCdna())
453 AlignFrame af = Desktop.getAlignFrameFor(complement);
454 ((SplitFrame) af.getSplitViewContainer())
456 af.setMenusForViewport();
460 ap.setSelected(true);
461 ap.alignFrame.setMenusForViewport();
466 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
467 .indexOf("devel") > -1
468 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
469 .indexOf("test") > -1)
471 formatMenu.add(vsel);
473 addFocusListener(new FocusAdapter()
476 public void focusGained(FocusEvent e)
478 Jalview.setCurrentAlignFrame(AlignFrame.this);
485 * Change the filename and format for the alignment, and enable the 'reload'
486 * button functionality.
493 public void setFileName(String file, FileFormatI format)
496 setFileFormat(format);
497 reload.setEnabled(true);
501 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
504 void addKeyListener()
506 addKeyListener(new KeyAdapter()
509 public void keyPressed(KeyEvent evt)
511 if (viewport.cursorMode
512 && ((evt.getKeyCode() >= KeyEvent.VK_0
513 && evt.getKeyCode() <= KeyEvent.VK_9)
514 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
515 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
516 && Character.isDigit(evt.getKeyChar()))
518 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
521 switch (evt.getKeyCode())
524 case 27: // escape key
525 deselectAllSequenceMenuItem_actionPerformed(null);
529 case KeyEvent.VK_DOWN:
530 if (evt.isAltDown() || !viewport.cursorMode)
532 moveSelectedSequences(false);
534 if (viewport.cursorMode)
536 alignPanel.getSeqPanel().moveCursor(0, 1);
541 if (evt.isAltDown() || !viewport.cursorMode)
543 moveSelectedSequences(true);
545 if (viewport.cursorMode)
547 alignPanel.getSeqPanel().moveCursor(0, -1);
552 case KeyEvent.VK_LEFT:
553 if (evt.isAltDown() || !viewport.cursorMode)
555 slideSequences(false,
556 alignPanel.getSeqPanel().getKeyboardNo1());
560 alignPanel.getSeqPanel().moveCursor(-1, 0);
565 case KeyEvent.VK_RIGHT:
566 if (evt.isAltDown() || !viewport.cursorMode)
568 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
572 alignPanel.getSeqPanel().moveCursor(1, 0);
576 case KeyEvent.VK_SPACE:
577 if (viewport.cursorMode)
579 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
580 || evt.isShiftDown() || evt.isAltDown());
584 // case KeyEvent.VK_A:
585 // if (viewport.cursorMode)
587 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
588 // //System.out.println("A");
592 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
593 * System.out.println("closing bracket"); } break;
595 case KeyEvent.VK_DELETE:
596 case KeyEvent.VK_BACK_SPACE:
597 if (!viewport.cursorMode)
599 cut_actionPerformed(null);
603 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
604 || evt.isShiftDown() || evt.isAltDown());
610 if (viewport.cursorMode)
612 alignPanel.getSeqPanel().setCursorRow();
616 if (viewport.cursorMode && !evt.isControlDown())
618 alignPanel.getSeqPanel().setCursorColumn();
622 if (viewport.cursorMode)
624 alignPanel.getSeqPanel().setCursorPosition();
628 case KeyEvent.VK_ENTER:
629 case KeyEvent.VK_COMMA:
630 if (viewport.cursorMode)
632 alignPanel.getSeqPanel().setCursorRowAndColumn();
637 if (viewport.cursorMode)
639 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
643 if (viewport.cursorMode)
645 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
650 viewport.cursorMode = !viewport.cursorMode;
651 statusBar.setText(MessageManager
652 .formatMessage("label.keyboard_editing_mode", new String[]
653 { (viewport.cursorMode ? "on" : "off") }));
654 if (viewport.cursorMode)
656 ViewportRanges ranges = viewport.getRanges();
657 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
659 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
662 alignPanel.getSeqPanel().seqCanvas.repaint();
668 Help.showHelpWindow();
669 } catch (Exception ex)
671 ex.printStackTrace();
676 boolean toggleSeqs = !evt.isControlDown();
677 boolean toggleCols = !evt.isShiftDown();
678 toggleHiddenRegions(toggleSeqs, toggleCols);
683 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
684 boolean modifyExisting = true; // always modify, don't clear
685 // evt.isShiftDown();
686 boolean invertHighlighted = evt.isAltDown();
687 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
691 case KeyEvent.VK_PAGE_UP:
692 viewport.getRanges().pageUp();
694 case KeyEvent.VK_PAGE_DOWN:
695 viewport.getRanges().pageDown();
701 public void keyReleased(KeyEvent evt)
703 switch (evt.getKeyCode())
705 case KeyEvent.VK_LEFT:
706 if (evt.isAltDown() || !viewport.cursorMode)
708 viewport.firePropertyChange("alignment", null,
709 viewport.getAlignment().getSequences());
713 case KeyEvent.VK_RIGHT:
714 if (evt.isAltDown() || !viewport.cursorMode)
716 viewport.firePropertyChange("alignment", null,
717 viewport.getAlignment().getSequences());
725 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
727 ap.alignFrame = this;
728 avc = new jalview.controller.AlignViewController(this, viewport,
733 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
735 int aSize = alignPanels.size();
737 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
739 if (aSize == 1 && ap.av.viewName == null)
741 this.getContentPane().add(ap, BorderLayout.CENTER);
747 setInitialTabVisible();
750 expandViews.setEnabled(true);
751 gatherViews.setEnabled(true);
752 tabbedPane.addTab(ap.av.viewName, ap);
754 ap.setVisible(false);
759 if (ap.av.isPadGaps())
761 ap.av.getAlignment().padGaps();
763 ap.av.updateConservation(ap);
764 ap.av.updateConsensus(ap);
765 ap.av.updateStrucConsensus(ap);
769 public void setInitialTabVisible()
771 expandViews.setEnabled(true);
772 gatherViews.setEnabled(true);
773 tabbedPane.setVisible(true);
774 AlignmentPanel first = alignPanels.get(0);
775 tabbedPane.addTab(first.av.viewName, first);
776 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
779 public AlignViewport getViewport()
784 /* Set up intrinsic listeners for dynamically generated GUI bits. */
785 private void addServiceListeners()
787 final java.beans.PropertyChangeListener thisListener;
788 Desktop.instance.addJalviewPropertyChangeListener("services",
789 thisListener = new java.beans.PropertyChangeListener()
792 public void propertyChange(PropertyChangeEvent evt)
794 // // System.out.println("Discoverer property change.");
795 // if (evt.getPropertyName().equals("services"))
797 SwingUtilities.invokeLater(new Runnable()
804 "Rebuild WS Menu for service change");
805 BuildWebServiceMenu();
812 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
815 public void internalFrameClosed(
816 javax.swing.event.InternalFrameEvent evt)
818 // System.out.println("deregistering discoverer listener");
819 Desktop.instance.removeJalviewPropertyChangeListener("services",
821 closeMenuItem_actionPerformed(true);
824 // Finally, build the menu once to get current service state
825 new Thread(new Runnable()
830 BuildWebServiceMenu();
836 * Configure menu items that vary according to whether the alignment is
837 * nucleotide or protein
839 public void setGUINucleotide()
841 AlignmentI al = getViewport().getAlignment();
842 boolean nucleotide = al.isNucleotide();
844 loadVcf.setVisible(nucleotide);
845 showTranslation.setVisible(nucleotide);
846 showReverse.setVisible(nucleotide);
847 showReverseComplement.setVisible(nucleotide);
848 conservationMenuItem.setEnabled(!nucleotide);
850 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
851 showGroupConservation.setEnabled(!nucleotide);
853 showComplementMenuItem
854 .setText(nucleotide ? MessageManager.getString("label.protein")
855 : MessageManager.getString("label.nucleotide"));
859 * set up menus for the current viewport. This may be called after any
860 * operation that affects the data in the current view (selection changed,
861 * etc) to update the menus to reflect the new state.
864 public void setMenusForViewport()
866 setMenusFromViewport(viewport);
870 * Need to call this method when tabs are selected for multiple views, or when
871 * loading from Jalview2XML.java
876 void setMenusFromViewport(AlignViewport av)
878 padGapsMenuitem.setSelected(av.isPadGaps());
879 colourTextMenuItem.setSelected(av.isShowColourText());
880 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
881 modifyPID.setEnabled(abovePIDThreshold.isSelected());
882 conservationMenuItem.setSelected(av.getConservationSelected());
883 modifyConservation.setEnabled(conservationMenuItem.isSelected());
884 seqLimits.setSelected(av.getShowJVSuffix());
885 idRightAlign.setSelected(av.isRightAlignIds());
886 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
887 renderGapsMenuItem.setSelected(av.isRenderGaps());
888 wrapMenuItem.setSelected(av.getWrapAlignment());
889 scaleAbove.setVisible(av.getWrapAlignment());
890 scaleLeft.setVisible(av.getWrapAlignment());
891 scaleRight.setVisible(av.getWrapAlignment());
892 annotationPanelMenuItem.setState(av.isShowAnnotation());
894 * Show/hide annotations only enabled if annotation panel is shown
896 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
897 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
898 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
899 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
900 viewBoxesMenuItem.setSelected(av.getShowBoxes());
901 viewTextMenuItem.setSelected(av.getShowText());
902 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
903 showGroupConsensus.setSelected(av.isShowGroupConsensus());
904 showGroupConservation.setSelected(av.isShowGroupConservation());
905 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
906 showSequenceLogo.setSelected(av.isShowSequenceLogo());
907 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
909 ColourMenuHelper.setColourSelected(colourMenu,
910 av.getGlobalColourScheme());
912 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
913 hiddenMarkers.setState(av.getShowHiddenMarkers());
914 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
915 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
916 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
917 autoCalculate.setSelected(av.autoCalculateConsensus);
918 sortByTree.setSelected(av.sortByTree);
919 listenToViewSelections.setSelected(av.followSelection);
921 showProducts.setEnabled(canShowProducts());
922 setGroovyEnabled(Desktop.getGroovyConsole() != null);
928 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
932 public void setGroovyEnabled(boolean b)
934 runGroovy.setEnabled(b);
937 private IProgressIndicator progressBar;
942 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
945 public void setProgressBar(String message, long id)
947 progressBar.setProgressBar(message, id);
951 public void registerHandler(final long id,
952 final IProgressIndicatorHandler handler)
954 progressBar.registerHandler(id, handler);
959 * @return true if any progress bars are still active
962 public boolean operationInProgress()
964 return progressBar.operationInProgress();
968 public void setStatus(String text)
970 statusBar.setText(text);
974 * Added so Castor Mapping file can obtain Jalview Version
976 public String getVersion()
978 return jalview.bin.Cache.getProperty("VERSION");
981 public FeatureRenderer getFeatureRenderer()
983 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
987 public void fetchSequence_actionPerformed(ActionEvent e)
989 new jalview.gui.SequenceFetcher(this);
993 public void addFromFile_actionPerformed(ActionEvent e)
995 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
999 public void reload_actionPerformed(ActionEvent e)
1001 if (fileName != null)
1003 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1004 // originating file's format
1005 // TODO: work out how to recover feature settings for correct view(s) when
1006 // file is reloaded.
1007 if (FileFormat.Jalview.equals(currentFileFormat))
1009 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1010 for (int i = 0; i < frames.length; i++)
1012 if (frames[i] instanceof AlignFrame && frames[i] != this
1013 && ((AlignFrame) frames[i]).fileName != null
1014 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1018 frames[i].setSelected(true);
1019 Desktop.instance.closeAssociatedWindows();
1020 } catch (java.beans.PropertyVetoException ex)
1026 Desktop.instance.closeAssociatedWindows();
1028 FileLoader loader = new FileLoader();
1029 DataSourceType protocol = fileName.startsWith("http:")
1030 ? DataSourceType.URL
1031 : DataSourceType.FILE;
1032 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1036 Rectangle bounds = this.getBounds();
1038 FileLoader loader = new FileLoader();
1039 DataSourceType protocol = fileName.startsWith("http:")
1040 ? DataSourceType.URL
1041 : DataSourceType.FILE;
1042 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1043 protocol, currentFileFormat);
1045 newframe.setBounds(bounds);
1046 if (featureSettings != null && featureSettings.isShowing())
1048 final Rectangle fspos = featureSettings.frame.getBounds();
1049 // TODO: need a 'show feature settings' function that takes bounds -
1050 // need to refactor Desktop.addFrame
1051 newframe.featureSettings_actionPerformed(null);
1052 final FeatureSettings nfs = newframe.featureSettings;
1053 SwingUtilities.invokeLater(new Runnable()
1058 nfs.frame.setBounds(fspos);
1061 this.featureSettings.close();
1062 this.featureSettings = null;
1064 this.closeMenuItem_actionPerformed(true);
1070 public void addFromText_actionPerformed(ActionEvent e)
1073 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1077 public void addFromURL_actionPerformed(ActionEvent e)
1079 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1083 public void save_actionPerformed(ActionEvent e)
1085 if (fileName == null || (currentFileFormat == null)
1086 || fileName.startsWith("http"))
1088 saveAs_actionPerformed(null);
1092 saveAlignment(fileName, currentFileFormat);
1103 public void saveAs_actionPerformed(ActionEvent e)
1105 String format = currentFileFormat == null ? null
1106 : currentFileFormat.getName();
1107 JalviewFileChooser chooser = JalviewFileChooser
1108 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1110 chooser.setFileView(new JalviewFileView());
1111 chooser.setDialogTitle(
1112 MessageManager.getString("label.save_alignment_to_file"));
1113 chooser.setToolTipText(MessageManager.getString("action.save"));
1115 int value = chooser.showSaveDialog(this);
1117 if (value == JalviewFileChooser.APPROVE_OPTION)
1119 currentFileFormat = chooser.getSelectedFormat();
1120 while (currentFileFormat == null)
1122 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1123 MessageManager.getString(
1124 "label.select_file_format_before_saving"),
1125 MessageManager.getString("label.file_format_not_specified"),
1126 JvOptionPane.WARNING_MESSAGE);
1127 currentFileFormat = chooser.getSelectedFormat();
1128 value = chooser.showSaveDialog(this);
1129 if (value != JalviewFileChooser.APPROVE_OPTION)
1135 fileName = chooser.getSelectedFile().getPath();
1137 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1139 Cache.setProperty("LAST_DIRECTORY", fileName);
1140 saveAlignment(fileName, currentFileFormat);
1144 public boolean saveAlignment(String file, FileFormatI format)
1146 boolean success = true;
1148 if (FileFormat.Jalview.equals(format))
1150 String shortName = title;
1152 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1154 shortName = shortName.substring(
1155 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1158 success = new Jalview2XML().saveAlignment(this, file, shortName);
1160 statusBar.setText(MessageManager.formatMessage(
1161 "label.successfully_saved_to_file_in_format", new Object[]
1162 { fileName, format }));
1167 AlignmentExportData exportData = getAlignmentForExport(format,
1169 if (exportData.getSettings().isCancelled())
1173 FormatAdapter f = new FormatAdapter(alignPanel,
1174 exportData.getSettings());
1175 String output = f.formatSequences(format, exportData.getAlignment(), // class
1179 // occur in the distant future
1180 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1181 f.getCacheSuffixDefault(format),
1182 viewport.getAlignment().getHiddenColumns());
1192 PrintWriter out = new PrintWriter(new FileWriter(file));
1196 this.setTitle(file);
1197 statusBar.setText(MessageManager.formatMessage(
1198 "label.successfully_saved_to_file_in_format", new Object[]
1199 { fileName, format.getName() }));
1200 } catch (Exception ex)
1203 ex.printStackTrace();
1210 JvOptionPane.showInternalMessageDialog(this, MessageManager
1211 .formatMessage("label.couldnt_save_file", new Object[]
1213 MessageManager.getString("label.error_saving_file"),
1214 JvOptionPane.WARNING_MESSAGE);
1220 private void warningMessage(String warning, String title)
1222 if (new jalview.util.Platform().isHeadless())
1224 System.err.println("Warning: " + title + "\nWarning: " + warning);
1229 JvOptionPane.showInternalMessageDialog(this, warning, title,
1230 JvOptionPane.WARNING_MESSAGE);
1242 protected void outputText_actionPerformed(ActionEvent e)
1244 FileFormatI fileFormat = FileFormats.getInstance()
1245 .forName(e.getActionCommand());
1246 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1248 if (exportData.getSettings().isCancelled())
1252 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1253 cap.setForInput(null);
1256 FileFormatI format = fileFormat;
1257 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1258 .formatSequences(format, exportData.getAlignment(),
1259 exportData.getOmitHidden(),
1260 exportData.getStartEndPostions(),
1261 viewport.getAlignment().getHiddenColumns()));
1262 Desktop.addInternalFrame(cap, MessageManager
1263 .formatMessage("label.alignment_output_command", new Object[]
1264 { e.getActionCommand() }), 600, 500);
1265 } catch (OutOfMemoryError oom)
1267 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1274 public static AlignmentExportData getAlignmentForExport(
1275 FileFormatI format, AlignViewportI viewport,
1276 AlignExportSettingI exportSettings)
1278 AlignmentI alignmentToExport = null;
1279 AlignExportSettingI settings = exportSettings;
1280 String[] omitHidden = null;
1282 HiddenSequences hiddenSeqs = viewport.getAlignment()
1283 .getHiddenSequences();
1285 alignmentToExport = viewport.getAlignment();
1287 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1288 if (settings == null)
1290 settings = new AlignExportSettings(hasHiddenSeqs,
1291 viewport.hasHiddenColumns(), format);
1293 // settings.isExportAnnotations();
1295 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1297 omitHidden = viewport.getViewAsString(false,
1298 settings.isExportHiddenSequences());
1301 int[] alignmentStartEnd = new int[2];
1302 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1304 alignmentToExport = hiddenSeqs.getFullAlignment();
1308 alignmentToExport = viewport.getAlignment();
1310 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1311 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1312 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1313 omitHidden, alignmentStartEnd, settings);
1324 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1326 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1327 htmlSVG.exportHTML(null);
1331 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1333 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1334 bjs.exportHTML(null);
1337 public void createImageMap(File file, String image)
1339 alignPanel.makePNGImageMap(file, image);
1349 public void createPNG(File f)
1351 alignPanel.makePNG(f);
1361 public void createEPS(File f)
1363 alignPanel.makeEPS(f);
1367 public void createSVG(File f)
1369 alignPanel.makeSVG(f);
1373 public void pageSetup_actionPerformed(ActionEvent e)
1375 PrinterJob printJob = PrinterJob.getPrinterJob();
1376 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1386 public void printMenuItem_actionPerformed(ActionEvent e)
1388 // Putting in a thread avoids Swing painting problems
1389 PrintThread thread = new PrintThread(alignPanel);
1394 public void exportFeatures_actionPerformed(ActionEvent e)
1396 new AnnotationExporter(alignPanel).exportFeatures();
1400 public void exportAnnotations_actionPerformed(ActionEvent e)
1402 new AnnotationExporter(alignPanel).exportAnnotations();
1406 public void associatedData_actionPerformed(ActionEvent e)
1408 // Pick the tree file
1409 JalviewFileChooser chooser = new JalviewFileChooser(
1410 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1411 chooser.setFileView(new JalviewFileView());
1412 chooser.setDialogTitle(
1413 MessageManager.getString("label.load_jalview_annotations"));
1414 chooser.setToolTipText(
1415 MessageManager.getString("label.load_jalview_annotations"));
1417 int value = chooser.showOpenDialog(null);
1419 if (value == JalviewFileChooser.APPROVE_OPTION)
1421 String choice = chooser.getSelectedFile().getPath();
1422 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1423 loadJalviewDataFile(choice, null, null, null);
1429 * Close the current view or all views in the alignment frame. If the frame
1430 * only contains one view then the alignment will be removed from memory.
1432 * @param closeAllTabs
1435 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1437 if (alignPanels != null && alignPanels.size() < 2)
1439 closeAllTabs = true;
1444 if (alignPanels != null)
1448 if (this.isClosed())
1450 // really close all the windows - otherwise wait till
1451 // setClosed(true) is called
1452 for (int i = 0; i < alignPanels.size(); i++)
1454 AlignmentPanel ap = alignPanels.get(i);
1461 closeView(alignPanel);
1468 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1469 * be called recursively, with the frame now in 'closed' state
1471 this.setClosed(true);
1473 } catch (Exception ex)
1475 ex.printStackTrace();
1480 * Close the specified panel and close up tabs appropriately.
1482 * @param panelToClose
1484 public void closeView(AlignmentPanel panelToClose)
1486 int index = tabbedPane.getSelectedIndex();
1487 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1488 alignPanels.remove(panelToClose);
1489 panelToClose.closePanel();
1490 panelToClose = null;
1492 tabbedPane.removeTabAt(closedindex);
1493 tabbedPane.validate();
1495 if (index > closedindex || index == tabbedPane.getTabCount())
1497 // modify currently selected tab index if necessary.
1501 this.tabSelectionChanged(index);
1507 void updateEditMenuBar()
1510 if (viewport.getHistoryList().size() > 0)
1512 undoMenuItem.setEnabled(true);
1513 CommandI command = viewport.getHistoryList().peek();
1514 undoMenuItem.setText(MessageManager
1515 .formatMessage("label.undo_command", new Object[]
1516 { command.getDescription() }));
1520 undoMenuItem.setEnabled(false);
1521 undoMenuItem.setText(MessageManager.getString("action.undo"));
1524 if (viewport.getRedoList().size() > 0)
1526 redoMenuItem.setEnabled(true);
1528 CommandI command = viewport.getRedoList().peek();
1529 redoMenuItem.setText(MessageManager
1530 .formatMessage("label.redo_command", new Object[]
1531 { command.getDescription() }));
1535 redoMenuItem.setEnabled(false);
1536 redoMenuItem.setText(MessageManager.getString("action.redo"));
1541 public void addHistoryItem(CommandI command)
1543 if (command.getSize() > 0)
1545 viewport.addToHistoryList(command);
1546 viewport.clearRedoList();
1547 updateEditMenuBar();
1548 viewport.updateHiddenColumns();
1549 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1550 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1551 // viewport.getColumnSelection()
1552 // .getHiddenColumns().size() > 0);
1558 * @return alignment objects for all views
1560 AlignmentI[] getViewAlignments()
1562 if (alignPanels != null)
1564 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1566 for (AlignmentPanel ap : alignPanels)
1568 als[i++] = ap.av.getAlignment();
1572 if (viewport != null)
1574 return new AlignmentI[] { viewport.getAlignment() };
1586 protected void undoMenuItem_actionPerformed(ActionEvent e)
1588 if (viewport.getHistoryList().isEmpty())
1592 CommandI command = viewport.getHistoryList().pop();
1593 viewport.addToRedoList(command);
1594 command.undoCommand(getViewAlignments());
1596 AlignmentViewport originalSource = getOriginatingSource(command);
1597 updateEditMenuBar();
1599 if (originalSource != null)
1601 if (originalSource != viewport)
1604 "Implementation worry: mismatch of viewport origin for undo");
1606 originalSource.updateHiddenColumns();
1607 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1609 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1610 // viewport.getColumnSelection()
1611 // .getHiddenColumns().size() > 0);
1612 originalSource.firePropertyChange("alignment", null,
1613 originalSource.getAlignment().getSequences());
1624 protected void redoMenuItem_actionPerformed(ActionEvent e)
1626 if (viewport.getRedoList().size() < 1)
1631 CommandI command = viewport.getRedoList().pop();
1632 viewport.addToHistoryList(command);
1633 command.doCommand(getViewAlignments());
1635 AlignmentViewport originalSource = getOriginatingSource(command);
1636 updateEditMenuBar();
1638 if (originalSource != null)
1641 if (originalSource != viewport)
1644 "Implementation worry: mismatch of viewport origin for redo");
1646 originalSource.updateHiddenColumns();
1647 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1649 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1650 // viewport.getColumnSelection()
1651 // .getHiddenColumns().size() > 0);
1652 originalSource.firePropertyChange("alignment", null,
1653 originalSource.getAlignment().getSequences());
1657 AlignmentViewport getOriginatingSource(CommandI command)
1659 AlignmentViewport originalSource = null;
1660 // For sequence removal and addition, we need to fire
1661 // the property change event FROM the viewport where the
1662 // original alignment was altered
1663 AlignmentI al = null;
1664 if (command instanceof EditCommand)
1666 EditCommand editCommand = (EditCommand) command;
1667 al = editCommand.getAlignment();
1668 List<Component> comps = PaintRefresher.components
1669 .get(viewport.getSequenceSetId());
1671 for (Component comp : comps)
1673 if (comp instanceof AlignmentPanel)
1675 if (al == ((AlignmentPanel) comp).av.getAlignment())
1677 originalSource = ((AlignmentPanel) comp).av;
1684 if (originalSource == null)
1686 // The original view is closed, we must validate
1687 // the current view against the closed view first
1690 PaintRefresher.validateSequences(al, viewport.getAlignment());
1693 originalSource = viewport;
1696 return originalSource;
1705 public void moveSelectedSequences(boolean up)
1707 SequenceGroup sg = viewport.getSelectionGroup();
1713 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1714 viewport.getHiddenRepSequences(), up);
1715 alignPanel.paintAlignment(true, false);
1718 synchronized void slideSequences(boolean right, int size)
1720 List<SequenceI> sg = new ArrayList<>();
1721 if (viewport.cursorMode)
1723 sg.add(viewport.getAlignment()
1724 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1726 else if (viewport.getSelectionGroup() != null
1727 && viewport.getSelectionGroup().getSize() != viewport
1728 .getAlignment().getHeight())
1730 sg = viewport.getSelectionGroup()
1731 .getSequences(viewport.getHiddenRepSequences());
1739 List<SequenceI> invertGroup = new ArrayList<>();
1741 for (SequenceI seq : viewport.getAlignment().getSequences())
1743 if (!sg.contains(seq))
1745 invertGroup.add(seq);
1749 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1751 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1752 for (int i = 0; i < invertGroup.size(); i++)
1754 seqs2[i] = invertGroup.get(i);
1757 SlideSequencesCommand ssc;
1760 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1761 viewport.getGapCharacter());
1765 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1766 viewport.getGapCharacter());
1769 int groupAdjustment = 0;
1770 if (ssc.getGapsInsertedBegin() && right)
1772 if (viewport.cursorMode)
1774 alignPanel.getSeqPanel().moveCursor(size, 0);
1778 groupAdjustment = size;
1781 else if (!ssc.getGapsInsertedBegin() && !right)
1783 if (viewport.cursorMode)
1785 alignPanel.getSeqPanel().moveCursor(-size, 0);
1789 groupAdjustment = -size;
1793 if (groupAdjustment != 0)
1795 viewport.getSelectionGroup().setStartRes(
1796 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1797 viewport.getSelectionGroup().setEndRes(
1798 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1802 * just extend the last slide command if compatible; but not if in
1803 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1805 boolean appendHistoryItem = false;
1806 Deque<CommandI> historyList = viewport.getHistoryList();
1807 boolean inSplitFrame = getSplitViewContainer() != null;
1808 if (!inSplitFrame && historyList != null && historyList.size() > 0
1809 && historyList.peek() instanceof SlideSequencesCommand)
1811 appendHistoryItem = ssc.appendSlideCommand(
1812 (SlideSequencesCommand) historyList.peek());
1815 if (!appendHistoryItem)
1817 addHistoryItem(ssc);
1830 protected void copy_actionPerformed(ActionEvent e)
1832 if (viewport.getSelectionGroup() == null)
1836 // TODO: preserve the ordering of displayed alignment annotation in any
1837 // internal paste (particularly sequence associated annotation)
1838 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1839 String[] omitHidden = null;
1841 if (viewport.hasHiddenColumns())
1843 omitHidden = viewport.getViewAsString(true);
1846 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1847 seqs, omitHidden, null);
1849 StringSelection ss = new StringSelection(output);
1853 jalview.gui.Desktop.internalCopy = true;
1854 // Its really worth setting the clipboard contents
1855 // to empty before setting the large StringSelection!!
1856 Toolkit.getDefaultToolkit().getSystemClipboard()
1857 .setContents(new StringSelection(""), null);
1859 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1861 } catch (OutOfMemoryError er)
1863 new OOMWarning("copying region", er);
1867 HiddenColumns hiddenColumns = null;
1868 if (viewport.hasHiddenColumns())
1870 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1871 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1873 // create new HiddenColumns object with copy of hidden regions
1874 // between startRes and endRes, offset by startRes
1875 hiddenColumns = new HiddenColumns(
1876 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1877 hiddenCutoff, hiddenOffset);
1880 Desktop.jalviewClipboard = new Object[] { seqs,
1881 viewport.getAlignment().getDataset(), hiddenColumns };
1882 statusBar.setText(MessageManager.formatMessage(
1883 "label.copied_sequences_to_clipboard", new Object[]
1884 { Integer.valueOf(seqs.length).toString() }));
1894 protected void pasteNew_actionPerformed(ActionEvent e)
1906 protected void pasteThis_actionPerformed(ActionEvent e)
1912 * Paste contents of Jalview clipboard
1914 * @param newAlignment
1915 * true to paste to a new alignment, otherwise add to this.
1917 void paste(boolean newAlignment)
1919 boolean externalPaste = true;
1922 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1923 Transferable contents = c.getContents(this);
1925 if (contents == null)
1934 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1935 if (str.length() < 1)
1940 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1942 } catch (OutOfMemoryError er)
1944 new OOMWarning("Out of memory pasting sequences!!", er);
1948 SequenceI[] sequences;
1949 boolean annotationAdded = false;
1950 AlignmentI alignment = null;
1952 if (Desktop.jalviewClipboard != null)
1954 // The clipboard was filled from within Jalview, we must use the
1956 // And dataset from the copied alignment
1957 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1958 // be doubly sure that we create *new* sequence objects.
1959 sequences = new SequenceI[newseq.length];
1960 for (int i = 0; i < newseq.length; i++)
1962 sequences[i] = new Sequence(newseq[i]);
1964 alignment = new Alignment(sequences);
1965 externalPaste = false;
1969 // parse the clipboard as an alignment.
1970 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1972 sequences = alignment.getSequencesArray();
1976 ArrayList<Integer> newGraphGroups = new ArrayList<>();
1982 if (Desktop.jalviewClipboard != null)
1984 // dataset is inherited
1985 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1989 // new dataset is constructed
1990 alignment.setDataset(null);
1992 alwidth = alignment.getWidth() + 1;
1996 AlignmentI pastedal = alignment; // preserve pasted alignment object
1997 // Add pasted sequences and dataset into existing alignment.
1998 alignment = viewport.getAlignment();
1999 alwidth = alignment.getWidth() + 1;
2000 // decide if we need to import sequences from an existing dataset
2001 boolean importDs = Desktop.jalviewClipboard != null
2002 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2003 // importDs==true instructs us to copy over new dataset sequences from
2004 // an existing alignment
2005 Vector newDs = (importDs) ? new Vector() : null; // used to create
2006 // minimum dataset set
2008 for (int i = 0; i < sequences.length; i++)
2012 newDs.addElement(null);
2014 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2016 if (importDs && ds != null)
2018 if (!newDs.contains(ds))
2020 newDs.setElementAt(ds, i);
2021 ds = new Sequence(ds);
2022 // update with new dataset sequence
2023 sequences[i].setDatasetSequence(ds);
2027 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2032 // copy and derive new dataset sequence
2033 sequences[i] = sequences[i].deriveSequence();
2034 alignment.getDataset()
2035 .addSequence(sequences[i].getDatasetSequence());
2036 // TODO: avoid creation of duplicate dataset sequences with a
2037 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2039 alignment.addSequence(sequences[i]); // merges dataset
2043 newDs.clear(); // tidy up
2045 if (alignment.getAlignmentAnnotation() != null)
2047 for (AlignmentAnnotation alan : alignment
2048 .getAlignmentAnnotation())
2050 if (alan.graphGroup > fgroup)
2052 fgroup = alan.graphGroup;
2056 if (pastedal.getAlignmentAnnotation() != null)
2058 // Add any annotation attached to alignment.
2059 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2060 for (int i = 0; i < alann.length; i++)
2062 annotationAdded = true;
2063 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2065 AlignmentAnnotation newann = new AlignmentAnnotation(
2067 if (newann.graphGroup > -1)
2069 if (newGraphGroups.size() <= newann.graphGroup
2070 || newGraphGroups.get(newann.graphGroup) == null)
2072 for (int q = newGraphGroups
2073 .size(); q <= newann.graphGroup; q++)
2075 newGraphGroups.add(q, null);
2077 newGraphGroups.set(newann.graphGroup,
2078 new Integer(++fgroup));
2080 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2084 newann.padAnnotation(alwidth);
2085 alignment.addAnnotation(newann);
2095 addHistoryItem(new EditCommand(
2096 MessageManager.getString("label.add_sequences"),
2097 Action.PASTE, sequences, 0, alignment.getWidth(),
2100 // Add any annotations attached to sequences
2101 for (int i = 0; i < sequences.length; i++)
2103 if (sequences[i].getAnnotation() != null)
2105 AlignmentAnnotation newann;
2106 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2108 annotationAdded = true;
2109 newann = sequences[i].getAnnotation()[a];
2110 newann.adjustForAlignment();
2111 newann.padAnnotation(alwidth);
2112 if (newann.graphGroup > -1)
2114 if (newann.graphGroup > -1)
2116 if (newGraphGroups.size() <= newann.graphGroup
2117 || newGraphGroups.get(newann.graphGroup) == null)
2119 for (int q = newGraphGroups
2120 .size(); q <= newann.graphGroup; q++)
2122 newGraphGroups.add(q, null);
2124 newGraphGroups.set(newann.graphGroup,
2125 new Integer(++fgroup));
2127 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2131 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2135 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2143 // propagate alignment changed.
2144 viewport.getRanges().setEndSeq(alignment.getHeight());
2145 if (annotationAdded)
2147 // Duplicate sequence annotation in all views.
2148 AlignmentI[] alview = this.getViewAlignments();
2149 for (int i = 0; i < sequences.length; i++)
2151 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2156 for (int avnum = 0; avnum < alview.length; avnum++)
2158 if (alview[avnum] != alignment)
2160 // duplicate in a view other than the one with input focus
2161 int avwidth = alview[avnum].getWidth() + 1;
2162 // this relies on sann being preserved after we
2163 // modify the sequence's annotation array for each duplication
2164 for (int a = 0; a < sann.length; a++)
2166 AlignmentAnnotation newann = new AlignmentAnnotation(
2168 sequences[i].addAlignmentAnnotation(newann);
2169 newann.padAnnotation(avwidth);
2170 alview[avnum].addAnnotation(newann); // annotation was
2171 // duplicated earlier
2172 // TODO JAL-1145 graphGroups are not updated for sequence
2173 // annotation added to several views. This may cause
2175 alview[avnum].setAnnotationIndex(newann, a);
2180 buildSortByAnnotationScoresMenu();
2182 viewport.firePropertyChange("alignment", null,
2183 alignment.getSequences());
2184 if (alignPanels != null)
2186 for (AlignmentPanel ap : alignPanels)
2188 ap.validateAnnotationDimensions(false);
2193 alignPanel.validateAnnotationDimensions(false);
2199 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2201 String newtitle = new String("Copied sequences");
2203 if (Desktop.jalviewClipboard != null
2204 && Desktop.jalviewClipboard[2] != null)
2206 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2207 af.viewport.setHiddenColumns(hc);
2210 // >>>This is a fix for the moment, until a better solution is
2212 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2213 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2214 .getFeatureRenderer());
2216 // TODO: maintain provenance of an alignment, rather than just make the
2217 // title a concatenation of operations.
2220 if (title.startsWith("Copied sequences"))
2226 newtitle = newtitle.concat("- from " + title);
2231 newtitle = new String("Pasted sequences");
2234 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2239 } catch (Exception ex)
2241 ex.printStackTrace();
2242 System.out.println("Exception whilst pasting: " + ex);
2243 // could be anything being pasted in here
2249 protected void expand_newalign(ActionEvent e)
2253 AlignmentI alignment = AlignmentUtils
2254 .expandContext(getViewport().getAlignment(), -1);
2255 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2257 String newtitle = new String("Flanking alignment");
2259 if (Desktop.jalviewClipboard != null
2260 && Desktop.jalviewClipboard[2] != null)
2262 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2263 af.viewport.setHiddenColumns(hc);
2266 // >>>This is a fix for the moment, until a better solution is
2268 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2269 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2270 .getFeatureRenderer());
2272 // TODO: maintain provenance of an alignment, rather than just make the
2273 // title a concatenation of operations.
2275 if (title.startsWith("Copied sequences"))
2281 newtitle = newtitle.concat("- from " + title);
2285 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2287 } catch (Exception ex)
2289 ex.printStackTrace();
2290 System.out.println("Exception whilst pasting: " + ex);
2291 // could be anything being pasted in here
2292 } catch (OutOfMemoryError oom)
2294 new OOMWarning("Viewing flanking region of alignment", oom);
2305 protected void cut_actionPerformed(ActionEvent e)
2307 copy_actionPerformed(null);
2308 delete_actionPerformed(null);
2318 protected void delete_actionPerformed(ActionEvent evt)
2321 SequenceGroup sg = viewport.getSelectionGroup();
2328 * If the cut affects all sequences, warn, remove highlighted columns
2330 if (sg.getSize() == viewport.getAlignment().getHeight())
2332 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2333 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2334 if (isEntireAlignWidth)
2336 int confirm = JvOptionPane.showConfirmDialog(this,
2337 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2338 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2339 JvOptionPane.OK_CANCEL_OPTION);
2341 if (confirm == JvOptionPane.CANCEL_OPTION
2342 || confirm == JvOptionPane.CLOSED_OPTION)
2347 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2348 sg.getEndRes() + 1);
2350 SequenceI[] cut = sg.getSequences()
2351 .toArray(new SequenceI[sg.getSize()]);
2353 addHistoryItem(new EditCommand(
2354 MessageManager.getString("label.cut_sequences"), Action.CUT,
2355 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2356 viewport.getAlignment()));
2358 viewport.setSelectionGroup(null);
2359 viewport.sendSelection();
2360 viewport.getAlignment().deleteGroup(sg);
2362 viewport.firePropertyChange("alignment", null,
2363 viewport.getAlignment().getSequences());
2364 if (viewport.getAlignment().getHeight() < 1)
2368 this.setClosed(true);
2369 } catch (Exception ex)
2382 protected void deleteGroups_actionPerformed(ActionEvent e)
2384 if (avc.deleteGroups())
2386 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2387 alignPanel.updateAnnotation();
2388 alignPanel.paintAlignment(true, true);
2399 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2401 SequenceGroup sg = new SequenceGroup();
2403 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2405 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2408 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2409 viewport.setSelectionGroup(sg);
2410 viewport.sendSelection();
2411 // JAL-2034 - should delegate to
2412 // alignPanel to decide if overview needs
2414 alignPanel.paintAlignment(false, false);
2415 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2425 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2427 if (viewport.cursorMode)
2429 alignPanel.getSeqPanel().keyboardNo1 = null;
2430 alignPanel.getSeqPanel().keyboardNo2 = null;
2432 viewport.setSelectionGroup(null);
2433 viewport.getColumnSelection().clear();
2434 viewport.setSelectionGroup(null);
2435 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2436 // JAL-2034 - should delegate to
2437 // alignPanel to decide if overview needs
2439 alignPanel.paintAlignment(false, false);
2440 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2441 viewport.sendSelection();
2451 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2453 SequenceGroup sg = viewport.getSelectionGroup();
2457 selectAllSequenceMenuItem_actionPerformed(null);
2462 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2464 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2466 // JAL-2034 - should delegate to
2467 // alignPanel to decide if overview needs
2470 alignPanel.paintAlignment(true, false);
2471 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2472 viewport.sendSelection();
2476 public void invertColSel_actionPerformed(ActionEvent e)
2478 viewport.invertColumnSelection();
2479 alignPanel.paintAlignment(true, false);
2480 viewport.sendSelection();
2490 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2492 trimAlignment(true);
2502 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2504 trimAlignment(false);
2507 void trimAlignment(boolean trimLeft)
2509 ColumnSelection colSel = viewport.getColumnSelection();
2512 if (!colSel.isEmpty())
2516 column = colSel.getMin();
2520 column = colSel.getMax();
2524 if (viewport.getSelectionGroup() != null)
2526 seqs = viewport.getSelectionGroup()
2527 .getSequencesAsArray(viewport.getHiddenRepSequences());
2531 seqs = viewport.getAlignment().getSequencesArray();
2534 TrimRegionCommand trimRegion;
2537 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2538 column, viewport.getAlignment());
2539 viewport.getRanges().setStartRes(0);
2543 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2544 column, viewport.getAlignment());
2547 statusBar.setText(MessageManager
2548 .formatMessage("label.removed_columns", new String[]
2549 { Integer.valueOf(trimRegion.getSize()).toString() }));
2551 addHistoryItem(trimRegion);
2553 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2555 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2556 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2558 viewport.getAlignment().deleteGroup(sg);
2562 viewport.firePropertyChange("alignment", null,
2563 viewport.getAlignment().getSequences());
2574 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2576 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2579 if (viewport.getSelectionGroup() != null)
2581 seqs = viewport.getSelectionGroup()
2582 .getSequencesAsArray(viewport.getHiddenRepSequences());
2583 start = viewport.getSelectionGroup().getStartRes();
2584 end = viewport.getSelectionGroup().getEndRes();
2588 seqs = viewport.getAlignment().getSequencesArray();
2591 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2592 "Remove Gapped Columns", seqs, start, end,
2593 viewport.getAlignment());
2595 addHistoryItem(removeGapCols);
2597 statusBar.setText(MessageManager
2598 .formatMessage("label.removed_empty_columns", new Object[]
2599 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2601 // This is to maintain viewport position on first residue
2602 // of first sequence
2603 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2604 ViewportRanges ranges = viewport.getRanges();
2605 int startRes = seq.findPosition(ranges.getStartRes());
2606 // ShiftList shifts;
2607 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2608 // edit.alColumnChanges=shifts.getInverse();
2609 // if (viewport.hasHiddenColumns)
2610 // viewport.getColumnSelection().compensateForEdits(shifts);
2611 ranges.setStartRes(seq.findIndex(startRes) - 1);
2612 viewport.firePropertyChange("alignment", null,
2613 viewport.getAlignment().getSequences());
2624 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2626 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2629 if (viewport.getSelectionGroup() != null)
2631 seqs = viewport.getSelectionGroup()
2632 .getSequencesAsArray(viewport.getHiddenRepSequences());
2633 start = viewport.getSelectionGroup().getStartRes();
2634 end = viewport.getSelectionGroup().getEndRes();
2638 seqs = viewport.getAlignment().getSequencesArray();
2641 // This is to maintain viewport position on first residue
2642 // of first sequence
2643 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2644 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2646 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2647 viewport.getAlignment()));
2649 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2651 viewport.firePropertyChange("alignment", null,
2652 viewport.getAlignment().getSequences());
2663 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2665 viewport.setPadGaps(padGapsMenuitem.isSelected());
2666 viewport.firePropertyChange("alignment", null,
2667 viewport.getAlignment().getSequences());
2677 public void findMenuItem_actionPerformed(ActionEvent e)
2683 * Create a new view of the current alignment.
2686 public void newView_actionPerformed(ActionEvent e)
2688 newView(null, true);
2692 * Creates and shows a new view of the current alignment.
2695 * title of newly created view; if null, one will be generated
2696 * @param copyAnnotation
2697 * if true then duplicate all annnotation, groups and settings
2698 * @return new alignment panel, already displayed.
2700 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2703 * Create a new AlignmentPanel (with its own, new Viewport)
2705 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2706 if (!copyAnnotation)
2709 * remove all groups and annotation except for the automatic stuff
2711 newap.av.getAlignment().deleteAllGroups();
2712 newap.av.getAlignment().deleteAllAnnotations(false);
2715 newap.av.setGatherViewsHere(false);
2717 if (viewport.viewName == null)
2719 viewport.viewName = MessageManager
2720 .getString("label.view_name_original");
2724 * Views share the same edits undo and redo stacks
2726 newap.av.setHistoryList(viewport.getHistoryList());
2727 newap.av.setRedoList(viewport.getRedoList());
2730 * Views share the same mappings; need to deregister any new mappings
2731 * created by copyAlignPanel, and register the new reference to the shared
2734 newap.av.replaceMappings(viewport.getAlignment());
2737 * start up cDNA consensus (if applicable) now mappings are in place
2739 if (newap.av.initComplementConsensus())
2741 newap.refresh(true); // adjust layout of annotations
2744 newap.av.viewName = getNewViewName(viewTitle);
2746 addAlignmentPanel(newap, true);
2747 newap.alignmentChanged();
2749 if (alignPanels.size() == 2)
2751 viewport.setGatherViewsHere(true);
2753 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2758 * Make a new name for the view, ensuring it is unique within the current
2759 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2760 * these now use viewId. Unique view names are still desirable for usability.)
2765 protected String getNewViewName(String viewTitle)
2767 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2768 boolean addFirstIndex = false;
2769 if (viewTitle == null || viewTitle.trim().length() == 0)
2771 viewTitle = MessageManager.getString("action.view");
2772 addFirstIndex = true;
2776 index = 1;// we count from 1 if given a specific name
2778 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2780 List<Component> comps = PaintRefresher.components
2781 .get(viewport.getSequenceSetId());
2783 List<String> existingNames = getExistingViewNames(comps);
2785 while (existingNames.contains(newViewName))
2787 newViewName = viewTitle + " " + (++index);
2793 * Returns a list of distinct view names found in the given list of
2794 * components. View names are held on the viewport of an AlignmentPanel.
2799 protected List<String> getExistingViewNames(List<Component> comps)
2801 List<String> existingNames = new ArrayList<>();
2802 for (Component comp : comps)
2804 if (comp instanceof AlignmentPanel)
2806 AlignmentPanel ap = (AlignmentPanel) comp;
2807 if (!existingNames.contains(ap.av.viewName))
2809 existingNames.add(ap.av.viewName);
2813 return existingNames;
2817 * Explode tabbed views into separate windows.
2820 public void expandViews_actionPerformed(ActionEvent e)
2822 Desktop.explodeViews(this);
2826 * Gather views in separate windows back into a tabbed presentation.
2829 public void gatherViews_actionPerformed(ActionEvent e)
2831 Desktop.instance.gatherViews(this);
2841 public void font_actionPerformed(ActionEvent e)
2843 new FontChooser(alignPanel);
2853 protected void seqLimit_actionPerformed(ActionEvent e)
2855 viewport.setShowJVSuffix(seqLimits.isSelected());
2857 alignPanel.getIdPanel().getIdCanvas()
2858 .setPreferredSize(alignPanel.calculateIdWidth());
2859 alignPanel.paintAlignment(true, false);
2863 public void idRightAlign_actionPerformed(ActionEvent e)
2865 viewport.setRightAlignIds(idRightAlign.isSelected());
2866 alignPanel.paintAlignment(false, false);
2870 public void centreColumnLabels_actionPerformed(ActionEvent e)
2872 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2873 alignPanel.paintAlignment(false, false);
2879 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2882 protected void followHighlight_actionPerformed()
2885 * Set the 'follow' flag on the Viewport (and scroll to position if now
2888 final boolean state = this.followHighlightMenuItem.getState();
2889 viewport.setFollowHighlight(state);
2892 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2903 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2905 viewport.setColourText(colourTextMenuItem.isSelected());
2906 alignPanel.paintAlignment(false, false);
2916 public void wrapMenuItem_actionPerformed(ActionEvent e)
2918 scaleAbove.setVisible(wrapMenuItem.isSelected());
2919 scaleLeft.setVisible(wrapMenuItem.isSelected());
2920 scaleRight.setVisible(wrapMenuItem.isSelected());
2921 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2922 alignPanel.updateLayout();
2926 public void showAllSeqs_actionPerformed(ActionEvent e)
2928 viewport.showAllHiddenSeqs();
2932 public void showAllColumns_actionPerformed(ActionEvent e)
2934 viewport.showAllHiddenColumns();
2935 alignPanel.paintAlignment(true, true);
2936 viewport.sendSelection();
2940 public void hideSelSequences_actionPerformed(ActionEvent e)
2942 viewport.hideAllSelectedSeqs();
2946 * called by key handler and the hide all/show all menu items
2951 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2954 boolean hide = false;
2955 SequenceGroup sg = viewport.getSelectionGroup();
2956 if (!toggleSeqs && !toggleCols)
2958 // Hide everything by the current selection - this is a hack - we do the
2959 // invert and then hide
2960 // first check that there will be visible columns after the invert.
2961 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2962 && sg.getStartRes() <= sg.getEndRes()))
2964 // now invert the sequence set, if required - empty selection implies
2965 // that no hiding is required.
2968 invertSequenceMenuItem_actionPerformed(null);
2969 sg = viewport.getSelectionGroup();
2973 viewport.expandColSelection(sg, true);
2974 // finally invert the column selection and get the new sequence
2976 invertColSel_actionPerformed(null);
2983 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2985 hideSelSequences_actionPerformed(null);
2988 else if (!(toggleCols && viewport.hasSelectedColumns()))
2990 showAllSeqs_actionPerformed(null);
2996 if (viewport.hasSelectedColumns())
2998 hideSelColumns_actionPerformed(null);
3001 viewport.setSelectionGroup(sg);
3006 showAllColumns_actionPerformed(null);
3015 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3016 * event.ActionEvent)
3019 public void hideAllButSelection_actionPerformed(ActionEvent e)
3021 toggleHiddenRegions(false, false);
3022 viewport.sendSelection();
3029 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3033 public void hideAllSelection_actionPerformed(ActionEvent e)
3035 SequenceGroup sg = viewport.getSelectionGroup();
3036 viewport.expandColSelection(sg, false);
3037 viewport.hideAllSelectedSeqs();
3038 viewport.hideSelectedColumns();
3039 alignPanel.paintAlignment(true, true);
3040 viewport.sendSelection();
3047 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3051 public void showAllhidden_actionPerformed(ActionEvent e)
3053 viewport.showAllHiddenColumns();
3054 viewport.showAllHiddenSeqs();
3055 alignPanel.paintAlignment(true, true);
3056 viewport.sendSelection();
3060 public void hideSelColumns_actionPerformed(ActionEvent e)
3062 viewport.hideSelectedColumns();
3063 alignPanel.paintAlignment(true, true);
3064 viewport.sendSelection();
3068 public void hiddenMarkers_actionPerformed(ActionEvent e)
3070 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3081 protected void scaleAbove_actionPerformed(ActionEvent e)
3083 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3084 // TODO: do we actually need to update overview for scale above change ?
3085 alignPanel.paintAlignment(true, false);
3095 protected void scaleLeft_actionPerformed(ActionEvent e)
3097 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3098 alignPanel.paintAlignment(true, false);
3108 protected void scaleRight_actionPerformed(ActionEvent e)
3110 viewport.setScaleRightWrapped(scaleRight.isSelected());
3111 alignPanel.paintAlignment(true, false);
3121 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3123 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3124 alignPanel.paintAlignment(false, false);
3134 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3136 viewport.setShowText(viewTextMenuItem.isSelected());
3137 alignPanel.paintAlignment(false, false);
3147 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3149 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3150 alignPanel.paintAlignment(false, false);
3153 public FeatureSettings featureSettings;
3156 public FeatureSettingsControllerI getFeatureSettingsUI()
3158 return featureSettings;
3162 public void featureSettings_actionPerformed(ActionEvent e)
3164 if (featureSettings != null)
3166 featureSettings.close();
3167 featureSettings = null;
3169 if (!showSeqFeatures.isSelected())
3171 // make sure features are actually displayed
3172 showSeqFeatures.setSelected(true);
3173 showSeqFeatures_actionPerformed(null);
3175 featureSettings = new FeatureSettings(this);
3179 * Set or clear 'Show Sequence Features'
3185 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3187 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3188 alignPanel.paintAlignment(true, true);
3192 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3193 * the annotations panel as a whole.
3195 * The options to show/hide all annotations should be enabled when the panel
3196 * is shown, and disabled when the panel is hidden.
3201 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3203 final boolean setVisible = annotationPanelMenuItem.isSelected();
3204 viewport.setShowAnnotation(setVisible);
3205 this.showAllSeqAnnotations.setEnabled(setVisible);
3206 this.hideAllSeqAnnotations.setEnabled(setVisible);
3207 this.showAllAlAnnotations.setEnabled(setVisible);
3208 this.hideAllAlAnnotations.setEnabled(setVisible);
3209 alignPanel.updateLayout();
3213 public void alignmentProperties()
3215 JEditorPane editPane = new JEditorPane("text/html", "");
3216 editPane.setEditable(false);
3217 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3220 MessageManager.formatMessage("label.html_content", new Object[]
3221 { contents.toString() }));
3222 JInternalFrame frame = new JInternalFrame();
3223 frame.getContentPane().add(new JScrollPane(editPane));
3225 Desktop.addInternalFrame(frame, MessageManager
3226 .formatMessage("label.alignment_properties", new Object[]
3227 { getTitle() }), 500, 400);
3237 public void overviewMenuItem_actionPerformed(ActionEvent e)
3239 if (alignPanel.overviewPanel != null)
3244 JInternalFrame frame = new JInternalFrame();
3245 final OverviewPanel overview = new OverviewPanel(alignPanel);
3246 frame.setContentPane(overview);
3247 Desktop.addInternalFrame(frame, MessageManager
3248 .formatMessage("label.overview_params", new Object[]
3249 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3252 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3253 frame.addInternalFrameListener(
3254 new javax.swing.event.InternalFrameAdapter()
3257 public void internalFrameClosed(
3258 javax.swing.event.InternalFrameEvent evt)
3261 alignPanel.setOverviewPanel(null);
3264 if (getKeyListeners().length > 0)
3266 frame.addKeyListener(getKeyListeners()[0]);
3269 alignPanel.setOverviewPanel(overview);
3273 public void textColour_actionPerformed()
3275 new TextColourChooser().chooseColour(alignPanel, null);
3279 * public void covariationColour_actionPerformed() {
3281 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3285 public void annotationColour_actionPerformed()
3287 new AnnotationColourChooser(viewport, alignPanel);
3291 public void annotationColumn_actionPerformed(ActionEvent e)
3293 new AnnotationColumnChooser(viewport, alignPanel);
3297 * Action on the user checking or unchecking the option to apply the selected
3298 * colour scheme to all groups. If unchecked, groups may have their own
3299 * independent colour schemes.
3304 public void applyToAllGroups_actionPerformed(boolean selected)
3306 viewport.setColourAppliesToAllGroups(selected);
3310 * Action on user selecting a colour from the colour menu
3313 * the name (not the menu item label!) of the colour scheme
3316 public void changeColour_actionPerformed(String name)
3319 * 'User Defined' opens a panel to configure or load a
3320 * user-defined colour scheme
3322 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3324 new UserDefinedColours(alignPanel);
3329 * otherwise set the chosen colour scheme (or null for 'None')
3331 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3332 viewport.getAlignment(), viewport.getHiddenRepSequences());
3337 * Actions on setting or changing the alignment colour scheme
3342 public void changeColour(ColourSchemeI cs)
3344 // TODO: pull up to controller method
3345 ColourMenuHelper.setColourSelected(colourMenu, cs);
3347 viewport.setGlobalColourScheme(cs);
3349 alignPanel.paintAlignment(true, true);
3353 * Show the PID threshold slider panel
3356 protected void modifyPID_actionPerformed()
3358 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3359 alignPanel.getViewName());
3360 SliderPanel.showPIDSlider();
3364 * Show the Conservation slider panel
3367 protected void modifyConservation_actionPerformed()
3369 SliderPanel.setConservationSlider(alignPanel,
3370 viewport.getResidueShading(), alignPanel.getViewName());
3371 SliderPanel.showConservationSlider();
3375 * Action on selecting or deselecting (Colour) By Conservation
3378 public void conservationMenuItem_actionPerformed(boolean selected)
3380 modifyConservation.setEnabled(selected);
3381 viewport.setConservationSelected(selected);
3382 viewport.getResidueShading().setConservationApplied(selected);
3384 changeColour(viewport.getGlobalColourScheme());
3387 modifyConservation_actionPerformed();
3391 SliderPanel.hideConservationSlider();
3396 * Action on selecting or deselecting (Colour) Above PID Threshold
3399 public void abovePIDThreshold_actionPerformed(boolean selected)
3401 modifyPID.setEnabled(selected);
3402 viewport.setAbovePIDThreshold(selected);
3405 viewport.getResidueShading().setThreshold(0,
3406 viewport.isIgnoreGapsConsensus());
3409 changeColour(viewport.getGlobalColourScheme());
3412 modifyPID_actionPerformed();
3416 SliderPanel.hidePIDSlider();
3427 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3429 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3430 AlignmentSorter.sortByPID(viewport.getAlignment(),
3431 viewport.getAlignment().getSequenceAt(0));
3432 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3433 viewport.getAlignment()));
3434 alignPanel.paintAlignment(true, false);
3444 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3446 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3447 AlignmentSorter.sortByID(viewport.getAlignment());
3449 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3450 alignPanel.paintAlignment(true, false);
3460 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3462 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3463 AlignmentSorter.sortByLength(viewport.getAlignment());
3464 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3465 viewport.getAlignment()));
3466 alignPanel.paintAlignment(true, false);
3476 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3478 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3479 AlignmentSorter.sortByGroup(viewport.getAlignment());
3480 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3481 viewport.getAlignment()));
3483 alignPanel.paintAlignment(true, false);
3493 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3495 new RedundancyPanel(alignPanel, this);
3505 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3507 if ((viewport.getSelectionGroup() == null)
3508 || (viewport.getSelectionGroup().getSize() < 2))
3510 JvOptionPane.showInternalMessageDialog(this,
3511 MessageManager.getString(
3512 "label.you_must_select_least_two_sequences"),
3513 MessageManager.getString("label.invalid_selection"),
3514 JvOptionPane.WARNING_MESSAGE);
3518 JInternalFrame frame = new JInternalFrame();
3519 frame.setContentPane(new PairwiseAlignPanel(viewport));
3520 Desktop.addInternalFrame(frame,
3521 MessageManager.getString("action.pairwise_alignment"), 600,
3527 public void autoCalculate_actionPerformed(ActionEvent e)
3529 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3530 if (viewport.autoCalculateConsensus)
3532 viewport.firePropertyChange("alignment", null,
3533 viewport.getAlignment().getSequences());
3538 public void sortByTreeOption_actionPerformed(ActionEvent e)
3540 viewport.sortByTree = sortByTree.isSelected();
3544 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3546 viewport.followSelection = listenToViewSelections.isSelected();
3550 * Constructs a tree panel and adds it to the desktop
3553 * tree type (NJ or AV)
3555 * name of score model used to compute the tree
3557 * parameters for the distance or similarity calculation
3559 void newTreePanel(String type, String modelName,
3560 SimilarityParamsI options)
3562 String frameTitle = "";
3565 boolean onSelection = false;
3566 if (viewport.getSelectionGroup() != null
3567 && viewport.getSelectionGroup().getSize() > 0)
3569 SequenceGroup sg = viewport.getSelectionGroup();
3571 /* Decide if the selection is a column region */
3572 for (SequenceI _s : sg.getSequences())
3574 if (_s.getLength() < sg.getEndRes())
3576 JvOptionPane.showMessageDialog(Desktop.desktop,
3577 MessageManager.getString(
3578 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3579 MessageManager.getString(
3580 "label.sequences_selection_not_aligned"),
3581 JvOptionPane.WARNING_MESSAGE);
3590 if (viewport.getAlignment().getHeight() < 2)
3596 tp = new TreePanel(alignPanel, type, modelName, options);
3597 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3599 frameTitle += " from ";
3601 if (viewport.viewName != null)
3603 frameTitle += viewport.viewName + " of ";
3606 frameTitle += this.title;
3608 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3619 public void addSortByOrderMenuItem(String title,
3620 final AlignmentOrder order)
3622 final JMenuItem item = new JMenuItem(MessageManager
3623 .formatMessage("action.by_title_param", new Object[]
3626 item.addActionListener(new java.awt.event.ActionListener()
3629 public void actionPerformed(ActionEvent e)
3631 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3633 // TODO: JBPNote - have to map order entries to curent SequenceI
3635 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3637 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3638 viewport.getAlignment()));
3640 alignPanel.paintAlignment(true, false);
3646 * Add a new sort by annotation score menu item
3649 * the menu to add the option to
3651 * the label used to retrieve scores for each sequence on the
3654 public void addSortByAnnotScoreMenuItem(JMenu sort,
3655 final String scoreLabel)
3657 final JMenuItem item = new JMenuItem(scoreLabel);
3659 item.addActionListener(new java.awt.event.ActionListener()
3662 public void actionPerformed(ActionEvent e)
3664 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3665 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3666 viewport.getAlignment());// ,viewport.getSelectionGroup());
3667 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3668 viewport.getAlignment()));
3669 alignPanel.paintAlignment(true, false);
3675 * last hash for alignment's annotation array - used to minimise cost of
3678 protected int _annotationScoreVectorHash;
3681 * search the alignment and rebuild the sort by annotation score submenu the
3682 * last alignment annotation vector hash is stored to minimize cost of
3683 * rebuilding in subsequence calls.
3687 public void buildSortByAnnotationScoresMenu()
3689 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3694 if (viewport.getAlignment().getAlignmentAnnotation()
3695 .hashCode() != _annotationScoreVectorHash)
3697 sortByAnnotScore.removeAll();
3698 // almost certainly a quicker way to do this - but we keep it simple
3699 Hashtable scoreSorts = new Hashtable();
3700 AlignmentAnnotation aann[];
3701 for (SequenceI sqa : viewport.getAlignment().getSequences())
3703 aann = sqa.getAnnotation();
3704 for (int i = 0; aann != null && i < aann.length; i++)
3706 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3708 scoreSorts.put(aann[i].label, aann[i].label);
3712 Enumeration labels = scoreSorts.keys();
3713 while (labels.hasMoreElements())
3715 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3716 (String) labels.nextElement());
3718 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3721 _annotationScoreVectorHash = viewport.getAlignment()
3722 .getAlignmentAnnotation().hashCode();
3727 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3728 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3729 * call. Listeners are added to remove the menu item when the treePanel is
3730 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3734 public void buildTreeSortMenu()
3736 sortByTreeMenu.removeAll();
3738 List<Component> comps = PaintRefresher.components
3739 .get(viewport.getSequenceSetId());
3740 List<TreePanel> treePanels = new ArrayList<>();
3741 for (Component comp : comps)
3743 if (comp instanceof TreePanel)
3745 treePanels.add((TreePanel) comp);
3749 if (treePanels.size() < 1)
3751 sortByTreeMenu.setVisible(false);
3755 sortByTreeMenu.setVisible(true);
3757 for (final TreePanel tp : treePanels)
3759 final JMenuItem item = new JMenuItem(tp.getTitle());
3760 item.addActionListener(new java.awt.event.ActionListener()
3763 public void actionPerformed(ActionEvent e)
3765 tp.sortByTree_actionPerformed();
3766 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3771 sortByTreeMenu.add(item);
3775 public boolean sortBy(AlignmentOrder alorder, String undoname)
3777 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3778 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3779 if (undoname != null)
3781 addHistoryItem(new OrderCommand(undoname, oldOrder,
3782 viewport.getAlignment()));
3784 alignPanel.paintAlignment(true, false);
3789 * Work out whether the whole set of sequences or just the selected set will
3790 * be submitted for multiple alignment.
3793 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3795 // Now, check we have enough sequences
3796 AlignmentView msa = null;
3798 if ((viewport.getSelectionGroup() != null)
3799 && (viewport.getSelectionGroup().getSize() > 1))
3801 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3802 // some common interface!
3804 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3805 * SequenceI[sz = seqs.getSize(false)];
3807 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3808 * seqs.getSequenceAt(i); }
3810 msa = viewport.getAlignmentView(true);
3812 else if (viewport.getSelectionGroup() != null
3813 && viewport.getSelectionGroup().getSize() == 1)
3815 int option = JvOptionPane.showConfirmDialog(this,
3816 MessageManager.getString("warn.oneseq_msainput_selection"),
3817 MessageManager.getString("label.invalid_selection"),
3818 JvOptionPane.OK_CANCEL_OPTION);
3819 if (option == JvOptionPane.OK_OPTION)
3821 msa = viewport.getAlignmentView(false);
3826 msa = viewport.getAlignmentView(false);
3832 * Decides what is submitted to a secondary structure prediction service: the
3833 * first sequence in the alignment, or in the current selection, or, if the
3834 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3835 * region or the whole alignment. (where the first sequence in the set is the
3836 * one that the prediction will be for).
3838 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3840 AlignmentView seqs = null;
3842 if ((viewport.getSelectionGroup() != null)
3843 && (viewport.getSelectionGroup().getSize() > 0))
3845 seqs = viewport.getAlignmentView(true);
3849 seqs = viewport.getAlignmentView(false);
3851 // limit sequences - JBPNote in future - could spawn multiple prediction
3853 // TODO: viewport.getAlignment().isAligned is a global state - the local
3854 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3855 if (!viewport.getAlignment().isAligned(false))
3857 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3858 // TODO: if seqs.getSequences().length>1 then should really have warned
3872 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3874 // Pick the tree file
3875 JalviewFileChooser chooser = new JalviewFileChooser(
3876 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3877 chooser.setFileView(new JalviewFileView());
3878 chooser.setDialogTitle(
3879 MessageManager.getString("label.select_newick_like_tree_file"));
3880 chooser.setToolTipText(
3881 MessageManager.getString("label.load_tree_file"));
3883 int value = chooser.showOpenDialog(null);
3885 if (value == JalviewFileChooser.APPROVE_OPTION)
3887 String filePath = chooser.getSelectedFile().getPath();
3888 Cache.setProperty("LAST_DIRECTORY", filePath);
3889 NewickFile fin = null;
3892 fin = new NewickFile(filePath, DataSourceType.FILE);
3893 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3894 } catch (Exception ex)
3896 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3897 MessageManager.getString("label.problem_reading_tree_file"),
3898 JvOptionPane.WARNING_MESSAGE);
3899 ex.printStackTrace();
3901 if (fin != null && fin.hasWarningMessage())
3903 JvOptionPane.showMessageDialog(Desktop.desktop,
3904 fin.getWarningMessage(),
3906 .getString("label.possible_problem_with_tree_file"),
3907 JvOptionPane.WARNING_MESSAGE);
3912 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3914 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3917 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3918 int h, int x, int y)
3920 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3924 * Add a treeviewer for the tree extracted from a Newick file object to the
3925 * current alignment view
3932 * Associated alignment input data (or null)
3941 * @return TreePanel handle
3943 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3944 AlignmentView input, int w, int h, int x, int y)
3946 TreePanel tp = null;
3952 if (nf.getTree() != null)
3954 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3960 tp.setLocation(x, y);
3963 Desktop.addInternalFrame(tp, treeTitle, w, h);
3965 } catch (Exception ex)
3967 ex.printStackTrace();
3973 private boolean buildingMenu = false;
3976 * Generates menu items and listener event actions for web service clients
3979 public void BuildWebServiceMenu()
3981 while (buildingMenu)
3985 System.err.println("Waiting for building menu to finish.");
3987 } catch (Exception e)
3991 final AlignFrame me = this;
3992 buildingMenu = true;
3993 new Thread(new Runnable()
3998 final List<JMenuItem> legacyItems = new ArrayList<>();
4001 // System.err.println("Building ws menu again "
4002 // + Thread.currentThread());
4003 // TODO: add support for context dependent disabling of services based
4005 // alignment and current selection
4006 // TODO: add additional serviceHandle parameter to specify abstract
4008 // class independently of AbstractName
4009 // TODO: add in rediscovery GUI function to restart discoverer
4010 // TODO: group services by location as well as function and/or
4012 // object broker mechanism.
4013 final Vector<JMenu> wsmenu = new Vector<>();
4014 final IProgressIndicator af = me;
4017 * do not i18n these strings - they are hard-coded in class
4018 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4019 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4021 final JMenu msawsmenu = new JMenu("Alignment");
4022 final JMenu secstrmenu = new JMenu(
4023 "Secondary Structure Prediction");
4024 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4025 final JMenu analymenu = new JMenu("Analysis");
4026 final JMenu dismenu = new JMenu("Protein Disorder");
4027 // JAL-940 - only show secondary structure prediction services from
4028 // the legacy server
4029 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4031 Discoverer.services != null && (Discoverer.services.size() > 0))
4033 // TODO: refactor to allow list of AbstractName/Handler bindings to
4035 // stored or retrieved from elsewhere
4036 // No MSAWS used any more:
4037 // Vector msaws = null; // (Vector)
4038 // Discoverer.services.get("MsaWS");
4039 Vector secstrpr = (Vector) Discoverer.services
4041 if (secstrpr != null)
4043 // Add any secondary structure prediction services
4044 for (int i = 0, j = secstrpr.size(); i < j; i++)
4046 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4048 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4049 .getServiceClient(sh);
4050 int p = secstrmenu.getItemCount();
4051 impl.attachWSMenuEntry(secstrmenu, me);
4052 int q = secstrmenu.getItemCount();
4053 for (int litm = p; litm < q; litm++)
4055 legacyItems.add(secstrmenu.getItem(litm));
4061 // Add all submenus in the order they should appear on the web
4063 wsmenu.add(msawsmenu);
4064 wsmenu.add(secstrmenu);
4065 wsmenu.add(dismenu);
4066 wsmenu.add(analymenu);
4067 // No search services yet
4068 // wsmenu.add(seqsrchmenu);
4070 javax.swing.SwingUtilities.invokeLater(new Runnable()
4077 webService.removeAll();
4078 // first, add discovered services onto the webservices menu
4079 if (wsmenu.size() > 0)
4081 for (int i = 0, j = wsmenu.size(); i < j; i++)
4083 webService.add(wsmenu.get(i));
4088 webService.add(me.webServiceNoServices);
4090 // TODO: move into separate menu builder class.
4091 boolean new_sspred = false;
4092 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4094 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4095 if (jws2servs != null)
4097 if (jws2servs.hasServices())
4099 jws2servs.attachWSMenuEntry(webService, me);
4100 for (Jws2Instance sv : jws2servs.getServices())
4102 if (sv.description.toLowerCase().contains("jpred"))
4104 for (JMenuItem jmi : legacyItems)
4106 jmi.setVisible(false);
4112 if (jws2servs.isRunning())
4114 JMenuItem tm = new JMenuItem(
4115 "Still discovering JABA Services");
4116 tm.setEnabled(false);
4121 build_urlServiceMenu(me.webService);
4122 build_fetchdbmenu(webService);
4123 for (JMenu item : wsmenu)
4125 if (item.getItemCount() == 0)
4127 item.setEnabled(false);
4131 item.setEnabled(true);
4134 } catch (Exception e)
4137 "Exception during web service menu building process.",
4142 } catch (Exception e)
4145 buildingMenu = false;
4152 * construct any groupURL type service menu entries.
4156 private void build_urlServiceMenu(JMenu webService)
4158 // TODO: remove this code when 2.7 is released
4159 // DEBUG - alignmentView
4161 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4162 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4164 * @Override public void actionPerformed(ActionEvent e) {
4165 * jalview.datamodel.AlignmentView
4166 * .testSelectionViews(af.viewport.getAlignment(),
4167 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4169 * }); webService.add(testAlView);
4171 // TODO: refactor to RestClient discoverer and merge menu entries for
4172 // rest-style services with other types of analysis/calculation service
4173 // SHmmr test client - still being implemented.
4174 // DEBUG - alignmentView
4176 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4179 client.attachWSMenuEntry(
4180 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4186 * Searches the alignment sequences for xRefs and builds the Show
4187 * Cross-References menu (formerly called Show Products), with database
4188 * sources for which cross-references are found (protein sources for a
4189 * nucleotide alignment and vice versa)
4191 * @return true if Show Cross-references menu should be enabled
4193 public boolean canShowProducts()
4195 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4196 AlignmentI dataset = viewport.getAlignment().getDataset();
4198 showProducts.removeAll();
4199 final boolean dna = viewport.getAlignment().isNucleotide();
4201 if (seqs == null || seqs.length == 0)
4203 // nothing to see here.
4207 boolean showp = false;
4210 List<String> ptypes = new CrossRef(seqs, dataset)
4211 .findXrefSourcesForSequences(dna);
4213 for (final String source : ptypes)
4216 final AlignFrame af = this;
4217 JMenuItem xtype = new JMenuItem(source);
4218 xtype.addActionListener(new ActionListener()
4221 public void actionPerformed(ActionEvent e)
4223 showProductsFor(af.viewport.getSequenceSelection(), dna,
4227 showProducts.add(xtype);
4229 showProducts.setVisible(showp);
4230 showProducts.setEnabled(showp);
4231 } catch (Exception e)
4234 "canShowProducts threw an exception - please report to help@jalview.org",
4242 * Finds and displays cross-references for the selected sequences (protein
4243 * products for nucleotide sequences, dna coding sequences for peptides).
4246 * the sequences to show cross-references for
4248 * true if from a nucleotide alignment (so showing proteins)
4250 * the database to show cross-references for
4252 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4253 final String source)
4255 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4260 * Construct and display a new frame containing the translation of this
4261 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4264 public void showTranslation_actionPerformed(ActionEvent e)
4266 AlignmentI al = null;
4269 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4271 al = dna.translateCdna();
4272 } catch (Exception ex)
4274 jalview.bin.Cache.log.error(
4275 "Exception during translation. Please report this !", ex);
4276 final String msg = MessageManager.getString(
4277 "label.error_when_translating_sequences_submit_bug_report");
4278 final String errorTitle = MessageManager
4279 .getString("label.implementation_error")
4280 + MessageManager.getString("label.translation_failed");
4281 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4282 JvOptionPane.ERROR_MESSAGE);
4285 if (al == null || al.getHeight() == 0)
4287 final String msg = MessageManager.getString(
4288 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4289 final String errorTitle = MessageManager
4290 .getString("label.translation_failed");
4291 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4292 JvOptionPane.WARNING_MESSAGE);
4296 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4297 af.setFileFormat(this.currentFileFormat);
4298 final String newTitle = MessageManager
4299 .formatMessage("label.translation_of_params", new Object[]
4300 { this.getTitle() });
4301 af.setTitle(newTitle);
4302 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4304 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4305 viewport.openSplitFrame(af, new Alignment(seqs));
4309 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4316 * Set the file format
4320 public void setFileFormat(FileFormatI format)
4322 this.currentFileFormat = format;
4326 * Try to load a features file onto the alignment.
4329 * contents or path to retrieve file
4331 * access mode of file (see jalview.io.AlignFile)
4332 * @return true if features file was parsed correctly.
4334 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4336 return avc.parseFeaturesFile(file, sourceType,
4337 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4342 public void refreshFeatureUI(boolean enableIfNecessary)
4344 // note - currently this is only still here rather than in the controller
4345 // because of the featureSettings hard reference that is yet to be
4347 if (enableIfNecessary)
4349 viewport.setShowSequenceFeatures(true);
4350 showSeqFeatures.setSelected(true);
4356 public void dragEnter(DropTargetDragEvent evt)
4361 public void dragExit(DropTargetEvent evt)
4366 public void dragOver(DropTargetDragEvent evt)
4371 public void dropActionChanged(DropTargetDragEvent evt)
4376 public void drop(DropTargetDropEvent evt)
4378 // JAL-1552 - acceptDrop required before getTransferable call for
4379 // Java's Transferable for native dnd
4380 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4381 Transferable t = evt.getTransferable();
4382 final AlignFrame thisaf = this;
4383 final List<String> files = new ArrayList<>();
4384 List<DataSourceType> protocols = new ArrayList<>();
4388 Desktop.transferFromDropTarget(files, protocols, evt, t);
4389 } catch (Exception e)
4391 e.printStackTrace();
4395 new Thread(new Runnable()
4402 // check to see if any of these files have names matching sequences
4405 SequenceIdMatcher idm = new SequenceIdMatcher(
4406 viewport.getAlignment().getSequencesArray());
4408 * Object[] { String,SequenceI}
4410 ArrayList<Object[]> filesmatched = new ArrayList<>();
4411 ArrayList<String> filesnotmatched = new ArrayList<>();
4412 for (int i = 0; i < files.size(); i++)
4414 String file = files.get(i).toString();
4416 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4417 if (protocol == DataSourceType.FILE)
4419 File fl = new File(file);
4420 pdbfn = fl.getName();
4422 else if (protocol == DataSourceType.URL)
4424 URL url = new URL(file);
4425 pdbfn = url.getFile();
4427 if (pdbfn.length() > 0)
4429 // attempt to find a match in the alignment
4430 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4431 int l = 0, c = pdbfn.indexOf(".");
4432 while (mtch == null && c != -1)
4437 } while ((c = pdbfn.indexOf(".", l)) > l);
4440 pdbfn = pdbfn.substring(0, l);
4442 mtch = idm.findAllIdMatches(pdbfn);
4446 FileFormatI type = null;
4449 type = new IdentifyFile().identify(file, protocol);
4450 } catch (Exception ex)
4454 if (type != null && type.isStructureFile())
4456 filesmatched.add(new Object[] { file, protocol, mtch });
4460 // File wasn't named like one of the sequences or wasn't a PDB
4462 filesnotmatched.add(file);
4466 if (filesmatched.size() > 0)
4468 boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4471 String msg = MessageManager.formatMessage(
4472 "label.automatically_associate_structure_files_with_sequences_same_name",
4474 { Integer.valueOf(filesmatched.size())
4476 String ttl = MessageManager.getString(
4477 "label.automatically_associate_structure_files_by_name");
4478 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4479 ttl, JvOptionPane.YES_NO_OPTION);
4480 autoAssociate = choice == JvOptionPane.YES_OPTION;
4484 for (Object[] fm : filesmatched)
4486 // try and associate
4487 // TODO: may want to set a standard ID naming formalism for
4488 // associating PDB files which have no IDs.
4489 for (SequenceI toassoc : (SequenceI[]) fm[2])
4491 PDBEntry pe = new AssociatePdbFileWithSeq()
4492 .associatePdbWithSeq((String) fm[0],
4493 (DataSourceType) fm[1], toassoc, false,
4497 System.err.println("Associated file : "
4498 + ((String) fm[0]) + " with "
4499 + toassoc.getDisplayId(true));
4503 // TODO: do we need to update overview ? only if features are
4505 alignPanel.paintAlignment(true, false);
4511 * add declined structures as sequences
4513 for (Object[] o : filesmatched)
4515 filesnotmatched.add((String) o[0]);
4519 if (filesnotmatched.size() > 0)
4521 if (assocfiles > 0 && (Cache.getDefault(
4522 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4523 || JvOptionPane.showConfirmDialog(thisaf,
4524 "<html>" + MessageManager.formatMessage(
4525 "label.ignore_unmatched_dropped_files_info",
4528 filesnotmatched.size())
4531 MessageManager.getString(
4532 "label.ignore_unmatched_dropped_files"),
4533 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4537 for (String fn : filesnotmatched)
4539 loadJalviewDataFile(fn, null, null, null);
4543 } catch (Exception ex)
4545 ex.printStackTrace();
4553 * Attempt to load a "dropped" file or URL string, by testing in turn for
4555 * <li>an Annotation file</li>
4556 * <li>a JNet file</li>
4557 * <li>a features file</li>
4558 * <li>else try to interpret as an alignment file</li>
4562 * either a filename or a URL string.
4564 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4565 FileFormatI format, SequenceI assocSeq)
4569 if (sourceType == null)
4571 sourceType = FormatAdapter.checkProtocol(file);
4573 // if the file isn't identified, or not positively identified as some
4574 // other filetype (PFAM is default unidentified alignment file type) then
4575 // try to parse as annotation.
4576 boolean isAnnotation = (format == null
4577 || FileFormat.Pfam.equals(format))
4578 ? new AnnotationFile().annotateAlignmentView(viewport,
4584 // first see if its a T-COFFEE score file
4585 TCoffeeScoreFile tcf = null;
4588 tcf = new TCoffeeScoreFile(file, sourceType);
4591 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4595 new TCoffeeColourScheme(viewport.getAlignment()));
4596 isAnnotation = true;
4597 statusBar.setText(MessageManager.getString(
4598 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4602 // some problem - if no warning its probable that the ID matching
4603 // process didn't work
4604 JvOptionPane.showMessageDialog(Desktop.desktop,
4605 tcf.getWarningMessage() == null
4606 ? MessageManager.getString(
4607 "label.check_file_matches_sequence_ids_alignment")
4608 : tcf.getWarningMessage(),
4609 MessageManager.getString(
4610 "label.problem_reading_tcoffee_score_file"),
4611 JvOptionPane.WARNING_MESSAGE);
4618 } catch (Exception x)
4621 "Exception when processing data source as T-COFFEE score file",
4627 // try to see if its a JNet 'concise' style annotation file *before*
4629 // try to parse it as a features file
4632 format = new IdentifyFile().identify(file, sourceType);
4634 if (FileFormat.ScoreMatrix == format)
4636 ScoreMatrixFile sm = new ScoreMatrixFile(
4637 new FileParse(file, sourceType));
4639 // todo: i18n this message
4640 statusBar.setText(MessageManager.formatMessage(
4641 "label.successfully_loaded_matrix",
4642 sm.getMatrixName()));
4644 else if (FileFormat.Jnet.equals(format))
4646 JPredFile predictions = new JPredFile(file, sourceType);
4647 new JnetAnnotationMaker();
4648 JnetAnnotationMaker.add_annotation(predictions,
4649 viewport.getAlignment(), 0, false);
4650 viewport.getAlignment().setupJPredAlignment();
4651 isAnnotation = true;
4653 // else if (IdentifyFile.FeaturesFile.equals(format))
4654 else if (FileFormat.Features.equals(format))
4656 if (parseFeaturesFile(file, sourceType))
4658 alignPanel.paintAlignment(true, true);
4663 new FileLoader().LoadFile(viewport, file, sourceType, format);
4670 alignPanel.adjustAnnotationHeight();
4671 viewport.updateSequenceIdColours();
4672 buildSortByAnnotationScoresMenu();
4673 alignPanel.paintAlignment(true, true);
4675 } catch (Exception ex)
4677 ex.printStackTrace();
4678 } catch (OutOfMemoryError oom)
4683 } catch (Exception x)
4688 + (sourceType != null
4689 ? (sourceType == DataSourceType.PASTE
4691 : "using " + sourceType + " from "
4695 ? "(parsing as '" + format + "' file)"
4697 oom, Desktop.desktop);
4702 * Method invoked by the ChangeListener on the tabbed pane, in other words
4703 * when a different tabbed pane is selected by the user or programmatically.
4706 public void tabSelectionChanged(int index)
4710 alignPanel = alignPanels.get(index);
4711 viewport = alignPanel.av;
4712 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4713 setMenusFromViewport(viewport);
4717 * 'focus' any colour slider that is open to the selected viewport
4719 if (viewport.getConservationSelected())
4721 SliderPanel.setConservationSlider(alignPanel,
4722 viewport.getResidueShading(), alignPanel.getViewName());
4726 SliderPanel.hideConservationSlider();
4728 if (viewport.getAbovePIDThreshold())
4730 SliderPanel.setPIDSliderSource(alignPanel,
4731 viewport.getResidueShading(), alignPanel.getViewName());
4735 SliderPanel.hidePIDSlider();
4739 * If there is a frame linked to this one in a SplitPane, switch it to the
4740 * same view tab index. No infinite recursion of calls should happen, since
4741 * tabSelectionChanged() should not get invoked on setting the selected
4742 * index to an unchanged value. Guard against setting an invalid index
4743 * before the new view peer tab has been created.
4745 final AlignViewportI peer = viewport.getCodingComplement();
4748 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4749 .getAlignPanel().alignFrame;
4750 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4752 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4758 * On right mouse click on view tab, prompt for and set new view name.
4761 public void tabbedPane_mousePressed(MouseEvent e)
4763 if (e.isPopupTrigger())
4765 String msg = MessageManager.getString("label.enter_view_name");
4766 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4767 JvOptionPane.QUESTION_MESSAGE);
4771 viewport.viewName = reply;
4772 // TODO warn if reply is in getExistingViewNames()?
4773 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4778 public AlignViewport getCurrentView()
4784 * Open the dialog for regex description parsing.
4787 protected void extractScores_actionPerformed(ActionEvent e)
4789 ParseProperties pp = new jalview.analysis.ParseProperties(
4790 viewport.getAlignment());
4791 // TODO: verify regex and introduce GUI dialog for version 2.5
4792 // if (pp.getScoresFromDescription("col", "score column ",
4793 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4795 if (pp.getScoresFromDescription("description column",
4796 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4798 buildSortByAnnotationScoresMenu();
4806 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4810 protected void showDbRefs_actionPerformed(ActionEvent e)
4812 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4818 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4822 protected void showNpFeats_actionPerformed(ActionEvent e)
4824 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4828 * find the viewport amongst the tabs in this alignment frame and close that
4833 public boolean closeView(AlignViewportI av)
4837 this.closeMenuItem_actionPerformed(false);
4840 Component[] comp = tabbedPane.getComponents();
4841 for (int i = 0; comp != null && i < comp.length; i++)
4843 if (comp[i] instanceof AlignmentPanel)
4845 if (((AlignmentPanel) comp[i]).av == av)
4848 closeView((AlignmentPanel) comp[i]);
4856 protected void build_fetchdbmenu(JMenu webService)
4858 // Temporary hack - DBRef Fetcher always top level ws entry.
4859 // TODO We probably want to store a sequence database checklist in
4860 // preferences and have checkboxes.. rather than individual sources selected
4862 final JMenu rfetch = new JMenu(
4863 MessageManager.getString("action.fetch_db_references"));
4864 rfetch.setToolTipText(MessageManager.getString(
4865 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4866 webService.add(rfetch);
4868 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4869 MessageManager.getString("option.trim_retrieved_seqs"));
4870 trimrs.setToolTipText(
4871 MessageManager.getString("label.trim_retrieved_sequences"));
4873 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4874 trimrs.addActionListener(new ActionListener()
4877 public void actionPerformed(ActionEvent e)
4879 trimrs.setSelected(trimrs.isSelected());
4880 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4881 Boolean.valueOf(trimrs.isSelected()).toString());
4885 JMenuItem fetchr = new JMenuItem(
4886 MessageManager.getString("label.standard_databases"));
4887 fetchr.setToolTipText(
4888 MessageManager.getString("label.fetch_embl_uniprot"));
4889 fetchr.addActionListener(new ActionListener()
4893 public void actionPerformed(ActionEvent e)
4895 new Thread(new Runnable()
4900 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4901 .getAlignment().isNucleotide();
4902 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4903 alignPanel.av.getSequenceSelection(),
4904 alignPanel.alignFrame, null,
4905 alignPanel.alignFrame.featureSettings, isNucleotide);
4906 dbRefFetcher.addListener(new FetchFinishedListenerI()
4909 public void finished()
4911 AlignFrame.this.setMenusForViewport();
4914 dbRefFetcher.fetchDBRefs(false);
4922 final AlignFrame me = this;
4923 new Thread(new Runnable()
4928 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4929 .getSequenceFetcherSingleton(me);
4930 javax.swing.SwingUtilities.invokeLater(new Runnable()
4935 String[] dbclasses = sf.getOrderedSupportedSources();
4936 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4937 // jalview.util.QuickSort.sort(otherdb, otherdb);
4938 List<DbSourceProxy> otherdb;
4939 JMenu dfetch = new JMenu();
4940 JMenu ifetch = new JMenu();
4941 JMenuItem fetchr = null;
4942 int comp = 0, icomp = 0, mcomp = 15;
4943 String mname = null;
4945 for (String dbclass : dbclasses)
4947 otherdb = sf.getSourceProxy(dbclass);
4948 // add a single entry for this class, or submenu allowing 'fetch
4950 if (otherdb == null || otherdb.size() < 1)
4954 // List<DbSourceProxy> dbs=otherdb;
4955 // otherdb=new ArrayList<DbSourceProxy>();
4956 // for (DbSourceProxy db:dbs)
4958 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4962 mname = "From " + dbclass;
4964 if (otherdb.size() == 1)
4966 final DbSourceProxy[] dassource = otherdb
4967 .toArray(new DbSourceProxy[0]);
4968 DbSourceProxy src = otherdb.get(0);
4969 fetchr = new JMenuItem(src.getDbSource());
4970 fetchr.addActionListener(new ActionListener()
4974 public void actionPerformed(ActionEvent e)
4976 new Thread(new Runnable()
4982 boolean isNucleotide = alignPanel.alignFrame
4983 .getViewport().getAlignment()
4985 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4986 alignPanel.av.getSequenceSelection(),
4987 alignPanel.alignFrame, dassource,
4988 alignPanel.alignFrame.featureSettings,
4991 .addListener(new FetchFinishedListenerI()
4994 public void finished()
4996 AlignFrame.this.setMenusForViewport();
4999 dbRefFetcher.fetchDBRefs(false);
5005 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5006 MessageManager.formatMessage(
5007 "label.fetch_retrieve_from", new Object[]
5008 { src.getDbName() })));
5014 final DbSourceProxy[] dassource = otherdb
5015 .toArray(new DbSourceProxy[0]);
5017 DbSourceProxy src = otherdb.get(0);
5018 fetchr = new JMenuItem(MessageManager
5019 .formatMessage("label.fetch_all_param", new Object[]
5020 { src.getDbSource() }));
5021 fetchr.addActionListener(new ActionListener()
5024 public void actionPerformed(ActionEvent e)
5026 new Thread(new Runnable()
5032 boolean isNucleotide = alignPanel.alignFrame
5033 .getViewport().getAlignment()
5035 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5036 alignPanel.av.getSequenceSelection(),
5037 alignPanel.alignFrame, dassource,
5038 alignPanel.alignFrame.featureSettings,
5041 .addListener(new FetchFinishedListenerI()
5044 public void finished()
5046 AlignFrame.this.setMenusForViewport();
5049 dbRefFetcher.fetchDBRefs(false);
5055 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5056 MessageManager.formatMessage(
5057 "label.fetch_retrieve_from_all_sources",
5059 { Integer.valueOf(otherdb.size())
5061 src.getDbSource(), src.getDbName() })));
5064 // and then build the rest of the individual menus
5065 ifetch = new JMenu(MessageManager.formatMessage(
5066 "label.source_from_db_source", new Object[]
5067 { src.getDbSource() }));
5069 String imname = null;
5071 for (DbSourceProxy sproxy : otherdb)
5073 String dbname = sproxy.getDbName();
5074 String sname = dbname.length() > 5
5075 ? dbname.substring(0, 5) + "..."
5077 String msname = dbname.length() > 10
5078 ? dbname.substring(0, 10) + "..."
5082 imname = MessageManager
5083 .formatMessage("label.from_msname", new Object[]
5086 fetchr = new JMenuItem(msname);
5087 final DbSourceProxy[] dassrc = { sproxy };
5088 fetchr.addActionListener(new ActionListener()
5092 public void actionPerformed(ActionEvent e)
5094 new Thread(new Runnable()
5100 boolean isNucleotide = alignPanel.alignFrame
5101 .getViewport().getAlignment()
5103 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5104 alignPanel.av.getSequenceSelection(),
5105 alignPanel.alignFrame, dassrc,
5106 alignPanel.alignFrame.featureSettings,
5109 .addListener(new FetchFinishedListenerI()
5112 public void finished()
5114 AlignFrame.this.setMenusForViewport();
5117 dbRefFetcher.fetchDBRefs(false);
5123 fetchr.setToolTipText(
5124 "<html>" + MessageManager.formatMessage(
5125 "label.fetch_retrieve_from", new Object[]
5129 if (++icomp >= mcomp || i == (otherdb.size()))
5131 ifetch.setText(MessageManager.formatMessage(
5132 "label.source_to_target", imname, sname));
5134 ifetch = new JMenu();
5142 if (comp >= mcomp || dbi >= (dbclasses.length))
5144 dfetch.setText(MessageManager.formatMessage(
5145 "label.source_to_target", mname, dbclass));
5147 dfetch = new JMenu();
5160 * Left justify the whole alignment.
5163 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5165 AlignmentI al = viewport.getAlignment();
5167 viewport.firePropertyChange("alignment", null, al);
5171 * Right justify the whole alignment.
5174 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5176 AlignmentI al = viewport.getAlignment();
5178 viewport.firePropertyChange("alignment", null, al);
5182 public void setShowSeqFeatures(boolean b)
5184 showSeqFeatures.setSelected(b);
5185 viewport.setShowSequenceFeatures(b);
5192 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5193 * awt.event.ActionEvent)
5196 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5198 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5199 alignPanel.paintAlignment(false, false);
5206 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5210 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5212 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5213 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5221 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5222 * .event.ActionEvent)
5225 protected void showGroupConservation_actionPerformed(ActionEvent e)
5227 viewport.setShowGroupConservation(showGroupConservation.getState());
5228 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5235 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5236 * .event.ActionEvent)
5239 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5241 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5242 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5249 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5250 * .event.ActionEvent)
5253 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5255 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5256 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5260 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5262 showSequenceLogo.setState(true);
5263 viewport.setShowSequenceLogo(true);
5264 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5265 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5269 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5271 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5278 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5279 * .event.ActionEvent)
5282 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5284 if (avc.makeGroupsFromSelection())
5286 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5287 alignPanel.updateAnnotation();
5288 alignPanel.paintAlignment(true, true);
5292 public void clearAlignmentSeqRep()
5294 // TODO refactor alignmentseqrep to controller
5295 if (viewport.getAlignment().hasSeqrep())
5297 viewport.getAlignment().setSeqrep(null);
5298 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5299 alignPanel.updateAnnotation();
5300 alignPanel.paintAlignment(true, true);
5305 protected void createGroup_actionPerformed(ActionEvent e)
5307 if (avc.createGroup())
5309 if (applyAutoAnnotationSettings.isSelected())
5311 alignPanel.updateAnnotation(true, false);
5313 alignPanel.alignmentChanged();
5318 protected void unGroup_actionPerformed(ActionEvent e)
5322 alignPanel.alignmentChanged();
5327 * make the given alignmentPanel the currently selected tab
5329 * @param alignmentPanel
5331 public void setDisplayedView(AlignmentPanel alignmentPanel)
5333 if (!viewport.getSequenceSetId()
5334 .equals(alignmentPanel.av.getSequenceSetId()))
5336 throw new Error(MessageManager.getString(
5337 "error.implementation_error_cannot_show_view_alignment_frame"));
5339 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5340 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5342 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5347 * Action on selection of menu options to Show or Hide annotations.
5350 * @param forSequences
5351 * update sequence-related annotations
5352 * @param forAlignment
5353 * update non-sequence-related annotations
5356 protected void setAnnotationsVisibility(boolean visible,
5357 boolean forSequences, boolean forAlignment)
5359 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5360 .getAlignmentAnnotation();
5365 for (AlignmentAnnotation aa : anns)
5368 * don't display non-positional annotations on an alignment
5370 if (aa.annotations == null)
5374 boolean apply = (aa.sequenceRef == null && forAlignment)
5375 || (aa.sequenceRef != null && forSequences);
5378 aa.visible = visible;
5381 alignPanel.validateAnnotationDimensions(true);
5382 alignPanel.alignmentChanged();
5386 * Store selected annotation sort order for the view and repaint.
5389 protected void sortAnnotations_actionPerformed()
5391 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5393 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5394 alignPanel.paintAlignment(false, false);
5399 * @return alignment panels in this alignment frame
5401 public List<? extends AlignmentViewPanel> getAlignPanels()
5403 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5407 * Open a new alignment window, with the cDNA associated with this (protein)
5408 * alignment, aligned as is the protein.
5410 protected void viewAsCdna_actionPerformed()
5412 // TODO no longer a menu action - refactor as required
5413 final AlignmentI alignment = getViewport().getAlignment();
5414 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5415 if (mappings == null)
5419 List<SequenceI> cdnaSeqs = new ArrayList<>();
5420 for (SequenceI aaSeq : alignment.getSequences())
5422 for (AlignedCodonFrame acf : mappings)
5424 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5428 * There is a cDNA mapping for this protein sequence - add to new
5429 * alignment. It will share the same dataset sequence as other mapped
5430 * cDNA (no new mappings need to be created).
5432 final Sequence newSeq = new Sequence(dnaSeq);
5433 newSeq.setDatasetSequence(dnaSeq);
5434 cdnaSeqs.add(newSeq);
5438 if (cdnaSeqs.size() == 0)
5440 // show a warning dialog no mapped cDNA
5443 AlignmentI cdna = new Alignment(
5444 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5445 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5446 AlignFrame.DEFAULT_HEIGHT);
5447 cdna.alignAs(alignment);
5448 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5450 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5451 AlignFrame.DEFAULT_HEIGHT);
5455 * Set visibility of dna/protein complement view (available when shown in a
5461 protected void showComplement_actionPerformed(boolean show)
5463 SplitContainerI sf = getSplitViewContainer();
5466 sf.setComplementVisible(this, show);
5471 * Generate the reverse (optionally complemented) of the selected sequences,
5472 * and add them to the alignment
5475 protected void showReverse_actionPerformed(boolean complement)
5477 AlignmentI al = null;
5480 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5481 al = dna.reverseCdna(complement);
5482 viewport.addAlignment(al, "");
5483 addHistoryItem(new EditCommand(
5484 MessageManager.getString("label.add_sequences"), Action.PASTE,
5485 al.getSequencesArray(), 0, al.getWidth(),
5486 viewport.getAlignment()));
5487 } catch (Exception ex)
5489 System.err.println(ex.getMessage());
5495 * Try to run a script in the Groovy console, having first ensured that this
5496 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5497 * be targeted at this alignment.
5500 protected void runGroovy_actionPerformed()
5502 Jalview.setCurrentAlignFrame(this);
5503 groovy.ui.Console console = Desktop.getGroovyConsole();
5504 if (console != null)
5508 console.runScript();
5509 } catch (Exception ex)
5511 System.err.println((ex.toString()));
5512 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5513 MessageManager.getString("label.couldnt_run_groovy_script"),
5514 MessageManager.getString("label.groovy_support_failed"),
5515 JvOptionPane.ERROR_MESSAGE);
5520 System.err.println("Can't run Groovy script as console not found");
5525 * Hides columns containing (or not containing) a specified feature, provided
5526 * that would not leave all columns hidden
5528 * @param featureType
5529 * @param columnsContaining
5532 public boolean hideFeatureColumns(String featureType,
5533 boolean columnsContaining)
5535 boolean notForHiding = avc.markColumnsContainingFeatures(
5536 columnsContaining, false, false, featureType);
5539 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5540 false, featureType))
5542 getViewport().hideSelectedColumns();
5550 protected void selectHighlightedColumns_actionPerformed(
5551 ActionEvent actionEvent)
5553 // include key modifier check in case user selects from menu
5554 avc.markHighlightedColumns(
5555 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5556 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5557 | ActionEvent.CTRL_MASK)) != 0);
5561 * Rebuilds the Colour menu, including any user-defined colours which have
5562 * been loaded either on startup or during the session
5564 public void buildColourMenu()
5566 colourMenu.removeAll();
5568 colourMenu.add(applyToAllGroups);
5569 colourMenu.add(textColour);
5570 colourMenu.addSeparator();
5572 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5573 viewport.getAlignment(), false);
5575 colourMenu.add(annotationColour);
5576 bg.add(annotationColour);
5577 colourMenu.addSeparator();
5578 colourMenu.add(conservationMenuItem);
5579 colourMenu.add(modifyConservation);
5580 colourMenu.add(abovePIDThreshold);
5581 colourMenu.add(modifyPID);
5583 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5584 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5588 * Open a dialog (if not already open) that allows the user to select and
5589 * calculate PCA or Tree analysis
5591 protected void openTreePcaDialog()
5593 if (alignPanel.getCalculationDialog() == null)
5595 new CalculationChooser(AlignFrame.this);
5600 protected void loadVcf_actionPerformed()
5602 JalviewFileChooser chooser = new JalviewFileChooser(
5603 Cache.getProperty("LAST_DIRECTORY"));
5604 chooser.setFileView(new JalviewFileView());
5605 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5606 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5608 int value = chooser.showOpenDialog(null);
5610 if (value == JalviewFileChooser.APPROVE_OPTION)
5612 String choice = chooser.getSelectedFile().getPath();
5613 Cache.setProperty("LAST_DIRECTORY", choice);
5614 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5615 new VCFLoader(choice).loadVCF(seqs, this);
5621 class PrintThread extends Thread
5625 public PrintThread(AlignmentPanel ap)
5630 static PageFormat pf;
5635 PrinterJob printJob = PrinterJob.getPrinterJob();
5639 printJob.setPrintable(ap, pf);
5643 printJob.setPrintable(ap);
5646 if (printJob.printDialog())
5651 } catch (Exception PrintException)
5653 PrintException.printStackTrace();