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.BackupFiles;
68 import jalview.io.BioJsHTMLOutput;
69 import jalview.io.DataSourceType;
70 import jalview.io.FileFormat;
71 import jalview.io.FileFormatI;
72 import jalview.io.FileFormats;
73 import jalview.io.FileLoader;
74 import jalview.io.FileParse;
75 import jalview.io.FormatAdapter;
76 import jalview.io.HtmlSvgOutput;
77 import jalview.io.IdentifyFile;
78 import jalview.io.JPredFile;
79 import jalview.io.JalviewFileChooser;
80 import jalview.io.JalviewFileView;
81 import jalview.io.JnetAnnotationMaker;
82 import jalview.io.NewickFile;
83 import jalview.io.ScoreMatrixFile;
84 import jalview.io.TCoffeeScoreFile;
85 import jalview.io.vcf.VCFLoader;
86 import jalview.jbgui.GAlignFrame;
87 import jalview.schemes.ColourSchemeI;
88 import jalview.schemes.ColourSchemes;
89 import jalview.schemes.ResidueColourScheme;
90 import jalview.schemes.TCoffeeColourScheme;
91 import jalview.util.MessageManager;
92 import jalview.viewmodel.AlignmentViewport;
93 import jalview.viewmodel.ViewportRanges;
94 import jalview.ws.DBRefFetcher;
95 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
96 import jalview.ws.jws1.Discoverer;
97 import jalview.ws.jws2.Jws2Discoverer;
98 import jalview.ws.jws2.jabaws2.Jws2Instance;
99 import jalview.ws.seqfetcher.DbSourceProxy;
101 import java.awt.BorderLayout;
102 import java.awt.Component;
103 import java.awt.Rectangle;
104 import java.awt.Toolkit;
105 import java.awt.datatransfer.Clipboard;
106 import java.awt.datatransfer.DataFlavor;
107 import java.awt.datatransfer.StringSelection;
108 import java.awt.datatransfer.Transferable;
109 import java.awt.dnd.DnDConstants;
110 import java.awt.dnd.DropTargetDragEvent;
111 import java.awt.dnd.DropTargetDropEvent;
112 import java.awt.dnd.DropTargetEvent;
113 import java.awt.dnd.DropTargetListener;
114 import java.awt.event.ActionEvent;
115 import java.awt.event.ActionListener;
116 import java.awt.event.FocusAdapter;
117 import java.awt.event.FocusEvent;
118 import java.awt.event.ItemEvent;
119 import java.awt.event.ItemListener;
120 import java.awt.event.KeyAdapter;
121 import java.awt.event.KeyEvent;
122 import java.awt.event.MouseEvent;
123 import java.awt.print.PageFormat;
124 import java.awt.print.PrinterJob;
125 import java.beans.PropertyChangeEvent;
127 import java.io.FileWriter;
128 import java.io.PrintWriter;
130 import java.util.ArrayList;
131 import java.util.Arrays;
132 import java.util.Deque;
133 import java.util.Enumeration;
134 import java.util.Hashtable;
135 import java.util.List;
136 import java.util.Vector;
138 import javax.swing.JCheckBoxMenuItem;
139 import javax.swing.JEditorPane;
140 import javax.swing.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());
1190 // create backupfiles object and get new temp filename destination
1191 BackupFiles backupfiles = new BackupFiles(file);
1195 PrintWriter out = new PrintWriter(
1196 new FileWriter(backupfiles.getTempFilePath()));
1200 this.setTitle(file);
1201 statusBar.setText(MessageManager.formatMessage(
1202 "label.successfully_saved_to_file_in_format", new Object[]
1203 { fileName, format.getName() }));
1204 } catch (Exception ex)
1207 ex.printStackTrace();
1210 backupfiles.setWriteSuccess(success);
1211 // do the backup file roll and rename the temp file to actual file
1212 success = backupfiles.rollBackupsAndRenameTempFile();
1219 JvOptionPane.showInternalMessageDialog(this, MessageManager
1220 .formatMessage("label.couldnt_save_file", new Object[]
1222 MessageManager.getString("label.error_saving_file"),
1223 JvOptionPane.WARNING_MESSAGE);
1229 private void warningMessage(String warning, String title)
1231 if (new jalview.util.Platform().isHeadless())
1233 System.err.println("Warning: " + title + "\nWarning: " + warning);
1238 JvOptionPane.showInternalMessageDialog(this, warning, title,
1239 JvOptionPane.WARNING_MESSAGE);
1251 protected void outputText_actionPerformed(ActionEvent e)
1253 FileFormatI fileFormat = FileFormats.getInstance()
1254 .forName(e.getActionCommand());
1255 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1257 if (exportData.getSettings().isCancelled())
1261 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1262 cap.setForInput(null);
1265 FileFormatI format = fileFormat;
1266 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1267 .formatSequences(format, exportData.getAlignment(),
1268 exportData.getOmitHidden(),
1269 exportData.getStartEndPostions(),
1270 viewport.getAlignment().getHiddenColumns()));
1271 Desktop.addInternalFrame(cap, MessageManager
1272 .formatMessage("label.alignment_output_command", new Object[]
1273 { e.getActionCommand() }), 600, 500);
1274 } catch (OutOfMemoryError oom)
1276 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1283 public static AlignmentExportData getAlignmentForExport(
1284 FileFormatI format, AlignViewportI viewport,
1285 AlignExportSettingI exportSettings)
1287 AlignmentI alignmentToExport = null;
1288 AlignExportSettingI settings = exportSettings;
1289 String[] omitHidden = null;
1291 HiddenSequences hiddenSeqs = viewport.getAlignment()
1292 .getHiddenSequences();
1294 alignmentToExport = viewport.getAlignment();
1296 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1297 if (settings == null)
1299 settings = new AlignExportSettings(hasHiddenSeqs,
1300 viewport.hasHiddenColumns(), format);
1302 // settings.isExportAnnotations();
1304 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1306 omitHidden = viewport.getViewAsString(false,
1307 settings.isExportHiddenSequences());
1310 int[] alignmentStartEnd = new int[2];
1311 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1313 alignmentToExport = hiddenSeqs.getFullAlignment();
1317 alignmentToExport = viewport.getAlignment();
1319 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1320 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1321 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1322 omitHidden, alignmentStartEnd, settings);
1333 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1335 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1336 htmlSVG.exportHTML(null);
1340 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1342 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1343 bjs.exportHTML(null);
1346 public void createImageMap(File file, String image)
1348 alignPanel.makePNGImageMap(file, image);
1358 public void createPNG(File f)
1360 alignPanel.makePNG(f);
1370 public void createEPS(File f)
1372 alignPanel.makeEPS(f);
1376 public void createSVG(File f)
1378 alignPanel.makeSVG(f);
1382 public void pageSetup_actionPerformed(ActionEvent e)
1384 PrinterJob printJob = PrinterJob.getPrinterJob();
1385 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1395 public void printMenuItem_actionPerformed(ActionEvent e)
1397 // Putting in a thread avoids Swing painting problems
1398 PrintThread thread = new PrintThread(alignPanel);
1403 public void exportFeatures_actionPerformed(ActionEvent e)
1405 new AnnotationExporter(alignPanel).exportFeatures();
1409 public void exportAnnotations_actionPerformed(ActionEvent e)
1411 new AnnotationExporter(alignPanel).exportAnnotations();
1415 public void associatedData_actionPerformed(ActionEvent e)
1417 // Pick the tree file
1418 JalviewFileChooser chooser = new JalviewFileChooser(
1419 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1420 chooser.setFileView(new JalviewFileView());
1421 chooser.setDialogTitle(
1422 MessageManager.getString("label.load_jalview_annotations"));
1423 chooser.setToolTipText(
1424 MessageManager.getString("label.load_jalview_annotations"));
1426 int value = chooser.showOpenDialog(null);
1428 if (value == JalviewFileChooser.APPROVE_OPTION)
1430 String choice = chooser.getSelectedFile().getPath();
1431 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1432 loadJalviewDataFile(choice, null, null, null);
1438 * Close the current view or all views in the alignment frame. If the frame
1439 * only contains one view then the alignment will be removed from memory.
1441 * @param closeAllTabs
1444 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1446 if (alignPanels != null && alignPanels.size() < 2)
1448 closeAllTabs = true;
1453 if (alignPanels != null)
1457 if (this.isClosed())
1459 // really close all the windows - otherwise wait till
1460 // setClosed(true) is called
1461 for (int i = 0; i < alignPanels.size(); i++)
1463 AlignmentPanel ap = alignPanels.get(i);
1470 closeView(alignPanel);
1477 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1478 * be called recursively, with the frame now in 'closed' state
1480 this.setClosed(true);
1482 } catch (Exception ex)
1484 ex.printStackTrace();
1489 * Close the specified panel and close up tabs appropriately.
1491 * @param panelToClose
1493 public void closeView(AlignmentPanel panelToClose)
1495 int index = tabbedPane.getSelectedIndex();
1496 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1497 alignPanels.remove(panelToClose);
1498 panelToClose.closePanel();
1499 panelToClose = null;
1501 tabbedPane.removeTabAt(closedindex);
1502 tabbedPane.validate();
1504 if (index > closedindex || index == tabbedPane.getTabCount())
1506 // modify currently selected tab index if necessary.
1510 this.tabSelectionChanged(index);
1516 void updateEditMenuBar()
1519 if (viewport.getHistoryList().size() > 0)
1521 undoMenuItem.setEnabled(true);
1522 CommandI command = viewport.getHistoryList().peek();
1523 undoMenuItem.setText(MessageManager
1524 .formatMessage("label.undo_command", new Object[]
1525 { command.getDescription() }));
1529 undoMenuItem.setEnabled(false);
1530 undoMenuItem.setText(MessageManager.getString("action.undo"));
1533 if (viewport.getRedoList().size() > 0)
1535 redoMenuItem.setEnabled(true);
1537 CommandI command = viewport.getRedoList().peek();
1538 redoMenuItem.setText(MessageManager
1539 .formatMessage("label.redo_command", new Object[]
1540 { command.getDescription() }));
1544 redoMenuItem.setEnabled(false);
1545 redoMenuItem.setText(MessageManager.getString("action.redo"));
1550 public void addHistoryItem(CommandI command)
1552 if (command.getSize() > 0)
1554 viewport.addToHistoryList(command);
1555 viewport.clearRedoList();
1556 updateEditMenuBar();
1557 viewport.updateHiddenColumns();
1558 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1559 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1560 // viewport.getColumnSelection()
1561 // .getHiddenColumns().size() > 0);
1567 * @return alignment objects for all views
1569 AlignmentI[] getViewAlignments()
1571 if (alignPanels != null)
1573 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1575 for (AlignmentPanel ap : alignPanels)
1577 als[i++] = ap.av.getAlignment();
1581 if (viewport != null)
1583 return new AlignmentI[] { viewport.getAlignment() };
1595 protected void undoMenuItem_actionPerformed(ActionEvent e)
1597 if (viewport.getHistoryList().isEmpty())
1601 CommandI command = viewport.getHistoryList().pop();
1602 viewport.addToRedoList(command);
1603 command.undoCommand(getViewAlignments());
1605 AlignmentViewport originalSource = getOriginatingSource(command);
1606 updateEditMenuBar();
1608 if (originalSource != null)
1610 if (originalSource != viewport)
1613 "Implementation worry: mismatch of viewport origin for undo");
1615 originalSource.updateHiddenColumns();
1616 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1618 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1619 // viewport.getColumnSelection()
1620 // .getHiddenColumns().size() > 0);
1621 originalSource.firePropertyChange("alignment", null,
1622 originalSource.getAlignment().getSequences());
1633 protected void redoMenuItem_actionPerformed(ActionEvent e)
1635 if (viewport.getRedoList().size() < 1)
1640 CommandI command = viewport.getRedoList().pop();
1641 viewport.addToHistoryList(command);
1642 command.doCommand(getViewAlignments());
1644 AlignmentViewport originalSource = getOriginatingSource(command);
1645 updateEditMenuBar();
1647 if (originalSource != null)
1650 if (originalSource != viewport)
1653 "Implementation worry: mismatch of viewport origin for redo");
1655 originalSource.updateHiddenColumns();
1656 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1658 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1659 // viewport.getColumnSelection()
1660 // .getHiddenColumns().size() > 0);
1661 originalSource.firePropertyChange("alignment", null,
1662 originalSource.getAlignment().getSequences());
1666 AlignmentViewport getOriginatingSource(CommandI command)
1668 AlignmentViewport originalSource = null;
1669 // For sequence removal and addition, we need to fire
1670 // the property change event FROM the viewport where the
1671 // original alignment was altered
1672 AlignmentI al = null;
1673 if (command instanceof EditCommand)
1675 EditCommand editCommand = (EditCommand) command;
1676 al = editCommand.getAlignment();
1677 List<Component> comps = PaintRefresher.components
1678 .get(viewport.getSequenceSetId());
1680 for (Component comp : comps)
1682 if (comp instanceof AlignmentPanel)
1684 if (al == ((AlignmentPanel) comp).av.getAlignment())
1686 originalSource = ((AlignmentPanel) comp).av;
1693 if (originalSource == null)
1695 // The original view is closed, we must validate
1696 // the current view against the closed view first
1699 PaintRefresher.validateSequences(al, viewport.getAlignment());
1702 originalSource = viewport;
1705 return originalSource;
1714 public void moveSelectedSequences(boolean up)
1716 SequenceGroup sg = viewport.getSelectionGroup();
1722 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1723 viewport.getHiddenRepSequences(), up);
1724 alignPanel.paintAlignment(true, false);
1727 synchronized void slideSequences(boolean right, int size)
1729 List<SequenceI> sg = new ArrayList<>();
1730 if (viewport.cursorMode)
1732 sg.add(viewport.getAlignment()
1733 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1735 else if (viewport.getSelectionGroup() != null
1736 && viewport.getSelectionGroup().getSize() != viewport
1737 .getAlignment().getHeight())
1739 sg = viewport.getSelectionGroup()
1740 .getSequences(viewport.getHiddenRepSequences());
1748 List<SequenceI> invertGroup = new ArrayList<>();
1750 for (SequenceI seq : viewport.getAlignment().getSequences())
1752 if (!sg.contains(seq))
1754 invertGroup.add(seq);
1758 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1760 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1761 for (int i = 0; i < invertGroup.size(); i++)
1763 seqs2[i] = invertGroup.get(i);
1766 SlideSequencesCommand ssc;
1769 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1770 viewport.getGapCharacter());
1774 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1775 viewport.getGapCharacter());
1778 int groupAdjustment = 0;
1779 if (ssc.getGapsInsertedBegin() && right)
1781 if (viewport.cursorMode)
1783 alignPanel.getSeqPanel().moveCursor(size, 0);
1787 groupAdjustment = size;
1790 else if (!ssc.getGapsInsertedBegin() && !right)
1792 if (viewport.cursorMode)
1794 alignPanel.getSeqPanel().moveCursor(-size, 0);
1798 groupAdjustment = -size;
1802 if (groupAdjustment != 0)
1804 viewport.getSelectionGroup().setStartRes(
1805 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1806 viewport.getSelectionGroup().setEndRes(
1807 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1811 * just extend the last slide command if compatible; but not if in
1812 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1814 boolean appendHistoryItem = false;
1815 Deque<CommandI> historyList = viewport.getHistoryList();
1816 boolean inSplitFrame = getSplitViewContainer() != null;
1817 if (!inSplitFrame && historyList != null && historyList.size() > 0
1818 && historyList.peek() instanceof SlideSequencesCommand)
1820 appendHistoryItem = ssc.appendSlideCommand(
1821 (SlideSequencesCommand) historyList.peek());
1824 if (!appendHistoryItem)
1826 addHistoryItem(ssc);
1839 protected void copy_actionPerformed(ActionEvent e)
1841 if (viewport.getSelectionGroup() == null)
1845 // TODO: preserve the ordering of displayed alignment annotation in any
1846 // internal paste (particularly sequence associated annotation)
1847 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1848 String[] omitHidden = null;
1850 if (viewport.hasHiddenColumns())
1852 omitHidden = viewport.getViewAsString(true);
1855 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1856 seqs, omitHidden, null);
1858 StringSelection ss = new StringSelection(output);
1862 jalview.gui.Desktop.internalCopy = true;
1863 // Its really worth setting the clipboard contents
1864 // to empty before setting the large StringSelection!!
1865 Toolkit.getDefaultToolkit().getSystemClipboard()
1866 .setContents(new StringSelection(""), null);
1868 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1870 } catch (OutOfMemoryError er)
1872 new OOMWarning("copying region", er);
1876 HiddenColumns hiddenColumns = null;
1877 if (viewport.hasHiddenColumns())
1879 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1880 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1882 // create new HiddenColumns object with copy of hidden regions
1883 // between startRes and endRes, offset by startRes
1884 hiddenColumns = new HiddenColumns(
1885 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1886 hiddenCutoff, hiddenOffset);
1889 Desktop.jalviewClipboard = new Object[] { seqs,
1890 viewport.getAlignment().getDataset(), hiddenColumns };
1891 statusBar.setText(MessageManager.formatMessage(
1892 "label.copied_sequences_to_clipboard", new Object[]
1893 { Integer.valueOf(seqs.length).toString() }));
1903 protected void pasteNew_actionPerformed(ActionEvent e)
1915 protected void pasteThis_actionPerformed(ActionEvent e)
1921 * Paste contents of Jalview clipboard
1923 * @param newAlignment
1924 * true to paste to a new alignment, otherwise add to this.
1926 void paste(boolean newAlignment)
1928 boolean externalPaste = true;
1931 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1932 Transferable contents = c.getContents(this);
1934 if (contents == null)
1943 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1944 if (str.length() < 1)
1949 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1951 } catch (OutOfMemoryError er)
1953 new OOMWarning("Out of memory pasting sequences!!", er);
1957 SequenceI[] sequences;
1958 boolean annotationAdded = false;
1959 AlignmentI alignment = null;
1961 if (Desktop.jalviewClipboard != null)
1963 // The clipboard was filled from within Jalview, we must use the
1965 // And dataset from the copied alignment
1966 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1967 // be doubly sure that we create *new* sequence objects.
1968 sequences = new SequenceI[newseq.length];
1969 for (int i = 0; i < newseq.length; i++)
1971 sequences[i] = new Sequence(newseq[i]);
1973 alignment = new Alignment(sequences);
1974 externalPaste = false;
1978 // parse the clipboard as an alignment.
1979 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1981 sequences = alignment.getSequencesArray();
1985 ArrayList<Integer> newGraphGroups = new ArrayList<>();
1991 if (Desktop.jalviewClipboard != null)
1993 // dataset is inherited
1994 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1998 // new dataset is constructed
1999 alignment.setDataset(null);
2001 alwidth = alignment.getWidth() + 1;
2005 AlignmentI pastedal = alignment; // preserve pasted alignment object
2006 // Add pasted sequences and dataset into existing alignment.
2007 alignment = viewport.getAlignment();
2008 alwidth = alignment.getWidth() + 1;
2009 // decide if we need to import sequences from an existing dataset
2010 boolean importDs = Desktop.jalviewClipboard != null
2011 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2012 // importDs==true instructs us to copy over new dataset sequences from
2013 // an existing alignment
2014 Vector newDs = (importDs) ? new Vector() : null; // used to create
2015 // minimum dataset set
2017 for (int i = 0; i < sequences.length; i++)
2021 newDs.addElement(null);
2023 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2025 if (importDs && ds != null)
2027 if (!newDs.contains(ds))
2029 newDs.setElementAt(ds, i);
2030 ds = new Sequence(ds);
2031 // update with new dataset sequence
2032 sequences[i].setDatasetSequence(ds);
2036 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2041 // copy and derive new dataset sequence
2042 sequences[i] = sequences[i].deriveSequence();
2043 alignment.getDataset()
2044 .addSequence(sequences[i].getDatasetSequence());
2045 // TODO: avoid creation of duplicate dataset sequences with a
2046 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2048 alignment.addSequence(sequences[i]); // merges dataset
2052 newDs.clear(); // tidy up
2054 if (alignment.getAlignmentAnnotation() != null)
2056 for (AlignmentAnnotation alan : alignment
2057 .getAlignmentAnnotation())
2059 if (alan.graphGroup > fgroup)
2061 fgroup = alan.graphGroup;
2065 if (pastedal.getAlignmentAnnotation() != null)
2067 // Add any annotation attached to alignment.
2068 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2069 for (int i = 0; i < alann.length; i++)
2071 annotationAdded = true;
2072 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2074 AlignmentAnnotation newann = new AlignmentAnnotation(
2076 if (newann.graphGroup > -1)
2078 if (newGraphGroups.size() <= newann.graphGroup
2079 || newGraphGroups.get(newann.graphGroup) == null)
2081 for (int q = newGraphGroups
2082 .size(); q <= newann.graphGroup; q++)
2084 newGraphGroups.add(q, null);
2086 newGraphGroups.set(newann.graphGroup,
2087 new Integer(++fgroup));
2089 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2093 newann.padAnnotation(alwidth);
2094 alignment.addAnnotation(newann);
2104 addHistoryItem(new EditCommand(
2105 MessageManager.getString("label.add_sequences"),
2106 Action.PASTE, sequences, 0, alignment.getWidth(),
2109 // Add any annotations attached to sequences
2110 for (int i = 0; i < sequences.length; i++)
2112 if (sequences[i].getAnnotation() != null)
2114 AlignmentAnnotation newann;
2115 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2117 annotationAdded = true;
2118 newann = sequences[i].getAnnotation()[a];
2119 newann.adjustForAlignment();
2120 newann.padAnnotation(alwidth);
2121 if (newann.graphGroup > -1)
2123 if (newann.graphGroup > -1)
2125 if (newGraphGroups.size() <= newann.graphGroup
2126 || newGraphGroups.get(newann.graphGroup) == null)
2128 for (int q = newGraphGroups
2129 .size(); q <= newann.graphGroup; q++)
2131 newGraphGroups.add(q, null);
2133 newGraphGroups.set(newann.graphGroup,
2134 new Integer(++fgroup));
2136 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2140 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2144 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2152 // propagate alignment changed.
2153 viewport.getRanges().setEndSeq(alignment.getHeight());
2154 if (annotationAdded)
2156 // Duplicate sequence annotation in all views.
2157 AlignmentI[] alview = this.getViewAlignments();
2158 for (int i = 0; i < sequences.length; i++)
2160 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2165 for (int avnum = 0; avnum < alview.length; avnum++)
2167 if (alview[avnum] != alignment)
2169 // duplicate in a view other than the one with input focus
2170 int avwidth = alview[avnum].getWidth() + 1;
2171 // this relies on sann being preserved after we
2172 // modify the sequence's annotation array for each duplication
2173 for (int a = 0; a < sann.length; a++)
2175 AlignmentAnnotation newann = new AlignmentAnnotation(
2177 sequences[i].addAlignmentAnnotation(newann);
2178 newann.padAnnotation(avwidth);
2179 alview[avnum].addAnnotation(newann); // annotation was
2180 // duplicated earlier
2181 // TODO JAL-1145 graphGroups are not updated for sequence
2182 // annotation added to several views. This may cause
2184 alview[avnum].setAnnotationIndex(newann, a);
2189 buildSortByAnnotationScoresMenu();
2191 viewport.firePropertyChange("alignment", null,
2192 alignment.getSequences());
2193 if (alignPanels != null)
2195 for (AlignmentPanel ap : alignPanels)
2197 ap.validateAnnotationDimensions(false);
2202 alignPanel.validateAnnotationDimensions(false);
2208 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2210 String newtitle = new String("Copied sequences");
2212 if (Desktop.jalviewClipboard != null
2213 && Desktop.jalviewClipboard[2] != null)
2215 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2216 af.viewport.setHiddenColumns(hc);
2219 // >>>This is a fix for the moment, until a better solution is
2221 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2222 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2223 .getFeatureRenderer());
2225 // TODO: maintain provenance of an alignment, rather than just make the
2226 // title a concatenation of operations.
2229 if (title.startsWith("Copied sequences"))
2235 newtitle = newtitle.concat("- from " + title);
2240 newtitle = new String("Pasted sequences");
2243 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2248 } catch (Exception ex)
2250 ex.printStackTrace();
2251 System.out.println("Exception whilst pasting: " + ex);
2252 // could be anything being pasted in here
2258 protected void expand_newalign(ActionEvent e)
2262 AlignmentI alignment = AlignmentUtils
2263 .expandContext(getViewport().getAlignment(), -1);
2264 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2266 String newtitle = new String("Flanking alignment");
2268 if (Desktop.jalviewClipboard != null
2269 && Desktop.jalviewClipboard[2] != null)
2271 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2272 af.viewport.setHiddenColumns(hc);
2275 // >>>This is a fix for the moment, until a better solution is
2277 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2278 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2279 .getFeatureRenderer());
2281 // TODO: maintain provenance of an alignment, rather than just make the
2282 // title a concatenation of operations.
2284 if (title.startsWith("Copied sequences"))
2290 newtitle = newtitle.concat("- from " + title);
2294 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2296 } catch (Exception ex)
2298 ex.printStackTrace();
2299 System.out.println("Exception whilst pasting: " + ex);
2300 // could be anything being pasted in here
2301 } catch (OutOfMemoryError oom)
2303 new OOMWarning("Viewing flanking region of alignment", oom);
2314 protected void cut_actionPerformed(ActionEvent e)
2316 copy_actionPerformed(null);
2317 delete_actionPerformed(null);
2327 protected void delete_actionPerformed(ActionEvent evt)
2330 SequenceGroup sg = viewport.getSelectionGroup();
2337 * If the cut affects all sequences, warn, remove highlighted columns
2339 if (sg.getSize() == viewport.getAlignment().getHeight())
2341 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2342 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2343 if (isEntireAlignWidth)
2345 int confirm = JvOptionPane.showConfirmDialog(this,
2346 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2347 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2348 JvOptionPane.OK_CANCEL_OPTION);
2350 if (confirm == JvOptionPane.CANCEL_OPTION
2351 || confirm == JvOptionPane.CLOSED_OPTION)
2356 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2357 sg.getEndRes() + 1);
2359 SequenceI[] cut = sg.getSequences()
2360 .toArray(new SequenceI[sg.getSize()]);
2362 addHistoryItem(new EditCommand(
2363 MessageManager.getString("label.cut_sequences"), Action.CUT,
2364 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2365 viewport.getAlignment()));
2367 viewport.setSelectionGroup(null);
2368 viewport.sendSelection();
2369 viewport.getAlignment().deleteGroup(sg);
2371 viewport.firePropertyChange("alignment", null,
2372 viewport.getAlignment().getSequences());
2373 if (viewport.getAlignment().getHeight() < 1)
2377 this.setClosed(true);
2378 } catch (Exception ex)
2391 protected void deleteGroups_actionPerformed(ActionEvent e)
2393 if (avc.deleteGroups())
2395 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2396 alignPanel.updateAnnotation();
2397 alignPanel.paintAlignment(true, true);
2408 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2410 SequenceGroup sg = new SequenceGroup();
2412 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2414 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2417 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2418 viewport.setSelectionGroup(sg);
2419 viewport.sendSelection();
2420 // JAL-2034 - should delegate to
2421 // alignPanel to decide if overview needs
2423 alignPanel.paintAlignment(false, false);
2424 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2434 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2436 if (viewport.cursorMode)
2438 alignPanel.getSeqPanel().keyboardNo1 = null;
2439 alignPanel.getSeqPanel().keyboardNo2 = null;
2441 viewport.setSelectionGroup(null);
2442 viewport.getColumnSelection().clear();
2443 viewport.setSelectionGroup(null);
2444 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2445 // JAL-2034 - should delegate to
2446 // alignPanel to decide if overview needs
2448 alignPanel.paintAlignment(false, false);
2449 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2450 viewport.sendSelection();
2460 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2462 SequenceGroup sg = viewport.getSelectionGroup();
2466 selectAllSequenceMenuItem_actionPerformed(null);
2471 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2473 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2475 // JAL-2034 - should delegate to
2476 // alignPanel to decide if overview needs
2479 alignPanel.paintAlignment(true, false);
2480 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2481 viewport.sendSelection();
2485 public void invertColSel_actionPerformed(ActionEvent e)
2487 viewport.invertColumnSelection();
2488 alignPanel.paintAlignment(true, false);
2489 viewport.sendSelection();
2499 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2501 trimAlignment(true);
2511 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2513 trimAlignment(false);
2516 void trimAlignment(boolean trimLeft)
2518 ColumnSelection colSel = viewport.getColumnSelection();
2521 if (!colSel.isEmpty())
2525 column = colSel.getMin();
2529 column = colSel.getMax();
2533 if (viewport.getSelectionGroup() != null)
2535 seqs = viewport.getSelectionGroup()
2536 .getSequencesAsArray(viewport.getHiddenRepSequences());
2540 seqs = viewport.getAlignment().getSequencesArray();
2543 TrimRegionCommand trimRegion;
2546 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2547 column, viewport.getAlignment());
2548 viewport.getRanges().setStartRes(0);
2552 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2553 column, viewport.getAlignment());
2556 statusBar.setText(MessageManager
2557 .formatMessage("label.removed_columns", new String[]
2558 { Integer.valueOf(trimRegion.getSize()).toString() }));
2560 addHistoryItem(trimRegion);
2562 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2564 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2565 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2567 viewport.getAlignment().deleteGroup(sg);
2571 viewport.firePropertyChange("alignment", null,
2572 viewport.getAlignment().getSequences());
2583 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2585 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2588 if (viewport.getSelectionGroup() != null)
2590 seqs = viewport.getSelectionGroup()
2591 .getSequencesAsArray(viewport.getHiddenRepSequences());
2592 start = viewport.getSelectionGroup().getStartRes();
2593 end = viewport.getSelectionGroup().getEndRes();
2597 seqs = viewport.getAlignment().getSequencesArray();
2600 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2601 "Remove Gapped Columns", seqs, start, end,
2602 viewport.getAlignment());
2604 addHistoryItem(removeGapCols);
2606 statusBar.setText(MessageManager
2607 .formatMessage("label.removed_empty_columns", new Object[]
2608 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2610 // This is to maintain viewport position on first residue
2611 // of first sequence
2612 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2613 ViewportRanges ranges = viewport.getRanges();
2614 int startRes = seq.findPosition(ranges.getStartRes());
2615 // ShiftList shifts;
2616 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2617 // edit.alColumnChanges=shifts.getInverse();
2618 // if (viewport.hasHiddenColumns)
2619 // viewport.getColumnSelection().compensateForEdits(shifts);
2620 ranges.setStartRes(seq.findIndex(startRes) - 1);
2621 viewport.firePropertyChange("alignment", null,
2622 viewport.getAlignment().getSequences());
2633 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2635 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2638 if (viewport.getSelectionGroup() != null)
2640 seqs = viewport.getSelectionGroup()
2641 .getSequencesAsArray(viewport.getHiddenRepSequences());
2642 start = viewport.getSelectionGroup().getStartRes();
2643 end = viewport.getSelectionGroup().getEndRes();
2647 seqs = viewport.getAlignment().getSequencesArray();
2650 // This is to maintain viewport position on first residue
2651 // of first sequence
2652 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2653 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2655 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2656 viewport.getAlignment()));
2658 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2660 viewport.firePropertyChange("alignment", null,
2661 viewport.getAlignment().getSequences());
2672 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2674 viewport.setPadGaps(padGapsMenuitem.isSelected());
2675 viewport.firePropertyChange("alignment", null,
2676 viewport.getAlignment().getSequences());
2686 public void findMenuItem_actionPerformed(ActionEvent e)
2692 * Create a new view of the current alignment.
2695 public void newView_actionPerformed(ActionEvent e)
2697 newView(null, true);
2701 * Creates and shows a new view of the current alignment.
2704 * title of newly created view; if null, one will be generated
2705 * @param copyAnnotation
2706 * if true then duplicate all annnotation, groups and settings
2707 * @return new alignment panel, already displayed.
2709 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2712 * Create a new AlignmentPanel (with its own, new Viewport)
2714 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2715 if (!copyAnnotation)
2718 * remove all groups and annotation except for the automatic stuff
2720 newap.av.getAlignment().deleteAllGroups();
2721 newap.av.getAlignment().deleteAllAnnotations(false);
2724 newap.av.setGatherViewsHere(false);
2726 if (viewport.viewName == null)
2728 viewport.viewName = MessageManager
2729 .getString("label.view_name_original");
2733 * Views share the same edits undo and redo stacks
2735 newap.av.setHistoryList(viewport.getHistoryList());
2736 newap.av.setRedoList(viewport.getRedoList());
2739 * Views share the same mappings; need to deregister any new mappings
2740 * created by copyAlignPanel, and register the new reference to the shared
2743 newap.av.replaceMappings(viewport.getAlignment());
2746 * start up cDNA consensus (if applicable) now mappings are in place
2748 if (newap.av.initComplementConsensus())
2750 newap.refresh(true); // adjust layout of annotations
2753 newap.av.viewName = getNewViewName(viewTitle);
2755 addAlignmentPanel(newap, true);
2756 newap.alignmentChanged();
2758 if (alignPanels.size() == 2)
2760 viewport.setGatherViewsHere(true);
2762 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2767 * Make a new name for the view, ensuring it is unique within the current
2768 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2769 * these now use viewId. Unique view names are still desirable for usability.)
2774 protected String getNewViewName(String viewTitle)
2776 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2777 boolean addFirstIndex = false;
2778 if (viewTitle == null || viewTitle.trim().length() == 0)
2780 viewTitle = MessageManager.getString("action.view");
2781 addFirstIndex = true;
2785 index = 1;// we count from 1 if given a specific name
2787 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2789 List<Component> comps = PaintRefresher.components
2790 .get(viewport.getSequenceSetId());
2792 List<String> existingNames = getExistingViewNames(comps);
2794 while (existingNames.contains(newViewName))
2796 newViewName = viewTitle + " " + (++index);
2802 * Returns a list of distinct view names found in the given list of
2803 * components. View names are held on the viewport of an AlignmentPanel.
2808 protected List<String> getExistingViewNames(List<Component> comps)
2810 List<String> existingNames = new ArrayList<>();
2811 for (Component comp : comps)
2813 if (comp instanceof AlignmentPanel)
2815 AlignmentPanel ap = (AlignmentPanel) comp;
2816 if (!existingNames.contains(ap.av.viewName))
2818 existingNames.add(ap.av.viewName);
2822 return existingNames;
2826 * Explode tabbed views into separate windows.
2829 public void expandViews_actionPerformed(ActionEvent e)
2831 Desktop.explodeViews(this);
2835 * Gather views in separate windows back into a tabbed presentation.
2838 public void gatherViews_actionPerformed(ActionEvent e)
2840 Desktop.instance.gatherViews(this);
2850 public void font_actionPerformed(ActionEvent e)
2852 new FontChooser(alignPanel);
2862 protected void seqLimit_actionPerformed(ActionEvent e)
2864 viewport.setShowJVSuffix(seqLimits.isSelected());
2866 alignPanel.getIdPanel().getIdCanvas()
2867 .setPreferredSize(alignPanel.calculateIdWidth());
2868 alignPanel.paintAlignment(true, false);
2872 public void idRightAlign_actionPerformed(ActionEvent e)
2874 viewport.setRightAlignIds(idRightAlign.isSelected());
2875 alignPanel.paintAlignment(false, false);
2879 public void centreColumnLabels_actionPerformed(ActionEvent e)
2881 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2882 alignPanel.paintAlignment(false, false);
2888 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2891 protected void followHighlight_actionPerformed()
2894 * Set the 'follow' flag on the Viewport (and scroll to position if now
2897 final boolean state = this.followHighlightMenuItem.getState();
2898 viewport.setFollowHighlight(state);
2901 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2912 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2914 viewport.setColourText(colourTextMenuItem.isSelected());
2915 alignPanel.paintAlignment(false, false);
2925 public void wrapMenuItem_actionPerformed(ActionEvent e)
2927 scaleAbove.setVisible(wrapMenuItem.isSelected());
2928 scaleLeft.setVisible(wrapMenuItem.isSelected());
2929 scaleRight.setVisible(wrapMenuItem.isSelected());
2930 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2931 alignPanel.updateLayout();
2935 public void showAllSeqs_actionPerformed(ActionEvent e)
2937 viewport.showAllHiddenSeqs();
2941 public void showAllColumns_actionPerformed(ActionEvent e)
2943 viewport.showAllHiddenColumns();
2944 alignPanel.paintAlignment(true, true);
2945 viewport.sendSelection();
2949 public void hideSelSequences_actionPerformed(ActionEvent e)
2951 viewport.hideAllSelectedSeqs();
2955 * called by key handler and the hide all/show all menu items
2960 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2963 boolean hide = false;
2964 SequenceGroup sg = viewport.getSelectionGroup();
2965 if (!toggleSeqs && !toggleCols)
2967 // Hide everything by the current selection - this is a hack - we do the
2968 // invert and then hide
2969 // first check that there will be visible columns after the invert.
2970 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2971 && sg.getStartRes() <= sg.getEndRes()))
2973 // now invert the sequence set, if required - empty selection implies
2974 // that no hiding is required.
2977 invertSequenceMenuItem_actionPerformed(null);
2978 sg = viewport.getSelectionGroup();
2982 viewport.expandColSelection(sg, true);
2983 // finally invert the column selection and get the new sequence
2985 invertColSel_actionPerformed(null);
2992 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2994 hideSelSequences_actionPerformed(null);
2997 else if (!(toggleCols && viewport.hasSelectedColumns()))
2999 showAllSeqs_actionPerformed(null);
3005 if (viewport.hasSelectedColumns())
3007 hideSelColumns_actionPerformed(null);
3010 viewport.setSelectionGroup(sg);
3015 showAllColumns_actionPerformed(null);
3024 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3025 * event.ActionEvent)
3028 public void hideAllButSelection_actionPerformed(ActionEvent e)
3030 toggleHiddenRegions(false, false);
3031 viewport.sendSelection();
3038 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3042 public void hideAllSelection_actionPerformed(ActionEvent e)
3044 SequenceGroup sg = viewport.getSelectionGroup();
3045 viewport.expandColSelection(sg, false);
3046 viewport.hideAllSelectedSeqs();
3047 viewport.hideSelectedColumns();
3048 alignPanel.paintAlignment(true, true);
3049 viewport.sendSelection();
3056 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3060 public void showAllhidden_actionPerformed(ActionEvent e)
3062 viewport.showAllHiddenColumns();
3063 viewport.showAllHiddenSeqs();
3064 alignPanel.paintAlignment(true, true);
3065 viewport.sendSelection();
3069 public void hideSelColumns_actionPerformed(ActionEvent e)
3071 viewport.hideSelectedColumns();
3072 alignPanel.paintAlignment(true, true);
3073 viewport.sendSelection();
3077 public void hiddenMarkers_actionPerformed(ActionEvent e)
3079 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3090 protected void scaleAbove_actionPerformed(ActionEvent e)
3092 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3093 // TODO: do we actually need to update overview for scale above change ?
3094 alignPanel.paintAlignment(true, false);
3104 protected void scaleLeft_actionPerformed(ActionEvent e)
3106 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3107 alignPanel.paintAlignment(true, false);
3117 protected void scaleRight_actionPerformed(ActionEvent e)
3119 viewport.setScaleRightWrapped(scaleRight.isSelected());
3120 alignPanel.paintAlignment(true, false);
3130 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3132 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3133 alignPanel.paintAlignment(false, false);
3143 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3145 viewport.setShowText(viewTextMenuItem.isSelected());
3146 alignPanel.paintAlignment(false, false);
3156 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3158 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3159 alignPanel.paintAlignment(false, false);
3162 public FeatureSettings featureSettings;
3165 public FeatureSettingsControllerI getFeatureSettingsUI()
3167 return featureSettings;
3171 public void featureSettings_actionPerformed(ActionEvent e)
3173 if (featureSettings != null)
3175 featureSettings.close();
3176 featureSettings = null;
3178 if (!showSeqFeatures.isSelected())
3180 // make sure features are actually displayed
3181 showSeqFeatures.setSelected(true);
3182 showSeqFeatures_actionPerformed(null);
3184 featureSettings = new FeatureSettings(this);
3188 * Set or clear 'Show Sequence Features'
3194 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3196 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3197 alignPanel.paintAlignment(true, true);
3201 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3202 * the annotations panel as a whole.
3204 * The options to show/hide all annotations should be enabled when the panel
3205 * is shown, and disabled when the panel is hidden.
3210 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3212 final boolean setVisible = annotationPanelMenuItem.isSelected();
3213 viewport.setShowAnnotation(setVisible);
3214 this.showAllSeqAnnotations.setEnabled(setVisible);
3215 this.hideAllSeqAnnotations.setEnabled(setVisible);
3216 this.showAllAlAnnotations.setEnabled(setVisible);
3217 this.hideAllAlAnnotations.setEnabled(setVisible);
3218 alignPanel.updateLayout();
3222 public void alignmentProperties()
3224 JEditorPane editPane = new JEditorPane("text/html", "");
3225 editPane.setEditable(false);
3226 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3229 MessageManager.formatMessage("label.html_content", new Object[]
3230 { contents.toString() }));
3231 JInternalFrame frame = new JInternalFrame();
3232 frame.getContentPane().add(new JScrollPane(editPane));
3234 Desktop.addInternalFrame(frame, MessageManager
3235 .formatMessage("label.alignment_properties", new Object[]
3236 { getTitle() }), 500, 400);
3246 public void overviewMenuItem_actionPerformed(ActionEvent e)
3248 if (alignPanel.overviewPanel != null)
3253 JInternalFrame frame = new JInternalFrame();
3254 final OverviewPanel overview = new OverviewPanel(alignPanel);
3255 frame.setContentPane(overview);
3256 Desktop.addInternalFrame(frame, MessageManager
3257 .formatMessage("label.overview_params", new Object[]
3258 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3261 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3262 frame.addInternalFrameListener(
3263 new javax.swing.event.InternalFrameAdapter()
3266 public void internalFrameClosed(
3267 javax.swing.event.InternalFrameEvent evt)
3270 alignPanel.setOverviewPanel(null);
3273 if (getKeyListeners().length > 0)
3275 frame.addKeyListener(getKeyListeners()[0]);
3278 alignPanel.setOverviewPanel(overview);
3282 public void textColour_actionPerformed()
3284 new TextColourChooser().chooseColour(alignPanel, null);
3288 * public void covariationColour_actionPerformed() {
3290 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3294 public void annotationColour_actionPerformed()
3296 new AnnotationColourChooser(viewport, alignPanel);
3300 public void annotationColumn_actionPerformed(ActionEvent e)
3302 new AnnotationColumnChooser(viewport, alignPanel);
3306 * Action on the user checking or unchecking the option to apply the selected
3307 * colour scheme to all groups. If unchecked, groups may have their own
3308 * independent colour schemes.
3313 public void applyToAllGroups_actionPerformed(boolean selected)
3315 viewport.setColourAppliesToAllGroups(selected);
3319 * Action on user selecting a colour from the colour menu
3322 * the name (not the menu item label!) of the colour scheme
3325 public void changeColour_actionPerformed(String name)
3328 * 'User Defined' opens a panel to configure or load a
3329 * user-defined colour scheme
3331 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3333 new UserDefinedColours(alignPanel);
3338 * otherwise set the chosen colour scheme (or null for 'None')
3340 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3341 viewport.getAlignment(), viewport.getHiddenRepSequences());
3346 * Actions on setting or changing the alignment colour scheme
3351 public void changeColour(ColourSchemeI cs)
3353 // TODO: pull up to controller method
3354 ColourMenuHelper.setColourSelected(colourMenu, cs);
3356 viewport.setGlobalColourScheme(cs);
3358 alignPanel.paintAlignment(true, true);
3362 * Show the PID threshold slider panel
3365 protected void modifyPID_actionPerformed()
3367 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3368 alignPanel.getViewName());
3369 SliderPanel.showPIDSlider();
3373 * Show the Conservation slider panel
3376 protected void modifyConservation_actionPerformed()
3378 SliderPanel.setConservationSlider(alignPanel,
3379 viewport.getResidueShading(), alignPanel.getViewName());
3380 SliderPanel.showConservationSlider();
3384 * Action on selecting or deselecting (Colour) By Conservation
3387 public void conservationMenuItem_actionPerformed(boolean selected)
3389 modifyConservation.setEnabled(selected);
3390 viewport.setConservationSelected(selected);
3391 viewport.getResidueShading().setConservationApplied(selected);
3393 changeColour(viewport.getGlobalColourScheme());
3396 modifyConservation_actionPerformed();
3400 SliderPanel.hideConservationSlider();
3405 * Action on selecting or deselecting (Colour) Above PID Threshold
3408 public void abovePIDThreshold_actionPerformed(boolean selected)
3410 modifyPID.setEnabled(selected);
3411 viewport.setAbovePIDThreshold(selected);
3414 viewport.getResidueShading().setThreshold(0,
3415 viewport.isIgnoreGapsConsensus());
3418 changeColour(viewport.getGlobalColourScheme());
3421 modifyPID_actionPerformed();
3425 SliderPanel.hidePIDSlider();
3436 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3438 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3439 AlignmentSorter.sortByPID(viewport.getAlignment(),
3440 viewport.getAlignment().getSequenceAt(0));
3441 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3442 viewport.getAlignment()));
3443 alignPanel.paintAlignment(true, false);
3453 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3455 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3456 AlignmentSorter.sortByID(viewport.getAlignment());
3458 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3459 alignPanel.paintAlignment(true, false);
3469 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3471 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3472 AlignmentSorter.sortByLength(viewport.getAlignment());
3473 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3474 viewport.getAlignment()));
3475 alignPanel.paintAlignment(true, false);
3485 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3487 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3488 AlignmentSorter.sortByGroup(viewport.getAlignment());
3489 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3490 viewport.getAlignment()));
3492 alignPanel.paintAlignment(true, false);
3502 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3504 new RedundancyPanel(alignPanel, this);
3514 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3516 if ((viewport.getSelectionGroup() == null)
3517 || (viewport.getSelectionGroup().getSize() < 2))
3519 JvOptionPane.showInternalMessageDialog(this,
3520 MessageManager.getString(
3521 "label.you_must_select_least_two_sequences"),
3522 MessageManager.getString("label.invalid_selection"),
3523 JvOptionPane.WARNING_MESSAGE);
3527 JInternalFrame frame = new JInternalFrame();
3528 frame.setContentPane(new PairwiseAlignPanel(viewport));
3529 Desktop.addInternalFrame(frame,
3530 MessageManager.getString("action.pairwise_alignment"), 600,
3536 public void autoCalculate_actionPerformed(ActionEvent e)
3538 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3539 if (viewport.autoCalculateConsensus)
3541 viewport.firePropertyChange("alignment", null,
3542 viewport.getAlignment().getSequences());
3547 public void sortByTreeOption_actionPerformed(ActionEvent e)
3549 viewport.sortByTree = sortByTree.isSelected();
3553 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3555 viewport.followSelection = listenToViewSelections.isSelected();
3559 * Constructs a tree panel and adds it to the desktop
3562 * tree type (NJ or AV)
3564 * name of score model used to compute the tree
3566 * parameters for the distance or similarity calculation
3568 void newTreePanel(String type, String modelName,
3569 SimilarityParamsI options)
3571 String frameTitle = "";
3574 boolean onSelection = false;
3575 if (viewport.getSelectionGroup() != null
3576 && viewport.getSelectionGroup().getSize() > 0)
3578 SequenceGroup sg = viewport.getSelectionGroup();
3580 /* Decide if the selection is a column region */
3581 for (SequenceI _s : sg.getSequences())
3583 if (_s.getLength() < sg.getEndRes())
3585 JvOptionPane.showMessageDialog(Desktop.desktop,
3586 MessageManager.getString(
3587 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3588 MessageManager.getString(
3589 "label.sequences_selection_not_aligned"),
3590 JvOptionPane.WARNING_MESSAGE);
3599 if (viewport.getAlignment().getHeight() < 2)
3605 tp = new TreePanel(alignPanel, type, modelName, options);
3606 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3608 frameTitle += " from ";
3610 if (viewport.viewName != null)
3612 frameTitle += viewport.viewName + " of ";
3615 frameTitle += this.title;
3617 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3628 public void addSortByOrderMenuItem(String title,
3629 final AlignmentOrder order)
3631 final JMenuItem item = new JMenuItem(MessageManager
3632 .formatMessage("action.by_title_param", new Object[]
3635 item.addActionListener(new java.awt.event.ActionListener()
3638 public void actionPerformed(ActionEvent e)
3640 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3642 // TODO: JBPNote - have to map order entries to curent SequenceI
3644 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3646 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3647 viewport.getAlignment()));
3649 alignPanel.paintAlignment(true, false);
3655 * Add a new sort by annotation score menu item
3658 * the menu to add the option to
3660 * the label used to retrieve scores for each sequence on the
3663 public void addSortByAnnotScoreMenuItem(JMenu sort,
3664 final String scoreLabel)
3666 final JMenuItem item = new JMenuItem(scoreLabel);
3668 item.addActionListener(new java.awt.event.ActionListener()
3671 public void actionPerformed(ActionEvent e)
3673 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3674 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3675 viewport.getAlignment());// ,viewport.getSelectionGroup());
3676 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3677 viewport.getAlignment()));
3678 alignPanel.paintAlignment(true, false);
3684 * last hash for alignment's annotation array - used to minimise cost of
3687 protected int _annotationScoreVectorHash;
3690 * search the alignment and rebuild the sort by annotation score submenu the
3691 * last alignment annotation vector hash is stored to minimize cost of
3692 * rebuilding in subsequence calls.
3696 public void buildSortByAnnotationScoresMenu()
3698 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3703 if (viewport.getAlignment().getAlignmentAnnotation()
3704 .hashCode() != _annotationScoreVectorHash)
3706 sortByAnnotScore.removeAll();
3707 // almost certainly a quicker way to do this - but we keep it simple
3708 Hashtable scoreSorts = new Hashtable();
3709 AlignmentAnnotation aann[];
3710 for (SequenceI sqa : viewport.getAlignment().getSequences())
3712 aann = sqa.getAnnotation();
3713 for (int i = 0; aann != null && i < aann.length; i++)
3715 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3717 scoreSorts.put(aann[i].label, aann[i].label);
3721 Enumeration labels = scoreSorts.keys();
3722 while (labels.hasMoreElements())
3724 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3725 (String) labels.nextElement());
3727 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3730 _annotationScoreVectorHash = viewport.getAlignment()
3731 .getAlignmentAnnotation().hashCode();
3736 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3737 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3738 * call. Listeners are added to remove the menu item when the treePanel is
3739 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3743 public void buildTreeSortMenu()
3745 sortByTreeMenu.removeAll();
3747 List<Component> comps = PaintRefresher.components
3748 .get(viewport.getSequenceSetId());
3749 List<TreePanel> treePanels = new ArrayList<>();
3750 for (Component comp : comps)
3752 if (comp instanceof TreePanel)
3754 treePanels.add((TreePanel) comp);
3758 if (treePanels.size() < 1)
3760 sortByTreeMenu.setVisible(false);
3764 sortByTreeMenu.setVisible(true);
3766 for (final TreePanel tp : treePanels)
3768 final JMenuItem item = new JMenuItem(tp.getTitle());
3769 item.addActionListener(new java.awt.event.ActionListener()
3772 public void actionPerformed(ActionEvent e)
3774 tp.sortByTree_actionPerformed();
3775 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3780 sortByTreeMenu.add(item);
3784 public boolean sortBy(AlignmentOrder alorder, String undoname)
3786 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3787 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3788 if (undoname != null)
3790 addHistoryItem(new OrderCommand(undoname, oldOrder,
3791 viewport.getAlignment()));
3793 alignPanel.paintAlignment(true, false);
3798 * Work out whether the whole set of sequences or just the selected set will
3799 * be submitted for multiple alignment.
3802 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3804 // Now, check we have enough sequences
3805 AlignmentView msa = null;
3807 if ((viewport.getSelectionGroup() != null)
3808 && (viewport.getSelectionGroup().getSize() > 1))
3810 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3811 // some common interface!
3813 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3814 * SequenceI[sz = seqs.getSize(false)];
3816 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3817 * seqs.getSequenceAt(i); }
3819 msa = viewport.getAlignmentView(true);
3821 else if (viewport.getSelectionGroup() != null
3822 && viewport.getSelectionGroup().getSize() == 1)
3824 int option = JvOptionPane.showConfirmDialog(this,
3825 MessageManager.getString("warn.oneseq_msainput_selection"),
3826 MessageManager.getString("label.invalid_selection"),
3827 JvOptionPane.OK_CANCEL_OPTION);
3828 if (option == JvOptionPane.OK_OPTION)
3830 msa = viewport.getAlignmentView(false);
3835 msa = viewport.getAlignmentView(false);
3841 * Decides what is submitted to a secondary structure prediction service: the
3842 * first sequence in the alignment, or in the current selection, or, if the
3843 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3844 * region or the whole alignment. (where the first sequence in the set is the
3845 * one that the prediction will be for).
3847 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3849 AlignmentView seqs = null;
3851 if ((viewport.getSelectionGroup() != null)
3852 && (viewport.getSelectionGroup().getSize() > 0))
3854 seqs = viewport.getAlignmentView(true);
3858 seqs = viewport.getAlignmentView(false);
3860 // limit sequences - JBPNote in future - could spawn multiple prediction
3862 // TODO: viewport.getAlignment().isAligned is a global state - the local
3863 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3864 if (!viewport.getAlignment().isAligned(false))
3866 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3867 // TODO: if seqs.getSequences().length>1 then should really have warned
3881 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3883 // Pick the tree file
3884 JalviewFileChooser chooser = new JalviewFileChooser(
3885 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3886 chooser.setFileView(new JalviewFileView());
3887 chooser.setDialogTitle(
3888 MessageManager.getString("label.select_newick_like_tree_file"));
3889 chooser.setToolTipText(
3890 MessageManager.getString("label.load_tree_file"));
3892 int value = chooser.showOpenDialog(null);
3894 if (value == JalviewFileChooser.APPROVE_OPTION)
3896 String filePath = chooser.getSelectedFile().getPath();
3897 Cache.setProperty("LAST_DIRECTORY", filePath);
3898 NewickFile fin = null;
3901 fin = new NewickFile(filePath, DataSourceType.FILE);
3902 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3903 } catch (Exception ex)
3905 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3906 MessageManager.getString("label.problem_reading_tree_file"),
3907 JvOptionPane.WARNING_MESSAGE);
3908 ex.printStackTrace();
3910 if (fin != null && fin.hasWarningMessage())
3912 JvOptionPane.showMessageDialog(Desktop.desktop,
3913 fin.getWarningMessage(),
3915 .getString("label.possible_problem_with_tree_file"),
3916 JvOptionPane.WARNING_MESSAGE);
3921 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3923 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3926 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3927 int h, int x, int y)
3929 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3933 * Add a treeviewer for the tree extracted from a Newick file object to the
3934 * current alignment view
3941 * Associated alignment input data (or null)
3950 * @return TreePanel handle
3952 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3953 AlignmentView input, int w, int h, int x, int y)
3955 TreePanel tp = null;
3961 if (nf.getTree() != null)
3963 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3969 tp.setLocation(x, y);
3972 Desktop.addInternalFrame(tp, treeTitle, w, h);
3974 } catch (Exception ex)
3976 ex.printStackTrace();
3982 private boolean buildingMenu = false;
3985 * Generates menu items and listener event actions for web service clients
3988 public void BuildWebServiceMenu()
3990 while (buildingMenu)
3994 System.err.println("Waiting for building menu to finish.");
3996 } catch (Exception e)
4000 final AlignFrame me = this;
4001 buildingMenu = true;
4002 new Thread(new Runnable()
4007 final List<JMenuItem> legacyItems = new ArrayList<>();
4010 // System.err.println("Building ws menu again "
4011 // + Thread.currentThread());
4012 // TODO: add support for context dependent disabling of services based
4014 // alignment and current selection
4015 // TODO: add additional serviceHandle parameter to specify abstract
4017 // class independently of AbstractName
4018 // TODO: add in rediscovery GUI function to restart discoverer
4019 // TODO: group services by location as well as function and/or
4021 // object broker mechanism.
4022 final Vector<JMenu> wsmenu = new Vector<>();
4023 final IProgressIndicator af = me;
4026 * do not i18n these strings - they are hard-coded in class
4027 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4028 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4030 final JMenu msawsmenu = new JMenu("Alignment");
4031 final JMenu secstrmenu = new JMenu(
4032 "Secondary Structure Prediction");
4033 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4034 final JMenu analymenu = new JMenu("Analysis");
4035 final JMenu dismenu = new JMenu("Protein Disorder");
4036 // JAL-940 - only show secondary structure prediction services from
4037 // the legacy server
4038 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4040 Discoverer.services != null && (Discoverer.services.size() > 0))
4042 // TODO: refactor to allow list of AbstractName/Handler bindings to
4044 // stored or retrieved from elsewhere
4045 // No MSAWS used any more:
4046 // Vector msaws = null; // (Vector)
4047 // Discoverer.services.get("MsaWS");
4048 Vector secstrpr = (Vector) Discoverer.services
4050 if (secstrpr != null)
4052 // Add any secondary structure prediction services
4053 for (int i = 0, j = secstrpr.size(); i < j; i++)
4055 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4057 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4058 .getServiceClient(sh);
4059 int p = secstrmenu.getItemCount();
4060 impl.attachWSMenuEntry(secstrmenu, me);
4061 int q = secstrmenu.getItemCount();
4062 for (int litm = p; litm < q; litm++)
4064 legacyItems.add(secstrmenu.getItem(litm));
4070 // Add all submenus in the order they should appear on the web
4072 wsmenu.add(msawsmenu);
4073 wsmenu.add(secstrmenu);
4074 wsmenu.add(dismenu);
4075 wsmenu.add(analymenu);
4076 // No search services yet
4077 // wsmenu.add(seqsrchmenu);
4079 javax.swing.SwingUtilities.invokeLater(new Runnable()
4086 webService.removeAll();
4087 // first, add discovered services onto the webservices menu
4088 if (wsmenu.size() > 0)
4090 for (int i = 0, j = wsmenu.size(); i < j; i++)
4092 webService.add(wsmenu.get(i));
4097 webService.add(me.webServiceNoServices);
4099 // TODO: move into separate menu builder class.
4100 boolean new_sspred = false;
4101 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4103 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4104 if (jws2servs != null)
4106 if (jws2servs.hasServices())
4108 jws2servs.attachWSMenuEntry(webService, me);
4109 for (Jws2Instance sv : jws2servs.getServices())
4111 if (sv.description.toLowerCase().contains("jpred"))
4113 for (JMenuItem jmi : legacyItems)
4115 jmi.setVisible(false);
4121 if (jws2servs.isRunning())
4123 JMenuItem tm = new JMenuItem(
4124 "Still discovering JABA Services");
4125 tm.setEnabled(false);
4130 build_urlServiceMenu(me.webService);
4131 build_fetchdbmenu(webService);
4132 for (JMenu item : wsmenu)
4134 if (item.getItemCount() == 0)
4136 item.setEnabled(false);
4140 item.setEnabled(true);
4143 } catch (Exception e)
4146 "Exception during web service menu building process.",
4151 } catch (Exception e)
4154 buildingMenu = false;
4161 * construct any groupURL type service menu entries.
4165 private void build_urlServiceMenu(JMenu webService)
4167 // TODO: remove this code when 2.7 is released
4168 // DEBUG - alignmentView
4170 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4171 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4173 * @Override public void actionPerformed(ActionEvent e) {
4174 * jalview.datamodel.AlignmentView
4175 * .testSelectionViews(af.viewport.getAlignment(),
4176 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4178 * }); webService.add(testAlView);
4180 // TODO: refactor to RestClient discoverer and merge menu entries for
4181 // rest-style services with other types of analysis/calculation service
4182 // SHmmr test client - still being implemented.
4183 // DEBUG - alignmentView
4185 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4188 client.attachWSMenuEntry(
4189 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4195 * Searches the alignment sequences for xRefs and builds the Show
4196 * Cross-References menu (formerly called Show Products), with database
4197 * sources for which cross-references are found (protein sources for a
4198 * nucleotide alignment and vice versa)
4200 * @return true if Show Cross-references menu should be enabled
4202 public boolean canShowProducts()
4204 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4205 AlignmentI dataset = viewport.getAlignment().getDataset();
4207 showProducts.removeAll();
4208 final boolean dna = viewport.getAlignment().isNucleotide();
4210 if (seqs == null || seqs.length == 0)
4212 // nothing to see here.
4216 boolean showp = false;
4219 List<String> ptypes = new CrossRef(seqs, dataset)
4220 .findXrefSourcesForSequences(dna);
4222 for (final String source : ptypes)
4225 final AlignFrame af = this;
4226 JMenuItem xtype = new JMenuItem(source);
4227 xtype.addActionListener(new ActionListener()
4230 public void actionPerformed(ActionEvent e)
4232 showProductsFor(af.viewport.getSequenceSelection(), dna,
4236 showProducts.add(xtype);
4238 showProducts.setVisible(showp);
4239 showProducts.setEnabled(showp);
4240 } catch (Exception e)
4243 "canShowProducts threw an exception - please report to help@jalview.org",
4251 * Finds and displays cross-references for the selected sequences (protein
4252 * products for nucleotide sequences, dna coding sequences for peptides).
4255 * the sequences to show cross-references for
4257 * true if from a nucleotide alignment (so showing proteins)
4259 * the database to show cross-references for
4261 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4262 final String source)
4264 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4269 * Construct and display a new frame containing the translation of this
4270 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4273 public void showTranslation_actionPerformed(ActionEvent e)
4275 AlignmentI al = null;
4278 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4280 al = dna.translateCdna();
4281 } catch (Exception ex)
4283 jalview.bin.Cache.log.error(
4284 "Exception during translation. Please report this !", ex);
4285 final String msg = MessageManager.getString(
4286 "label.error_when_translating_sequences_submit_bug_report");
4287 final String errorTitle = MessageManager
4288 .getString("label.implementation_error")
4289 + MessageManager.getString("label.translation_failed");
4290 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4291 JvOptionPane.ERROR_MESSAGE);
4294 if (al == null || al.getHeight() == 0)
4296 final String msg = MessageManager.getString(
4297 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4298 final String errorTitle = MessageManager
4299 .getString("label.translation_failed");
4300 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4301 JvOptionPane.WARNING_MESSAGE);
4305 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4306 af.setFileFormat(this.currentFileFormat);
4307 final String newTitle = MessageManager
4308 .formatMessage("label.translation_of_params", new Object[]
4309 { this.getTitle() });
4310 af.setTitle(newTitle);
4311 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4313 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4314 viewport.openSplitFrame(af, new Alignment(seqs));
4318 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4325 * Set the file format
4329 public void setFileFormat(FileFormatI format)
4331 this.currentFileFormat = format;
4335 * Try to load a features file onto the alignment.
4338 * contents or path to retrieve file
4340 * access mode of file (see jalview.io.AlignFile)
4341 * @return true if features file was parsed correctly.
4343 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4345 return avc.parseFeaturesFile(file, sourceType,
4346 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4351 public void refreshFeatureUI(boolean enableIfNecessary)
4353 // note - currently this is only still here rather than in the controller
4354 // because of the featureSettings hard reference that is yet to be
4356 if (enableIfNecessary)
4358 viewport.setShowSequenceFeatures(true);
4359 showSeqFeatures.setSelected(true);
4365 public void dragEnter(DropTargetDragEvent evt)
4370 public void dragExit(DropTargetEvent evt)
4375 public void dragOver(DropTargetDragEvent evt)
4380 public void dropActionChanged(DropTargetDragEvent evt)
4385 public void drop(DropTargetDropEvent evt)
4387 // JAL-1552 - acceptDrop required before getTransferable call for
4388 // Java's Transferable for native dnd
4389 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4390 Transferable t = evt.getTransferable();
4391 final AlignFrame thisaf = this;
4392 final List<String> files = new ArrayList<>();
4393 List<DataSourceType> protocols = new ArrayList<>();
4397 Desktop.transferFromDropTarget(files, protocols, evt, t);
4398 } catch (Exception e)
4400 e.printStackTrace();
4404 new Thread(new Runnable()
4411 // check to see if any of these files have names matching sequences
4414 SequenceIdMatcher idm = new SequenceIdMatcher(
4415 viewport.getAlignment().getSequencesArray());
4417 * Object[] { String,SequenceI}
4419 ArrayList<Object[]> filesmatched = new ArrayList<>();
4420 ArrayList<String> filesnotmatched = new ArrayList<>();
4421 for (int i = 0; i < files.size(); i++)
4423 String file = files.get(i).toString();
4425 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4426 if (protocol == DataSourceType.FILE)
4428 File fl = new File(file);
4429 pdbfn = fl.getName();
4431 else if (protocol == DataSourceType.URL)
4433 URL url = new URL(file);
4434 pdbfn = url.getFile();
4436 if (pdbfn.length() > 0)
4438 // attempt to find a match in the alignment
4439 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4440 int l = 0, c = pdbfn.indexOf(".");
4441 while (mtch == null && c != -1)
4446 } while ((c = pdbfn.indexOf(".", l)) > l);
4449 pdbfn = pdbfn.substring(0, l);
4451 mtch = idm.findAllIdMatches(pdbfn);
4455 FileFormatI type = null;
4458 type = new IdentifyFile().identify(file, protocol);
4459 } catch (Exception ex)
4463 if (type != null && type.isStructureFile())
4465 filesmatched.add(new Object[] { file, protocol, mtch });
4469 // File wasn't named like one of the sequences or wasn't a PDB
4471 filesnotmatched.add(file);
4475 if (filesmatched.size() > 0)
4477 boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4480 String msg = MessageManager.formatMessage(
4481 "label.automatically_associate_structure_files_with_sequences_same_name",
4483 { Integer.valueOf(filesmatched.size())
4485 String ttl = MessageManager.getString(
4486 "label.automatically_associate_structure_files_by_name");
4487 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4488 ttl, JvOptionPane.YES_NO_OPTION);
4489 autoAssociate = choice == JvOptionPane.YES_OPTION;
4493 for (Object[] fm : filesmatched)
4495 // try and associate
4496 // TODO: may want to set a standard ID naming formalism for
4497 // associating PDB files which have no IDs.
4498 for (SequenceI toassoc : (SequenceI[]) fm[2])
4500 PDBEntry pe = new AssociatePdbFileWithSeq()
4501 .associatePdbWithSeq((String) fm[0],
4502 (DataSourceType) fm[1], toassoc, false,
4506 System.err.println("Associated file : "
4507 + ((String) fm[0]) + " with "
4508 + toassoc.getDisplayId(true));
4512 // TODO: do we need to update overview ? only if features are
4514 alignPanel.paintAlignment(true, false);
4520 * add declined structures as sequences
4522 for (Object[] o : filesmatched)
4524 filesnotmatched.add((String) o[0]);
4528 if (filesnotmatched.size() > 0)
4530 if (assocfiles > 0 && (Cache.getDefault(
4531 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4532 || JvOptionPane.showConfirmDialog(thisaf,
4533 "<html>" + MessageManager.formatMessage(
4534 "label.ignore_unmatched_dropped_files_info",
4537 filesnotmatched.size())
4540 MessageManager.getString(
4541 "label.ignore_unmatched_dropped_files"),
4542 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4546 for (String fn : filesnotmatched)
4548 loadJalviewDataFile(fn, null, null, null);
4552 } catch (Exception ex)
4554 ex.printStackTrace();
4562 * Attempt to load a "dropped" file or URL string, by testing in turn for
4564 * <li>an Annotation file</li>
4565 * <li>a JNet file</li>
4566 * <li>a features file</li>
4567 * <li>else try to interpret as an alignment file</li>
4571 * either a filename or a URL string.
4573 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4574 FileFormatI format, SequenceI assocSeq)
4578 if (sourceType == null)
4580 sourceType = FormatAdapter.checkProtocol(file);
4582 // if the file isn't identified, or not positively identified as some
4583 // other filetype (PFAM is default unidentified alignment file type) then
4584 // try to parse as annotation.
4585 boolean isAnnotation = (format == null
4586 || FileFormat.Pfam.equals(format))
4587 ? new AnnotationFile().annotateAlignmentView(viewport,
4593 // first see if its a T-COFFEE score file
4594 TCoffeeScoreFile tcf = null;
4597 tcf = new TCoffeeScoreFile(file, sourceType);
4600 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4604 new TCoffeeColourScheme(viewport.getAlignment()));
4605 isAnnotation = true;
4606 statusBar.setText(MessageManager.getString(
4607 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4611 // some problem - if no warning its probable that the ID matching
4612 // process didn't work
4613 JvOptionPane.showMessageDialog(Desktop.desktop,
4614 tcf.getWarningMessage() == null
4615 ? MessageManager.getString(
4616 "label.check_file_matches_sequence_ids_alignment")
4617 : tcf.getWarningMessage(),
4618 MessageManager.getString(
4619 "label.problem_reading_tcoffee_score_file"),
4620 JvOptionPane.WARNING_MESSAGE);
4627 } catch (Exception x)
4630 "Exception when processing data source as T-COFFEE score file",
4636 // try to see if its a JNet 'concise' style annotation file *before*
4638 // try to parse it as a features file
4641 format = new IdentifyFile().identify(file, sourceType);
4643 if (FileFormat.ScoreMatrix == format)
4645 ScoreMatrixFile sm = new ScoreMatrixFile(
4646 new FileParse(file, sourceType));
4648 // todo: i18n this message
4649 statusBar.setText(MessageManager.formatMessage(
4650 "label.successfully_loaded_matrix",
4651 sm.getMatrixName()));
4653 else if (FileFormat.Jnet.equals(format))
4655 JPredFile predictions = new JPredFile(file, sourceType);
4656 new JnetAnnotationMaker();
4657 JnetAnnotationMaker.add_annotation(predictions,
4658 viewport.getAlignment(), 0, false);
4659 viewport.getAlignment().setupJPredAlignment();
4660 isAnnotation = true;
4662 // else if (IdentifyFile.FeaturesFile.equals(format))
4663 else if (FileFormat.Features.equals(format))
4665 if (parseFeaturesFile(file, sourceType))
4667 alignPanel.paintAlignment(true, true);
4672 new FileLoader().LoadFile(viewport, file, sourceType, format);
4679 alignPanel.adjustAnnotationHeight();
4680 viewport.updateSequenceIdColours();
4681 buildSortByAnnotationScoresMenu();
4682 alignPanel.paintAlignment(true, true);
4684 } catch (Exception ex)
4686 ex.printStackTrace();
4687 } catch (OutOfMemoryError oom)
4692 } catch (Exception x)
4697 + (sourceType != null
4698 ? (sourceType == DataSourceType.PASTE
4700 : "using " + sourceType + " from "
4704 ? "(parsing as '" + format + "' file)"
4706 oom, Desktop.desktop);
4711 * Method invoked by the ChangeListener on the tabbed pane, in other words
4712 * when a different tabbed pane is selected by the user or programmatically.
4715 public void tabSelectionChanged(int index)
4719 alignPanel = alignPanels.get(index);
4720 viewport = alignPanel.av;
4721 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4722 setMenusFromViewport(viewport);
4726 * 'focus' any colour slider that is open to the selected viewport
4728 if (viewport.getConservationSelected())
4730 SliderPanel.setConservationSlider(alignPanel,
4731 viewport.getResidueShading(), alignPanel.getViewName());
4735 SliderPanel.hideConservationSlider();
4737 if (viewport.getAbovePIDThreshold())
4739 SliderPanel.setPIDSliderSource(alignPanel,
4740 viewport.getResidueShading(), alignPanel.getViewName());
4744 SliderPanel.hidePIDSlider();
4748 * If there is a frame linked to this one in a SplitPane, switch it to the
4749 * same view tab index. No infinite recursion of calls should happen, since
4750 * tabSelectionChanged() should not get invoked on setting the selected
4751 * index to an unchanged value. Guard against setting an invalid index
4752 * before the new view peer tab has been created.
4754 final AlignViewportI peer = viewport.getCodingComplement();
4757 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4758 .getAlignPanel().alignFrame;
4759 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4761 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4767 * On right mouse click on view tab, prompt for and set new view name.
4770 public void tabbedPane_mousePressed(MouseEvent e)
4772 if (e.isPopupTrigger())
4774 String msg = MessageManager.getString("label.enter_view_name");
4775 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4776 JvOptionPane.QUESTION_MESSAGE);
4780 viewport.viewName = reply;
4781 // TODO warn if reply is in getExistingViewNames()?
4782 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4787 public AlignViewport getCurrentView()
4793 * Open the dialog for regex description parsing.
4796 protected void extractScores_actionPerformed(ActionEvent e)
4798 ParseProperties pp = new jalview.analysis.ParseProperties(
4799 viewport.getAlignment());
4800 // TODO: verify regex and introduce GUI dialog for version 2.5
4801 // if (pp.getScoresFromDescription("col", "score column ",
4802 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4804 if (pp.getScoresFromDescription("description column",
4805 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4807 buildSortByAnnotationScoresMenu();
4815 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4819 protected void showDbRefs_actionPerformed(ActionEvent e)
4821 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4827 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4831 protected void showNpFeats_actionPerformed(ActionEvent e)
4833 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4837 * find the viewport amongst the tabs in this alignment frame and close that
4842 public boolean closeView(AlignViewportI av)
4846 this.closeMenuItem_actionPerformed(false);
4849 Component[] comp = tabbedPane.getComponents();
4850 for (int i = 0; comp != null && i < comp.length; i++)
4852 if (comp[i] instanceof AlignmentPanel)
4854 if (((AlignmentPanel) comp[i]).av == av)
4857 closeView((AlignmentPanel) comp[i]);
4865 protected void build_fetchdbmenu(JMenu webService)
4867 // Temporary hack - DBRef Fetcher always top level ws entry.
4868 // TODO We probably want to store a sequence database checklist in
4869 // preferences and have checkboxes.. rather than individual sources selected
4871 final JMenu rfetch = new JMenu(
4872 MessageManager.getString("action.fetch_db_references"));
4873 rfetch.setToolTipText(MessageManager.getString(
4874 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4875 webService.add(rfetch);
4877 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4878 MessageManager.getString("option.trim_retrieved_seqs"));
4879 trimrs.setToolTipText(
4880 MessageManager.getString("label.trim_retrieved_sequences"));
4882 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4883 trimrs.addActionListener(new ActionListener()
4886 public void actionPerformed(ActionEvent e)
4888 trimrs.setSelected(trimrs.isSelected());
4889 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4890 Boolean.valueOf(trimrs.isSelected()).toString());
4894 JMenuItem fetchr = new JMenuItem(
4895 MessageManager.getString("label.standard_databases"));
4896 fetchr.setToolTipText(
4897 MessageManager.getString("label.fetch_embl_uniprot"));
4898 fetchr.addActionListener(new ActionListener()
4902 public void actionPerformed(ActionEvent e)
4904 new Thread(new Runnable()
4909 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4910 .getAlignment().isNucleotide();
4911 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4912 alignPanel.av.getSequenceSelection(),
4913 alignPanel.alignFrame, null,
4914 alignPanel.alignFrame.featureSettings, isNucleotide);
4915 dbRefFetcher.addListener(new FetchFinishedListenerI()
4918 public void finished()
4920 AlignFrame.this.setMenusForViewport();
4923 dbRefFetcher.fetchDBRefs(false);
4931 final AlignFrame me = this;
4932 new Thread(new Runnable()
4937 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4938 .getSequenceFetcherSingleton(me);
4939 javax.swing.SwingUtilities.invokeLater(new Runnable()
4944 String[] dbclasses = sf.getOrderedSupportedSources();
4945 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4946 // jalview.util.QuickSort.sort(otherdb, otherdb);
4947 List<DbSourceProxy> otherdb;
4948 JMenu dfetch = new JMenu();
4949 JMenu ifetch = new JMenu();
4950 JMenuItem fetchr = null;
4951 int comp = 0, icomp = 0, mcomp = 15;
4952 String mname = null;
4954 for (String dbclass : dbclasses)
4956 otherdb = sf.getSourceProxy(dbclass);
4957 // add a single entry for this class, or submenu allowing 'fetch
4959 if (otherdb == null || otherdb.size() < 1)
4963 // List<DbSourceProxy> dbs=otherdb;
4964 // otherdb=new ArrayList<DbSourceProxy>();
4965 // for (DbSourceProxy db:dbs)
4967 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4971 mname = "From " + dbclass;
4973 if (otherdb.size() == 1)
4975 final DbSourceProxy[] dassource = otherdb
4976 .toArray(new DbSourceProxy[0]);
4977 DbSourceProxy src = otherdb.get(0);
4978 fetchr = new JMenuItem(src.getDbSource());
4979 fetchr.addActionListener(new ActionListener()
4983 public void actionPerformed(ActionEvent e)
4985 new Thread(new Runnable()
4991 boolean isNucleotide = alignPanel.alignFrame
4992 .getViewport().getAlignment()
4994 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4995 alignPanel.av.getSequenceSelection(),
4996 alignPanel.alignFrame, dassource,
4997 alignPanel.alignFrame.featureSettings,
5000 .addListener(new FetchFinishedListenerI()
5003 public void finished()
5005 AlignFrame.this.setMenusForViewport();
5008 dbRefFetcher.fetchDBRefs(false);
5014 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5015 MessageManager.formatMessage(
5016 "label.fetch_retrieve_from", new Object[]
5017 { src.getDbName() })));
5023 final DbSourceProxy[] dassource = otherdb
5024 .toArray(new DbSourceProxy[0]);
5026 DbSourceProxy src = otherdb.get(0);
5027 fetchr = new JMenuItem(MessageManager
5028 .formatMessage("label.fetch_all_param", new Object[]
5029 { src.getDbSource() }));
5030 fetchr.addActionListener(new ActionListener()
5033 public void actionPerformed(ActionEvent e)
5035 new Thread(new Runnable()
5041 boolean isNucleotide = alignPanel.alignFrame
5042 .getViewport().getAlignment()
5044 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5045 alignPanel.av.getSequenceSelection(),
5046 alignPanel.alignFrame, dassource,
5047 alignPanel.alignFrame.featureSettings,
5050 .addListener(new FetchFinishedListenerI()
5053 public void finished()
5055 AlignFrame.this.setMenusForViewport();
5058 dbRefFetcher.fetchDBRefs(false);
5064 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5065 MessageManager.formatMessage(
5066 "label.fetch_retrieve_from_all_sources",
5068 { Integer.valueOf(otherdb.size())
5070 src.getDbSource(), src.getDbName() })));
5073 // and then build the rest of the individual menus
5074 ifetch = new JMenu(MessageManager.formatMessage(
5075 "label.source_from_db_source", new Object[]
5076 { src.getDbSource() }));
5078 String imname = null;
5080 for (DbSourceProxy sproxy : otherdb)
5082 String dbname = sproxy.getDbName();
5083 String sname = dbname.length() > 5
5084 ? dbname.substring(0, 5) + "..."
5086 String msname = dbname.length() > 10
5087 ? dbname.substring(0, 10) + "..."
5091 imname = MessageManager
5092 .formatMessage("label.from_msname", new Object[]
5095 fetchr = new JMenuItem(msname);
5096 final DbSourceProxy[] dassrc = { sproxy };
5097 fetchr.addActionListener(new ActionListener()
5101 public void actionPerformed(ActionEvent e)
5103 new Thread(new Runnable()
5109 boolean isNucleotide = alignPanel.alignFrame
5110 .getViewport().getAlignment()
5112 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5113 alignPanel.av.getSequenceSelection(),
5114 alignPanel.alignFrame, dassrc,
5115 alignPanel.alignFrame.featureSettings,
5118 .addListener(new FetchFinishedListenerI()
5121 public void finished()
5123 AlignFrame.this.setMenusForViewport();
5126 dbRefFetcher.fetchDBRefs(false);
5132 fetchr.setToolTipText(
5133 "<html>" + MessageManager.formatMessage(
5134 "label.fetch_retrieve_from", new Object[]
5138 if (++icomp >= mcomp || i == (otherdb.size()))
5140 ifetch.setText(MessageManager.formatMessage(
5141 "label.source_to_target", imname, sname));
5143 ifetch = new JMenu();
5151 if (comp >= mcomp || dbi >= (dbclasses.length))
5153 dfetch.setText(MessageManager.formatMessage(
5154 "label.source_to_target", mname, dbclass));
5156 dfetch = new JMenu();
5169 * Left justify the whole alignment.
5172 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5174 AlignmentI al = viewport.getAlignment();
5176 viewport.firePropertyChange("alignment", null, al);
5180 * Right justify the whole alignment.
5183 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5185 AlignmentI al = viewport.getAlignment();
5187 viewport.firePropertyChange("alignment", null, al);
5191 public void setShowSeqFeatures(boolean b)
5193 showSeqFeatures.setSelected(b);
5194 viewport.setShowSequenceFeatures(b);
5201 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5202 * awt.event.ActionEvent)
5205 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5207 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5208 alignPanel.paintAlignment(false, false);
5215 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5219 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5221 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5222 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5230 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5231 * .event.ActionEvent)
5234 protected void showGroupConservation_actionPerformed(ActionEvent e)
5236 viewport.setShowGroupConservation(showGroupConservation.getState());
5237 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5244 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5245 * .event.ActionEvent)
5248 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5250 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5251 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5258 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5259 * .event.ActionEvent)
5262 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5264 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5265 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5269 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5271 showSequenceLogo.setState(true);
5272 viewport.setShowSequenceLogo(true);
5273 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5274 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5278 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5280 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5287 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5288 * .event.ActionEvent)
5291 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5293 if (avc.makeGroupsFromSelection())
5295 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5296 alignPanel.updateAnnotation();
5297 alignPanel.paintAlignment(true, true);
5301 public void clearAlignmentSeqRep()
5303 // TODO refactor alignmentseqrep to controller
5304 if (viewport.getAlignment().hasSeqrep())
5306 viewport.getAlignment().setSeqrep(null);
5307 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5308 alignPanel.updateAnnotation();
5309 alignPanel.paintAlignment(true, true);
5314 protected void createGroup_actionPerformed(ActionEvent e)
5316 if (avc.createGroup())
5318 if (applyAutoAnnotationSettings.isSelected())
5320 alignPanel.updateAnnotation(true, false);
5322 alignPanel.alignmentChanged();
5327 protected void unGroup_actionPerformed(ActionEvent e)
5331 alignPanel.alignmentChanged();
5336 * make the given alignmentPanel the currently selected tab
5338 * @param alignmentPanel
5340 public void setDisplayedView(AlignmentPanel alignmentPanel)
5342 if (!viewport.getSequenceSetId()
5343 .equals(alignmentPanel.av.getSequenceSetId()))
5345 throw new Error(MessageManager.getString(
5346 "error.implementation_error_cannot_show_view_alignment_frame"));
5348 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5349 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5351 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5356 * Action on selection of menu options to Show or Hide annotations.
5359 * @param forSequences
5360 * update sequence-related annotations
5361 * @param forAlignment
5362 * update non-sequence-related annotations
5365 protected void setAnnotationsVisibility(boolean visible,
5366 boolean forSequences, boolean forAlignment)
5368 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5369 .getAlignmentAnnotation();
5374 for (AlignmentAnnotation aa : anns)
5377 * don't display non-positional annotations on an alignment
5379 if (aa.annotations == null)
5383 boolean apply = (aa.sequenceRef == null && forAlignment)
5384 || (aa.sequenceRef != null && forSequences);
5387 aa.visible = visible;
5390 alignPanel.validateAnnotationDimensions(true);
5391 alignPanel.alignmentChanged();
5395 * Store selected annotation sort order for the view and repaint.
5398 protected void sortAnnotations_actionPerformed()
5400 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5402 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5403 alignPanel.paintAlignment(false, false);
5408 * @return alignment panels in this alignment frame
5410 public List<? extends AlignmentViewPanel> getAlignPanels()
5412 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5416 * Open a new alignment window, with the cDNA associated with this (protein)
5417 * alignment, aligned as is the protein.
5419 protected void viewAsCdna_actionPerformed()
5421 // TODO no longer a menu action - refactor as required
5422 final AlignmentI alignment = getViewport().getAlignment();
5423 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5424 if (mappings == null)
5428 List<SequenceI> cdnaSeqs = new ArrayList<>();
5429 for (SequenceI aaSeq : alignment.getSequences())
5431 for (AlignedCodonFrame acf : mappings)
5433 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5437 * There is a cDNA mapping for this protein sequence - add to new
5438 * alignment. It will share the same dataset sequence as other mapped
5439 * cDNA (no new mappings need to be created).
5441 final Sequence newSeq = new Sequence(dnaSeq);
5442 newSeq.setDatasetSequence(dnaSeq);
5443 cdnaSeqs.add(newSeq);
5447 if (cdnaSeqs.size() == 0)
5449 // show a warning dialog no mapped cDNA
5452 AlignmentI cdna = new Alignment(
5453 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5454 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5455 AlignFrame.DEFAULT_HEIGHT);
5456 cdna.alignAs(alignment);
5457 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5459 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5460 AlignFrame.DEFAULT_HEIGHT);
5464 * Set visibility of dna/protein complement view (available when shown in a
5470 protected void showComplement_actionPerformed(boolean show)
5472 SplitContainerI sf = getSplitViewContainer();
5475 sf.setComplementVisible(this, show);
5480 * Generate the reverse (optionally complemented) of the selected sequences,
5481 * and add them to the alignment
5484 protected void showReverse_actionPerformed(boolean complement)
5486 AlignmentI al = null;
5489 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5490 al = dna.reverseCdna(complement);
5491 viewport.addAlignment(al, "");
5492 addHistoryItem(new EditCommand(
5493 MessageManager.getString("label.add_sequences"), Action.PASTE,
5494 al.getSequencesArray(), 0, al.getWidth(),
5495 viewport.getAlignment()));
5496 } catch (Exception ex)
5498 System.err.println(ex.getMessage());
5504 * Try to run a script in the Groovy console, having first ensured that this
5505 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5506 * be targeted at this alignment.
5509 protected void runGroovy_actionPerformed()
5511 Jalview.setCurrentAlignFrame(this);
5512 groovy.ui.Console console = Desktop.getGroovyConsole();
5513 if (console != null)
5517 console.runScript();
5518 } catch (Exception ex)
5520 System.err.println((ex.toString()));
5521 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5522 MessageManager.getString("label.couldnt_run_groovy_script"),
5523 MessageManager.getString("label.groovy_support_failed"),
5524 JvOptionPane.ERROR_MESSAGE);
5529 System.err.println("Can't run Groovy script as console not found");
5534 * Hides columns containing (or not containing) a specified feature, provided
5535 * that would not leave all columns hidden
5537 * @param featureType
5538 * @param columnsContaining
5541 public boolean hideFeatureColumns(String featureType,
5542 boolean columnsContaining)
5544 boolean notForHiding = avc.markColumnsContainingFeatures(
5545 columnsContaining, false, false, featureType);
5548 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5549 false, featureType))
5551 getViewport().hideSelectedColumns();
5559 protected void selectHighlightedColumns_actionPerformed(
5560 ActionEvent actionEvent)
5562 // include key modifier check in case user selects from menu
5563 avc.markHighlightedColumns(
5564 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5565 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5566 | ActionEvent.CTRL_MASK)) != 0);
5570 * Rebuilds the Colour menu, including any user-defined colours which have
5571 * been loaded either on startup or during the session
5573 public void buildColourMenu()
5575 colourMenu.removeAll();
5577 colourMenu.add(applyToAllGroups);
5578 colourMenu.add(textColour);
5579 colourMenu.addSeparator();
5581 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5584 colourMenu.addSeparator();
5585 colourMenu.add(conservationMenuItem);
5586 colourMenu.add(modifyConservation);
5587 colourMenu.add(abovePIDThreshold);
5588 colourMenu.add(modifyPID);
5589 colourMenu.add(annotationColour);
5591 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5592 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5596 * Open a dialog (if not already open) that allows the user to select and
5597 * calculate PCA or Tree analysis
5599 protected void openTreePcaDialog()
5601 if (alignPanel.getCalculationDialog() == null)
5603 new CalculationChooser(AlignFrame.this);
5608 protected void loadVcf_actionPerformed()
5610 JalviewFileChooser chooser = new JalviewFileChooser(
5611 Cache.getProperty("LAST_DIRECTORY"));
5612 chooser.setFileView(new JalviewFileView());
5613 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5614 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5616 int value = chooser.showOpenDialog(null);
5618 if (value == JalviewFileChooser.APPROVE_OPTION)
5620 String choice = chooser.getSelectedFile().getPath();
5621 Cache.setProperty("LAST_DIRECTORY", choice);
5622 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5623 new VCFLoader(choice).loadVCF(seqs, this);
5629 class PrintThread extends Thread
5633 public PrintThread(AlignmentPanel ap)
5638 static PageFormat pf;
5643 PrinterJob printJob = PrinterJob.getPrinterJob();
5647 printJob.setPrintable(ap, pf);
5651 printJob.setPrintable(ap);
5654 if (printJob.printDialog())
5659 } catch (Exception PrintException)
5661 PrintException.printStackTrace();