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.getViewName() != null);
739 if (aSize == 1 && ap.av.getViewName() == null)
741 this.getContentPane().add(ap, BorderLayout.CENTER);
747 setInitialTabVisible();
750 expandViews.setEnabled(true);
751 gatherViews.setEnabled(true);
752 tabbedPane.addTab(ap.av.getViewName(), 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.getViewName(), 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 public 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 jalview.project.Jalview2XML().saveAlignment(this, file,
1161 statusBar.setText(MessageManager.formatMessage(
1162 "label.successfully_saved_to_file_in_format", new Object[]
1163 { fileName, format }));
1168 AlignmentExportData exportData = getAlignmentForExport(format,
1170 if (exportData.getSettings().isCancelled())
1174 FormatAdapter f = new FormatAdapter(alignPanel,
1175 exportData.getSettings());
1176 String output = f.formatSequences(format, exportData.getAlignment(), // class
1180 // occur in the distant future
1181 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1182 f.getCacheSuffixDefault(format),
1183 viewport.getAlignment().getHiddenColumns());
1191 // create backupfiles object and get new temp filename destination
1192 BackupFiles backupfiles = new BackupFiles(file);
1196 PrintWriter out = new PrintWriter(
1197 new FileWriter(backupfiles.getTempFilePath()));
1201 this.setTitle(file);
1202 statusBar.setText(MessageManager.formatMessage(
1203 "label.successfully_saved_to_file_in_format", new Object[]
1204 { fileName, format.getName() }));
1205 } catch (Exception ex)
1208 ex.printStackTrace();
1211 backupfiles.setWriteSuccess(success);
1212 // do the backup file roll and rename the temp file to actual file
1213 success = backupfiles.rollBackupsAndRenameTempFile();
1220 JvOptionPane.showInternalMessageDialog(this, MessageManager
1221 .formatMessage("label.couldnt_save_file", new Object[]
1223 MessageManager.getString("label.error_saving_file"),
1224 JvOptionPane.WARNING_MESSAGE);
1230 private void warningMessage(String warning, String title)
1232 if (new jalview.util.Platform().isHeadless())
1234 System.err.println("Warning: " + title + "\nWarning: " + warning);
1239 JvOptionPane.showInternalMessageDialog(this, warning, title,
1240 JvOptionPane.WARNING_MESSAGE);
1252 protected void outputText_actionPerformed(ActionEvent e)
1254 FileFormatI fileFormat = FileFormats.getInstance()
1255 .forName(e.getActionCommand());
1256 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1258 if (exportData.getSettings().isCancelled())
1262 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1263 cap.setForInput(null);
1266 FileFormatI format = fileFormat;
1267 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1268 .formatSequences(format, exportData.getAlignment(),
1269 exportData.getOmitHidden(),
1270 exportData.getStartEndPostions(),
1271 viewport.getAlignment().getHiddenColumns()));
1272 Desktop.addInternalFrame(cap, MessageManager
1273 .formatMessage("label.alignment_output_command", new Object[]
1274 { e.getActionCommand() }), 600, 500);
1275 } catch (OutOfMemoryError oom)
1277 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1284 public static AlignmentExportData getAlignmentForExport(
1285 FileFormatI format, AlignViewportI viewport,
1286 AlignExportSettingI exportSettings)
1288 AlignmentI alignmentToExport = null;
1289 AlignExportSettingI settings = exportSettings;
1290 String[] omitHidden = null;
1292 HiddenSequences hiddenSeqs = viewport.getAlignment()
1293 .getHiddenSequences();
1295 alignmentToExport = viewport.getAlignment();
1297 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1298 if (settings == null)
1300 settings = new AlignExportSettings(hasHiddenSeqs,
1301 viewport.hasHiddenColumns(), format);
1303 // settings.isExportAnnotations();
1305 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1307 omitHidden = viewport.getViewAsString(false,
1308 settings.isExportHiddenSequences());
1311 int[] alignmentStartEnd = new int[2];
1312 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1314 alignmentToExport = hiddenSeqs.getFullAlignment();
1318 alignmentToExport = viewport.getAlignment();
1320 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1321 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1322 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1323 omitHidden, alignmentStartEnd, settings);
1334 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1336 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1337 htmlSVG.exportHTML(null);
1341 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1343 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1344 bjs.exportHTML(null);
1347 public void createImageMap(File file, String image)
1349 alignPanel.makePNGImageMap(file, image);
1359 public void createPNG(File f)
1361 alignPanel.makePNG(f);
1371 public void createEPS(File f)
1373 alignPanel.makeEPS(f);
1377 public void createSVG(File f)
1379 alignPanel.makeSVG(f);
1383 public void pageSetup_actionPerformed(ActionEvent e)
1385 PrinterJob printJob = PrinterJob.getPrinterJob();
1386 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1396 public void printMenuItem_actionPerformed(ActionEvent e)
1398 // Putting in a thread avoids Swing painting problems
1399 PrintThread thread = new PrintThread(alignPanel);
1404 public void exportFeatures_actionPerformed(ActionEvent e)
1406 new AnnotationExporter(alignPanel).exportFeatures();
1410 public void exportAnnotations_actionPerformed(ActionEvent e)
1412 new AnnotationExporter(alignPanel).exportAnnotations();
1416 public void associatedData_actionPerformed(ActionEvent e)
1418 // Pick the tree file
1419 JalviewFileChooser chooser = new JalviewFileChooser(
1420 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1421 chooser.setFileView(new JalviewFileView());
1422 chooser.setDialogTitle(
1423 MessageManager.getString("label.load_jalview_annotations"));
1424 chooser.setToolTipText(
1425 MessageManager.getString("label.load_jalview_annotations"));
1427 int value = chooser.showOpenDialog(null);
1429 if (value == JalviewFileChooser.APPROVE_OPTION)
1431 String choice = chooser.getSelectedFile().getPath();
1432 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1433 loadJalviewDataFile(choice, null, null, null);
1439 * Close the current view or all views in the alignment frame. If the frame
1440 * only contains one view then the alignment will be removed from memory.
1442 * @param closeAllTabs
1445 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1447 if (alignPanels != null && alignPanels.size() < 2)
1449 closeAllTabs = true;
1454 if (alignPanels != null)
1458 if (this.isClosed())
1460 // really close all the windows - otherwise wait till
1461 // setClosed(true) is called
1462 for (int i = 0; i < alignPanels.size(); i++)
1464 AlignmentPanel ap = alignPanels.get(i);
1471 closeView(alignPanel);
1478 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1479 * be called recursively, with the frame now in 'closed' state
1481 this.setClosed(true);
1483 } catch (Exception ex)
1485 ex.printStackTrace();
1490 * Close the specified panel and close up tabs appropriately.
1492 * @param panelToClose
1494 public void closeView(AlignmentPanel panelToClose)
1496 int index = tabbedPane.getSelectedIndex();
1497 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1498 alignPanels.remove(panelToClose);
1499 panelToClose.closePanel();
1500 panelToClose = null;
1502 tabbedPane.removeTabAt(closedindex);
1503 tabbedPane.validate();
1505 if (index > closedindex || index == tabbedPane.getTabCount())
1507 // modify currently selected tab index if necessary.
1511 this.tabSelectionChanged(index);
1517 void updateEditMenuBar()
1520 if (viewport.getHistoryList().size() > 0)
1522 undoMenuItem.setEnabled(true);
1523 CommandI command = viewport.getHistoryList().peek();
1524 undoMenuItem.setText(MessageManager
1525 .formatMessage("label.undo_command", new Object[]
1526 { command.getDescription() }));
1530 undoMenuItem.setEnabled(false);
1531 undoMenuItem.setText(MessageManager.getString("action.undo"));
1534 if (viewport.getRedoList().size() > 0)
1536 redoMenuItem.setEnabled(true);
1538 CommandI command = viewport.getRedoList().peek();
1539 redoMenuItem.setText(MessageManager
1540 .formatMessage("label.redo_command", new Object[]
1541 { command.getDescription() }));
1545 redoMenuItem.setEnabled(false);
1546 redoMenuItem.setText(MessageManager.getString("action.redo"));
1551 public void addHistoryItem(CommandI command)
1553 if (command.getSize() > 0)
1555 viewport.addToHistoryList(command);
1556 viewport.clearRedoList();
1557 updateEditMenuBar();
1558 viewport.updateHiddenColumns();
1559 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1560 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1561 // viewport.getColumnSelection()
1562 // .getHiddenColumns().size() > 0);
1568 * @return alignment objects for all views
1570 AlignmentI[] getViewAlignments()
1572 if (alignPanels != null)
1574 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1576 for (AlignmentPanel ap : alignPanels)
1578 als[i++] = ap.av.getAlignment();
1582 if (viewport != null)
1584 return new AlignmentI[] { viewport.getAlignment() };
1596 protected void undoMenuItem_actionPerformed(ActionEvent e)
1598 if (viewport.getHistoryList().isEmpty())
1602 CommandI command = viewport.getHistoryList().pop();
1603 viewport.addToRedoList(command);
1604 command.undoCommand(getViewAlignments());
1606 AlignmentViewport originalSource = getOriginatingSource(command);
1607 updateEditMenuBar();
1609 if (originalSource != null)
1611 if (originalSource != viewport)
1614 "Implementation worry: mismatch of viewport origin for undo");
1616 originalSource.updateHiddenColumns();
1617 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1619 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1620 // viewport.getColumnSelection()
1621 // .getHiddenColumns().size() > 0);
1622 originalSource.firePropertyChange("alignment", null,
1623 originalSource.getAlignment().getSequences());
1634 protected void redoMenuItem_actionPerformed(ActionEvent e)
1636 if (viewport.getRedoList().size() < 1)
1641 CommandI command = viewport.getRedoList().pop();
1642 viewport.addToHistoryList(command);
1643 command.doCommand(getViewAlignments());
1645 AlignmentViewport originalSource = getOriginatingSource(command);
1646 updateEditMenuBar();
1648 if (originalSource != null)
1651 if (originalSource != viewport)
1654 "Implementation worry: mismatch of viewport origin for redo");
1656 originalSource.updateHiddenColumns();
1657 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1659 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1660 // viewport.getColumnSelection()
1661 // .getHiddenColumns().size() > 0);
1662 originalSource.firePropertyChange("alignment", null,
1663 originalSource.getAlignment().getSequences());
1667 AlignmentViewport getOriginatingSource(CommandI command)
1669 AlignmentViewport originalSource = null;
1670 // For sequence removal and addition, we need to fire
1671 // the property change event FROM the viewport where the
1672 // original alignment was altered
1673 AlignmentI al = null;
1674 if (command instanceof EditCommand)
1676 EditCommand editCommand = (EditCommand) command;
1677 al = editCommand.getAlignment();
1678 List<Component> comps = PaintRefresher.components
1679 .get(viewport.getSequenceSetId());
1681 for (Component comp : comps)
1683 if (comp instanceof AlignmentPanel)
1685 if (al == ((AlignmentPanel) comp).av.getAlignment())
1687 originalSource = ((AlignmentPanel) comp).av;
1694 if (originalSource == null)
1696 // The original view is closed, we must validate
1697 // the current view against the closed view first
1700 PaintRefresher.validateSequences(al, viewport.getAlignment());
1703 originalSource = viewport;
1706 return originalSource;
1715 public void moveSelectedSequences(boolean up)
1717 SequenceGroup sg = viewport.getSelectionGroup();
1723 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1724 viewport.getHiddenRepSequences(), up);
1725 alignPanel.paintAlignment(true, false);
1728 synchronized void slideSequences(boolean right, int size)
1730 List<SequenceI> sg = new ArrayList<>();
1731 if (viewport.cursorMode)
1733 sg.add(viewport.getAlignment()
1734 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1736 else if (viewport.getSelectionGroup() != null
1737 && viewport.getSelectionGroup().getSize() != viewport
1738 .getAlignment().getHeight())
1740 sg = viewport.getSelectionGroup()
1741 .getSequences(viewport.getHiddenRepSequences());
1749 List<SequenceI> invertGroup = new ArrayList<>();
1751 for (SequenceI seq : viewport.getAlignment().getSequences())
1753 if (!sg.contains(seq))
1755 invertGroup.add(seq);
1759 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1761 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1762 for (int i = 0; i < invertGroup.size(); i++)
1764 seqs2[i] = invertGroup.get(i);
1767 SlideSequencesCommand ssc;
1770 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1771 viewport.getGapCharacter());
1775 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1776 viewport.getGapCharacter());
1779 int groupAdjustment = 0;
1780 if (ssc.getGapsInsertedBegin() && right)
1782 if (viewport.cursorMode)
1784 alignPanel.getSeqPanel().moveCursor(size, 0);
1788 groupAdjustment = size;
1791 else if (!ssc.getGapsInsertedBegin() && !right)
1793 if (viewport.cursorMode)
1795 alignPanel.getSeqPanel().moveCursor(-size, 0);
1799 groupAdjustment = -size;
1803 if (groupAdjustment != 0)
1805 viewport.getSelectionGroup().setStartRes(
1806 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1807 viewport.getSelectionGroup().setEndRes(
1808 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1812 * just extend the last slide command if compatible; but not if in
1813 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1815 boolean appendHistoryItem = false;
1816 Deque<CommandI> historyList = viewport.getHistoryList();
1817 boolean inSplitFrame = getSplitViewContainer() != null;
1818 if (!inSplitFrame && historyList != null && historyList.size() > 0
1819 && historyList.peek() instanceof SlideSequencesCommand)
1821 appendHistoryItem = ssc.appendSlideCommand(
1822 (SlideSequencesCommand) historyList.peek());
1825 if (!appendHistoryItem)
1827 addHistoryItem(ssc);
1840 protected void copy_actionPerformed(ActionEvent e)
1842 if (viewport.getSelectionGroup() == null)
1846 // TODO: preserve the ordering of displayed alignment annotation in any
1847 // internal paste (particularly sequence associated annotation)
1848 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1849 String[] omitHidden = null;
1851 if (viewport.hasHiddenColumns())
1853 omitHidden = viewport.getViewAsString(true);
1856 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1857 seqs, omitHidden, null);
1859 StringSelection ss = new StringSelection(output);
1863 jalview.gui.Desktop.internalCopy = true;
1864 // Its really worth setting the clipboard contents
1865 // to empty before setting the large StringSelection!!
1866 Toolkit.getDefaultToolkit().getSystemClipboard()
1867 .setContents(new StringSelection(""), null);
1869 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1871 } catch (OutOfMemoryError er)
1873 new OOMWarning("copying region", er);
1877 HiddenColumns hiddenColumns = null;
1878 if (viewport.hasHiddenColumns())
1880 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1881 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1883 // create new HiddenColumns object with copy of hidden regions
1884 // between startRes and endRes, offset by startRes
1885 hiddenColumns = new HiddenColumns(
1886 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1887 hiddenCutoff, hiddenOffset);
1890 Desktop.jalviewClipboard = new Object[] { seqs,
1891 viewport.getAlignment().getDataset(), hiddenColumns };
1892 statusBar.setText(MessageManager.formatMessage(
1893 "label.copied_sequences_to_clipboard", new Object[]
1894 { Integer.valueOf(seqs.length).toString() }));
1904 protected void pasteNew_actionPerformed(ActionEvent e)
1916 protected void pasteThis_actionPerformed(ActionEvent e)
1922 * Paste contents of Jalview clipboard
1924 * @param newAlignment
1925 * true to paste to a new alignment, otherwise add to this.
1927 void paste(boolean newAlignment)
1929 boolean externalPaste = true;
1932 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1933 Transferable contents = c.getContents(this);
1935 if (contents == null)
1944 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1945 if (str.length() < 1)
1950 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1952 } catch (OutOfMemoryError er)
1954 new OOMWarning("Out of memory pasting sequences!!", er);
1958 SequenceI[] sequences;
1959 boolean annotationAdded = false;
1960 AlignmentI alignment = null;
1962 if (Desktop.jalviewClipboard != null)
1964 // The clipboard was filled from within Jalview, we must use the
1966 // And dataset from the copied alignment
1967 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1968 // be doubly sure that we create *new* sequence objects.
1969 sequences = new SequenceI[newseq.length];
1970 for (int i = 0; i < newseq.length; i++)
1972 sequences[i] = new Sequence(newseq[i]);
1974 alignment = new Alignment(sequences);
1975 externalPaste = false;
1979 // parse the clipboard as an alignment.
1980 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1982 sequences = alignment.getSequencesArray();
1986 ArrayList<Integer> newGraphGroups = new ArrayList<>();
1992 if (Desktop.jalviewClipboard != null)
1994 // dataset is inherited
1995 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1999 // new dataset is constructed
2000 alignment.setDataset(null);
2002 alwidth = alignment.getWidth() + 1;
2006 AlignmentI pastedal = alignment; // preserve pasted alignment object
2007 // Add pasted sequences and dataset into existing alignment.
2008 alignment = viewport.getAlignment();
2009 alwidth = alignment.getWidth() + 1;
2010 // decide if we need to import sequences from an existing dataset
2011 boolean importDs = Desktop.jalviewClipboard != null
2012 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2013 // importDs==true instructs us to copy over new dataset sequences from
2014 // an existing alignment
2015 Vector newDs = (importDs) ? new Vector() : null; // used to create
2016 // minimum dataset set
2018 for (int i = 0; i < sequences.length; i++)
2022 newDs.addElement(null);
2024 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2026 if (importDs && ds != null)
2028 if (!newDs.contains(ds))
2030 newDs.setElementAt(ds, i);
2031 ds = new Sequence(ds);
2032 // update with new dataset sequence
2033 sequences[i].setDatasetSequence(ds);
2037 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2042 // copy and derive new dataset sequence
2043 sequences[i] = sequences[i].deriveSequence();
2044 alignment.getDataset()
2045 .addSequence(sequences[i].getDatasetSequence());
2046 // TODO: avoid creation of duplicate dataset sequences with a
2047 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2049 alignment.addSequence(sequences[i]); // merges dataset
2053 newDs.clear(); // tidy up
2055 if (alignment.getAlignmentAnnotation() != null)
2057 for (AlignmentAnnotation alan : alignment
2058 .getAlignmentAnnotation())
2060 if (alan.graphGroup > fgroup)
2062 fgroup = alan.graphGroup;
2066 if (pastedal.getAlignmentAnnotation() != null)
2068 // Add any annotation attached to alignment.
2069 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2070 for (int i = 0; i < alann.length; i++)
2072 annotationAdded = true;
2073 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2075 AlignmentAnnotation newann = new AlignmentAnnotation(
2077 if (newann.graphGroup > -1)
2079 if (newGraphGroups.size() <= newann.graphGroup
2080 || newGraphGroups.get(newann.graphGroup) == null)
2082 for (int q = newGraphGroups
2083 .size(); q <= newann.graphGroup; q++)
2085 newGraphGroups.add(q, null);
2087 newGraphGroups.set(newann.graphGroup,
2088 new Integer(++fgroup));
2090 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2094 newann.padAnnotation(alwidth);
2095 alignment.addAnnotation(newann);
2105 addHistoryItem(new EditCommand(
2106 MessageManager.getString("label.add_sequences"),
2107 Action.PASTE, sequences, 0, alignment.getWidth(),
2110 // Add any annotations attached to sequences
2111 for (int i = 0; i < sequences.length; i++)
2113 if (sequences[i].getAnnotation() != null)
2115 AlignmentAnnotation newann;
2116 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2118 annotationAdded = true;
2119 newann = sequences[i].getAnnotation()[a];
2120 newann.adjustForAlignment();
2121 newann.padAnnotation(alwidth);
2122 if (newann.graphGroup > -1)
2124 if (newann.graphGroup > -1)
2126 if (newGraphGroups.size() <= newann.graphGroup
2127 || newGraphGroups.get(newann.graphGroup) == null)
2129 for (int q = newGraphGroups
2130 .size(); q <= newann.graphGroup; q++)
2132 newGraphGroups.add(q, null);
2134 newGraphGroups.set(newann.graphGroup,
2135 new Integer(++fgroup));
2137 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2141 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2145 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2153 // propagate alignment changed.
2154 viewport.getRanges().setEndSeq(alignment.getHeight());
2155 if (annotationAdded)
2157 // Duplicate sequence annotation in all views.
2158 AlignmentI[] alview = this.getViewAlignments();
2159 for (int i = 0; i < sequences.length; i++)
2161 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2166 for (int avnum = 0; avnum < alview.length; avnum++)
2168 if (alview[avnum] != alignment)
2170 // duplicate in a view other than the one with input focus
2171 int avwidth = alview[avnum].getWidth() + 1;
2172 // this relies on sann being preserved after we
2173 // modify the sequence's annotation array for each duplication
2174 for (int a = 0; a < sann.length; a++)
2176 AlignmentAnnotation newann = new AlignmentAnnotation(
2178 sequences[i].addAlignmentAnnotation(newann);
2179 newann.padAnnotation(avwidth);
2180 alview[avnum].addAnnotation(newann); // annotation was
2181 // duplicated earlier
2182 // TODO JAL-1145 graphGroups are not updated for sequence
2183 // annotation added to several views. This may cause
2185 alview[avnum].setAnnotationIndex(newann, a);
2190 buildSortByAnnotationScoresMenu();
2192 viewport.firePropertyChange("alignment", null,
2193 alignment.getSequences());
2194 if (alignPanels != null)
2196 for (AlignmentPanel ap : alignPanels)
2198 ap.validateAnnotationDimensions(false);
2203 alignPanel.validateAnnotationDimensions(false);
2209 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2211 String newtitle = new String("Copied sequences");
2213 if (Desktop.jalviewClipboard != null
2214 && Desktop.jalviewClipboard[2] != null)
2216 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2217 af.viewport.setHiddenColumns(hc);
2220 // >>>This is a fix for the moment, until a better solution is
2222 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2223 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2224 .getFeatureRenderer());
2226 // TODO: maintain provenance of an alignment, rather than just make the
2227 // title a concatenation of operations.
2230 if (title.startsWith("Copied sequences"))
2236 newtitle = newtitle.concat("- from " + title);
2241 newtitle = new String("Pasted sequences");
2244 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2249 } catch (Exception ex)
2251 ex.printStackTrace();
2252 System.out.println("Exception whilst pasting: " + ex);
2253 // could be anything being pasted in here
2259 protected void expand_newalign(ActionEvent e)
2263 AlignmentI alignment = AlignmentUtils
2264 .expandContext(getViewport().getAlignment(), -1);
2265 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2267 String newtitle = new String("Flanking alignment");
2269 if (Desktop.jalviewClipboard != null
2270 && Desktop.jalviewClipboard[2] != null)
2272 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2273 af.viewport.setHiddenColumns(hc);
2276 // >>>This is a fix for the moment, until a better solution is
2278 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2279 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2280 .getFeatureRenderer());
2282 // TODO: maintain provenance of an alignment, rather than just make the
2283 // title a concatenation of operations.
2285 if (title.startsWith("Copied sequences"))
2291 newtitle = newtitle.concat("- from " + title);
2295 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2297 } catch (Exception ex)
2299 ex.printStackTrace();
2300 System.out.println("Exception whilst pasting: " + ex);
2301 // could be anything being pasted in here
2302 } catch (OutOfMemoryError oom)
2304 new OOMWarning("Viewing flanking region of alignment", oom);
2315 protected void cut_actionPerformed(ActionEvent e)
2317 copy_actionPerformed(null);
2318 delete_actionPerformed(null);
2328 protected void delete_actionPerformed(ActionEvent evt)
2331 SequenceGroup sg = viewport.getSelectionGroup();
2338 * If the cut affects all sequences, warn, remove highlighted columns
2340 if (sg.getSize() == viewport.getAlignment().getHeight())
2342 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2343 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2344 if (isEntireAlignWidth)
2346 int confirm = JvOptionPane.showConfirmDialog(this,
2347 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2348 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2349 JvOptionPane.OK_CANCEL_OPTION);
2351 if (confirm == JvOptionPane.CANCEL_OPTION
2352 || confirm == JvOptionPane.CLOSED_OPTION)
2357 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2358 sg.getEndRes() + 1);
2360 SequenceI[] cut = sg.getSequences()
2361 .toArray(new SequenceI[sg.getSize()]);
2363 addHistoryItem(new EditCommand(
2364 MessageManager.getString("label.cut_sequences"), Action.CUT,
2365 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2366 viewport.getAlignment()));
2368 viewport.setSelectionGroup(null);
2369 viewport.sendSelection();
2370 viewport.getAlignment().deleteGroup(sg);
2372 viewport.firePropertyChange("alignment", null,
2373 viewport.getAlignment().getSequences());
2374 if (viewport.getAlignment().getHeight() < 1)
2378 this.setClosed(true);
2379 } catch (Exception ex)
2392 protected void deleteGroups_actionPerformed(ActionEvent e)
2394 if (avc.deleteGroups())
2396 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2397 alignPanel.updateAnnotation();
2398 alignPanel.paintAlignment(true, true);
2409 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2411 SequenceGroup sg = new SequenceGroup();
2413 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2415 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2418 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2419 viewport.setSelectionGroup(sg);
2420 viewport.sendSelection();
2421 // JAL-2034 - should delegate to
2422 // alignPanel to decide if overview needs
2424 alignPanel.paintAlignment(false, false);
2425 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2435 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2437 if (viewport.cursorMode)
2439 alignPanel.getSeqPanel().keyboardNo1 = null;
2440 alignPanel.getSeqPanel().keyboardNo2 = null;
2442 viewport.setSelectionGroup(null);
2443 viewport.getColumnSelection().clear();
2444 viewport.setSelectionGroup(null);
2445 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2446 // JAL-2034 - should delegate to
2447 // alignPanel to decide if overview needs
2449 alignPanel.paintAlignment(false, false);
2450 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2451 viewport.sendSelection();
2461 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2463 SequenceGroup sg = viewport.getSelectionGroup();
2467 selectAllSequenceMenuItem_actionPerformed(null);
2472 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2474 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2476 // JAL-2034 - should delegate to
2477 // alignPanel to decide if overview needs
2480 alignPanel.paintAlignment(true, false);
2481 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2482 viewport.sendSelection();
2486 public void invertColSel_actionPerformed(ActionEvent e)
2488 viewport.invertColumnSelection();
2489 alignPanel.paintAlignment(true, false);
2490 viewport.sendSelection();
2500 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2502 trimAlignment(true);
2512 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2514 trimAlignment(false);
2517 void trimAlignment(boolean trimLeft)
2519 ColumnSelection colSel = viewport.getColumnSelection();
2522 if (!colSel.isEmpty())
2526 column = colSel.getMin();
2530 column = colSel.getMax();
2534 if (viewport.getSelectionGroup() != null)
2536 seqs = viewport.getSelectionGroup()
2537 .getSequencesAsArray(viewport.getHiddenRepSequences());
2541 seqs = viewport.getAlignment().getSequencesArray();
2544 TrimRegionCommand trimRegion;
2547 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2548 column, viewport.getAlignment());
2549 viewport.getRanges().setStartRes(0);
2553 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2554 column, viewport.getAlignment());
2557 statusBar.setText(MessageManager
2558 .formatMessage("label.removed_columns", new String[]
2559 { Integer.valueOf(trimRegion.getSize()).toString() }));
2561 addHistoryItem(trimRegion);
2563 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2565 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2566 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2568 viewport.getAlignment().deleteGroup(sg);
2572 viewport.firePropertyChange("alignment", null,
2573 viewport.getAlignment().getSequences());
2584 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2586 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2589 if (viewport.getSelectionGroup() != null)
2591 seqs = viewport.getSelectionGroup()
2592 .getSequencesAsArray(viewport.getHiddenRepSequences());
2593 start = viewport.getSelectionGroup().getStartRes();
2594 end = viewport.getSelectionGroup().getEndRes();
2598 seqs = viewport.getAlignment().getSequencesArray();
2601 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2602 "Remove Gapped Columns", seqs, start, end,
2603 viewport.getAlignment());
2605 addHistoryItem(removeGapCols);
2607 statusBar.setText(MessageManager
2608 .formatMessage("label.removed_empty_columns", new Object[]
2609 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2611 // This is to maintain viewport position on first residue
2612 // of first sequence
2613 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2614 ViewportRanges ranges = viewport.getRanges();
2615 int startRes = seq.findPosition(ranges.getStartRes());
2616 // ShiftList shifts;
2617 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2618 // edit.alColumnChanges=shifts.getInverse();
2619 // if (viewport.hasHiddenColumns)
2620 // viewport.getColumnSelection().compensateForEdits(shifts);
2621 ranges.setStartRes(seq.findIndex(startRes) - 1);
2622 viewport.firePropertyChange("alignment", null,
2623 viewport.getAlignment().getSequences());
2634 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2636 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2639 if (viewport.getSelectionGroup() != null)
2641 seqs = viewport.getSelectionGroup()
2642 .getSequencesAsArray(viewport.getHiddenRepSequences());
2643 start = viewport.getSelectionGroup().getStartRes();
2644 end = viewport.getSelectionGroup().getEndRes();
2648 seqs = viewport.getAlignment().getSequencesArray();
2651 // This is to maintain viewport position on first residue
2652 // of first sequence
2653 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2654 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2656 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2657 viewport.getAlignment()));
2659 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2661 viewport.firePropertyChange("alignment", null,
2662 viewport.getAlignment().getSequences());
2673 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2675 viewport.setPadGaps(padGapsMenuitem.isSelected());
2676 viewport.firePropertyChange("alignment", null,
2677 viewport.getAlignment().getSequences());
2687 public void findMenuItem_actionPerformed(ActionEvent e)
2693 * Create a new view of the current alignment.
2696 public void newView_actionPerformed(ActionEvent e)
2698 newView(null, true);
2702 * Creates and shows a new view of the current alignment.
2705 * title of newly created view; if null, one will be generated
2706 * @param copyAnnotation
2707 * if true then duplicate all annnotation, groups and settings
2708 * @return new alignment panel, already displayed.
2710 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2713 * Create a new AlignmentPanel (with its own, new Viewport)
2715 AlignmentPanel newap = new jalview.project.Jalview2XML()
2716 .copyAlignPanel(alignPanel);
2717 if (!copyAnnotation)
2720 * remove all groups and annotation except for the automatic stuff
2722 newap.av.getAlignment().deleteAllGroups();
2723 newap.av.getAlignment().deleteAllAnnotations(false);
2726 newap.av.setGatherViewsHere(false);
2728 if (viewport.getViewName() == null)
2730 viewport.setViewName(MessageManager
2731 .getString("label.view_name_original"));
2735 * Views share the same edits undo and redo stacks
2737 newap.av.setHistoryList(viewport.getHistoryList());
2738 newap.av.setRedoList(viewport.getRedoList());
2741 * Views share the same mappings; need to deregister any new mappings
2742 * created by copyAlignPanel, and register the new reference to the shared
2745 newap.av.replaceMappings(viewport.getAlignment());
2748 * start up cDNA consensus (if applicable) now mappings are in place
2750 if (newap.av.initComplementConsensus())
2752 newap.refresh(true); // adjust layout of annotations
2755 newap.av.setViewName(getNewViewName(viewTitle));
2757 addAlignmentPanel(newap, true);
2758 newap.alignmentChanged();
2760 if (alignPanels.size() == 2)
2762 viewport.setGatherViewsHere(true);
2764 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2769 * Make a new name for the view, ensuring it is unique within the current
2770 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2771 * these now use viewId. Unique view names are still desirable for usability.)
2776 protected String getNewViewName(String viewTitle)
2778 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2779 boolean addFirstIndex = false;
2780 if (viewTitle == null || viewTitle.trim().length() == 0)
2782 viewTitle = MessageManager.getString("action.view");
2783 addFirstIndex = true;
2787 index = 1;// we count from 1 if given a specific name
2789 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2791 List<Component> comps = PaintRefresher.components
2792 .get(viewport.getSequenceSetId());
2794 List<String> existingNames = getExistingViewNames(comps);
2796 while (existingNames.contains(newViewName))
2798 newViewName = viewTitle + " " + (++index);
2804 * Returns a list of distinct view names found in the given list of
2805 * components. View names are held on the viewport of an AlignmentPanel.
2810 protected List<String> getExistingViewNames(List<Component> comps)
2812 List<String> existingNames = new ArrayList<>();
2813 for (Component comp : comps)
2815 if (comp instanceof AlignmentPanel)
2817 AlignmentPanel ap = (AlignmentPanel) comp;
2818 if (!existingNames.contains(ap.av.getViewName()))
2820 existingNames.add(ap.av.getViewName());
2824 return existingNames;
2828 * Explode tabbed views into separate windows.
2831 public void expandViews_actionPerformed(ActionEvent e)
2833 Desktop.explodeViews(this);
2837 * Gather views in separate windows back into a tabbed presentation.
2840 public void gatherViews_actionPerformed(ActionEvent e)
2842 Desktop.instance.gatherViews(this);
2852 public void font_actionPerformed(ActionEvent e)
2854 new FontChooser(alignPanel);
2864 protected void seqLimit_actionPerformed(ActionEvent e)
2866 viewport.setShowJVSuffix(seqLimits.isSelected());
2868 alignPanel.getIdPanel().getIdCanvas()
2869 .setPreferredSize(alignPanel.calculateIdWidth());
2870 alignPanel.paintAlignment(true, false);
2874 public void idRightAlign_actionPerformed(ActionEvent e)
2876 viewport.setRightAlignIds(idRightAlign.isSelected());
2877 alignPanel.paintAlignment(false, false);
2881 public void centreColumnLabels_actionPerformed(ActionEvent e)
2883 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2884 alignPanel.paintAlignment(false, false);
2890 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2893 protected void followHighlight_actionPerformed()
2896 * Set the 'follow' flag on the Viewport (and scroll to position if now
2899 final boolean state = this.followHighlightMenuItem.getState();
2900 viewport.setFollowHighlight(state);
2903 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2914 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2916 viewport.setColourText(colourTextMenuItem.isSelected());
2917 alignPanel.paintAlignment(false, false);
2927 public void wrapMenuItem_actionPerformed(ActionEvent e)
2929 scaleAbove.setVisible(wrapMenuItem.isSelected());
2930 scaleLeft.setVisible(wrapMenuItem.isSelected());
2931 scaleRight.setVisible(wrapMenuItem.isSelected());
2932 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2933 alignPanel.updateLayout();
2937 public void showAllSeqs_actionPerformed(ActionEvent e)
2939 viewport.showAllHiddenSeqs();
2943 public void showAllColumns_actionPerformed(ActionEvent e)
2945 viewport.showAllHiddenColumns();
2946 alignPanel.paintAlignment(true, true);
2947 viewport.sendSelection();
2951 public void hideSelSequences_actionPerformed(ActionEvent e)
2953 viewport.hideAllSelectedSeqs();
2957 * called by key handler and the hide all/show all menu items
2962 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2965 boolean hide = false;
2966 SequenceGroup sg = viewport.getSelectionGroup();
2967 if (!toggleSeqs && !toggleCols)
2969 // Hide everything by the current selection - this is a hack - we do the
2970 // invert and then hide
2971 // first check that there will be visible columns after the invert.
2972 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2973 && sg.getStartRes() <= sg.getEndRes()))
2975 // now invert the sequence set, if required - empty selection implies
2976 // that no hiding is required.
2979 invertSequenceMenuItem_actionPerformed(null);
2980 sg = viewport.getSelectionGroup();
2984 viewport.expandColSelection(sg, true);
2985 // finally invert the column selection and get the new sequence
2987 invertColSel_actionPerformed(null);
2994 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2996 hideSelSequences_actionPerformed(null);
2999 else if (!(toggleCols && viewport.hasSelectedColumns()))
3001 showAllSeqs_actionPerformed(null);
3007 if (viewport.hasSelectedColumns())
3009 hideSelColumns_actionPerformed(null);
3012 viewport.setSelectionGroup(sg);
3017 showAllColumns_actionPerformed(null);
3026 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3027 * event.ActionEvent)
3030 public void hideAllButSelection_actionPerformed(ActionEvent e)
3032 toggleHiddenRegions(false, false);
3033 viewport.sendSelection();
3040 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3044 public void hideAllSelection_actionPerformed(ActionEvent e)
3046 SequenceGroup sg = viewport.getSelectionGroup();
3047 viewport.expandColSelection(sg, false);
3048 viewport.hideAllSelectedSeqs();
3049 viewport.hideSelectedColumns();
3050 alignPanel.paintAlignment(true, true);
3051 viewport.sendSelection();
3058 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3062 public void showAllhidden_actionPerformed(ActionEvent e)
3064 viewport.showAllHiddenColumns();
3065 viewport.showAllHiddenSeqs();
3066 alignPanel.paintAlignment(true, true);
3067 viewport.sendSelection();
3071 public void hideSelColumns_actionPerformed(ActionEvent e)
3073 viewport.hideSelectedColumns();
3074 alignPanel.paintAlignment(true, true);
3075 viewport.sendSelection();
3079 public void hiddenMarkers_actionPerformed(ActionEvent e)
3081 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3092 protected void scaleAbove_actionPerformed(ActionEvent e)
3094 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3095 // TODO: do we actually need to update overview for scale above change ?
3096 alignPanel.paintAlignment(true, false);
3106 protected void scaleLeft_actionPerformed(ActionEvent e)
3108 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3109 alignPanel.paintAlignment(true, false);
3119 protected void scaleRight_actionPerformed(ActionEvent e)
3121 viewport.setScaleRightWrapped(scaleRight.isSelected());
3122 alignPanel.paintAlignment(true, false);
3132 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3134 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3135 alignPanel.paintAlignment(false, false);
3145 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3147 viewport.setShowText(viewTextMenuItem.isSelected());
3148 alignPanel.paintAlignment(false, false);
3158 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3160 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3161 alignPanel.paintAlignment(false, false);
3164 public FeatureSettings featureSettings;
3167 public FeatureSettingsControllerI getFeatureSettingsUI()
3169 return featureSettings;
3173 public void featureSettings_actionPerformed(ActionEvent e)
3175 if (featureSettings != null)
3177 featureSettings.close();
3178 featureSettings = null;
3180 if (!showSeqFeatures.isSelected())
3182 // make sure features are actually displayed
3183 showSeqFeatures.setSelected(true);
3184 showSeqFeatures_actionPerformed(null);
3186 featureSettings = new FeatureSettings(this);
3190 * Set or clear 'Show Sequence Features'
3196 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3198 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3199 alignPanel.paintAlignment(true, true);
3203 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3204 * the annotations panel as a whole.
3206 * The options to show/hide all annotations should be enabled when the panel
3207 * is shown, and disabled when the panel is hidden.
3212 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3214 final boolean setVisible = annotationPanelMenuItem.isSelected();
3215 viewport.setShowAnnotation(setVisible);
3216 this.showAllSeqAnnotations.setEnabled(setVisible);
3217 this.hideAllSeqAnnotations.setEnabled(setVisible);
3218 this.showAllAlAnnotations.setEnabled(setVisible);
3219 this.hideAllAlAnnotations.setEnabled(setVisible);
3220 alignPanel.updateLayout();
3224 public void alignmentProperties()
3226 JEditorPane editPane = new JEditorPane("text/html", "");
3227 editPane.setEditable(false);
3228 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3231 MessageManager.formatMessage("label.html_content", new Object[]
3232 { contents.toString() }));
3233 JInternalFrame frame = new JInternalFrame();
3234 frame.getContentPane().add(new JScrollPane(editPane));
3236 Desktop.addInternalFrame(frame, MessageManager
3237 .formatMessage("label.alignment_properties", new Object[]
3238 { getTitle() }), 500, 400);
3248 public void overviewMenuItem_actionPerformed(ActionEvent e)
3250 if (alignPanel.overviewPanel != null)
3255 JInternalFrame frame = new JInternalFrame();
3256 final OverviewPanel overview = new OverviewPanel(alignPanel);
3257 frame.setContentPane(overview);
3258 Desktop.addInternalFrame(frame, MessageManager
3259 .formatMessage("label.overview_params", new Object[]
3260 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3263 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3264 frame.addInternalFrameListener(
3265 new javax.swing.event.InternalFrameAdapter()
3268 public void internalFrameClosed(
3269 javax.swing.event.InternalFrameEvent evt)
3272 alignPanel.setOverviewPanel(null);
3275 if (getKeyListeners().length > 0)
3277 frame.addKeyListener(getKeyListeners()[0]);
3280 alignPanel.setOverviewPanel(overview);
3284 public void textColour_actionPerformed()
3286 new TextColourChooser().chooseColour(alignPanel, null);
3290 * public void covariationColour_actionPerformed() {
3292 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3296 public void annotationColour_actionPerformed()
3298 new AnnotationColourChooser(viewport, alignPanel);
3302 public void annotationColumn_actionPerformed(ActionEvent e)
3304 new AnnotationColumnChooser(viewport, alignPanel);
3308 * Action on the user checking or unchecking the option to apply the selected
3309 * colour scheme to all groups. If unchecked, groups may have their own
3310 * independent colour schemes.
3315 public void applyToAllGroups_actionPerformed(boolean selected)
3317 viewport.setColourAppliesToAllGroups(selected);
3321 * Action on user selecting a colour from the colour menu
3324 * the name (not the menu item label!) of the colour scheme
3327 public void changeColour_actionPerformed(String name)
3330 * 'User Defined' opens a panel to configure or load a
3331 * user-defined colour scheme
3333 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3335 new UserDefinedColours(alignPanel);
3340 * otherwise set the chosen colour scheme (or null for 'None')
3342 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3343 viewport.getAlignment(), viewport.getHiddenRepSequences());
3348 * Actions on setting or changing the alignment colour scheme
3353 public void changeColour(ColourSchemeI cs)
3355 // TODO: pull up to controller method
3356 ColourMenuHelper.setColourSelected(colourMenu, cs);
3358 viewport.setGlobalColourScheme(cs);
3360 alignPanel.paintAlignment(true, true);
3364 * Show the PID threshold slider panel
3367 protected void modifyPID_actionPerformed()
3369 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3370 alignPanel.getViewName());
3371 SliderPanel.showPIDSlider();
3375 * Show the Conservation slider panel
3378 protected void modifyConservation_actionPerformed()
3380 SliderPanel.setConservationSlider(alignPanel,
3381 viewport.getResidueShading(), alignPanel.getViewName());
3382 SliderPanel.showConservationSlider();
3386 * Action on selecting or deselecting (Colour) By Conservation
3389 public void conservationMenuItem_actionPerformed(boolean selected)
3391 modifyConservation.setEnabled(selected);
3392 viewport.setConservationSelected(selected);
3393 viewport.getResidueShading().setConservationApplied(selected);
3395 changeColour(viewport.getGlobalColourScheme());
3398 modifyConservation_actionPerformed();
3402 SliderPanel.hideConservationSlider();
3407 * Action on selecting or deselecting (Colour) Above PID Threshold
3410 public void abovePIDThreshold_actionPerformed(boolean selected)
3412 modifyPID.setEnabled(selected);
3413 viewport.setAbovePIDThreshold(selected);
3416 viewport.getResidueShading().setThreshold(0,
3417 viewport.isIgnoreGapsConsensus());
3420 changeColour(viewport.getGlobalColourScheme());
3423 modifyPID_actionPerformed();
3427 SliderPanel.hidePIDSlider();
3438 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3440 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3441 AlignmentSorter.sortByPID(viewport.getAlignment(),
3442 viewport.getAlignment().getSequenceAt(0));
3443 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3444 viewport.getAlignment()));
3445 alignPanel.paintAlignment(true, false);
3455 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3457 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3458 AlignmentSorter.sortByID(viewport.getAlignment());
3460 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3461 alignPanel.paintAlignment(true, false);
3471 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3473 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3474 AlignmentSorter.sortByLength(viewport.getAlignment());
3475 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3476 viewport.getAlignment()));
3477 alignPanel.paintAlignment(true, false);
3487 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3489 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3490 AlignmentSorter.sortByGroup(viewport.getAlignment());
3491 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3492 viewport.getAlignment()));
3494 alignPanel.paintAlignment(true, false);
3504 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3506 new RedundancyPanel(alignPanel, this);
3516 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3518 if ((viewport.getSelectionGroup() == null)
3519 || (viewport.getSelectionGroup().getSize() < 2))
3521 JvOptionPane.showInternalMessageDialog(this,
3522 MessageManager.getString(
3523 "label.you_must_select_least_two_sequences"),
3524 MessageManager.getString("label.invalid_selection"),
3525 JvOptionPane.WARNING_MESSAGE);
3529 JInternalFrame frame = new JInternalFrame();
3530 frame.setContentPane(new PairwiseAlignPanel(viewport));
3531 Desktop.addInternalFrame(frame,
3532 MessageManager.getString("action.pairwise_alignment"), 600,
3538 public void autoCalculate_actionPerformed(ActionEvent e)
3540 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3541 if (viewport.autoCalculateConsensus)
3543 viewport.firePropertyChange("alignment", null,
3544 viewport.getAlignment().getSequences());
3549 public void sortByTreeOption_actionPerformed(ActionEvent e)
3551 viewport.sortByTree = sortByTree.isSelected();
3555 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3557 viewport.followSelection = listenToViewSelections.isSelected();
3561 * Constructs a tree panel and adds it to the desktop
3564 * tree type (NJ or AV)
3566 * name of score model used to compute the tree
3568 * parameters for the distance or similarity calculation
3570 void newTreePanel(String type, String modelName,
3571 SimilarityParamsI options)
3573 String frameTitle = "";
3576 boolean onSelection = false;
3577 if (viewport.getSelectionGroup() != null
3578 && viewport.getSelectionGroup().getSize() > 0)
3580 SequenceGroup sg = viewport.getSelectionGroup();
3582 /* Decide if the selection is a column region */
3583 for (SequenceI _s : sg.getSequences())
3585 if (_s.getLength() < sg.getEndRes())
3587 JvOptionPane.showMessageDialog(Desktop.desktop,
3588 MessageManager.getString(
3589 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3590 MessageManager.getString(
3591 "label.sequences_selection_not_aligned"),
3592 JvOptionPane.WARNING_MESSAGE);
3601 if (viewport.getAlignment().getHeight() < 2)
3607 tp = new TreePanel(alignPanel, type, modelName, options);
3608 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3610 frameTitle += " from ";
3612 if (viewport.getViewName() != null)
3614 frameTitle += viewport.getViewName() + " of ";
3617 frameTitle += this.title;
3619 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3630 public void addSortByOrderMenuItem(String title,
3631 final AlignmentOrder order)
3633 final JMenuItem item = new JMenuItem(MessageManager
3634 .formatMessage("action.by_title_param", new Object[]
3637 item.addActionListener(new java.awt.event.ActionListener()
3640 public void actionPerformed(ActionEvent e)
3642 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3644 // TODO: JBPNote - have to map order entries to curent SequenceI
3646 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3648 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3649 viewport.getAlignment()));
3651 alignPanel.paintAlignment(true, false);
3657 * Add a new sort by annotation score menu item
3660 * the menu to add the option to
3662 * the label used to retrieve scores for each sequence on the
3665 public void addSortByAnnotScoreMenuItem(JMenu sort,
3666 final String scoreLabel)
3668 final JMenuItem item = new JMenuItem(scoreLabel);
3670 item.addActionListener(new java.awt.event.ActionListener()
3673 public void actionPerformed(ActionEvent e)
3675 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3676 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3677 viewport.getAlignment());// ,viewport.getSelectionGroup());
3678 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3679 viewport.getAlignment()));
3680 alignPanel.paintAlignment(true, false);
3686 * last hash for alignment's annotation array - used to minimise cost of
3689 protected int _annotationScoreVectorHash;
3692 * search the alignment and rebuild the sort by annotation score submenu the
3693 * last alignment annotation vector hash is stored to minimize cost of
3694 * rebuilding in subsequence calls.
3698 public void buildSortByAnnotationScoresMenu()
3700 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3705 if (viewport.getAlignment().getAlignmentAnnotation()
3706 .hashCode() != _annotationScoreVectorHash)
3708 sortByAnnotScore.removeAll();
3709 // almost certainly a quicker way to do this - but we keep it simple
3710 Hashtable scoreSorts = new Hashtable();
3711 AlignmentAnnotation aann[];
3712 for (SequenceI sqa : viewport.getAlignment().getSequences())
3714 aann = sqa.getAnnotation();
3715 for (int i = 0; aann != null && i < aann.length; i++)
3717 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3719 scoreSorts.put(aann[i].label, aann[i].label);
3723 Enumeration labels = scoreSorts.keys();
3724 while (labels.hasMoreElements())
3726 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3727 (String) labels.nextElement());
3729 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3732 _annotationScoreVectorHash = viewport.getAlignment()
3733 .getAlignmentAnnotation().hashCode();
3738 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3739 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3740 * call. Listeners are added to remove the menu item when the treePanel is
3741 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3745 public void buildTreeSortMenu()
3747 sortByTreeMenu.removeAll();
3749 List<Component> comps = PaintRefresher.components
3750 .get(viewport.getSequenceSetId());
3751 List<TreePanel> treePanels = new ArrayList<>();
3752 for (Component comp : comps)
3754 if (comp instanceof TreePanel)
3756 treePanels.add((TreePanel) comp);
3760 if (treePanels.size() < 1)
3762 sortByTreeMenu.setVisible(false);
3766 sortByTreeMenu.setVisible(true);
3768 for (final TreePanel tp : treePanels)
3770 final JMenuItem item = new JMenuItem(tp.getTitle());
3771 item.addActionListener(new java.awt.event.ActionListener()
3774 public void actionPerformed(ActionEvent e)
3776 tp.sortByTree_actionPerformed();
3777 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3782 sortByTreeMenu.add(item);
3786 public boolean sortBy(AlignmentOrder alorder, String undoname)
3788 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3789 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3790 if (undoname != null)
3792 addHistoryItem(new OrderCommand(undoname, oldOrder,
3793 viewport.getAlignment()));
3795 alignPanel.paintAlignment(true, false);
3800 * Work out whether the whole set of sequences or just the selected set will
3801 * be submitted for multiple alignment.
3804 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3806 // Now, check we have enough sequences
3807 AlignmentView msa = null;
3809 if ((viewport.getSelectionGroup() != null)
3810 && (viewport.getSelectionGroup().getSize() > 1))
3812 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3813 // some common interface!
3815 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3816 * SequenceI[sz = seqs.getSize(false)];
3818 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3819 * seqs.getSequenceAt(i); }
3821 msa = viewport.getAlignmentView(true);
3823 else if (viewport.getSelectionGroup() != null
3824 && viewport.getSelectionGroup().getSize() == 1)
3826 int option = JvOptionPane.showConfirmDialog(this,
3827 MessageManager.getString("warn.oneseq_msainput_selection"),
3828 MessageManager.getString("label.invalid_selection"),
3829 JvOptionPane.OK_CANCEL_OPTION);
3830 if (option == JvOptionPane.OK_OPTION)
3832 msa = viewport.getAlignmentView(false);
3837 msa = viewport.getAlignmentView(false);
3843 * Decides what is submitted to a secondary structure prediction service: the
3844 * first sequence in the alignment, or in the current selection, or, if the
3845 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3846 * region or the whole alignment. (where the first sequence in the set is the
3847 * one that the prediction will be for).
3849 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3851 AlignmentView seqs = null;
3853 if ((viewport.getSelectionGroup() != null)
3854 && (viewport.getSelectionGroup().getSize() > 0))
3856 seqs = viewport.getAlignmentView(true);
3860 seqs = viewport.getAlignmentView(false);
3862 // limit sequences - JBPNote in future - could spawn multiple prediction
3864 // TODO: viewport.getAlignment().isAligned is a global state - the local
3865 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3866 if (!viewport.getAlignment().isAligned(false))
3868 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3869 // TODO: if seqs.getSequences().length>1 then should really have warned
3883 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3885 // Pick the tree file
3886 JalviewFileChooser chooser = new JalviewFileChooser(
3887 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3888 chooser.setFileView(new JalviewFileView());
3889 chooser.setDialogTitle(
3890 MessageManager.getString("label.select_newick_like_tree_file"));
3891 chooser.setToolTipText(
3892 MessageManager.getString("label.load_tree_file"));
3894 int value = chooser.showOpenDialog(null);
3896 if (value == JalviewFileChooser.APPROVE_OPTION)
3898 String filePath = chooser.getSelectedFile().getPath();
3899 Cache.setProperty("LAST_DIRECTORY", filePath);
3900 NewickFile fin = null;
3903 fin = new NewickFile(filePath, DataSourceType.FILE);
3904 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3905 } catch (Exception ex)
3907 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3908 MessageManager.getString("label.problem_reading_tree_file"),
3909 JvOptionPane.WARNING_MESSAGE);
3910 ex.printStackTrace();
3912 if (fin != null && fin.hasWarningMessage())
3914 JvOptionPane.showMessageDialog(Desktop.desktop,
3915 fin.getWarningMessage(),
3917 .getString("label.possible_problem_with_tree_file"),
3918 JvOptionPane.WARNING_MESSAGE);
3923 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3925 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3928 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3929 int h, int x, int y)
3931 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3935 * Add a treeviewer for the tree extracted from a Newick file object to the
3936 * current alignment view
3943 * Associated alignment input data (or null)
3952 * @return TreePanel handle
3954 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3955 AlignmentView input, int w, int h, int x, int y)
3957 TreePanel tp = null;
3963 if (nf.getTree() != null)
3965 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3971 tp.setLocation(x, y);
3974 Desktop.addInternalFrame(tp, treeTitle, w, h);
3976 } catch (Exception ex)
3978 ex.printStackTrace();
3984 private boolean buildingMenu = false;
3987 * Generates menu items and listener event actions for web service clients
3990 public void BuildWebServiceMenu()
3992 while (buildingMenu)
3996 System.err.println("Waiting for building menu to finish.");
3998 } catch (Exception e)
4002 final AlignFrame me = this;
4003 buildingMenu = true;
4004 new Thread(new Runnable()
4009 final List<JMenuItem> legacyItems = new ArrayList<>();
4012 // System.err.println("Building ws menu again "
4013 // + Thread.currentThread());
4014 // TODO: add support for context dependent disabling of services based
4016 // alignment and current selection
4017 // TODO: add additional serviceHandle parameter to specify abstract
4019 // class independently of AbstractName
4020 // TODO: add in rediscovery GUI function to restart discoverer
4021 // TODO: group services by location as well as function and/or
4023 // object broker mechanism.
4024 final Vector<JMenu> wsmenu = new Vector<>();
4025 final IProgressIndicator af = me;
4028 * do not i18n these strings - they are hard-coded in class
4029 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4030 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4032 final JMenu msawsmenu = new JMenu("Alignment");
4033 final JMenu secstrmenu = new JMenu(
4034 "Secondary Structure Prediction");
4035 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4036 final JMenu analymenu = new JMenu("Analysis");
4037 final JMenu dismenu = new JMenu("Protein Disorder");
4038 // JAL-940 - only show secondary structure prediction services from
4039 // the legacy server
4040 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4042 Discoverer.services != null && (Discoverer.services.size() > 0))
4044 // TODO: refactor to allow list of AbstractName/Handler bindings to
4046 // stored or retrieved from elsewhere
4047 // No MSAWS used any more:
4048 // Vector msaws = null; // (Vector)
4049 // Discoverer.services.get("MsaWS");
4050 Vector secstrpr = (Vector) Discoverer.services
4052 if (secstrpr != null)
4054 // Add any secondary structure prediction services
4055 for (int i = 0, j = secstrpr.size(); i < j; i++)
4057 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4059 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4060 .getServiceClient(sh);
4061 int p = secstrmenu.getItemCount();
4062 impl.attachWSMenuEntry(secstrmenu, me);
4063 int q = secstrmenu.getItemCount();
4064 for (int litm = p; litm < q; litm++)
4066 legacyItems.add(secstrmenu.getItem(litm));
4072 // Add all submenus in the order they should appear on the web
4074 wsmenu.add(msawsmenu);
4075 wsmenu.add(secstrmenu);
4076 wsmenu.add(dismenu);
4077 wsmenu.add(analymenu);
4078 // No search services yet
4079 // wsmenu.add(seqsrchmenu);
4081 javax.swing.SwingUtilities.invokeLater(new Runnable()
4088 webService.removeAll();
4089 // first, add discovered services onto the webservices menu
4090 if (wsmenu.size() > 0)
4092 for (int i = 0, j = wsmenu.size(); i < j; i++)
4094 webService.add(wsmenu.get(i));
4099 webService.add(me.webServiceNoServices);
4101 // TODO: move into separate menu builder class.
4102 boolean new_sspred = false;
4103 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4105 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4106 if (jws2servs != null)
4108 if (jws2servs.hasServices())
4110 jws2servs.attachWSMenuEntry(webService, me);
4111 for (Jws2Instance sv : jws2servs.getServices())
4113 if (sv.description.toLowerCase().contains("jpred"))
4115 for (JMenuItem jmi : legacyItems)
4117 jmi.setVisible(false);
4123 if (jws2servs.isRunning())
4125 JMenuItem tm = new JMenuItem(
4126 "Still discovering JABA Services");
4127 tm.setEnabled(false);
4132 build_urlServiceMenu(me.webService);
4133 build_fetchdbmenu(webService);
4134 for (JMenu item : wsmenu)
4136 if (item.getItemCount() == 0)
4138 item.setEnabled(false);
4142 item.setEnabled(true);
4145 } catch (Exception e)
4148 "Exception during web service menu building process.",
4153 } catch (Exception e)
4156 buildingMenu = false;
4163 * construct any groupURL type service menu entries.
4167 private void build_urlServiceMenu(JMenu webService)
4169 // TODO: remove this code when 2.7 is released
4170 // DEBUG - alignmentView
4172 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4173 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4175 * @Override public void actionPerformed(ActionEvent e) {
4176 * jalview.datamodel.AlignmentView
4177 * .testSelectionViews(af.viewport.getAlignment(),
4178 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4180 * }); webService.add(testAlView);
4182 // TODO: refactor to RestClient discoverer and merge menu entries for
4183 // rest-style services with other types of analysis/calculation service
4184 // SHmmr test client - still being implemented.
4185 // DEBUG - alignmentView
4187 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4190 client.attachWSMenuEntry(
4191 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4197 * Searches the alignment sequences for xRefs and builds the Show
4198 * Cross-References menu (formerly called Show Products), with database
4199 * sources for which cross-references are found (protein sources for a
4200 * nucleotide alignment and vice versa)
4202 * @return true if Show Cross-references menu should be enabled
4204 public boolean canShowProducts()
4206 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4207 AlignmentI dataset = viewport.getAlignment().getDataset();
4209 showProducts.removeAll();
4210 final boolean dna = viewport.getAlignment().isNucleotide();
4212 if (seqs == null || seqs.length == 0)
4214 // nothing to see here.
4218 boolean showp = false;
4221 List<String> ptypes = new CrossRef(seqs, dataset)
4222 .findXrefSourcesForSequences(dna);
4224 for (final String source : ptypes)
4227 final AlignFrame af = this;
4228 JMenuItem xtype = new JMenuItem(source);
4229 xtype.addActionListener(new ActionListener()
4232 public void actionPerformed(ActionEvent e)
4234 showProductsFor(af.viewport.getSequenceSelection(), dna,
4238 showProducts.add(xtype);
4240 showProducts.setVisible(showp);
4241 showProducts.setEnabled(showp);
4242 } catch (Exception e)
4245 "canShowProducts threw an exception - please report to help@jalview.org",
4253 * Finds and displays cross-references for the selected sequences (protein
4254 * products for nucleotide sequences, dna coding sequences for peptides).
4257 * the sequences to show cross-references for
4259 * true if from a nucleotide alignment (so showing proteins)
4261 * the database to show cross-references for
4263 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4264 final String source)
4266 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4271 * Construct and display a new frame containing the translation of this
4272 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4275 public void showTranslation_actionPerformed(ActionEvent e)
4277 AlignmentI al = null;
4280 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4282 al = dna.translateCdna();
4283 } catch (Exception ex)
4285 jalview.bin.Cache.log.error(
4286 "Exception during translation. Please report this !", ex);
4287 final String msg = MessageManager.getString(
4288 "label.error_when_translating_sequences_submit_bug_report");
4289 final String errorTitle = MessageManager
4290 .getString("label.implementation_error")
4291 + MessageManager.getString("label.translation_failed");
4292 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4293 JvOptionPane.ERROR_MESSAGE);
4296 if (al == null || al.getHeight() == 0)
4298 final String msg = MessageManager.getString(
4299 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4300 final String errorTitle = MessageManager
4301 .getString("label.translation_failed");
4302 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4303 JvOptionPane.WARNING_MESSAGE);
4307 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4308 af.setFileFormat(this.currentFileFormat);
4309 final String newTitle = MessageManager
4310 .formatMessage("label.translation_of_params", new Object[]
4311 { this.getTitle() });
4312 af.setTitle(newTitle);
4313 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4315 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4316 viewport.openSplitFrame(af, new Alignment(seqs));
4320 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4327 * Set the file format
4331 public void setFileFormat(FileFormatI format)
4333 this.currentFileFormat = format;
4337 * Try to load a features file onto the alignment.
4340 * contents or path to retrieve file
4342 * access mode of file (see jalview.io.AlignFile)
4343 * @return true if features file was parsed correctly.
4345 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4347 return avc.parseFeaturesFile(file, sourceType,
4348 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4353 public void refreshFeatureUI(boolean enableIfNecessary)
4355 // note - currently this is only still here rather than in the controller
4356 // because of the featureSettings hard reference that is yet to be
4358 if (enableIfNecessary)
4360 viewport.setShowSequenceFeatures(true);
4361 showSeqFeatures.setSelected(true);
4367 public void dragEnter(DropTargetDragEvent evt)
4372 public void dragExit(DropTargetEvent evt)
4377 public void dragOver(DropTargetDragEvent evt)
4382 public void dropActionChanged(DropTargetDragEvent evt)
4387 public void drop(DropTargetDropEvent evt)
4389 // JAL-1552 - acceptDrop required before getTransferable call for
4390 // Java's Transferable for native dnd
4391 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4392 Transferable t = evt.getTransferable();
4393 final AlignFrame thisaf = this;
4394 final List<String> files = new ArrayList<>();
4395 List<DataSourceType> protocols = new ArrayList<>();
4399 Desktop.transferFromDropTarget(files, protocols, evt, t);
4400 } catch (Exception e)
4402 e.printStackTrace();
4406 new Thread(new Runnable()
4413 // check to see if any of these files have names matching sequences
4416 SequenceIdMatcher idm = new SequenceIdMatcher(
4417 viewport.getAlignment().getSequencesArray());
4419 * Object[] { String,SequenceI}
4421 ArrayList<Object[]> filesmatched = new ArrayList<>();
4422 ArrayList<String> filesnotmatched = new ArrayList<>();
4423 for (int i = 0; i < files.size(); i++)
4425 String file = files.get(i).toString();
4427 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4428 if (protocol == DataSourceType.FILE)
4430 File fl = new File(file);
4431 pdbfn = fl.getName();
4433 else if (protocol == DataSourceType.URL)
4435 URL url = new URL(file);
4436 pdbfn = url.getFile();
4438 if (pdbfn.length() > 0)
4440 // attempt to find a match in the alignment
4441 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4442 int l = 0, c = pdbfn.indexOf(".");
4443 while (mtch == null && c != -1)
4448 } while ((c = pdbfn.indexOf(".", l)) > l);
4451 pdbfn = pdbfn.substring(0, l);
4453 mtch = idm.findAllIdMatches(pdbfn);
4457 FileFormatI type = null;
4460 type = new IdentifyFile().identify(file, protocol);
4461 } catch (Exception ex)
4465 if (type != null && type.isStructureFile())
4467 filesmatched.add(new Object[] { file, protocol, mtch });
4471 // File wasn't named like one of the sequences or wasn't a PDB
4473 filesnotmatched.add(file);
4477 if (filesmatched.size() > 0)
4479 boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4482 String msg = MessageManager.formatMessage(
4483 "label.automatically_associate_structure_files_with_sequences_same_name",
4485 { Integer.valueOf(filesmatched.size())
4487 String ttl = MessageManager.getString(
4488 "label.automatically_associate_structure_files_by_name");
4489 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4490 ttl, JvOptionPane.YES_NO_OPTION);
4491 autoAssociate = choice == JvOptionPane.YES_OPTION;
4495 for (Object[] fm : filesmatched)
4497 // try and associate
4498 // TODO: may want to set a standard ID naming formalism for
4499 // associating PDB files which have no IDs.
4500 for (SequenceI toassoc : (SequenceI[]) fm[2])
4502 PDBEntry pe = new AssociatePdbFileWithSeq()
4503 .associatePdbWithSeq((String) fm[0],
4504 (DataSourceType) fm[1], toassoc, false,
4508 System.err.println("Associated file : "
4509 + ((String) fm[0]) + " with "
4510 + toassoc.getDisplayId(true));
4514 // TODO: do we need to update overview ? only if features are
4516 alignPanel.paintAlignment(true, false);
4522 * add declined structures as sequences
4524 for (Object[] o : filesmatched)
4526 filesnotmatched.add((String) o[0]);
4530 if (filesnotmatched.size() > 0)
4532 if (assocfiles > 0 && (Cache.getDefault(
4533 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4534 || JvOptionPane.showConfirmDialog(thisaf,
4535 "<html>" + MessageManager.formatMessage(
4536 "label.ignore_unmatched_dropped_files_info",
4539 filesnotmatched.size())
4542 MessageManager.getString(
4543 "label.ignore_unmatched_dropped_files"),
4544 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4548 for (String fn : filesnotmatched)
4550 loadJalviewDataFile(fn, null, null, null);
4554 } catch (Exception ex)
4556 ex.printStackTrace();
4564 * Attempt to load a "dropped" file or URL string, by testing in turn for
4566 * <li>an Annotation file</li>
4567 * <li>a JNet file</li>
4568 * <li>a features file</li>
4569 * <li>else try to interpret as an alignment file</li>
4573 * either a filename or a URL string.
4575 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4576 FileFormatI format, SequenceI assocSeq)
4580 if (sourceType == null)
4582 sourceType = FormatAdapter.checkProtocol(file);
4584 // if the file isn't identified, or not positively identified as some
4585 // other filetype (PFAM is default unidentified alignment file type) then
4586 // try to parse as annotation.
4587 boolean isAnnotation = (format == null
4588 || FileFormat.Pfam.equals(format))
4589 ? new AnnotationFile().annotateAlignmentView(viewport,
4595 // first see if its a T-COFFEE score file
4596 TCoffeeScoreFile tcf = null;
4599 tcf = new TCoffeeScoreFile(file, sourceType);
4602 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4606 new TCoffeeColourScheme(viewport.getAlignment()));
4607 isAnnotation = true;
4608 statusBar.setText(MessageManager.getString(
4609 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4613 // some problem - if no warning its probable that the ID matching
4614 // process didn't work
4615 JvOptionPane.showMessageDialog(Desktop.desktop,
4616 tcf.getWarningMessage() == null
4617 ? MessageManager.getString(
4618 "label.check_file_matches_sequence_ids_alignment")
4619 : tcf.getWarningMessage(),
4620 MessageManager.getString(
4621 "label.problem_reading_tcoffee_score_file"),
4622 JvOptionPane.WARNING_MESSAGE);
4629 } catch (Exception x)
4632 "Exception when processing data source as T-COFFEE score file",
4638 // try to see if its a JNet 'concise' style annotation file *before*
4640 // try to parse it as a features file
4643 format = new IdentifyFile().identify(file, sourceType);
4645 if (FileFormat.ScoreMatrix == format)
4647 ScoreMatrixFile sm = new ScoreMatrixFile(
4648 new FileParse(file, sourceType));
4650 // todo: i18n this message
4651 statusBar.setText(MessageManager.formatMessage(
4652 "label.successfully_loaded_matrix",
4653 sm.getMatrixName()));
4655 else if (FileFormat.Jnet.equals(format))
4657 JPredFile predictions = new JPredFile(file, sourceType);
4658 new JnetAnnotationMaker();
4659 JnetAnnotationMaker.add_annotation(predictions,
4660 viewport.getAlignment(), 0, false);
4661 viewport.getAlignment().setupJPredAlignment();
4662 isAnnotation = true;
4664 // else if (IdentifyFile.FeaturesFile.equals(format))
4665 else if (FileFormat.Features.equals(format))
4667 if (parseFeaturesFile(file, sourceType))
4669 alignPanel.paintAlignment(true, true);
4674 new FileLoader().LoadFile(viewport, file, sourceType, format);
4681 alignPanel.adjustAnnotationHeight();
4682 viewport.updateSequenceIdColours();
4683 buildSortByAnnotationScoresMenu();
4684 alignPanel.paintAlignment(true, true);
4686 } catch (Exception ex)
4688 ex.printStackTrace();
4689 } catch (OutOfMemoryError oom)
4694 } catch (Exception x)
4699 + (sourceType != null
4700 ? (sourceType == DataSourceType.PASTE
4702 : "using " + sourceType + " from "
4706 ? "(parsing as '" + format + "' file)"
4708 oom, Desktop.desktop);
4713 * Method invoked by the ChangeListener on the tabbed pane, in other words
4714 * when a different tabbed pane is selected by the user or programmatically.
4717 public void tabSelectionChanged(int index)
4721 alignPanel = alignPanels.get(index);
4722 viewport = alignPanel.av;
4723 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4724 setMenusFromViewport(viewport);
4728 * 'focus' any colour slider that is open to the selected viewport
4730 if (viewport.getConservationSelected())
4732 SliderPanel.setConservationSlider(alignPanel,
4733 viewport.getResidueShading(), alignPanel.getViewName());
4737 SliderPanel.hideConservationSlider();
4739 if (viewport.getAbovePIDThreshold())
4741 SliderPanel.setPIDSliderSource(alignPanel,
4742 viewport.getResidueShading(), alignPanel.getViewName());
4746 SliderPanel.hidePIDSlider();
4750 * If there is a frame linked to this one in a SplitPane, switch it to the
4751 * same view tab index. No infinite recursion of calls should happen, since
4752 * tabSelectionChanged() should not get invoked on setting the selected
4753 * index to an unchanged value. Guard against setting an invalid index
4754 * before the new view peer tab has been created.
4756 final AlignViewportI peer = viewport.getCodingComplement();
4759 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4760 .getAlignPanel().alignFrame;
4761 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4763 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4769 * On right mouse click on view tab, prompt for and set new view name.
4772 public void tabbedPane_mousePressed(MouseEvent e)
4774 if (e.isPopupTrigger())
4776 String msg = MessageManager.getString("label.enter_view_name");
4777 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4778 JvOptionPane.QUESTION_MESSAGE);
4782 viewport.setViewName(reply);
4783 // TODO warn if reply is in getExistingViewNames()?
4784 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4789 public AlignViewport getCurrentView()
4795 * Open the dialog for regex description parsing.
4798 protected void extractScores_actionPerformed(ActionEvent e)
4800 ParseProperties pp = new jalview.analysis.ParseProperties(
4801 viewport.getAlignment());
4802 // TODO: verify regex and introduce GUI dialog for version 2.5
4803 // if (pp.getScoresFromDescription("col", "score column ",
4804 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4806 if (pp.getScoresFromDescription("description column",
4807 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4809 buildSortByAnnotationScoresMenu();
4817 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4821 protected void showDbRefs_actionPerformed(ActionEvent e)
4823 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4829 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4833 protected void showNpFeats_actionPerformed(ActionEvent e)
4835 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4839 * find the viewport amongst the tabs in this alignment frame and close that
4844 public boolean closeView(AlignViewportI av)
4848 this.closeMenuItem_actionPerformed(false);
4851 Component[] comp = tabbedPane.getComponents();
4852 for (int i = 0; comp != null && i < comp.length; i++)
4854 if (comp[i] instanceof AlignmentPanel)
4856 if (((AlignmentPanel) comp[i]).av == av)
4859 closeView((AlignmentPanel) comp[i]);
4867 protected void build_fetchdbmenu(JMenu webService)
4869 // Temporary hack - DBRef Fetcher always top level ws entry.
4870 // TODO We probably want to store a sequence database checklist in
4871 // preferences and have checkboxes.. rather than individual sources selected
4873 final JMenu rfetch = new JMenu(
4874 MessageManager.getString("action.fetch_db_references"));
4875 rfetch.setToolTipText(MessageManager.getString(
4876 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4877 webService.add(rfetch);
4879 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4880 MessageManager.getString("option.trim_retrieved_seqs"));
4881 trimrs.setToolTipText(
4882 MessageManager.getString("label.trim_retrieved_sequences"));
4884 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4885 trimrs.addActionListener(new ActionListener()
4888 public void actionPerformed(ActionEvent e)
4890 trimrs.setSelected(trimrs.isSelected());
4891 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4892 Boolean.valueOf(trimrs.isSelected()).toString());
4896 JMenuItem fetchr = new JMenuItem(
4897 MessageManager.getString("label.standard_databases"));
4898 fetchr.setToolTipText(
4899 MessageManager.getString("label.fetch_embl_uniprot"));
4900 fetchr.addActionListener(new ActionListener()
4904 public void actionPerformed(ActionEvent e)
4906 new Thread(new Runnable()
4911 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4912 .getAlignment().isNucleotide();
4913 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4914 alignPanel.av.getSequenceSelection(),
4915 alignPanel.alignFrame, null,
4916 alignPanel.alignFrame.featureSettings, isNucleotide);
4917 dbRefFetcher.addListener(new FetchFinishedListenerI()
4920 public void finished()
4922 AlignFrame.this.setMenusForViewport();
4925 dbRefFetcher.fetchDBRefs(false);
4933 final AlignFrame me = this;
4934 new Thread(new Runnable()
4939 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4940 .getSequenceFetcherSingleton(me);
4941 javax.swing.SwingUtilities.invokeLater(new Runnable()
4946 String[] dbclasses = sf.getOrderedSupportedSources();
4947 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4948 // jalview.util.QuickSort.sort(otherdb, otherdb);
4949 List<DbSourceProxy> otherdb;
4950 JMenu dfetch = new JMenu();
4951 JMenu ifetch = new JMenu();
4952 JMenuItem fetchr = null;
4953 int comp = 0, icomp = 0, mcomp = 15;
4954 String mname = null;
4956 for (String dbclass : dbclasses)
4958 otherdb = sf.getSourceProxy(dbclass);
4959 // add a single entry for this class, or submenu allowing 'fetch
4961 if (otherdb == null || otherdb.size() < 1)
4965 // List<DbSourceProxy> dbs=otherdb;
4966 // otherdb=new ArrayList<DbSourceProxy>();
4967 // for (DbSourceProxy db:dbs)
4969 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4973 mname = "From " + dbclass;
4975 if (otherdb.size() == 1)
4977 final DbSourceProxy[] dassource = otherdb
4978 .toArray(new DbSourceProxy[0]);
4979 DbSourceProxy src = otherdb.get(0);
4980 fetchr = new JMenuItem(src.getDbSource());
4981 fetchr.addActionListener(new ActionListener()
4985 public void actionPerformed(ActionEvent e)
4987 new Thread(new Runnable()
4993 boolean isNucleotide = alignPanel.alignFrame
4994 .getViewport().getAlignment()
4996 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4997 alignPanel.av.getSequenceSelection(),
4998 alignPanel.alignFrame, dassource,
4999 alignPanel.alignFrame.featureSettings,
5002 .addListener(new FetchFinishedListenerI()
5005 public void finished()
5007 AlignFrame.this.setMenusForViewport();
5010 dbRefFetcher.fetchDBRefs(false);
5016 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5017 MessageManager.formatMessage(
5018 "label.fetch_retrieve_from", new Object[]
5019 { src.getDbName() })));
5025 final DbSourceProxy[] dassource = otherdb
5026 .toArray(new DbSourceProxy[0]);
5028 DbSourceProxy src = otherdb.get(0);
5029 fetchr = new JMenuItem(MessageManager
5030 .formatMessage("label.fetch_all_param", new Object[]
5031 { src.getDbSource() }));
5032 fetchr.addActionListener(new ActionListener()
5035 public void actionPerformed(ActionEvent e)
5037 new Thread(new Runnable()
5043 boolean isNucleotide = alignPanel.alignFrame
5044 .getViewport().getAlignment()
5046 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5047 alignPanel.av.getSequenceSelection(),
5048 alignPanel.alignFrame, dassource,
5049 alignPanel.alignFrame.featureSettings,
5052 .addListener(new FetchFinishedListenerI()
5055 public void finished()
5057 AlignFrame.this.setMenusForViewport();
5060 dbRefFetcher.fetchDBRefs(false);
5066 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5067 MessageManager.formatMessage(
5068 "label.fetch_retrieve_from_all_sources",
5070 { Integer.valueOf(otherdb.size())
5072 src.getDbSource(), src.getDbName() })));
5075 // and then build the rest of the individual menus
5076 ifetch = new JMenu(MessageManager.formatMessage(
5077 "label.source_from_db_source", new Object[]
5078 { src.getDbSource() }));
5080 String imname = null;
5082 for (DbSourceProxy sproxy : otherdb)
5084 String dbname = sproxy.getDbName();
5085 String sname = dbname.length() > 5
5086 ? dbname.substring(0, 5) + "..."
5088 String msname = dbname.length() > 10
5089 ? dbname.substring(0, 10) + "..."
5093 imname = MessageManager
5094 .formatMessage("label.from_msname", new Object[]
5097 fetchr = new JMenuItem(msname);
5098 final DbSourceProxy[] dassrc = { sproxy };
5099 fetchr.addActionListener(new ActionListener()
5103 public void actionPerformed(ActionEvent e)
5105 new Thread(new Runnable()
5111 boolean isNucleotide = alignPanel.alignFrame
5112 .getViewport().getAlignment()
5114 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5115 alignPanel.av.getSequenceSelection(),
5116 alignPanel.alignFrame, dassrc,
5117 alignPanel.alignFrame.featureSettings,
5120 .addListener(new FetchFinishedListenerI()
5123 public void finished()
5125 AlignFrame.this.setMenusForViewport();
5128 dbRefFetcher.fetchDBRefs(false);
5134 fetchr.setToolTipText(
5135 "<html>" + MessageManager.formatMessage(
5136 "label.fetch_retrieve_from", new Object[]
5140 if (++icomp >= mcomp || i == (otherdb.size()))
5142 ifetch.setText(MessageManager.formatMessage(
5143 "label.source_to_target", imname, sname));
5145 ifetch = new JMenu();
5153 if (comp >= mcomp || dbi >= (dbclasses.length))
5155 dfetch.setText(MessageManager.formatMessage(
5156 "label.source_to_target", mname, dbclass));
5158 dfetch = new JMenu();
5171 * Left justify the whole alignment.
5174 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5176 AlignmentI al = viewport.getAlignment();
5178 viewport.firePropertyChange("alignment", null, al);
5182 * Right justify the whole alignment.
5185 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5187 AlignmentI al = viewport.getAlignment();
5189 viewport.firePropertyChange("alignment", null, al);
5193 public void setShowSeqFeatures(boolean b)
5195 showSeqFeatures.setSelected(b);
5196 viewport.setShowSequenceFeatures(b);
5203 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5204 * awt.event.ActionEvent)
5207 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5209 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5210 alignPanel.paintAlignment(false, false);
5217 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5221 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5223 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5224 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5232 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5233 * .event.ActionEvent)
5236 protected void showGroupConservation_actionPerformed(ActionEvent e)
5238 viewport.setShowGroupConservation(showGroupConservation.getState());
5239 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5246 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5247 * .event.ActionEvent)
5250 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5252 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5253 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5260 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5261 * .event.ActionEvent)
5264 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5266 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5267 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5271 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5273 showSequenceLogo.setState(true);
5274 viewport.setShowSequenceLogo(true);
5275 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5276 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5280 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5282 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5289 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5290 * .event.ActionEvent)
5293 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5295 if (avc.makeGroupsFromSelection())
5297 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5298 alignPanel.updateAnnotation();
5299 alignPanel.paintAlignment(true, true);
5303 public void clearAlignmentSeqRep()
5305 // TODO refactor alignmentseqrep to controller
5306 if (viewport.getAlignment().hasSeqrep())
5308 viewport.getAlignment().setSeqrep(null);
5309 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5310 alignPanel.updateAnnotation();
5311 alignPanel.paintAlignment(true, true);
5316 protected void createGroup_actionPerformed(ActionEvent e)
5318 if (avc.createGroup())
5320 if (applyAutoAnnotationSettings.isSelected())
5322 alignPanel.updateAnnotation(true, false);
5324 alignPanel.alignmentChanged();
5329 protected void unGroup_actionPerformed(ActionEvent e)
5333 alignPanel.alignmentChanged();
5338 * make the given alignmentPanel the currently selected tab
5340 * @param alignmentPanel
5342 public void setDisplayedView(AlignmentPanel alignmentPanel)
5344 if (!viewport.getSequenceSetId()
5345 .equals(alignmentPanel.av.getSequenceSetId()))
5347 throw new Error(MessageManager.getString(
5348 "error.implementation_error_cannot_show_view_alignment_frame"));
5350 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5351 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5353 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5358 * Action on selection of menu options to Show or Hide annotations.
5361 * @param forSequences
5362 * update sequence-related annotations
5363 * @param forAlignment
5364 * update non-sequence-related annotations
5367 protected void setAnnotationsVisibility(boolean visible,
5368 boolean forSequences, boolean forAlignment)
5370 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5371 .getAlignmentAnnotation();
5376 for (AlignmentAnnotation aa : anns)
5379 * don't display non-positional annotations on an alignment
5381 if (aa.annotations == null)
5385 boolean apply = (aa.sequenceRef == null && forAlignment)
5386 || (aa.sequenceRef != null && forSequences);
5389 aa.visible = visible;
5392 alignPanel.validateAnnotationDimensions(true);
5393 alignPanel.alignmentChanged();
5397 * Store selected annotation sort order for the view and repaint.
5400 protected void sortAnnotations_actionPerformed()
5402 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5404 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5405 alignPanel.paintAlignment(false, false);
5410 * @return alignment panels in this alignment frame
5412 public List<? extends AlignmentViewPanel> getAlignPanels()
5414 // alignPanels is never null
5415 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5420 * Open a new alignment window, with the cDNA associated with this (protein)
5421 * alignment, aligned as is the protein.
5423 protected void viewAsCdna_actionPerformed()
5425 // TODO no longer a menu action - refactor as required
5426 final AlignmentI alignment = getViewport().getAlignment();
5427 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5428 if (mappings == null)
5432 List<SequenceI> cdnaSeqs = new ArrayList<>();
5433 for (SequenceI aaSeq : alignment.getSequences())
5435 for (AlignedCodonFrame acf : mappings)
5437 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5441 * There is a cDNA mapping for this protein sequence - add to new
5442 * alignment. It will share the same dataset sequence as other mapped
5443 * cDNA (no new mappings need to be created).
5445 final Sequence newSeq = new Sequence(dnaSeq);
5446 newSeq.setDatasetSequence(dnaSeq);
5447 cdnaSeqs.add(newSeq);
5451 if (cdnaSeqs.size() == 0)
5453 // show a warning dialog no mapped cDNA
5456 AlignmentI cdna = new Alignment(
5457 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5458 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5459 AlignFrame.DEFAULT_HEIGHT);
5460 cdna.alignAs(alignment);
5461 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5463 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5464 AlignFrame.DEFAULT_HEIGHT);
5468 * Set visibility of dna/protein complement view (available when shown in a
5474 protected void showComplement_actionPerformed(boolean show)
5476 SplitContainerI sf = getSplitViewContainer();
5479 sf.setComplementVisible(this, show);
5484 * Generate the reverse (optionally complemented) of the selected sequences,
5485 * and add them to the alignment
5488 protected void showReverse_actionPerformed(boolean complement)
5490 AlignmentI al = null;
5493 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5494 al = dna.reverseCdna(complement);
5495 viewport.addAlignment(al, "");
5496 addHistoryItem(new EditCommand(
5497 MessageManager.getString("label.add_sequences"), Action.PASTE,
5498 al.getSequencesArray(), 0, al.getWidth(),
5499 viewport.getAlignment()));
5500 } catch (Exception ex)
5502 System.err.println(ex.getMessage());
5508 * Try to run a script in the Groovy console, having first ensured that this
5509 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5510 * be targeted at this alignment.
5513 protected void runGroovy_actionPerformed()
5515 Jalview.setCurrentAlignFrame(this);
5516 groovy.ui.Console console = Desktop.getGroovyConsole();
5517 if (console != null)
5521 console.runScript();
5522 } catch (Exception ex)
5524 System.err.println((ex.toString()));
5525 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5526 MessageManager.getString("label.couldnt_run_groovy_script"),
5527 MessageManager.getString("label.groovy_support_failed"),
5528 JvOptionPane.ERROR_MESSAGE);
5533 System.err.println("Can't run Groovy script as console not found");
5538 * Hides columns containing (or not containing) a specified feature, provided
5539 * that would not leave all columns hidden
5541 * @param featureType
5542 * @param columnsContaining
5545 public boolean hideFeatureColumns(String featureType,
5546 boolean columnsContaining)
5548 boolean notForHiding = avc.markColumnsContainingFeatures(
5549 columnsContaining, false, false, featureType);
5552 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5553 false, featureType))
5555 getViewport().hideSelectedColumns();
5563 protected void selectHighlightedColumns_actionPerformed(
5564 ActionEvent actionEvent)
5566 // include key modifier check in case user selects from menu
5567 avc.markHighlightedColumns(
5568 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5569 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5570 | ActionEvent.CTRL_MASK)) != 0);
5574 * Rebuilds the Colour menu, including any user-defined colours which have
5575 * been loaded either on startup or during the session
5577 public void buildColourMenu()
5579 colourMenu.removeAll();
5581 colourMenu.add(applyToAllGroups);
5582 colourMenu.add(textColour);
5583 colourMenu.addSeparator();
5585 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5588 colourMenu.addSeparator();
5589 colourMenu.add(conservationMenuItem);
5590 colourMenu.add(modifyConservation);
5591 colourMenu.add(abovePIDThreshold);
5592 colourMenu.add(modifyPID);
5593 colourMenu.add(annotationColour);
5595 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5596 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5600 * Open a dialog (if not already open) that allows the user to select and
5601 * calculate PCA or Tree analysis
5603 protected void openTreePcaDialog()
5605 if (alignPanel.getCalculationDialog() == null)
5607 new CalculationChooser(AlignFrame.this);
5612 protected void loadVcf_actionPerformed()
5614 JalviewFileChooser chooser = new JalviewFileChooser(
5615 Cache.getProperty("LAST_DIRECTORY"));
5616 chooser.setFileView(new JalviewFileView());
5617 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5618 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5620 int value = chooser.showOpenDialog(null);
5622 if (value == JalviewFileChooser.APPROVE_OPTION)
5624 String choice = chooser.getSelectedFile().getPath();
5625 Cache.setProperty("LAST_DIRECTORY", choice);
5626 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5627 new VCFLoader(choice).loadVCF(seqs, this);
5633 class PrintThread extends Thread
5637 public PrintThread(AlignmentPanel ap)
5642 static PageFormat pf;
5647 PrinterJob printJob = PrinterJob.getPrinterJob();
5651 printJob.setPrintable(ap, pf);
5655 printJob.setPrintable(ap);
5658 if (printJob.printDialog())
5663 } catch (Exception PrintException)
5665 PrintException.printStackTrace();