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 * Sets the text of the status bar. Note that setting a null or empty value
969 * will cause the status bar to be hidden, with possibly undesirable flicker
970 * of the screen layout.
973 public void setStatus(String text)
975 statusBar.setText(text);
979 * Added so Castor Mapping file can obtain Jalview Version
981 public String getVersion()
983 return jalview.bin.Cache.getProperty("VERSION");
986 public FeatureRenderer getFeatureRenderer()
988 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
992 public void fetchSequence_actionPerformed(ActionEvent e)
994 new jalview.gui.SequenceFetcher(this);
998 public void addFromFile_actionPerformed(ActionEvent e)
1000 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1004 public void reload_actionPerformed(ActionEvent e)
1006 if (fileName != null)
1008 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1009 // originating file's format
1010 // TODO: work out how to recover feature settings for correct view(s) when
1011 // file is reloaded.
1012 if (FileFormat.Jalview.equals(currentFileFormat))
1014 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1015 for (int i = 0; i < frames.length; i++)
1017 if (frames[i] instanceof AlignFrame && frames[i] != this
1018 && ((AlignFrame) frames[i]).fileName != null
1019 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1023 frames[i].setSelected(true);
1024 Desktop.instance.closeAssociatedWindows();
1025 } catch (java.beans.PropertyVetoException ex)
1031 Desktop.instance.closeAssociatedWindows();
1033 FileLoader loader = new FileLoader();
1034 DataSourceType protocol = fileName.startsWith("http:")
1035 ? DataSourceType.URL
1036 : DataSourceType.FILE;
1037 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1041 Rectangle bounds = this.getBounds();
1043 FileLoader loader = new FileLoader();
1044 DataSourceType protocol = fileName.startsWith("http:")
1045 ? DataSourceType.URL
1046 : DataSourceType.FILE;
1047 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1048 protocol, currentFileFormat);
1050 newframe.setBounds(bounds);
1051 if (featureSettings != null && featureSettings.isShowing())
1053 final Rectangle fspos = featureSettings.frame.getBounds();
1054 // TODO: need a 'show feature settings' function that takes bounds -
1055 // need to refactor Desktop.addFrame
1056 newframe.featureSettings_actionPerformed(null);
1057 final FeatureSettings nfs = newframe.featureSettings;
1058 SwingUtilities.invokeLater(new Runnable()
1063 nfs.frame.setBounds(fspos);
1066 this.featureSettings.close();
1067 this.featureSettings = null;
1069 this.closeMenuItem_actionPerformed(true);
1075 public void addFromText_actionPerformed(ActionEvent e)
1078 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1082 public void addFromURL_actionPerformed(ActionEvent e)
1084 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1088 public void save_actionPerformed(ActionEvent e)
1090 if (fileName == null || (currentFileFormat == null)
1091 || fileName.startsWith("http"))
1093 saveAs_actionPerformed(null);
1097 saveAlignment(fileName, currentFileFormat);
1108 public void saveAs_actionPerformed(ActionEvent e)
1110 String format = currentFileFormat == null ? null
1111 : currentFileFormat.getName();
1112 JalviewFileChooser chooser = JalviewFileChooser
1113 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1115 chooser.setFileView(new JalviewFileView());
1116 chooser.setDialogTitle(
1117 MessageManager.getString("label.save_alignment_to_file"));
1118 chooser.setToolTipText(MessageManager.getString("action.save"));
1120 int value = chooser.showSaveDialog(this);
1122 if (value == JalviewFileChooser.APPROVE_OPTION)
1124 currentFileFormat = chooser.getSelectedFormat();
1125 while (currentFileFormat == null)
1127 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1128 MessageManager.getString(
1129 "label.select_file_format_before_saving"),
1130 MessageManager.getString("label.file_format_not_specified"),
1131 JvOptionPane.WARNING_MESSAGE);
1132 currentFileFormat = chooser.getSelectedFormat();
1133 value = chooser.showSaveDialog(this);
1134 if (value != JalviewFileChooser.APPROVE_OPTION)
1140 fileName = chooser.getSelectedFile().getPath();
1142 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1144 Cache.setProperty("LAST_DIRECTORY", fileName);
1145 saveAlignment(fileName, currentFileFormat);
1149 public boolean saveAlignment(String file, FileFormatI format)
1151 boolean success = true;
1153 if (FileFormat.Jalview.equals(format))
1155 String shortName = title;
1157 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1159 shortName = shortName.substring(
1160 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1163 success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1166 statusBar.setText(MessageManager.formatMessage(
1167 "label.successfully_saved_to_file_in_format", new Object[]
1168 { fileName, format }));
1173 AlignmentExportData exportData = getAlignmentForExport(format,
1175 if (exportData.getSettings().isCancelled())
1179 FormatAdapter f = new FormatAdapter(alignPanel,
1180 exportData.getSettings());
1181 String output = f.formatSequences(format, exportData.getAlignment(), // class
1185 // occur in the distant future
1186 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1187 f.getCacheSuffixDefault(format),
1188 viewport.getAlignment().getHiddenColumns());
1196 // create backupfiles object and get new temp filename destination
1197 BackupFiles backupfiles = new BackupFiles(file);
1201 PrintWriter out = new PrintWriter(
1202 new FileWriter(backupfiles.getTempFilePath()));
1206 this.setTitle(file);
1207 statusBar.setText(MessageManager.formatMessage(
1208 "label.successfully_saved_to_file_in_format", new Object[]
1209 { fileName, format.getName() }));
1210 } catch (Exception ex)
1213 ex.printStackTrace();
1216 backupfiles.setWriteSuccess(success);
1217 // do the backup file roll and rename the temp file to actual file
1218 success = backupfiles.rollBackupsAndRenameTempFile();
1225 JvOptionPane.showInternalMessageDialog(this, MessageManager
1226 .formatMessage("label.couldnt_save_file", new Object[]
1228 MessageManager.getString("label.error_saving_file"),
1229 JvOptionPane.WARNING_MESSAGE);
1235 private void warningMessage(String warning, String title)
1237 if (new jalview.util.Platform().isHeadless())
1239 System.err.println("Warning: " + title + "\nWarning: " + warning);
1244 JvOptionPane.showInternalMessageDialog(this, warning, title,
1245 JvOptionPane.WARNING_MESSAGE);
1257 protected void outputText_actionPerformed(ActionEvent e)
1259 FileFormatI fileFormat = FileFormats.getInstance()
1260 .forName(e.getActionCommand());
1261 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1263 if (exportData.getSettings().isCancelled())
1267 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1268 cap.setForInput(null);
1271 FileFormatI format = fileFormat;
1272 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1273 .formatSequences(format, exportData.getAlignment(),
1274 exportData.getOmitHidden(),
1275 exportData.getStartEndPostions(),
1276 viewport.getAlignment().getHiddenColumns()));
1277 Desktop.addInternalFrame(cap, MessageManager
1278 .formatMessage("label.alignment_output_command", new Object[]
1279 { e.getActionCommand() }), 600, 500);
1280 } catch (OutOfMemoryError oom)
1282 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1289 public static AlignmentExportData getAlignmentForExport(
1290 FileFormatI format, AlignViewportI viewport,
1291 AlignExportSettingI exportSettings)
1293 AlignmentI alignmentToExport = null;
1294 AlignExportSettingI settings = exportSettings;
1295 String[] omitHidden = null;
1297 HiddenSequences hiddenSeqs = viewport.getAlignment()
1298 .getHiddenSequences();
1300 alignmentToExport = viewport.getAlignment();
1302 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1303 if (settings == null)
1305 settings = new AlignExportSettings(hasHiddenSeqs,
1306 viewport.hasHiddenColumns(), format);
1308 // settings.isExportAnnotations();
1310 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1312 omitHidden = viewport.getViewAsString(false,
1313 settings.isExportHiddenSequences());
1316 int[] alignmentStartEnd = new int[2];
1317 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1319 alignmentToExport = hiddenSeqs.getFullAlignment();
1323 alignmentToExport = viewport.getAlignment();
1325 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1326 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1327 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1328 omitHidden, alignmentStartEnd, settings);
1339 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1341 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1342 htmlSVG.exportHTML(null);
1346 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1348 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1349 bjs.exportHTML(null);
1352 public void createImageMap(File file, String image)
1354 alignPanel.makePNGImageMap(file, image);
1364 public void createPNG(File f)
1366 alignPanel.makePNG(f);
1376 public void createEPS(File f)
1378 alignPanel.makeEPS(f);
1382 public void createSVG(File f)
1384 alignPanel.makeSVG(f);
1388 public void pageSetup_actionPerformed(ActionEvent e)
1390 PrinterJob printJob = PrinterJob.getPrinterJob();
1391 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1401 public void printMenuItem_actionPerformed(ActionEvent e)
1403 // Putting in a thread avoids Swing painting problems
1404 PrintThread thread = new PrintThread(alignPanel);
1409 public void exportFeatures_actionPerformed(ActionEvent e)
1411 new AnnotationExporter(alignPanel).exportFeatures();
1415 public void exportAnnotations_actionPerformed(ActionEvent e)
1417 new AnnotationExporter(alignPanel).exportAnnotations();
1421 public void associatedData_actionPerformed(ActionEvent e)
1423 // Pick the tree file
1424 JalviewFileChooser chooser = new JalviewFileChooser(
1425 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1426 chooser.setFileView(new JalviewFileView());
1427 chooser.setDialogTitle(
1428 MessageManager.getString("label.load_jalview_annotations"));
1429 chooser.setToolTipText(
1430 MessageManager.getString("label.load_jalview_annotations"));
1432 int value = chooser.showOpenDialog(null);
1434 if (value == JalviewFileChooser.APPROVE_OPTION)
1436 String choice = chooser.getSelectedFile().getPath();
1437 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1438 loadJalviewDataFile(choice, null, null, null);
1444 * Close the current view or all views in the alignment frame. If the frame
1445 * only contains one view then the alignment will be removed from memory.
1447 * @param closeAllTabs
1450 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1452 if (alignPanels != null && alignPanels.size() < 2)
1454 closeAllTabs = true;
1459 if (alignPanels != null)
1463 if (this.isClosed())
1465 // really close all the windows - otherwise wait till
1466 // setClosed(true) is called
1467 for (int i = 0; i < alignPanels.size(); i++)
1469 AlignmentPanel ap = alignPanels.get(i);
1476 closeView(alignPanel);
1483 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1484 * be called recursively, with the frame now in 'closed' state
1486 this.setClosed(true);
1488 } catch (Exception ex)
1490 ex.printStackTrace();
1495 * Close the specified panel and close up tabs appropriately.
1497 * @param panelToClose
1499 public void closeView(AlignmentPanel panelToClose)
1501 int index = tabbedPane.getSelectedIndex();
1502 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1503 alignPanels.remove(panelToClose);
1504 panelToClose.closePanel();
1505 panelToClose = null;
1507 tabbedPane.removeTabAt(closedindex);
1508 tabbedPane.validate();
1510 if (index > closedindex || index == tabbedPane.getTabCount())
1512 // modify currently selected tab index if necessary.
1516 this.tabSelectionChanged(index);
1522 void updateEditMenuBar()
1525 if (viewport.getHistoryList().size() > 0)
1527 undoMenuItem.setEnabled(true);
1528 CommandI command = viewport.getHistoryList().peek();
1529 undoMenuItem.setText(MessageManager
1530 .formatMessage("label.undo_command", new Object[]
1531 { command.getDescription() }));
1535 undoMenuItem.setEnabled(false);
1536 undoMenuItem.setText(MessageManager.getString("action.undo"));
1539 if (viewport.getRedoList().size() > 0)
1541 redoMenuItem.setEnabled(true);
1543 CommandI command = viewport.getRedoList().peek();
1544 redoMenuItem.setText(MessageManager
1545 .formatMessage("label.redo_command", new Object[]
1546 { command.getDescription() }));
1550 redoMenuItem.setEnabled(false);
1551 redoMenuItem.setText(MessageManager.getString("action.redo"));
1556 public void addHistoryItem(CommandI command)
1558 if (command.getSize() > 0)
1560 viewport.addToHistoryList(command);
1561 viewport.clearRedoList();
1562 updateEditMenuBar();
1563 viewport.updateHiddenColumns();
1564 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1565 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1566 // viewport.getColumnSelection()
1567 // .getHiddenColumns().size() > 0);
1573 * @return alignment objects for all views
1575 AlignmentI[] getViewAlignments()
1577 if (alignPanels != null)
1579 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1581 for (AlignmentPanel ap : alignPanels)
1583 als[i++] = ap.av.getAlignment();
1587 if (viewport != null)
1589 return new AlignmentI[] { viewport.getAlignment() };
1601 protected void undoMenuItem_actionPerformed(ActionEvent e)
1603 if (viewport.getHistoryList().isEmpty())
1607 CommandI command = viewport.getHistoryList().pop();
1608 viewport.addToRedoList(command);
1609 command.undoCommand(getViewAlignments());
1611 AlignmentViewport originalSource = getOriginatingSource(command);
1612 updateEditMenuBar();
1614 if (originalSource != null)
1616 if (originalSource != viewport)
1619 "Implementation worry: mismatch of viewport origin for undo");
1621 originalSource.updateHiddenColumns();
1622 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1624 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1625 // viewport.getColumnSelection()
1626 // .getHiddenColumns().size() > 0);
1627 originalSource.firePropertyChange("alignment", null,
1628 originalSource.getAlignment().getSequences());
1639 protected void redoMenuItem_actionPerformed(ActionEvent e)
1641 if (viewport.getRedoList().size() < 1)
1646 CommandI command = viewport.getRedoList().pop();
1647 viewport.addToHistoryList(command);
1648 command.doCommand(getViewAlignments());
1650 AlignmentViewport originalSource = getOriginatingSource(command);
1651 updateEditMenuBar();
1653 if (originalSource != null)
1656 if (originalSource != viewport)
1659 "Implementation worry: mismatch of viewport origin for redo");
1661 originalSource.updateHiddenColumns();
1662 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1664 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1665 // viewport.getColumnSelection()
1666 // .getHiddenColumns().size() > 0);
1667 originalSource.firePropertyChange("alignment", null,
1668 originalSource.getAlignment().getSequences());
1672 AlignmentViewport getOriginatingSource(CommandI command)
1674 AlignmentViewport originalSource = null;
1675 // For sequence removal and addition, we need to fire
1676 // the property change event FROM the viewport where the
1677 // original alignment was altered
1678 AlignmentI al = null;
1679 if (command instanceof EditCommand)
1681 EditCommand editCommand = (EditCommand) command;
1682 al = editCommand.getAlignment();
1683 List<Component> comps = PaintRefresher.components
1684 .get(viewport.getSequenceSetId());
1686 for (Component comp : comps)
1688 if (comp instanceof AlignmentPanel)
1690 if (al == ((AlignmentPanel) comp).av.getAlignment())
1692 originalSource = ((AlignmentPanel) comp).av;
1699 if (originalSource == null)
1701 // The original view is closed, we must validate
1702 // the current view against the closed view first
1705 PaintRefresher.validateSequences(al, viewport.getAlignment());
1708 originalSource = viewport;
1711 return originalSource;
1720 public void moveSelectedSequences(boolean up)
1722 SequenceGroup sg = viewport.getSelectionGroup();
1728 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1729 viewport.getHiddenRepSequences(), up);
1730 alignPanel.paintAlignment(true, false);
1733 synchronized void slideSequences(boolean right, int size)
1735 List<SequenceI> sg = new ArrayList<>();
1736 if (viewport.cursorMode)
1738 sg.add(viewport.getAlignment()
1739 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1741 else if (viewport.getSelectionGroup() != null
1742 && viewport.getSelectionGroup().getSize() != viewport
1743 .getAlignment().getHeight())
1745 sg = viewport.getSelectionGroup()
1746 .getSequences(viewport.getHiddenRepSequences());
1754 List<SequenceI> invertGroup = new ArrayList<>();
1756 for (SequenceI seq : viewport.getAlignment().getSequences())
1758 if (!sg.contains(seq))
1760 invertGroup.add(seq);
1764 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1766 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1767 for (int i = 0; i < invertGroup.size(); i++)
1769 seqs2[i] = invertGroup.get(i);
1772 SlideSequencesCommand ssc;
1775 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1776 viewport.getGapCharacter());
1780 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1781 viewport.getGapCharacter());
1784 int groupAdjustment = 0;
1785 if (ssc.getGapsInsertedBegin() && right)
1787 if (viewport.cursorMode)
1789 alignPanel.getSeqPanel().moveCursor(size, 0);
1793 groupAdjustment = size;
1796 else if (!ssc.getGapsInsertedBegin() && !right)
1798 if (viewport.cursorMode)
1800 alignPanel.getSeqPanel().moveCursor(-size, 0);
1804 groupAdjustment = -size;
1808 if (groupAdjustment != 0)
1810 viewport.getSelectionGroup().setStartRes(
1811 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1812 viewport.getSelectionGroup().setEndRes(
1813 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1817 * just extend the last slide command if compatible; but not if in
1818 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1820 boolean appendHistoryItem = false;
1821 Deque<CommandI> historyList = viewport.getHistoryList();
1822 boolean inSplitFrame = getSplitViewContainer() != null;
1823 if (!inSplitFrame && historyList != null && historyList.size() > 0
1824 && historyList.peek() instanceof SlideSequencesCommand)
1826 appendHistoryItem = ssc.appendSlideCommand(
1827 (SlideSequencesCommand) historyList.peek());
1830 if (!appendHistoryItem)
1832 addHistoryItem(ssc);
1845 protected void copy_actionPerformed(ActionEvent e)
1847 if (viewport.getSelectionGroup() == null)
1851 // TODO: preserve the ordering of displayed alignment annotation in any
1852 // internal paste (particularly sequence associated annotation)
1853 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1854 String[] omitHidden = null;
1856 if (viewport.hasHiddenColumns())
1858 omitHidden = viewport.getViewAsString(true);
1861 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1862 seqs, omitHidden, null);
1864 StringSelection ss = new StringSelection(output);
1868 jalview.gui.Desktop.internalCopy = true;
1869 // Its really worth setting the clipboard contents
1870 // to empty before setting the large StringSelection!!
1871 Toolkit.getDefaultToolkit().getSystemClipboard()
1872 .setContents(new StringSelection(""), null);
1874 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1876 } catch (OutOfMemoryError er)
1878 new OOMWarning("copying region", er);
1882 HiddenColumns hiddenColumns = null;
1883 if (viewport.hasHiddenColumns())
1885 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1886 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1888 // create new HiddenColumns object with copy of hidden regions
1889 // between startRes and endRes, offset by startRes
1890 hiddenColumns = new HiddenColumns(
1891 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1892 hiddenCutoff, hiddenOffset);
1895 Desktop.jalviewClipboard = new Object[] { seqs,
1896 viewport.getAlignment().getDataset(), hiddenColumns };
1897 statusBar.setText(MessageManager.formatMessage(
1898 "label.copied_sequences_to_clipboard", new Object[]
1899 { Integer.valueOf(seqs.length).toString() }));
1909 protected void pasteNew_actionPerformed(ActionEvent e)
1921 protected void pasteThis_actionPerformed(ActionEvent e)
1927 * Paste contents of Jalview clipboard
1929 * @param newAlignment
1930 * true to paste to a new alignment, otherwise add to this.
1932 void paste(boolean newAlignment)
1934 boolean externalPaste = true;
1937 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1938 Transferable contents = c.getContents(this);
1940 if (contents == null)
1949 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1950 if (str.length() < 1)
1955 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1957 } catch (OutOfMemoryError er)
1959 new OOMWarning("Out of memory pasting sequences!!", er);
1963 SequenceI[] sequences;
1964 boolean annotationAdded = false;
1965 AlignmentI alignment = null;
1967 if (Desktop.jalviewClipboard != null)
1969 // The clipboard was filled from within Jalview, we must use the
1971 // And dataset from the copied alignment
1972 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1973 // be doubly sure that we create *new* sequence objects.
1974 sequences = new SequenceI[newseq.length];
1975 for (int i = 0; i < newseq.length; i++)
1977 sequences[i] = new Sequence(newseq[i]);
1979 alignment = new Alignment(sequences);
1980 externalPaste = false;
1984 // parse the clipboard as an alignment.
1985 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1987 sequences = alignment.getSequencesArray();
1991 ArrayList<Integer> newGraphGroups = new ArrayList<>();
1997 if (Desktop.jalviewClipboard != null)
1999 // dataset is inherited
2000 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2004 // new dataset is constructed
2005 alignment.setDataset(null);
2007 alwidth = alignment.getWidth() + 1;
2011 AlignmentI pastedal = alignment; // preserve pasted alignment object
2012 // Add pasted sequences and dataset into existing alignment.
2013 alignment = viewport.getAlignment();
2014 alwidth = alignment.getWidth() + 1;
2015 // decide if we need to import sequences from an existing dataset
2016 boolean importDs = Desktop.jalviewClipboard != null
2017 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2018 // importDs==true instructs us to copy over new dataset sequences from
2019 // an existing alignment
2020 Vector newDs = (importDs) ? new Vector() : null; // used to create
2021 // minimum dataset set
2023 for (int i = 0; i < sequences.length; i++)
2027 newDs.addElement(null);
2029 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2031 if (importDs && ds != null)
2033 if (!newDs.contains(ds))
2035 newDs.setElementAt(ds, i);
2036 ds = new Sequence(ds);
2037 // update with new dataset sequence
2038 sequences[i].setDatasetSequence(ds);
2042 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2047 // copy and derive new dataset sequence
2048 sequences[i] = sequences[i].deriveSequence();
2049 alignment.getDataset()
2050 .addSequence(sequences[i].getDatasetSequence());
2051 // TODO: avoid creation of duplicate dataset sequences with a
2052 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2054 alignment.addSequence(sequences[i]); // merges dataset
2058 newDs.clear(); // tidy up
2060 if (alignment.getAlignmentAnnotation() != null)
2062 for (AlignmentAnnotation alan : alignment
2063 .getAlignmentAnnotation())
2065 if (alan.graphGroup > fgroup)
2067 fgroup = alan.graphGroup;
2071 if (pastedal.getAlignmentAnnotation() != null)
2073 // Add any annotation attached to alignment.
2074 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2075 for (int i = 0; i < alann.length; i++)
2077 annotationAdded = true;
2078 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2080 AlignmentAnnotation newann = new AlignmentAnnotation(
2082 if (newann.graphGroup > -1)
2084 if (newGraphGroups.size() <= newann.graphGroup
2085 || newGraphGroups.get(newann.graphGroup) == null)
2087 for (int q = newGraphGroups
2088 .size(); q <= newann.graphGroup; q++)
2090 newGraphGroups.add(q, null);
2092 newGraphGroups.set(newann.graphGroup,
2093 new Integer(++fgroup));
2095 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2099 newann.padAnnotation(alwidth);
2100 alignment.addAnnotation(newann);
2110 addHistoryItem(new EditCommand(
2111 MessageManager.getString("label.add_sequences"),
2112 Action.PASTE, sequences, 0, alignment.getWidth(),
2115 // Add any annotations attached to sequences
2116 for (int i = 0; i < sequences.length; i++)
2118 if (sequences[i].getAnnotation() != null)
2120 AlignmentAnnotation newann;
2121 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2123 annotationAdded = true;
2124 newann = sequences[i].getAnnotation()[a];
2125 newann.adjustForAlignment();
2126 newann.padAnnotation(alwidth);
2127 if (newann.graphGroup > -1)
2129 if (newann.graphGroup > -1)
2131 if (newGraphGroups.size() <= newann.graphGroup
2132 || newGraphGroups.get(newann.graphGroup) == null)
2134 for (int q = newGraphGroups
2135 .size(); q <= newann.graphGroup; q++)
2137 newGraphGroups.add(q, null);
2139 newGraphGroups.set(newann.graphGroup,
2140 new Integer(++fgroup));
2142 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2146 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2150 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2158 // propagate alignment changed.
2159 viewport.getRanges().setEndSeq(alignment.getHeight());
2160 if (annotationAdded)
2162 // Duplicate sequence annotation in all views.
2163 AlignmentI[] alview = this.getViewAlignments();
2164 for (int i = 0; i < sequences.length; i++)
2166 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2171 for (int avnum = 0; avnum < alview.length; avnum++)
2173 if (alview[avnum] != alignment)
2175 // duplicate in a view other than the one with input focus
2176 int avwidth = alview[avnum].getWidth() + 1;
2177 // this relies on sann being preserved after we
2178 // modify the sequence's annotation array for each duplication
2179 for (int a = 0; a < sann.length; a++)
2181 AlignmentAnnotation newann = new AlignmentAnnotation(
2183 sequences[i].addAlignmentAnnotation(newann);
2184 newann.padAnnotation(avwidth);
2185 alview[avnum].addAnnotation(newann); // annotation was
2186 // duplicated earlier
2187 // TODO JAL-1145 graphGroups are not updated for sequence
2188 // annotation added to several views. This may cause
2190 alview[avnum].setAnnotationIndex(newann, a);
2195 buildSortByAnnotationScoresMenu();
2197 viewport.firePropertyChange("alignment", null,
2198 alignment.getSequences());
2199 if (alignPanels != null)
2201 for (AlignmentPanel ap : alignPanels)
2203 ap.validateAnnotationDimensions(false);
2208 alignPanel.validateAnnotationDimensions(false);
2214 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2216 String newtitle = new String("Copied sequences");
2218 if (Desktop.jalviewClipboard != null
2219 && Desktop.jalviewClipboard[2] != null)
2221 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2222 af.viewport.setHiddenColumns(hc);
2225 // >>>This is a fix for the moment, until a better solution is
2227 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2228 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2229 .getFeatureRenderer());
2231 // TODO: maintain provenance of an alignment, rather than just make the
2232 // title a concatenation of operations.
2235 if (title.startsWith("Copied sequences"))
2241 newtitle = newtitle.concat("- from " + title);
2246 newtitle = new String("Pasted sequences");
2249 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2254 } catch (Exception ex)
2256 ex.printStackTrace();
2257 System.out.println("Exception whilst pasting: " + ex);
2258 // could be anything being pasted in here
2264 protected void expand_newalign(ActionEvent e)
2268 AlignmentI alignment = AlignmentUtils
2269 .expandContext(getViewport().getAlignment(), -1);
2270 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2272 String newtitle = new String("Flanking alignment");
2274 if (Desktop.jalviewClipboard != null
2275 && Desktop.jalviewClipboard[2] != null)
2277 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2278 af.viewport.setHiddenColumns(hc);
2281 // >>>This is a fix for the moment, until a better solution is
2283 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2284 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2285 .getFeatureRenderer());
2287 // TODO: maintain provenance of an alignment, rather than just make the
2288 // title a concatenation of operations.
2290 if (title.startsWith("Copied sequences"))
2296 newtitle = newtitle.concat("- from " + title);
2300 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2302 } catch (Exception ex)
2304 ex.printStackTrace();
2305 System.out.println("Exception whilst pasting: " + ex);
2306 // could be anything being pasted in here
2307 } catch (OutOfMemoryError oom)
2309 new OOMWarning("Viewing flanking region of alignment", oom);
2320 protected void cut_actionPerformed(ActionEvent e)
2322 copy_actionPerformed(null);
2323 delete_actionPerformed(null);
2333 protected void delete_actionPerformed(ActionEvent evt)
2336 SequenceGroup sg = viewport.getSelectionGroup();
2343 * If the cut affects all sequences, warn, remove highlighted columns
2345 if (sg.getSize() == viewport.getAlignment().getHeight())
2347 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2348 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2349 if (isEntireAlignWidth)
2351 int confirm = JvOptionPane.showConfirmDialog(this,
2352 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2353 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2354 JvOptionPane.OK_CANCEL_OPTION);
2356 if (confirm == JvOptionPane.CANCEL_OPTION
2357 || confirm == JvOptionPane.CLOSED_OPTION)
2362 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2363 sg.getEndRes() + 1);
2365 SequenceI[] cut = sg.getSequences()
2366 .toArray(new SequenceI[sg.getSize()]);
2368 addHistoryItem(new EditCommand(
2369 MessageManager.getString("label.cut_sequences"), Action.CUT,
2370 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2371 viewport.getAlignment()));
2373 viewport.setSelectionGroup(null);
2374 viewport.sendSelection();
2375 viewport.getAlignment().deleteGroup(sg);
2377 viewport.firePropertyChange("alignment", null,
2378 viewport.getAlignment().getSequences());
2379 if (viewport.getAlignment().getHeight() < 1)
2383 this.setClosed(true);
2384 } catch (Exception ex)
2397 protected void deleteGroups_actionPerformed(ActionEvent e)
2399 if (avc.deleteGroups())
2401 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2402 alignPanel.updateAnnotation();
2403 alignPanel.paintAlignment(true, true);
2414 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2416 SequenceGroup sg = new SequenceGroup(
2417 viewport.getAlignment().getSequences());
2419 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2420 viewport.setSelectionGroup(sg);
2421 viewport.isSelectionGroupChanged(true);
2422 viewport.sendSelection();
2423 // JAL-2034 - should delegate to
2424 // alignPanel to decide if overview needs
2426 alignPanel.paintAlignment(false, false);
2427 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2437 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2439 if (viewport.cursorMode)
2441 alignPanel.getSeqPanel().keyboardNo1 = null;
2442 alignPanel.getSeqPanel().keyboardNo2 = null;
2444 viewport.setSelectionGroup(null);
2445 viewport.getColumnSelection().clear();
2446 viewport.setSelectionGroup(null);
2447 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2448 // JAL-2034 - should delegate to
2449 // alignPanel to decide if overview needs
2451 alignPanel.paintAlignment(false, false);
2452 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2453 viewport.sendSelection();
2463 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2465 SequenceGroup sg = viewport.getSelectionGroup();
2469 selectAllSequenceMenuItem_actionPerformed(null);
2474 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2476 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2478 // JAL-2034 - should delegate to
2479 // alignPanel to decide if overview needs
2482 alignPanel.paintAlignment(true, false);
2483 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2484 viewport.sendSelection();
2488 public void invertColSel_actionPerformed(ActionEvent e)
2490 viewport.invertColumnSelection();
2491 alignPanel.paintAlignment(true, false);
2492 viewport.sendSelection();
2502 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2504 trimAlignment(true);
2514 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2516 trimAlignment(false);
2519 void trimAlignment(boolean trimLeft)
2521 ColumnSelection colSel = viewport.getColumnSelection();
2524 if (!colSel.isEmpty())
2528 column = colSel.getMin();
2532 column = colSel.getMax();
2536 if (viewport.getSelectionGroup() != null)
2538 seqs = viewport.getSelectionGroup()
2539 .getSequencesAsArray(viewport.getHiddenRepSequences());
2543 seqs = viewport.getAlignment().getSequencesArray();
2546 TrimRegionCommand trimRegion;
2549 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2550 column, viewport.getAlignment());
2551 viewport.getRanges().setStartRes(0);
2555 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2556 column, viewport.getAlignment());
2559 statusBar.setText(MessageManager
2560 .formatMessage("label.removed_columns", new String[]
2561 { Integer.valueOf(trimRegion.getSize()).toString() }));
2563 addHistoryItem(trimRegion);
2565 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2567 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2568 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2570 viewport.getAlignment().deleteGroup(sg);
2574 viewport.firePropertyChange("alignment", null,
2575 viewport.getAlignment().getSequences());
2586 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2588 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2591 if (viewport.getSelectionGroup() != null)
2593 seqs = viewport.getSelectionGroup()
2594 .getSequencesAsArray(viewport.getHiddenRepSequences());
2595 start = viewport.getSelectionGroup().getStartRes();
2596 end = viewport.getSelectionGroup().getEndRes();
2600 seqs = viewport.getAlignment().getSequencesArray();
2603 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2604 "Remove Gapped Columns", seqs, start, end,
2605 viewport.getAlignment());
2607 addHistoryItem(removeGapCols);
2609 statusBar.setText(MessageManager
2610 .formatMessage("label.removed_empty_columns", new Object[]
2611 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2613 // This is to maintain viewport position on first residue
2614 // of first sequence
2615 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2616 ViewportRanges ranges = viewport.getRanges();
2617 int startRes = seq.findPosition(ranges.getStartRes());
2618 // ShiftList shifts;
2619 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2620 // edit.alColumnChanges=shifts.getInverse();
2621 // if (viewport.hasHiddenColumns)
2622 // viewport.getColumnSelection().compensateForEdits(shifts);
2623 ranges.setStartRes(seq.findIndex(startRes) - 1);
2624 viewport.firePropertyChange("alignment", null,
2625 viewport.getAlignment().getSequences());
2636 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2638 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2641 if (viewport.getSelectionGroup() != null)
2643 seqs = viewport.getSelectionGroup()
2644 .getSequencesAsArray(viewport.getHiddenRepSequences());
2645 start = viewport.getSelectionGroup().getStartRes();
2646 end = viewport.getSelectionGroup().getEndRes();
2650 seqs = viewport.getAlignment().getSequencesArray();
2653 // This is to maintain viewport position on first residue
2654 // of first sequence
2655 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2656 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2658 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2659 viewport.getAlignment()));
2661 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2663 viewport.firePropertyChange("alignment", null,
2664 viewport.getAlignment().getSequences());
2675 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2677 viewport.setPadGaps(padGapsMenuitem.isSelected());
2678 viewport.firePropertyChange("alignment", null,
2679 viewport.getAlignment().getSequences());
2689 public void findMenuItem_actionPerformed(ActionEvent e)
2695 * Create a new view of the current alignment.
2698 public void newView_actionPerformed(ActionEvent e)
2700 newView(null, true);
2704 * Creates and shows a new view of the current alignment.
2707 * title of newly created view; if null, one will be generated
2708 * @param copyAnnotation
2709 * if true then duplicate all annnotation, groups and settings
2710 * @return new alignment panel, already displayed.
2712 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2715 * Create a new AlignmentPanel (with its own, new Viewport)
2717 AlignmentPanel newap = new jalview.project.Jalview2XML()
2718 .copyAlignPanel(alignPanel);
2719 if (!copyAnnotation)
2722 * remove all groups and annotation except for the automatic stuff
2724 newap.av.getAlignment().deleteAllGroups();
2725 newap.av.getAlignment().deleteAllAnnotations(false);
2728 newap.av.setGatherViewsHere(false);
2730 if (viewport.getViewName() == null)
2732 viewport.setViewName(MessageManager
2733 .getString("label.view_name_original"));
2737 * Views share the same edits undo and redo stacks
2739 newap.av.setHistoryList(viewport.getHistoryList());
2740 newap.av.setRedoList(viewport.getRedoList());
2743 * Views share the same mappings; need to deregister any new mappings
2744 * created by copyAlignPanel, and register the new reference to the shared
2747 newap.av.replaceMappings(viewport.getAlignment());
2750 * start up cDNA consensus (if applicable) now mappings are in place
2752 if (newap.av.initComplementConsensus())
2754 newap.refresh(true); // adjust layout of annotations
2757 newap.av.setViewName(getNewViewName(viewTitle));
2759 addAlignmentPanel(newap, true);
2760 newap.alignmentChanged();
2762 if (alignPanels.size() == 2)
2764 viewport.setGatherViewsHere(true);
2766 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2771 * Make a new name for the view, ensuring it is unique within the current
2772 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2773 * these now use viewId. Unique view names are still desirable for usability.)
2778 protected String getNewViewName(String viewTitle)
2780 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2781 boolean addFirstIndex = false;
2782 if (viewTitle == null || viewTitle.trim().length() == 0)
2784 viewTitle = MessageManager.getString("action.view");
2785 addFirstIndex = true;
2789 index = 1;// we count from 1 if given a specific name
2791 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2793 List<Component> comps = PaintRefresher.components
2794 .get(viewport.getSequenceSetId());
2796 List<String> existingNames = getExistingViewNames(comps);
2798 while (existingNames.contains(newViewName))
2800 newViewName = viewTitle + " " + (++index);
2806 * Returns a list of distinct view names found in the given list of
2807 * components. View names are held on the viewport of an AlignmentPanel.
2812 protected List<String> getExistingViewNames(List<Component> comps)
2814 List<String> existingNames = new ArrayList<>();
2815 for (Component comp : comps)
2817 if (comp instanceof AlignmentPanel)
2819 AlignmentPanel ap = (AlignmentPanel) comp;
2820 if (!existingNames.contains(ap.av.getViewName()))
2822 existingNames.add(ap.av.getViewName());
2826 return existingNames;
2830 * Explode tabbed views into separate windows.
2833 public void expandViews_actionPerformed(ActionEvent e)
2835 Desktop.explodeViews(this);
2839 * Gather views in separate windows back into a tabbed presentation.
2842 public void gatherViews_actionPerformed(ActionEvent e)
2844 Desktop.instance.gatherViews(this);
2854 public void font_actionPerformed(ActionEvent e)
2856 new FontChooser(alignPanel);
2866 protected void seqLimit_actionPerformed(ActionEvent e)
2868 viewport.setShowJVSuffix(seqLimits.isSelected());
2870 alignPanel.getIdPanel().getIdCanvas()
2871 .setPreferredSize(alignPanel.calculateIdWidth());
2872 alignPanel.paintAlignment(true, false);
2876 public void idRightAlign_actionPerformed(ActionEvent e)
2878 viewport.setRightAlignIds(idRightAlign.isSelected());
2879 alignPanel.paintAlignment(false, false);
2883 public void centreColumnLabels_actionPerformed(ActionEvent e)
2885 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2886 alignPanel.paintAlignment(false, false);
2892 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2895 protected void followHighlight_actionPerformed()
2898 * Set the 'follow' flag on the Viewport (and scroll to position if now
2901 final boolean state = this.followHighlightMenuItem.getState();
2902 viewport.setFollowHighlight(state);
2905 alignPanel.scrollToPosition(viewport.getSearchResults());
2916 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2918 viewport.setColourText(colourTextMenuItem.isSelected());
2919 alignPanel.paintAlignment(false, false);
2929 public void wrapMenuItem_actionPerformed(ActionEvent e)
2931 scaleAbove.setVisible(wrapMenuItem.isSelected());
2932 scaleLeft.setVisible(wrapMenuItem.isSelected());
2933 scaleRight.setVisible(wrapMenuItem.isSelected());
2934 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2935 alignPanel.updateLayout();
2939 public void showAllSeqs_actionPerformed(ActionEvent e)
2941 viewport.showAllHiddenSeqs();
2945 public void showAllColumns_actionPerformed(ActionEvent e)
2947 viewport.showAllHiddenColumns();
2948 alignPanel.paintAlignment(true, true);
2949 viewport.sendSelection();
2953 public void hideSelSequences_actionPerformed(ActionEvent e)
2955 viewport.hideAllSelectedSeqs();
2959 * called by key handler and the hide all/show all menu items
2964 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2967 boolean hide = false;
2968 SequenceGroup sg = viewport.getSelectionGroup();
2969 if (!toggleSeqs && !toggleCols)
2971 // Hide everything by the current selection - this is a hack - we do the
2972 // invert and then hide
2973 // first check that there will be visible columns after the invert.
2974 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2975 && sg.getStartRes() <= sg.getEndRes()))
2977 // now invert the sequence set, if required - empty selection implies
2978 // that no hiding is required.
2981 invertSequenceMenuItem_actionPerformed(null);
2982 sg = viewport.getSelectionGroup();
2986 viewport.expandColSelection(sg, true);
2987 // finally invert the column selection and get the new sequence
2989 invertColSel_actionPerformed(null);
2996 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2998 hideSelSequences_actionPerformed(null);
3001 else if (!(toggleCols && viewport.hasSelectedColumns()))
3003 showAllSeqs_actionPerformed(null);
3009 if (viewport.hasSelectedColumns())
3011 hideSelColumns_actionPerformed(null);
3014 viewport.setSelectionGroup(sg);
3019 showAllColumns_actionPerformed(null);
3028 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3029 * event.ActionEvent)
3032 public void hideAllButSelection_actionPerformed(ActionEvent e)
3034 toggleHiddenRegions(false, false);
3035 viewport.sendSelection();
3042 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3046 public void hideAllSelection_actionPerformed(ActionEvent e)
3048 SequenceGroup sg = viewport.getSelectionGroup();
3049 viewport.expandColSelection(sg, false);
3050 viewport.hideAllSelectedSeqs();
3051 viewport.hideSelectedColumns();
3052 alignPanel.updateLayout();
3053 alignPanel.paintAlignment(true, true);
3054 viewport.sendSelection();
3061 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3065 public void showAllhidden_actionPerformed(ActionEvent e)
3067 viewport.showAllHiddenColumns();
3068 viewport.showAllHiddenSeqs();
3069 alignPanel.paintAlignment(true, true);
3070 viewport.sendSelection();
3074 public void hideSelColumns_actionPerformed(ActionEvent e)
3076 viewport.hideSelectedColumns();
3077 alignPanel.updateLayout();
3078 alignPanel.paintAlignment(true, true);
3079 viewport.sendSelection();
3083 public void hiddenMarkers_actionPerformed(ActionEvent e)
3085 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3096 protected void scaleAbove_actionPerformed(ActionEvent e)
3098 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3099 // TODO: do we actually need to update overview for scale above change ?
3100 alignPanel.paintAlignment(true, false);
3110 protected void scaleLeft_actionPerformed(ActionEvent e)
3112 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3113 alignPanel.paintAlignment(true, false);
3123 protected void scaleRight_actionPerformed(ActionEvent e)
3125 viewport.setScaleRightWrapped(scaleRight.isSelected());
3126 alignPanel.paintAlignment(true, false);
3136 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3138 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3139 alignPanel.paintAlignment(false, false);
3149 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3151 viewport.setShowText(viewTextMenuItem.isSelected());
3152 alignPanel.paintAlignment(false, false);
3162 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3164 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3165 alignPanel.paintAlignment(false, false);
3168 public FeatureSettings featureSettings;
3171 public FeatureSettingsControllerI getFeatureSettingsUI()
3173 return featureSettings;
3177 public void featureSettings_actionPerformed(ActionEvent e)
3179 if (featureSettings != null)
3181 featureSettings.close();
3182 featureSettings = null;
3184 if (!showSeqFeatures.isSelected())
3186 // make sure features are actually displayed
3187 showSeqFeatures.setSelected(true);
3188 showSeqFeatures_actionPerformed(null);
3190 featureSettings = new FeatureSettings(this);
3194 * Set or clear 'Show Sequence Features'
3200 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3202 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3203 alignPanel.paintAlignment(true, true);
3207 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3208 * the annotations panel as a whole.
3210 * The options to show/hide all annotations should be enabled when the panel
3211 * is shown, and disabled when the panel is hidden.
3216 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3218 final boolean setVisible = annotationPanelMenuItem.isSelected();
3219 viewport.setShowAnnotation(setVisible);
3220 this.showAllSeqAnnotations.setEnabled(setVisible);
3221 this.hideAllSeqAnnotations.setEnabled(setVisible);
3222 this.showAllAlAnnotations.setEnabled(setVisible);
3223 this.hideAllAlAnnotations.setEnabled(setVisible);
3224 alignPanel.updateLayout();
3228 public void alignmentProperties()
3230 JEditorPane editPane = new JEditorPane("text/html", "");
3231 editPane.setEditable(false);
3232 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3235 MessageManager.formatMessage("label.html_content", new Object[]
3236 { contents.toString() }));
3237 JInternalFrame frame = new JInternalFrame();
3238 frame.getContentPane().add(new JScrollPane(editPane));
3240 Desktop.addInternalFrame(frame, MessageManager
3241 .formatMessage("label.alignment_properties", new Object[]
3242 { getTitle() }), 500, 400);
3252 public void overviewMenuItem_actionPerformed(ActionEvent e)
3254 if (alignPanel.overviewPanel != null)
3259 JInternalFrame frame = new JInternalFrame();
3260 final OverviewPanel overview = new OverviewPanel(alignPanel);
3261 frame.setContentPane(overview);
3262 Desktop.addInternalFrame(frame, MessageManager
3263 .formatMessage("label.overview_params", new Object[]
3264 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3267 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3268 frame.addInternalFrameListener(
3269 new javax.swing.event.InternalFrameAdapter()
3272 public void internalFrameClosed(
3273 javax.swing.event.InternalFrameEvent evt)
3276 alignPanel.setOverviewPanel(null);
3279 if (getKeyListeners().length > 0)
3281 frame.addKeyListener(getKeyListeners()[0]);
3284 alignPanel.setOverviewPanel(overview);
3288 public void textColour_actionPerformed()
3290 new TextColourChooser().chooseColour(alignPanel, null);
3294 * public void covariationColour_actionPerformed() {
3296 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3300 public void annotationColour_actionPerformed()
3302 new AnnotationColourChooser(viewport, alignPanel);
3306 public void annotationColumn_actionPerformed(ActionEvent e)
3308 new AnnotationColumnChooser(viewport, alignPanel);
3312 * Action on the user checking or unchecking the option to apply the selected
3313 * colour scheme to all groups. If unchecked, groups may have their own
3314 * independent colour schemes.
3319 public void applyToAllGroups_actionPerformed(boolean selected)
3321 viewport.setColourAppliesToAllGroups(selected);
3325 * Action on user selecting a colour from the colour menu
3328 * the name (not the menu item label!) of the colour scheme
3331 public void changeColour_actionPerformed(String name)
3334 * 'User Defined' opens a panel to configure or load a
3335 * user-defined colour scheme
3337 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3339 new UserDefinedColours(alignPanel);
3344 * otherwise set the chosen colour scheme (or null for 'None')
3346 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3347 viewport.getAlignment(), viewport.getHiddenRepSequences());
3352 * Actions on setting or changing the alignment colour scheme
3357 public void changeColour(ColourSchemeI cs)
3359 // TODO: pull up to controller method
3360 ColourMenuHelper.setColourSelected(colourMenu, cs);
3362 viewport.setGlobalColourScheme(cs);
3364 alignPanel.paintAlignment(true, true);
3368 * Show the PID threshold slider panel
3371 protected void modifyPID_actionPerformed()
3373 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3374 alignPanel.getViewName());
3375 SliderPanel.showPIDSlider();
3379 * Show the Conservation slider panel
3382 protected void modifyConservation_actionPerformed()
3384 SliderPanel.setConservationSlider(alignPanel,
3385 viewport.getResidueShading(), alignPanel.getViewName());
3386 SliderPanel.showConservationSlider();
3390 * Action on selecting or deselecting (Colour) By Conservation
3393 public void conservationMenuItem_actionPerformed(boolean selected)
3395 modifyConservation.setEnabled(selected);
3396 viewport.setConservationSelected(selected);
3397 viewport.getResidueShading().setConservationApplied(selected);
3399 changeColour(viewport.getGlobalColourScheme());
3402 modifyConservation_actionPerformed();
3406 SliderPanel.hideConservationSlider();
3411 * Action on selecting or deselecting (Colour) Above PID Threshold
3414 public void abovePIDThreshold_actionPerformed(boolean selected)
3416 modifyPID.setEnabled(selected);
3417 viewport.setAbovePIDThreshold(selected);
3420 viewport.getResidueShading().setThreshold(0,
3421 viewport.isIgnoreGapsConsensus());
3424 changeColour(viewport.getGlobalColourScheme());
3427 modifyPID_actionPerformed();
3431 SliderPanel.hidePIDSlider();
3442 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3444 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3445 AlignmentSorter.sortByPID(viewport.getAlignment(),
3446 viewport.getAlignment().getSequenceAt(0));
3447 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3448 viewport.getAlignment()));
3449 alignPanel.paintAlignment(true, false);
3459 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3461 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3462 AlignmentSorter.sortByID(viewport.getAlignment());
3464 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3465 alignPanel.paintAlignment(true, false);
3475 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3477 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3478 AlignmentSorter.sortByLength(viewport.getAlignment());
3479 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3480 viewport.getAlignment()));
3481 alignPanel.paintAlignment(true, false);
3491 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3493 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3494 AlignmentSorter.sortByGroup(viewport.getAlignment());
3495 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3496 viewport.getAlignment()));
3498 alignPanel.paintAlignment(true, false);
3508 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3510 new RedundancyPanel(alignPanel, this);
3520 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3522 if ((viewport.getSelectionGroup() == null)
3523 || (viewport.getSelectionGroup().getSize() < 2))
3525 JvOptionPane.showInternalMessageDialog(this,
3526 MessageManager.getString(
3527 "label.you_must_select_least_two_sequences"),
3528 MessageManager.getString("label.invalid_selection"),
3529 JvOptionPane.WARNING_MESSAGE);
3533 JInternalFrame frame = new JInternalFrame();
3534 frame.setContentPane(new PairwiseAlignPanel(viewport));
3535 Desktop.addInternalFrame(frame,
3536 MessageManager.getString("action.pairwise_alignment"), 600,
3542 public void autoCalculate_actionPerformed(ActionEvent e)
3544 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3545 if (viewport.autoCalculateConsensus)
3547 viewport.firePropertyChange("alignment", null,
3548 viewport.getAlignment().getSequences());
3553 public void sortByTreeOption_actionPerformed(ActionEvent e)
3555 viewport.sortByTree = sortByTree.isSelected();
3559 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3561 viewport.followSelection = listenToViewSelections.isSelected();
3565 * Constructs a tree panel and adds it to the desktop
3568 * tree type (NJ or AV)
3570 * name of score model used to compute the tree
3572 * parameters for the distance or similarity calculation
3574 void newTreePanel(String type, String modelName,
3575 SimilarityParamsI options)
3577 String frameTitle = "";
3580 boolean onSelection = false;
3581 if (viewport.getSelectionGroup() != null
3582 && viewport.getSelectionGroup().getSize() > 0)
3584 SequenceGroup sg = viewport.getSelectionGroup();
3586 /* Decide if the selection is a column region */
3587 for (SequenceI _s : sg.getSequences())
3589 if (_s.getLength() < sg.getEndRes())
3591 JvOptionPane.showMessageDialog(Desktop.desktop,
3592 MessageManager.getString(
3593 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3594 MessageManager.getString(
3595 "label.sequences_selection_not_aligned"),
3596 JvOptionPane.WARNING_MESSAGE);
3605 if (viewport.getAlignment().getHeight() < 2)
3611 tp = new TreePanel(alignPanel, type, modelName, options);
3612 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3614 frameTitle += " from ";
3616 if (viewport.getViewName() != null)
3618 frameTitle += viewport.getViewName() + " of ";
3621 frameTitle += this.title;
3623 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3634 public void addSortByOrderMenuItem(String title,
3635 final AlignmentOrder order)
3637 final JMenuItem item = new JMenuItem(MessageManager
3638 .formatMessage("action.by_title_param", new Object[]
3641 item.addActionListener(new java.awt.event.ActionListener()
3644 public void actionPerformed(ActionEvent e)
3646 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3648 // TODO: JBPNote - have to map order entries to curent SequenceI
3650 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3652 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3653 viewport.getAlignment()));
3655 alignPanel.paintAlignment(true, false);
3661 * Add a new sort by annotation score menu item
3664 * the menu to add the option to
3666 * the label used to retrieve scores for each sequence on the
3669 public void addSortByAnnotScoreMenuItem(JMenu sort,
3670 final String scoreLabel)
3672 final JMenuItem item = new JMenuItem(scoreLabel);
3674 item.addActionListener(new java.awt.event.ActionListener()
3677 public void actionPerformed(ActionEvent e)
3679 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3680 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3681 viewport.getAlignment());// ,viewport.getSelectionGroup());
3682 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3683 viewport.getAlignment()));
3684 alignPanel.paintAlignment(true, false);
3690 * last hash for alignment's annotation array - used to minimise cost of
3693 protected int _annotationScoreVectorHash;
3696 * search the alignment and rebuild the sort by annotation score submenu the
3697 * last alignment annotation vector hash is stored to minimize cost of
3698 * rebuilding in subsequence calls.
3702 public void buildSortByAnnotationScoresMenu()
3704 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3709 if (viewport.getAlignment().getAlignmentAnnotation()
3710 .hashCode() != _annotationScoreVectorHash)
3712 sortByAnnotScore.removeAll();
3713 // almost certainly a quicker way to do this - but we keep it simple
3714 Hashtable scoreSorts = new Hashtable();
3715 AlignmentAnnotation aann[];
3716 for (SequenceI sqa : viewport.getAlignment().getSequences())
3718 aann = sqa.getAnnotation();
3719 for (int i = 0; aann != null && i < aann.length; i++)
3721 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3723 scoreSorts.put(aann[i].label, aann[i].label);
3727 Enumeration labels = scoreSorts.keys();
3728 while (labels.hasMoreElements())
3730 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3731 (String) labels.nextElement());
3733 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3736 _annotationScoreVectorHash = viewport.getAlignment()
3737 .getAlignmentAnnotation().hashCode();
3742 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3743 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3744 * call. Listeners are added to remove the menu item when the treePanel is
3745 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3749 public void buildTreeSortMenu()
3751 sortByTreeMenu.removeAll();
3753 List<Component> comps = PaintRefresher.components
3754 .get(viewport.getSequenceSetId());
3755 List<TreePanel> treePanels = new ArrayList<>();
3756 for (Component comp : comps)
3758 if (comp instanceof TreePanel)
3760 treePanels.add((TreePanel) comp);
3764 if (treePanels.size() < 1)
3766 sortByTreeMenu.setVisible(false);
3770 sortByTreeMenu.setVisible(true);
3772 for (final TreePanel tp : treePanels)
3774 final JMenuItem item = new JMenuItem(tp.getTitle());
3775 item.addActionListener(new java.awt.event.ActionListener()
3778 public void actionPerformed(ActionEvent e)
3780 tp.sortByTree_actionPerformed();
3781 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3786 sortByTreeMenu.add(item);
3790 public boolean sortBy(AlignmentOrder alorder, String undoname)
3792 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3793 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3794 if (undoname != null)
3796 addHistoryItem(new OrderCommand(undoname, oldOrder,
3797 viewport.getAlignment()));
3799 alignPanel.paintAlignment(true, false);
3804 * Work out whether the whole set of sequences or just the selected set will
3805 * be submitted for multiple alignment.
3808 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3810 // Now, check we have enough sequences
3811 AlignmentView msa = null;
3813 if ((viewport.getSelectionGroup() != null)
3814 && (viewport.getSelectionGroup().getSize() > 1))
3816 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3817 // some common interface!
3819 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3820 * SequenceI[sz = seqs.getSize(false)];
3822 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3823 * seqs.getSequenceAt(i); }
3825 msa = viewport.getAlignmentView(true);
3827 else if (viewport.getSelectionGroup() != null
3828 && viewport.getSelectionGroup().getSize() == 1)
3830 int option = JvOptionPane.showConfirmDialog(this,
3831 MessageManager.getString("warn.oneseq_msainput_selection"),
3832 MessageManager.getString("label.invalid_selection"),
3833 JvOptionPane.OK_CANCEL_OPTION);
3834 if (option == JvOptionPane.OK_OPTION)
3836 msa = viewport.getAlignmentView(false);
3841 msa = viewport.getAlignmentView(false);
3847 * Decides what is submitted to a secondary structure prediction service: the
3848 * first sequence in the alignment, or in the current selection, or, if the
3849 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3850 * region or the whole alignment. (where the first sequence in the set is the
3851 * one that the prediction will be for).
3853 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3855 AlignmentView seqs = null;
3857 if ((viewport.getSelectionGroup() != null)
3858 && (viewport.getSelectionGroup().getSize() > 0))
3860 seqs = viewport.getAlignmentView(true);
3864 seqs = viewport.getAlignmentView(false);
3866 // limit sequences - JBPNote in future - could spawn multiple prediction
3868 // TODO: viewport.getAlignment().isAligned is a global state - the local
3869 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3870 if (!viewport.getAlignment().isAligned(false))
3872 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3873 // TODO: if seqs.getSequences().length>1 then should really have warned
3887 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3889 // Pick the tree file
3890 JalviewFileChooser chooser = new JalviewFileChooser(
3891 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3892 chooser.setFileView(new JalviewFileView());
3893 chooser.setDialogTitle(
3894 MessageManager.getString("label.select_newick_like_tree_file"));
3895 chooser.setToolTipText(
3896 MessageManager.getString("label.load_tree_file"));
3898 int value = chooser.showOpenDialog(null);
3900 if (value == JalviewFileChooser.APPROVE_OPTION)
3902 String filePath = chooser.getSelectedFile().getPath();
3903 Cache.setProperty("LAST_DIRECTORY", filePath);
3904 NewickFile fin = null;
3907 fin = new NewickFile(filePath, DataSourceType.FILE);
3908 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3909 } catch (Exception ex)
3911 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3912 MessageManager.getString("label.problem_reading_tree_file"),
3913 JvOptionPane.WARNING_MESSAGE);
3914 ex.printStackTrace();
3916 if (fin != null && fin.hasWarningMessage())
3918 JvOptionPane.showMessageDialog(Desktop.desktop,
3919 fin.getWarningMessage(),
3921 .getString("label.possible_problem_with_tree_file"),
3922 JvOptionPane.WARNING_MESSAGE);
3927 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3929 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3932 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3933 int h, int x, int y)
3935 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3939 * Add a treeviewer for the tree extracted from a Newick file object to the
3940 * current alignment view
3947 * Associated alignment input data (or null)
3956 * @return TreePanel handle
3958 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3959 AlignmentView input, int w, int h, int x, int y)
3961 TreePanel tp = null;
3967 if (nf.getTree() != null)
3969 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3975 tp.setLocation(x, y);
3978 Desktop.addInternalFrame(tp, treeTitle, w, h);
3980 } catch (Exception ex)
3982 ex.printStackTrace();
3988 private boolean buildingMenu = false;
3991 * Generates menu items and listener event actions for web service clients
3994 public void BuildWebServiceMenu()
3996 while (buildingMenu)
4000 System.err.println("Waiting for building menu to finish.");
4002 } catch (Exception e)
4006 final AlignFrame me = this;
4007 buildingMenu = true;
4008 new Thread(new Runnable()
4013 final List<JMenuItem> legacyItems = new ArrayList<>();
4016 // System.err.println("Building ws menu again "
4017 // + Thread.currentThread());
4018 // TODO: add support for context dependent disabling of services based
4020 // alignment and current selection
4021 // TODO: add additional serviceHandle parameter to specify abstract
4023 // class independently of AbstractName
4024 // TODO: add in rediscovery GUI function to restart discoverer
4025 // TODO: group services by location as well as function and/or
4027 // object broker mechanism.
4028 final Vector<JMenu> wsmenu = new Vector<>();
4029 final IProgressIndicator af = me;
4032 * do not i18n these strings - they are hard-coded in class
4033 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4034 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4036 final JMenu msawsmenu = new JMenu("Alignment");
4037 final JMenu secstrmenu = new JMenu(
4038 "Secondary Structure Prediction");
4039 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4040 final JMenu analymenu = new JMenu("Analysis");
4041 final JMenu dismenu = new JMenu("Protein Disorder");
4042 // JAL-940 - only show secondary structure prediction services from
4043 // the legacy server
4044 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4046 Discoverer.services != null && (Discoverer.services.size() > 0))
4048 // TODO: refactor to allow list of AbstractName/Handler bindings to
4050 // stored or retrieved from elsewhere
4051 // No MSAWS used any more:
4052 // Vector msaws = null; // (Vector)
4053 // Discoverer.services.get("MsaWS");
4054 Vector secstrpr = (Vector) Discoverer.services
4056 if (secstrpr != null)
4058 // Add any secondary structure prediction services
4059 for (int i = 0, j = secstrpr.size(); i < j; i++)
4061 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4063 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4064 .getServiceClient(sh);
4065 int p = secstrmenu.getItemCount();
4066 impl.attachWSMenuEntry(secstrmenu, me);
4067 int q = secstrmenu.getItemCount();
4068 for (int litm = p; litm < q; litm++)
4070 legacyItems.add(secstrmenu.getItem(litm));
4076 // Add all submenus in the order they should appear on the web
4078 wsmenu.add(msawsmenu);
4079 wsmenu.add(secstrmenu);
4080 wsmenu.add(dismenu);
4081 wsmenu.add(analymenu);
4082 // No search services yet
4083 // wsmenu.add(seqsrchmenu);
4085 javax.swing.SwingUtilities.invokeLater(new Runnable()
4092 webService.removeAll();
4093 // first, add discovered services onto the webservices menu
4094 if (wsmenu.size() > 0)
4096 for (int i = 0, j = wsmenu.size(); i < j; i++)
4098 webService.add(wsmenu.get(i));
4103 webService.add(me.webServiceNoServices);
4105 // TODO: move into separate menu builder class.
4106 boolean new_sspred = false;
4107 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4109 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4110 if (jws2servs != null)
4112 if (jws2servs.hasServices())
4114 jws2servs.attachWSMenuEntry(webService, me);
4115 for (Jws2Instance sv : jws2servs.getServices())
4117 if (sv.description.toLowerCase().contains("jpred"))
4119 for (JMenuItem jmi : legacyItems)
4121 jmi.setVisible(false);
4127 if (jws2servs.isRunning())
4129 JMenuItem tm = new JMenuItem(
4130 "Still discovering JABA Services");
4131 tm.setEnabled(false);
4136 build_urlServiceMenu(me.webService);
4137 build_fetchdbmenu(webService);
4138 for (JMenu item : wsmenu)
4140 if (item.getItemCount() == 0)
4142 item.setEnabled(false);
4146 item.setEnabled(true);
4149 } catch (Exception e)
4152 "Exception during web service menu building process.",
4157 } catch (Exception e)
4160 buildingMenu = false;
4167 * construct any groupURL type service menu entries.
4171 private void build_urlServiceMenu(JMenu webService)
4173 // TODO: remove this code when 2.7 is released
4174 // DEBUG - alignmentView
4176 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4177 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4179 * @Override public void actionPerformed(ActionEvent e) {
4180 * jalview.datamodel.AlignmentView
4181 * .testSelectionViews(af.viewport.getAlignment(),
4182 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4184 * }); webService.add(testAlView);
4186 // TODO: refactor to RestClient discoverer and merge menu entries for
4187 // rest-style services with other types of analysis/calculation service
4188 // SHmmr test client - still being implemented.
4189 // DEBUG - alignmentView
4191 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4194 client.attachWSMenuEntry(
4195 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4201 * Searches the alignment sequences for xRefs and builds the Show
4202 * Cross-References menu (formerly called Show Products), with database
4203 * sources for which cross-references are found (protein sources for a
4204 * nucleotide alignment and vice versa)
4206 * @return true if Show Cross-references menu should be enabled
4208 public boolean canShowProducts()
4210 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4211 AlignmentI dataset = viewport.getAlignment().getDataset();
4213 showProducts.removeAll();
4214 final boolean dna = viewport.getAlignment().isNucleotide();
4216 if (seqs == null || seqs.length == 0)
4218 // nothing to see here.
4222 boolean showp = false;
4225 List<String> ptypes = new CrossRef(seqs, dataset)
4226 .findXrefSourcesForSequences(dna);
4228 for (final String source : ptypes)
4231 final AlignFrame af = this;
4232 JMenuItem xtype = new JMenuItem(source);
4233 xtype.addActionListener(new ActionListener()
4236 public void actionPerformed(ActionEvent e)
4238 showProductsFor(af.viewport.getSequenceSelection(), dna,
4242 showProducts.add(xtype);
4244 showProducts.setVisible(showp);
4245 showProducts.setEnabled(showp);
4246 } catch (Exception e)
4249 "canShowProducts threw an exception - please report to help@jalview.org",
4257 * Finds and displays cross-references for the selected sequences (protein
4258 * products for nucleotide sequences, dna coding sequences for peptides).
4261 * the sequences to show cross-references for
4263 * true if from a nucleotide alignment (so showing proteins)
4265 * the database to show cross-references for
4267 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4268 final String source)
4270 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4275 * Construct and display a new frame containing the translation of this
4276 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4279 public void showTranslation_actionPerformed(ActionEvent e)
4281 AlignmentI al = null;
4284 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4286 al = dna.translateCdna();
4287 } catch (Exception ex)
4289 jalview.bin.Cache.log.error(
4290 "Exception during translation. Please report this !", ex);
4291 final String msg = MessageManager.getString(
4292 "label.error_when_translating_sequences_submit_bug_report");
4293 final String errorTitle = MessageManager
4294 .getString("label.implementation_error")
4295 + MessageManager.getString("label.translation_failed");
4296 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4297 JvOptionPane.ERROR_MESSAGE);
4300 if (al == null || al.getHeight() == 0)
4302 final String msg = MessageManager.getString(
4303 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4304 final String errorTitle = MessageManager
4305 .getString("label.translation_failed");
4306 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4307 JvOptionPane.WARNING_MESSAGE);
4311 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4312 af.setFileFormat(this.currentFileFormat);
4313 final String newTitle = MessageManager
4314 .formatMessage("label.translation_of_params", new Object[]
4315 { this.getTitle() });
4316 af.setTitle(newTitle);
4317 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4319 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4320 viewport.openSplitFrame(af, new Alignment(seqs));
4324 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4331 * Set the file format
4335 public void setFileFormat(FileFormatI format)
4337 this.currentFileFormat = format;
4341 * Try to load a features file onto the alignment.
4344 * contents or path to retrieve file
4346 * access mode of file (see jalview.io.AlignFile)
4347 * @return true if features file was parsed correctly.
4349 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4351 return avc.parseFeaturesFile(file, sourceType,
4352 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4357 public void refreshFeatureUI(boolean enableIfNecessary)
4359 // note - currently this is only still here rather than in the controller
4360 // because of the featureSettings hard reference that is yet to be
4362 if (enableIfNecessary)
4364 viewport.setShowSequenceFeatures(true);
4365 showSeqFeatures.setSelected(true);
4371 public void dragEnter(DropTargetDragEvent evt)
4376 public void dragExit(DropTargetEvent evt)
4381 public void dragOver(DropTargetDragEvent evt)
4386 public void dropActionChanged(DropTargetDragEvent evt)
4391 public void drop(DropTargetDropEvent evt)
4393 // JAL-1552 - acceptDrop required before getTransferable call for
4394 // Java's Transferable for native dnd
4395 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4396 Transferable t = evt.getTransferable();
4397 final AlignFrame thisaf = this;
4398 final List<String> files = new ArrayList<>();
4399 List<DataSourceType> protocols = new ArrayList<>();
4403 Desktop.transferFromDropTarget(files, protocols, evt, t);
4404 } catch (Exception e)
4406 e.printStackTrace();
4410 new Thread(new Runnable()
4417 // check to see if any of these files have names matching sequences
4420 SequenceIdMatcher idm = new SequenceIdMatcher(
4421 viewport.getAlignment().getSequencesArray());
4423 * Object[] { String,SequenceI}
4425 ArrayList<Object[]> filesmatched = new ArrayList<>();
4426 ArrayList<String> filesnotmatched = new ArrayList<>();
4427 for (int i = 0; i < files.size(); i++)
4429 String file = files.get(i).toString();
4431 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4432 if (protocol == DataSourceType.FILE)
4434 File fl = new File(file);
4435 pdbfn = fl.getName();
4437 else if (protocol == DataSourceType.URL)
4439 URL url = new URL(file);
4440 pdbfn = url.getFile();
4442 if (pdbfn.length() > 0)
4444 // attempt to find a match in the alignment
4445 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4446 int l = 0, c = pdbfn.indexOf(".");
4447 while (mtch == null && c != -1)
4452 } while ((c = pdbfn.indexOf(".", l)) > l);
4455 pdbfn = pdbfn.substring(0, l);
4457 mtch = idm.findAllIdMatches(pdbfn);
4461 FileFormatI type = null;
4464 type = new IdentifyFile().identify(file, protocol);
4465 } catch (Exception ex)
4469 if (type != null && type.isStructureFile())
4471 filesmatched.add(new Object[] { file, protocol, mtch });
4475 // File wasn't named like one of the sequences or wasn't a PDB
4477 filesnotmatched.add(file);
4481 if (filesmatched.size() > 0)
4483 boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4486 String msg = MessageManager.formatMessage(
4487 "label.automatically_associate_structure_files_with_sequences_same_name",
4489 { Integer.valueOf(filesmatched.size())
4491 String ttl = MessageManager.getString(
4492 "label.automatically_associate_structure_files_by_name");
4493 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4494 ttl, JvOptionPane.YES_NO_OPTION);
4495 autoAssociate = choice == JvOptionPane.YES_OPTION;
4499 for (Object[] fm : filesmatched)
4501 // try and associate
4502 // TODO: may want to set a standard ID naming formalism for
4503 // associating PDB files which have no IDs.
4504 for (SequenceI toassoc : (SequenceI[]) fm[2])
4506 PDBEntry pe = new AssociatePdbFileWithSeq()
4507 .associatePdbWithSeq((String) fm[0],
4508 (DataSourceType) fm[1], toassoc, false,
4512 System.err.println("Associated file : "
4513 + ((String) fm[0]) + " with "
4514 + toassoc.getDisplayId(true));
4518 // TODO: do we need to update overview ? only if features are
4520 alignPanel.paintAlignment(true, false);
4526 * add declined structures as sequences
4528 for (Object[] o : filesmatched)
4530 filesnotmatched.add((String) o[0]);
4534 if (filesnotmatched.size() > 0)
4536 if (assocfiles > 0 && (Cache.getDefault(
4537 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4538 || JvOptionPane.showConfirmDialog(thisaf,
4539 "<html>" + MessageManager.formatMessage(
4540 "label.ignore_unmatched_dropped_files_info",
4543 filesnotmatched.size())
4546 MessageManager.getString(
4547 "label.ignore_unmatched_dropped_files"),
4548 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4552 for (String fn : filesnotmatched)
4554 loadJalviewDataFile(fn, null, null, null);
4558 } catch (Exception ex)
4560 ex.printStackTrace();
4568 * Attempt to load a "dropped" file or URL string, by testing in turn for
4570 * <li>an Annotation file</li>
4571 * <li>a JNet file</li>
4572 * <li>a features file</li>
4573 * <li>else try to interpret as an alignment file</li>
4577 * either a filename or a URL string.
4579 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4580 FileFormatI format, SequenceI assocSeq)
4584 if (sourceType == null)
4586 sourceType = FormatAdapter.checkProtocol(file);
4588 // if the file isn't identified, or not positively identified as some
4589 // other filetype (PFAM is default unidentified alignment file type) then
4590 // try to parse as annotation.
4591 boolean isAnnotation = (format == null
4592 || FileFormat.Pfam.equals(format))
4593 ? new AnnotationFile().annotateAlignmentView(viewport,
4599 // first see if its a T-COFFEE score file
4600 TCoffeeScoreFile tcf = null;
4603 tcf = new TCoffeeScoreFile(file, sourceType);
4606 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4610 new TCoffeeColourScheme(viewport.getAlignment()));
4611 isAnnotation = true;
4612 statusBar.setText(MessageManager.getString(
4613 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4617 // some problem - if no warning its probable that the ID matching
4618 // process didn't work
4619 JvOptionPane.showMessageDialog(Desktop.desktop,
4620 tcf.getWarningMessage() == null
4621 ? MessageManager.getString(
4622 "label.check_file_matches_sequence_ids_alignment")
4623 : tcf.getWarningMessage(),
4624 MessageManager.getString(
4625 "label.problem_reading_tcoffee_score_file"),
4626 JvOptionPane.WARNING_MESSAGE);
4633 } catch (Exception x)
4636 "Exception when processing data source as T-COFFEE score file",
4642 // try to see if its a JNet 'concise' style annotation file *before*
4644 // try to parse it as a features file
4647 format = new IdentifyFile().identify(file, sourceType);
4649 if (FileFormat.ScoreMatrix == format)
4651 ScoreMatrixFile sm = new ScoreMatrixFile(
4652 new FileParse(file, sourceType));
4654 // todo: i18n this message
4655 statusBar.setText(MessageManager.formatMessage(
4656 "label.successfully_loaded_matrix",
4657 sm.getMatrixName()));
4659 else if (FileFormat.Jnet.equals(format))
4661 JPredFile predictions = new JPredFile(file, sourceType);
4662 new JnetAnnotationMaker();
4663 JnetAnnotationMaker.add_annotation(predictions,
4664 viewport.getAlignment(), 0, false);
4665 viewport.getAlignment().setupJPredAlignment();
4666 isAnnotation = true;
4668 // else if (IdentifyFile.FeaturesFile.equals(format))
4669 else if (FileFormat.Features.equals(format))
4671 if (parseFeaturesFile(file, sourceType))
4673 alignPanel.paintAlignment(true, true);
4678 new FileLoader().LoadFile(viewport, file, sourceType, format);
4685 alignPanel.adjustAnnotationHeight();
4686 viewport.updateSequenceIdColours();
4687 buildSortByAnnotationScoresMenu();
4688 alignPanel.paintAlignment(true, true);
4690 } catch (Exception ex)
4692 ex.printStackTrace();
4693 } catch (OutOfMemoryError oom)
4698 } catch (Exception x)
4703 + (sourceType != null
4704 ? (sourceType == DataSourceType.PASTE
4706 : "using " + sourceType + " from "
4710 ? "(parsing as '" + format + "' file)"
4712 oom, Desktop.desktop);
4717 * Method invoked by the ChangeListener on the tabbed pane, in other words
4718 * when a different tabbed pane is selected by the user or programmatically.
4721 public void tabSelectionChanged(int index)
4725 alignPanel = alignPanels.get(index);
4726 viewport = alignPanel.av;
4727 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4728 setMenusFromViewport(viewport);
4732 * 'focus' any colour slider that is open to the selected viewport
4734 if (viewport.getConservationSelected())
4736 SliderPanel.setConservationSlider(alignPanel,
4737 viewport.getResidueShading(), alignPanel.getViewName());
4741 SliderPanel.hideConservationSlider();
4743 if (viewport.getAbovePIDThreshold())
4745 SliderPanel.setPIDSliderSource(alignPanel,
4746 viewport.getResidueShading(), alignPanel.getViewName());
4750 SliderPanel.hidePIDSlider();
4754 * If there is a frame linked to this one in a SplitPane, switch it to the
4755 * same view tab index. No infinite recursion of calls should happen, since
4756 * tabSelectionChanged() should not get invoked on setting the selected
4757 * index to an unchanged value. Guard against setting an invalid index
4758 * before the new view peer tab has been created.
4760 final AlignViewportI peer = viewport.getCodingComplement();
4763 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4764 .getAlignPanel().alignFrame;
4765 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4767 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4773 * On right mouse click on view tab, prompt for and set new view name.
4776 public void tabbedPane_mousePressed(MouseEvent e)
4778 if (e.isPopupTrigger())
4780 String msg = MessageManager.getString("label.enter_view_name");
4781 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4782 JvOptionPane.QUESTION_MESSAGE);
4786 viewport.setViewName(reply);
4787 // TODO warn if reply is in getExistingViewNames()?
4788 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4793 public AlignViewport getCurrentView()
4799 * Open the dialog for regex description parsing.
4802 protected void extractScores_actionPerformed(ActionEvent e)
4804 ParseProperties pp = new jalview.analysis.ParseProperties(
4805 viewport.getAlignment());
4806 // TODO: verify regex and introduce GUI dialog for version 2.5
4807 // if (pp.getScoresFromDescription("col", "score column ",
4808 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4810 if (pp.getScoresFromDescription("description column",
4811 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4813 buildSortByAnnotationScoresMenu();
4821 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4825 protected void showDbRefs_actionPerformed(ActionEvent e)
4827 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4833 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4837 protected void showNpFeats_actionPerformed(ActionEvent e)
4839 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4843 * find the viewport amongst the tabs in this alignment frame and close that
4848 public boolean closeView(AlignViewportI av)
4852 this.closeMenuItem_actionPerformed(false);
4855 Component[] comp = tabbedPane.getComponents();
4856 for (int i = 0; comp != null && i < comp.length; i++)
4858 if (comp[i] instanceof AlignmentPanel)
4860 if (((AlignmentPanel) comp[i]).av == av)
4863 closeView((AlignmentPanel) comp[i]);
4871 protected void build_fetchdbmenu(JMenu webService)
4873 // Temporary hack - DBRef Fetcher always top level ws entry.
4874 // TODO We probably want to store a sequence database checklist in
4875 // preferences and have checkboxes.. rather than individual sources selected
4877 final JMenu rfetch = new JMenu(
4878 MessageManager.getString("action.fetch_db_references"));
4879 rfetch.setToolTipText(MessageManager.getString(
4880 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4881 webService.add(rfetch);
4883 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4884 MessageManager.getString("option.trim_retrieved_seqs"));
4885 trimrs.setToolTipText(
4886 MessageManager.getString("label.trim_retrieved_sequences"));
4888 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4889 trimrs.addActionListener(new ActionListener()
4892 public void actionPerformed(ActionEvent e)
4894 trimrs.setSelected(trimrs.isSelected());
4895 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4896 Boolean.valueOf(trimrs.isSelected()).toString());
4900 JMenuItem fetchr = new JMenuItem(
4901 MessageManager.getString("label.standard_databases"));
4902 fetchr.setToolTipText(
4903 MessageManager.getString("label.fetch_embl_uniprot"));
4904 fetchr.addActionListener(new ActionListener()
4908 public void actionPerformed(ActionEvent e)
4910 new Thread(new Runnable()
4915 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4916 .getAlignment().isNucleotide();
4917 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4918 alignPanel.av.getSequenceSelection(),
4919 alignPanel.alignFrame, null,
4920 alignPanel.alignFrame.featureSettings, isNucleotide);
4921 dbRefFetcher.addListener(new FetchFinishedListenerI()
4924 public void finished()
4926 AlignFrame.this.setMenusForViewport();
4929 dbRefFetcher.fetchDBRefs(false);
4937 final AlignFrame me = this;
4938 new Thread(new Runnable()
4943 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4944 .getSequenceFetcherSingleton(me);
4945 javax.swing.SwingUtilities.invokeLater(new Runnable()
4950 String[] dbclasses = sf.getOrderedSupportedSources();
4951 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4952 // jalview.util.QuickSort.sort(otherdb, otherdb);
4953 List<DbSourceProxy> otherdb;
4954 JMenu dfetch = new JMenu();
4955 JMenu ifetch = new JMenu();
4956 JMenuItem fetchr = null;
4957 int comp = 0, icomp = 0, mcomp = 15;
4958 String mname = null;
4960 for (String dbclass : dbclasses)
4962 otherdb = sf.getSourceProxy(dbclass);
4963 // add a single entry for this class, or submenu allowing 'fetch
4965 if (otherdb == null || otherdb.size() < 1)
4969 // List<DbSourceProxy> dbs=otherdb;
4970 // otherdb=new ArrayList<DbSourceProxy>();
4971 // for (DbSourceProxy db:dbs)
4973 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4977 mname = "From " + dbclass;
4979 if (otherdb.size() == 1)
4981 final DbSourceProxy[] dassource = otherdb
4982 .toArray(new DbSourceProxy[0]);
4983 DbSourceProxy src = otherdb.get(0);
4984 fetchr = new JMenuItem(src.getDbSource());
4985 fetchr.addActionListener(new ActionListener()
4989 public void actionPerformed(ActionEvent e)
4991 new Thread(new Runnable()
4997 boolean isNucleotide = alignPanel.alignFrame
4998 .getViewport().getAlignment()
5000 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5001 alignPanel.av.getSequenceSelection(),
5002 alignPanel.alignFrame, dassource,
5003 alignPanel.alignFrame.featureSettings,
5006 .addListener(new FetchFinishedListenerI()
5009 public void finished()
5011 AlignFrame.this.setMenusForViewport();
5014 dbRefFetcher.fetchDBRefs(false);
5020 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5021 MessageManager.formatMessage(
5022 "label.fetch_retrieve_from", new Object[]
5023 { src.getDbName() })));
5029 final DbSourceProxy[] dassource = otherdb
5030 .toArray(new DbSourceProxy[0]);
5032 DbSourceProxy src = otherdb.get(0);
5033 fetchr = new JMenuItem(MessageManager
5034 .formatMessage("label.fetch_all_param", new Object[]
5035 { src.getDbSource() }));
5036 fetchr.addActionListener(new ActionListener()
5039 public void actionPerformed(ActionEvent e)
5041 new Thread(new Runnable()
5047 boolean isNucleotide = alignPanel.alignFrame
5048 .getViewport().getAlignment()
5050 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5051 alignPanel.av.getSequenceSelection(),
5052 alignPanel.alignFrame, dassource,
5053 alignPanel.alignFrame.featureSettings,
5056 .addListener(new FetchFinishedListenerI()
5059 public void finished()
5061 AlignFrame.this.setMenusForViewport();
5064 dbRefFetcher.fetchDBRefs(false);
5070 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5071 MessageManager.formatMessage(
5072 "label.fetch_retrieve_from_all_sources",
5074 { Integer.valueOf(otherdb.size())
5076 src.getDbSource(), src.getDbName() })));
5079 // and then build the rest of the individual menus
5080 ifetch = new JMenu(MessageManager.formatMessage(
5081 "label.source_from_db_source", new Object[]
5082 { src.getDbSource() }));
5084 String imname = null;
5086 for (DbSourceProxy sproxy : otherdb)
5088 String dbname = sproxy.getDbName();
5089 String sname = dbname.length() > 5
5090 ? dbname.substring(0, 5) + "..."
5092 String msname = dbname.length() > 10
5093 ? dbname.substring(0, 10) + "..."
5097 imname = MessageManager
5098 .formatMessage("label.from_msname", new Object[]
5101 fetchr = new JMenuItem(msname);
5102 final DbSourceProxy[] dassrc = { sproxy };
5103 fetchr.addActionListener(new ActionListener()
5107 public void actionPerformed(ActionEvent e)
5109 new Thread(new Runnable()
5115 boolean isNucleotide = alignPanel.alignFrame
5116 .getViewport().getAlignment()
5118 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5119 alignPanel.av.getSequenceSelection(),
5120 alignPanel.alignFrame, dassrc,
5121 alignPanel.alignFrame.featureSettings,
5124 .addListener(new FetchFinishedListenerI()
5127 public void finished()
5129 AlignFrame.this.setMenusForViewport();
5132 dbRefFetcher.fetchDBRefs(false);
5138 fetchr.setToolTipText(
5139 "<html>" + MessageManager.formatMessage(
5140 "label.fetch_retrieve_from", new Object[]
5144 if (++icomp >= mcomp || i == (otherdb.size()))
5146 ifetch.setText(MessageManager.formatMessage(
5147 "label.source_to_target", imname, sname));
5149 ifetch = new JMenu();
5157 if (comp >= mcomp || dbi >= (dbclasses.length))
5159 dfetch.setText(MessageManager.formatMessage(
5160 "label.source_to_target", mname, dbclass));
5162 dfetch = new JMenu();
5175 * Left justify the whole alignment.
5178 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5180 AlignmentI al = viewport.getAlignment();
5182 viewport.firePropertyChange("alignment", null, al);
5186 * Right justify the whole alignment.
5189 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5191 AlignmentI al = viewport.getAlignment();
5193 viewport.firePropertyChange("alignment", null, al);
5197 public void setShowSeqFeatures(boolean b)
5199 showSeqFeatures.setSelected(b);
5200 viewport.setShowSequenceFeatures(b);
5207 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5208 * awt.event.ActionEvent)
5211 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5213 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5214 alignPanel.paintAlignment(false, false);
5221 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5225 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5227 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5228 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5236 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5237 * .event.ActionEvent)
5240 protected void showGroupConservation_actionPerformed(ActionEvent e)
5242 viewport.setShowGroupConservation(showGroupConservation.getState());
5243 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5250 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5251 * .event.ActionEvent)
5254 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5256 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5257 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5264 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5265 * .event.ActionEvent)
5268 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5270 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5271 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5275 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5277 showSequenceLogo.setState(true);
5278 viewport.setShowSequenceLogo(true);
5279 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5280 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5284 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5286 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5293 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5294 * .event.ActionEvent)
5297 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5299 if (avc.makeGroupsFromSelection())
5301 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5302 alignPanel.updateAnnotation();
5303 alignPanel.paintAlignment(true, true);
5307 public void clearAlignmentSeqRep()
5309 // TODO refactor alignmentseqrep to controller
5310 if (viewport.getAlignment().hasSeqrep())
5312 viewport.getAlignment().setSeqrep(null);
5313 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5314 alignPanel.updateAnnotation();
5315 alignPanel.paintAlignment(true, true);
5320 protected void createGroup_actionPerformed(ActionEvent e)
5322 if (avc.createGroup())
5324 if (applyAutoAnnotationSettings.isSelected())
5326 alignPanel.updateAnnotation(true, false);
5328 alignPanel.alignmentChanged();
5333 protected void unGroup_actionPerformed(ActionEvent e)
5337 alignPanel.alignmentChanged();
5342 * make the given alignmentPanel the currently selected tab
5344 * @param alignmentPanel
5346 public void setDisplayedView(AlignmentPanel alignmentPanel)
5348 if (!viewport.getSequenceSetId()
5349 .equals(alignmentPanel.av.getSequenceSetId()))
5351 throw new Error(MessageManager.getString(
5352 "error.implementation_error_cannot_show_view_alignment_frame"));
5354 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5355 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5357 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5362 * Action on selection of menu options to Show or Hide annotations.
5365 * @param forSequences
5366 * update sequence-related annotations
5367 * @param forAlignment
5368 * update non-sequence-related annotations
5371 protected void setAnnotationsVisibility(boolean visible,
5372 boolean forSequences, boolean forAlignment)
5374 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5375 .getAlignmentAnnotation();
5380 for (AlignmentAnnotation aa : anns)
5383 * don't display non-positional annotations on an alignment
5385 if (aa.annotations == null)
5389 boolean apply = (aa.sequenceRef == null && forAlignment)
5390 || (aa.sequenceRef != null && forSequences);
5393 aa.visible = visible;
5396 alignPanel.validateAnnotationDimensions(true);
5397 alignPanel.alignmentChanged();
5401 * Store selected annotation sort order for the view and repaint.
5404 protected void sortAnnotations_actionPerformed()
5406 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5408 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5409 alignPanel.paintAlignment(false, false);
5414 * @return alignment panels in this alignment frame
5416 public List<? extends AlignmentViewPanel> getAlignPanels()
5418 // alignPanels is never null
5419 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5424 * Open a new alignment window, with the cDNA associated with this (protein)
5425 * alignment, aligned as is the protein.
5427 protected void viewAsCdna_actionPerformed()
5429 // TODO no longer a menu action - refactor as required
5430 final AlignmentI alignment = getViewport().getAlignment();
5431 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5432 if (mappings == null)
5436 List<SequenceI> cdnaSeqs = new ArrayList<>();
5437 for (SequenceI aaSeq : alignment.getSequences())
5439 for (AlignedCodonFrame acf : mappings)
5441 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5445 * There is a cDNA mapping for this protein sequence - add to new
5446 * alignment. It will share the same dataset sequence as other mapped
5447 * cDNA (no new mappings need to be created).
5449 final Sequence newSeq = new Sequence(dnaSeq);
5450 newSeq.setDatasetSequence(dnaSeq);
5451 cdnaSeqs.add(newSeq);
5455 if (cdnaSeqs.size() == 0)
5457 // show a warning dialog no mapped cDNA
5460 AlignmentI cdna = new Alignment(
5461 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5462 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5463 AlignFrame.DEFAULT_HEIGHT);
5464 cdna.alignAs(alignment);
5465 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5467 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5468 AlignFrame.DEFAULT_HEIGHT);
5472 * Set visibility of dna/protein complement view (available when shown in a
5478 protected void showComplement_actionPerformed(boolean show)
5480 SplitContainerI sf = getSplitViewContainer();
5483 sf.setComplementVisible(this, show);
5488 * Generate the reverse (optionally complemented) of the selected sequences,
5489 * and add them to the alignment
5492 protected void showReverse_actionPerformed(boolean complement)
5494 AlignmentI al = null;
5497 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5498 al = dna.reverseCdna(complement);
5499 viewport.addAlignment(al, "");
5500 addHistoryItem(new EditCommand(
5501 MessageManager.getString("label.add_sequences"), Action.PASTE,
5502 al.getSequencesArray(), 0, al.getWidth(),
5503 viewport.getAlignment()));
5504 } catch (Exception ex)
5506 System.err.println(ex.getMessage());
5512 * Try to run a script in the Groovy console, having first ensured that this
5513 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5514 * be targeted at this alignment.
5517 protected void runGroovy_actionPerformed()
5519 Jalview.setCurrentAlignFrame(this);
5520 groovy.ui.Console console = Desktop.getGroovyConsole();
5521 if (console != null)
5525 console.runScript();
5526 } catch (Exception ex)
5528 System.err.println((ex.toString()));
5529 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5530 MessageManager.getString("label.couldnt_run_groovy_script"),
5531 MessageManager.getString("label.groovy_support_failed"),
5532 JvOptionPane.ERROR_MESSAGE);
5537 System.err.println("Can't run Groovy script as console not found");
5542 * Hides columns containing (or not containing) a specified feature, provided
5543 * that would not leave all columns hidden
5545 * @param featureType
5546 * @param columnsContaining
5549 public boolean hideFeatureColumns(String featureType,
5550 boolean columnsContaining)
5552 boolean notForHiding = avc.markColumnsContainingFeatures(
5553 columnsContaining, false, false, featureType);
5556 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5557 false, featureType))
5559 getViewport().hideSelectedColumns();
5567 protected void selectHighlightedColumns_actionPerformed(
5568 ActionEvent actionEvent)
5570 // include key modifier check in case user selects from menu
5571 avc.markHighlightedColumns(
5572 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5573 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5574 | ActionEvent.CTRL_MASK)) != 0);
5578 * Rebuilds the Colour menu, including any user-defined colours which have
5579 * been loaded either on startup or during the session
5581 public void buildColourMenu()
5583 colourMenu.removeAll();
5585 colourMenu.add(applyToAllGroups);
5586 colourMenu.add(textColour);
5587 colourMenu.addSeparator();
5589 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5592 colourMenu.addSeparator();
5593 colourMenu.add(conservationMenuItem);
5594 colourMenu.add(modifyConservation);
5595 colourMenu.add(abovePIDThreshold);
5596 colourMenu.add(modifyPID);
5597 colourMenu.add(annotationColour);
5599 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5600 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5604 * Open a dialog (if not already open) that allows the user to select and
5605 * calculate PCA or Tree analysis
5607 protected void openTreePcaDialog()
5609 if (alignPanel.getCalculationDialog() == null)
5611 new CalculationChooser(AlignFrame.this);
5616 protected void loadVcf_actionPerformed()
5618 JalviewFileChooser chooser = new JalviewFileChooser(
5619 Cache.getProperty("LAST_DIRECTORY"));
5620 chooser.setFileView(new JalviewFileView());
5621 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5622 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5624 int value = chooser.showOpenDialog(null);
5626 if (value == JalviewFileChooser.APPROVE_OPTION)
5628 String choice = chooser.getSelectedFile().getPath();
5629 Cache.setProperty("LAST_DIRECTORY", choice);
5630 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5631 new VCFLoader(choice).loadVCF(seqs, this);
5637 class PrintThread extends Thread
5641 public PrintThread(AlignmentPanel ap)
5646 static PageFormat pf;
5651 PrinterJob printJob = PrinterJob.getPrinterJob();
5655 printJob.setPrintable(ap, pf);
5659 printJob.setPrintable(ap);
5662 if (printJob.printDialog())
5667 } catch (Exception PrintException)
5669 PrintException.printStackTrace();