2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.SimilarityParamsI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenColumns;
57 import jalview.datamodel.HiddenSequences;
58 import jalview.datamodel.PDBEntry;
59 import jalview.datamodel.SeqCigar;
60 import jalview.datamodel.Sequence;
61 import jalview.datamodel.SequenceGroup;
62 import jalview.datamodel.SequenceI;
63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.DataSourceType;
69 import jalview.io.FileFormat;
70 import jalview.io.FileFormatI;
71 import jalview.io.FileFormats;
72 import jalview.io.FileLoader;
73 import jalview.io.FileParse;
74 import jalview.io.FormatAdapter;
75 import jalview.io.HtmlSvgOutput;
76 import jalview.io.IdentifyFile;
77 import jalview.io.JPredFile;
78 import jalview.io.JalviewFileChooser;
79 import jalview.io.JalviewFileView;
80 import jalview.io.JnetAnnotationMaker;
81 import jalview.io.NewickFile;
82 import jalview.io.ScoreMatrixFile;
83 import jalview.io.TCoffeeScoreFile;
84 import jalview.io.vcf.VCFLoader;
85 import jalview.jbgui.GAlignFrame;
86 import jalview.schemes.ColourSchemeI;
87 import jalview.schemes.ColourSchemes;
88 import jalview.schemes.ResidueColourScheme;
89 import jalview.schemes.TCoffeeColourScheme;
90 import jalview.util.MessageManager;
91 import jalview.viewmodel.AlignmentViewport;
92 import jalview.viewmodel.ViewportRanges;
93 import jalview.ws.DBRefFetcher;
94 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
95 import jalview.ws.jws1.Discoverer;
96 import jalview.ws.jws2.Jws2Discoverer;
97 import jalview.ws.jws2.jabaws2.Jws2Instance;
98 import jalview.ws.seqfetcher.DbSourceProxy;
100 import java.awt.BorderLayout;
101 import java.awt.Component;
102 import java.awt.Rectangle;
103 import java.awt.Toolkit;
104 import java.awt.datatransfer.Clipboard;
105 import java.awt.datatransfer.DataFlavor;
106 import java.awt.datatransfer.StringSelection;
107 import java.awt.datatransfer.Transferable;
108 import java.awt.dnd.DnDConstants;
109 import java.awt.dnd.DropTargetDragEvent;
110 import java.awt.dnd.DropTargetDropEvent;
111 import java.awt.dnd.DropTargetEvent;
112 import java.awt.dnd.DropTargetListener;
113 import java.awt.event.ActionEvent;
114 import java.awt.event.ActionListener;
115 import java.awt.event.FocusAdapter;
116 import java.awt.event.FocusEvent;
117 import java.awt.event.ItemEvent;
118 import java.awt.event.ItemListener;
119 import java.awt.event.KeyAdapter;
120 import java.awt.event.KeyEvent;
121 import java.awt.event.MouseEvent;
122 import java.awt.print.PageFormat;
123 import java.awt.print.PrinterJob;
124 import java.beans.PropertyChangeEvent;
126 import java.io.FileWriter;
127 import java.io.PrintWriter;
129 import java.util.ArrayList;
130 import java.util.Arrays;
131 import java.util.Deque;
132 import java.util.Enumeration;
133 import java.util.Hashtable;
134 import java.util.List;
135 import java.util.Vector;
137 import javax.swing.JCheckBoxMenuItem;
138 import javax.swing.JEditorPane;
139 import javax.swing.JInternalFrame;
140 import javax.swing.JLayeredPane;
141 import javax.swing.JMenu;
142 import javax.swing.JMenuItem;
143 import javax.swing.JScrollPane;
144 import javax.swing.SwingUtilities;
150 * @version $Revision$
152 public class AlignFrame extends GAlignFrame implements DropTargetListener,
153 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
156 public static final int DEFAULT_WIDTH = 700;
158 public static final int DEFAULT_HEIGHT = 500;
161 * The currently displayed panel (selected tabbed view if more than one)
163 public AlignmentPanel alignPanel;
165 AlignViewport viewport;
167 public AlignViewControllerI avc;
169 List<AlignmentPanel> alignPanels = new ArrayList<>();
172 * Last format used to load or save alignments in this window
174 FileFormatI currentFileFormat = null;
177 * Current filename for this alignment
179 String fileName = null;
182 * Creates a new AlignFrame object with specific width and height.
188 public AlignFrame(AlignmentI al, int width, int height)
190 this(al, null, width, height);
194 * Creates a new AlignFrame object with specific width, height and
200 * @param sequenceSetId
202 public AlignFrame(AlignmentI al, int width, int height,
203 String sequenceSetId)
205 this(al, null, width, height, sequenceSetId);
209 * Creates a new AlignFrame object with specific width, height and
215 * @param sequenceSetId
218 public AlignFrame(AlignmentI al, int width, int height,
219 String sequenceSetId, String viewId)
221 this(al, null, width, height, sequenceSetId, viewId);
225 * new alignment window with hidden columns
229 * @param hiddenColumns
230 * ColumnSelection or null
232 * Width of alignment frame
236 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
239 this(al, hiddenColumns, width, height, null);
243 * Create alignment frame for al with hiddenColumns, a specific width and
244 * height, and specific sequenceId
247 * @param hiddenColumns
250 * @param sequenceSetId
253 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
254 int height, String sequenceSetId)
256 this(al, hiddenColumns, width, height, sequenceSetId, null);
260 * Create alignment frame for al with hiddenColumns, a specific width and
261 * height, and specific sequenceId
264 * @param hiddenColumns
267 * @param sequenceSetId
272 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
273 int height, String sequenceSetId, String viewId)
275 setSize(width, height);
277 if (al.getDataset() == null)
282 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
284 alignPanel = new AlignmentPanel(this, viewport);
286 addAlignmentPanel(alignPanel, true);
290 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
291 HiddenColumns hiddenColumns, int width, int height)
293 setSize(width, height);
295 if (al.getDataset() == null)
300 viewport = new AlignViewport(al, hiddenColumns);
302 if (hiddenSeqs != null && hiddenSeqs.length > 0)
304 viewport.hideSequence(hiddenSeqs);
306 alignPanel = new AlignmentPanel(this, viewport);
307 addAlignmentPanel(alignPanel, true);
312 * Make a new AlignFrame from existing alignmentPanels
319 public AlignFrame(AlignmentPanel ap)
323 addAlignmentPanel(ap, false);
328 * initalise the alignframe from the underlying viewport data and the
333 if (!Jalview.isHeadlessMode())
335 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
338 avc = new jalview.controller.AlignViewController(this, viewport,
340 if (viewport.getAlignmentConservationAnnotation() == null)
342 // BLOSUM62Colour.setEnabled(false);
343 conservationMenuItem.setEnabled(false);
344 modifyConservation.setEnabled(false);
345 // PIDColour.setEnabled(false);
346 // abovePIDThreshold.setEnabled(false);
347 // modifyPID.setEnabled(false);
350 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
353 if (sortby.equals("Id"))
355 sortIDMenuItem_actionPerformed(null);
357 else if (sortby.equals("Pairwise Identity"))
359 sortPairwiseMenuItem_actionPerformed(null);
363 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
365 setMenusFromViewport(viewport);
366 buildSortByAnnotationScoresMenu();
367 calculateTree.addActionListener(new ActionListener()
371 public void actionPerformed(ActionEvent e)
378 if (Desktop.desktop != null)
380 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
382 * BH 2018 ignore service listeners
388 addServiceListeners();
393 if (viewport.getWrapAlignment())
395 wrapMenuItem_actionPerformed(null);
398 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
400 this.overviewMenuItem_actionPerformed(null);
405 final List<AlignmentPanel> selviews = new ArrayList<>();
406 final List<AlignmentPanel> origview = new ArrayList<>();
407 final String menuLabel = MessageManager
408 .getString("label.copy_format_from");
409 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
410 new ViewSetProvider()
414 public AlignmentPanel[] getAllAlignmentPanels()
417 origview.add(alignPanel);
418 // make an array of all alignment panels except for this one
419 List<AlignmentPanel> aps = new ArrayList<>(
420 Arrays.asList(Desktop.getAlignmentPanels(null)));
421 aps.remove(AlignFrame.this.alignPanel);
422 return aps.toArray(new AlignmentPanel[aps.size()]);
424 }, selviews, new ItemListener()
428 public void itemStateChanged(ItemEvent e)
430 if (origview.size() > 0)
432 final AlignmentPanel ap = origview.get(0);
435 * Copy the ViewStyle of the selected panel to 'this one'.
436 * Don't change value of 'scaleProteinAsCdna' unless copying
439 ViewStyleI vs = selviews.get(0).getAlignViewport()
441 boolean fromSplitFrame = selviews.get(0)
442 .getAlignViewport().getCodingComplement() != null;
445 vs.setScaleProteinAsCdna(ap.getAlignViewport()
446 .getViewStyle().isScaleProteinAsCdna());
448 ap.getAlignViewport().setViewStyle(vs);
451 * Also rescale ViewStyle of SplitFrame complement if there is
452 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
453 * the whole ViewStyle (allow cDNA protein to have different
456 AlignViewportI complement = ap.getAlignViewport()
457 .getCodingComplement();
458 if (complement != null && vs.isScaleProteinAsCdna())
460 AlignFrame af = Desktop.getAlignFrameFor(complement);
461 ((SplitFrame) af.getSplitViewContainer())
463 af.setMenusForViewport();
467 ap.setSelected(true);
468 ap.alignFrame.setMenusForViewport();
473 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
474 .indexOf("devel") > -1
475 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
476 .indexOf("test") > -1)
478 formatMenu.add(vsel);
480 addFocusListener(new FocusAdapter()
483 public void focusGained(FocusEvent e)
485 Jalview.setCurrentAlignFrame(AlignFrame.this);
492 * Change the filename and format for the alignment, and enable the 'reload'
493 * button functionality.
500 public void setFileName(String file, FileFormatI format)
503 setFileFormat(format);
504 reload.setEnabled(true);
508 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
511 void addKeyListener()
513 addKeyListener(new KeyAdapter()
516 public void keyPressed(KeyEvent evt)
518 if (viewport.cursorMode
519 && ((evt.getKeyCode() >= KeyEvent.VK_0
520 && evt.getKeyCode() <= KeyEvent.VK_9)
521 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
522 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
523 && Character.isDigit(evt.getKeyChar()))
525 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
528 switch (evt.getKeyCode())
531 case 27: // escape key
532 deselectAllSequenceMenuItem_actionPerformed(null);
536 case KeyEvent.VK_DOWN:
537 if (evt.isAltDown() || !viewport.cursorMode)
539 moveSelectedSequences(false);
541 if (viewport.cursorMode)
543 alignPanel.getSeqPanel().moveCursor(0, 1);
548 if (evt.isAltDown() || !viewport.cursorMode)
550 moveSelectedSequences(true);
552 if (viewport.cursorMode)
554 alignPanel.getSeqPanel().moveCursor(0, -1);
559 case KeyEvent.VK_LEFT:
560 if (evt.isAltDown() || !viewport.cursorMode)
562 slideSequences(false,
563 alignPanel.getSeqPanel().getKeyboardNo1());
567 alignPanel.getSeqPanel().moveCursor(-1, 0);
572 case KeyEvent.VK_RIGHT:
573 if (evt.isAltDown() || !viewport.cursorMode)
575 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
579 alignPanel.getSeqPanel().moveCursor(1, 0);
583 case KeyEvent.VK_SPACE:
584 if (viewport.cursorMode)
586 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
587 || evt.isShiftDown() || evt.isAltDown());
591 // case KeyEvent.VK_A:
592 // if (viewport.cursorMode)
594 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
595 // //System.out.println("A");
599 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
600 * System.out.println("closing bracket"); } break;
602 case KeyEvent.VK_DELETE:
603 case KeyEvent.VK_BACK_SPACE:
604 if (!viewport.cursorMode)
606 cut_actionPerformed(null);
610 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
611 || evt.isShiftDown() || evt.isAltDown());
617 if (viewport.cursorMode)
619 alignPanel.getSeqPanel().setCursorRow();
623 if (viewport.cursorMode && !evt.isControlDown())
625 alignPanel.getSeqPanel().setCursorColumn();
629 if (viewport.cursorMode)
631 alignPanel.getSeqPanel().setCursorPosition();
635 case KeyEvent.VK_ENTER:
636 case KeyEvent.VK_COMMA:
637 if (viewport.cursorMode)
639 alignPanel.getSeqPanel().setCursorRowAndColumn();
644 if (viewport.cursorMode)
646 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
650 if (viewport.cursorMode)
652 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
657 viewport.cursorMode = !viewport.cursorMode;
658 statusBar.setText(MessageManager
659 .formatMessage("label.keyboard_editing_mode", new String[]
660 { (viewport.cursorMode ? "on" : "off") }));
661 if (viewport.cursorMode)
663 ViewportRanges ranges = viewport.getRanges();
664 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
666 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
669 alignPanel.getSeqPanel().seqCanvas.repaint();
675 Help.showHelpWindow();
676 } catch (Exception ex)
678 ex.printStackTrace();
683 boolean toggleSeqs = !evt.isControlDown();
684 boolean toggleCols = !evt.isShiftDown();
685 toggleHiddenRegions(toggleSeqs, toggleCols);
690 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
691 boolean modifyExisting = true; // always modify, don't clear
692 // evt.isShiftDown();
693 boolean invertHighlighted = evt.isAltDown();
694 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
698 case KeyEvent.VK_PAGE_UP:
699 viewport.getRanges().pageUp();
701 case KeyEvent.VK_PAGE_DOWN:
702 viewport.getRanges().pageDown();
708 public void keyReleased(KeyEvent evt)
710 switch (evt.getKeyCode())
712 case KeyEvent.VK_LEFT:
713 if (evt.isAltDown() || !viewport.cursorMode)
715 viewport.firePropertyChange("alignment", null,
716 viewport.getAlignment().getSequences());
720 case KeyEvent.VK_RIGHT:
721 if (evt.isAltDown() || !viewport.cursorMode)
723 viewport.firePropertyChange("alignment", null,
724 viewport.getAlignment().getSequences());
732 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
734 ap.alignFrame = this;
735 avc = new jalview.controller.AlignViewController(this, viewport,
740 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
742 int aSize = alignPanels.size();
744 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
746 if (aSize == 1 && ap.av.viewName == null)
748 this.getContentPane().add(ap, BorderLayout.CENTER);
754 setInitialTabVisible();
757 expandViews.setEnabled(true);
758 gatherViews.setEnabled(true);
759 tabbedPane.addTab(ap.av.viewName, ap);
761 ap.setVisible(false);
766 if (ap.av.isPadGaps())
768 ap.av.getAlignment().padGaps();
770 ap.av.updateConservation(ap);
771 ap.av.updateConsensus(ap);
772 ap.av.updateStrucConsensus(ap);
776 public void setInitialTabVisible()
778 expandViews.setEnabled(true);
779 gatherViews.setEnabled(true);
780 tabbedPane.setVisible(true);
781 AlignmentPanel first = alignPanels.get(0);
782 tabbedPane.addTab(first.av.viewName, first);
783 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
786 public AlignViewport getViewport()
791 /* Set up intrinsic listeners for dynamically generated GUI bits. */
792 private void addServiceListeners()
794 final java.beans.PropertyChangeListener thisListener;
795 Desktop.instance.addJalviewPropertyChangeListener("services",
796 thisListener = new java.beans.PropertyChangeListener()
799 public void propertyChange(PropertyChangeEvent evt)
801 // // System.out.println("Discoverer property change.");
802 // if (evt.getPropertyName().equals("services"))
804 SwingUtilities.invokeLater(new Runnable()
811 "Rebuild WS Menu for service change");
812 BuildWebServiceMenu();
819 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
822 public void internalFrameClosed(
823 javax.swing.event.InternalFrameEvent evt)
825 // System.out.println("deregistering discoverer listener");
826 Desktop.instance.removeJalviewPropertyChangeListener("services",
828 closeMenuItem_actionPerformed(true);
831 // Finally, build the menu once to get current service state
832 new Thread(new Runnable()
837 BuildWebServiceMenu();
843 * Configure menu items that vary according to whether the alignment is
844 * nucleotide or protein
846 public void setGUINucleotide()
848 AlignmentI al = getViewport().getAlignment();
849 boolean nucleotide = al.isNucleotide();
851 loadVcf.setVisible(nucleotide);
852 showTranslation.setVisible(nucleotide);
853 showReverse.setVisible(nucleotide);
854 showReverseComplement.setVisible(nucleotide);
855 conservationMenuItem.setEnabled(!nucleotide);
857 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
858 showGroupConservation.setEnabled(!nucleotide);
860 showComplementMenuItem
861 .setText(nucleotide ? MessageManager.getString("label.protein")
862 : MessageManager.getString("label.nucleotide"));
866 * set up menus for the current viewport. This may be called after any
867 * operation that affects the data in the current view (selection changed,
868 * etc) to update the menus to reflect the new state.
871 public void setMenusForViewport()
873 setMenusFromViewport(viewport);
877 * Need to call this method when tabs are selected for multiple views, or when
878 * loading from Jalview2XML.java
883 void setMenusFromViewport(AlignViewport av)
885 padGapsMenuitem.setSelected(av.isPadGaps());
886 colourTextMenuItem.setSelected(av.isShowColourText());
887 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
888 modifyPID.setEnabled(abovePIDThreshold.isSelected());
889 conservationMenuItem.setSelected(av.getConservationSelected());
890 modifyConservation.setEnabled(conservationMenuItem.isSelected());
891 seqLimits.setSelected(av.getShowJVSuffix());
892 idRightAlign.setSelected(av.isRightAlignIds());
893 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
894 renderGapsMenuItem.setSelected(av.isRenderGaps());
895 wrapMenuItem.setSelected(av.getWrapAlignment());
896 scaleAbove.setVisible(av.getWrapAlignment());
897 scaleLeft.setVisible(av.getWrapAlignment());
898 scaleRight.setVisible(av.getWrapAlignment());
899 annotationPanelMenuItem.setState(av.isShowAnnotation());
901 * Show/hide annotations only enabled if annotation panel is shown
903 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
904 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
905 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
906 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
907 viewBoxesMenuItem.setSelected(av.getShowBoxes());
908 viewTextMenuItem.setSelected(av.getShowText());
909 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
910 showGroupConsensus.setSelected(av.isShowGroupConsensus());
911 showGroupConservation.setSelected(av.isShowGroupConservation());
912 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
913 showSequenceLogo.setSelected(av.isShowSequenceLogo());
914 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
916 ColourMenuHelper.setColourSelected(colourMenu,
917 av.getGlobalColourScheme());
919 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
920 hiddenMarkers.setState(av.getShowHiddenMarkers());
921 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
922 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
923 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
924 autoCalculate.setSelected(av.autoCalculateConsensus);
925 sortByTree.setSelected(av.sortByTree);
926 listenToViewSelections.setSelected(av.followSelection);
928 showProducts.setEnabled(canShowProducts());
929 setGroovyEnabled(Desktop.getGroovyConsole() != null);
935 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
939 public void setGroovyEnabled(boolean b)
941 runGroovy.setEnabled(b);
944 private IProgressIndicator progressBar;
949 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
952 public void setProgressBar(String message, long id)
954 progressBar.setProgressBar(message, id);
958 public void registerHandler(final long id,
959 final IProgressIndicatorHandler handler)
961 progressBar.registerHandler(id, handler);
966 * @return true if any progress bars are still active
969 public boolean operationInProgress()
971 return progressBar.operationInProgress();
975 public void setStatus(String text)
977 statusBar.setText(text);
981 * Added so Castor Mapping file can obtain Jalview Version
983 public String getVersion()
985 return jalview.bin.Cache.getProperty("VERSION");
988 public FeatureRenderer getFeatureRenderer()
990 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
994 public void fetchSequence_actionPerformed(ActionEvent e)
996 new jalview.gui.SequenceFetcher(this);
1000 public void addFromFile_actionPerformed(ActionEvent e)
1002 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1006 public void reload_actionPerformed(ActionEvent e)
1008 if (fileName != null)
1010 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1011 // originating file's format
1012 // TODO: work out how to recover feature settings for correct view(s) when
1013 // file is reloaded.
1014 if (FileFormat.Jalview.equals(currentFileFormat))
1016 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1017 for (int i = 0; i < frames.length; i++)
1019 if (frames[i] instanceof AlignFrame && frames[i] != this
1020 && ((AlignFrame) frames[i]).fileName != null
1021 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1025 frames[i].setSelected(true);
1026 Desktop.instance.closeAssociatedWindows();
1027 } catch (java.beans.PropertyVetoException ex)
1033 Desktop.instance.closeAssociatedWindows();
1035 FileLoader loader = new FileLoader();
1036 DataSourceType protocol = fileName.startsWith("http:")
1037 ? DataSourceType.URL
1038 : DataSourceType.FILE;
1039 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1043 Rectangle bounds = this.getBounds();
1045 FileLoader loader = new FileLoader();
1046 DataSourceType protocol = fileName.startsWith("http:")
1047 ? DataSourceType.URL
1048 : DataSourceType.FILE;
1049 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1050 protocol, currentFileFormat);
1052 newframe.setBounds(bounds);
1053 if (featureSettings != null && featureSettings.isShowing())
1055 final Rectangle fspos = featureSettings.frame.getBounds();
1056 // TODO: need a 'show feature settings' function that takes bounds -
1057 // need to refactor Desktop.addFrame
1058 newframe.featureSettings_actionPerformed(null);
1059 final FeatureSettings nfs = newframe.featureSettings;
1060 SwingUtilities.invokeLater(new Runnable()
1065 nfs.frame.setBounds(fspos);
1068 this.featureSettings.close();
1069 this.featureSettings = null;
1071 this.closeMenuItem_actionPerformed(true);
1077 public void addFromText_actionPerformed(ActionEvent e)
1080 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1084 public void addFromURL_actionPerformed(ActionEvent e)
1086 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1090 public void save_actionPerformed(ActionEvent e)
1092 if (fileName == null || (currentFileFormat == null)
1093 || fileName.startsWith("http"))
1095 saveAs_actionPerformed(null);
1099 saveAlignment(fileName, currentFileFormat);
1110 public void saveAs_actionPerformed(ActionEvent e)
1112 String format = currentFileFormat == null ? null
1113 : currentFileFormat.getName();
1114 JalviewFileChooser chooser = JalviewFileChooser
1115 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1117 chooser.setFileView(new JalviewFileView());
1118 chooser.setDialogTitle(
1119 MessageManager.getString("label.save_alignment_to_file"));
1120 chooser.setToolTipText(MessageManager.getString("action.save"));
1122 int value = chooser.showSaveDialog(this);
1124 if (value == JalviewFileChooser.APPROVE_OPTION)
1126 currentFileFormat = chooser.getSelectedFormat();
1127 while (currentFileFormat == null)
1129 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1130 MessageManager.getString(
1131 "label.select_file_format_before_saving"),
1132 MessageManager.getString("label.file_format_not_specified"),
1133 JvOptionPane.WARNING_MESSAGE);
1134 currentFileFormat = chooser.getSelectedFormat();
1135 value = chooser.showSaveDialog(this);
1136 if (value != JalviewFileChooser.APPROVE_OPTION)
1142 fileName = chooser.getSelectedFile().getPath();
1144 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1146 Cache.setProperty("LAST_DIRECTORY", fileName);
1147 saveAlignment(fileName, currentFileFormat);
1151 public boolean saveAlignment(String file, FileFormatI format)
1153 boolean success = true;
1155 if (FileFormat.Jalview.equals(format))
1157 String shortName = title;
1159 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1161 shortName = shortName.substring(
1162 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1165 success = new Jalview2XML().saveAlignment(this, file, shortName);
1167 statusBar.setText(MessageManager.formatMessage(
1168 "label.successfully_saved_to_file_in_format", new Object[]
1169 { fileName, format }));
1174 AlignmentExportData exportData = getAlignmentForExport(format,
1176 if (exportData.getSettings().isCancelled())
1180 FormatAdapter f = new FormatAdapter(alignPanel,
1181 exportData.getSettings());
1182 String output = f.formatSequences(format, exportData.getAlignment(), // class
1186 // occur in the distant future
1187 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1188 f.getCacheSuffixDefault(format),
1189 viewport.getAlignment().getHiddenColumns());
1199 PrintWriter out = new PrintWriter(new FileWriter(file));
1203 this.setTitle(file);
1204 statusBar.setText(MessageManager.formatMessage(
1205 "label.successfully_saved_to_file_in_format", new Object[]
1206 { fileName, format.getName() }));
1207 } catch (Exception ex)
1210 ex.printStackTrace();
1217 JvOptionPane.showInternalMessageDialog(this, MessageManager
1218 .formatMessage("label.couldnt_save_file", new Object[]
1220 MessageManager.getString("label.error_saving_file"),
1221 JvOptionPane.WARNING_MESSAGE);
1227 private void warningMessage(String warning, String title)
1229 if (new jalview.util.Platform().isHeadless())
1231 System.err.println("Warning: " + title + "\nWarning: " + warning);
1236 JvOptionPane.showInternalMessageDialog(this, warning, title,
1237 JvOptionPane.WARNING_MESSAGE);
1249 protected void outputText_actionPerformed(ActionEvent e)
1251 FileFormatI fileFormat = FileFormats.getInstance()
1252 .forName(e.getActionCommand());
1253 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1255 if (exportData.getSettings().isCancelled())
1259 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1260 cap.setForInput(null);
1263 FileFormatI format = fileFormat;
1264 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1265 .formatSequences(format, exportData.getAlignment(),
1266 exportData.getOmitHidden(),
1267 exportData.getStartEndPostions(),
1268 viewport.getAlignment().getHiddenColumns()));
1269 Desktop.addInternalFrame(cap, MessageManager
1270 .formatMessage("label.alignment_output_command", new Object[]
1271 { e.getActionCommand() }), 600, 500);
1272 } catch (OutOfMemoryError oom)
1274 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1281 public static AlignmentExportData getAlignmentForExport(
1282 FileFormatI format, AlignViewportI viewport,
1283 AlignExportSettingI exportSettings)
1285 AlignmentI alignmentToExport = null;
1286 AlignExportSettingI settings = exportSettings;
1287 String[] omitHidden = null;
1289 HiddenSequences hiddenSeqs = viewport.getAlignment()
1290 .getHiddenSequences();
1292 alignmentToExport = viewport.getAlignment();
1294 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1295 if (settings == null)
1297 settings = new AlignExportSettings(hasHiddenSeqs,
1298 viewport.hasHiddenColumns(), format);
1300 // settings.isExportAnnotations();
1302 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1304 omitHidden = viewport.getViewAsString(false,
1305 settings.isExportHiddenSequences());
1308 int[] alignmentStartEnd = new int[2];
1309 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1311 alignmentToExport = hiddenSeqs.getFullAlignment();
1315 alignmentToExport = viewport.getAlignment();
1317 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1318 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1319 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1320 omitHidden, alignmentStartEnd, settings);
1331 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1333 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1334 htmlSVG.exportHTML(null);
1338 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1340 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1341 bjs.exportHTML(null);
1344 public void createImageMap(File file, String image)
1346 alignPanel.makePNGImageMap(file, image);
1356 public void createPNG(File f)
1358 alignPanel.makePNG(f);
1368 public void createEPS(File f)
1370 alignPanel.makeEPS(f);
1374 public void createSVG(File f)
1376 alignPanel.makeSVG(f);
1380 public void pageSetup_actionPerformed(ActionEvent e)
1382 PrinterJob printJob = PrinterJob.getPrinterJob();
1383 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1393 public void printMenuItem_actionPerformed(ActionEvent e)
1395 // Putting in a thread avoids Swing painting problems
1396 PrintThread thread = new PrintThread(alignPanel);
1401 public void exportFeatures_actionPerformed(ActionEvent e)
1403 new AnnotationExporter(alignPanel).exportFeatures();
1407 public void exportAnnotations_actionPerformed(ActionEvent e)
1409 new AnnotationExporter(alignPanel).exportAnnotations();
1413 public void associatedData_actionPerformed(ActionEvent e)
1415 // Pick the tree file
1416 JalviewFileChooser chooser = new JalviewFileChooser(
1417 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1418 chooser.setFileView(new JalviewFileView());
1419 chooser.setDialogTitle(
1420 MessageManager.getString("label.load_jalview_annotations"));
1421 chooser.setToolTipText(
1422 MessageManager.getString("label.load_jalview_annotations"));
1424 int value = chooser.showOpenDialog(null);
1426 if (value == JalviewFileChooser.APPROVE_OPTION)
1428 String choice = chooser.getSelectedFile().getPath();
1429 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1430 loadJalviewDataFile(choice, null, null, null);
1436 * Close the current view or all views in the alignment frame. If the frame
1437 * only contains one view then the alignment will be removed from memory.
1439 * @param closeAllTabs
1442 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1444 if (alignPanels != null && alignPanels.size() < 2)
1446 closeAllTabs = true;
1451 if (alignPanels != null)
1455 if (this.isClosed())
1457 // really close all the windows - otherwise wait till
1458 // setClosed(true) is called
1459 for (int i = 0; i < alignPanels.size(); i++)
1461 AlignmentPanel ap = alignPanels.get(i);
1468 closeView(alignPanel);
1475 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1476 * be called recursively, with the frame now in 'closed' state
1478 this.setClosed(true);
1480 } catch (Exception ex)
1482 ex.printStackTrace();
1487 * Close the specified panel and close up tabs appropriately.
1489 * @param panelToClose
1491 public void closeView(AlignmentPanel panelToClose)
1493 int index = tabbedPane.getSelectedIndex();
1494 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1495 alignPanels.remove(panelToClose);
1496 panelToClose.closePanel();
1497 panelToClose = null;
1499 tabbedPane.removeTabAt(closedindex);
1500 tabbedPane.validate();
1502 if (index > closedindex || index == tabbedPane.getTabCount())
1504 // modify currently selected tab index if necessary.
1508 this.tabSelectionChanged(index);
1514 void updateEditMenuBar()
1517 if (viewport.getHistoryList().size() > 0)
1519 undoMenuItem.setEnabled(true);
1520 CommandI command = viewport.getHistoryList().peek();
1521 undoMenuItem.setText(MessageManager
1522 .formatMessage("label.undo_command", new Object[]
1523 { command.getDescription() }));
1527 undoMenuItem.setEnabled(false);
1528 undoMenuItem.setText(MessageManager.getString("action.undo"));
1531 if (viewport.getRedoList().size() > 0)
1533 redoMenuItem.setEnabled(true);
1535 CommandI command = viewport.getRedoList().peek();
1536 redoMenuItem.setText(MessageManager
1537 .formatMessage("label.redo_command", new Object[]
1538 { command.getDescription() }));
1542 redoMenuItem.setEnabled(false);
1543 redoMenuItem.setText(MessageManager.getString("action.redo"));
1548 public void addHistoryItem(CommandI command)
1550 if (command.getSize() > 0)
1552 viewport.addToHistoryList(command);
1553 viewport.clearRedoList();
1554 updateEditMenuBar();
1555 viewport.updateHiddenColumns();
1556 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1557 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1558 // viewport.getColumnSelection()
1559 // .getHiddenColumns().size() > 0);
1565 * @return alignment objects for all views
1567 AlignmentI[] getViewAlignments()
1569 if (alignPanels != null)
1571 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1573 for (AlignmentPanel ap : alignPanels)
1575 als[i++] = ap.av.getAlignment();
1579 if (viewport != null)
1581 return new AlignmentI[] { viewport.getAlignment() };
1593 protected void undoMenuItem_actionPerformed(ActionEvent e)
1595 if (viewport.getHistoryList().isEmpty())
1599 CommandI command = viewport.getHistoryList().pop();
1600 viewport.addToRedoList(command);
1601 command.undoCommand(getViewAlignments());
1603 AlignmentViewport originalSource = getOriginatingSource(command);
1604 updateEditMenuBar();
1606 if (originalSource != null)
1608 if (originalSource != viewport)
1611 "Implementation worry: mismatch of viewport origin for undo");
1613 originalSource.updateHiddenColumns();
1614 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1616 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1617 // viewport.getColumnSelection()
1618 // .getHiddenColumns().size() > 0);
1619 originalSource.firePropertyChange("alignment", null,
1620 originalSource.getAlignment().getSequences());
1631 protected void redoMenuItem_actionPerformed(ActionEvent e)
1633 if (viewport.getRedoList().size() < 1)
1638 CommandI command = viewport.getRedoList().pop();
1639 viewport.addToHistoryList(command);
1640 command.doCommand(getViewAlignments());
1642 AlignmentViewport originalSource = getOriginatingSource(command);
1643 updateEditMenuBar();
1645 if (originalSource != null)
1648 if (originalSource != viewport)
1651 "Implementation worry: mismatch of viewport origin for redo");
1653 originalSource.updateHiddenColumns();
1654 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1656 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1657 // viewport.getColumnSelection()
1658 // .getHiddenColumns().size() > 0);
1659 originalSource.firePropertyChange("alignment", null,
1660 originalSource.getAlignment().getSequences());
1664 AlignmentViewport getOriginatingSource(CommandI command)
1666 AlignmentViewport originalSource = null;
1667 // For sequence removal and addition, we need to fire
1668 // the property change event FROM the viewport where the
1669 // original alignment was altered
1670 AlignmentI al = null;
1671 if (command instanceof EditCommand)
1673 EditCommand editCommand = (EditCommand) command;
1674 al = editCommand.getAlignment();
1675 List<Component> comps = PaintRefresher.components
1676 .get(viewport.getSequenceSetId());
1678 for (Component comp : comps)
1680 if (comp instanceof AlignmentPanel)
1682 if (al == ((AlignmentPanel) comp).av.getAlignment())
1684 originalSource = ((AlignmentPanel) comp).av;
1691 if (originalSource == null)
1693 // The original view is closed, we must validate
1694 // the current view against the closed view first
1697 PaintRefresher.validateSequences(al, viewport.getAlignment());
1700 originalSource = viewport;
1703 return originalSource;
1712 public void moveSelectedSequences(boolean up)
1714 SequenceGroup sg = viewport.getSelectionGroup();
1720 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1721 viewport.getHiddenRepSequences(), up);
1722 alignPanel.paintAlignment(true, false);
1725 synchronized void slideSequences(boolean right, int size)
1727 List<SequenceI> sg = new ArrayList<>();
1728 if (viewport.cursorMode)
1730 sg.add(viewport.getAlignment()
1731 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1733 else if (viewport.getSelectionGroup() != null
1734 && viewport.getSelectionGroup().getSize() != viewport
1735 .getAlignment().getHeight())
1737 sg = viewport.getSelectionGroup()
1738 .getSequences(viewport.getHiddenRepSequences());
1746 List<SequenceI> invertGroup = new ArrayList<>();
1748 for (SequenceI seq : viewport.getAlignment().getSequences())
1750 if (!sg.contains(seq))
1752 invertGroup.add(seq);
1756 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1758 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1759 for (int i = 0; i < invertGroup.size(); i++)
1761 seqs2[i] = invertGroup.get(i);
1764 SlideSequencesCommand ssc;
1767 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1768 viewport.getGapCharacter());
1772 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1773 viewport.getGapCharacter());
1776 int groupAdjustment = 0;
1777 if (ssc.getGapsInsertedBegin() && right)
1779 if (viewport.cursorMode)
1781 alignPanel.getSeqPanel().moveCursor(size, 0);
1785 groupAdjustment = size;
1788 else if (!ssc.getGapsInsertedBegin() && !right)
1790 if (viewport.cursorMode)
1792 alignPanel.getSeqPanel().moveCursor(-size, 0);
1796 groupAdjustment = -size;
1800 if (groupAdjustment != 0)
1802 viewport.getSelectionGroup().setStartRes(
1803 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1804 viewport.getSelectionGroup().setEndRes(
1805 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1809 * just extend the last slide command if compatible; but not if in
1810 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1812 boolean appendHistoryItem = false;
1813 Deque<CommandI> historyList = viewport.getHistoryList();
1814 boolean inSplitFrame = getSplitViewContainer() != null;
1815 if (!inSplitFrame && historyList != null && historyList.size() > 0
1816 && historyList.peek() instanceof SlideSequencesCommand)
1818 appendHistoryItem = ssc.appendSlideCommand(
1819 (SlideSequencesCommand) historyList.peek());
1822 if (!appendHistoryItem)
1824 addHistoryItem(ssc);
1837 protected void copy_actionPerformed(ActionEvent e)
1839 if (viewport.getSelectionGroup() == null)
1843 // TODO: preserve the ordering of displayed alignment annotation in any
1844 // internal paste (particularly sequence associated annotation)
1845 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1846 String[] omitHidden = null;
1848 if (viewport.hasHiddenColumns())
1850 omitHidden = viewport.getViewAsString(true);
1853 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1854 seqs, omitHidden, null);
1856 StringSelection ss = new StringSelection(output);
1860 jalview.gui.Desktop.internalCopy = true;
1861 // Its really worth setting the clipboard contents
1862 // to empty before setting the large StringSelection!!
1863 Toolkit.getDefaultToolkit().getSystemClipboard()
1864 .setContents(new StringSelection(""), null);
1866 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1868 } catch (OutOfMemoryError er)
1870 new OOMWarning("copying region", er);
1874 HiddenColumns hiddenColumns = null;
1875 if (viewport.hasHiddenColumns())
1877 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1878 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1880 // create new HiddenColumns object with copy of hidden regions
1881 // between startRes and endRes, offset by startRes
1882 hiddenColumns = new HiddenColumns(
1883 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1884 hiddenCutoff, hiddenOffset);
1887 Desktop.jalviewClipboard = new Object[] { seqs,
1888 viewport.getAlignment().getDataset(), hiddenColumns };
1889 statusBar.setText(MessageManager.formatMessage(
1890 "label.copied_sequences_to_clipboard", new Object[]
1891 { Integer.valueOf(seqs.length).toString() }));
1901 protected void pasteNew_actionPerformed(ActionEvent e)
1913 protected void pasteThis_actionPerformed(ActionEvent e)
1919 * Paste contents of Jalview clipboard
1921 * @param newAlignment
1922 * true to paste to a new alignment, otherwise add to this.
1924 void paste(boolean newAlignment)
1926 boolean externalPaste = true;
1929 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1930 Transferable contents = c.getContents(this);
1932 if (contents == null)
1941 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1942 if (str.length() < 1)
1947 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1949 } catch (OutOfMemoryError er)
1951 new OOMWarning("Out of memory pasting sequences!!", er);
1955 SequenceI[] sequences;
1956 boolean annotationAdded = false;
1957 AlignmentI alignment = null;
1959 if (Desktop.jalviewClipboard != null)
1961 // The clipboard was filled from within Jalview, we must use the
1963 // And dataset from the copied alignment
1964 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1965 // be doubly sure that we create *new* sequence objects.
1966 sequences = new SequenceI[newseq.length];
1967 for (int i = 0; i < newseq.length; i++)
1969 sequences[i] = new Sequence(newseq[i]);
1971 alignment = new Alignment(sequences);
1972 externalPaste = false;
1976 // parse the clipboard as an alignment.
1977 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1979 sequences = alignment.getSequencesArray();
1983 ArrayList<Integer> newGraphGroups = new ArrayList<>();
1989 if (Desktop.jalviewClipboard != null)
1991 // dataset is inherited
1992 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1996 // new dataset is constructed
1997 alignment.setDataset(null);
1999 alwidth = alignment.getWidth() + 1;
2003 AlignmentI pastedal = alignment; // preserve pasted alignment object
2004 // Add pasted sequences and dataset into existing alignment.
2005 alignment = viewport.getAlignment();
2006 alwidth = alignment.getWidth() + 1;
2007 // decide if we need to import sequences from an existing dataset
2008 boolean importDs = Desktop.jalviewClipboard != null
2009 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2010 // importDs==true instructs us to copy over new dataset sequences from
2011 // an existing alignment
2012 Vector newDs = (importDs) ? new Vector() : null; // used to create
2013 // minimum dataset set
2015 for (int i = 0; i < sequences.length; i++)
2019 newDs.addElement(null);
2021 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2023 if (importDs && ds != null)
2025 if (!newDs.contains(ds))
2027 newDs.setElementAt(ds, i);
2028 ds = new Sequence(ds);
2029 // update with new dataset sequence
2030 sequences[i].setDatasetSequence(ds);
2034 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2039 // copy and derive new dataset sequence
2040 sequences[i] = sequences[i].deriveSequence();
2041 alignment.getDataset()
2042 .addSequence(sequences[i].getDatasetSequence());
2043 // TODO: avoid creation of duplicate dataset sequences with a
2044 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2046 alignment.addSequence(sequences[i]); // merges dataset
2050 newDs.clear(); // tidy up
2052 if (alignment.getAlignmentAnnotation() != null)
2054 for (AlignmentAnnotation alan : alignment
2055 .getAlignmentAnnotation())
2057 if (alan.graphGroup > fgroup)
2059 fgroup = alan.graphGroup;
2063 if (pastedal.getAlignmentAnnotation() != null)
2065 // Add any annotation attached to alignment.
2066 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2067 for (int i = 0; i < alann.length; i++)
2069 annotationAdded = true;
2070 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2072 AlignmentAnnotation newann = new AlignmentAnnotation(
2074 if (newann.graphGroup > -1)
2076 if (newGraphGroups.size() <= newann.graphGroup
2077 || newGraphGroups.get(newann.graphGroup) == null)
2079 for (int q = newGraphGroups
2080 .size(); q <= newann.graphGroup; q++)
2082 newGraphGroups.add(q, null);
2084 newGraphGroups.set(newann.graphGroup,
2085 new Integer(++fgroup));
2087 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2091 newann.padAnnotation(alwidth);
2092 alignment.addAnnotation(newann);
2102 addHistoryItem(new EditCommand(
2103 MessageManager.getString("label.add_sequences"),
2104 Action.PASTE, sequences, 0, alignment.getWidth(),
2107 // Add any annotations attached to sequences
2108 for (int i = 0; i < sequences.length; i++)
2110 if (sequences[i].getAnnotation() != null)
2112 AlignmentAnnotation newann;
2113 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2115 annotationAdded = true;
2116 newann = sequences[i].getAnnotation()[a];
2117 newann.adjustForAlignment();
2118 newann.padAnnotation(alwidth);
2119 if (newann.graphGroup > -1)
2121 if (newann.graphGroup > -1)
2123 if (newGraphGroups.size() <= newann.graphGroup
2124 || newGraphGroups.get(newann.graphGroup) == null)
2126 for (int q = newGraphGroups
2127 .size(); q <= newann.graphGroup; q++)
2129 newGraphGroups.add(q, null);
2131 newGraphGroups.set(newann.graphGroup,
2132 new Integer(++fgroup));
2134 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2138 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2142 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2150 // propagate alignment changed.
2151 viewport.getRanges().setEndSeq(alignment.getHeight());
2152 if (annotationAdded)
2154 // Duplicate sequence annotation in all views.
2155 AlignmentI[] alview = this.getViewAlignments();
2156 for (int i = 0; i < sequences.length; i++)
2158 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2163 for (int avnum = 0; avnum < alview.length; avnum++)
2165 if (alview[avnum] != alignment)
2167 // duplicate in a view other than the one with input focus
2168 int avwidth = alview[avnum].getWidth() + 1;
2169 // this relies on sann being preserved after we
2170 // modify the sequence's annotation array for each duplication
2171 for (int a = 0; a < sann.length; a++)
2173 AlignmentAnnotation newann = new AlignmentAnnotation(
2175 sequences[i].addAlignmentAnnotation(newann);
2176 newann.padAnnotation(avwidth);
2177 alview[avnum].addAnnotation(newann); // annotation was
2178 // duplicated earlier
2179 // TODO JAL-1145 graphGroups are not updated for sequence
2180 // annotation added to several views. This may cause
2182 alview[avnum].setAnnotationIndex(newann, a);
2187 buildSortByAnnotationScoresMenu();
2189 viewport.firePropertyChange("alignment", null,
2190 alignment.getSequences());
2191 if (alignPanels != null)
2193 for (AlignmentPanel ap : alignPanels)
2195 ap.validateAnnotationDimensions(false);
2200 alignPanel.validateAnnotationDimensions(false);
2206 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2208 String newtitle = new String("Copied sequences");
2210 if (Desktop.jalviewClipboard != null
2211 && Desktop.jalviewClipboard[2] != null)
2213 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2214 af.viewport.setHiddenColumns(hc);
2217 // >>>This is a fix for the moment, until a better solution is
2219 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2220 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2221 .getFeatureRenderer());
2223 // TODO: maintain provenance of an alignment, rather than just make the
2224 // title a concatenation of operations.
2227 if (title.startsWith("Copied sequences"))
2233 newtitle = newtitle.concat("- from " + title);
2238 newtitle = new String("Pasted sequences");
2241 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2246 } catch (Exception ex)
2248 ex.printStackTrace();
2249 System.out.println("Exception whilst pasting: " + ex);
2250 // could be anything being pasted in here
2256 protected void expand_newalign(ActionEvent e)
2260 AlignmentI alignment = AlignmentUtils
2261 .expandContext(getViewport().getAlignment(), -1);
2262 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2264 String newtitle = new String("Flanking alignment");
2266 if (Desktop.jalviewClipboard != null
2267 && Desktop.jalviewClipboard[2] != null)
2269 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2270 af.viewport.setHiddenColumns(hc);
2273 // >>>This is a fix for the moment, until a better solution is
2275 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2276 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2277 .getFeatureRenderer());
2279 // TODO: maintain provenance of an alignment, rather than just make the
2280 // title a concatenation of operations.
2282 if (title.startsWith("Copied sequences"))
2288 newtitle = newtitle.concat("- from " + title);
2292 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2294 } catch (Exception ex)
2296 ex.printStackTrace();
2297 System.out.println("Exception whilst pasting: " + ex);
2298 // could be anything being pasted in here
2299 } catch (OutOfMemoryError oom)
2301 new OOMWarning("Viewing flanking region of alignment", oom);
2312 protected void cut_actionPerformed(ActionEvent e)
2314 copy_actionPerformed(null);
2315 delete_actionPerformed(null);
2325 protected void delete_actionPerformed(ActionEvent evt)
2328 SequenceGroup sg = viewport.getSelectionGroup();
2335 * If the cut affects all sequences, warn, remove highlighted columns
2337 if (sg.getSize() == viewport.getAlignment().getHeight())
2339 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2340 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2341 if (isEntireAlignWidth)
2343 int confirm = JvOptionPane.showConfirmDialog(this,
2344 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2345 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2346 JvOptionPane.OK_CANCEL_OPTION);
2348 if (confirm == JvOptionPane.CANCEL_OPTION
2349 || confirm == JvOptionPane.CLOSED_OPTION)
2354 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2355 sg.getEndRes() + 1);
2357 SequenceI[] cut = sg.getSequences()
2358 .toArray(new SequenceI[sg.getSize()]);
2360 addHistoryItem(new EditCommand(
2361 MessageManager.getString("label.cut_sequences"), Action.CUT,
2362 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2363 viewport.getAlignment()));
2365 viewport.setSelectionGroup(null);
2366 viewport.sendSelection();
2367 viewport.getAlignment().deleteGroup(sg);
2369 viewport.firePropertyChange("alignment", null,
2370 viewport.getAlignment().getSequences());
2371 if (viewport.getAlignment().getHeight() < 1)
2375 this.setClosed(true);
2376 } catch (Exception ex)
2389 protected void deleteGroups_actionPerformed(ActionEvent e)
2391 if (avc.deleteGroups())
2393 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2394 alignPanel.updateAnnotation();
2395 alignPanel.paintAlignment(true, true);
2406 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2408 SequenceGroup sg = new SequenceGroup();
2410 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2412 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2415 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2416 viewport.setSelectionGroup(sg);
2417 viewport.sendSelection();
2418 // JAL-2034 - should delegate to
2419 // alignPanel to decide if overview needs
2421 alignPanel.paintAlignment(false, false);
2422 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2432 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2434 if (viewport.cursorMode)
2436 alignPanel.getSeqPanel().keyboardNo1 = null;
2437 alignPanel.getSeqPanel().keyboardNo2 = null;
2439 viewport.setSelectionGroup(null);
2440 viewport.getColumnSelection().clear();
2441 viewport.setSelectionGroup(null);
2442 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2443 // JAL-2034 - should delegate to
2444 // alignPanel to decide if overview needs
2446 alignPanel.paintAlignment(false, false);
2447 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2448 viewport.sendSelection();
2458 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2460 SequenceGroup sg = viewport.getSelectionGroup();
2464 selectAllSequenceMenuItem_actionPerformed(null);
2469 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2471 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2473 // JAL-2034 - should delegate to
2474 // alignPanel to decide if overview needs
2477 alignPanel.paintAlignment(true, false);
2478 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2479 viewport.sendSelection();
2483 public void invertColSel_actionPerformed(ActionEvent e)
2485 viewport.invertColumnSelection();
2486 alignPanel.paintAlignment(true, false);
2487 viewport.sendSelection();
2497 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2499 trimAlignment(true);
2509 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2511 trimAlignment(false);
2514 void trimAlignment(boolean trimLeft)
2516 ColumnSelection colSel = viewport.getColumnSelection();
2519 if (!colSel.isEmpty())
2523 column = colSel.getMin();
2527 column = colSel.getMax();
2531 if (viewport.getSelectionGroup() != null)
2533 seqs = viewport.getSelectionGroup()
2534 .getSequencesAsArray(viewport.getHiddenRepSequences());
2538 seqs = viewport.getAlignment().getSequencesArray();
2541 TrimRegionCommand trimRegion;
2544 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2545 column, viewport.getAlignment());
2546 viewport.getRanges().setStartRes(0);
2550 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2551 column, viewport.getAlignment());
2554 statusBar.setText(MessageManager
2555 .formatMessage("label.removed_columns", new String[]
2556 { Integer.valueOf(trimRegion.getSize()).toString() }));
2558 addHistoryItem(trimRegion);
2560 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2562 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2563 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2565 viewport.getAlignment().deleteGroup(sg);
2569 viewport.firePropertyChange("alignment", null,
2570 viewport.getAlignment().getSequences());
2581 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2583 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2586 if (viewport.getSelectionGroup() != null)
2588 seqs = viewport.getSelectionGroup()
2589 .getSequencesAsArray(viewport.getHiddenRepSequences());
2590 start = viewport.getSelectionGroup().getStartRes();
2591 end = viewport.getSelectionGroup().getEndRes();
2595 seqs = viewport.getAlignment().getSequencesArray();
2598 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2599 "Remove Gapped Columns", seqs, start, end,
2600 viewport.getAlignment());
2602 addHistoryItem(removeGapCols);
2604 statusBar.setText(MessageManager
2605 .formatMessage("label.removed_empty_columns", new Object[]
2606 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2608 // This is to maintain viewport position on first residue
2609 // of first sequence
2610 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2611 ViewportRanges ranges = viewport.getRanges();
2612 int startRes = seq.findPosition(ranges.getStartRes());
2613 // ShiftList shifts;
2614 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2615 // edit.alColumnChanges=shifts.getInverse();
2616 // if (viewport.hasHiddenColumns)
2617 // viewport.getColumnSelection().compensateForEdits(shifts);
2618 ranges.setStartRes(seq.findIndex(startRes) - 1);
2619 viewport.firePropertyChange("alignment", null,
2620 viewport.getAlignment().getSequences());
2631 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2633 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2636 if (viewport.getSelectionGroup() != null)
2638 seqs = viewport.getSelectionGroup()
2639 .getSequencesAsArray(viewport.getHiddenRepSequences());
2640 start = viewport.getSelectionGroup().getStartRes();
2641 end = viewport.getSelectionGroup().getEndRes();
2645 seqs = viewport.getAlignment().getSequencesArray();
2648 // This is to maintain viewport position on first residue
2649 // of first sequence
2650 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2651 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2653 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2654 viewport.getAlignment()));
2656 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2658 viewport.firePropertyChange("alignment", null,
2659 viewport.getAlignment().getSequences());
2670 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2672 viewport.setPadGaps(padGapsMenuitem.isSelected());
2673 viewport.firePropertyChange("alignment", null,
2674 viewport.getAlignment().getSequences());
2684 public void findMenuItem_actionPerformed(ActionEvent e)
2690 * Create a new view of the current alignment.
2693 public void newView_actionPerformed(ActionEvent e)
2695 newView(null, true);
2699 * Creates and shows a new view of the current alignment.
2702 * title of newly created view; if null, one will be generated
2703 * @param copyAnnotation
2704 * if true then duplicate all annnotation, groups and settings
2705 * @return new alignment panel, already displayed.
2707 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2710 * Create a new AlignmentPanel (with its own, new Viewport)
2712 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2713 if (!copyAnnotation)
2716 * remove all groups and annotation except for the automatic stuff
2718 newap.av.getAlignment().deleteAllGroups();
2719 newap.av.getAlignment().deleteAllAnnotations(false);
2722 newap.av.setGatherViewsHere(false);
2724 if (viewport.viewName == null)
2726 viewport.viewName = MessageManager
2727 .getString("label.view_name_original");
2731 * Views share the same edits undo and redo stacks
2733 newap.av.setHistoryList(viewport.getHistoryList());
2734 newap.av.setRedoList(viewport.getRedoList());
2737 * Views share the same mappings; need to deregister any new mappings
2738 * created by copyAlignPanel, and register the new reference to the shared
2741 newap.av.replaceMappings(viewport.getAlignment());
2744 * start up cDNA consensus (if applicable) now mappings are in place
2746 if (newap.av.initComplementConsensus())
2748 newap.refresh(true); // adjust layout of annotations
2751 newap.av.viewName = getNewViewName(viewTitle);
2753 addAlignmentPanel(newap, true);
2754 newap.alignmentChanged();
2756 if (alignPanels.size() == 2)
2758 viewport.setGatherViewsHere(true);
2760 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2765 * Make a new name for the view, ensuring it is unique within the current
2766 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2767 * these now use viewId. Unique view names are still desirable for usability.)
2772 protected String getNewViewName(String viewTitle)
2774 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2775 boolean addFirstIndex = false;
2776 if (viewTitle == null || viewTitle.trim().length() == 0)
2778 viewTitle = MessageManager.getString("action.view");
2779 addFirstIndex = true;
2783 index = 1;// we count from 1 if given a specific name
2785 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2787 List<Component> comps = PaintRefresher.components
2788 .get(viewport.getSequenceSetId());
2790 List<String> existingNames = getExistingViewNames(comps);
2792 while (existingNames.contains(newViewName))
2794 newViewName = viewTitle + " " + (++index);
2800 * Returns a list of distinct view names found in the given list of
2801 * components. View names are held on the viewport of an AlignmentPanel.
2806 protected List<String> getExistingViewNames(List<Component> comps)
2808 List<String> existingNames = new ArrayList<>();
2809 for (Component comp : comps)
2811 if (comp instanceof AlignmentPanel)
2813 AlignmentPanel ap = (AlignmentPanel) comp;
2814 if (!existingNames.contains(ap.av.viewName))
2816 existingNames.add(ap.av.viewName);
2820 return existingNames;
2824 * Explode tabbed views into separate windows.
2827 public void expandViews_actionPerformed(ActionEvent e)
2829 Desktop.explodeViews(this);
2833 * Gather views in separate windows back into a tabbed presentation.
2836 public void gatherViews_actionPerformed(ActionEvent e)
2838 Desktop.instance.gatherViews(this);
2848 public void font_actionPerformed(ActionEvent e)
2850 new FontChooser(alignPanel);
2860 protected void seqLimit_actionPerformed(ActionEvent e)
2862 viewport.setShowJVSuffix(seqLimits.isSelected());
2864 alignPanel.getIdPanel().getIdCanvas()
2865 .setPreferredSize(alignPanel.calculateIdWidth());
2866 alignPanel.paintAlignment(true, false);
2870 public void idRightAlign_actionPerformed(ActionEvent e)
2872 viewport.setRightAlignIds(idRightAlign.isSelected());
2873 alignPanel.paintAlignment(false, false);
2877 public void centreColumnLabels_actionPerformed(ActionEvent e)
2879 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2880 alignPanel.paintAlignment(false, false);
2886 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2889 protected void followHighlight_actionPerformed()
2892 * Set the 'follow' flag on the Viewport (and scroll to position if now
2895 final boolean state = this.followHighlightMenuItem.getState();
2896 viewport.setFollowHighlight(state);
2899 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2910 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2912 viewport.setColourText(colourTextMenuItem.isSelected());
2913 alignPanel.paintAlignment(false, false);
2923 public void wrapMenuItem_actionPerformed(ActionEvent e)
2925 scaleAbove.setVisible(wrapMenuItem.isSelected());
2926 scaleLeft.setVisible(wrapMenuItem.isSelected());
2927 scaleRight.setVisible(wrapMenuItem.isSelected());
2928 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2929 alignPanel.updateLayout();
2933 public void showAllSeqs_actionPerformed(ActionEvent e)
2935 viewport.showAllHiddenSeqs();
2939 public void showAllColumns_actionPerformed(ActionEvent e)
2941 viewport.showAllHiddenColumns();
2942 alignPanel.paintAlignment(true, true);
2943 viewport.sendSelection();
2947 public void hideSelSequences_actionPerformed(ActionEvent e)
2949 viewport.hideAllSelectedSeqs();
2953 * called by key handler and the hide all/show all menu items
2958 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2961 boolean hide = false;
2962 SequenceGroup sg = viewport.getSelectionGroup();
2963 if (!toggleSeqs && !toggleCols)
2965 // Hide everything by the current selection - this is a hack - we do the
2966 // invert and then hide
2967 // first check that there will be visible columns after the invert.
2968 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2969 && sg.getStartRes() <= sg.getEndRes()))
2971 // now invert the sequence set, if required - empty selection implies
2972 // that no hiding is required.
2975 invertSequenceMenuItem_actionPerformed(null);
2976 sg = viewport.getSelectionGroup();
2980 viewport.expandColSelection(sg, true);
2981 // finally invert the column selection and get the new sequence
2983 invertColSel_actionPerformed(null);
2990 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2992 hideSelSequences_actionPerformed(null);
2995 else if (!(toggleCols && viewport.hasSelectedColumns()))
2997 showAllSeqs_actionPerformed(null);
3003 if (viewport.hasSelectedColumns())
3005 hideSelColumns_actionPerformed(null);
3008 viewport.setSelectionGroup(sg);
3013 showAllColumns_actionPerformed(null);
3022 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3023 * event.ActionEvent)
3026 public void hideAllButSelection_actionPerformed(ActionEvent e)
3028 toggleHiddenRegions(false, false);
3029 viewport.sendSelection();
3036 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3040 public void hideAllSelection_actionPerformed(ActionEvent e)
3042 SequenceGroup sg = viewport.getSelectionGroup();
3043 viewport.expandColSelection(sg, false);
3044 viewport.hideAllSelectedSeqs();
3045 viewport.hideSelectedColumns();
3046 alignPanel.paintAlignment(true, true);
3047 viewport.sendSelection();
3054 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3058 public void showAllhidden_actionPerformed(ActionEvent e)
3060 viewport.showAllHiddenColumns();
3061 viewport.showAllHiddenSeqs();
3062 alignPanel.paintAlignment(true, true);
3063 viewport.sendSelection();
3067 public void hideSelColumns_actionPerformed(ActionEvent e)
3069 viewport.hideSelectedColumns();
3070 alignPanel.paintAlignment(true, true);
3071 viewport.sendSelection();
3075 public void hiddenMarkers_actionPerformed(ActionEvent e)
3077 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3088 protected void scaleAbove_actionPerformed(ActionEvent e)
3090 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3091 // TODO: do we actually need to update overview for scale above change ?
3092 alignPanel.paintAlignment(true, false);
3102 protected void scaleLeft_actionPerformed(ActionEvent e)
3104 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3105 alignPanel.paintAlignment(true, false);
3115 protected void scaleRight_actionPerformed(ActionEvent e)
3117 viewport.setScaleRightWrapped(scaleRight.isSelected());
3118 alignPanel.paintAlignment(true, false);
3128 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3130 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3131 alignPanel.paintAlignment(false, false);
3141 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3143 viewport.setShowText(viewTextMenuItem.isSelected());
3144 alignPanel.paintAlignment(false, false);
3154 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3156 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3157 alignPanel.paintAlignment(false, false);
3160 public FeatureSettings featureSettings;
3163 public FeatureSettingsControllerI getFeatureSettingsUI()
3165 return featureSettings;
3169 public void featureSettings_actionPerformed(ActionEvent e)
3171 if (featureSettings != null)
3173 featureSettings.close();
3174 featureSettings = null;
3176 if (!showSeqFeatures.isSelected())
3178 // make sure features are actually displayed
3179 showSeqFeatures.setSelected(true);
3180 showSeqFeatures_actionPerformed(null);
3182 featureSettings = new FeatureSettings(this);
3186 * Set or clear 'Show Sequence Features'
3192 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3194 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3195 alignPanel.paintAlignment(true, true);
3199 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3200 * the annotations panel as a whole.
3202 * The options to show/hide all annotations should be enabled when the panel
3203 * is shown, and disabled when the panel is hidden.
3208 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3210 final boolean setVisible = annotationPanelMenuItem.isSelected();
3211 viewport.setShowAnnotation(setVisible);
3212 this.showAllSeqAnnotations.setEnabled(setVisible);
3213 this.hideAllSeqAnnotations.setEnabled(setVisible);
3214 this.showAllAlAnnotations.setEnabled(setVisible);
3215 this.hideAllAlAnnotations.setEnabled(setVisible);
3216 alignPanel.updateLayout();
3220 public void alignmentProperties()
3222 JEditorPane editPane = new JEditorPane("text/html", "");
3223 editPane.setEditable(false);
3224 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3227 MessageManager.formatMessage("label.html_content", new Object[]
3228 { contents.toString() }));
3229 JInternalFrame frame = new JInternalFrame();
3230 frame.getContentPane().add(new JScrollPane(editPane));
3232 Desktop.addInternalFrame(frame, MessageManager
3233 .formatMessage("label.alignment_properties", new Object[]
3234 { getTitle() }), 500, 400);
3244 public void overviewMenuItem_actionPerformed(ActionEvent e)
3246 if (alignPanel.overviewPanel != null)
3251 JInternalFrame frame = new JInternalFrame();
3252 final OverviewPanel overview = new OverviewPanel(alignPanel);
3253 frame.setContentPane(overview);
3254 Desktop.addInternalFrame(frame, MessageManager
3255 .formatMessage("label.overview_params", new Object[]
3256 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3259 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3260 frame.addInternalFrameListener(
3261 new javax.swing.event.InternalFrameAdapter()
3264 public void internalFrameClosed(
3265 javax.swing.event.InternalFrameEvent evt)
3268 alignPanel.setOverviewPanel(null);
3271 if (getKeyListeners().length > 0)
3273 frame.addKeyListener(getKeyListeners()[0]);
3276 alignPanel.setOverviewPanel(overview);
3280 public void textColour_actionPerformed()
3282 new TextColourChooser().chooseColour(alignPanel, null);
3286 * public void covariationColour_actionPerformed() {
3288 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3292 public void annotationColour_actionPerformed()
3294 new AnnotationColourChooser(viewport, alignPanel);
3298 public void annotationColumn_actionPerformed(ActionEvent e)
3300 new AnnotationColumnChooser(viewport, alignPanel);
3304 * Action on the user checking or unchecking the option to apply the selected
3305 * colour scheme to all groups. If unchecked, groups may have their own
3306 * independent colour schemes.
3311 public void applyToAllGroups_actionPerformed(boolean selected)
3313 viewport.setColourAppliesToAllGroups(selected);
3317 * Action on user selecting a colour from the colour menu
3320 * the name (not the menu item label!) of the colour scheme
3323 public void changeColour_actionPerformed(String name)
3326 * 'User Defined' opens a panel to configure or load a
3327 * user-defined colour scheme
3329 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3331 new UserDefinedColours(alignPanel);
3336 * otherwise set the chosen colour scheme (or null for 'None')
3338 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3339 viewport.getAlignment(), viewport.getHiddenRepSequences());
3344 * Actions on setting or changing the alignment colour scheme
3349 public void changeColour(ColourSchemeI cs)
3351 // TODO: pull up to controller method
3352 ColourMenuHelper.setColourSelected(colourMenu, cs);
3354 viewport.setGlobalColourScheme(cs);
3356 alignPanel.paintAlignment(true, true);
3360 * Show the PID threshold slider panel
3363 protected void modifyPID_actionPerformed()
3365 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3366 alignPanel.getViewName());
3367 SliderPanel.showPIDSlider();
3371 * Show the Conservation slider panel
3374 protected void modifyConservation_actionPerformed()
3376 SliderPanel.setConservationSlider(alignPanel,
3377 viewport.getResidueShading(), alignPanel.getViewName());
3378 SliderPanel.showConservationSlider();
3382 * Action on selecting or deselecting (Colour) By Conservation
3385 public void conservationMenuItem_actionPerformed(boolean selected)
3387 modifyConservation.setEnabled(selected);
3388 viewport.setConservationSelected(selected);
3389 viewport.getResidueShading().setConservationApplied(selected);
3391 changeColour(viewport.getGlobalColourScheme());
3394 modifyConservation_actionPerformed();
3398 SliderPanel.hideConservationSlider();
3403 * Action on selecting or deselecting (Colour) Above PID Threshold
3406 public void abovePIDThreshold_actionPerformed(boolean selected)
3408 modifyPID.setEnabled(selected);
3409 viewport.setAbovePIDThreshold(selected);
3412 viewport.getResidueShading().setThreshold(0,
3413 viewport.isIgnoreGapsConsensus());
3416 changeColour(viewport.getGlobalColourScheme());
3419 modifyPID_actionPerformed();
3423 SliderPanel.hidePIDSlider();
3434 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3436 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3437 AlignmentSorter.sortByPID(viewport.getAlignment(),
3438 viewport.getAlignment().getSequenceAt(0));
3439 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3440 viewport.getAlignment()));
3441 alignPanel.paintAlignment(true, false);
3451 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3453 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3454 AlignmentSorter.sortByID(viewport.getAlignment());
3456 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3457 alignPanel.paintAlignment(true, false);
3467 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3469 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3470 AlignmentSorter.sortByLength(viewport.getAlignment());
3471 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3472 viewport.getAlignment()));
3473 alignPanel.paintAlignment(true, false);
3483 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3485 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3486 AlignmentSorter.sortByGroup(viewport.getAlignment());
3487 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3488 viewport.getAlignment()));
3490 alignPanel.paintAlignment(true, false);
3500 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3502 new RedundancyPanel(alignPanel, this);
3512 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3514 if ((viewport.getSelectionGroup() == null)
3515 || (viewport.getSelectionGroup().getSize() < 2))
3517 JvOptionPane.showInternalMessageDialog(this,
3518 MessageManager.getString(
3519 "label.you_must_select_least_two_sequences"),
3520 MessageManager.getString("label.invalid_selection"),
3521 JvOptionPane.WARNING_MESSAGE);
3525 JInternalFrame frame = new JInternalFrame();
3526 frame.setContentPane(new PairwiseAlignPanel(viewport));
3527 Desktop.addInternalFrame(frame,
3528 MessageManager.getString("action.pairwise_alignment"), 600,
3534 public void autoCalculate_actionPerformed(ActionEvent e)
3536 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3537 if (viewport.autoCalculateConsensus)
3539 viewport.firePropertyChange("alignment", null,
3540 viewport.getAlignment().getSequences());
3545 public void sortByTreeOption_actionPerformed(ActionEvent e)
3547 viewport.sortByTree = sortByTree.isSelected();
3551 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3553 viewport.followSelection = listenToViewSelections.isSelected();
3557 * Constructs a tree panel and adds it to the desktop
3560 * tree type (NJ or AV)
3562 * name of score model used to compute the tree
3564 * parameters for the distance or similarity calculation
3566 void newTreePanel(String type, String modelName,
3567 SimilarityParamsI options)
3569 String frameTitle = "";
3572 boolean onSelection = false;
3573 if (viewport.getSelectionGroup() != null
3574 && viewport.getSelectionGroup().getSize() > 0)
3576 SequenceGroup sg = viewport.getSelectionGroup();
3578 /* Decide if the selection is a column region */
3579 for (SequenceI _s : sg.getSequences())
3581 if (_s.getLength() < sg.getEndRes())
3583 JvOptionPane.showMessageDialog(Desktop.desktop,
3584 MessageManager.getString(
3585 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3586 MessageManager.getString(
3587 "label.sequences_selection_not_aligned"),
3588 JvOptionPane.WARNING_MESSAGE);
3597 if (viewport.getAlignment().getHeight() < 2)
3603 tp = new TreePanel(alignPanel, type, modelName, options);
3604 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3606 frameTitle += " from ";
3608 if (viewport.viewName != null)
3610 frameTitle += viewport.viewName + " of ";
3613 frameTitle += this.title;
3615 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3626 public void addSortByOrderMenuItem(String title,
3627 final AlignmentOrder order)
3629 final JMenuItem item = new JMenuItem(MessageManager
3630 .formatMessage("action.by_title_param", new Object[]
3633 item.addActionListener(new java.awt.event.ActionListener()
3636 public void actionPerformed(ActionEvent e)
3638 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3640 // TODO: JBPNote - have to map order entries to curent SequenceI
3642 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3644 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3645 viewport.getAlignment()));
3647 alignPanel.paintAlignment(true, false);
3653 * Add a new sort by annotation score menu item
3656 * the menu to add the option to
3658 * the label used to retrieve scores for each sequence on the
3661 public void addSortByAnnotScoreMenuItem(JMenu sort,
3662 final String scoreLabel)
3664 final JMenuItem item = new JMenuItem(scoreLabel);
3666 item.addActionListener(new java.awt.event.ActionListener()
3669 public void actionPerformed(ActionEvent e)
3671 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3672 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3673 viewport.getAlignment());// ,viewport.getSelectionGroup());
3674 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3675 viewport.getAlignment()));
3676 alignPanel.paintAlignment(true, false);
3682 * last hash for alignment's annotation array - used to minimise cost of
3685 protected int _annotationScoreVectorHash;
3688 * search the alignment and rebuild the sort by annotation score submenu the
3689 * last alignment annotation vector hash is stored to minimize cost of
3690 * rebuilding in subsequence calls.
3694 public void buildSortByAnnotationScoresMenu()
3696 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3701 if (viewport.getAlignment().getAlignmentAnnotation()
3702 .hashCode() != _annotationScoreVectorHash)
3704 sortByAnnotScore.removeAll();
3705 // almost certainly a quicker way to do this - but we keep it simple
3706 Hashtable scoreSorts = new Hashtable();
3707 AlignmentAnnotation aann[];
3708 for (SequenceI sqa : viewport.getAlignment().getSequences())
3710 aann = sqa.getAnnotation();
3711 for (int i = 0; aann != null && i < aann.length; i++)
3713 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3715 scoreSorts.put(aann[i].label, aann[i].label);
3719 Enumeration labels = scoreSorts.keys();
3720 while (labels.hasMoreElements())
3722 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3723 (String) labels.nextElement());
3725 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3728 _annotationScoreVectorHash = viewport.getAlignment()
3729 .getAlignmentAnnotation().hashCode();
3734 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3735 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3736 * call. Listeners are added to remove the menu item when the treePanel is
3737 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3741 public void buildTreeSortMenu()
3743 sortByTreeMenu.removeAll();
3745 List<Component> comps = PaintRefresher.components
3746 .get(viewport.getSequenceSetId());
3747 List<TreePanel> treePanels = new ArrayList<>();
3748 for (Component comp : comps)
3750 if (comp instanceof TreePanel)
3752 treePanels.add((TreePanel) comp);
3756 if (treePanels.size() < 1)
3758 sortByTreeMenu.setVisible(false);
3762 sortByTreeMenu.setVisible(true);
3764 for (final TreePanel tp : treePanels)
3766 final JMenuItem item = new JMenuItem(tp.getTitle());
3767 item.addActionListener(new java.awt.event.ActionListener()
3770 public void actionPerformed(ActionEvent e)
3772 tp.sortByTree_actionPerformed();
3773 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3778 sortByTreeMenu.add(item);
3782 public boolean sortBy(AlignmentOrder alorder, String undoname)
3784 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3785 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3786 if (undoname != null)
3788 addHistoryItem(new OrderCommand(undoname, oldOrder,
3789 viewport.getAlignment()));
3791 alignPanel.paintAlignment(true, false);
3796 * Work out whether the whole set of sequences or just the selected set will
3797 * be submitted for multiple alignment.
3800 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3802 // Now, check we have enough sequences
3803 AlignmentView msa = null;
3805 if ((viewport.getSelectionGroup() != null)
3806 && (viewport.getSelectionGroup().getSize() > 1))
3808 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3809 // some common interface!
3811 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3812 * SequenceI[sz = seqs.getSize(false)];
3814 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3815 * seqs.getSequenceAt(i); }
3817 msa = viewport.getAlignmentView(true);
3819 else if (viewport.getSelectionGroup() != null
3820 && viewport.getSelectionGroup().getSize() == 1)
3822 int option = JvOptionPane.showConfirmDialog(this,
3823 MessageManager.getString("warn.oneseq_msainput_selection"),
3824 MessageManager.getString("label.invalid_selection"),
3825 JvOptionPane.OK_CANCEL_OPTION);
3826 if (option == JvOptionPane.OK_OPTION)
3828 msa = viewport.getAlignmentView(false);
3833 msa = viewport.getAlignmentView(false);
3839 * Decides what is submitted to a secondary structure prediction service: the
3840 * first sequence in the alignment, or in the current selection, or, if the
3841 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3842 * region or the whole alignment. (where the first sequence in the set is the
3843 * one that the prediction will be for).
3845 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3847 AlignmentView seqs = null;
3849 if ((viewport.getSelectionGroup() != null)
3850 && (viewport.getSelectionGroup().getSize() > 0))
3852 seqs = viewport.getAlignmentView(true);
3856 seqs = viewport.getAlignmentView(false);
3858 // limit sequences - JBPNote in future - could spawn multiple prediction
3860 // TODO: viewport.getAlignment().isAligned is a global state - the local
3861 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3862 if (!viewport.getAlignment().isAligned(false))
3864 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3865 // TODO: if seqs.getSequences().length>1 then should really have warned
3879 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3881 // Pick the tree file
3882 JalviewFileChooser chooser = new JalviewFileChooser(
3883 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3884 chooser.setFileView(new JalviewFileView());
3885 chooser.setDialogTitle(
3886 MessageManager.getString("label.select_newick_like_tree_file"));
3887 chooser.setToolTipText(
3888 MessageManager.getString("label.load_tree_file"));
3890 int value = chooser.showOpenDialog(null);
3892 if (value == JalviewFileChooser.APPROVE_OPTION)
3894 String filePath = chooser.getSelectedFile().getPath();
3895 Cache.setProperty("LAST_DIRECTORY", filePath);
3896 NewickFile fin = null;
3899 fin = new NewickFile(filePath, DataSourceType.FILE);
3900 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3901 } catch (Exception ex)
3903 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3904 MessageManager.getString("label.problem_reading_tree_file"),
3905 JvOptionPane.WARNING_MESSAGE);
3906 ex.printStackTrace();
3908 if (fin != null && fin.hasWarningMessage())
3910 JvOptionPane.showMessageDialog(Desktop.desktop,
3911 fin.getWarningMessage(),
3913 .getString("label.possible_problem_with_tree_file"),
3914 JvOptionPane.WARNING_MESSAGE);
3919 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3921 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3924 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3925 int h, int x, int y)
3927 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3931 * Add a treeviewer for the tree extracted from a Newick file object to the
3932 * current alignment view
3939 * Associated alignment input data (or null)
3948 * @return TreePanel handle
3950 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3951 AlignmentView input, int w, int h, int x, int y)
3953 TreePanel tp = null;
3959 if (nf.getTree() != null)
3961 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3967 tp.setLocation(x, y);
3970 Desktop.addInternalFrame(tp, treeTitle, w, h);
3972 } catch (Exception ex)
3974 ex.printStackTrace();
3980 private boolean buildingMenu = false;
3983 * Generates menu items and listener event actions for web service clients
3986 public void BuildWebServiceMenu()
3988 while (buildingMenu)
3992 System.err.println("Waiting for building menu to finish.");
3994 } catch (Exception e)
3998 final AlignFrame me = this;
3999 buildingMenu = true;
4000 new Thread(new Runnable()
4005 final List<JMenuItem> legacyItems = new ArrayList<>();
4008 // System.err.println("Building ws menu again "
4009 // + Thread.currentThread());
4010 // TODO: add support for context dependent disabling of services based
4012 // alignment and current selection
4013 // TODO: add additional serviceHandle parameter to specify abstract
4015 // class independently of AbstractName
4016 // TODO: add in rediscovery GUI function to restart discoverer
4017 // TODO: group services by location as well as function and/or
4019 // object broker mechanism.
4020 final Vector<JMenu> wsmenu = new Vector<>();
4021 final IProgressIndicator af = me;
4024 * do not i18n these strings - they are hard-coded in class
4025 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4026 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4028 final JMenu msawsmenu = new JMenu("Alignment");
4029 final JMenu secstrmenu = new JMenu(
4030 "Secondary Structure Prediction");
4031 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4032 final JMenu analymenu = new JMenu("Analysis");
4033 final JMenu dismenu = new JMenu("Protein Disorder");
4034 // JAL-940 - only show secondary structure prediction services from
4035 // the legacy server
4036 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4038 Discoverer.services != null && (Discoverer.services.size() > 0))
4040 // TODO: refactor to allow list of AbstractName/Handler bindings to
4042 // stored or retrieved from elsewhere
4043 // No MSAWS used any more:
4044 // Vector msaws = null; // (Vector)
4045 // Discoverer.services.get("MsaWS");
4046 Vector secstrpr = (Vector) Discoverer.services
4048 if (secstrpr != null)
4050 // Add any secondary structure prediction services
4051 for (int i = 0, j = secstrpr.size(); i < j; i++)
4053 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4055 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4056 .getServiceClient(sh);
4057 int p = secstrmenu.getItemCount();
4058 impl.attachWSMenuEntry(secstrmenu, me);
4059 int q = secstrmenu.getItemCount();
4060 for (int litm = p; litm < q; litm++)
4062 legacyItems.add(secstrmenu.getItem(litm));
4068 // Add all submenus in the order they should appear on the web
4070 wsmenu.add(msawsmenu);
4071 wsmenu.add(secstrmenu);
4072 wsmenu.add(dismenu);
4073 wsmenu.add(analymenu);
4074 // No search services yet
4075 // wsmenu.add(seqsrchmenu);
4077 javax.swing.SwingUtilities.invokeLater(new Runnable()
4084 webService.removeAll();
4085 // first, add discovered services onto the webservices menu
4086 if (wsmenu.size() > 0)
4088 for (int i = 0, j = wsmenu.size(); i < j; i++)
4090 webService.add(wsmenu.get(i));
4095 webService.add(me.webServiceNoServices);
4097 // TODO: move into separate menu builder class.
4098 boolean new_sspred = false;
4099 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4101 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4102 if (jws2servs != null)
4104 if (jws2servs.hasServices())
4106 jws2servs.attachWSMenuEntry(webService, me);
4107 for (Jws2Instance sv : jws2servs.getServices())
4109 if (sv.description.toLowerCase().contains("jpred"))
4111 for (JMenuItem jmi : legacyItems)
4113 jmi.setVisible(false);
4119 if (jws2servs.isRunning())
4121 JMenuItem tm = new JMenuItem(
4122 "Still discovering JABA Services");
4123 tm.setEnabled(false);
4128 build_urlServiceMenu(me.webService);
4129 build_fetchdbmenu(webService);
4130 for (JMenu item : wsmenu)
4132 if (item.getItemCount() == 0)
4134 item.setEnabled(false);
4138 item.setEnabled(true);
4141 } catch (Exception e)
4144 "Exception during web service menu building process.",
4149 } catch (Exception e)
4152 buildingMenu = false;
4159 * construct any groupURL type service menu entries.
4163 private void build_urlServiceMenu(JMenu webService)
4165 // TODO: remove this code when 2.7 is released
4166 // DEBUG - alignmentView
4168 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4169 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4171 * @Override public void actionPerformed(ActionEvent e) {
4172 * jalview.datamodel.AlignmentView
4173 * .testSelectionViews(af.viewport.getAlignment(),
4174 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4176 * }); webService.add(testAlView);
4178 // TODO: refactor to RestClient discoverer and merge menu entries for
4179 // rest-style services with other types of analysis/calculation service
4180 // SHmmr test client - still being implemented.
4181 // DEBUG - alignmentView
4183 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4186 client.attachWSMenuEntry(
4187 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4193 * Searches the alignment sequences for xRefs and builds the Show
4194 * Cross-References menu (formerly called Show Products), with database
4195 * sources for which cross-references are found (protein sources for a
4196 * nucleotide alignment and vice versa)
4198 * @return true if Show Cross-references menu should be enabled
4200 public boolean canShowProducts()
4202 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4203 AlignmentI dataset = viewport.getAlignment().getDataset();
4205 showProducts.removeAll();
4206 final boolean dna = viewport.getAlignment().isNucleotide();
4208 if (seqs == null || seqs.length == 0)
4210 // nothing to see here.
4214 boolean showp = false;
4217 List<String> ptypes = new CrossRef(seqs, dataset)
4218 .findXrefSourcesForSequences(dna);
4220 for (final String source : ptypes)
4223 final AlignFrame af = this;
4224 JMenuItem xtype = new JMenuItem(source);
4225 xtype.addActionListener(new ActionListener()
4228 public void actionPerformed(ActionEvent e)
4230 showProductsFor(af.viewport.getSequenceSelection(), dna,
4234 showProducts.add(xtype);
4236 showProducts.setVisible(showp);
4237 showProducts.setEnabled(showp);
4238 } catch (Exception e)
4241 "canShowProducts threw an exception - please report to help@jalview.org",
4249 * Finds and displays cross-references for the selected sequences (protein
4250 * products for nucleotide sequences, dna coding sequences for peptides).
4253 * the sequences to show cross-references for
4255 * true if from a nucleotide alignment (so showing proteins)
4257 * the database to show cross-references for
4259 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4260 final String source)
4262 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4267 * Construct and display a new frame containing the translation of this
4268 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4271 public void showTranslation_actionPerformed(ActionEvent e)
4273 AlignmentI al = null;
4276 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4278 al = dna.translateCdna();
4279 } catch (Exception ex)
4281 jalview.bin.Cache.log.error(
4282 "Exception during translation. Please report this !", ex);
4283 final String msg = MessageManager.getString(
4284 "label.error_when_translating_sequences_submit_bug_report");
4285 final String errorTitle = MessageManager
4286 .getString("label.implementation_error")
4287 + MessageManager.getString("label.translation_failed");
4288 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4289 JvOptionPane.ERROR_MESSAGE);
4292 if (al == null || al.getHeight() == 0)
4294 final String msg = MessageManager.getString(
4295 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4296 final String errorTitle = MessageManager
4297 .getString("label.translation_failed");
4298 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4299 JvOptionPane.WARNING_MESSAGE);
4303 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4304 af.setFileFormat(this.currentFileFormat);
4305 final String newTitle = MessageManager
4306 .formatMessage("label.translation_of_params", new Object[]
4307 { this.getTitle() });
4308 af.setTitle(newTitle);
4309 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4311 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4312 viewport.openSplitFrame(af, new Alignment(seqs));
4316 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4323 * Set the file format
4327 public void setFileFormat(FileFormatI format)
4329 this.currentFileFormat = format;
4333 * Try to load a features file onto the alignment.
4336 * contents or path to retrieve file
4338 * access mode of file (see jalview.io.AlignFile)
4339 * @return true if features file was parsed correctly.
4341 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4343 return avc.parseFeaturesFile(file, sourceType,
4344 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4349 public void refreshFeatureUI(boolean enableIfNecessary)
4351 // note - currently this is only still here rather than in the controller
4352 // because of the featureSettings hard reference that is yet to be
4354 if (enableIfNecessary)
4356 viewport.setShowSequenceFeatures(true);
4357 showSeqFeatures.setSelected(true);
4363 public void dragEnter(DropTargetDragEvent evt)
4368 public void dragExit(DropTargetEvent evt)
4373 public void dragOver(DropTargetDragEvent evt)
4378 public void dropActionChanged(DropTargetDragEvent evt)
4383 public void drop(DropTargetDropEvent evt)
4385 // JAL-1552 - acceptDrop required before getTransferable call for
4386 // Java's Transferable for native dnd
4387 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4388 Transferable t = evt.getTransferable();
4389 final AlignFrame thisaf = this;
4390 final List<String> files = new ArrayList<>();
4391 List<DataSourceType> protocols = new ArrayList<>();
4395 Desktop.transferFromDropTarget(files, protocols, evt, t);
4396 } catch (Exception e)
4398 e.printStackTrace();
4402 new Thread(new Runnable()
4409 // check to see if any of these files have names matching sequences
4412 SequenceIdMatcher idm = new SequenceIdMatcher(
4413 viewport.getAlignment().getSequencesArray());
4415 * Object[] { String,SequenceI}
4417 ArrayList<Object[]> filesmatched = new ArrayList<>();
4418 ArrayList<String> filesnotmatched = new ArrayList<>();
4419 for (int i = 0; i < files.size(); i++)
4421 String file = files.get(i).toString();
4423 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4424 if (protocol == DataSourceType.FILE)
4426 File fl = new File(file);
4427 pdbfn = fl.getName();
4429 else if (protocol == DataSourceType.URL)
4431 URL url = new URL(file);
4432 pdbfn = url.getFile();
4434 if (pdbfn.length() > 0)
4436 // attempt to find a match in the alignment
4437 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4438 int l = 0, c = pdbfn.indexOf(".");
4439 while (mtch == null && c != -1)
4444 } while ((c = pdbfn.indexOf(".", l)) > l);
4447 pdbfn = pdbfn.substring(0, l);
4449 mtch = idm.findAllIdMatches(pdbfn);
4453 FileFormatI type = null;
4456 type = new IdentifyFile().identify(file, protocol);
4457 } catch (Exception ex)
4461 if (type != null && type.isStructureFile())
4463 filesmatched.add(new Object[] { file, protocol, mtch });
4467 // File wasn't named like one of the sequences or wasn't a PDB
4469 filesnotmatched.add(file);
4473 if (filesmatched.size() > 0)
4475 boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4478 String msg = MessageManager.formatMessage(
4479 "label.automatically_associate_structure_files_with_sequences_same_name",
4481 { Integer.valueOf(filesmatched.size())
4483 String ttl = MessageManager.getString(
4484 "label.automatically_associate_structure_files_by_name");
4485 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4486 ttl, JvOptionPane.YES_NO_OPTION);
4487 autoAssociate = choice == JvOptionPane.YES_OPTION;
4491 for (Object[] fm : filesmatched)
4493 // try and associate
4494 // TODO: may want to set a standard ID naming formalism for
4495 // associating PDB files which have no IDs.
4496 for (SequenceI toassoc : (SequenceI[]) fm[2])
4498 PDBEntry pe = new AssociatePdbFileWithSeq()
4499 .associatePdbWithSeq((String) fm[0],
4500 (DataSourceType) fm[1], toassoc, false,
4504 System.err.println("Associated file : "
4505 + ((String) fm[0]) + " with "
4506 + toassoc.getDisplayId(true));
4510 // TODO: do we need to update overview ? only if features are
4512 alignPanel.paintAlignment(true, false);
4518 * add declined structures as sequences
4520 for (Object[] o : filesmatched)
4522 filesnotmatched.add((String) o[0]);
4526 if (filesnotmatched.size() > 0)
4528 if (assocfiles > 0 && (Cache.getDefault(
4529 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4530 || JvOptionPane.showConfirmDialog(thisaf,
4531 "<html>" + MessageManager.formatMessage(
4532 "label.ignore_unmatched_dropped_files_info",
4535 filesnotmatched.size())
4538 MessageManager.getString(
4539 "label.ignore_unmatched_dropped_files"),
4540 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4544 for (String fn : filesnotmatched)
4546 loadJalviewDataFile(fn, null, null, null);
4550 } catch (Exception ex)
4552 ex.printStackTrace();
4560 * Attempt to load a "dropped" file or URL string, by testing in turn for
4562 * <li>an Annotation file</li>
4563 * <li>a JNet file</li>
4564 * <li>a features file</li>
4565 * <li>else try to interpret as an alignment file</li>
4569 * either a filename or a URL string.
4571 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4572 FileFormatI format, SequenceI assocSeq)
4576 if (sourceType == null)
4578 sourceType = FormatAdapter.checkProtocol(file);
4580 // if the file isn't identified, or not positively identified as some
4581 // other filetype (PFAM is default unidentified alignment file type) then
4582 // try to parse as annotation.
4583 boolean isAnnotation = (format == null
4584 || FileFormat.Pfam.equals(format))
4585 ? new AnnotationFile().annotateAlignmentView(viewport,
4591 // first see if its a T-COFFEE score file
4592 TCoffeeScoreFile tcf = null;
4595 tcf = new TCoffeeScoreFile(file, sourceType);
4598 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4602 new TCoffeeColourScheme(viewport.getAlignment()));
4603 isAnnotation = true;
4604 statusBar.setText(MessageManager.getString(
4605 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4609 // some problem - if no warning its probable that the ID matching
4610 // process didn't work
4611 JvOptionPane.showMessageDialog(Desktop.desktop,
4612 tcf.getWarningMessage() == null
4613 ? MessageManager.getString(
4614 "label.check_file_matches_sequence_ids_alignment")
4615 : tcf.getWarningMessage(),
4616 MessageManager.getString(
4617 "label.problem_reading_tcoffee_score_file"),
4618 JvOptionPane.WARNING_MESSAGE);
4625 } catch (Exception x)
4628 "Exception when processing data source as T-COFFEE score file",
4634 // try to see if its a JNet 'concise' style annotation file *before*
4636 // try to parse it as a features file
4639 format = new IdentifyFile().identify(file, sourceType);
4641 if (FileFormat.ScoreMatrix == format)
4643 ScoreMatrixFile sm = new ScoreMatrixFile(
4644 new FileParse(file, sourceType));
4646 // todo: i18n this message
4647 statusBar.setText(MessageManager.formatMessage(
4648 "label.successfully_loaded_matrix",
4649 sm.getMatrixName()));
4651 else if (FileFormat.Jnet.equals(format))
4653 JPredFile predictions = new JPredFile(file, sourceType);
4654 new JnetAnnotationMaker();
4655 JnetAnnotationMaker.add_annotation(predictions,
4656 viewport.getAlignment(), 0, false);
4657 viewport.getAlignment().setupJPredAlignment();
4658 isAnnotation = true;
4660 // else if (IdentifyFile.FeaturesFile.equals(format))
4661 else if (FileFormat.Features.equals(format))
4663 if (parseFeaturesFile(file, sourceType))
4665 alignPanel.paintAlignment(true, true);
4670 new FileLoader().LoadFile(viewport, file, sourceType, format);
4677 alignPanel.adjustAnnotationHeight();
4678 viewport.updateSequenceIdColours();
4679 buildSortByAnnotationScoresMenu();
4680 alignPanel.paintAlignment(true, true);
4682 } catch (Exception ex)
4684 ex.printStackTrace();
4685 } catch (OutOfMemoryError oom)
4690 } catch (Exception x)
4695 + (sourceType != null
4696 ? (sourceType == DataSourceType.PASTE
4698 : "using " + sourceType + " from "
4702 ? "(parsing as '" + format + "' file)"
4704 oom, Desktop.desktop);
4709 * Method invoked by the ChangeListener on the tabbed pane, in other words
4710 * when a different tabbed pane is selected by the user or programmatically.
4713 public void tabSelectionChanged(int index)
4717 alignPanel = alignPanels.get(index);
4718 viewport = alignPanel.av;
4719 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4720 setMenusFromViewport(viewport);
4724 * 'focus' any colour slider that is open to the selected viewport
4726 if (viewport.getConservationSelected())
4728 SliderPanel.setConservationSlider(alignPanel,
4729 viewport.getResidueShading(), alignPanel.getViewName());
4733 SliderPanel.hideConservationSlider();
4735 if (viewport.getAbovePIDThreshold())
4737 SliderPanel.setPIDSliderSource(alignPanel,
4738 viewport.getResidueShading(), alignPanel.getViewName());
4742 SliderPanel.hidePIDSlider();
4746 * If there is a frame linked to this one in a SplitPane, switch it to the
4747 * same view tab index. No infinite recursion of calls should happen, since
4748 * tabSelectionChanged() should not get invoked on setting the selected
4749 * index to an unchanged value. Guard against setting an invalid index
4750 * before the new view peer tab has been created.
4752 final AlignViewportI peer = viewport.getCodingComplement();
4755 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4756 .getAlignPanel().alignFrame;
4757 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4759 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4765 * On right mouse click on view tab, prompt for and set new view name.
4768 public void tabbedPane_mousePressed(MouseEvent e)
4770 if (e.isPopupTrigger())
4772 String msg = MessageManager.getString("label.enter_view_name");
4773 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4774 JvOptionPane.QUESTION_MESSAGE);
4778 viewport.viewName = reply;
4779 // TODO warn if reply is in getExistingViewNames()?
4780 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4785 public AlignViewport getCurrentView()
4791 * Open the dialog for regex description parsing.
4794 protected void extractScores_actionPerformed(ActionEvent e)
4796 ParseProperties pp = new jalview.analysis.ParseProperties(
4797 viewport.getAlignment());
4798 // TODO: verify regex and introduce GUI dialog for version 2.5
4799 // if (pp.getScoresFromDescription("col", "score column ",
4800 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4802 if (pp.getScoresFromDescription("description column",
4803 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4805 buildSortByAnnotationScoresMenu();
4813 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4817 protected void showDbRefs_actionPerformed(ActionEvent e)
4819 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4825 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4829 protected void showNpFeats_actionPerformed(ActionEvent e)
4831 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4835 * find the viewport amongst the tabs in this alignment frame and close that
4840 public boolean closeView(AlignViewportI av)
4844 this.closeMenuItem_actionPerformed(false);
4847 Component[] comp = tabbedPane.getComponents();
4848 for (int i = 0; comp != null && i < comp.length; i++)
4850 if (comp[i] instanceof AlignmentPanel)
4852 if (((AlignmentPanel) comp[i]).av == av)
4855 closeView((AlignmentPanel) comp[i]);
4863 protected void build_fetchdbmenu(JMenu webService)
4865 // Temporary hack - DBRef Fetcher always top level ws entry.
4866 // TODO We probably want to store a sequence database checklist in
4867 // preferences and have checkboxes.. rather than individual sources selected
4869 final JMenu rfetch = new JMenu(
4870 MessageManager.getString("action.fetch_db_references"));
4871 rfetch.setToolTipText(MessageManager.getString(
4872 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4873 webService.add(rfetch);
4875 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4876 MessageManager.getString("option.trim_retrieved_seqs"));
4877 trimrs.setToolTipText(
4878 MessageManager.getString("label.trim_retrieved_sequences"));
4880 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4881 trimrs.addActionListener(new ActionListener()
4884 public void actionPerformed(ActionEvent e)
4886 trimrs.setSelected(trimrs.isSelected());
4887 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4888 Boolean.valueOf(trimrs.isSelected()).toString());
4892 JMenuItem fetchr = new JMenuItem(
4893 MessageManager.getString("label.standard_databases"));
4894 fetchr.setToolTipText(
4895 MessageManager.getString("label.fetch_embl_uniprot"));
4896 fetchr.addActionListener(new ActionListener()
4900 public void actionPerformed(ActionEvent e)
4902 new Thread(new Runnable()
4907 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4908 .getAlignment().isNucleotide();
4909 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4910 alignPanel.av.getSequenceSelection(),
4911 alignPanel.alignFrame, null,
4912 alignPanel.alignFrame.featureSettings, isNucleotide);
4913 dbRefFetcher.addListener(new FetchFinishedListenerI()
4916 public void finished()
4918 AlignFrame.this.setMenusForViewport();
4921 dbRefFetcher.fetchDBRefs(false);
4929 final AlignFrame me = this;
4930 new Thread(new Runnable()
4935 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4936 .getSequenceFetcherSingleton(me);
4937 javax.swing.SwingUtilities.invokeLater(new Runnable()
4942 String[] dbclasses = sf.getOrderedSupportedSources();
4943 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4944 // jalview.util.QuickSort.sort(otherdb, otherdb);
4945 List<DbSourceProxy> otherdb;
4946 JMenu dfetch = new JMenu();
4947 JMenu ifetch = new JMenu();
4948 JMenuItem fetchr = null;
4949 int comp = 0, icomp = 0, mcomp = 15;
4950 String mname = null;
4952 for (String dbclass : dbclasses)
4954 otherdb = sf.getSourceProxy(dbclass);
4955 // add a single entry for this class, or submenu allowing 'fetch
4957 if (otherdb == null || otherdb.size() < 1)
4961 // List<DbSourceProxy> dbs=otherdb;
4962 // otherdb=new ArrayList<DbSourceProxy>();
4963 // for (DbSourceProxy db:dbs)
4965 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4969 mname = "From " + dbclass;
4971 if (otherdb.size() == 1)
4973 final DbSourceProxy[] dassource = otherdb
4974 .toArray(new DbSourceProxy[0]);
4975 DbSourceProxy src = otherdb.get(0);
4976 fetchr = new JMenuItem(src.getDbSource());
4977 fetchr.addActionListener(new ActionListener()
4981 public void actionPerformed(ActionEvent e)
4983 new Thread(new Runnable()
4989 boolean isNucleotide = alignPanel.alignFrame
4990 .getViewport().getAlignment()
4992 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4993 alignPanel.av.getSequenceSelection(),
4994 alignPanel.alignFrame, dassource,
4995 alignPanel.alignFrame.featureSettings,
4998 .addListener(new FetchFinishedListenerI()
5001 public void finished()
5003 AlignFrame.this.setMenusForViewport();
5006 dbRefFetcher.fetchDBRefs(false);
5012 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5013 MessageManager.formatMessage(
5014 "label.fetch_retrieve_from", new Object[]
5015 { src.getDbName() })));
5021 final DbSourceProxy[] dassource = otherdb
5022 .toArray(new DbSourceProxy[0]);
5024 DbSourceProxy src = otherdb.get(0);
5025 fetchr = new JMenuItem(MessageManager
5026 .formatMessage("label.fetch_all_param", new Object[]
5027 { src.getDbSource() }));
5028 fetchr.addActionListener(new ActionListener()
5031 public void actionPerformed(ActionEvent e)
5033 new Thread(new Runnable()
5039 boolean isNucleotide = alignPanel.alignFrame
5040 .getViewport().getAlignment()
5042 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5043 alignPanel.av.getSequenceSelection(),
5044 alignPanel.alignFrame, dassource,
5045 alignPanel.alignFrame.featureSettings,
5048 .addListener(new FetchFinishedListenerI()
5051 public void finished()
5053 AlignFrame.this.setMenusForViewport();
5056 dbRefFetcher.fetchDBRefs(false);
5062 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5063 MessageManager.formatMessage(
5064 "label.fetch_retrieve_from_all_sources",
5066 { Integer.valueOf(otherdb.size())
5068 src.getDbSource(), src.getDbName() })));
5071 // and then build the rest of the individual menus
5072 ifetch = new JMenu(MessageManager.formatMessage(
5073 "label.source_from_db_source", new Object[]
5074 { src.getDbSource() }));
5076 String imname = null;
5078 for (DbSourceProxy sproxy : otherdb)
5080 String dbname = sproxy.getDbName();
5081 String sname = dbname.length() > 5
5082 ? dbname.substring(0, 5) + "..."
5084 String msname = dbname.length() > 10
5085 ? dbname.substring(0, 10) + "..."
5089 imname = MessageManager
5090 .formatMessage("label.from_msname", new Object[]
5093 fetchr = new JMenuItem(msname);
5094 final DbSourceProxy[] dassrc = { sproxy };
5095 fetchr.addActionListener(new ActionListener()
5099 public void actionPerformed(ActionEvent e)
5101 new Thread(new Runnable()
5107 boolean isNucleotide = alignPanel.alignFrame
5108 .getViewport().getAlignment()
5110 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5111 alignPanel.av.getSequenceSelection(),
5112 alignPanel.alignFrame, dassrc,
5113 alignPanel.alignFrame.featureSettings,
5116 .addListener(new FetchFinishedListenerI()
5119 public void finished()
5121 AlignFrame.this.setMenusForViewport();
5124 dbRefFetcher.fetchDBRefs(false);
5130 fetchr.setToolTipText(
5131 "<html>" + MessageManager.formatMessage(
5132 "label.fetch_retrieve_from", new Object[]
5136 if (++icomp >= mcomp || i == (otherdb.size()))
5138 ifetch.setText(MessageManager.formatMessage(
5139 "label.source_to_target", imname, sname));
5141 ifetch = new JMenu();
5149 if (comp >= mcomp || dbi >= (dbclasses.length))
5151 dfetch.setText(MessageManager.formatMessage(
5152 "label.source_to_target", mname, dbclass));
5154 dfetch = new JMenu();
5167 * Left justify the whole alignment.
5170 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5172 AlignmentI al = viewport.getAlignment();
5174 viewport.firePropertyChange("alignment", null, al);
5178 * Right justify the whole alignment.
5181 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5183 AlignmentI al = viewport.getAlignment();
5185 viewport.firePropertyChange("alignment", null, al);
5189 public void setShowSeqFeatures(boolean b)
5191 showSeqFeatures.setSelected(b);
5192 viewport.setShowSequenceFeatures(b);
5199 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5200 * awt.event.ActionEvent)
5203 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5205 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5206 alignPanel.paintAlignment(false, false);
5213 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5217 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5219 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5220 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5228 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5229 * .event.ActionEvent)
5232 protected void showGroupConservation_actionPerformed(ActionEvent e)
5234 viewport.setShowGroupConservation(showGroupConservation.getState());
5235 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5242 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5243 * .event.ActionEvent)
5246 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5248 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5249 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5256 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5257 * .event.ActionEvent)
5260 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5262 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5263 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5267 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5269 showSequenceLogo.setState(true);
5270 viewport.setShowSequenceLogo(true);
5271 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5272 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5276 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5278 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5285 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5286 * .event.ActionEvent)
5289 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5291 if (avc.makeGroupsFromSelection())
5293 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5294 alignPanel.updateAnnotation();
5295 alignPanel.paintAlignment(true, true);
5299 public void clearAlignmentSeqRep()
5301 // TODO refactor alignmentseqrep to controller
5302 if (viewport.getAlignment().hasSeqrep())
5304 viewport.getAlignment().setSeqrep(null);
5305 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5306 alignPanel.updateAnnotation();
5307 alignPanel.paintAlignment(true, true);
5312 protected void createGroup_actionPerformed(ActionEvent e)
5314 if (avc.createGroup())
5316 alignPanel.alignmentChanged();
5321 protected void unGroup_actionPerformed(ActionEvent e)
5325 alignPanel.alignmentChanged();
5330 * make the given alignmentPanel the currently selected tab
5332 * @param alignmentPanel
5334 public void setDisplayedView(AlignmentPanel alignmentPanel)
5336 if (!viewport.getSequenceSetId()
5337 .equals(alignmentPanel.av.getSequenceSetId()))
5339 throw new Error(MessageManager.getString(
5340 "error.implementation_error_cannot_show_view_alignment_frame"));
5342 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5343 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5345 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5350 * Action on selection of menu options to Show or Hide annotations.
5353 * @param forSequences
5354 * update sequence-related annotations
5355 * @param forAlignment
5356 * update non-sequence-related annotations
5359 protected void setAnnotationsVisibility(boolean visible,
5360 boolean forSequences, boolean forAlignment)
5362 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5363 .getAlignmentAnnotation();
5368 for (AlignmentAnnotation aa : anns)
5371 * don't display non-positional annotations on an alignment
5373 if (aa.annotations == null)
5377 boolean apply = (aa.sequenceRef == null && forAlignment)
5378 || (aa.sequenceRef != null && forSequences);
5381 aa.visible = visible;
5384 alignPanel.validateAnnotationDimensions(true);
5385 alignPanel.alignmentChanged();
5389 * Store selected annotation sort order for the view and repaint.
5392 protected void sortAnnotations_actionPerformed()
5394 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5396 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5397 alignPanel.paintAlignment(false, false);
5402 * @return alignment panels in this alignment frame
5404 public List<? extends AlignmentViewPanel> getAlignPanels()
5406 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5410 * Open a new alignment window, with the cDNA associated with this (protein)
5411 * alignment, aligned as is the protein.
5413 protected void viewAsCdna_actionPerformed()
5415 // TODO no longer a menu action - refactor as required
5416 final AlignmentI alignment = getViewport().getAlignment();
5417 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5418 if (mappings == null)
5422 List<SequenceI> cdnaSeqs = new ArrayList<>();
5423 for (SequenceI aaSeq : alignment.getSequences())
5425 for (AlignedCodonFrame acf : mappings)
5427 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5431 * There is a cDNA mapping for this protein sequence - add to new
5432 * alignment. It will share the same dataset sequence as other mapped
5433 * cDNA (no new mappings need to be created).
5435 final Sequence newSeq = new Sequence(dnaSeq);
5436 newSeq.setDatasetSequence(dnaSeq);
5437 cdnaSeqs.add(newSeq);
5441 if (cdnaSeqs.size() == 0)
5443 // show a warning dialog no mapped cDNA
5446 AlignmentI cdna = new Alignment(
5447 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5448 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5449 AlignFrame.DEFAULT_HEIGHT);
5450 cdna.alignAs(alignment);
5451 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5453 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5454 AlignFrame.DEFAULT_HEIGHT);
5458 * Set visibility of dna/protein complement view (available when shown in a
5464 protected void showComplement_actionPerformed(boolean show)
5466 SplitContainerI sf = getSplitViewContainer();
5469 sf.setComplementVisible(this, show);
5474 * Generate the reverse (optionally complemented) of the selected sequences,
5475 * and add them to the alignment
5478 protected void showReverse_actionPerformed(boolean complement)
5480 AlignmentI al = null;
5483 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5484 al = dna.reverseCdna(complement);
5485 viewport.addAlignment(al, "");
5486 addHistoryItem(new EditCommand(
5487 MessageManager.getString("label.add_sequences"), Action.PASTE,
5488 al.getSequencesArray(), 0, al.getWidth(),
5489 viewport.getAlignment()));
5490 } catch (Exception ex)
5492 System.err.println(ex.getMessage());
5498 * Try to run a script in the Groovy console, having first ensured that this
5499 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5500 * be targeted at this alignment.
5503 protected void runGroovy_actionPerformed()
5505 Jalview.setCurrentAlignFrame(this);
5506 groovy.ui.Console console = Desktop.getGroovyConsole();
5507 if (console != null)
5511 console.runScript();
5512 } catch (Exception ex)
5514 System.err.println((ex.toString()));
5515 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5516 MessageManager.getString("label.couldnt_run_groovy_script"),
5517 MessageManager.getString("label.groovy_support_failed"),
5518 JvOptionPane.ERROR_MESSAGE);
5523 System.err.println("Can't run Groovy script as console not found");
5528 * Hides columns containing (or not containing) a specified feature, provided
5529 * that would not leave all columns hidden
5531 * @param featureType
5532 * @param columnsContaining
5535 public boolean hideFeatureColumns(String featureType,
5536 boolean columnsContaining)
5538 boolean notForHiding = avc.markColumnsContainingFeatures(
5539 columnsContaining, false, false, featureType);
5542 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5543 false, featureType))
5545 getViewport().hideSelectedColumns();
5553 protected void selectHighlightedColumns_actionPerformed(
5554 ActionEvent actionEvent)
5556 // include key modifier check in case user selects from menu
5557 avc.markHighlightedColumns(
5558 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5559 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5560 | ActionEvent.CTRL_MASK)) != 0);
5564 * Rebuilds the Colour menu, including any user-defined colours which have
5565 * been loaded either on startup or during the session
5567 public void buildColourMenu()
5569 colourMenu.removeAll();
5571 colourMenu.add(applyToAllGroups);
5572 colourMenu.add(textColour);
5573 colourMenu.addSeparator();
5575 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5578 colourMenu.addSeparator();
5579 colourMenu.add(conservationMenuItem);
5580 colourMenu.add(modifyConservation);
5581 colourMenu.add(abovePIDThreshold);
5582 colourMenu.add(modifyPID);
5583 colourMenu.add(annotationColour);
5585 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5586 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5590 * Open a dialog (if not already open) that allows the user to select and
5591 * calculate PCA or Tree analysis
5593 protected void openTreePcaDialog()
5595 if (alignPanel.getCalculationDialog() == null)
5597 new CalculationChooser(AlignFrame.this);
5602 protected void loadVcf_actionPerformed()
5604 JalviewFileChooser chooser = new JalviewFileChooser(
5605 Cache.getProperty("LAST_DIRECTORY"));
5606 chooser.setFileView(new JalviewFileView());
5607 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5608 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5610 int value = chooser.showOpenDialog(null);
5612 if (value == JalviewFileChooser.APPROVE_OPTION)
5614 String choice = chooser.getSelectedFile().getPath();
5615 Cache.setProperty("LAST_DIRECTORY", choice);
5616 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5617 new VCFLoader(choice).loadVCF(seqs, this);
5623 class PrintThread extends Thread
5627 public PrintThread(AlignmentPanel ap)
5632 static PageFormat pf;
5637 PrinterJob printJob = PrinterJob.getPrinterJob();
5641 printJob.setPrintable(ap, pf);
5645 printJob.setPrintable(ap);
5648 if (printJob.printDialog())
5653 } catch (Exception PrintException)
5655 PrintException.printStackTrace();