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.GeneticCodeI;
28 import jalview.analysis.ParseProperties;
29 import jalview.analysis.SequenceIdMatcher;
30 import jalview.api.AlignExportSettingI;
31 import jalview.api.AlignViewControllerGuiI;
32 import jalview.api.AlignViewControllerI;
33 import jalview.api.AlignViewportI;
34 import jalview.api.AlignmentViewPanel;
35 import jalview.api.FeatureSettingsControllerI;
36 import jalview.api.FeatureSettingsModelI;
37 import jalview.api.SplitContainerI;
38 import jalview.api.ViewStyleI;
39 import jalview.api.analysis.SimilarityParamsI;
40 import jalview.bin.Cache;
41 import jalview.bin.Jalview;
42 import jalview.commands.CommandI;
43 import jalview.commands.EditCommand;
44 import jalview.commands.EditCommand.Action;
45 import jalview.commands.OrderCommand;
46 import jalview.commands.RemoveGapColCommand;
47 import jalview.commands.RemoveGapsCommand;
48 import jalview.commands.SlideSequencesCommand;
49 import jalview.commands.TrimRegionCommand;
50 import jalview.datamodel.AlignedCodonFrame;
51 import jalview.datamodel.Alignment;
52 import jalview.datamodel.AlignmentAnnotation;
53 import jalview.datamodel.AlignmentExportData;
54 import jalview.datamodel.AlignmentI;
55 import jalview.datamodel.AlignmentOrder;
56 import jalview.datamodel.AlignmentView;
57 import jalview.datamodel.ColumnSelection;
58 import jalview.datamodel.HiddenColumns;
59 import jalview.datamodel.HiddenSequences;
60 import jalview.datamodel.PDBEntry;
61 import jalview.datamodel.SeqCigar;
62 import jalview.datamodel.Sequence;
63 import jalview.datamodel.SequenceGroup;
64 import jalview.datamodel.SequenceI;
65 import jalview.gui.ColourMenuHelper.ColourChangeListener;
66 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
67 import jalview.io.AlignmentProperties;
68 import jalview.io.AnnotationFile;
69 import jalview.io.BackupFiles;
70 import jalview.io.BioJsHTMLOutput;
71 import jalview.io.DataSourceType;
72 import jalview.io.FileFormat;
73 import jalview.io.FileFormatI;
74 import jalview.io.FileFormats;
75 import jalview.io.FileLoader;
76 import jalview.io.FileParse;
77 import jalview.io.FormatAdapter;
78 import jalview.io.HtmlSvgOutput;
79 import jalview.io.IdentifyFile;
80 import jalview.io.JPredFile;
81 import jalview.io.JalviewFileChooser;
82 import jalview.io.JalviewFileView;
83 import jalview.io.JnetAnnotationMaker;
84 import jalview.io.NewickFile;
85 import jalview.io.ScoreMatrixFile;
86 import jalview.io.TCoffeeScoreFile;
87 import jalview.io.vcf.VCFLoader;
88 import jalview.jbgui.GAlignFrame;
89 import jalview.schemes.ColourSchemeI;
90 import jalview.schemes.ColourSchemes;
91 import jalview.schemes.ResidueColourScheme;
92 import jalview.schemes.TCoffeeColourScheme;
93 import jalview.util.MessageManager;
94 import jalview.viewmodel.AlignmentViewport;
95 import jalview.viewmodel.ViewportRanges;
96 import jalview.ws.DBRefFetcher;
97 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
98 import jalview.ws.jws1.Discoverer;
99 import jalview.ws.jws2.Jws2Discoverer;
100 import jalview.ws.jws2.jabaws2.Jws2Instance;
101 import jalview.ws.seqfetcher.DbSourceProxy;
103 import java.awt.BorderLayout;
104 import java.awt.Component;
105 import java.awt.Rectangle;
106 import java.awt.Toolkit;
107 import java.awt.datatransfer.Clipboard;
108 import java.awt.datatransfer.DataFlavor;
109 import java.awt.datatransfer.StringSelection;
110 import java.awt.datatransfer.Transferable;
111 import java.awt.dnd.DnDConstants;
112 import java.awt.dnd.DropTargetDragEvent;
113 import java.awt.dnd.DropTargetDropEvent;
114 import java.awt.dnd.DropTargetEvent;
115 import java.awt.dnd.DropTargetListener;
116 import java.awt.event.ActionEvent;
117 import java.awt.event.ActionListener;
118 import java.awt.event.FocusAdapter;
119 import java.awt.event.FocusEvent;
120 import java.awt.event.ItemEvent;
121 import java.awt.event.ItemListener;
122 import java.awt.event.KeyAdapter;
123 import java.awt.event.KeyEvent;
124 import java.awt.event.MouseEvent;
125 import java.awt.print.PageFormat;
126 import java.awt.print.PrinterJob;
127 import java.beans.PropertyChangeEvent;
129 import java.io.FileWriter;
130 import java.io.PrintWriter;
132 import java.util.ArrayList;
133 import java.util.Arrays;
134 import java.util.Deque;
135 import java.util.Enumeration;
136 import java.util.Hashtable;
137 import java.util.List;
138 import java.util.Vector;
140 import javax.swing.ButtonGroup;
141 import javax.swing.JCheckBoxMenuItem;
142 import javax.swing.JEditorPane;
143 import javax.swing.JInternalFrame;
144 import javax.swing.JLayeredPane;
145 import javax.swing.JMenu;
146 import javax.swing.JMenuItem;
147 import javax.swing.JScrollPane;
148 import javax.swing.SwingUtilities;
154 * @version $Revision$
156 public class AlignFrame extends GAlignFrame implements DropTargetListener,
157 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
160 public static final int DEFAULT_WIDTH = 700;
162 public static final int DEFAULT_HEIGHT = 500;
165 * The currently displayed panel (selected tabbed view if more than one)
167 public AlignmentPanel alignPanel;
169 AlignViewport viewport;
171 public AlignViewControllerI avc;
173 List<AlignmentPanel> alignPanels = new ArrayList<>();
176 * Last format used to load or save alignments in this window
178 FileFormatI currentFileFormat = null;
181 * Current filename for this alignment
183 String fileName = null;
186 * Creates a new AlignFrame object with specific width and height.
192 public AlignFrame(AlignmentI al, int width, int height)
194 this(al, null, width, height);
198 * Creates a new AlignFrame object with specific width, height and
204 * @param sequenceSetId
206 public AlignFrame(AlignmentI al, int width, int height,
207 String sequenceSetId)
209 this(al, null, width, height, sequenceSetId);
213 * Creates a new AlignFrame object with specific width, height and
219 * @param sequenceSetId
222 public AlignFrame(AlignmentI al, int width, int height,
223 String sequenceSetId, String viewId)
225 this(al, null, width, height, sequenceSetId, viewId);
229 * new alignment window with hidden columns
233 * @param hiddenColumns
234 * ColumnSelection or null
236 * Width of alignment frame
240 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
243 this(al, hiddenColumns, width, height, null);
247 * Create alignment frame for al with hiddenColumns, a specific width and
248 * height, and specific sequenceId
251 * @param hiddenColumns
254 * @param sequenceSetId
257 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
258 int height, String sequenceSetId)
260 this(al, hiddenColumns, width, height, sequenceSetId, null);
264 * Create alignment frame for al with hiddenColumns, a specific width and
265 * height, and specific sequenceId
268 * @param hiddenColumns
271 * @param sequenceSetId
276 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
277 int height, String sequenceSetId, String viewId)
279 setSize(width, height);
281 if (al.getDataset() == null)
286 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
288 alignPanel = new AlignmentPanel(this, viewport);
290 addAlignmentPanel(alignPanel, true);
294 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
295 HiddenColumns hiddenColumns, int width, int height)
297 setSize(width, height);
299 if (al.getDataset() == null)
304 viewport = new AlignViewport(al, hiddenColumns);
306 if (hiddenSeqs != null && hiddenSeqs.length > 0)
308 viewport.hideSequence(hiddenSeqs);
310 alignPanel = new AlignmentPanel(this, viewport);
311 addAlignmentPanel(alignPanel, true);
316 * Make a new AlignFrame from existing alignmentPanels
323 public AlignFrame(AlignmentPanel ap)
327 addAlignmentPanel(ap, false);
332 * initalise the alignframe from the underlying viewport data and the
337 if (!Jalview.isHeadlessMode())
339 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
342 avc = new jalview.controller.AlignViewController(this, viewport,
344 if (viewport.getAlignmentConservationAnnotation() == null)
346 // BLOSUM62Colour.setEnabled(false);
347 conservationMenuItem.setEnabled(false);
348 modifyConservation.setEnabled(false);
349 // PIDColour.setEnabled(false);
350 // abovePIDThreshold.setEnabled(false);
351 // modifyPID.setEnabled(false);
354 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
357 if (sortby.equals("Id"))
359 sortIDMenuItem_actionPerformed(null);
361 else if (sortby.equals("Pairwise Identity"))
363 sortPairwiseMenuItem_actionPerformed(null);
367 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
369 setMenusFromViewport(viewport);
370 buildSortByAnnotationScoresMenu();
371 calculateTree.addActionListener(new ActionListener()
375 public void actionPerformed(ActionEvent e)
382 if (Desktop.desktop != null)
384 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
385 addServiceListeners();
389 if (viewport.getWrapAlignment())
391 wrapMenuItem_actionPerformed(null);
394 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
396 this.overviewMenuItem_actionPerformed(null);
401 final List<AlignmentPanel> selviews = new ArrayList<>();
402 final List<AlignmentPanel> origview = new ArrayList<>();
403 final String menuLabel = MessageManager
404 .getString("label.copy_format_from");
405 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
406 new ViewSetProvider()
410 public AlignmentPanel[] getAllAlignmentPanels()
413 origview.add(alignPanel);
414 // make an array of all alignment panels except for this one
415 List<AlignmentPanel> aps = new ArrayList<>(
416 Arrays.asList(Desktop.getAlignmentPanels(null)));
417 aps.remove(AlignFrame.this.alignPanel);
418 return aps.toArray(new AlignmentPanel[aps.size()]);
420 }, selviews, new ItemListener()
424 public void itemStateChanged(ItemEvent e)
426 if (origview.size() > 0)
428 final AlignmentPanel ap = origview.get(0);
431 * Copy the ViewStyle of the selected panel to 'this one'.
432 * Don't change value of 'scaleProteinAsCdna' unless copying
435 ViewStyleI vs = selviews.get(0).getAlignViewport()
437 boolean fromSplitFrame = selviews.get(0)
438 .getAlignViewport().getCodingComplement() != null;
441 vs.setScaleProteinAsCdna(ap.getAlignViewport()
442 .getViewStyle().isScaleProteinAsCdna());
444 ap.getAlignViewport().setViewStyle(vs);
447 * Also rescale ViewStyle of SplitFrame complement if there is
448 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
449 * the whole ViewStyle (allow cDNA protein to have different
452 AlignViewportI complement = ap.getAlignViewport()
453 .getCodingComplement();
454 if (complement != null && vs.isScaleProteinAsCdna())
456 AlignFrame af = Desktop.getAlignFrameFor(complement);
457 ((SplitFrame) af.getSplitViewContainer())
459 af.setMenusForViewport();
463 ap.setSelected(true);
464 ap.alignFrame.setMenusForViewport();
469 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
470 .indexOf("devel") > -1
471 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
472 .indexOf("test") > -1)
474 formatMenu.add(vsel);
476 addFocusListener(new FocusAdapter()
479 public void focusGained(FocusEvent e)
481 Jalview.setCurrentAlignFrame(AlignFrame.this);
488 * Change the filename and format for the alignment, and enable the 'reload'
489 * button functionality.
496 public void setFileName(String file, FileFormatI format)
499 setFileFormat(format);
500 reload.setEnabled(true);
504 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
507 void addKeyListener()
509 addKeyListener(new KeyAdapter()
512 public void keyPressed(KeyEvent evt)
514 if (viewport.cursorMode
515 && ((evt.getKeyCode() >= KeyEvent.VK_0
516 && evt.getKeyCode() <= KeyEvent.VK_9)
517 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
518 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
519 && Character.isDigit(evt.getKeyChar()))
521 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
524 switch (evt.getKeyCode())
527 case 27: // escape key
528 deselectAllSequenceMenuItem_actionPerformed(null);
532 case KeyEvent.VK_DOWN:
533 if (evt.isAltDown() || !viewport.cursorMode)
535 moveSelectedSequences(false);
537 if (viewport.cursorMode)
539 alignPanel.getSeqPanel().moveCursor(0, 1);
544 if (evt.isAltDown() || !viewport.cursorMode)
546 moveSelectedSequences(true);
548 if (viewport.cursorMode)
550 alignPanel.getSeqPanel().moveCursor(0, -1);
555 case KeyEvent.VK_LEFT:
556 if (evt.isAltDown() || !viewport.cursorMode)
558 slideSequences(false,
559 alignPanel.getSeqPanel().getKeyboardNo1());
563 alignPanel.getSeqPanel().moveCursor(-1, 0);
568 case KeyEvent.VK_RIGHT:
569 if (evt.isAltDown() || !viewport.cursorMode)
571 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
575 alignPanel.getSeqPanel().moveCursor(1, 0);
579 case KeyEvent.VK_SPACE:
580 if (viewport.cursorMode)
582 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
583 || evt.isShiftDown() || evt.isAltDown());
587 // case KeyEvent.VK_A:
588 // if (viewport.cursorMode)
590 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
591 // //System.out.println("A");
595 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
596 * System.out.println("closing bracket"); } break;
598 case KeyEvent.VK_DELETE:
599 case KeyEvent.VK_BACK_SPACE:
600 if (!viewport.cursorMode)
602 cut_actionPerformed(null);
606 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
607 || evt.isShiftDown() || evt.isAltDown());
613 if (viewport.cursorMode)
615 alignPanel.getSeqPanel().setCursorRow();
619 if (viewport.cursorMode && !evt.isControlDown())
621 alignPanel.getSeqPanel().setCursorColumn();
625 if (viewport.cursorMode)
627 alignPanel.getSeqPanel().setCursorPosition();
631 case KeyEvent.VK_ENTER:
632 case KeyEvent.VK_COMMA:
633 if (viewport.cursorMode)
635 alignPanel.getSeqPanel().setCursorRowAndColumn();
640 if (viewport.cursorMode)
642 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
646 if (viewport.cursorMode)
648 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
653 viewport.cursorMode = !viewport.cursorMode;
654 statusBar.setText(MessageManager
655 .formatMessage("label.keyboard_editing_mode", new String[]
656 { (viewport.cursorMode ? "on" : "off") }));
657 if (viewport.cursorMode)
659 ViewportRanges ranges = viewport.getRanges();
660 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
662 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
665 alignPanel.getSeqPanel().seqCanvas.repaint();
671 Help.showHelpWindow();
672 } catch (Exception ex)
674 ex.printStackTrace();
679 boolean toggleSeqs = !evt.isControlDown();
680 boolean toggleCols = !evt.isShiftDown();
681 toggleHiddenRegions(toggleSeqs, toggleCols);
686 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
687 boolean modifyExisting = true; // always modify, don't clear
688 // evt.isShiftDown();
689 boolean invertHighlighted = evt.isAltDown();
690 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
694 case KeyEvent.VK_PAGE_UP:
695 viewport.getRanges().pageUp();
697 case KeyEvent.VK_PAGE_DOWN:
698 viewport.getRanges().pageDown();
704 public void keyReleased(KeyEvent evt)
706 switch (evt.getKeyCode())
708 case KeyEvent.VK_LEFT:
709 if (evt.isAltDown() || !viewport.cursorMode)
711 viewport.firePropertyChange("alignment", null,
712 viewport.getAlignment().getSequences());
716 case KeyEvent.VK_RIGHT:
717 if (evt.isAltDown() || !viewport.cursorMode)
719 viewport.firePropertyChange("alignment", null,
720 viewport.getAlignment().getSequences());
728 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
730 ap.alignFrame = this;
731 avc = new jalview.controller.AlignViewController(this, viewport,
736 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
738 int aSize = alignPanels.size();
740 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
742 if (aSize == 1 && ap.av.getViewName() == null)
744 this.getContentPane().add(ap, BorderLayout.CENTER);
750 setInitialTabVisible();
753 expandViews.setEnabled(true);
754 gatherViews.setEnabled(true);
755 tabbedPane.addTab(ap.av.getViewName(), ap);
757 ap.setVisible(false);
762 if (ap.av.isPadGaps())
764 ap.av.getAlignment().padGaps();
766 ap.av.updateConservation(ap);
767 ap.av.updateConsensus(ap);
768 ap.av.updateStrucConsensus(ap);
772 public void setInitialTabVisible()
774 expandViews.setEnabled(true);
775 gatherViews.setEnabled(true);
776 tabbedPane.setVisible(true);
777 AlignmentPanel first = alignPanels.get(0);
778 tabbedPane.addTab(first.av.getViewName(), first);
779 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
782 public AlignViewport getViewport()
787 /* Set up intrinsic listeners for dynamically generated GUI bits. */
788 private void addServiceListeners()
790 final java.beans.PropertyChangeListener thisListener;
791 Desktop.instance.addJalviewPropertyChangeListener("services",
792 thisListener = new java.beans.PropertyChangeListener()
795 public void propertyChange(PropertyChangeEvent evt)
797 // // System.out.println("Discoverer property change.");
798 // if (evt.getPropertyName().equals("services"))
800 SwingUtilities.invokeLater(new Runnable()
807 "Rebuild WS Menu for service change");
808 BuildWebServiceMenu();
815 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
818 public void internalFrameClosed(
819 javax.swing.event.InternalFrameEvent evt)
821 // System.out.println("deregistering discoverer listener");
822 Desktop.instance.removeJalviewPropertyChangeListener("services",
824 closeMenuItem_actionPerformed(true);
827 // Finally, build the menu once to get current service state
828 new Thread(new Runnable()
833 BuildWebServiceMenu();
839 * Configure menu items that vary according to whether the alignment is
840 * nucleotide or protein
842 public void setGUINucleotide()
844 AlignmentI al = getViewport().getAlignment();
845 boolean nucleotide = al.isNucleotide();
847 loadVcf.setVisible(nucleotide);
848 showTranslation.setVisible(nucleotide);
849 showReverse.setVisible(nucleotide);
850 showReverseComplement.setVisible(nucleotide);
851 conservationMenuItem.setEnabled(!nucleotide);
853 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
854 showGroupConservation.setEnabled(!nucleotide);
856 showComplementMenuItem
857 .setText(nucleotide ? MessageManager.getString("label.protein")
858 : MessageManager.getString("label.nucleotide"));
862 * set up menus for the current viewport. This may be called after any
863 * operation that affects the data in the current view (selection changed,
864 * etc) to update the menus to reflect the new state.
867 public void setMenusForViewport()
869 setMenusFromViewport(viewport);
873 * Need to call this method when tabs are selected for multiple views, or when
874 * loading from Jalview2XML.java
879 public void setMenusFromViewport(AlignViewport av)
881 padGapsMenuitem.setSelected(av.isPadGaps());
882 colourTextMenuItem.setSelected(av.isShowColourText());
883 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
884 modifyPID.setEnabled(abovePIDThreshold.isSelected());
885 conservationMenuItem.setSelected(av.getConservationSelected());
886 modifyConservation.setEnabled(conservationMenuItem.isSelected());
887 seqLimits.setSelected(av.getShowJVSuffix());
888 idRightAlign.setSelected(av.isRightAlignIds());
889 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
890 renderGapsMenuItem.setSelected(av.isRenderGaps());
891 wrapMenuItem.setSelected(av.getWrapAlignment());
892 scaleAbove.setVisible(av.getWrapAlignment());
893 scaleLeft.setVisible(av.getWrapAlignment());
894 scaleRight.setVisible(av.getWrapAlignment());
895 annotationPanelMenuItem.setState(av.isShowAnnotation());
897 * Show/hide annotations only enabled if annotation panel is shown
899 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
900 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
901 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
902 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
903 viewBoxesMenuItem.setSelected(av.getShowBoxes());
904 viewTextMenuItem.setSelected(av.getShowText());
905 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
906 showGroupConsensus.setSelected(av.isShowGroupConsensus());
907 showGroupConservation.setSelected(av.isShowGroupConservation());
908 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
909 showSequenceLogo.setSelected(av.isShowSequenceLogo());
910 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
912 ColourMenuHelper.setColourSelected(colourMenu,
913 av.getGlobalColourScheme());
915 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
916 hiddenMarkers.setState(av.getShowHiddenMarkers());
917 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
918 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
919 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
920 autoCalculate.setSelected(av.autoCalculateConsensus);
921 sortByTree.setSelected(av.sortByTree);
922 listenToViewSelections.setSelected(av.followSelection);
924 showProducts.setEnabled(canShowProducts());
925 setGroovyEnabled(Desktop.getGroovyConsole() != null);
931 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
935 public void setGroovyEnabled(boolean b)
937 runGroovy.setEnabled(b);
940 private IProgressIndicator progressBar;
945 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
948 public void setProgressBar(String message, long id)
950 progressBar.setProgressBar(message, id);
954 public void registerHandler(final long id,
955 final IProgressIndicatorHandler handler)
957 progressBar.registerHandler(id, handler);
962 * @return true if any progress bars are still active
965 public boolean operationInProgress()
967 return progressBar.operationInProgress();
971 * Sets the text of the status bar. Note that setting a null or empty value
972 * will cause the status bar to be hidden, with possibly undesirable flicker
973 * of the screen layout.
976 public void setStatus(String text)
978 statusBar.setText(text == null || text.isEmpty() ? " " : text);
982 * Added so Castor Mapping file can obtain Jalview Version
984 public String getVersion()
986 return jalview.bin.Cache.getProperty("VERSION");
989 public FeatureRenderer getFeatureRenderer()
991 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
995 public void fetchSequence_actionPerformed(ActionEvent e)
997 new jalview.gui.SequenceFetcher(this);
1001 public void addFromFile_actionPerformed(ActionEvent e)
1003 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1007 public void reload_actionPerformed(ActionEvent e)
1009 if (fileName != null)
1011 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1012 // originating file's format
1013 // TODO: work out how to recover feature settings for correct view(s) when
1014 // file is reloaded.
1015 if (FileFormat.Jalview.equals(currentFileFormat))
1017 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1018 for (int i = 0; i < frames.length; i++)
1020 if (frames[i] instanceof AlignFrame && frames[i] != this
1021 && ((AlignFrame) frames[i]).fileName != null
1022 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1026 frames[i].setSelected(true);
1027 Desktop.instance.closeAssociatedWindows();
1028 } catch (java.beans.PropertyVetoException ex)
1034 Desktop.instance.closeAssociatedWindows();
1036 FileLoader loader = new FileLoader();
1037 DataSourceType protocol = fileName.startsWith("http:")
1038 ? DataSourceType.URL
1039 : DataSourceType.FILE;
1040 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1044 Rectangle bounds = this.getBounds();
1046 FileLoader loader = new FileLoader();
1047 DataSourceType protocol = fileName.startsWith("http:")
1048 ? DataSourceType.URL
1049 : DataSourceType.FILE;
1050 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1051 protocol, currentFileFormat);
1053 newframe.setBounds(bounds);
1054 if (featureSettings != null && featureSettings.isShowing())
1056 final Rectangle fspos = featureSettings.frame.getBounds();
1057 // TODO: need a 'show feature settings' function that takes bounds -
1058 // need to refactor Desktop.addFrame
1059 newframe.featureSettings_actionPerformed(null);
1060 final FeatureSettings nfs = newframe.featureSettings;
1061 SwingUtilities.invokeLater(new Runnable()
1066 nfs.frame.setBounds(fspos);
1069 this.featureSettings.close();
1070 this.featureSettings = null;
1072 this.closeMenuItem_actionPerformed(true);
1078 public void addFromText_actionPerformed(ActionEvent e)
1081 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1085 public void addFromURL_actionPerformed(ActionEvent e)
1087 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1091 public void save_actionPerformed(ActionEvent e)
1093 if (fileName == null || (currentFileFormat == null)
1094 || fileName.startsWith("http"))
1096 saveAs_actionPerformed(null);
1100 saveAlignment(fileName, currentFileFormat);
1111 public void saveAs_actionPerformed(ActionEvent e)
1113 String format = currentFileFormat == null ? null
1114 : currentFileFormat.getName();
1115 JalviewFileChooser chooser = JalviewFileChooser
1116 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1118 chooser.setFileView(new JalviewFileView());
1119 chooser.setDialogTitle(
1120 MessageManager.getString("label.save_alignment_to_file"));
1121 chooser.setToolTipText(MessageManager.getString("action.save"));
1123 int value = chooser.showSaveDialog(this);
1125 if (value == JalviewFileChooser.APPROVE_OPTION)
1127 currentFileFormat = chooser.getSelectedFormat();
1128 while (currentFileFormat == null)
1130 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1131 MessageManager.getString(
1132 "label.select_file_format_before_saving"),
1133 MessageManager.getString("label.file_format_not_specified"),
1134 JvOptionPane.WARNING_MESSAGE);
1135 currentFileFormat = chooser.getSelectedFormat();
1136 value = chooser.showSaveDialog(this);
1137 if (value != JalviewFileChooser.APPROVE_OPTION)
1143 fileName = chooser.getSelectedFile().getPath();
1145 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1147 Cache.setProperty("LAST_DIRECTORY", fileName);
1148 saveAlignment(fileName, currentFileFormat);
1152 public boolean saveAlignment(String file, FileFormatI format)
1154 boolean success = true;
1156 if (FileFormat.Jalview.equals(format))
1158 String shortName = title;
1160 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1162 shortName = shortName.substring(
1163 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1166 success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1169 statusBar.setText(MessageManager.formatMessage(
1170 "label.successfully_saved_to_file_in_format", new Object[]
1171 { fileName, format }));
1176 AlignmentExportData exportData = getAlignmentForExport(format,
1178 if (exportData.getSettings().isCancelled())
1182 FormatAdapter f = new FormatAdapter(alignPanel,
1183 exportData.getSettings());
1184 String output = f.formatSequences(format, exportData.getAlignment(), // class
1188 // occur in the distant future
1189 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1190 f.getCacheSuffixDefault(format),
1191 viewport.getAlignment().getHiddenColumns());
1199 // create backupfiles object and get new temp filename destination
1200 BackupFiles backupfiles = new BackupFiles(file);
1204 PrintWriter out = new PrintWriter(
1205 new FileWriter(backupfiles.getTempFilePath()));
1209 this.setTitle(file);
1210 statusBar.setText(MessageManager.formatMessage(
1211 "label.successfully_saved_to_file_in_format", new Object[]
1212 { fileName, format.getName() }));
1213 } catch (Exception ex)
1216 ex.printStackTrace();
1219 backupfiles.setWriteSuccess(success);
1220 // do the backup file roll and rename the temp file to actual file
1221 success = backupfiles.rollBackupsAndRenameTempFile();
1228 JvOptionPane.showInternalMessageDialog(this, MessageManager
1229 .formatMessage("label.couldnt_save_file", new Object[]
1231 MessageManager.getString("label.error_saving_file"),
1232 JvOptionPane.WARNING_MESSAGE);
1238 private void warningMessage(String warning, String title)
1240 if (new jalview.util.Platform().isHeadless())
1242 System.err.println("Warning: " + title + "\nWarning: " + warning);
1247 JvOptionPane.showInternalMessageDialog(this, warning, title,
1248 JvOptionPane.WARNING_MESSAGE);
1260 protected void outputText_actionPerformed(ActionEvent e)
1262 FileFormatI fileFormat = FileFormats.getInstance()
1263 .forName(e.getActionCommand());
1264 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1266 if (exportData.getSettings().isCancelled())
1270 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1271 cap.setForInput(null);
1274 FileFormatI format = fileFormat;
1275 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1276 .formatSequences(format, exportData.getAlignment(),
1277 exportData.getOmitHidden(),
1278 exportData.getStartEndPostions(),
1279 viewport.getAlignment().getHiddenColumns()));
1280 Desktop.addInternalFrame(cap, MessageManager
1281 .formatMessage("label.alignment_output_command", new Object[]
1282 { e.getActionCommand() }), 600, 500);
1283 } catch (OutOfMemoryError oom)
1285 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1292 public static AlignmentExportData getAlignmentForExport(
1293 FileFormatI format, AlignViewportI viewport,
1294 AlignExportSettingI exportSettings)
1296 AlignmentI alignmentToExport = null;
1297 AlignExportSettingI settings = exportSettings;
1298 String[] omitHidden = null;
1300 HiddenSequences hiddenSeqs = viewport.getAlignment()
1301 .getHiddenSequences();
1303 alignmentToExport = viewport.getAlignment();
1305 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1306 if (settings == null)
1308 settings = new AlignExportSettings(hasHiddenSeqs,
1309 viewport.hasHiddenColumns(), format);
1311 // settings.isExportAnnotations();
1313 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1315 omitHidden = viewport.getViewAsString(false,
1316 settings.isExportHiddenSequences());
1319 int[] alignmentStartEnd = new int[2];
1320 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1322 alignmentToExport = hiddenSeqs.getFullAlignment();
1326 alignmentToExport = viewport.getAlignment();
1328 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1329 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1330 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1331 omitHidden, alignmentStartEnd, settings);
1342 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1344 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1345 htmlSVG.exportHTML(null);
1349 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1351 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1352 bjs.exportHTML(null);
1355 public void createImageMap(File file, String image)
1357 alignPanel.makePNGImageMap(file, image);
1367 public void createPNG(File f)
1369 alignPanel.makePNG(f);
1379 public void createEPS(File f)
1381 alignPanel.makeEPS(f);
1385 public void createSVG(File f)
1387 alignPanel.makeSVG(f);
1391 public void pageSetup_actionPerformed(ActionEvent e)
1393 PrinterJob printJob = PrinterJob.getPrinterJob();
1394 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1404 public void printMenuItem_actionPerformed(ActionEvent e)
1406 // Putting in a thread avoids Swing painting problems
1407 PrintThread thread = new PrintThread(alignPanel);
1412 public void exportFeatures_actionPerformed(ActionEvent e)
1414 new AnnotationExporter(alignPanel).exportFeatures();
1418 public void exportAnnotations_actionPerformed(ActionEvent e)
1420 new AnnotationExporter(alignPanel).exportAnnotations();
1424 public void associatedData_actionPerformed(ActionEvent e)
1426 // Pick the tree file
1427 JalviewFileChooser chooser = new JalviewFileChooser(
1428 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1429 chooser.setFileView(new JalviewFileView());
1430 chooser.setDialogTitle(
1431 MessageManager.getString("label.load_jalview_annotations"));
1432 chooser.setToolTipText(
1433 MessageManager.getString("label.load_jalview_annotations"));
1435 int value = chooser.showOpenDialog(null);
1437 if (value == JalviewFileChooser.APPROVE_OPTION)
1439 String choice = chooser.getSelectedFile().getPath();
1440 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1441 loadJalviewDataFile(choice, null, null, null);
1447 * Close the current view or all views in the alignment frame. If the frame
1448 * only contains one view then the alignment will be removed from memory.
1450 * @param closeAllTabs
1453 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1455 if (alignPanels != null && alignPanels.size() < 2)
1457 closeAllTabs = true;
1462 if (alignPanels != null)
1466 if (this.isClosed())
1468 // really close all the windows - otherwise wait till
1469 // setClosed(true) is called
1470 for (int i = 0; i < alignPanels.size(); i++)
1472 AlignmentPanel ap = alignPanels.get(i);
1479 closeView(alignPanel);
1484 if (featureSettings != null && featureSettings.isOpen())
1486 featureSettings.close();
1487 featureSettings = null;
1490 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1491 * be called recursively, with the frame now in 'closed' state
1493 this.setClosed(true);
1495 } catch (Exception ex)
1497 ex.printStackTrace();
1502 * Close the specified panel and close up tabs appropriately.
1504 * @param panelToClose
1506 public void closeView(AlignmentPanel panelToClose)
1508 int index = tabbedPane.getSelectedIndex();
1509 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1510 alignPanels.remove(panelToClose);
1511 panelToClose.closePanel();
1512 panelToClose = null;
1514 tabbedPane.removeTabAt(closedindex);
1515 tabbedPane.validate();
1517 if (index > closedindex || index == tabbedPane.getTabCount())
1519 // modify currently selected tab index if necessary.
1523 this.tabSelectionChanged(index);
1529 void updateEditMenuBar()
1532 if (viewport.getHistoryList().size() > 0)
1534 undoMenuItem.setEnabled(true);
1535 CommandI command = viewport.getHistoryList().peek();
1536 undoMenuItem.setText(MessageManager
1537 .formatMessage("label.undo_command", new Object[]
1538 { command.getDescription() }));
1542 undoMenuItem.setEnabled(false);
1543 undoMenuItem.setText(MessageManager.getString("action.undo"));
1546 if (viewport.getRedoList().size() > 0)
1548 redoMenuItem.setEnabled(true);
1550 CommandI command = viewport.getRedoList().peek();
1551 redoMenuItem.setText(MessageManager
1552 .formatMessage("label.redo_command", new Object[]
1553 { command.getDescription() }));
1557 redoMenuItem.setEnabled(false);
1558 redoMenuItem.setText(MessageManager.getString("action.redo"));
1563 public void addHistoryItem(CommandI command)
1565 if (command.getSize() > 0)
1567 viewport.addToHistoryList(command);
1568 viewport.clearRedoList();
1569 updateEditMenuBar();
1570 viewport.updateHiddenColumns();
1571 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1572 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1573 // viewport.getColumnSelection()
1574 // .getHiddenColumns().size() > 0);
1580 * @return alignment objects for all views
1582 AlignmentI[] getViewAlignments()
1584 if (alignPanels != null)
1586 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1588 for (AlignmentPanel ap : alignPanels)
1590 als[i++] = ap.av.getAlignment();
1594 if (viewport != null)
1596 return new AlignmentI[] { viewport.getAlignment() };
1608 protected void undoMenuItem_actionPerformed(ActionEvent e)
1610 if (viewport.getHistoryList().isEmpty())
1614 CommandI command = viewport.getHistoryList().pop();
1615 viewport.addToRedoList(command);
1616 command.undoCommand(getViewAlignments());
1618 AlignmentViewport originalSource = getOriginatingSource(command);
1619 updateEditMenuBar();
1621 if (originalSource != null)
1623 if (originalSource != viewport)
1626 "Implementation worry: mismatch of viewport origin for undo");
1628 originalSource.updateHiddenColumns();
1629 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1631 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1632 // viewport.getColumnSelection()
1633 // .getHiddenColumns().size() > 0);
1634 originalSource.firePropertyChange("alignment", null,
1635 originalSource.getAlignment().getSequences());
1646 protected void redoMenuItem_actionPerformed(ActionEvent e)
1648 if (viewport.getRedoList().size() < 1)
1653 CommandI command = viewport.getRedoList().pop();
1654 viewport.addToHistoryList(command);
1655 command.doCommand(getViewAlignments());
1657 AlignmentViewport originalSource = getOriginatingSource(command);
1658 updateEditMenuBar();
1660 if (originalSource != null)
1663 if (originalSource != viewport)
1666 "Implementation worry: mismatch of viewport origin for redo");
1668 originalSource.updateHiddenColumns();
1669 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1671 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1672 // viewport.getColumnSelection()
1673 // .getHiddenColumns().size() > 0);
1674 originalSource.firePropertyChange("alignment", null,
1675 originalSource.getAlignment().getSequences());
1679 AlignmentViewport getOriginatingSource(CommandI command)
1681 AlignmentViewport originalSource = null;
1682 // For sequence removal and addition, we need to fire
1683 // the property change event FROM the viewport where the
1684 // original alignment was altered
1685 AlignmentI al = null;
1686 if (command instanceof EditCommand)
1688 EditCommand editCommand = (EditCommand) command;
1689 al = editCommand.getAlignment();
1690 List<Component> comps = PaintRefresher.components
1691 .get(viewport.getSequenceSetId());
1693 for (Component comp : comps)
1695 if (comp instanceof AlignmentPanel)
1697 if (al == ((AlignmentPanel) comp).av.getAlignment())
1699 originalSource = ((AlignmentPanel) comp).av;
1706 if (originalSource == null)
1708 // The original view is closed, we must validate
1709 // the current view against the closed view first
1712 PaintRefresher.validateSequences(al, viewport.getAlignment());
1715 originalSource = viewport;
1718 return originalSource;
1727 public void moveSelectedSequences(boolean up)
1729 SequenceGroup sg = viewport.getSelectionGroup();
1735 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1736 viewport.getHiddenRepSequences(), up);
1737 alignPanel.paintAlignment(true, false);
1740 synchronized void slideSequences(boolean right, int size)
1742 List<SequenceI> sg = new ArrayList<>();
1743 if (viewport.cursorMode)
1745 sg.add(viewport.getAlignment()
1746 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1748 else if (viewport.getSelectionGroup() != null
1749 && viewport.getSelectionGroup().getSize() != viewport
1750 .getAlignment().getHeight())
1752 sg = viewport.getSelectionGroup()
1753 .getSequences(viewport.getHiddenRepSequences());
1761 List<SequenceI> invertGroup = new ArrayList<>();
1763 for (SequenceI seq : viewport.getAlignment().getSequences())
1765 if (!sg.contains(seq))
1767 invertGroup.add(seq);
1771 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1773 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1774 for (int i = 0; i < invertGroup.size(); i++)
1776 seqs2[i] = invertGroup.get(i);
1779 SlideSequencesCommand ssc;
1782 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1783 viewport.getGapCharacter());
1787 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1788 viewport.getGapCharacter());
1791 int groupAdjustment = 0;
1792 if (ssc.getGapsInsertedBegin() && right)
1794 if (viewport.cursorMode)
1796 alignPanel.getSeqPanel().moveCursor(size, 0);
1800 groupAdjustment = size;
1803 else if (!ssc.getGapsInsertedBegin() && !right)
1805 if (viewport.cursorMode)
1807 alignPanel.getSeqPanel().moveCursor(-size, 0);
1811 groupAdjustment = -size;
1815 if (groupAdjustment != 0)
1817 viewport.getSelectionGroup().setStartRes(
1818 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1819 viewport.getSelectionGroup().setEndRes(
1820 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1824 * just extend the last slide command if compatible; but not if in
1825 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1827 boolean appendHistoryItem = false;
1828 Deque<CommandI> historyList = viewport.getHistoryList();
1829 boolean inSplitFrame = getSplitViewContainer() != null;
1830 if (!inSplitFrame && historyList != null && historyList.size() > 0
1831 && historyList.peek() instanceof SlideSequencesCommand)
1833 appendHistoryItem = ssc.appendSlideCommand(
1834 (SlideSequencesCommand) historyList.peek());
1837 if (!appendHistoryItem)
1839 addHistoryItem(ssc);
1852 protected void copy_actionPerformed(ActionEvent e)
1854 if (viewport.getSelectionGroup() == null)
1858 // TODO: preserve the ordering of displayed alignment annotation in any
1859 // internal paste (particularly sequence associated annotation)
1860 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1861 String[] omitHidden = null;
1863 if (viewport.hasHiddenColumns())
1865 omitHidden = viewport.getViewAsString(true);
1868 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1869 seqs, omitHidden, null);
1871 StringSelection ss = new StringSelection(output);
1875 jalview.gui.Desktop.internalCopy = true;
1876 // Its really worth setting the clipboard contents
1877 // to empty before setting the large StringSelection!!
1878 Toolkit.getDefaultToolkit().getSystemClipboard()
1879 .setContents(new StringSelection(""), null);
1881 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1883 } catch (OutOfMemoryError er)
1885 new OOMWarning("copying region", er);
1889 HiddenColumns hiddenColumns = null;
1890 if (viewport.hasHiddenColumns())
1892 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1893 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1895 // create new HiddenColumns object with copy of hidden regions
1896 // between startRes and endRes, offset by startRes
1897 hiddenColumns = new HiddenColumns(
1898 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1899 hiddenCutoff, hiddenOffset);
1902 Desktop.jalviewClipboard = new Object[] { seqs,
1903 viewport.getAlignment().getDataset(), hiddenColumns };
1904 statusBar.setText(MessageManager.formatMessage(
1905 "label.copied_sequences_to_clipboard", new Object[]
1906 { Integer.valueOf(seqs.length).toString() }));
1916 protected void pasteNew_actionPerformed(ActionEvent e)
1928 protected void pasteThis_actionPerformed(ActionEvent e)
1934 * Paste contents of Jalview clipboard
1936 * @param newAlignment
1937 * true to paste to a new alignment, otherwise add to this.
1939 void paste(boolean newAlignment)
1941 boolean externalPaste = true;
1944 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1945 Transferable contents = c.getContents(this);
1947 if (contents == null)
1956 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1957 if (str.length() < 1)
1962 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1964 } catch (OutOfMemoryError er)
1966 new OOMWarning("Out of memory pasting sequences!!", er);
1970 SequenceI[] sequences;
1971 boolean annotationAdded = false;
1972 AlignmentI alignment = null;
1974 if (Desktop.jalviewClipboard != null)
1976 // The clipboard was filled from within Jalview, we must use the
1978 // And dataset from the copied alignment
1979 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1980 // be doubly sure that we create *new* sequence objects.
1981 sequences = new SequenceI[newseq.length];
1982 for (int i = 0; i < newseq.length; i++)
1984 sequences[i] = new Sequence(newseq[i]);
1986 alignment = new Alignment(sequences);
1987 externalPaste = false;
1991 // parse the clipboard as an alignment.
1992 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1994 sequences = alignment.getSequencesArray();
1998 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2004 if (Desktop.jalviewClipboard != null)
2006 // dataset is inherited
2007 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2011 // new dataset is constructed
2012 alignment.setDataset(null);
2014 alwidth = alignment.getWidth() + 1;
2018 AlignmentI pastedal = alignment; // preserve pasted alignment object
2019 // Add pasted sequences and dataset into existing alignment.
2020 alignment = viewport.getAlignment();
2021 alwidth = alignment.getWidth() + 1;
2022 // decide if we need to import sequences from an existing dataset
2023 boolean importDs = Desktop.jalviewClipboard != null
2024 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2025 // importDs==true instructs us to copy over new dataset sequences from
2026 // an existing alignment
2027 Vector newDs = (importDs) ? new Vector() : null; // used to create
2028 // minimum dataset set
2030 for (int i = 0; i < sequences.length; i++)
2034 newDs.addElement(null);
2036 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2038 if (importDs && ds != null)
2040 if (!newDs.contains(ds))
2042 newDs.setElementAt(ds, i);
2043 ds = new Sequence(ds);
2044 // update with new dataset sequence
2045 sequences[i].setDatasetSequence(ds);
2049 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2054 // copy and derive new dataset sequence
2055 sequences[i] = sequences[i].deriveSequence();
2056 alignment.getDataset()
2057 .addSequence(sequences[i].getDatasetSequence());
2058 // TODO: avoid creation of duplicate dataset sequences with a
2059 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2061 alignment.addSequence(sequences[i]); // merges dataset
2065 newDs.clear(); // tidy up
2067 if (alignment.getAlignmentAnnotation() != null)
2069 for (AlignmentAnnotation alan : alignment
2070 .getAlignmentAnnotation())
2072 if (alan.graphGroup > fgroup)
2074 fgroup = alan.graphGroup;
2078 if (pastedal.getAlignmentAnnotation() != null)
2080 // Add any annotation attached to alignment.
2081 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2082 for (int i = 0; i < alann.length; i++)
2084 annotationAdded = true;
2085 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2087 AlignmentAnnotation newann = new AlignmentAnnotation(
2089 if (newann.graphGroup > -1)
2091 if (newGraphGroups.size() <= newann.graphGroup
2092 || newGraphGroups.get(newann.graphGroup) == null)
2094 for (int q = newGraphGroups
2095 .size(); q <= newann.graphGroup; q++)
2097 newGraphGroups.add(q, null);
2099 newGraphGroups.set(newann.graphGroup,
2100 Integer.valueOf(++fgroup));
2102 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2106 newann.padAnnotation(alwidth);
2107 alignment.addAnnotation(newann);
2117 addHistoryItem(new EditCommand(
2118 MessageManager.getString("label.add_sequences"),
2119 Action.PASTE, sequences, 0, alignment.getWidth(),
2122 // Add any annotations attached to sequences
2123 for (int i = 0; i < sequences.length; i++)
2125 if (sequences[i].getAnnotation() != null)
2127 AlignmentAnnotation newann;
2128 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2130 annotationAdded = true;
2131 newann = sequences[i].getAnnotation()[a];
2132 newann.adjustForAlignment();
2133 newann.padAnnotation(alwidth);
2134 if (newann.graphGroup > -1)
2136 if (newann.graphGroup > -1)
2138 if (newGraphGroups.size() <= newann.graphGroup
2139 || newGraphGroups.get(newann.graphGroup) == null)
2141 for (int q = newGraphGroups
2142 .size(); q <= newann.graphGroup; q++)
2144 newGraphGroups.add(q, null);
2146 newGraphGroups.set(newann.graphGroup,
2147 Integer.valueOf(++fgroup));
2149 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2153 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2157 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2165 // propagate alignment changed.
2166 viewport.getRanges().setEndSeq(alignment.getHeight());
2167 if (annotationAdded)
2169 // Duplicate sequence annotation in all views.
2170 AlignmentI[] alview = this.getViewAlignments();
2171 for (int i = 0; i < sequences.length; i++)
2173 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2178 for (int avnum = 0; avnum < alview.length; avnum++)
2180 if (alview[avnum] != alignment)
2182 // duplicate in a view other than the one with input focus
2183 int avwidth = alview[avnum].getWidth() + 1;
2184 // this relies on sann being preserved after we
2185 // modify the sequence's annotation array for each duplication
2186 for (int a = 0; a < sann.length; a++)
2188 AlignmentAnnotation newann = new AlignmentAnnotation(
2190 sequences[i].addAlignmentAnnotation(newann);
2191 newann.padAnnotation(avwidth);
2192 alview[avnum].addAnnotation(newann); // annotation was
2193 // duplicated earlier
2194 // TODO JAL-1145 graphGroups are not updated for sequence
2195 // annotation added to several views. This may cause
2197 alview[avnum].setAnnotationIndex(newann, a);
2202 buildSortByAnnotationScoresMenu();
2204 viewport.firePropertyChange("alignment", null,
2205 alignment.getSequences());
2206 if (alignPanels != null)
2208 for (AlignmentPanel ap : alignPanels)
2210 ap.validateAnnotationDimensions(false);
2215 alignPanel.validateAnnotationDimensions(false);
2221 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2223 String newtitle = new String("Copied sequences");
2225 if (Desktop.jalviewClipboard != null
2226 && Desktop.jalviewClipboard[2] != null)
2228 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2229 af.viewport.setHiddenColumns(hc);
2232 // >>>This is a fix for the moment, until a better solution is
2234 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2235 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2236 .getFeatureRenderer());
2238 // TODO: maintain provenance of an alignment, rather than just make the
2239 // title a concatenation of operations.
2242 if (title.startsWith("Copied sequences"))
2248 newtitle = newtitle.concat("- from " + title);
2253 newtitle = new String("Pasted sequences");
2256 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2261 } catch (Exception ex)
2263 ex.printStackTrace();
2264 System.out.println("Exception whilst pasting: " + ex);
2265 // could be anything being pasted in here
2271 protected void expand_newalign(ActionEvent e)
2275 AlignmentI alignment = AlignmentUtils
2276 .expandContext(getViewport().getAlignment(), -1);
2277 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2279 String newtitle = new String("Flanking alignment");
2281 if (Desktop.jalviewClipboard != null
2282 && Desktop.jalviewClipboard[2] != null)
2284 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2285 af.viewport.setHiddenColumns(hc);
2288 // >>>This is a fix for the moment, until a better solution is
2290 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2291 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2292 .getFeatureRenderer());
2294 // TODO: maintain provenance of an alignment, rather than just make the
2295 // title a concatenation of operations.
2297 if (title.startsWith("Copied sequences"))
2303 newtitle = newtitle.concat("- from " + title);
2307 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2309 } catch (Exception ex)
2311 ex.printStackTrace();
2312 System.out.println("Exception whilst pasting: " + ex);
2313 // could be anything being pasted in here
2314 } catch (OutOfMemoryError oom)
2316 new OOMWarning("Viewing flanking region of alignment", oom);
2327 protected void cut_actionPerformed(ActionEvent e)
2329 copy_actionPerformed(null);
2330 delete_actionPerformed(null);
2340 protected void delete_actionPerformed(ActionEvent evt)
2343 SequenceGroup sg = viewport.getSelectionGroup();
2350 * If the cut affects all sequences, warn, remove highlighted columns
2352 if (sg.getSize() == viewport.getAlignment().getHeight())
2354 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2355 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2356 if (isEntireAlignWidth)
2358 int confirm = JvOptionPane.showConfirmDialog(this,
2359 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2360 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2361 JvOptionPane.OK_CANCEL_OPTION);
2363 if (confirm == JvOptionPane.CANCEL_OPTION
2364 || confirm == JvOptionPane.CLOSED_OPTION)
2369 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2370 sg.getEndRes() + 1);
2372 SequenceI[] cut = sg.getSequences()
2373 .toArray(new SequenceI[sg.getSize()]);
2375 addHistoryItem(new EditCommand(
2376 MessageManager.getString("label.cut_sequences"), Action.CUT,
2377 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2378 viewport.getAlignment()));
2380 viewport.setSelectionGroup(null);
2381 viewport.sendSelection();
2382 viewport.getAlignment().deleteGroup(sg);
2384 viewport.firePropertyChange("alignment", null,
2385 viewport.getAlignment().getSequences());
2386 if (viewport.getAlignment().getHeight() < 1)
2390 this.setClosed(true);
2391 } catch (Exception ex)
2404 protected void deleteGroups_actionPerformed(ActionEvent e)
2406 if (avc.deleteGroups())
2408 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2409 alignPanel.updateAnnotation();
2410 alignPanel.paintAlignment(true, true);
2421 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2423 SequenceGroup sg = new SequenceGroup(
2424 viewport.getAlignment().getSequences());
2426 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2427 viewport.setSelectionGroup(sg);
2428 viewport.isSelectionGroupChanged(true);
2429 viewport.sendSelection();
2430 // JAL-2034 - should delegate to
2431 // alignPanel to decide if overview needs
2433 alignPanel.paintAlignment(false, false);
2434 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2444 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2446 if (viewport.cursorMode)
2448 alignPanel.getSeqPanel().keyboardNo1 = null;
2449 alignPanel.getSeqPanel().keyboardNo2 = null;
2451 viewport.setSelectionGroup(null);
2452 viewport.getColumnSelection().clear();
2453 viewport.setSelectionGroup(null);
2454 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2455 // JAL-2034 - should delegate to
2456 // alignPanel to decide if overview needs
2458 alignPanel.paintAlignment(false, false);
2459 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2460 viewport.sendSelection();
2470 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2472 SequenceGroup sg = viewport.getSelectionGroup();
2476 selectAllSequenceMenuItem_actionPerformed(null);
2481 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2483 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2485 // JAL-2034 - should delegate to
2486 // alignPanel to decide if overview needs
2489 alignPanel.paintAlignment(true, false);
2490 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2491 viewport.sendSelection();
2495 public void invertColSel_actionPerformed(ActionEvent e)
2497 viewport.invertColumnSelection();
2498 alignPanel.paintAlignment(true, false);
2499 viewport.sendSelection();
2509 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2511 trimAlignment(true);
2521 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2523 trimAlignment(false);
2526 void trimAlignment(boolean trimLeft)
2528 ColumnSelection colSel = viewport.getColumnSelection();
2531 if (!colSel.isEmpty())
2535 column = colSel.getMin();
2539 column = colSel.getMax();
2543 if (viewport.getSelectionGroup() != null)
2545 seqs = viewport.getSelectionGroup()
2546 .getSequencesAsArray(viewport.getHiddenRepSequences());
2550 seqs = viewport.getAlignment().getSequencesArray();
2553 TrimRegionCommand trimRegion;
2556 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2557 column, viewport.getAlignment());
2558 viewport.getRanges().setStartRes(0);
2562 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2563 column, viewport.getAlignment());
2566 statusBar.setText(MessageManager
2567 .formatMessage("label.removed_columns", new String[]
2568 { Integer.valueOf(trimRegion.getSize()).toString() }));
2570 addHistoryItem(trimRegion);
2572 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2574 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2575 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2577 viewport.getAlignment().deleteGroup(sg);
2581 viewport.firePropertyChange("alignment", null,
2582 viewport.getAlignment().getSequences());
2593 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2595 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2598 if (viewport.getSelectionGroup() != null)
2600 seqs = viewport.getSelectionGroup()
2601 .getSequencesAsArray(viewport.getHiddenRepSequences());
2602 start = viewport.getSelectionGroup().getStartRes();
2603 end = viewport.getSelectionGroup().getEndRes();
2607 seqs = viewport.getAlignment().getSequencesArray();
2610 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2611 "Remove Gapped Columns", seqs, start, end,
2612 viewport.getAlignment());
2614 addHistoryItem(removeGapCols);
2616 statusBar.setText(MessageManager
2617 .formatMessage("label.removed_empty_columns", new Object[]
2618 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2620 // This is to maintain viewport position on first residue
2621 // of first sequence
2622 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2623 ViewportRanges ranges = viewport.getRanges();
2624 int startRes = seq.findPosition(ranges.getStartRes());
2625 // ShiftList shifts;
2626 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2627 // edit.alColumnChanges=shifts.getInverse();
2628 // if (viewport.hasHiddenColumns)
2629 // viewport.getColumnSelection().compensateForEdits(shifts);
2630 ranges.setStartRes(seq.findIndex(startRes) - 1);
2631 viewport.firePropertyChange("alignment", null,
2632 viewport.getAlignment().getSequences());
2643 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2645 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2648 if (viewport.getSelectionGroup() != null)
2650 seqs = viewport.getSelectionGroup()
2651 .getSequencesAsArray(viewport.getHiddenRepSequences());
2652 start = viewport.getSelectionGroup().getStartRes();
2653 end = viewport.getSelectionGroup().getEndRes();
2657 seqs = viewport.getAlignment().getSequencesArray();
2660 // This is to maintain viewport position on first residue
2661 // of first sequence
2662 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2663 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2665 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2666 viewport.getAlignment()));
2668 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2670 viewport.firePropertyChange("alignment", null,
2671 viewport.getAlignment().getSequences());
2682 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2684 viewport.setPadGaps(padGapsMenuitem.isSelected());
2685 viewport.firePropertyChange("alignment", null,
2686 viewport.getAlignment().getSequences());
2696 public void findMenuItem_actionPerformed(ActionEvent e)
2702 * Create a new view of the current alignment.
2705 public void newView_actionPerformed(ActionEvent e)
2707 newView(null, true);
2711 * Creates and shows a new view of the current alignment.
2714 * title of newly created view; if null, one will be generated
2715 * @param copyAnnotation
2716 * if true then duplicate all annnotation, groups and settings
2717 * @return new alignment panel, already displayed.
2719 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2722 * Create a new AlignmentPanel (with its own, new Viewport)
2724 AlignmentPanel newap = new jalview.project.Jalview2XML()
2725 .copyAlignPanel(alignPanel);
2726 if (!copyAnnotation)
2729 * remove all groups and annotation except for the automatic stuff
2731 newap.av.getAlignment().deleteAllGroups();
2732 newap.av.getAlignment().deleteAllAnnotations(false);
2735 newap.av.setGatherViewsHere(false);
2737 if (viewport.getViewName() == null)
2739 viewport.setViewName(MessageManager
2740 .getString("label.view_name_original"));
2744 * Views share the same edits undo and redo stacks
2746 newap.av.setHistoryList(viewport.getHistoryList());
2747 newap.av.setRedoList(viewport.getRedoList());
2750 * copy any visualisation settings that are not saved in the project
2752 newap.av.setColourAppliesToAllGroups(
2753 viewport.getColourAppliesToAllGroups());
2756 * Views share the same mappings; need to deregister any new mappings
2757 * created by copyAlignPanel, and register the new reference to the shared
2760 newap.av.replaceMappings(viewport.getAlignment());
2763 * start up cDNA consensus (if applicable) now mappings are in place
2765 if (newap.av.initComplementConsensus())
2767 newap.refresh(true); // adjust layout of annotations
2770 newap.av.setViewName(getNewViewName(viewTitle));
2772 addAlignmentPanel(newap, true);
2773 newap.alignmentChanged();
2775 if (alignPanels.size() == 2)
2777 viewport.setGatherViewsHere(true);
2779 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2784 * Make a new name for the view, ensuring it is unique within the current
2785 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2786 * these now use viewId. Unique view names are still desirable for usability.)
2791 protected String getNewViewName(String viewTitle)
2793 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2794 boolean addFirstIndex = false;
2795 if (viewTitle == null || viewTitle.trim().length() == 0)
2797 viewTitle = MessageManager.getString("action.view");
2798 addFirstIndex = true;
2802 index = 1;// we count from 1 if given a specific name
2804 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2806 List<Component> comps = PaintRefresher.components
2807 .get(viewport.getSequenceSetId());
2809 List<String> existingNames = getExistingViewNames(comps);
2811 while (existingNames.contains(newViewName))
2813 newViewName = viewTitle + " " + (++index);
2819 * Returns a list of distinct view names found in the given list of
2820 * components. View names are held on the viewport of an AlignmentPanel.
2825 protected List<String> getExistingViewNames(List<Component> comps)
2827 List<String> existingNames = new ArrayList<>();
2828 for (Component comp : comps)
2830 if (comp instanceof AlignmentPanel)
2832 AlignmentPanel ap = (AlignmentPanel) comp;
2833 if (!existingNames.contains(ap.av.getViewName()))
2835 existingNames.add(ap.av.getViewName());
2839 return existingNames;
2843 * Explode tabbed views into separate windows.
2846 public void expandViews_actionPerformed(ActionEvent e)
2848 Desktop.explodeViews(this);
2852 * Gather views in separate windows back into a tabbed presentation.
2855 public void gatherViews_actionPerformed(ActionEvent e)
2857 Desktop.instance.gatherViews(this);
2867 public void font_actionPerformed(ActionEvent e)
2869 new FontChooser(alignPanel);
2879 protected void seqLimit_actionPerformed(ActionEvent e)
2881 viewport.setShowJVSuffix(seqLimits.isSelected());
2883 alignPanel.getIdPanel().getIdCanvas()
2884 .setPreferredSize(alignPanel.calculateIdWidth());
2885 alignPanel.paintAlignment(true, false);
2889 public void idRightAlign_actionPerformed(ActionEvent e)
2891 viewport.setRightAlignIds(idRightAlign.isSelected());
2892 alignPanel.paintAlignment(false, false);
2896 public void centreColumnLabels_actionPerformed(ActionEvent e)
2898 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2899 alignPanel.paintAlignment(false, false);
2905 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2908 protected void followHighlight_actionPerformed()
2911 * Set the 'follow' flag on the Viewport (and scroll to position if now
2914 final boolean state = this.followHighlightMenuItem.getState();
2915 viewport.setFollowHighlight(state);
2918 alignPanel.scrollToPosition(viewport.getSearchResults());
2929 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2931 viewport.setColourText(colourTextMenuItem.isSelected());
2932 alignPanel.paintAlignment(false, false);
2942 public void wrapMenuItem_actionPerformed(ActionEvent e)
2944 scaleAbove.setVisible(wrapMenuItem.isSelected());
2945 scaleLeft.setVisible(wrapMenuItem.isSelected());
2946 scaleRight.setVisible(wrapMenuItem.isSelected());
2947 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2948 alignPanel.updateLayout();
2952 public void showAllSeqs_actionPerformed(ActionEvent e)
2954 viewport.showAllHiddenSeqs();
2958 public void showAllColumns_actionPerformed(ActionEvent e)
2960 viewport.showAllHiddenColumns();
2961 alignPanel.paintAlignment(true, true);
2962 viewport.sendSelection();
2966 public void hideSelSequences_actionPerformed(ActionEvent e)
2968 viewport.hideAllSelectedSeqs();
2972 * called by key handler and the hide all/show all menu items
2977 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2980 boolean hide = false;
2981 SequenceGroup sg = viewport.getSelectionGroup();
2982 if (!toggleSeqs && !toggleCols)
2984 // Hide everything by the current selection - this is a hack - we do the
2985 // invert and then hide
2986 // first check that there will be visible columns after the invert.
2987 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2988 && sg.getStartRes() <= sg.getEndRes()))
2990 // now invert the sequence set, if required - empty selection implies
2991 // that no hiding is required.
2994 invertSequenceMenuItem_actionPerformed(null);
2995 sg = viewport.getSelectionGroup();
2999 viewport.expandColSelection(sg, true);
3000 // finally invert the column selection and get the new sequence
3002 invertColSel_actionPerformed(null);
3009 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3011 hideSelSequences_actionPerformed(null);
3014 else if (!(toggleCols && viewport.hasSelectedColumns()))
3016 showAllSeqs_actionPerformed(null);
3022 if (viewport.hasSelectedColumns())
3024 hideSelColumns_actionPerformed(null);
3027 viewport.setSelectionGroup(sg);
3032 showAllColumns_actionPerformed(null);
3041 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3042 * event.ActionEvent)
3045 public void hideAllButSelection_actionPerformed(ActionEvent e)
3047 toggleHiddenRegions(false, false);
3048 viewport.sendSelection();
3055 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3059 public void hideAllSelection_actionPerformed(ActionEvent e)
3061 SequenceGroup sg = viewport.getSelectionGroup();
3062 viewport.expandColSelection(sg, false);
3063 viewport.hideAllSelectedSeqs();
3064 viewport.hideSelectedColumns();
3065 alignPanel.updateLayout();
3066 alignPanel.paintAlignment(true, true);
3067 viewport.sendSelection();
3074 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3078 public void showAllhidden_actionPerformed(ActionEvent e)
3080 viewport.showAllHiddenColumns();
3081 viewport.showAllHiddenSeqs();
3082 alignPanel.paintAlignment(true, true);
3083 viewport.sendSelection();
3087 public void hideSelColumns_actionPerformed(ActionEvent e)
3089 viewport.hideSelectedColumns();
3090 alignPanel.updateLayout();
3091 alignPanel.paintAlignment(true, true);
3092 viewport.sendSelection();
3096 public void hiddenMarkers_actionPerformed(ActionEvent e)
3098 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3109 protected void scaleAbove_actionPerformed(ActionEvent e)
3111 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3112 alignPanel.updateLayout();
3113 alignPanel.paintAlignment(true, false);
3123 protected void scaleLeft_actionPerformed(ActionEvent e)
3125 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3126 alignPanel.updateLayout();
3127 alignPanel.paintAlignment(true, false);
3137 protected void scaleRight_actionPerformed(ActionEvent e)
3139 viewport.setScaleRightWrapped(scaleRight.isSelected());
3140 alignPanel.updateLayout();
3141 alignPanel.paintAlignment(true, false);
3151 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3153 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3154 alignPanel.paintAlignment(false, false);
3164 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3166 viewport.setShowText(viewTextMenuItem.isSelected());
3167 alignPanel.paintAlignment(false, false);
3177 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3179 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3180 alignPanel.paintAlignment(false, false);
3183 public FeatureSettings featureSettings;
3186 public FeatureSettingsControllerI getFeatureSettingsUI()
3188 return featureSettings;
3192 public void featureSettings_actionPerformed(ActionEvent e)
3194 showFeatureSettingsUI();
3198 public FeatureSettingsControllerI showFeatureSettingsUI()
3200 if (featureSettings != null)
3202 featureSettings.closeOldSettings();
3203 featureSettings = null;
3205 if (!showSeqFeatures.isSelected())
3207 // make sure features are actually displayed
3208 showSeqFeatures.setSelected(true);
3209 showSeqFeatures_actionPerformed(null);
3211 featureSettings = new FeatureSettings(this);
3212 return featureSettings;
3216 * Set or clear 'Show Sequence Features'
3222 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3224 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3225 alignPanel.paintAlignment(true, true);
3229 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3230 * the annotations panel as a whole.
3232 * The options to show/hide all annotations should be enabled when the panel
3233 * is shown, and disabled when the panel is hidden.
3238 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3240 final boolean setVisible = annotationPanelMenuItem.isSelected();
3241 viewport.setShowAnnotation(setVisible);
3242 this.showAllSeqAnnotations.setEnabled(setVisible);
3243 this.hideAllSeqAnnotations.setEnabled(setVisible);
3244 this.showAllAlAnnotations.setEnabled(setVisible);
3245 this.hideAllAlAnnotations.setEnabled(setVisible);
3246 alignPanel.updateLayout();
3250 public void alignmentProperties()
3252 JEditorPane editPane = new JEditorPane("text/html", "");
3253 editPane.setEditable(false);
3254 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3257 MessageManager.formatMessage("label.html_content", new Object[]
3258 { contents.toString() }));
3259 JInternalFrame frame = new JInternalFrame();
3260 frame.getContentPane().add(new JScrollPane(editPane));
3262 Desktop.addInternalFrame(frame, MessageManager
3263 .formatMessage("label.alignment_properties", new Object[]
3264 { getTitle() }), 500, 400);
3274 public void overviewMenuItem_actionPerformed(ActionEvent e)
3276 if (alignPanel.overviewPanel != null)
3281 JInternalFrame frame = new JInternalFrame();
3282 final OverviewPanel overview = new OverviewPanel(alignPanel);
3283 frame.setContentPane(overview);
3284 Desktop.addInternalFrame(frame, MessageManager
3285 .formatMessage("label.overview_params", new Object[]
3286 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3289 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3290 frame.addInternalFrameListener(
3291 new javax.swing.event.InternalFrameAdapter()
3294 public void internalFrameClosed(
3295 javax.swing.event.InternalFrameEvent evt)
3298 alignPanel.setOverviewPanel(null);
3301 if (getKeyListeners().length > 0)
3303 frame.addKeyListener(getKeyListeners()[0]);
3306 alignPanel.setOverviewPanel(overview);
3310 public void textColour_actionPerformed()
3312 new TextColourChooser().chooseColour(alignPanel, null);
3316 * public void covariationColour_actionPerformed() {
3318 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3322 public void annotationColour_actionPerformed()
3324 new AnnotationColourChooser(viewport, alignPanel);
3328 public void annotationColumn_actionPerformed(ActionEvent e)
3330 new AnnotationColumnChooser(viewport, alignPanel);
3334 * Action on the user checking or unchecking the option to apply the selected
3335 * colour scheme to all groups. If unchecked, groups may have their own
3336 * independent colour schemes.
3341 public void applyToAllGroups_actionPerformed(boolean selected)
3343 viewport.setColourAppliesToAllGroups(selected);
3347 * Action on user selecting a colour from the colour menu
3350 * the name (not the menu item label!) of the colour scheme
3353 public void changeColour_actionPerformed(String name)
3356 * 'User Defined' opens a panel to configure or load a
3357 * user-defined colour scheme
3359 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3361 new UserDefinedColours(alignPanel);
3366 * otherwise set the chosen colour scheme (or null for 'None')
3368 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3370 viewport.getAlignment(), viewport.getHiddenRepSequences());
3375 * Actions on setting or changing the alignment colour scheme
3380 public void changeColour(ColourSchemeI cs)
3382 // TODO: pull up to controller method
3383 ColourMenuHelper.setColourSelected(colourMenu, cs);
3385 viewport.setGlobalColourScheme(cs);
3387 alignPanel.paintAlignment(true, true);
3391 * Show the PID threshold slider panel
3394 protected void modifyPID_actionPerformed()
3396 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3397 alignPanel.getViewName());
3398 SliderPanel.showPIDSlider();
3402 * Show the Conservation slider panel
3405 protected void modifyConservation_actionPerformed()
3407 SliderPanel.setConservationSlider(alignPanel,
3408 viewport.getResidueShading(), alignPanel.getViewName());
3409 SliderPanel.showConservationSlider();
3413 * Action on selecting or deselecting (Colour) By Conservation
3416 public void conservationMenuItem_actionPerformed(boolean selected)
3418 modifyConservation.setEnabled(selected);
3419 viewport.setConservationSelected(selected);
3420 viewport.getResidueShading().setConservationApplied(selected);
3422 changeColour(viewport.getGlobalColourScheme());
3425 modifyConservation_actionPerformed();
3429 SliderPanel.hideConservationSlider();
3434 * Action on selecting or deselecting (Colour) Above PID Threshold
3437 public void abovePIDThreshold_actionPerformed(boolean selected)
3439 modifyPID.setEnabled(selected);
3440 viewport.setAbovePIDThreshold(selected);
3443 viewport.getResidueShading().setThreshold(0,
3444 viewport.isIgnoreGapsConsensus());
3447 changeColour(viewport.getGlobalColourScheme());
3450 modifyPID_actionPerformed();
3454 SliderPanel.hidePIDSlider();
3465 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3467 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3468 AlignmentSorter.sortByPID(viewport.getAlignment(),
3469 viewport.getAlignment().getSequenceAt(0));
3470 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3471 viewport.getAlignment()));
3472 alignPanel.paintAlignment(true, false);
3482 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3484 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3485 AlignmentSorter.sortByID(viewport.getAlignment());
3487 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3488 alignPanel.paintAlignment(true, false);
3498 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3500 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3501 AlignmentSorter.sortByLength(viewport.getAlignment());
3502 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3503 viewport.getAlignment()));
3504 alignPanel.paintAlignment(true, false);
3514 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3516 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3517 AlignmentSorter.sortByGroup(viewport.getAlignment());
3518 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3519 viewport.getAlignment()));
3521 alignPanel.paintAlignment(true, false);
3531 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3533 new RedundancyPanel(alignPanel, this);
3543 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3545 if ((viewport.getSelectionGroup() == null)
3546 || (viewport.getSelectionGroup().getSize() < 2))
3548 JvOptionPane.showInternalMessageDialog(this,
3549 MessageManager.getString(
3550 "label.you_must_select_least_two_sequences"),
3551 MessageManager.getString("label.invalid_selection"),
3552 JvOptionPane.WARNING_MESSAGE);
3556 JInternalFrame frame = new JInternalFrame();
3557 frame.setContentPane(new PairwiseAlignPanel(viewport));
3558 Desktop.addInternalFrame(frame,
3559 MessageManager.getString("action.pairwise_alignment"), 600,
3565 public void autoCalculate_actionPerformed(ActionEvent e)
3567 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3568 if (viewport.autoCalculateConsensus)
3570 viewport.firePropertyChange("alignment", null,
3571 viewport.getAlignment().getSequences());
3576 public void sortByTreeOption_actionPerformed(ActionEvent e)
3578 viewport.sortByTree = sortByTree.isSelected();
3582 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3584 viewport.followSelection = listenToViewSelections.isSelected();
3588 * Constructs a tree panel and adds it to the desktop
3591 * tree type (NJ or AV)
3593 * name of score model used to compute the tree
3595 * parameters for the distance or similarity calculation
3597 void newTreePanel(String type, String modelName,
3598 SimilarityParamsI options)
3600 String frameTitle = "";
3603 boolean onSelection = false;
3604 if (viewport.getSelectionGroup() != null
3605 && viewport.getSelectionGroup().getSize() > 0)
3607 SequenceGroup sg = viewport.getSelectionGroup();
3609 /* Decide if the selection is a column region */
3610 for (SequenceI _s : sg.getSequences())
3612 if (_s.getLength() < sg.getEndRes())
3614 JvOptionPane.showMessageDialog(Desktop.desktop,
3615 MessageManager.getString(
3616 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3617 MessageManager.getString(
3618 "label.sequences_selection_not_aligned"),
3619 JvOptionPane.WARNING_MESSAGE);
3628 if (viewport.getAlignment().getHeight() < 2)
3634 tp = new TreePanel(alignPanel, type, modelName, options);
3635 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3637 frameTitle += " from ";
3639 if (viewport.getViewName() != null)
3641 frameTitle += viewport.getViewName() + " of ";
3644 frameTitle += this.title;
3646 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3657 public void addSortByOrderMenuItem(String title,
3658 final AlignmentOrder order)
3660 final JMenuItem item = new JMenuItem(MessageManager
3661 .formatMessage("action.by_title_param", new Object[]
3664 item.addActionListener(new java.awt.event.ActionListener()
3667 public void actionPerformed(ActionEvent e)
3669 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3671 // TODO: JBPNote - have to map order entries to curent SequenceI
3673 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3675 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3676 viewport.getAlignment()));
3678 alignPanel.paintAlignment(true, false);
3684 * Add a new sort by annotation score menu item
3687 * the menu to add the option to
3689 * the label used to retrieve scores for each sequence on the
3692 public void addSortByAnnotScoreMenuItem(JMenu sort,
3693 final String scoreLabel)
3695 final JMenuItem item = new JMenuItem(scoreLabel);
3697 item.addActionListener(new java.awt.event.ActionListener()
3700 public void actionPerformed(ActionEvent e)
3702 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3703 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3704 viewport.getAlignment());// ,viewport.getSelectionGroup());
3705 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3706 viewport.getAlignment()));
3707 alignPanel.paintAlignment(true, false);
3713 * last hash for alignment's annotation array - used to minimise cost of
3716 protected int _annotationScoreVectorHash;
3719 * search the alignment and rebuild the sort by annotation score submenu the
3720 * last alignment annotation vector hash is stored to minimize cost of
3721 * rebuilding in subsequence calls.
3725 public void buildSortByAnnotationScoresMenu()
3727 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3732 if (viewport.getAlignment().getAlignmentAnnotation()
3733 .hashCode() != _annotationScoreVectorHash)
3735 sortByAnnotScore.removeAll();
3736 // almost certainly a quicker way to do this - but we keep it simple
3737 Hashtable scoreSorts = new Hashtable();
3738 AlignmentAnnotation aann[];
3739 for (SequenceI sqa : viewport.getAlignment().getSequences())
3741 aann = sqa.getAnnotation();
3742 for (int i = 0; aann != null && i < aann.length; i++)
3744 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3746 scoreSorts.put(aann[i].label, aann[i].label);
3750 Enumeration labels = scoreSorts.keys();
3751 while (labels.hasMoreElements())
3753 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3754 (String) labels.nextElement());
3756 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3759 _annotationScoreVectorHash = viewport.getAlignment()
3760 .getAlignmentAnnotation().hashCode();
3765 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3766 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3767 * call. Listeners are added to remove the menu item when the treePanel is
3768 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3772 public void buildTreeSortMenu()
3774 sortByTreeMenu.removeAll();
3776 List<Component> comps = PaintRefresher.components
3777 .get(viewport.getSequenceSetId());
3778 List<TreePanel> treePanels = new ArrayList<>();
3779 for (Component comp : comps)
3781 if (comp instanceof TreePanel)
3783 treePanels.add((TreePanel) comp);
3787 if (treePanels.size() < 1)
3789 sortByTreeMenu.setVisible(false);
3793 sortByTreeMenu.setVisible(true);
3795 for (final TreePanel tp : treePanels)
3797 final JMenuItem item = new JMenuItem(tp.getTitle());
3798 item.addActionListener(new java.awt.event.ActionListener()
3801 public void actionPerformed(ActionEvent e)
3803 tp.sortByTree_actionPerformed();
3804 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3809 sortByTreeMenu.add(item);
3813 public boolean sortBy(AlignmentOrder alorder, String undoname)
3815 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3816 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3817 if (undoname != null)
3819 addHistoryItem(new OrderCommand(undoname, oldOrder,
3820 viewport.getAlignment()));
3822 alignPanel.paintAlignment(true, false);
3827 * Work out whether the whole set of sequences or just the selected set will
3828 * be submitted for multiple alignment.
3831 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3833 // Now, check we have enough sequences
3834 AlignmentView msa = null;
3836 if ((viewport.getSelectionGroup() != null)
3837 && (viewport.getSelectionGroup().getSize() > 1))
3839 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3840 // some common interface!
3842 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3843 * SequenceI[sz = seqs.getSize(false)];
3845 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3846 * seqs.getSequenceAt(i); }
3848 msa = viewport.getAlignmentView(true);
3850 else if (viewport.getSelectionGroup() != null
3851 && viewport.getSelectionGroup().getSize() == 1)
3853 int option = JvOptionPane.showConfirmDialog(this,
3854 MessageManager.getString("warn.oneseq_msainput_selection"),
3855 MessageManager.getString("label.invalid_selection"),
3856 JvOptionPane.OK_CANCEL_OPTION);
3857 if (option == JvOptionPane.OK_OPTION)
3859 msa = viewport.getAlignmentView(false);
3864 msa = viewport.getAlignmentView(false);
3870 * Decides what is submitted to a secondary structure prediction service: the
3871 * first sequence in the alignment, or in the current selection, or, if the
3872 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3873 * region or the whole alignment. (where the first sequence in the set is the
3874 * one that the prediction will be for).
3876 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3878 AlignmentView seqs = null;
3880 if ((viewport.getSelectionGroup() != null)
3881 && (viewport.getSelectionGroup().getSize() > 0))
3883 seqs = viewport.getAlignmentView(true);
3887 seqs = viewport.getAlignmentView(false);
3889 // limit sequences - JBPNote in future - could spawn multiple prediction
3891 // TODO: viewport.getAlignment().isAligned is a global state - the local
3892 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3893 if (!viewport.getAlignment().isAligned(false))
3895 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3896 // TODO: if seqs.getSequences().length>1 then should really have warned
3910 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3912 // Pick the tree file
3913 JalviewFileChooser chooser = new JalviewFileChooser(
3914 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3915 chooser.setFileView(new JalviewFileView());
3916 chooser.setDialogTitle(
3917 MessageManager.getString("label.select_newick_like_tree_file"));
3918 chooser.setToolTipText(
3919 MessageManager.getString("label.load_tree_file"));
3921 int value = chooser.showOpenDialog(null);
3923 if (value == JalviewFileChooser.APPROVE_OPTION)
3925 String filePath = chooser.getSelectedFile().getPath();
3926 Cache.setProperty("LAST_DIRECTORY", filePath);
3927 NewickFile fin = null;
3930 fin = new NewickFile(filePath, DataSourceType.FILE);
3931 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3932 } catch (Exception ex)
3934 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3935 MessageManager.getString("label.problem_reading_tree_file"),
3936 JvOptionPane.WARNING_MESSAGE);
3937 ex.printStackTrace();
3939 if (fin != null && fin.hasWarningMessage())
3941 JvOptionPane.showMessageDialog(Desktop.desktop,
3942 fin.getWarningMessage(),
3944 .getString("label.possible_problem_with_tree_file"),
3945 JvOptionPane.WARNING_MESSAGE);
3950 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3952 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3955 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3956 int h, int x, int y)
3958 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3962 * Add a treeviewer for the tree extracted from a Newick file object to the
3963 * current alignment view
3970 * Associated alignment input data (or null)
3979 * @return TreePanel handle
3981 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3982 AlignmentView input, int w, int h, int x, int y)
3984 TreePanel tp = null;
3990 if (nf.getTree() != null)
3992 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3998 tp.setLocation(x, y);
4001 Desktop.addInternalFrame(tp, treeTitle, w, h);
4003 } catch (Exception ex)
4005 ex.printStackTrace();
4011 private boolean buildingMenu = false;
4014 * Generates menu items and listener event actions for web service clients
4017 public void BuildWebServiceMenu()
4019 while (buildingMenu)
4023 System.err.println("Waiting for building menu to finish.");
4025 } catch (Exception e)
4029 final AlignFrame me = this;
4030 buildingMenu = true;
4031 new Thread(new Runnable()
4036 final List<JMenuItem> legacyItems = new ArrayList<>();
4039 // System.err.println("Building ws menu again "
4040 // + Thread.currentThread());
4041 // TODO: add support for context dependent disabling of services based
4043 // alignment and current selection
4044 // TODO: add additional serviceHandle parameter to specify abstract
4046 // class independently of AbstractName
4047 // TODO: add in rediscovery GUI function to restart discoverer
4048 // TODO: group services by location as well as function and/or
4050 // object broker mechanism.
4051 final Vector<JMenu> wsmenu = new Vector<>();
4052 final IProgressIndicator af = me;
4055 * do not i18n these strings - they are hard-coded in class
4056 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4057 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4059 final JMenu msawsmenu = new JMenu("Alignment");
4060 final JMenu secstrmenu = new JMenu(
4061 "Secondary Structure Prediction");
4062 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4063 final JMenu analymenu = new JMenu("Analysis");
4064 final JMenu dismenu = new JMenu("Protein Disorder");
4065 // JAL-940 - only show secondary structure prediction services from
4066 // the legacy server
4067 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4069 Discoverer.services != null && (Discoverer.services.size() > 0))
4071 // TODO: refactor to allow list of AbstractName/Handler bindings to
4073 // stored or retrieved from elsewhere
4074 // No MSAWS used any more:
4075 // Vector msaws = null; // (Vector)
4076 // Discoverer.services.get("MsaWS");
4077 Vector secstrpr = (Vector) Discoverer.services
4079 if (secstrpr != null)
4081 // Add any secondary structure prediction services
4082 for (int i = 0, j = secstrpr.size(); i < j; i++)
4084 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4086 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4087 .getServiceClient(sh);
4088 int p = secstrmenu.getItemCount();
4089 impl.attachWSMenuEntry(secstrmenu, me);
4090 int q = secstrmenu.getItemCount();
4091 for (int litm = p; litm < q; litm++)
4093 legacyItems.add(secstrmenu.getItem(litm));
4099 // Add all submenus in the order they should appear on the web
4101 wsmenu.add(msawsmenu);
4102 wsmenu.add(secstrmenu);
4103 wsmenu.add(dismenu);
4104 wsmenu.add(analymenu);
4105 // No search services yet
4106 // wsmenu.add(seqsrchmenu);
4108 javax.swing.SwingUtilities.invokeLater(new Runnable()
4115 webService.removeAll();
4116 // first, add discovered services onto the webservices menu
4117 if (wsmenu.size() > 0)
4119 for (int i = 0, j = wsmenu.size(); i < j; i++)
4121 webService.add(wsmenu.get(i));
4126 webService.add(me.webServiceNoServices);
4128 // TODO: move into separate menu builder class.
4129 boolean new_sspred = false;
4130 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4132 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4133 if (jws2servs != null)
4135 if (jws2servs.hasServices())
4137 jws2servs.attachWSMenuEntry(webService, me);
4138 for (Jws2Instance sv : jws2servs.getServices())
4140 if (sv.description.toLowerCase().contains("jpred"))
4142 for (JMenuItem jmi : legacyItems)
4144 jmi.setVisible(false);
4150 if (jws2servs.isRunning())
4152 JMenuItem tm = new JMenuItem(
4153 "Still discovering JABA Services");
4154 tm.setEnabled(false);
4159 build_urlServiceMenu(me.webService);
4160 build_fetchdbmenu(webService);
4161 for (JMenu item : wsmenu)
4163 if (item.getItemCount() == 0)
4165 item.setEnabled(false);
4169 item.setEnabled(true);
4172 } catch (Exception e)
4175 "Exception during web service menu building process.",
4180 } catch (Exception e)
4183 buildingMenu = false;
4190 * construct any groupURL type service menu entries.
4194 private void build_urlServiceMenu(JMenu webService)
4196 // TODO: remove this code when 2.7 is released
4197 // DEBUG - alignmentView
4199 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4200 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4202 * @Override public void actionPerformed(ActionEvent e) {
4203 * jalview.datamodel.AlignmentView
4204 * .testSelectionViews(af.viewport.getAlignment(),
4205 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4207 * }); webService.add(testAlView);
4209 // TODO: refactor to RestClient discoverer and merge menu entries for
4210 // rest-style services with other types of analysis/calculation service
4211 // SHmmr test client - still being implemented.
4212 // DEBUG - alignmentView
4214 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4217 client.attachWSMenuEntry(
4218 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4224 * Searches the alignment sequences for xRefs and builds the Show
4225 * Cross-References menu (formerly called Show Products), with database
4226 * sources for which cross-references are found (protein sources for a
4227 * nucleotide alignment and vice versa)
4229 * @return true if Show Cross-references menu should be enabled
4231 public boolean canShowProducts()
4233 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4234 AlignmentI dataset = viewport.getAlignment().getDataset();
4236 showProducts.removeAll();
4237 final boolean dna = viewport.getAlignment().isNucleotide();
4239 if (seqs == null || seqs.length == 0)
4241 // nothing to see here.
4245 boolean showp = false;
4248 List<String> ptypes = new CrossRef(seqs, dataset)
4249 .findXrefSourcesForSequences(dna);
4251 for (final String source : ptypes)
4254 final AlignFrame af = this;
4255 JMenuItem xtype = new JMenuItem(source);
4256 xtype.addActionListener(new ActionListener()
4259 public void actionPerformed(ActionEvent e)
4261 showProductsFor(af.viewport.getSequenceSelection(), dna,
4265 showProducts.add(xtype);
4267 showProducts.setVisible(showp);
4268 showProducts.setEnabled(showp);
4269 } catch (Exception e)
4272 "canShowProducts threw an exception - please report to help@jalview.org",
4280 * Finds and displays cross-references for the selected sequences (protein
4281 * products for nucleotide sequences, dna coding sequences for peptides).
4284 * the sequences to show cross-references for
4286 * true if from a nucleotide alignment (so showing proteins)
4288 * the database to show cross-references for
4290 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4291 final String source)
4293 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4298 * Construct and display a new frame containing the translation of this
4299 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4302 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4304 AlignmentI al = null;
4307 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4309 al = dna.translateCdna(codeTable);
4310 } catch (Exception ex)
4312 jalview.bin.Cache.log.error(
4313 "Exception during translation. Please report this !", ex);
4314 final String msg = MessageManager.getString(
4315 "label.error_when_translating_sequences_submit_bug_report");
4316 final String errorTitle = MessageManager
4317 .getString("label.implementation_error")
4318 + MessageManager.getString("label.translation_failed");
4319 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4320 JvOptionPane.ERROR_MESSAGE);
4323 if (al == null || al.getHeight() == 0)
4325 final String msg = MessageManager.getString(
4326 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4327 final String errorTitle = MessageManager
4328 .getString("label.translation_failed");
4329 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4330 JvOptionPane.WARNING_MESSAGE);
4334 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4335 af.setFileFormat(this.currentFileFormat);
4336 final String newTitle = MessageManager
4337 .formatMessage("label.translation_of_params", new Object[]
4338 { this.getTitle(), codeTable.getId() });
4339 af.setTitle(newTitle);
4340 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4342 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4343 viewport.openSplitFrame(af, new Alignment(seqs));
4347 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4354 * Set the file format
4358 public void setFileFormat(FileFormatI format)
4360 this.currentFileFormat = format;
4364 * Try to load a features file onto the alignment.
4367 * contents or path to retrieve file
4369 * access mode of file (see jalview.io.AlignFile)
4370 * @return true if features file was parsed correctly.
4372 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4374 return avc.parseFeaturesFile(file, sourceType,
4375 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4380 public void refreshFeatureUI(boolean enableIfNecessary)
4382 // note - currently this is only still here rather than in the controller
4383 // because of the featureSettings hard reference that is yet to be
4385 if (enableIfNecessary)
4387 viewport.setShowSequenceFeatures(true);
4388 showSeqFeatures.setSelected(true);
4394 public void dragEnter(DropTargetDragEvent evt)
4399 public void dragExit(DropTargetEvent evt)
4404 public void dragOver(DropTargetDragEvent evt)
4409 public void dropActionChanged(DropTargetDragEvent evt)
4414 public void drop(DropTargetDropEvent evt)
4416 // JAL-1552 - acceptDrop required before getTransferable call for
4417 // Java's Transferable for native dnd
4418 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4419 Transferable t = evt.getTransferable();
4420 final AlignFrame thisaf = this;
4421 final List<String> files = new ArrayList<>();
4422 List<DataSourceType> protocols = new ArrayList<>();
4426 Desktop.transferFromDropTarget(files, protocols, evt, t);
4427 } catch (Exception e)
4429 e.printStackTrace();
4433 new Thread(new Runnable()
4440 // check to see if any of these files have names matching sequences
4443 SequenceIdMatcher idm = new SequenceIdMatcher(
4444 viewport.getAlignment().getSequencesArray());
4446 * Object[] { String,SequenceI}
4448 ArrayList<Object[]> filesmatched = new ArrayList<>();
4449 ArrayList<String> filesnotmatched = new ArrayList<>();
4450 for (int i = 0; i < files.size(); i++)
4452 String file = files.get(i).toString();
4454 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4455 if (protocol == DataSourceType.FILE)
4457 File fl = new File(file);
4458 pdbfn = fl.getName();
4460 else if (protocol == DataSourceType.URL)
4462 URL url = new URL(file);
4463 pdbfn = url.getFile();
4465 if (pdbfn.length() > 0)
4467 // attempt to find a match in the alignment
4468 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4469 int l = 0, c = pdbfn.indexOf(".");
4470 while (mtch == null && c != -1)
4475 } while ((c = pdbfn.indexOf(".", l)) > l);
4478 pdbfn = pdbfn.substring(0, l);
4480 mtch = idm.findAllIdMatches(pdbfn);
4484 FileFormatI type = null;
4487 type = new IdentifyFile().identify(file, protocol);
4488 } catch (Exception ex)
4492 if (type != null && type.isStructureFile())
4494 filesmatched.add(new Object[] { file, protocol, mtch });
4498 // File wasn't named like one of the sequences or wasn't a PDB
4500 filesnotmatched.add(file);
4504 if (filesmatched.size() > 0)
4506 boolean autoAssociate = Cache
4507 .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4510 String msg = MessageManager.formatMessage(
4511 "label.automatically_associate_structure_files_with_sequences_same_name",
4513 { Integer.valueOf(filesmatched.size())
4515 String ttl = MessageManager.getString(
4516 "label.automatically_associate_structure_files_by_name");
4517 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4518 ttl, JvOptionPane.YES_NO_OPTION);
4519 autoAssociate = choice == JvOptionPane.YES_OPTION;
4523 for (Object[] fm : filesmatched)
4525 // try and associate
4526 // TODO: may want to set a standard ID naming formalism for
4527 // associating PDB files which have no IDs.
4528 for (SequenceI toassoc : (SequenceI[]) fm[2])
4530 PDBEntry pe = new AssociatePdbFileWithSeq()
4531 .associatePdbWithSeq((String) fm[0],
4532 (DataSourceType) fm[1], toassoc, false,
4536 System.err.println("Associated file : "
4537 + ((String) fm[0]) + " with "
4538 + toassoc.getDisplayId(true));
4542 // TODO: do we need to update overview ? only if features are
4544 alignPanel.paintAlignment(true, false);
4550 * add declined structures as sequences
4552 for (Object[] o : filesmatched)
4554 filesnotmatched.add((String) o[0]);
4558 if (filesnotmatched.size() > 0)
4560 if (assocfiles > 0 && (Cache.getDefault(
4561 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4562 || JvOptionPane.showConfirmDialog(thisaf,
4563 "<html>" + MessageManager.formatMessage(
4564 "label.ignore_unmatched_dropped_files_info",
4567 filesnotmatched.size())
4570 MessageManager.getString(
4571 "label.ignore_unmatched_dropped_files"),
4572 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4576 for (String fn : filesnotmatched)
4578 loadJalviewDataFile(fn, null, null, null);
4582 } catch (Exception ex)
4584 ex.printStackTrace();
4592 * Attempt to load a "dropped" file or URL string, by testing in turn for
4594 * <li>an Annotation file</li>
4595 * <li>a JNet file</li>
4596 * <li>a features file</li>
4597 * <li>else try to interpret as an alignment file</li>
4601 * either a filename or a URL string.
4603 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4604 FileFormatI format, SequenceI assocSeq)
4608 if (sourceType == null)
4610 sourceType = FormatAdapter.checkProtocol(file);
4612 // if the file isn't identified, or not positively identified as some
4613 // other filetype (PFAM is default unidentified alignment file type) then
4614 // try to parse as annotation.
4615 boolean isAnnotation = (format == null
4616 || FileFormat.Pfam.equals(format))
4617 ? new AnnotationFile().annotateAlignmentView(viewport,
4623 // first see if its a T-COFFEE score file
4624 TCoffeeScoreFile tcf = null;
4627 tcf = new TCoffeeScoreFile(file, sourceType);
4630 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4634 new TCoffeeColourScheme(viewport.getAlignment()));
4635 isAnnotation = true;
4636 statusBar.setText(MessageManager.getString(
4637 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4641 // some problem - if no warning its probable that the ID matching
4642 // process didn't work
4643 JvOptionPane.showMessageDialog(Desktop.desktop,
4644 tcf.getWarningMessage() == null
4645 ? MessageManager.getString(
4646 "label.check_file_matches_sequence_ids_alignment")
4647 : tcf.getWarningMessage(),
4648 MessageManager.getString(
4649 "label.problem_reading_tcoffee_score_file"),
4650 JvOptionPane.WARNING_MESSAGE);
4657 } catch (Exception x)
4660 "Exception when processing data source as T-COFFEE score file",
4666 // try to see if its a JNet 'concise' style annotation file *before*
4668 // try to parse it as a features file
4671 format = new IdentifyFile().identify(file, sourceType);
4673 if (FileFormat.ScoreMatrix == format)
4675 ScoreMatrixFile sm = new ScoreMatrixFile(
4676 new FileParse(file, sourceType));
4678 // todo: i18n this message
4679 statusBar.setText(MessageManager.formatMessage(
4680 "label.successfully_loaded_matrix",
4681 sm.getMatrixName()));
4683 else if (FileFormat.Jnet.equals(format))
4685 JPredFile predictions = new JPredFile(file, sourceType);
4686 new JnetAnnotationMaker();
4687 JnetAnnotationMaker.add_annotation(predictions,
4688 viewport.getAlignment(), 0, false);
4689 viewport.getAlignment().setupJPredAlignment();
4690 isAnnotation = true;
4692 // else if (IdentifyFile.FeaturesFile.equals(format))
4693 else if (FileFormat.Features.equals(format))
4695 if (parseFeaturesFile(file, sourceType))
4697 SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4698 if (splitFrame != null)
4700 splitFrame.repaint();
4704 alignPanel.paintAlignment(true, true);
4710 new FileLoader().LoadFile(viewport, file, sourceType, format);
4717 alignPanel.adjustAnnotationHeight();
4718 viewport.updateSequenceIdColours();
4719 buildSortByAnnotationScoresMenu();
4720 alignPanel.paintAlignment(true, true);
4722 } catch (Exception ex)
4724 ex.printStackTrace();
4725 } catch (OutOfMemoryError oom)
4730 } catch (Exception x)
4735 + (sourceType != null
4736 ? (sourceType == DataSourceType.PASTE
4738 : "using " + sourceType + " from "
4742 ? "(parsing as '" + format + "' file)"
4744 oom, Desktop.desktop);
4749 * Method invoked by the ChangeListener on the tabbed pane, in other words
4750 * when a different tabbed pane is selected by the user or programmatically.
4753 public void tabSelectionChanged(int index)
4757 alignPanel = alignPanels.get(index);
4758 viewport = alignPanel.av;
4759 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4760 setMenusFromViewport(viewport);
4761 if (featureSettings != null && featureSettings.isOpen()
4762 && featureSettings.fr.getViewport() != viewport)
4764 if (viewport.isShowSequenceFeatures())
4766 // refresh the featureSettings to reflect UI change
4767 showFeatureSettingsUI();
4771 // close feature settings for this view.
4772 featureSettings.close();
4779 * 'focus' any colour slider that is open to the selected viewport
4781 if (viewport.getConservationSelected())
4783 SliderPanel.setConservationSlider(alignPanel,
4784 viewport.getResidueShading(), alignPanel.getViewName());
4788 SliderPanel.hideConservationSlider();
4790 if (viewport.getAbovePIDThreshold())
4792 SliderPanel.setPIDSliderSource(alignPanel,
4793 viewport.getResidueShading(), alignPanel.getViewName());
4797 SliderPanel.hidePIDSlider();
4801 * If there is a frame linked to this one in a SplitPane, switch it to the
4802 * same view tab index. No infinite recursion of calls should happen, since
4803 * tabSelectionChanged() should not get invoked on setting the selected
4804 * index to an unchanged value. Guard against setting an invalid index
4805 * before the new view peer tab has been created.
4807 final AlignViewportI peer = viewport.getCodingComplement();
4810 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4811 .getAlignPanel().alignFrame;
4812 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4814 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4820 * On right mouse click on view tab, prompt for and set new view name.
4823 public void tabbedPane_mousePressed(MouseEvent e)
4825 if (e.isPopupTrigger())
4827 String msg = MessageManager.getString("label.enter_view_name");
4828 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4829 JvOptionPane.QUESTION_MESSAGE);
4833 viewport.setViewName(reply);
4834 // TODO warn if reply is in getExistingViewNames()?
4835 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4840 public AlignViewport getCurrentView()
4846 * Open the dialog for regex description parsing.
4849 protected void extractScores_actionPerformed(ActionEvent e)
4851 ParseProperties pp = new jalview.analysis.ParseProperties(
4852 viewport.getAlignment());
4853 // TODO: verify regex and introduce GUI dialog for version 2.5
4854 // if (pp.getScoresFromDescription("col", "score column ",
4855 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4857 if (pp.getScoresFromDescription("description column",
4858 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4860 buildSortByAnnotationScoresMenu();
4868 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4872 protected void showDbRefs_actionPerformed(ActionEvent e)
4874 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4880 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4884 protected void showNpFeats_actionPerformed(ActionEvent e)
4886 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4890 * find the viewport amongst the tabs in this alignment frame and close that
4895 public boolean closeView(AlignViewportI av)
4899 this.closeMenuItem_actionPerformed(false);
4902 Component[] comp = tabbedPane.getComponents();
4903 for (int i = 0; comp != null && i < comp.length; i++)
4905 if (comp[i] instanceof AlignmentPanel)
4907 if (((AlignmentPanel) comp[i]).av == av)
4910 closeView((AlignmentPanel) comp[i]);
4918 protected void build_fetchdbmenu(JMenu webService)
4920 // Temporary hack - DBRef Fetcher always top level ws entry.
4921 // TODO We probably want to store a sequence database checklist in
4922 // preferences and have checkboxes.. rather than individual sources selected
4924 final JMenu rfetch = new JMenu(
4925 MessageManager.getString("action.fetch_db_references"));
4926 rfetch.setToolTipText(MessageManager.getString(
4927 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4928 webService.add(rfetch);
4930 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4931 MessageManager.getString("option.trim_retrieved_seqs"));
4932 trimrs.setToolTipText(
4933 MessageManager.getString("label.trim_retrieved_sequences"));
4935 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4936 trimrs.addActionListener(new ActionListener()
4939 public void actionPerformed(ActionEvent e)
4941 trimrs.setSelected(trimrs.isSelected());
4942 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4943 Boolean.valueOf(trimrs.isSelected()).toString());
4947 JMenuItem fetchr = new JMenuItem(
4948 MessageManager.getString("label.standard_databases"));
4949 fetchr.setToolTipText(
4950 MessageManager.getString("label.fetch_embl_uniprot"));
4951 fetchr.addActionListener(new ActionListener()
4955 public void actionPerformed(ActionEvent e)
4957 new Thread(new Runnable()
4962 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4963 .getAlignment().isNucleotide();
4964 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4965 alignPanel.av.getSequenceSelection(),
4966 alignPanel.alignFrame, null,
4967 alignPanel.alignFrame.featureSettings, isNucleotide);
4968 dbRefFetcher.addListener(new FetchFinishedListenerI()
4971 public void finished()
4974 for (FeatureSettingsModelI srcSettings : dbRefFetcher
4975 .getFeatureSettingsModels())
4978 alignPanel.av.mergeFeaturesStyle(srcSettings);
4980 AlignFrame.this.setMenusForViewport();
4983 dbRefFetcher.fetchDBRefs(false);
4991 final AlignFrame me = this;
4992 new Thread(new Runnable()
4997 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4998 .getSequenceFetcherSingleton(me);
4999 javax.swing.SwingUtilities.invokeLater(new Runnable()
5004 String[] dbclasses = sf.getOrderedSupportedSources();
5005 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5006 // jalview.util.QuickSort.sort(otherdb, otherdb);
5007 List<DbSourceProxy> otherdb;
5008 JMenu dfetch = new JMenu();
5009 JMenu ifetch = new JMenu();
5010 JMenuItem fetchr = null;
5011 int comp = 0, icomp = 0, mcomp = 15;
5012 String mname = null;
5014 for (String dbclass : dbclasses)
5016 otherdb = sf.getSourceProxy(dbclass);
5017 // add a single entry for this class, or submenu allowing 'fetch
5019 if (otherdb == null || otherdb.size() < 1)
5023 // List<DbSourceProxy> dbs=otherdb;
5024 // otherdb=new ArrayList<DbSourceProxy>();
5025 // for (DbSourceProxy db:dbs)
5027 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5031 mname = "From " + dbclass;
5033 if (otherdb.size() == 1)
5035 final DbSourceProxy[] dassource = otherdb
5036 .toArray(new DbSourceProxy[0]);
5037 DbSourceProxy src = otherdb.get(0);
5038 fetchr = new JMenuItem(src.getDbSource());
5039 fetchr.addActionListener(new ActionListener()
5043 public void actionPerformed(ActionEvent e)
5045 new Thread(new Runnable()
5051 boolean isNucleotide = alignPanel.alignFrame
5052 .getViewport().getAlignment()
5054 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5055 alignPanel.av.getSequenceSelection(),
5056 alignPanel.alignFrame, dassource,
5057 alignPanel.alignFrame.featureSettings,
5060 .addListener(new FetchFinishedListenerI()
5063 public void finished()
5065 FeatureSettingsModelI srcSettings = dassource[0]
5066 .getFeatureColourScheme();
5067 alignPanel.av.mergeFeaturesStyle(
5069 AlignFrame.this.setMenusForViewport();
5072 dbRefFetcher.fetchDBRefs(false);
5078 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5079 MessageManager.formatMessage(
5080 "label.fetch_retrieve_from", new Object[]
5081 { src.getDbName() })));
5087 final DbSourceProxy[] dassource = otherdb
5088 .toArray(new DbSourceProxy[0]);
5090 DbSourceProxy src = otherdb.get(0);
5091 fetchr = new JMenuItem(MessageManager
5092 .formatMessage("label.fetch_all_param", new Object[]
5093 { src.getDbSource() }));
5094 fetchr.addActionListener(new ActionListener()
5097 public void actionPerformed(ActionEvent e)
5099 new Thread(new Runnable()
5105 boolean isNucleotide = alignPanel.alignFrame
5106 .getViewport().getAlignment()
5108 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5109 alignPanel.av.getSequenceSelection(),
5110 alignPanel.alignFrame, dassource,
5111 alignPanel.alignFrame.featureSettings,
5114 .addListener(new FetchFinishedListenerI()
5117 public void finished()
5119 AlignFrame.this.setMenusForViewport();
5122 dbRefFetcher.fetchDBRefs(false);
5128 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5129 MessageManager.formatMessage(
5130 "label.fetch_retrieve_from_all_sources",
5132 { Integer.valueOf(otherdb.size())
5134 src.getDbSource(), src.getDbName() })));
5137 // and then build the rest of the individual menus
5138 ifetch = new JMenu(MessageManager.formatMessage(
5139 "label.source_from_db_source", new Object[]
5140 { src.getDbSource() }));
5142 String imname = null;
5144 for (DbSourceProxy sproxy : otherdb)
5146 String dbname = sproxy.getDbName();
5147 String sname = dbname.length() > 5
5148 ? dbname.substring(0, 5) + "..."
5150 String msname = dbname.length() > 10
5151 ? dbname.substring(0, 10) + "..."
5155 imname = MessageManager
5156 .formatMessage("label.from_msname", new Object[]
5159 fetchr = new JMenuItem(msname);
5160 final DbSourceProxy[] dassrc = { sproxy };
5161 fetchr.addActionListener(new ActionListener()
5165 public void actionPerformed(ActionEvent e)
5167 new Thread(new Runnable()
5173 boolean isNucleotide = alignPanel.alignFrame
5174 .getViewport().getAlignment()
5176 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5177 alignPanel.av.getSequenceSelection(),
5178 alignPanel.alignFrame, dassrc,
5179 alignPanel.alignFrame.featureSettings,
5182 .addListener(new FetchFinishedListenerI()
5185 public void finished()
5187 AlignFrame.this.setMenusForViewport();
5190 dbRefFetcher.fetchDBRefs(false);
5196 fetchr.setToolTipText(
5197 "<html>" + MessageManager.formatMessage(
5198 "label.fetch_retrieve_from", new Object[]
5202 if (++icomp >= mcomp || i == (otherdb.size()))
5204 ifetch.setText(MessageManager.formatMessage(
5205 "label.source_to_target", imname, sname));
5207 ifetch = new JMenu();
5215 if (comp >= mcomp || dbi >= (dbclasses.length))
5217 dfetch.setText(MessageManager.formatMessage(
5218 "label.source_to_target", mname, dbclass));
5220 dfetch = new JMenu();
5233 * Left justify the whole alignment.
5236 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5238 AlignmentI al = viewport.getAlignment();
5240 viewport.firePropertyChange("alignment", null, al);
5244 * Right justify the whole alignment.
5247 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5249 AlignmentI al = viewport.getAlignment();
5251 viewport.firePropertyChange("alignment", null, al);
5255 public void setShowSeqFeatures(boolean b)
5257 showSeqFeatures.setSelected(b);
5258 viewport.setShowSequenceFeatures(b);
5265 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5266 * awt.event.ActionEvent)
5269 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5271 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5272 alignPanel.paintAlignment(false, false);
5279 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5283 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5285 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5286 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5294 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5295 * .event.ActionEvent)
5298 protected void showGroupConservation_actionPerformed(ActionEvent e)
5300 viewport.setShowGroupConservation(showGroupConservation.getState());
5301 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5308 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5309 * .event.ActionEvent)
5312 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5314 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5315 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5322 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5323 * .event.ActionEvent)
5326 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5328 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5329 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5333 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5335 showSequenceLogo.setState(true);
5336 viewport.setShowSequenceLogo(true);
5337 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5338 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5342 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5344 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5351 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5352 * .event.ActionEvent)
5355 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5357 if (avc.makeGroupsFromSelection())
5359 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5360 alignPanel.updateAnnotation();
5361 alignPanel.paintAlignment(true,
5362 viewport.needToUpdateStructureViews());
5366 public void clearAlignmentSeqRep()
5368 // TODO refactor alignmentseqrep to controller
5369 if (viewport.getAlignment().hasSeqrep())
5371 viewport.getAlignment().setSeqrep(null);
5372 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5373 alignPanel.updateAnnotation();
5374 alignPanel.paintAlignment(true, true);
5379 protected void createGroup_actionPerformed(ActionEvent e)
5381 if (avc.createGroup())
5383 if (applyAutoAnnotationSettings.isSelected())
5385 alignPanel.updateAnnotation(true, false);
5387 alignPanel.alignmentChanged();
5392 protected void unGroup_actionPerformed(ActionEvent e)
5396 alignPanel.alignmentChanged();
5401 * make the given alignmentPanel the currently selected tab
5403 * @param alignmentPanel
5405 public void setDisplayedView(AlignmentPanel alignmentPanel)
5407 if (!viewport.getSequenceSetId()
5408 .equals(alignmentPanel.av.getSequenceSetId()))
5410 throw new Error(MessageManager.getString(
5411 "error.implementation_error_cannot_show_view_alignment_frame"));
5413 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5414 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5416 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5421 * Action on selection of menu options to Show or Hide annotations.
5424 * @param forSequences
5425 * update sequence-related annotations
5426 * @param forAlignment
5427 * update non-sequence-related annotations
5430 protected void setAnnotationsVisibility(boolean visible,
5431 boolean forSequences, boolean forAlignment)
5433 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5434 .getAlignmentAnnotation();
5439 for (AlignmentAnnotation aa : anns)
5442 * don't display non-positional annotations on an alignment
5444 if (aa.annotations == null)
5448 boolean apply = (aa.sequenceRef == null && forAlignment)
5449 || (aa.sequenceRef != null && forSequences);
5452 aa.visible = visible;
5455 alignPanel.validateAnnotationDimensions(true);
5456 alignPanel.alignmentChanged();
5460 * Store selected annotation sort order for the view and repaint.
5463 protected void sortAnnotations_actionPerformed()
5465 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5467 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5468 alignPanel.paintAlignment(false, false);
5473 * @return alignment panels in this alignment frame
5475 public List<? extends AlignmentViewPanel> getAlignPanels()
5477 // alignPanels is never null
5478 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5483 * Open a new alignment window, with the cDNA associated with this (protein)
5484 * alignment, aligned as is the protein.
5486 protected void viewAsCdna_actionPerformed()
5488 // TODO no longer a menu action - refactor as required
5489 final AlignmentI alignment = getViewport().getAlignment();
5490 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5491 if (mappings == null)
5495 List<SequenceI> cdnaSeqs = new ArrayList<>();
5496 for (SequenceI aaSeq : alignment.getSequences())
5498 for (AlignedCodonFrame acf : mappings)
5500 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5504 * There is a cDNA mapping for this protein sequence - add to new
5505 * alignment. It will share the same dataset sequence as other mapped
5506 * cDNA (no new mappings need to be created).
5508 final Sequence newSeq = new Sequence(dnaSeq);
5509 newSeq.setDatasetSequence(dnaSeq);
5510 cdnaSeqs.add(newSeq);
5514 if (cdnaSeqs.size() == 0)
5516 // show a warning dialog no mapped cDNA
5519 AlignmentI cdna = new Alignment(
5520 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5521 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5522 AlignFrame.DEFAULT_HEIGHT);
5523 cdna.alignAs(alignment);
5524 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5526 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5527 AlignFrame.DEFAULT_HEIGHT);
5531 * Set visibility of dna/protein complement view (available when shown in a
5537 protected void showComplement_actionPerformed(boolean show)
5539 SplitContainerI sf = getSplitViewContainer();
5542 sf.setComplementVisible(this, show);
5547 * Generate the reverse (optionally complemented) of the selected sequences,
5548 * and add them to the alignment
5551 protected void showReverse_actionPerformed(boolean complement)
5553 AlignmentI al = null;
5556 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5557 al = dna.reverseCdna(complement);
5558 viewport.addAlignment(al, "");
5559 addHistoryItem(new EditCommand(
5560 MessageManager.getString("label.add_sequences"), Action.PASTE,
5561 al.getSequencesArray(), 0, al.getWidth(),
5562 viewport.getAlignment()));
5563 } catch (Exception ex)
5565 System.err.println(ex.getMessage());
5571 * Try to run a script in the Groovy console, having first ensured that this
5572 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5573 * be targeted at this alignment.
5576 protected void runGroovy_actionPerformed()
5578 Jalview.setCurrentAlignFrame(this);
5579 groovy.ui.Console console = Desktop.getGroovyConsole();
5580 if (console != null)
5584 console.runScript();
5585 } catch (Exception ex)
5587 System.err.println((ex.toString()));
5588 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5589 MessageManager.getString("label.couldnt_run_groovy_script"),
5590 MessageManager.getString("label.groovy_support_failed"),
5591 JvOptionPane.ERROR_MESSAGE);
5596 System.err.println("Can't run Groovy script as console not found");
5601 * Hides columns containing (or not containing) a specified feature, provided
5602 * that would not leave all columns hidden
5604 * @param featureType
5605 * @param columnsContaining
5608 public boolean hideFeatureColumns(String featureType,
5609 boolean columnsContaining)
5611 boolean notForHiding = avc.markColumnsContainingFeatures(
5612 columnsContaining, false, false, featureType);
5615 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5616 false, featureType))
5618 getViewport().hideSelectedColumns();
5626 protected void selectHighlightedColumns_actionPerformed(
5627 ActionEvent actionEvent)
5629 // include key modifier check in case user selects from menu
5630 avc.markHighlightedColumns(
5631 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5632 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5633 | ActionEvent.CTRL_MASK)) != 0);
5637 * Rebuilds the Colour menu, including any user-defined colours which have
5638 * been loaded either on startup or during the session
5640 public void buildColourMenu()
5642 colourMenu.removeAll();
5644 colourMenu.add(applyToAllGroups);
5645 colourMenu.add(textColour);
5646 colourMenu.addSeparator();
5648 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5649 viewport.getAlignment(), false);
5651 colourMenu.add(annotationColour);
5652 bg.add(annotationColour);
5653 colourMenu.addSeparator();
5654 colourMenu.add(conservationMenuItem);
5655 colourMenu.add(modifyConservation);
5656 colourMenu.add(abovePIDThreshold);
5657 colourMenu.add(modifyPID);
5659 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5660 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5664 * Open a dialog (if not already open) that allows the user to select and
5665 * calculate PCA or Tree analysis
5667 protected void openTreePcaDialog()
5669 if (alignPanel.getCalculationDialog() == null)
5671 new CalculationChooser(AlignFrame.this);
5676 protected void loadVcf_actionPerformed()
5678 JalviewFileChooser chooser = new JalviewFileChooser(
5679 Cache.getProperty("LAST_DIRECTORY"));
5680 chooser.setFileView(new JalviewFileView());
5681 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5682 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5684 int value = chooser.showOpenDialog(null);
5686 if (value == JalviewFileChooser.APPROVE_OPTION)
5688 String choice = chooser.getSelectedFile().getPath();
5689 Cache.setProperty("LAST_DIRECTORY", choice);
5690 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5691 new VCFLoader(choice).loadVCF(seqs, this);
5696 private Rectangle lastFeatureSettingsBounds = null;
5698 public void setFeatureSettingsGeometry(Rectangle bounds)
5700 lastFeatureSettingsBounds = bounds;
5704 public Rectangle getFeatureSettingsGeometry()
5706 return lastFeatureSettingsBounds;
5710 class PrintThread extends Thread
5714 public PrintThread(AlignmentPanel ap)
5719 static PageFormat pf;
5724 PrinterJob printJob = PrinterJob.getPrinterJob();
5728 printJob.setPrintable(ap, pf);
5732 printJob.setPrintable(ap);
5735 if (printJob.printDialog())
5740 } catch (Exception PrintException)
5742 PrintException.printStackTrace();