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.hmmer.HMMAlign;
68 import jalview.hmmer.HMMBuild;
69 import jalview.hmmer.HMMERParamStore;
70 import jalview.hmmer.HMMERPreset;
71 import jalview.hmmer.HMMSearch;
72 import jalview.hmmer.HmmerCommand;
73 import jalview.hmmer.JackHMMER;
74 import jalview.io.AlignmentProperties;
75 import jalview.io.AnnotationFile;
76 import jalview.io.BackupFiles;
77 import jalview.io.BioJsHTMLOutput;
78 import jalview.io.DataSourceType;
79 import jalview.io.FileFormat;
80 import jalview.io.FileFormatI;
81 import jalview.io.FileFormats;
82 import jalview.io.FileLoader;
83 import jalview.io.FileParse;
84 import jalview.io.FormatAdapter;
85 import jalview.io.HtmlSvgOutput;
86 import jalview.io.IdentifyFile;
87 import jalview.io.JPredFile;
88 import jalview.io.JalviewFileChooser;
89 import jalview.io.JalviewFileView;
90 import jalview.io.JnetAnnotationMaker;
91 import jalview.io.NewickFile;
92 import jalview.io.ScoreMatrixFile;
93 import jalview.io.TCoffeeScoreFile;
94 import jalview.io.vcf.VCFLoader;
95 import jalview.jbgui.GAlignFrame;
96 import jalview.schemes.ColourSchemeI;
97 import jalview.schemes.ColourSchemes;
98 import jalview.schemes.ResidueColourScheme;
99 import jalview.schemes.TCoffeeColourScheme;
100 import jalview.util.MessageManager;
101 import jalview.viewmodel.AlignmentViewport;
102 import jalview.viewmodel.ViewportRanges;
103 import jalview.ws.DBRefFetcher;
104 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
105 import jalview.ws.jws1.Discoverer;
106 import jalview.ws.jws2.Jws2Discoverer;
107 import jalview.ws.jws2.jabaws2.Jws2Instance;
108 import jalview.ws.params.ArgumentI;
109 import jalview.ws.params.ParamDatastoreI;
110 import jalview.ws.params.WsParamSetI;
111 import jalview.ws.seqfetcher.DbSourceProxy;
113 import java.awt.BorderLayout;
114 import java.awt.Component;
115 import java.awt.Rectangle;
116 import java.awt.Toolkit;
117 import java.awt.datatransfer.Clipboard;
118 import java.awt.datatransfer.DataFlavor;
119 import java.awt.datatransfer.StringSelection;
120 import java.awt.datatransfer.Transferable;
121 import java.awt.dnd.DnDConstants;
122 import java.awt.dnd.DropTargetDragEvent;
123 import java.awt.dnd.DropTargetDropEvent;
124 import java.awt.dnd.DropTargetEvent;
125 import java.awt.dnd.DropTargetListener;
126 import java.awt.event.ActionEvent;
127 import java.awt.event.ActionListener;
128 import java.awt.event.FocusAdapter;
129 import java.awt.event.FocusEvent;
130 import java.awt.event.ItemEvent;
131 import java.awt.event.ItemListener;
132 import java.awt.event.KeyAdapter;
133 import java.awt.event.KeyEvent;
134 import java.awt.event.MouseEvent;
135 import java.awt.print.PageFormat;
136 import java.awt.print.PrinterJob;
137 import java.beans.PropertyChangeEvent;
139 import java.io.FileWriter;
140 import java.io.IOException;
141 import java.io.PrintWriter;
143 import java.util.ArrayList;
144 import java.util.Arrays;
145 import java.util.Deque;
146 import java.util.HashSet;
147 import java.util.List;
148 import java.util.Set;
149 import java.util.Vector;
151 import javax.swing.ButtonGroup;
152 import javax.swing.JCheckBoxMenuItem;
153 import javax.swing.JEditorPane;
154 import javax.swing.JFileChooser;
155 import javax.swing.JInternalFrame;
156 import javax.swing.JLayeredPane;
157 import javax.swing.JMenu;
158 import javax.swing.JMenuItem;
159 import javax.swing.JOptionPane;
160 import javax.swing.JScrollPane;
161 import javax.swing.SwingUtilities;
167 * @version $Revision$
169 public class AlignFrame extends GAlignFrame implements DropTargetListener,
170 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
172 public static final int DEFAULT_WIDTH = 700;
174 public static final int DEFAULT_HEIGHT = 500;
177 * The currently displayed panel (selected tabbed view if more than one)
179 public AlignmentPanel alignPanel;
181 AlignViewport viewport;
183 public AlignViewControllerI avc;
185 List<AlignmentPanel> alignPanels = new ArrayList<>();
188 * Last format used to load or save alignments in this window
190 FileFormatI currentFileFormat = null;
193 * Current filename for this alignment
195 String fileName = null;
199 * Creates a new AlignFrame object with specific width and height.
205 public AlignFrame(AlignmentI al, int width, int height)
207 this(al, null, width, height);
211 * Creates a new AlignFrame object with specific width, height and
217 * @param sequenceSetId
219 public AlignFrame(AlignmentI al, int width, int height,
220 String sequenceSetId)
222 this(al, null, width, height, sequenceSetId);
226 * Creates a new AlignFrame object with specific width, height and
232 * @param sequenceSetId
235 public AlignFrame(AlignmentI al, int width, int height,
236 String sequenceSetId, String viewId)
238 this(al, null, width, height, sequenceSetId, viewId);
242 * new alignment window with hidden columns
246 * @param hiddenColumns
247 * ColumnSelection or null
249 * Width of alignment frame
253 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
256 this(al, hiddenColumns, width, height, null);
260 * Create alignment frame for al with hiddenColumns, a specific width and
261 * height, and specific sequenceId
264 * @param hiddenColumns
267 * @param sequenceSetId
270 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
271 int height, String sequenceSetId)
273 this(al, hiddenColumns, width, height, sequenceSetId, null);
277 * Create alignment frame for al with hiddenColumns, a specific width and
278 * height, and specific sequenceId
281 * @param hiddenColumns
284 * @param sequenceSetId
289 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
290 int height, String sequenceSetId, String viewId)
292 setSize(width, height);
294 if (al.getDataset() == null)
299 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
301 alignPanel = new AlignmentPanel(this, viewport);
303 addAlignmentPanel(alignPanel, true);
307 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
308 HiddenColumns hiddenColumns, int width, int height)
310 setSize(width, height);
312 if (al.getDataset() == null)
317 viewport = new AlignViewport(al, hiddenColumns);
319 if (hiddenSeqs != null && hiddenSeqs.length > 0)
321 viewport.hideSequence(hiddenSeqs);
323 alignPanel = new AlignmentPanel(this, viewport);
324 addAlignmentPanel(alignPanel, true);
329 * Make a new AlignFrame from existing alignmentPanels
336 public AlignFrame(AlignmentPanel ap)
340 addAlignmentPanel(ap, false);
345 * initalise the alignframe from the underlying viewport data and the
350 if (!Jalview.isHeadlessMode())
352 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
355 avc = new jalview.controller.AlignViewController(this, viewport,
357 if (viewport.getAlignmentConservationAnnotation() == null)
359 // BLOSUM62Colour.setEnabled(false);
360 conservationMenuItem.setEnabled(false);
361 modifyConservation.setEnabled(false);
362 // PIDColour.setEnabled(false);
363 // abovePIDThreshold.setEnabled(false);
364 // modifyPID.setEnabled(false);
367 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
370 if (sortby.equals("Id"))
372 sortIDMenuItem_actionPerformed(null);
374 else if (sortby.equals("Pairwise Identity"))
376 sortPairwiseMenuItem_actionPerformed(null);
380 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
382 setMenusFromViewport(viewport);
383 buildSortByAnnotationScoresMenu();
384 calculateTree.addActionListener(new ActionListener()
388 public void actionPerformed(ActionEvent e)
395 if (Desktop.desktop != null)
397 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
398 addServiceListeners();
402 if (viewport.getWrapAlignment())
404 wrapMenuItem_actionPerformed(null);
407 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
409 this.overviewMenuItem_actionPerformed(null);
414 final List<AlignmentPanel> selviews = new ArrayList<>();
415 final List<AlignmentPanel> origview = new ArrayList<>();
416 final String menuLabel = MessageManager
417 .getString("label.copy_format_from");
418 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
419 new ViewSetProvider()
423 public AlignmentPanel[] getAllAlignmentPanels()
426 origview.add(alignPanel);
427 // make an array of all alignment panels except for this one
428 List<AlignmentPanel> aps = new ArrayList<>(
429 Arrays.asList(Desktop.getAlignmentPanels(null)));
430 aps.remove(AlignFrame.this.alignPanel);
431 return aps.toArray(new AlignmentPanel[aps.size()]);
433 }, selviews, new ItemListener()
437 public void itemStateChanged(ItemEvent e)
439 if (origview.size() > 0)
441 final AlignmentPanel ap = origview.get(0);
444 * Copy the ViewStyle of the selected panel to 'this one'.
445 * Don't change value of 'scaleProteinAsCdna' unless copying
448 ViewStyleI vs = selviews.get(0).getAlignViewport()
450 boolean fromSplitFrame = selviews.get(0)
451 .getAlignViewport().getCodingComplement() != null;
454 vs.setScaleProteinAsCdna(ap.getAlignViewport()
455 .getViewStyle().isScaleProteinAsCdna());
457 ap.getAlignViewport().setViewStyle(vs);
460 * Also rescale ViewStyle of SplitFrame complement if there is
461 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
462 * the whole ViewStyle (allow cDNA protein to have different
465 AlignViewportI complement = ap.getAlignViewport()
466 .getCodingComplement();
467 if (complement != null && vs.isScaleProteinAsCdna())
469 AlignFrame af = Desktop.getAlignFrameFor(complement);
470 ((SplitFrame) af.getSplitViewContainer())
472 af.setMenusForViewport();
476 ap.setSelected(true);
477 ap.alignFrame.setMenusForViewport();
482 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
483 .indexOf("devel") > -1
484 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
485 .indexOf("test") > -1)
487 formatMenu.add(vsel);
489 addFocusListener(new FocusAdapter()
492 public void focusGained(FocusEvent e)
494 Jalview.setCurrentAlignFrame(AlignFrame.this);
501 * Change the filename and format for the alignment, and enable the 'reload'
502 * button functionality.
509 public void setFileName(String file, FileFormatI format)
512 setFileFormat(format);
513 reload.setEnabled(true);
517 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
520 void addKeyListener()
522 addKeyListener(new KeyAdapter()
525 public void keyPressed(KeyEvent evt)
527 if (viewport.cursorMode
528 && ((evt.getKeyCode() >= KeyEvent.VK_0
529 && evt.getKeyCode() <= KeyEvent.VK_9)
530 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
531 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
532 && Character.isDigit(evt.getKeyChar()))
534 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
537 switch (evt.getKeyCode())
540 case 27: // escape key
541 deselectAllSequenceMenuItem_actionPerformed(null);
545 case KeyEvent.VK_DOWN:
546 if (evt.isAltDown() || !viewport.cursorMode)
548 moveSelectedSequences(false);
550 if (viewport.cursorMode)
552 alignPanel.getSeqPanel().moveCursor(0, 1);
557 if (evt.isAltDown() || !viewport.cursorMode)
559 moveSelectedSequences(true);
561 if (viewport.cursorMode)
563 alignPanel.getSeqPanel().moveCursor(0, -1);
568 case KeyEvent.VK_LEFT:
569 if (evt.isAltDown() || !viewport.cursorMode)
571 slideSequences(false,
572 alignPanel.getSeqPanel().getKeyboardNo1());
576 alignPanel.getSeqPanel().moveCursor(-1, 0);
581 case KeyEvent.VK_RIGHT:
582 if (evt.isAltDown() || !viewport.cursorMode)
584 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
588 alignPanel.getSeqPanel().moveCursor(1, 0);
592 case KeyEvent.VK_SPACE:
593 if (viewport.cursorMode)
595 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
596 || evt.isShiftDown() || evt.isAltDown());
600 // case KeyEvent.VK_A:
601 // if (viewport.cursorMode)
603 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
604 // //System.out.println("A");
608 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
609 * System.out.println("closing bracket"); } break;
611 case KeyEvent.VK_DELETE:
612 case KeyEvent.VK_BACK_SPACE:
613 if (!viewport.cursorMode)
615 cut_actionPerformed(null);
619 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
620 || evt.isShiftDown() || evt.isAltDown());
626 if (viewport.cursorMode)
628 alignPanel.getSeqPanel().setCursorRow();
632 if (viewport.cursorMode && !evt.isControlDown())
634 alignPanel.getSeqPanel().setCursorColumn();
638 if (viewport.cursorMode)
640 alignPanel.getSeqPanel().setCursorPosition();
644 case KeyEvent.VK_ENTER:
645 case KeyEvent.VK_COMMA:
646 if (viewport.cursorMode)
648 alignPanel.getSeqPanel().setCursorRowAndColumn();
653 if (viewport.cursorMode)
655 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
659 if (viewport.cursorMode)
661 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
666 viewport.cursorMode = !viewport.cursorMode;
667 statusBar.setText(MessageManager
668 .formatMessage("label.keyboard_editing_mode", new String[]
669 { (viewport.cursorMode ? "on" : "off") }));
670 if (viewport.cursorMode)
672 ViewportRanges ranges = viewport.getRanges();
673 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
675 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
678 alignPanel.getSeqPanel().seqCanvas.repaint();
684 Help.showHelpWindow();
685 } catch (Exception ex)
687 ex.printStackTrace();
692 boolean toggleSeqs = !evt.isControlDown();
693 boolean toggleCols = !evt.isShiftDown();
694 toggleHiddenRegions(toggleSeqs, toggleCols);
699 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
700 boolean modifyExisting = true; // always modify, don't clear
701 // evt.isShiftDown();
702 boolean invertHighlighted = evt.isAltDown();
703 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
707 case KeyEvent.VK_PAGE_UP:
708 viewport.getRanges().pageUp();
710 case KeyEvent.VK_PAGE_DOWN:
711 viewport.getRanges().pageDown();
717 public void keyReleased(KeyEvent evt)
719 switch (evt.getKeyCode())
721 case KeyEvent.VK_LEFT:
722 if (evt.isAltDown() || !viewport.cursorMode)
724 viewport.firePropertyChange("alignment", null,
725 viewport.getAlignment().getSequences());
729 case KeyEvent.VK_RIGHT:
730 if (evt.isAltDown() || !viewport.cursorMode)
732 viewport.firePropertyChange("alignment", null,
733 viewport.getAlignment().getSequences());
741 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
743 ap.alignFrame = this;
744 avc = new jalview.controller.AlignViewController(this, viewport,
749 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
751 int aSize = alignPanels.size();
753 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
755 if (aSize == 1 && ap.av.getViewName() == null)
757 this.getContentPane().add(ap, BorderLayout.CENTER);
763 setInitialTabVisible();
766 expandViews.setEnabled(true);
767 gatherViews.setEnabled(true);
768 tabbedPane.addTab(ap.av.getViewName(), ap);
770 ap.setVisible(false);
775 if (ap.av.isPadGaps())
777 ap.av.getAlignment().padGaps();
779 ap.av.updateConservation(ap);
780 ap.av.updateConsensus(ap);
781 ap.av.updateStrucConsensus(ap);
782 ap.av.initInformationWorker(ap);
786 public void setInitialTabVisible()
788 expandViews.setEnabled(true);
789 gatherViews.setEnabled(true);
790 tabbedPane.setVisible(true);
791 AlignmentPanel first = alignPanels.get(0);
792 tabbedPane.addTab(first.av.getViewName(), first);
793 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
796 public AlignViewport getViewport()
801 /* Set up intrinsic listeners for dynamically generated GUI bits. */
802 private void addServiceListeners()
804 final java.beans.PropertyChangeListener thisListener;
805 Desktop.instance.addJalviewPropertyChangeListener("services",
806 thisListener = new java.beans.PropertyChangeListener()
809 public void propertyChange(PropertyChangeEvent evt)
811 // // System.out.println("Discoverer property change.");
812 // if (evt.getPropertyName().equals("services"))
814 SwingUtilities.invokeLater(new Runnable()
821 "Rebuild WS Menu for service change");
822 BuildWebServiceMenu();
829 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
832 public void internalFrameClosed(
833 javax.swing.event.InternalFrameEvent evt)
835 // System.out.println("deregistering discoverer listener");
836 Desktop.instance.removeJalviewPropertyChangeListener("services",
838 closeMenuItem_actionPerformed(true);
841 // Finally, build the menu once to get current service state
842 new Thread(new Runnable()
847 BuildWebServiceMenu();
853 * Configure menu items that vary according to whether the alignment is
854 * nucleotide or protein
856 public void setGUINucleotide()
858 AlignmentI al = getViewport().getAlignment();
859 boolean nucleotide = al.isNucleotide();
861 loadVcf.setVisible(nucleotide);
862 showTranslation.setVisible(nucleotide);
863 showReverse.setVisible(nucleotide);
864 showReverseComplement.setVisible(nucleotide);
865 conservationMenuItem.setEnabled(!nucleotide);
867 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
868 showGroupConservation.setEnabled(!nucleotide);
870 showComplementMenuItem
871 .setText(nucleotide ? MessageManager.getString("label.protein")
872 : MessageManager.getString("label.nucleotide"));
876 * set up menus for the current viewport. This may be called after any
877 * operation that affects the data in the current view (selection changed,
878 * etc) to update the menus to reflect the new state.
881 public void setMenusForViewport()
883 setMenusFromViewport(viewport);
887 * Need to call this method when tabs are selected for multiple views, or when
888 * loading from Jalview2XML.java
893 public void setMenusFromViewport(AlignViewport av)
895 padGapsMenuitem.setSelected(av.isPadGaps());
896 colourTextMenuItem.setSelected(av.isShowColourText());
897 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
898 modifyPID.setEnabled(abovePIDThreshold.isSelected());
899 conservationMenuItem.setSelected(av.getConservationSelected());
900 modifyConservation.setEnabled(conservationMenuItem.isSelected());
901 seqLimits.setSelected(av.getShowJVSuffix());
902 idRightAlign.setSelected(av.isRightAlignIds());
903 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
904 renderGapsMenuItem.setSelected(av.isRenderGaps());
905 wrapMenuItem.setSelected(av.getWrapAlignment());
906 scaleAbove.setVisible(av.getWrapAlignment());
907 scaleLeft.setVisible(av.getWrapAlignment());
908 scaleRight.setVisible(av.getWrapAlignment());
909 annotationPanelMenuItem.setState(av.isShowAnnotation());
911 * Show/hide annotations only enabled if annotation panel is shown
913 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
914 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
915 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
916 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
917 viewBoxesMenuItem.setSelected(av.getShowBoxes());
918 viewTextMenuItem.setSelected(av.getShowText());
919 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
920 showGroupConsensus.setSelected(av.isShowGroupConsensus());
921 showGroupConservation.setSelected(av.isShowGroupConservation());
922 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
923 showSequenceLogo.setSelected(av.isShowSequenceLogo());
924 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
925 showInformationHistogram.setSelected(av.isShowInformationHistogram());
926 showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
927 normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
929 ColourMenuHelper.setColourSelected(colourMenu,
930 av.getGlobalColourScheme());
932 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
933 hiddenMarkers.setState(av.getShowHiddenMarkers());
934 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
935 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
936 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
937 autoCalculate.setSelected(av.autoCalculateConsensus);
938 sortByTree.setSelected(av.sortByTree);
939 listenToViewSelections.setSelected(av.followSelection);
941 showProducts.setEnabled(canShowProducts());
942 setGroovyEnabled(Desktop.getGroovyConsole() != null);
948 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
952 public void setGroovyEnabled(boolean b)
954 runGroovy.setEnabled(b);
957 private IProgressIndicator progressBar;
962 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
965 public void setProgressBar(String message, long id)
967 progressBar.setProgressBar(message, id);
971 public void registerHandler(final long id,
972 final IProgressIndicatorHandler handler)
974 progressBar.registerHandler(id, handler);
979 * @return true if any progress bars are still active
982 public boolean operationInProgress()
984 return progressBar.operationInProgress();
988 * Sets the text of the status bar. Note that setting a null or empty value
989 * will cause the status bar to be hidden, with possibly undesirable flicker
990 * of the screen layout.
993 public void setStatus(String text)
995 statusBar.setText(text == null || text.isEmpty() ? " " : text);
999 * Added so Castor Mapping file can obtain Jalview Version
1001 public String getVersion()
1003 return jalview.bin.Cache.getProperty("VERSION");
1006 public FeatureRenderer getFeatureRenderer()
1008 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1012 public void fetchSequence_actionPerformed(ActionEvent e)
1014 new jalview.gui.SequenceFetcher(this);
1018 public void addFromFile_actionPerformed(ActionEvent e)
1020 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1024 public void hmmBuild_actionPerformed(boolean withDefaults)
1026 if (!alignmentIsSufficient(1))
1032 * get default parameters, and optionally show a dialog
1033 * to allow them to be modified
1035 ParamDatastoreI store = HMMERParamStore.forBuild(viewport);
1036 List<ArgumentI> args = store.getServiceParameters();
1040 WsParamSetI set = new HMMERPreset();
1041 WsJobParameters params = new WsJobParameters(store, set, args);
1042 if (params.showRunDialog())
1044 args = params.getJobParams();
1048 return; // user cancelled
1051 new Thread(new HMMBuild(this, args)).start();
1055 public void hmmAlign_actionPerformed(boolean withDefaults)
1057 if (!(checkForHMM() && alignmentIsSufficient(2)))
1063 * get default parameters, and optionally show a dialog
1064 * to allow them to be modified
1066 ParamDatastoreI store = HMMERParamStore.forAlign(viewport);
1067 List<ArgumentI> args = store.getServiceParameters();
1071 WsParamSetI set = new HMMERPreset();
1072 WsJobParameters params = new WsJobParameters(store, set, args);
1073 if (params.showRunDialog())
1075 args = params.getJobParams();
1079 return; // user cancelled
1082 new Thread(new HMMAlign(this, args)).start();
1086 public void hmmSearch_actionPerformed(boolean withDefaults)
1094 * get default parameters, and (if requested) show
1095 * dialog to allow modification
1097 ParamDatastoreI store = HMMERParamStore.forSearch(viewport);
1098 List<ArgumentI> args = store.getServiceParameters();
1102 WsParamSetI set = new HMMERPreset();
1103 WsJobParameters params = new WsJobParameters(store, set, args);
1104 if (params.showRunDialog())
1106 args = params.getJobParams();
1110 return; // user cancelled
1113 new Thread(new HMMSearch(this, args)).start();
1114 alignPanel.repaint();
1118 public void jackhmmer_actionPerformed(boolean withDefaults)
1122 * get default parameters, and (if requested) show
1123 * dialog to allow modification
1126 ParamDatastoreI store = HMMERParamStore.forJackhmmer(viewport);
1127 List<ArgumentI> args = store.getServiceParameters();
1131 WsParamSetI set = new HMMERPreset();
1132 WsJobParameters params = new WsJobParameters(store, set, args);
1133 if (params.showRunDialog())
1135 args = params.getJobParams();
1139 return; // user cancelled
1142 new Thread(new JackHMMER(this, args)).start();
1143 alignPanel.repaint();
1148 * Checks if the alignment has at least one hidden Markov model, if not shows
1149 * a dialog advising to run hmmbuild or load an HMM profile
1153 private boolean checkForHMM()
1155 if (viewport.getAlignment().getHmmSequences().isEmpty())
1157 JOptionPane.showMessageDialog(this,
1158 MessageManager.getString("warn.no_hmm"));
1165 protected void filterByEValue_actionPerformed()
1167 viewport.filterByEvalue(inputDouble("Enter E-Value Cutoff"));
1171 protected void filterByScore_actionPerformed()
1173 viewport.filterByScore(inputDouble("Enter Bit Score Threshold"));
1176 private double inputDouble(String message)
1180 while(d == null || d <= 0)
1182 str = JOptionPane.showInputDialog(this.alignPanel, message);
1185 d = Double.valueOf(str);
1187 catch (NumberFormatException e)
1195 * Checks if the alignment contains the required number of sequences.
1200 public boolean alignmentIsSufficient(int required)
1202 if (getViewport().getAlignment().getSequences().size() < required)
1204 JOptionPane.showMessageDialog(this,
1205 MessageManager.getString("label.not_enough_sequences"));
1212 * Opens a file browser and adds the selected file, if in Fasta, Stockholm or
1213 * Pfam format, to the list held under preference key "HMMSEARCH_DBS" (as a
1214 * comma-separated list)
1217 public void addDatabase_actionPerformed() throws IOException
1219 if (Cache.getProperty(Preferences.HMMSEARCH_DBS) == null)
1221 Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
1224 String path = openFileChooser(false);
1225 if (path != null && new File(path).exists())
1227 IdentifyFile identifier = new IdentifyFile();
1228 FileFormatI format = identifier.identify(path, DataSourceType.FILE);
1229 if (format == FileFormat.Fasta || format == FileFormat.Stockholm
1230 || format == FileFormat.Pfam)
1232 String currentDbPaths = Cache
1233 .getProperty(Preferences.HMMSEARCH_DBS);
1234 currentDbPaths += Preferences.COMMA + path;
1235 Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
1239 JOptionPane.showMessageDialog(this,
1240 MessageManager.getString("warn.invalid_format"));
1246 * Opens a file chooser, optionally restricted to selecting folders
1247 * (directories) only. Answers the path to the selected file or folder, or
1248 * null if none is chosen.
1253 protected String openFileChooser(boolean forFolder)
1255 // TODO duplicates GPreferences method - relocate to JalviewFileChooser?
1256 String choice = null;
1257 JFileChooser chooser = new JFileChooser();
1260 chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
1262 chooser.setDialogTitle(
1263 MessageManager.getString("label.open_local_file"));
1264 chooser.setToolTipText(MessageManager.getString("action.open"));
1266 int value = chooser.showOpenDialog(this);
1268 if (value == JFileChooser.APPROVE_OPTION)
1270 choice = chooser.getSelectedFile().getPath();
1276 public void reload_actionPerformed(ActionEvent e)
1278 if (fileName != null)
1280 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1281 // originating file's format
1282 // TODO: work out how to recover feature settings for correct view(s) when
1283 // file is reloaded.
1284 if (FileFormat.Jalview.equals(currentFileFormat))
1286 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1287 for (int i = 0; i < frames.length; i++)
1289 if (frames[i] instanceof AlignFrame && frames[i] != this
1290 && ((AlignFrame) frames[i]).fileName != null
1291 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1295 frames[i].setSelected(true);
1296 Desktop.instance.closeAssociatedWindows();
1297 } catch (java.beans.PropertyVetoException ex)
1303 Desktop.instance.closeAssociatedWindows();
1305 FileLoader loader = new FileLoader();
1306 DataSourceType protocol = fileName.startsWith("http:")
1307 ? DataSourceType.URL
1308 : DataSourceType.FILE;
1309 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1313 Rectangle bounds = this.getBounds();
1315 FileLoader loader = new FileLoader();
1316 DataSourceType protocol = fileName.startsWith("http:")
1317 ? DataSourceType.URL
1318 : DataSourceType.FILE;
1319 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1320 protocol, currentFileFormat);
1322 newframe.setBounds(bounds);
1323 if (featureSettings != null && featureSettings.isShowing())
1325 final Rectangle fspos = featureSettings.frame.getBounds();
1326 // TODO: need a 'show feature settings' function that takes bounds -
1327 // need to refactor Desktop.addFrame
1328 newframe.featureSettings_actionPerformed(null);
1329 final FeatureSettings nfs = newframe.featureSettings;
1330 SwingUtilities.invokeLater(new Runnable()
1335 nfs.frame.setBounds(fspos);
1338 this.featureSettings.close();
1339 this.featureSettings = null;
1341 this.closeMenuItem_actionPerformed(true);
1347 public void addFromText_actionPerformed(ActionEvent e)
1350 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1354 public void addFromURL_actionPerformed(ActionEvent e)
1356 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1360 public void save_actionPerformed(ActionEvent e)
1362 if (fileName == null || (currentFileFormat == null)
1363 || fileName.startsWith("http"))
1365 saveAs_actionPerformed(null);
1369 saveAlignment(fileName, currentFileFormat);
1380 public void saveAs_actionPerformed(ActionEvent e)
1382 String format = currentFileFormat == null ? null
1383 : currentFileFormat.getName();
1384 JalviewFileChooser chooser = JalviewFileChooser
1385 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1387 chooser.setFileView(new JalviewFileView());
1388 chooser.setDialogTitle(
1389 MessageManager.getString("label.save_alignment_to_file"));
1390 chooser.setToolTipText(MessageManager.getString("action.save"));
1392 int value = chooser.showSaveDialog(this);
1394 if (value == JalviewFileChooser.APPROVE_OPTION)
1396 currentFileFormat = chooser.getSelectedFormat();
1397 while (currentFileFormat == null)
1399 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1400 MessageManager.getString(
1401 "label.select_file_format_before_saving"),
1402 MessageManager.getString("label.file_format_not_specified"),
1403 JvOptionPane.WARNING_MESSAGE);
1404 currentFileFormat = chooser.getSelectedFormat();
1405 value = chooser.showSaveDialog(this);
1406 if (value != JalviewFileChooser.APPROVE_OPTION)
1412 fileName = chooser.getSelectedFile().getPath();
1414 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1416 Cache.setProperty("LAST_DIRECTORY", fileName);
1417 saveAlignment(fileName, currentFileFormat);
1421 public boolean saveAlignment(String file, FileFormatI format)
1423 boolean success = true;
1425 if (FileFormat.Jalview.equals(format))
1427 String shortName = title;
1429 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1431 shortName = shortName.substring(
1432 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1435 success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1438 statusBar.setText(MessageManager.formatMessage(
1439 "label.successfully_saved_to_file_in_format", new Object[]
1440 { fileName, format }));
1445 AlignmentExportData exportData = getAlignmentForExport(format,
1447 if (exportData.getSettings().isCancelled())
1451 FormatAdapter f = new FormatAdapter(alignPanel,
1452 exportData.getSettings());
1453 String output = f.formatSequences(format, exportData.getAlignment(), // class
1457 // occur in the distant future
1458 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1459 f.getCacheSuffixDefault(format),
1460 viewport.getAlignment().getHiddenColumns());
1468 // create backupfiles object and get new temp filename destination
1469 BackupFiles backupfiles = new BackupFiles(file);
1473 PrintWriter out = new PrintWriter(
1474 new FileWriter(backupfiles.getTempFilePath()));
1478 this.setTitle(file);
1479 statusBar.setText(MessageManager.formatMessage(
1480 "label.successfully_saved_to_file_in_format", new Object[]
1481 { fileName, format.getName() }));
1482 } catch (Exception ex)
1485 ex.printStackTrace();
1488 backupfiles.setWriteSuccess(success);
1489 // do the backup file roll and rename the temp file to actual file
1490 success = backupfiles.rollBackupsAndRenameTempFile();
1497 JvOptionPane.showInternalMessageDialog(this, MessageManager
1498 .formatMessage("label.couldnt_save_file", new Object[]
1500 MessageManager.getString("label.error_saving_file"),
1501 JvOptionPane.WARNING_MESSAGE);
1507 private void warningMessage(String warning, String title)
1509 if (new jalview.util.Platform().isHeadless())
1511 System.err.println("Warning: " + title + "\nWarning: " + warning);
1516 JvOptionPane.showInternalMessageDialog(this, warning, title,
1517 JvOptionPane.WARNING_MESSAGE);
1529 protected void outputText_actionPerformed(ActionEvent e)
1531 FileFormatI fileFormat = FileFormats.getInstance()
1532 .forName(e.getActionCommand());
1533 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1535 if (exportData.getSettings().isCancelled())
1539 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1540 cap.setForInput(null);
1543 FileFormatI format = fileFormat;
1544 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1545 .formatSequences(format, exportData.getAlignment(),
1546 exportData.getOmitHidden(),
1547 exportData.getStartEndPostions(),
1548 viewport.getAlignment().getHiddenColumns()));
1549 Desktop.addInternalFrame(cap, MessageManager
1550 .formatMessage("label.alignment_output_command", new Object[]
1551 { e.getActionCommand() }), 600, 500);
1552 } catch (OutOfMemoryError oom)
1554 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1561 public static AlignmentExportData getAlignmentForExport(
1562 FileFormatI format, AlignViewportI viewport,
1563 AlignExportSettingI exportSettings)
1565 AlignmentI alignmentToExport = null;
1566 AlignExportSettingI settings = exportSettings;
1567 String[] omitHidden = null;
1569 HiddenSequences hiddenSeqs = viewport.getAlignment()
1570 .getHiddenSequences();
1572 alignmentToExport = viewport.getAlignment();
1574 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1575 if (settings == null)
1577 settings = new AlignExportSettings(hasHiddenSeqs,
1578 viewport.hasHiddenColumns(), format);
1580 // settings.isExportAnnotations();
1582 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1584 omitHidden = viewport.getViewAsString(false,
1585 settings.isExportHiddenSequences());
1588 int[] alignmentStartEnd = new int[2];
1589 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1591 alignmentToExport = hiddenSeqs.getFullAlignment();
1595 alignmentToExport = viewport.getAlignment();
1597 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1598 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1599 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1600 omitHidden, alignmentStartEnd, settings);
1611 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1613 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1614 htmlSVG.exportHTML(null);
1618 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1620 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1621 bjs.exportHTML(null);
1624 public void createImageMap(File file, String image)
1626 alignPanel.makePNGImageMap(file, image);
1636 public void createPNG(File f)
1638 alignPanel.makePNG(f);
1648 public void createEPS(File f)
1650 alignPanel.makeEPS(f);
1654 public void createSVG(File f)
1656 alignPanel.makeSVG(f);
1660 public void pageSetup_actionPerformed(ActionEvent e)
1662 PrinterJob printJob = PrinterJob.getPrinterJob();
1663 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1673 public void printMenuItem_actionPerformed(ActionEvent e)
1675 // Putting in a thread avoids Swing painting problems
1676 PrintThread thread = new PrintThread(alignPanel);
1681 public void exportFeatures_actionPerformed(ActionEvent e)
1683 new AnnotationExporter(alignPanel).exportFeatures();
1687 public void exportAnnotations_actionPerformed(ActionEvent e)
1689 new AnnotationExporter(alignPanel).exportAnnotations();
1693 public void associatedData_actionPerformed(ActionEvent e)
1694 throws IOException, InterruptedException
1696 // Pick the tree file
1697 JalviewFileChooser chooser = new JalviewFileChooser(
1698 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1699 chooser.setFileView(new JalviewFileView());
1700 chooser.setDialogTitle(
1701 MessageManager.getString("label.load_jalview_annotations"));
1702 chooser.setToolTipText(
1703 MessageManager.getString("label.load_jalview_annotations"));
1705 int value = chooser.showOpenDialog(null);
1707 if (value == JalviewFileChooser.APPROVE_OPTION)
1709 String choice = chooser.getSelectedFile().getPath();
1710 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1711 loadJalviewDataFile(choice, null, null, null);
1717 * Close the current view or all views in the alignment frame. If the frame
1718 * only contains one view then the alignment will be removed from memory.
1720 * @param closeAllTabs
1723 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1725 if (alignPanels != null && alignPanels.size() < 2)
1727 closeAllTabs = true;
1732 if (alignPanels != null)
1736 if (this.isClosed())
1738 // really close all the windows - otherwise wait till
1739 // setClosed(true) is called
1740 for (int i = 0; i < alignPanels.size(); i++)
1742 AlignmentPanel ap = alignPanels.get(i);
1749 closeView(alignPanel);
1756 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1757 * be called recursively, with the frame now in 'closed' state
1759 this.setClosed(true);
1761 } catch (Exception ex)
1763 ex.printStackTrace();
1768 * Close the specified panel and close up tabs appropriately.
1770 * @param panelToClose
1772 public void closeView(AlignmentPanel panelToClose)
1774 int index = tabbedPane.getSelectedIndex();
1775 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1776 alignPanels.remove(panelToClose);
1777 panelToClose.closePanel();
1778 panelToClose = null;
1780 tabbedPane.removeTabAt(closedindex);
1781 tabbedPane.validate();
1783 if (index > closedindex || index == tabbedPane.getTabCount())
1785 // modify currently selected tab index if necessary.
1789 this.tabSelectionChanged(index);
1795 void updateEditMenuBar()
1798 if (viewport.getHistoryList().size() > 0)
1800 undoMenuItem.setEnabled(true);
1801 CommandI command = viewport.getHistoryList().peek();
1802 undoMenuItem.setText(MessageManager
1803 .formatMessage("label.undo_command", new Object[]
1804 { command.getDescription() }));
1808 undoMenuItem.setEnabled(false);
1809 undoMenuItem.setText(MessageManager.getString("action.undo"));
1812 if (viewport.getRedoList().size() > 0)
1814 redoMenuItem.setEnabled(true);
1816 CommandI command = viewport.getRedoList().peek();
1817 redoMenuItem.setText(MessageManager
1818 .formatMessage("label.redo_command", new Object[]
1819 { command.getDescription() }));
1823 redoMenuItem.setEnabled(false);
1824 redoMenuItem.setText(MessageManager.getString("action.redo"));
1829 public void addHistoryItem(CommandI command)
1831 if (command.getSize() > 0)
1833 viewport.addToHistoryList(command);
1834 viewport.clearRedoList();
1835 updateEditMenuBar();
1836 viewport.updateHiddenColumns();
1837 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1838 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1839 // viewport.getColumnSelection()
1840 // .getHiddenColumns().size() > 0);
1846 * @return alignment objects for all views
1848 AlignmentI[] getViewAlignments()
1850 if (alignPanels != null)
1852 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1854 for (AlignmentPanel ap : alignPanels)
1856 als[i++] = ap.av.getAlignment();
1860 if (viewport != null)
1862 return new AlignmentI[] { viewport.getAlignment() };
1874 protected void undoMenuItem_actionPerformed(ActionEvent e)
1876 if (viewport.getHistoryList().isEmpty())
1880 CommandI command = viewport.getHistoryList().pop();
1881 viewport.addToRedoList(command);
1882 command.undoCommand(getViewAlignments());
1884 AlignmentViewport originalSource = getOriginatingSource(command);
1885 updateEditMenuBar();
1887 if (originalSource != null)
1889 if (originalSource != viewport)
1892 "Implementation worry: mismatch of viewport origin for undo");
1894 originalSource.updateHiddenColumns();
1895 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1897 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1898 // viewport.getColumnSelection()
1899 // .getHiddenColumns().size() > 0);
1900 originalSource.firePropertyChange("alignment", null,
1901 originalSource.getAlignment().getSequences());
1912 protected void redoMenuItem_actionPerformed(ActionEvent e)
1914 if (viewport.getRedoList().size() < 1)
1919 CommandI command = viewport.getRedoList().pop();
1920 viewport.addToHistoryList(command);
1921 command.doCommand(getViewAlignments());
1923 AlignmentViewport originalSource = getOriginatingSource(command);
1924 updateEditMenuBar();
1926 if (originalSource != null)
1929 if (originalSource != viewport)
1932 "Implementation worry: mismatch of viewport origin for redo");
1934 originalSource.updateHiddenColumns();
1935 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1937 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1938 // viewport.getColumnSelection()
1939 // .getHiddenColumns().size() > 0);
1940 originalSource.firePropertyChange("alignment", null,
1941 originalSource.getAlignment().getSequences());
1945 AlignmentViewport getOriginatingSource(CommandI command)
1947 AlignmentViewport originalSource = null;
1948 // For sequence removal and addition, we need to fire
1949 // the property change event FROM the viewport where the
1950 // original alignment was altered
1951 AlignmentI al = null;
1952 if (command instanceof EditCommand)
1954 EditCommand editCommand = (EditCommand) command;
1955 al = editCommand.getAlignment();
1956 List<Component> comps = PaintRefresher.components
1957 .get(viewport.getSequenceSetId());
1959 for (Component comp : comps)
1961 if (comp instanceof AlignmentPanel)
1963 if (al == ((AlignmentPanel) comp).av.getAlignment())
1965 originalSource = ((AlignmentPanel) comp).av;
1972 if (originalSource == null)
1974 // The original view is closed, we must validate
1975 // the current view against the closed view first
1978 PaintRefresher.validateSequences(al, viewport.getAlignment());
1981 originalSource = viewport;
1984 return originalSource;
1993 public void moveSelectedSequences(boolean up)
1995 SequenceGroup sg = viewport.getSelectionGroup();
2001 viewport.getAlignment().moveSelectedSequencesByOne(sg,
2002 viewport.getHiddenRepSequences(), up);
2003 alignPanel.paintAlignment(true, false);
2006 synchronized void slideSequences(boolean right, int size)
2008 List<SequenceI> sg = new ArrayList<>();
2009 if (viewport.cursorMode)
2011 sg.add(viewport.getAlignment()
2012 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
2014 else if (viewport.getSelectionGroup() != null
2015 && viewport.getSelectionGroup().getSize() != viewport
2016 .getAlignment().getHeight())
2018 sg = viewport.getSelectionGroup()
2019 .getSequences(viewport.getHiddenRepSequences());
2027 List<SequenceI> invertGroup = new ArrayList<>();
2029 for (SequenceI seq : viewport.getAlignment().getSequences())
2031 if (!sg.contains(seq))
2033 invertGroup.add(seq);
2037 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
2039 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
2040 for (int i = 0; i < invertGroup.size(); i++)
2042 seqs2[i] = invertGroup.get(i);
2045 SlideSequencesCommand ssc;
2048 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
2049 viewport.getGapCharacter());
2053 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
2054 viewport.getGapCharacter());
2057 int groupAdjustment = 0;
2058 if (ssc.getGapsInsertedBegin() && right)
2060 if (viewport.cursorMode)
2062 alignPanel.getSeqPanel().moveCursor(size, 0);
2066 groupAdjustment = size;
2069 else if (!ssc.getGapsInsertedBegin() && !right)
2071 if (viewport.cursorMode)
2073 alignPanel.getSeqPanel().moveCursor(-size, 0);
2077 groupAdjustment = -size;
2081 if (groupAdjustment != 0)
2083 viewport.getSelectionGroup().setStartRes(
2084 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
2085 viewport.getSelectionGroup().setEndRes(
2086 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
2090 * just extend the last slide command if compatible; but not if in
2091 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
2093 boolean appendHistoryItem = false;
2094 Deque<CommandI> historyList = viewport.getHistoryList();
2095 boolean inSplitFrame = getSplitViewContainer() != null;
2096 if (!inSplitFrame && historyList != null && historyList.size() > 0
2097 && historyList.peek() instanceof SlideSequencesCommand)
2099 appendHistoryItem = ssc.appendSlideCommand(
2100 (SlideSequencesCommand) historyList.peek());
2103 if (!appendHistoryItem)
2105 addHistoryItem(ssc);
2118 protected void copy_actionPerformed(ActionEvent e)
2120 if (viewport.getSelectionGroup() == null)
2124 // TODO: preserve the ordering of displayed alignment annotation in any
2125 // internal paste (particularly sequence associated annotation)
2126 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
2127 String[] omitHidden = null;
2129 if (viewport.hasHiddenColumns())
2131 omitHidden = viewport.getViewAsString(true);
2134 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2135 seqs, omitHidden, null);
2137 StringSelection ss = new StringSelection(output);
2141 jalview.gui.Desktop.internalCopy = true;
2142 // Its really worth setting the clipboard contents
2143 // to empty before setting the large StringSelection!!
2144 Toolkit.getDefaultToolkit().getSystemClipboard()
2145 .setContents(new StringSelection(""), null);
2147 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2149 } catch (OutOfMemoryError er)
2151 new OOMWarning("copying region", er);
2155 HiddenColumns hiddenColumns = null;
2156 if (viewport.hasHiddenColumns())
2158 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2159 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2161 // create new HiddenColumns object with copy of hidden regions
2162 // between startRes and endRes, offset by startRes
2163 hiddenColumns = new HiddenColumns(
2164 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
2165 hiddenCutoff, hiddenOffset);
2168 Desktop.jalviewClipboard = new Object[] { seqs,
2169 viewport.getAlignment().getDataset(), hiddenColumns };
2170 statusBar.setText(MessageManager.formatMessage(
2171 "label.copied_sequences_to_clipboard", new Object[]
2172 { Integer.valueOf(seqs.length).toString() }));
2180 * @throws InterruptedException
2181 * @throws IOException
2184 protected void pasteNew_actionPerformed(ActionEvent e)
2185 throws IOException, InterruptedException
2195 * @throws InterruptedException
2196 * @throws IOException
2199 protected void pasteThis_actionPerformed(ActionEvent e)
2200 throws IOException, InterruptedException
2206 * Paste contents of Jalview clipboard
2208 * @param newAlignment
2209 * true to paste to a new alignment, otherwise add to this.
2210 * @throws InterruptedException
2211 * @throws IOException
2213 void paste(boolean newAlignment) throws IOException, InterruptedException
2215 boolean externalPaste = true;
2218 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2219 Transferable contents = c.getContents(this);
2221 if (contents == null)
2230 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2231 if (str.length() < 1)
2236 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2238 } catch (OutOfMemoryError er)
2240 new OOMWarning("Out of memory pasting sequences!!", er);
2244 SequenceI[] sequences;
2245 boolean annotationAdded = false;
2246 AlignmentI alignment = null;
2248 if (Desktop.jalviewClipboard != null)
2250 // The clipboard was filled from within Jalview, we must use the
2252 // And dataset from the copied alignment
2253 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2254 // be doubly sure that we create *new* sequence objects.
2255 sequences = new SequenceI[newseq.length];
2256 for (int i = 0; i < newseq.length; i++)
2258 sequences[i] = new Sequence(newseq[i]);
2260 alignment = new Alignment(sequences);
2261 externalPaste = false;
2265 // parse the clipboard as an alignment.
2266 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2268 sequences = alignment.getSequencesArray();
2272 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2278 if (Desktop.jalviewClipboard != null)
2280 // dataset is inherited
2281 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2285 // new dataset is constructed
2286 alignment.setDataset(null);
2288 alwidth = alignment.getWidth() + 1;
2292 AlignmentI pastedal = alignment; // preserve pasted alignment object
2293 // Add pasted sequences and dataset into existing alignment.
2294 alignment = viewport.getAlignment();
2295 alwidth = alignment.getWidth() + 1;
2296 // decide if we need to import sequences from an existing dataset
2297 boolean importDs = Desktop.jalviewClipboard != null
2298 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2299 // importDs==true instructs us to copy over new dataset sequences from
2300 // an existing alignment
2301 Vector newDs = (importDs) ? new Vector() : null; // used to create
2302 // minimum dataset set
2304 for (int i = 0; i < sequences.length; i++)
2308 newDs.addElement(null);
2310 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2312 if (importDs && ds != null)
2314 if (!newDs.contains(ds))
2316 newDs.setElementAt(ds, i);
2317 ds = new Sequence(ds);
2318 // update with new dataset sequence
2319 sequences[i].setDatasetSequence(ds);
2323 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2328 // copy and derive new dataset sequence
2329 sequences[i] = sequences[i].deriveSequence();
2330 alignment.getDataset()
2331 .addSequence(sequences[i].getDatasetSequence());
2332 // TODO: avoid creation of duplicate dataset sequences with a
2333 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2335 alignment.addSequence(sequences[i]); // merges dataset
2339 newDs.clear(); // tidy up
2341 if (alignment.getAlignmentAnnotation() != null)
2343 for (AlignmentAnnotation alan : alignment
2344 .getAlignmentAnnotation())
2346 if (alan.graphGroup > fgroup)
2348 fgroup = alan.graphGroup;
2352 if (pastedal.getAlignmentAnnotation() != null)
2354 // Add any annotation attached to alignment.
2355 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2356 for (int i = 0; i < alann.length; i++)
2358 annotationAdded = true;
2359 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2361 AlignmentAnnotation newann = new AlignmentAnnotation(
2363 if (newann.graphGroup > -1)
2365 if (newGraphGroups.size() <= newann.graphGroup
2366 || newGraphGroups.get(newann.graphGroup) == null)
2368 for (int q = newGraphGroups
2369 .size(); q <= newann.graphGroup; q++)
2371 newGraphGroups.add(q, null);
2373 newGraphGroups.set(newann.graphGroup,
2374 Integer.valueOf(++fgroup));
2376 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2380 newann.padAnnotation(alwidth);
2381 alignment.addAnnotation(newann);
2391 addHistoryItem(new EditCommand(
2392 MessageManager.getString("label.add_sequences"),
2393 Action.PASTE, sequences, 0, alignment.getWidth(),
2396 // Add any annotations attached to sequences
2397 for (int i = 0; i < sequences.length; i++)
2399 if (sequences[i].getAnnotation() != null)
2401 AlignmentAnnotation newann;
2402 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2404 annotationAdded = true;
2405 newann = sequences[i].getAnnotation()[a];
2406 newann.adjustForAlignment();
2407 newann.padAnnotation(alwidth);
2408 if (newann.graphGroup > -1)
2410 if (newann.graphGroup > -1)
2412 if (newGraphGroups.size() <= newann.graphGroup
2413 || newGraphGroups.get(newann.graphGroup) == null)
2415 for (int q = newGraphGroups
2416 .size(); q <= newann.graphGroup; q++)
2418 newGraphGroups.add(q, null);
2420 newGraphGroups.set(newann.graphGroup,
2421 Integer.valueOf(++fgroup));
2423 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2427 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2431 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2439 // propagate alignment changed.
2440 viewport.getRanges().setEndSeq(alignment.getHeight());
2441 if (annotationAdded)
2443 // Duplicate sequence annotation in all views.
2444 AlignmentI[] alview = this.getViewAlignments();
2445 for (int i = 0; i < sequences.length; i++)
2447 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2452 for (int avnum = 0; avnum < alview.length; avnum++)
2454 if (alview[avnum] != alignment)
2456 // duplicate in a view other than the one with input focus
2457 int avwidth = alview[avnum].getWidth() + 1;
2458 // this relies on sann being preserved after we
2459 // modify the sequence's annotation array for each duplication
2460 for (int a = 0; a < sann.length; a++)
2462 AlignmentAnnotation newann = new AlignmentAnnotation(
2464 sequences[i].addAlignmentAnnotation(newann);
2465 newann.padAnnotation(avwidth);
2466 alview[avnum].addAnnotation(newann); // annotation was
2467 // duplicated earlier
2468 // TODO JAL-1145 graphGroups are not updated for sequence
2469 // annotation added to several views. This may cause
2471 alview[avnum].setAnnotationIndex(newann, a);
2476 buildSortByAnnotationScoresMenu();
2478 viewport.firePropertyChange("alignment", null,
2479 alignment.getSequences());
2480 if (alignPanels != null)
2482 for (AlignmentPanel ap : alignPanels)
2484 ap.validateAnnotationDimensions(false);
2489 alignPanel.validateAnnotationDimensions(false);
2495 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2497 String newtitle = new String("Copied sequences");
2499 if (Desktop.jalviewClipboard != null
2500 && Desktop.jalviewClipboard[2] != null)
2502 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2503 af.viewport.setHiddenColumns(hc);
2506 // >>>This is a fix for the moment, until a better solution is
2508 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2509 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2510 .getFeatureRenderer());
2512 // TODO: maintain provenance of an alignment, rather than just make the
2513 // title a concatenation of operations.
2516 if (title.startsWith("Copied sequences"))
2522 newtitle = newtitle.concat("- from " + title);
2527 newtitle = new String("Pasted sequences");
2530 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2535 } catch (Exception ex)
2537 ex.printStackTrace();
2538 System.out.println("Exception whilst pasting: " + ex);
2539 // could be anything being pasted in here
2544 protected void expand_newalign(ActionEvent e)
2548 AlignmentI alignment = AlignmentUtils
2549 .expandContext(getViewport().getAlignment(), -1);
2550 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2552 String newtitle = new String("Flanking alignment");
2554 if (Desktop.jalviewClipboard != null
2555 && Desktop.jalviewClipboard[2] != null)
2557 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2558 af.viewport.setHiddenColumns(hc);
2561 // >>>This is a fix for the moment, until a better solution is
2563 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2564 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2565 .getFeatureRenderer());
2567 // TODO: maintain provenance of an alignment, rather than just make the
2568 // title a concatenation of operations.
2570 if (title.startsWith("Copied sequences"))
2576 newtitle = newtitle.concat("- from " + title);
2580 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2582 } catch (Exception ex)
2584 ex.printStackTrace();
2585 System.out.println("Exception whilst pasting: " + ex);
2586 // could be anything being pasted in here
2587 } catch (OutOfMemoryError oom)
2589 new OOMWarning("Viewing flanking region of alignment", oom);
2600 protected void cut_actionPerformed(ActionEvent e)
2602 copy_actionPerformed(null);
2603 delete_actionPerformed(null);
2613 protected void delete_actionPerformed(ActionEvent evt)
2616 SequenceGroup sg = viewport.getSelectionGroup();
2623 * If the cut affects all sequences, warn, remove highlighted columns
2625 if (sg.getSize() == viewport.getAlignment().getHeight())
2627 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2628 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2629 if (isEntireAlignWidth)
2631 int confirm = JvOptionPane.showConfirmDialog(this,
2632 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2633 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2634 JvOptionPane.OK_CANCEL_OPTION);
2636 if (confirm == JvOptionPane.CANCEL_OPTION
2637 || confirm == JvOptionPane.CLOSED_OPTION)
2642 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2643 sg.getEndRes() + 1);
2645 SequenceI[] cut = sg.getSequences()
2646 .toArray(new SequenceI[sg.getSize()]);
2648 addHistoryItem(new EditCommand(
2649 MessageManager.getString("label.cut_sequences"), Action.CUT,
2650 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2651 viewport.getAlignment()));
2653 viewport.setSelectionGroup(null);
2654 viewport.sendSelection();
2655 viewport.getAlignment().deleteGroup(sg);
2657 viewport.firePropertyChange("alignment", null,
2658 viewport.getAlignment().getSequences());
2659 if (viewport.getAlignment().getHeight() < 1)
2663 this.setClosed(true);
2664 } catch (Exception ex)
2677 protected void deleteGroups_actionPerformed(ActionEvent e)
2679 if (avc.deleteGroups())
2681 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2682 alignPanel.updateAnnotation();
2683 alignPanel.paintAlignment(true, true);
2694 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2696 SequenceGroup sg = new SequenceGroup(
2697 viewport.getAlignment().getSequences());
2699 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2700 viewport.setSelectionGroup(sg);
2701 viewport.isSelectionGroupChanged(true);
2702 viewport.sendSelection();
2703 // JAL-2034 - should delegate to
2704 // alignPanel to decide if overview needs
2706 alignPanel.paintAlignment(false, false);
2707 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2717 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2719 if (viewport.cursorMode)
2721 alignPanel.getSeqPanel().keyboardNo1 = null;
2722 alignPanel.getSeqPanel().keyboardNo2 = null;
2724 viewport.setSelectionGroup(null);
2725 viewport.getColumnSelection().clear();
2726 viewport.setSelectionGroup(null);
2727 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2728 // JAL-2034 - should delegate to
2729 // alignPanel to decide if overview needs
2731 alignPanel.paintAlignment(false, false);
2732 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2733 viewport.sendSelection();
2743 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2745 SequenceGroup sg = viewport.getSelectionGroup();
2749 selectAllSequenceMenuItem_actionPerformed(null);
2754 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2756 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2758 // JAL-2034 - should delegate to
2759 // alignPanel to decide if overview needs
2762 alignPanel.paintAlignment(true, false);
2763 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2764 viewport.sendSelection();
2768 public void invertColSel_actionPerformed(ActionEvent e)
2770 viewport.invertColumnSelection();
2771 alignPanel.paintAlignment(true, false);
2772 viewport.sendSelection();
2782 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2784 trimAlignment(true);
2794 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2796 trimAlignment(false);
2799 void trimAlignment(boolean trimLeft)
2801 ColumnSelection colSel = viewport.getColumnSelection();
2804 if (!colSel.isEmpty())
2808 column = colSel.getMin();
2812 column = colSel.getMax();
2816 if (viewport.getSelectionGroup() != null)
2818 seqs = viewport.getSelectionGroup()
2819 .getSequencesAsArray(viewport.getHiddenRepSequences());
2823 seqs = viewport.getAlignment().getSequencesArray();
2826 TrimRegionCommand trimRegion;
2829 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2830 column, viewport.getAlignment());
2831 viewport.getRanges().setStartRes(0);
2835 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2836 column, viewport.getAlignment());
2839 statusBar.setText(MessageManager
2840 .formatMessage("label.removed_columns", new String[]
2841 { Integer.valueOf(trimRegion.getSize()).toString() }));
2843 addHistoryItem(trimRegion);
2845 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2847 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2848 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2850 viewport.getAlignment().deleteGroup(sg);
2854 viewport.firePropertyChange("alignment", null,
2855 viewport.getAlignment().getSequences());
2866 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2868 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2871 if (viewport.getSelectionGroup() != null)
2873 seqs = viewport.getSelectionGroup()
2874 .getSequencesAsArray(viewport.getHiddenRepSequences());
2875 start = viewport.getSelectionGroup().getStartRes();
2876 end = viewport.getSelectionGroup().getEndRes();
2880 seqs = viewport.getAlignment().getSequencesArray();
2883 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2884 "Remove Gapped Columns", seqs, start, end,
2885 viewport.getAlignment());
2887 addHistoryItem(removeGapCols);
2889 statusBar.setText(MessageManager
2890 .formatMessage("label.removed_empty_columns", new Object[]
2891 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2893 // This is to maintain viewport position on first residue
2894 // of first sequence
2895 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2896 ViewportRanges ranges = viewport.getRanges();
2897 int startRes = seq.findPosition(ranges.getStartRes());
2898 // ShiftList shifts;
2899 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2900 // edit.alColumnChanges=shifts.getInverse();
2901 // if (viewport.hasHiddenColumns)
2902 // viewport.getColumnSelection().compensateForEdits(shifts);
2903 ranges.setStartRes(seq.findIndex(startRes) - 1);
2904 viewport.firePropertyChange("alignment", null,
2905 viewport.getAlignment().getSequences());
2916 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2918 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2921 if (viewport.getSelectionGroup() != null)
2923 seqs = viewport.getSelectionGroup()
2924 .getSequencesAsArray(viewport.getHiddenRepSequences());
2925 start = viewport.getSelectionGroup().getStartRes();
2926 end = viewport.getSelectionGroup().getEndRes();
2930 seqs = viewport.getAlignment().getSequencesArray();
2933 // This is to maintain viewport position on first residue
2934 // of first sequence
2935 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2936 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2938 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2939 viewport.getAlignment()));
2941 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2943 viewport.firePropertyChange("alignment", null,
2944 viewport.getAlignment().getSequences());
2955 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2957 viewport.setPadGaps(padGapsMenuitem.isSelected());
2958 viewport.firePropertyChange("alignment", null,
2959 viewport.getAlignment().getSequences());
2969 public void findMenuItem_actionPerformed(ActionEvent e)
2975 * Create a new view of the current alignment.
2978 public void newView_actionPerformed(ActionEvent e)
2980 newView(null, true);
2984 * Creates and shows a new view of the current alignment.
2987 * title of newly created view; if null, one will be generated
2988 * @param copyAnnotation
2989 * if true then duplicate all annnotation, groups and settings
2990 * @return new alignment panel, already displayed.
2992 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2995 * Create a new AlignmentPanel (with its own, new Viewport)
2997 AlignmentPanel newap = new jalview.project.Jalview2XML()
2998 .copyAlignPanel(alignPanel);
2999 if (!copyAnnotation)
3002 * remove all groups and annotation except for the automatic stuff
3004 newap.av.getAlignment().deleteAllGroups();
3005 newap.av.getAlignment().deleteAllAnnotations(false);
3008 newap.av.setGatherViewsHere(false);
3010 if (viewport.getViewName() == null)
3012 viewport.setViewName(MessageManager
3013 .getString("label.view_name_original"));
3017 * Views share the same edits undo and redo stacks
3019 newap.av.setHistoryList(viewport.getHistoryList());
3020 newap.av.setRedoList(viewport.getRedoList());
3023 * copy any visualisation settings that are not saved in the project
3025 newap.av.setColourAppliesToAllGroups(
3026 viewport.getColourAppliesToAllGroups());
3029 * Views share the same mappings; need to deregister any new mappings
3030 * created by copyAlignPanel, and register the new reference to the shared
3033 newap.av.replaceMappings(viewport.getAlignment());
3036 * start up cDNA consensus (if applicable) now mappings are in place
3038 if (newap.av.initComplementConsensus())
3040 newap.refresh(true); // adjust layout of annotations
3043 newap.av.setViewName(getNewViewName(viewTitle));
3045 addAlignmentPanel(newap, true);
3046 newap.alignmentChanged();
3048 if (alignPanels.size() == 2)
3050 viewport.setGatherViewsHere(true);
3052 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
3057 * Make a new name for the view, ensuring it is unique within the current
3058 * sequenceSetId. (This used to be essential for Jalview Project archives, but
3059 * these now use viewId. Unique view names are still desirable for usability.)
3064 protected String getNewViewName(String viewTitle)
3066 int index = Desktop.getViewCount(viewport.getSequenceSetId());
3067 boolean addFirstIndex = false;
3068 if (viewTitle == null || viewTitle.trim().length() == 0)
3070 viewTitle = MessageManager.getString("action.view");
3071 addFirstIndex = true;
3075 index = 1;// we count from 1 if given a specific name
3077 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
3079 List<Component> comps = PaintRefresher.components
3080 .get(viewport.getSequenceSetId());
3082 List<String> existingNames = getExistingViewNames(comps);
3084 while (existingNames.contains(newViewName))
3086 newViewName = viewTitle + " " + (++index);
3092 * Returns a list of distinct view names found in the given list of
3093 * components. View names are held on the viewport of an AlignmentPanel.
3098 protected List<String> getExistingViewNames(List<Component> comps)
3100 List<String> existingNames = new ArrayList<>();
3101 for (Component comp : comps)
3103 if (comp instanceof AlignmentPanel)
3105 AlignmentPanel ap = (AlignmentPanel) comp;
3106 if (!existingNames.contains(ap.av.getViewName()))
3108 existingNames.add(ap.av.getViewName());
3112 return existingNames;
3116 * Explode tabbed views into separate windows.
3119 public void expandViews_actionPerformed(ActionEvent e)
3121 Desktop.explodeViews(this);
3125 * Gather views in separate windows back into a tabbed presentation.
3128 public void gatherViews_actionPerformed(ActionEvent e)
3130 Desktop.instance.gatherViews(this);
3140 public void font_actionPerformed(ActionEvent e)
3142 new FontChooser(alignPanel);
3152 protected void seqLimit_actionPerformed(ActionEvent e)
3154 viewport.setShowJVSuffix(seqLimits.isSelected());
3156 alignPanel.getIdPanel().getIdCanvas()
3157 .setPreferredSize(alignPanel.calculateIdWidth());
3158 alignPanel.paintAlignment(true, false);
3162 public void idRightAlign_actionPerformed(ActionEvent e)
3164 viewport.setRightAlignIds(idRightAlign.isSelected());
3165 alignPanel.paintAlignment(false, false);
3169 public void centreColumnLabels_actionPerformed(ActionEvent e)
3171 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3172 alignPanel.paintAlignment(false, false);
3178 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3181 protected void followHighlight_actionPerformed()
3184 * Set the 'follow' flag on the Viewport (and scroll to position if now
3187 final boolean state = this.followHighlightMenuItem.getState();
3188 viewport.setFollowHighlight(state);
3191 alignPanel.scrollToPosition(viewport.getSearchResults());
3202 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3204 viewport.setColourText(colourTextMenuItem.isSelected());
3205 alignPanel.paintAlignment(false, false);
3215 public void wrapMenuItem_actionPerformed(ActionEvent e)
3217 scaleAbove.setVisible(wrapMenuItem.isSelected());
3218 scaleLeft.setVisible(wrapMenuItem.isSelected());
3219 scaleRight.setVisible(wrapMenuItem.isSelected());
3220 viewport.setWrapAlignment(wrapMenuItem.isSelected());
3221 alignPanel.updateLayout();
3225 public void showAllSeqs_actionPerformed(ActionEvent e)
3227 viewport.showAllHiddenSeqs();
3231 public void showAllColumns_actionPerformed(ActionEvent e)
3233 viewport.showAllHiddenColumns();
3234 alignPanel.paintAlignment(true, true);
3235 viewport.sendSelection();
3239 public void hideSelSequences_actionPerformed(ActionEvent e)
3241 viewport.hideAllSelectedSeqs();
3245 * called by key handler and the hide all/show all menu items
3250 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3253 boolean hide = false;
3254 SequenceGroup sg = viewport.getSelectionGroup();
3255 if (!toggleSeqs && !toggleCols)
3257 // Hide everything by the current selection - this is a hack - we do the
3258 // invert and then hide
3259 // first check that there will be visible columns after the invert.
3260 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3261 && sg.getStartRes() <= sg.getEndRes()))
3263 // now invert the sequence set, if required - empty selection implies
3264 // that no hiding is required.
3267 invertSequenceMenuItem_actionPerformed(null);
3268 sg = viewport.getSelectionGroup();
3272 viewport.expandColSelection(sg, true);
3273 // finally invert the column selection and get the new sequence
3275 invertColSel_actionPerformed(null);
3282 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3284 hideSelSequences_actionPerformed(null);
3287 else if (!(toggleCols && viewport.hasSelectedColumns()))
3289 showAllSeqs_actionPerformed(null);
3295 if (viewport.hasSelectedColumns())
3297 hideSelColumns_actionPerformed(null);
3300 viewport.setSelectionGroup(sg);
3305 showAllColumns_actionPerformed(null);
3314 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3315 * event.ActionEvent)
3318 public void hideAllButSelection_actionPerformed(ActionEvent e)
3320 toggleHiddenRegions(false, false);
3321 viewport.sendSelection();
3328 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3332 public void hideAllSelection_actionPerformed(ActionEvent e)
3334 SequenceGroup sg = viewport.getSelectionGroup();
3335 viewport.expandColSelection(sg, false);
3336 viewport.hideAllSelectedSeqs();
3337 viewport.hideSelectedColumns();
3338 alignPanel.updateLayout();
3339 alignPanel.paintAlignment(true, true);
3340 viewport.sendSelection();
3347 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3351 public void showAllhidden_actionPerformed(ActionEvent e)
3353 viewport.showAllHiddenColumns();
3354 viewport.showAllHiddenSeqs();
3355 alignPanel.paintAlignment(true, true);
3356 viewport.sendSelection();
3360 public void hideSelColumns_actionPerformed(ActionEvent e)
3362 viewport.hideSelectedColumns();
3363 alignPanel.updateLayout();
3364 alignPanel.paintAlignment(true, true);
3365 viewport.sendSelection();
3369 public void hiddenMarkers_actionPerformed(ActionEvent e)
3371 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3382 protected void scaleAbove_actionPerformed(ActionEvent e)
3384 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3385 alignPanel.updateLayout();
3386 alignPanel.paintAlignment(true, false);
3396 protected void scaleLeft_actionPerformed(ActionEvent e)
3398 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3399 alignPanel.updateLayout();
3400 alignPanel.paintAlignment(true, false);
3410 protected void scaleRight_actionPerformed(ActionEvent e)
3412 viewport.setScaleRightWrapped(scaleRight.isSelected());
3413 alignPanel.updateLayout();
3414 alignPanel.paintAlignment(true, false);
3424 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3426 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3427 alignPanel.paintAlignment(false, false);
3437 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3439 viewport.setShowText(viewTextMenuItem.isSelected());
3440 alignPanel.paintAlignment(false, false);
3450 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3452 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3453 alignPanel.paintAlignment(false, false);
3456 public FeatureSettings featureSettings;
3459 public FeatureSettingsControllerI getFeatureSettingsUI()
3461 return featureSettings;
3465 public void featureSettings_actionPerformed(ActionEvent e)
3467 if (featureSettings != null)
3469 featureSettings.close();
3470 featureSettings = null;
3472 if (!showSeqFeatures.isSelected())
3474 // make sure features are actually displayed
3475 showSeqFeatures.setSelected(true);
3476 showSeqFeatures_actionPerformed(null);
3478 featureSettings = new FeatureSettings(this);
3482 * Set or clear 'Show Sequence Features'
3488 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3490 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3491 alignPanel.paintAlignment(true, true);
3495 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3496 * the annotations panel as a whole.
3498 * The options to show/hide all annotations should be enabled when the panel
3499 * is shown, and disabled when the panel is hidden.
3504 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3506 final boolean setVisible = annotationPanelMenuItem.isSelected();
3507 viewport.setShowAnnotation(setVisible);
3508 this.showAllSeqAnnotations.setEnabled(setVisible);
3509 this.hideAllSeqAnnotations.setEnabled(setVisible);
3510 this.showAllAlAnnotations.setEnabled(setVisible);
3511 this.hideAllAlAnnotations.setEnabled(setVisible);
3512 alignPanel.updateLayout();
3516 public void alignmentProperties()
3518 JEditorPane editPane = new JEditorPane("text/html", "");
3519 editPane.setEditable(false);
3520 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3523 MessageManager.formatMessage("label.html_content", new Object[]
3524 { contents.toString() }));
3525 JInternalFrame frame = new JInternalFrame();
3526 frame.getContentPane().add(new JScrollPane(editPane));
3528 Desktop.addInternalFrame(frame, MessageManager
3529 .formatMessage("label.alignment_properties", new Object[]
3530 { getTitle() }), 500, 400);
3540 public void overviewMenuItem_actionPerformed(ActionEvent e)
3542 if (alignPanel.overviewPanel != null)
3547 JInternalFrame frame = new JInternalFrame();
3548 final OverviewPanel overview = new OverviewPanel(alignPanel);
3549 frame.setContentPane(overview);
3550 Desktop.addInternalFrame(frame, MessageManager
3551 .formatMessage("label.overview_params", new Object[]
3552 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3555 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3556 frame.addInternalFrameListener(
3557 new javax.swing.event.InternalFrameAdapter()
3560 public void internalFrameClosed(
3561 javax.swing.event.InternalFrameEvent evt)
3564 alignPanel.setOverviewPanel(null);
3567 if (getKeyListeners().length > 0)
3569 frame.addKeyListener(getKeyListeners()[0]);
3572 alignPanel.setOverviewPanel(overview);
3576 public void textColour_actionPerformed()
3578 new TextColourChooser().chooseColour(alignPanel, null);
3582 * public void covariationColour_actionPerformed() {
3584 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3588 public void annotationColour_actionPerformed()
3590 new AnnotationColourChooser(viewport, alignPanel);
3594 public void annotationColumn_actionPerformed(ActionEvent e)
3596 new AnnotationColumnChooser(viewport, alignPanel);
3600 * Action on the user checking or unchecking the option to apply the selected
3601 * colour scheme to all groups. If unchecked, groups may have their own
3602 * independent colour schemes.
3607 public void applyToAllGroups_actionPerformed(boolean selected)
3609 viewport.setColourAppliesToAllGroups(selected);
3613 * Action on user selecting a colour from the colour menu
3616 * the name (not the menu item label!) of the colour scheme
3619 public void changeColour_actionPerformed(String name)
3622 * 'User Defined' opens a panel to configure or load a
3623 * user-defined colour scheme
3625 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3627 new UserDefinedColours(alignPanel);
3632 * otherwise set the chosen colour scheme (or null for 'None')
3634 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3636 viewport.getAlignment(), viewport.getHiddenRepSequences());
3641 * Actions on setting or changing the alignment colour scheme
3646 public void changeColour(ColourSchemeI cs)
3648 // TODO: pull up to controller method
3649 ColourMenuHelper.setColourSelected(colourMenu, cs);
3651 viewport.setGlobalColourScheme(cs);
3653 alignPanel.paintAlignment(true, true);
3657 * Show the PID threshold slider panel
3660 protected void modifyPID_actionPerformed()
3662 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3663 alignPanel.getViewName());
3664 SliderPanel.showPIDSlider();
3668 * Show the Conservation slider panel
3671 protected void modifyConservation_actionPerformed()
3673 SliderPanel.setConservationSlider(alignPanel,
3674 viewport.getResidueShading(), alignPanel.getViewName());
3675 SliderPanel.showConservationSlider();
3679 * Action on selecting or deselecting (Colour) By Conservation
3682 public void conservationMenuItem_actionPerformed(boolean selected)
3684 modifyConservation.setEnabled(selected);
3685 viewport.setConservationSelected(selected);
3686 viewport.getResidueShading().setConservationApplied(selected);
3688 changeColour(viewport.getGlobalColourScheme());
3691 modifyConservation_actionPerformed();
3695 SliderPanel.hideConservationSlider();
3700 * Action on selecting or deselecting (Colour) Above PID Threshold
3703 public void abovePIDThreshold_actionPerformed(boolean selected)
3705 modifyPID.setEnabled(selected);
3706 viewport.setAbovePIDThreshold(selected);
3709 viewport.getResidueShading().setThreshold(0,
3710 viewport.isIgnoreGapsConsensus());
3713 changeColour(viewport.getGlobalColourScheme());
3716 modifyPID_actionPerformed();
3720 SliderPanel.hidePIDSlider();
3731 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3733 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3734 AlignmentSorter.sortByPID(viewport.getAlignment(),
3735 viewport.getAlignment().getSequenceAt(0));
3736 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3737 viewport.getAlignment()));
3738 alignPanel.paintAlignment(true, false);
3748 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3750 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3751 AlignmentSorter.sortByID(viewport.getAlignment());
3753 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3754 alignPanel.paintAlignment(true, false);
3764 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3766 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3767 AlignmentSorter.sortByLength(viewport.getAlignment());
3768 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3769 viewport.getAlignment()));
3770 alignPanel.paintAlignment(true, false);
3780 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3782 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3783 AlignmentSorter.sortByGroup(viewport.getAlignment());
3784 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3785 viewport.getAlignment()));
3787 alignPanel.paintAlignment(true, false);
3797 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3799 new RedundancyPanel(alignPanel, this);
3809 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3811 if ((viewport.getSelectionGroup() == null)
3812 || (viewport.getSelectionGroup().getSize() < 2))
3814 JvOptionPane.showInternalMessageDialog(this,
3815 MessageManager.getString(
3816 "label.you_must_select_least_two_sequences"),
3817 MessageManager.getString("label.invalid_selection"),
3818 JvOptionPane.WARNING_MESSAGE);
3822 JInternalFrame frame = new JInternalFrame();
3823 frame.setContentPane(new PairwiseAlignPanel(viewport));
3824 Desktop.addInternalFrame(frame,
3825 MessageManager.getString("action.pairwise_alignment"), 600,
3831 public void autoCalculate_actionPerformed(ActionEvent e)
3833 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3834 if (viewport.autoCalculateConsensus)
3836 viewport.firePropertyChange("alignment", null,
3837 viewport.getAlignment().getSequences());
3842 public void sortByTreeOption_actionPerformed(ActionEvent e)
3844 viewport.sortByTree = sortByTree.isSelected();
3848 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3850 viewport.followSelection = listenToViewSelections.isSelected();
3854 * Constructs a tree panel and adds it to the desktop
3857 * tree type (NJ or AV)
3859 * name of score model used to compute the tree
3861 * parameters for the distance or similarity calculation
3863 void newTreePanel(String type, String modelName,
3864 SimilarityParamsI options)
3866 String frameTitle = "";
3869 boolean onSelection = false;
3870 if (viewport.getSelectionGroup() != null
3871 && viewport.getSelectionGroup().getSize() > 0)
3873 SequenceGroup sg = viewport.getSelectionGroup();
3875 /* Decide if the selection is a column region */
3876 for (SequenceI _s : sg.getSequences())
3878 if (_s.getLength() < sg.getEndRes())
3880 JvOptionPane.showMessageDialog(Desktop.desktop,
3881 MessageManager.getString(
3882 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3883 MessageManager.getString(
3884 "label.sequences_selection_not_aligned"),
3885 JvOptionPane.WARNING_MESSAGE);
3894 if (viewport.getAlignment().getHeight() < 2)
3900 tp = new TreePanel(alignPanel, type, modelName, options);
3901 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3903 frameTitle += " from ";
3905 if (viewport.getViewName() != null)
3907 frameTitle += viewport.getViewName() + " of ";
3910 frameTitle += this.title;
3912 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3923 public void addSortByOrderMenuItem(String title,
3924 final AlignmentOrder order)
3926 final JMenuItem item = new JMenuItem(MessageManager
3927 .formatMessage("action.by_title_param", new Object[]
3930 item.addActionListener(new java.awt.event.ActionListener()
3933 public void actionPerformed(ActionEvent e)
3935 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3937 // TODO: JBPNote - have to map order entries to curent SequenceI
3939 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3941 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3942 viewport.getAlignment()));
3944 alignPanel.paintAlignment(true, false);
3950 * Add a new sort by annotation score menu item
3953 * the menu to add the option to
3955 * the label used to retrieve scores for each sequence on the
3958 public void addSortByAnnotScoreMenuItem(JMenu sort,
3959 final String scoreLabel)
3961 final JMenuItem item = new JMenuItem(scoreLabel);
3963 item.addActionListener(new java.awt.event.ActionListener()
3966 public void actionPerformed(ActionEvent e)
3968 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3969 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3970 viewport.getAlignment());// ,viewport.getSelectionGroup());
3971 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3972 viewport.getAlignment()));
3973 alignPanel.paintAlignment(true, false);
3979 * last hash for alignment's annotation array - used to minimise cost of
3982 protected int _annotationScoreVectorHash;
3985 * search the alignment and rebuild the sort by annotation score submenu the
3986 * last alignment annotation vector hash is stored to minimize cost of
3987 * rebuilding in subsequence calls.
3991 public void buildSortByAnnotationScoresMenu()
3993 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3998 if (viewport.getAlignment().getAlignmentAnnotation()
3999 .hashCode() == _annotationScoreVectorHash)
4004 sortByAnnotScore.removeAll();
4005 Set<String> scoreSorts = new HashSet<>();
4006 for (SequenceI sqa : viewport.getAlignment().getSequences())
4008 AlignmentAnnotation[] anns = sqa.getAnnotation();
4009 for (int i = 0; anns != null && i < anns.length; i++)
4011 AlignmentAnnotation aa = anns[i];
4012 if (aa != null && aa.hasScore() && aa.sequenceRef != null)
4014 scoreSorts.add(aa.label);
4018 for (String label : scoreSorts)
4020 addSortByAnnotScoreMenuItem(sortByAnnotScore, label);
4022 sortByAnnotScore.setVisible(!scoreSorts.isEmpty());
4024 _annotationScoreVectorHash = viewport.getAlignment()
4025 .getAlignmentAnnotation().hashCode();
4029 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4030 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4031 * call. Listeners are added to remove the menu item when the treePanel is
4032 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4036 public void buildTreeSortMenu()
4038 sortByTreeMenu.removeAll();
4040 List<Component> comps = PaintRefresher.components
4041 .get(viewport.getSequenceSetId());
4042 List<TreePanel> treePanels = new ArrayList<>();
4043 for (Component comp : comps)
4045 if (comp instanceof TreePanel)
4047 treePanels.add((TreePanel) comp);
4051 if (treePanels.size() < 1)
4053 sortByTreeMenu.setVisible(false);
4057 sortByTreeMenu.setVisible(true);
4059 for (final TreePanel tp : treePanels)
4061 final JMenuItem item = new JMenuItem(tp.getTitle());
4062 item.addActionListener(new java.awt.event.ActionListener()
4065 public void actionPerformed(ActionEvent e)
4067 tp.sortByTree_actionPerformed();
4068 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4073 sortByTreeMenu.add(item);
4077 public boolean sortBy(AlignmentOrder alorder, String undoname)
4079 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4080 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4081 if (undoname != null)
4083 addHistoryItem(new OrderCommand(undoname, oldOrder,
4084 viewport.getAlignment()));
4086 alignPanel.paintAlignment(true, false);
4091 * Work out whether the whole set of sequences or just the selected set will
4092 * be submitted for multiple alignment.
4095 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4097 // Now, check we have enough sequences
4098 AlignmentView msa = null;
4100 if ((viewport.getSelectionGroup() != null)
4101 && (viewport.getSelectionGroup().getSize() > 1))
4103 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4104 // some common interface!
4106 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4107 * SequenceI[sz = seqs.getSize(false)];
4109 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4110 * seqs.getSequenceAt(i); }
4112 msa = viewport.getAlignmentView(true);
4114 else if (viewport.getSelectionGroup() != null
4115 && viewport.getSelectionGroup().getSize() == 1)
4117 int option = JvOptionPane.showConfirmDialog(this,
4118 MessageManager.getString("warn.oneseq_msainput_selection"),
4119 MessageManager.getString("label.invalid_selection"),
4120 JvOptionPane.OK_CANCEL_OPTION);
4121 if (option == JvOptionPane.OK_OPTION)
4123 msa = viewport.getAlignmentView(false);
4128 msa = viewport.getAlignmentView(false);
4134 * Decides what is submitted to a secondary structure prediction service: the
4135 * first sequence in the alignment, or in the current selection, or, if the
4136 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4137 * region or the whole alignment. (where the first sequence in the set is the
4138 * one that the prediction will be for).
4140 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4142 AlignmentView seqs = null;
4144 if ((viewport.getSelectionGroup() != null)
4145 && (viewport.getSelectionGroup().getSize() > 0))
4147 seqs = viewport.getAlignmentView(true);
4151 seqs = viewport.getAlignmentView(false);
4153 // limit sequences - JBPNote in future - could spawn multiple prediction
4155 // TODO: viewport.getAlignment().isAligned is a global state - the local
4156 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4157 if (!viewport.getAlignment().isAligned(false))
4159 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4160 // TODO: if seqs.getSequences().length>1 then should really have warned
4174 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4176 // Pick the tree file
4177 JalviewFileChooser chooser = new JalviewFileChooser(
4178 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4179 chooser.setFileView(new JalviewFileView());
4180 chooser.setDialogTitle(
4181 MessageManager.getString("label.select_newick_like_tree_file"));
4182 chooser.setToolTipText(
4183 MessageManager.getString("label.load_tree_file"));
4185 int value = chooser.showOpenDialog(null);
4187 if (value == JalviewFileChooser.APPROVE_OPTION)
4189 String filePath = chooser.getSelectedFile().getPath();
4190 Cache.setProperty("LAST_DIRECTORY", filePath);
4191 NewickFile fin = null;
4194 fin = new NewickFile(filePath, DataSourceType.FILE);
4195 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4196 } catch (Exception ex)
4198 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4199 MessageManager.getString("label.problem_reading_tree_file"),
4200 JvOptionPane.WARNING_MESSAGE);
4201 ex.printStackTrace();
4203 if (fin != null && fin.hasWarningMessage())
4205 JvOptionPane.showMessageDialog(Desktop.desktop,
4206 fin.getWarningMessage(),
4208 .getString("label.possible_problem_with_tree_file"),
4209 JvOptionPane.WARNING_MESSAGE);
4214 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4216 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4219 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4220 int h, int x, int y)
4222 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4226 * Add a treeviewer for the tree extracted from a Newick file object to the
4227 * current alignment view
4234 * Associated alignment input data (or null)
4243 * @return TreePanel handle
4245 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4246 AlignmentView input, int w, int h, int x, int y)
4248 TreePanel tp = null;
4254 if (nf.getTree() != null)
4256 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4262 tp.setLocation(x, y);
4265 Desktop.addInternalFrame(tp, treeTitle, w, h);
4267 } catch (Exception ex)
4269 ex.printStackTrace();
4275 private boolean buildingMenu = false;
4278 * Generates menu items and listener event actions for web service clients
4281 public void BuildWebServiceMenu()
4283 while (buildingMenu)
4287 System.err.println("Waiting for building menu to finish.");
4289 } catch (Exception e)
4293 final AlignFrame me = this;
4294 buildingMenu = true;
4295 new Thread(new Runnable()
4300 final List<JMenuItem> legacyItems = new ArrayList<>();
4303 // System.err.println("Building ws menu again "
4304 // + Thread.currentThread());
4305 // TODO: add support for context dependent disabling of services based
4307 // alignment and current selection
4308 // TODO: add additional serviceHandle parameter to specify abstract
4310 // class independently of AbstractName
4311 // TODO: add in rediscovery GUI function to restart discoverer
4312 // TODO: group services by location as well as function and/or
4314 // object broker mechanism.
4315 final Vector<JMenu> wsmenu = new Vector<>();
4316 final IProgressIndicator af = me;
4319 * do not i18n these strings - they are hard-coded in class
4320 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4321 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4323 final JMenu msawsmenu = new JMenu("Alignment");
4324 final JMenu secstrmenu = new JMenu(
4325 "Secondary Structure Prediction");
4326 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4327 final JMenu analymenu = new JMenu("Analysis");
4328 final JMenu dismenu = new JMenu("Protein Disorder");
4329 // JAL-940 - only show secondary structure prediction services from
4330 // the legacy server
4331 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4333 Discoverer.services != null && (Discoverer.services.size() > 0))
4335 // TODO: refactor to allow list of AbstractName/Handler bindings to
4337 // stored or retrieved from elsewhere
4338 // No MSAWS used any more:
4339 // Vector msaws = null; // (Vector)
4340 // Discoverer.services.get("MsaWS");
4341 Vector secstrpr = (Vector) Discoverer.services
4343 if (secstrpr != null)
4345 // Add any secondary structure prediction services
4346 for (int i = 0, j = secstrpr.size(); i < j; i++)
4348 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4350 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4351 .getServiceClient(sh);
4352 int p = secstrmenu.getItemCount();
4353 impl.attachWSMenuEntry(secstrmenu, me);
4354 int q = secstrmenu.getItemCount();
4355 for (int litm = p; litm < q; litm++)
4357 legacyItems.add(secstrmenu.getItem(litm));
4363 // Add all submenus in the order they should appear on the web
4365 wsmenu.add(msawsmenu);
4366 wsmenu.add(secstrmenu);
4367 wsmenu.add(dismenu);
4368 wsmenu.add(analymenu);
4369 // No search services yet
4370 // wsmenu.add(seqsrchmenu);
4372 javax.swing.SwingUtilities.invokeLater(new Runnable()
4379 webService.removeAll();
4380 // first, add discovered services onto the webservices menu
4381 if (wsmenu.size() > 0)
4383 for (int i = 0, j = wsmenu.size(); i < j; i++)
4385 webService.add(wsmenu.get(i));
4390 webService.add(me.webServiceNoServices);
4392 // TODO: move into separate menu builder class.
4393 boolean new_sspred = false;
4394 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4396 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4397 if (jws2servs != null)
4399 if (jws2servs.hasServices())
4401 jws2servs.attachWSMenuEntry(webService, me);
4402 for (Jws2Instance sv : jws2servs.getServices())
4404 if (sv.description.toLowerCase().contains("jpred"))
4406 for (JMenuItem jmi : legacyItems)
4408 jmi.setVisible(false);
4414 if (jws2servs.isRunning())
4416 JMenuItem tm = new JMenuItem(
4417 "Still discovering JABA Services");
4418 tm.setEnabled(false);
4423 build_urlServiceMenu(me.webService);
4424 build_fetchdbmenu(webService);
4425 for (JMenu item : wsmenu)
4427 if (item.getItemCount() == 0)
4429 item.setEnabled(false);
4433 item.setEnabled(true);
4436 } catch (Exception e)
4439 "Exception during web service menu building process.",
4444 } catch (Exception e)
4447 buildingMenu = false;
4454 * construct any groupURL type service menu entries.
4458 private void build_urlServiceMenu(JMenu webService)
4460 // TODO: remove this code when 2.7 is released
4461 // DEBUG - alignmentView
4463 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4464 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4466 * @Override public void actionPerformed(ActionEvent e) {
4467 * jalview.datamodel.AlignmentView
4468 * .testSelectionViews(af.viewport.getAlignment(),
4469 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4471 * }); webService.add(testAlView);
4473 // TODO: refactor to RestClient discoverer and merge menu entries for
4474 // rest-style services with other types of analysis/calculation service
4475 // SHmmr test client - still being implemented.
4476 // DEBUG - alignmentView
4478 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4481 client.attachWSMenuEntry(
4482 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4488 * Searches the alignment sequences for xRefs and builds the Show
4489 * Cross-References menu (formerly called Show Products), with database
4490 * sources for which cross-references are found (protein sources for a
4491 * nucleotide alignment and vice versa)
4493 * @return true if Show Cross-references menu should be enabled
4495 public boolean canShowProducts()
4497 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4498 AlignmentI dataset = viewport.getAlignment().getDataset();
4500 showProducts.removeAll();
4501 final boolean dna = viewport.getAlignment().isNucleotide();
4503 if (seqs == null || seqs.length == 0)
4505 // nothing to see here.
4509 boolean showp = false;
4512 List<String> ptypes = new CrossRef(seqs, dataset)
4513 .findXrefSourcesForSequences(dna);
4515 for (final String source : ptypes)
4518 final AlignFrame af = this;
4519 JMenuItem xtype = new JMenuItem(source);
4520 xtype.addActionListener(new ActionListener()
4523 public void actionPerformed(ActionEvent e)
4525 showProductsFor(af.viewport.getSequenceSelection(), dna,
4529 showProducts.add(xtype);
4531 showProducts.setVisible(showp);
4532 showProducts.setEnabled(showp);
4533 } catch (Exception e)
4536 "canShowProducts threw an exception - please report to help@jalview.org",
4544 * Finds and displays cross-references for the selected sequences (protein
4545 * products for nucleotide sequences, dna coding sequences for peptides).
4548 * the sequences to show cross-references for
4550 * true if from a nucleotide alignment (so showing proteins)
4552 * the database to show cross-references for
4554 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4555 final String source)
4557 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4562 * Construct and display a new frame containing the translation of this
4563 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4566 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4568 AlignmentI al = null;
4571 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4573 al = dna.translateCdna(codeTable);
4574 } catch (Exception ex)
4576 jalview.bin.Cache.log.error(
4577 "Exception during translation. Please report this !", ex);
4578 final String msg = MessageManager.getString(
4579 "label.error_when_translating_sequences_submit_bug_report");
4580 final String errorTitle = MessageManager
4581 .getString("label.implementation_error")
4582 + MessageManager.getString("label.translation_failed");
4583 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4584 JvOptionPane.ERROR_MESSAGE);
4587 if (al == null || al.getHeight() == 0)
4589 final String msg = MessageManager.getString(
4590 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4591 final String errorTitle = MessageManager
4592 .getString("label.translation_failed");
4593 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4594 JvOptionPane.WARNING_MESSAGE);
4598 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4599 af.setFileFormat(this.currentFileFormat);
4600 final String newTitle = MessageManager
4601 .formatMessage("label.translation_of_params", new Object[]
4602 { this.getTitle(), codeTable.getId() });
4603 af.setTitle(newTitle);
4604 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4606 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4607 viewport.openSplitFrame(af, new Alignment(seqs));
4611 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4618 * Set the file format
4622 public void setFileFormat(FileFormatI format)
4624 this.currentFileFormat = format;
4628 * Try to load a features file onto the alignment.
4631 * contents or path to retrieve file
4633 * access mode of file (see jalview.io.AlignFile)
4634 * @return true if features file was parsed correctly.
4636 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4638 return avc.parseFeaturesFile(file, sourceType,
4639 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4644 public void refreshFeatureUI(boolean enableIfNecessary)
4646 // note - currently this is only still here rather than in the controller
4647 // because of the featureSettings hard reference that is yet to be
4649 if (enableIfNecessary)
4651 viewport.setShowSequenceFeatures(true);
4652 showSeqFeatures.setSelected(true);
4658 public void dragEnter(DropTargetDragEvent evt)
4663 public void dragExit(DropTargetEvent evt)
4668 public void dragOver(DropTargetDragEvent evt)
4673 public void dropActionChanged(DropTargetDragEvent evt)
4678 public void drop(DropTargetDropEvent evt)
4680 // JAL-1552 - acceptDrop required before getTransferable call for
4681 // Java's Transferable for native dnd
4682 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4683 Transferable t = evt.getTransferable();
4684 final AlignFrame thisaf = this;
4685 final List<String> files = new ArrayList<>();
4686 List<DataSourceType> protocols = new ArrayList<>();
4690 Desktop.transferFromDropTarget(files, protocols, evt, t);
4691 } catch (Exception e)
4693 e.printStackTrace();
4697 new Thread(new Runnable()
4704 // check to see if any of these files have names matching sequences
4707 SequenceIdMatcher idm = new SequenceIdMatcher(
4708 viewport.getAlignment().getSequencesArray());
4710 * Object[] { String,SequenceI}
4712 ArrayList<Object[]> filesmatched = new ArrayList<>();
4713 ArrayList<String> filesnotmatched = new ArrayList<>();
4714 for (int i = 0; i < files.size(); i++)
4716 String file = files.get(i).toString();
4718 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4719 if (protocol == DataSourceType.FILE)
4721 File fl = new File(file);
4722 pdbfn = fl.getName();
4724 else if (protocol == DataSourceType.URL)
4726 URL url = new URL(file);
4727 pdbfn = url.getFile();
4729 if (pdbfn.length() > 0)
4731 // attempt to find a match in the alignment
4732 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4733 int l = 0, c = pdbfn.indexOf(".");
4734 while (mtch == null && c != -1)
4739 } while ((c = pdbfn.indexOf(".", l)) > l);
4742 pdbfn = pdbfn.substring(0, l);
4744 mtch = idm.findAllIdMatches(pdbfn);
4748 FileFormatI type = null;
4751 type = new IdentifyFile().identify(file, protocol);
4752 } catch (Exception ex)
4756 if (type != null && type.isStructureFile())
4758 filesmatched.add(new Object[] { file, protocol, mtch });
4762 // File wasn't named like one of the sequences or wasn't a PDB
4764 filesnotmatched.add(file);
4768 if (filesmatched.size() > 0)
4770 boolean autoAssociate = Cache
4771 .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4774 String msg = MessageManager.formatMessage(
4775 "label.automatically_associate_structure_files_with_sequences_same_name",
4777 { Integer.valueOf(filesmatched.size())
4779 String ttl = MessageManager.getString(
4780 "label.automatically_associate_structure_files_by_name");
4781 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4782 ttl, JvOptionPane.YES_NO_OPTION);
4783 autoAssociate = choice == JvOptionPane.YES_OPTION;
4787 for (Object[] fm : filesmatched)
4789 // try and associate
4790 // TODO: may want to set a standard ID naming formalism for
4791 // associating PDB files which have no IDs.
4792 for (SequenceI toassoc : (SequenceI[]) fm[2])
4794 PDBEntry pe = new AssociatePdbFileWithSeq()
4795 .associatePdbWithSeq((String) fm[0],
4796 (DataSourceType) fm[1], toassoc, false,
4800 System.err.println("Associated file : "
4801 + ((String) fm[0]) + " with "
4802 + toassoc.getDisplayId(true));
4806 // TODO: do we need to update overview ? only if features are
4808 alignPanel.paintAlignment(true, false);
4814 * add declined structures as sequences
4816 for (Object[] o : filesmatched)
4818 filesnotmatched.add((String) o[0]);
4822 if (filesnotmatched.size() > 0)
4824 if (assocfiles > 0 && (Cache.getDefault(
4825 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4826 || JvOptionPane.showConfirmDialog(thisaf,
4827 "<html>" + MessageManager.formatMessage(
4828 "label.ignore_unmatched_dropped_files_info",
4831 filesnotmatched.size())
4834 MessageManager.getString(
4835 "label.ignore_unmatched_dropped_files"),
4836 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4840 for (String fn : filesnotmatched)
4842 loadJalviewDataFile(fn, null, null, null);
4846 } catch (Exception ex)
4848 ex.printStackTrace();
4856 * Attempt to load a "dropped" file or URL string, by testing in turn for
4858 * <li>an Annotation file</li>
4859 * <li>a JNet file</li>
4860 * <li>a features file</li>
4861 * <li>else try to interpret as an alignment file</li>
4865 * either a filename or a URL string.
4866 * @throws InterruptedException
4867 * @throws IOException
4869 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4870 FileFormatI format, SequenceI assocSeq)
4874 if (sourceType == null)
4876 sourceType = FormatAdapter.checkProtocol(file);
4878 // if the file isn't identified, or not positively identified as some
4879 // other filetype (PFAM is default unidentified alignment file type) then
4880 // try to parse as annotation.
4881 boolean isAnnotation = (format == null
4882 || FileFormat.Pfam.equals(format))
4883 ? new AnnotationFile().annotateAlignmentView(viewport,
4889 // first see if its a T-COFFEE score file
4890 TCoffeeScoreFile tcf = null;
4893 tcf = new TCoffeeScoreFile(file, sourceType);
4896 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4900 new TCoffeeColourScheme(viewport.getAlignment()));
4901 isAnnotation = true;
4902 statusBar.setText(MessageManager.getString(
4903 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4907 // some problem - if no warning its probable that the ID matching
4908 // process didn't work
4909 JvOptionPane.showMessageDialog(Desktop.desktop,
4910 tcf.getWarningMessage() == null
4911 ? MessageManager.getString(
4912 "label.check_file_matches_sequence_ids_alignment")
4913 : tcf.getWarningMessage(),
4914 MessageManager.getString(
4915 "label.problem_reading_tcoffee_score_file"),
4916 JvOptionPane.WARNING_MESSAGE);
4923 } catch (Exception x)
4926 "Exception when processing data source as T-COFFEE score file",
4932 // try to see if its a JNet 'concise' style annotation file *before*
4934 // try to parse it as a features file
4937 format = new IdentifyFile().identify(file, sourceType);
4939 if (FileFormat.ScoreMatrix == format)
4941 ScoreMatrixFile sm = new ScoreMatrixFile(
4942 new FileParse(file, sourceType));
4944 // todo: i18n this message
4945 statusBar.setText(MessageManager.formatMessage(
4946 "label.successfully_loaded_matrix",
4947 sm.getMatrixName()));
4949 else if (FileFormat.Jnet.equals(format))
4951 JPredFile predictions = new JPredFile(file, sourceType);
4952 new JnetAnnotationMaker();
4953 JnetAnnotationMaker.add_annotation(predictions,
4954 viewport.getAlignment(), 0, false);
4955 viewport.getAlignment().setupJPredAlignment();
4956 isAnnotation = true;
4958 // else if (IdentifyFile.FeaturesFile.equals(format))
4959 else if (FileFormat.Features.equals(format))
4961 if (parseFeaturesFile(file, sourceType))
4963 alignPanel.paintAlignment(true, true);
4968 new FileLoader().LoadFile(viewport, file, sourceType, format);
4974 alignPanel.adjustAnnotationHeight();
4975 viewport.updateSequenceIdColours();
4976 buildSortByAnnotationScoresMenu();
4977 alignPanel.paintAlignment(true, true);
4979 } catch (Exception ex)
4981 ex.printStackTrace();
4982 } catch (OutOfMemoryError oom)
4987 } catch (Exception x)
4992 + (sourceType != null
4993 ? (sourceType == DataSourceType.PASTE
4995 : "using " + sourceType + " from "
4999 ? "(parsing as '" + format + "' file)"
5001 oom, Desktop.desktop);
5006 * Method invoked by the ChangeListener on the tabbed pane, in other words
5007 * when a different tabbed pane is selected by the user or programmatically.
5010 public void tabSelectionChanged(int index)
5014 alignPanel = alignPanels.get(index);
5015 viewport = alignPanel.av;
5016 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5017 setMenusFromViewport(viewport);
5021 * 'focus' any colour slider that is open to the selected viewport
5023 if (viewport.getConservationSelected())
5025 SliderPanel.setConservationSlider(alignPanel,
5026 viewport.getResidueShading(), alignPanel.getViewName());
5030 SliderPanel.hideConservationSlider();
5032 if (viewport.getAbovePIDThreshold())
5034 SliderPanel.setPIDSliderSource(alignPanel,
5035 viewport.getResidueShading(), alignPanel.getViewName());
5039 SliderPanel.hidePIDSlider();
5043 * If there is a frame linked to this one in a SplitPane, switch it to the
5044 * same view tab index. No infinite recursion of calls should happen, since
5045 * tabSelectionChanged() should not get invoked on setting the selected
5046 * index to an unchanged value. Guard against setting an invalid index
5047 * before the new view peer tab has been created.
5049 final AlignViewportI peer = viewport.getCodingComplement();
5052 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
5053 .getAlignPanel().alignFrame;
5054 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5056 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5062 * On right mouse click on view tab, prompt for and set new view name.
5065 public void tabbedPane_mousePressed(MouseEvent e)
5067 if (e.isPopupTrigger())
5069 String msg = MessageManager.getString("label.enter_view_name");
5070 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
5071 JvOptionPane.QUESTION_MESSAGE);
5075 viewport.setViewName(reply);
5076 // TODO warn if reply is in getExistingViewNames()?
5077 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5082 public AlignViewport getCurrentView()
5088 * Open the dialog for regex description parsing.
5091 protected void extractScores_actionPerformed(ActionEvent e)
5093 ParseProperties pp = new jalview.analysis.ParseProperties(
5094 viewport.getAlignment());
5095 // TODO: verify regex and introduce GUI dialog for version 2.5
5096 // if (pp.getScoresFromDescription("col", "score column ",
5097 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5099 if (pp.getScoresFromDescription("description column",
5100 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5102 buildSortByAnnotationScoresMenu();
5110 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5114 protected void showDbRefs_actionPerformed(ActionEvent e)
5116 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5122 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5126 protected void showNpFeats_actionPerformed(ActionEvent e)
5128 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5132 * find the viewport amongst the tabs in this alignment frame and close that
5137 public boolean closeView(AlignViewportI av)
5141 this.closeMenuItem_actionPerformed(false);
5144 Component[] comp = tabbedPane.getComponents();
5145 for (int i = 0; comp != null && i < comp.length; i++)
5147 if (comp[i] instanceof AlignmentPanel)
5149 if (((AlignmentPanel) comp[i]).av == av)
5152 closeView((AlignmentPanel) comp[i]);
5160 protected void build_fetchdbmenu(JMenu webService)
5162 // Temporary hack - DBRef Fetcher always top level ws entry.
5163 // TODO We probably want to store a sequence database checklist in
5164 // preferences and have checkboxes.. rather than individual sources selected
5166 final JMenu rfetch = new JMenu(
5167 MessageManager.getString("action.fetch_db_references"));
5168 rfetch.setToolTipText(MessageManager.getString(
5169 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5170 webService.add(rfetch);
5172 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5173 MessageManager.getString("option.trim_retrieved_seqs"));
5174 trimrs.setToolTipText(
5175 MessageManager.getString("label.trim_retrieved_sequences"));
5177 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5178 trimrs.addActionListener(new ActionListener()
5181 public void actionPerformed(ActionEvent e)
5183 trimrs.setSelected(trimrs.isSelected());
5184 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5185 Boolean.valueOf(trimrs.isSelected()).toString());
5189 JMenuItem fetchr = new JMenuItem(
5190 MessageManager.getString("label.standard_databases"));
5191 fetchr.setToolTipText(
5192 MessageManager.getString("label.fetch_embl_uniprot"));
5193 fetchr.addActionListener(new ActionListener()
5197 public void actionPerformed(ActionEvent e)
5199 new Thread(new Runnable()
5204 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5205 .getAlignment().isNucleotide();
5206 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5207 alignPanel.av.getSequenceSelection(),
5208 alignPanel.alignFrame, null,
5209 alignPanel.alignFrame.featureSettings, isNucleotide);
5210 dbRefFetcher.addListener(new FetchFinishedListenerI()
5213 public void finished()
5216 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5217 .getFeatureSettingsModels())
5220 alignPanel.av.mergeFeaturesStyle(srcSettings);
5222 AlignFrame.this.setMenusForViewport();
5225 dbRefFetcher.fetchDBRefs(false);
5233 final AlignFrame me = this;
5234 new Thread(new Runnable()
5239 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5240 .getSequenceFetcherSingleton(me);
5241 javax.swing.SwingUtilities.invokeLater(new Runnable()
5246 String[] dbclasses = sf.getOrderedSupportedSources();
5247 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5248 // jalview.util.QuickSort.sort(otherdb, otherdb);
5249 List<DbSourceProxy> otherdb;
5250 JMenu dfetch = new JMenu();
5251 JMenu ifetch = new JMenu();
5252 JMenuItem fetchr = null;
5253 int comp = 0, icomp = 0, mcomp = 15;
5254 String mname = null;
5256 for (String dbclass : dbclasses)
5258 otherdb = sf.getSourceProxy(dbclass);
5259 // add a single entry for this class, or submenu allowing 'fetch
5261 if (otherdb == null || otherdb.size() < 1)
5265 // List<DbSourceProxy> dbs=otherdb;
5266 // otherdb=new ArrayList<DbSourceProxy>();
5267 // for (DbSourceProxy db:dbs)
5269 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5273 mname = "From " + dbclass;
5275 if (otherdb.size() == 1)
5277 final DbSourceProxy[] dassource = otherdb
5278 .toArray(new DbSourceProxy[0]);
5279 DbSourceProxy src = otherdb.get(0);
5280 fetchr = new JMenuItem(src.getDbSource());
5281 fetchr.addActionListener(new ActionListener()
5285 public void actionPerformed(ActionEvent e)
5287 new Thread(new Runnable()
5293 boolean isNucleotide = alignPanel.alignFrame
5294 .getViewport().getAlignment()
5296 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5297 alignPanel.av.getSequenceSelection(),
5298 alignPanel.alignFrame, dassource,
5299 alignPanel.alignFrame.featureSettings,
5302 .addListener(new FetchFinishedListenerI()
5305 public void finished()
5307 FeatureSettingsModelI srcSettings = dassource[0]
5308 .getFeatureColourScheme();
5309 alignPanel.av.mergeFeaturesStyle(
5311 AlignFrame.this.setMenusForViewport();
5314 dbRefFetcher.fetchDBRefs(false);
5320 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5321 MessageManager.formatMessage(
5322 "label.fetch_retrieve_from", new Object[]
5323 { src.getDbName() })));
5329 final DbSourceProxy[] dassource = otherdb
5330 .toArray(new DbSourceProxy[0]);
5332 DbSourceProxy src = otherdb.get(0);
5333 fetchr = new JMenuItem(MessageManager
5334 .formatMessage("label.fetch_all_param", new Object[]
5335 { src.getDbSource() }));
5336 fetchr.addActionListener(new ActionListener()
5339 public void actionPerformed(ActionEvent e)
5341 new Thread(new Runnable()
5347 boolean isNucleotide = alignPanel.alignFrame
5348 .getViewport().getAlignment()
5350 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5351 alignPanel.av.getSequenceSelection(),
5352 alignPanel.alignFrame, dassource,
5353 alignPanel.alignFrame.featureSettings,
5356 .addListener(new FetchFinishedListenerI()
5359 public void finished()
5361 AlignFrame.this.setMenusForViewport();
5364 dbRefFetcher.fetchDBRefs(false);
5370 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5371 MessageManager.formatMessage(
5372 "label.fetch_retrieve_from_all_sources",
5374 { Integer.valueOf(otherdb.size())
5376 src.getDbSource(), src.getDbName() })));
5379 // and then build the rest of the individual menus
5380 ifetch = new JMenu(MessageManager.formatMessage(
5381 "label.source_from_db_source", new Object[]
5382 { src.getDbSource() }));
5384 String imname = null;
5386 for (DbSourceProxy sproxy : otherdb)
5388 String dbname = sproxy.getDbName();
5389 String sname = dbname.length() > 5
5390 ? dbname.substring(0, 5) + "..."
5392 String msname = dbname.length() > 10
5393 ? dbname.substring(0, 10) + "..."
5397 imname = MessageManager
5398 .formatMessage("label.from_msname", new Object[]
5401 fetchr = new JMenuItem(msname);
5402 final DbSourceProxy[] dassrc = { sproxy };
5403 fetchr.addActionListener(new ActionListener()
5407 public void actionPerformed(ActionEvent e)
5409 new Thread(new Runnable()
5415 boolean isNucleotide = alignPanel.alignFrame
5416 .getViewport().getAlignment()
5418 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5419 alignPanel.av.getSequenceSelection(),
5420 alignPanel.alignFrame, dassrc,
5421 alignPanel.alignFrame.featureSettings,
5424 .addListener(new FetchFinishedListenerI()
5427 public void finished()
5429 AlignFrame.this.setMenusForViewport();
5432 dbRefFetcher.fetchDBRefs(false);
5438 fetchr.setToolTipText(
5439 "<html>" + MessageManager.formatMessage(
5440 "label.fetch_retrieve_from", new Object[]
5444 if (++icomp >= mcomp || i == (otherdb.size()))
5446 ifetch.setText(MessageManager.formatMessage(
5447 "label.source_to_target", imname, sname));
5449 ifetch = new JMenu();
5457 if (comp >= mcomp || dbi >= (dbclasses.length))
5459 dfetch.setText(MessageManager.formatMessage(
5460 "label.source_to_target", mname, dbclass));
5462 dfetch = new JMenu();
5475 * Left justify the whole alignment.
5478 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5480 AlignmentI al = viewport.getAlignment();
5482 viewport.firePropertyChange("alignment", null, al);
5486 * Right justify the whole alignment.
5489 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5491 AlignmentI al = viewport.getAlignment();
5493 viewport.firePropertyChange("alignment", null, al);
5497 public void setShowSeqFeatures(boolean b)
5499 showSeqFeatures.setSelected(b);
5500 viewport.setShowSequenceFeatures(b);
5507 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5508 * awt.event.ActionEvent)
5511 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5513 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5514 alignPanel.paintAlignment(false, false);
5521 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5525 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5527 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5528 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5536 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5537 * .event.ActionEvent)
5540 protected void showGroupConservation_actionPerformed(ActionEvent e)
5542 viewport.setShowGroupConservation(showGroupConservation.getState());
5543 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5550 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5551 * .event.ActionEvent)
5554 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5556 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5557 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5564 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5565 * .event.ActionEvent)
5568 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5570 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5571 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5575 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5577 showSequenceLogo.setState(true);
5578 viewport.setShowSequenceLogo(true);
5579 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5580 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5584 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5586 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5593 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5594 * .event.ActionEvent)
5597 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5599 if (avc.makeGroupsFromSelection())
5601 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5602 alignPanel.updateAnnotation();
5603 alignPanel.paintAlignment(true,
5604 viewport.needToUpdateStructureViews());
5608 public void clearAlignmentSeqRep()
5610 // TODO refactor alignmentseqrep to controller
5611 if (viewport.getAlignment().hasSeqrep())
5613 viewport.getAlignment().setSeqrep(null);
5614 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5615 alignPanel.updateAnnotation();
5616 alignPanel.paintAlignment(true, true);
5621 protected void createGroup_actionPerformed(ActionEvent e)
5623 if (avc.createGroup())
5625 if (applyAutoAnnotationSettings.isSelected())
5627 alignPanel.updateAnnotation(true, false);
5629 alignPanel.alignmentChanged();
5634 protected void unGroup_actionPerformed(ActionEvent e)
5638 alignPanel.alignmentChanged();
5643 * make the given alignmentPanel the currently selected tab
5645 * @param alignmentPanel
5647 public void setDisplayedView(AlignmentPanel alignmentPanel)
5649 if (!viewport.getSequenceSetId()
5650 .equals(alignmentPanel.av.getSequenceSetId()))
5652 throw new Error(MessageManager.getString(
5653 "error.implementation_error_cannot_show_view_alignment_frame"));
5655 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5656 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5658 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5663 * Action on selection of menu options to Show or Hide annotations.
5666 * @param forSequences
5667 * update sequence-related annotations
5668 * @param forAlignment
5669 * update non-sequence-related annotations
5672 protected void setAnnotationsVisibility(boolean visible,
5673 boolean forSequences, boolean forAlignment)
5675 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5676 .getAlignmentAnnotation();
5681 for (AlignmentAnnotation aa : anns)
5684 * don't display non-positional annotations on an alignment
5686 if (aa.annotations == null)
5690 boolean apply = (aa.sequenceRef == null && forAlignment)
5691 || (aa.sequenceRef != null && forSequences);
5694 aa.visible = visible;
5697 alignPanel.validateAnnotationDimensions(true);
5698 alignPanel.alignmentChanged();
5702 * Store selected annotation sort order for the view and repaint.
5705 protected void sortAnnotations_actionPerformed()
5707 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5709 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5710 alignPanel.paintAlignment(false, false);
5715 * @return alignment panels in this alignment frame
5717 public List<? extends AlignmentViewPanel> getAlignPanels()
5719 // alignPanels is never null
5720 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5725 * Open a new alignment window, with the cDNA associated with this (protein)
5726 * alignment, aligned as is the protein.
5728 protected void viewAsCdna_actionPerformed()
5730 // TODO no longer a menu action - refactor as required
5731 final AlignmentI alignment = getViewport().getAlignment();
5732 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5733 if (mappings == null)
5737 List<SequenceI> cdnaSeqs = new ArrayList<>();
5738 for (SequenceI aaSeq : alignment.getSequences())
5740 for (AlignedCodonFrame acf : mappings)
5742 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5746 * There is a cDNA mapping for this protein sequence - add to new
5747 * alignment. It will share the same dataset sequence as other mapped
5748 * cDNA (no new mappings need to be created).
5750 final Sequence newSeq = new Sequence(dnaSeq);
5751 newSeq.setDatasetSequence(dnaSeq);
5752 cdnaSeqs.add(newSeq);
5756 if (cdnaSeqs.size() == 0)
5758 // show a warning dialog no mapped cDNA
5761 AlignmentI cdna = new Alignment(
5762 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5763 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5764 AlignFrame.DEFAULT_HEIGHT);
5765 cdna.alignAs(alignment);
5766 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5768 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5769 AlignFrame.DEFAULT_HEIGHT);
5773 * Set visibility of dna/protein complement view (available when shown in a
5779 protected void showComplement_actionPerformed(boolean show)
5781 SplitContainerI sf = getSplitViewContainer();
5784 sf.setComplementVisible(this, show);
5789 * Generate the reverse (optionally complemented) of the selected sequences,
5790 * and add them to the alignment
5793 protected void showReverse_actionPerformed(boolean complement)
5795 AlignmentI al = null;
5798 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5799 al = dna.reverseCdna(complement);
5800 viewport.addAlignment(al, "");
5801 addHistoryItem(new EditCommand(
5802 MessageManager.getString("label.add_sequences"), Action.PASTE,
5803 al.getSequencesArray(), 0, al.getWidth(),
5804 viewport.getAlignment()));
5805 } catch (Exception ex)
5807 System.err.println(ex.getMessage());
5813 * Try to run a script in the Groovy console, having first ensured that this
5814 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5815 * be targeted at this alignment.
5818 protected void runGroovy_actionPerformed()
5820 Jalview.setCurrentAlignFrame(this);
5821 groovy.ui.Console console = Desktop.getGroovyConsole();
5822 if (console != null)
5826 console.runScript();
5827 } catch (Exception ex)
5829 System.err.println((ex.toString()));
5830 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5831 MessageManager.getString("label.couldnt_run_groovy_script"),
5832 MessageManager.getString("label.groovy_support_failed"),
5833 JvOptionPane.ERROR_MESSAGE);
5838 System.err.println("Can't run Groovy script as console not found");
5843 * Hides columns containing (or not containing) a specified feature, provided
5844 * that would not leave all columns hidden
5846 * @param featureType
5847 * @param columnsContaining
5850 public boolean hideFeatureColumns(String featureType,
5851 boolean columnsContaining)
5853 boolean notForHiding = avc.markColumnsContainingFeatures(
5854 columnsContaining, false, false, featureType);
5857 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5858 false, featureType))
5860 getViewport().hideSelectedColumns();
5868 protected void selectHighlightedColumns_actionPerformed(
5869 ActionEvent actionEvent)
5871 // include key modifier check in case user selects from menu
5872 avc.markHighlightedColumns(
5873 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5874 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5875 | ActionEvent.CTRL_MASK)) != 0);
5879 * Rebuilds the Colour menu, including any user-defined colours which have
5880 * been loaded either on startup or during the session
5882 public void buildColourMenu()
5884 colourMenu.removeAll();
5886 colourMenu.add(applyToAllGroups);
5887 colourMenu.add(textColour);
5888 colourMenu.addSeparator();
5890 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5891 viewport.getAlignment(), false);
5893 colourMenu.add(annotationColour);
5894 bg.add(annotationColour);
5895 colourMenu.addSeparator();
5896 colourMenu.add(conservationMenuItem);
5897 colourMenu.add(modifyConservation);
5898 colourMenu.add(abovePIDThreshold);
5899 colourMenu.add(modifyPID);
5901 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5902 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5906 * Open a dialog (if not already open) that allows the user to select and
5907 * calculate PCA or Tree analysis
5909 protected void openTreePcaDialog()
5911 if (alignPanel.getCalculationDialog() == null)
5913 new CalculationChooser(AlignFrame.this);
5918 * Sets the status of the HMMER menu
5920 public void updateHMMERStatus()
5922 hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
5926 protected void loadVcf_actionPerformed()
5928 JalviewFileChooser chooser = new JalviewFileChooser(
5929 Cache.getProperty("LAST_DIRECTORY"));
5930 chooser.setFileView(new JalviewFileView());
5931 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5932 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5934 int value = chooser.showOpenDialog(null);
5936 if (value == JalviewFileChooser.APPROVE_OPTION)
5938 String choice = chooser.getSelectedFile().getPath();
5939 Cache.setProperty("LAST_DIRECTORY", choice);
5940 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5941 new VCFLoader(choice).loadVCF(seqs, this);
5947 class PrintThread extends Thread
5951 public PrintThread(AlignmentPanel ap)
5956 static PageFormat pf;
5961 PrinterJob printJob = PrinterJob.getPrinterJob();
5965 printJob.setPrintable(ap, pf);
5969 printJob.setPrintable(ap);
5972 if (printJob.printDialog())
5977 } catch (Exception PrintException)
5979 PrintException.printStackTrace();