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;
112 import jalview.ws.slivkaws.SlivkaWSDiscoverer;
114 import java.awt.BorderLayout;
115 import java.awt.Component;
116 import java.awt.Rectangle;
117 import java.awt.Toolkit;
118 import java.awt.datatransfer.Clipboard;
119 import java.awt.datatransfer.DataFlavor;
120 import java.awt.datatransfer.StringSelection;
121 import java.awt.datatransfer.Transferable;
122 import java.awt.dnd.DnDConstants;
123 import java.awt.dnd.DropTargetDragEvent;
124 import java.awt.dnd.DropTargetDropEvent;
125 import java.awt.dnd.DropTargetEvent;
126 import java.awt.dnd.DropTargetListener;
127 import java.awt.event.ActionEvent;
128 import java.awt.event.ActionListener;
129 import java.awt.event.FocusAdapter;
130 import java.awt.event.FocusEvent;
131 import java.awt.event.ItemEvent;
132 import java.awt.event.ItemListener;
133 import java.awt.event.KeyAdapter;
134 import java.awt.event.KeyEvent;
135 import java.awt.event.MouseEvent;
136 import java.awt.print.PageFormat;
137 import java.awt.print.PrinterJob;
138 import java.beans.PropertyChangeEvent;
140 import java.io.FileWriter;
141 import java.io.IOException;
142 import java.io.PrintWriter;
144 import java.util.ArrayList;
145 import java.util.Arrays;
146 import java.util.Deque;
147 import java.util.HashSet;
148 import java.util.List;
149 import java.util.Set;
150 import java.util.Vector;
152 import javax.swing.ButtonGroup;
153 import javax.swing.JCheckBoxMenuItem;
154 import javax.swing.JEditorPane;
155 import javax.swing.JFileChooser;
156 import javax.swing.JInternalFrame;
157 import javax.swing.JLayeredPane;
158 import javax.swing.JMenu;
159 import javax.swing.JMenuItem;
160 import javax.swing.JOptionPane;
161 import javax.swing.JScrollPane;
162 import javax.swing.SwingUtilities;
168 * @version $Revision$
170 public class AlignFrame extends GAlignFrame implements DropTargetListener,
171 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
173 public static final int DEFAULT_WIDTH = 700;
175 public static final int DEFAULT_HEIGHT = 500;
178 * The currently displayed panel (selected tabbed view if more than one)
180 public AlignmentPanel alignPanel;
182 AlignViewport viewport;
184 public AlignViewControllerI avc;
186 List<AlignmentPanel> alignPanels = new ArrayList<>();
189 * Last format used to load or save alignments in this window
191 FileFormatI currentFileFormat = null;
194 * Current filename for this alignment
196 String fileName = null;
200 * Creates a new AlignFrame object with specific width and height.
206 public AlignFrame(AlignmentI al, int width, int height)
208 this(al, null, width, height);
212 * Creates a new AlignFrame object with specific width, height and
218 * @param sequenceSetId
220 public AlignFrame(AlignmentI al, int width, int height,
221 String sequenceSetId)
223 this(al, null, width, height, sequenceSetId);
227 * Creates a new AlignFrame object with specific width, height and
233 * @param sequenceSetId
236 public AlignFrame(AlignmentI al, int width, int height,
237 String sequenceSetId, String viewId)
239 this(al, null, width, height, sequenceSetId, viewId);
243 * new alignment window with hidden columns
247 * @param hiddenColumns
248 * ColumnSelection or null
250 * Width of alignment frame
254 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
257 this(al, hiddenColumns, width, height, null);
261 * Create alignment frame for al with hiddenColumns, a specific width and
262 * height, and specific sequenceId
265 * @param hiddenColumns
268 * @param sequenceSetId
271 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
272 int height, String sequenceSetId)
274 this(al, hiddenColumns, width, height, sequenceSetId, null);
278 * Create alignment frame for al with hiddenColumns, a specific width and
279 * height, and specific sequenceId
282 * @param hiddenColumns
285 * @param sequenceSetId
290 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
291 int height, String sequenceSetId, String viewId)
293 setSize(width, height);
295 if (al.getDataset() == null)
300 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
302 alignPanel = new AlignmentPanel(this, viewport);
304 addAlignmentPanel(alignPanel, true);
308 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
309 HiddenColumns hiddenColumns, int width, int height)
311 setSize(width, height);
313 if (al.getDataset() == null)
318 viewport = new AlignViewport(al, hiddenColumns);
320 if (hiddenSeqs != null && hiddenSeqs.length > 0)
322 viewport.hideSequence(hiddenSeqs);
324 alignPanel = new AlignmentPanel(this, viewport);
325 addAlignmentPanel(alignPanel, true);
330 * Make a new AlignFrame from existing alignmentPanels
337 public AlignFrame(AlignmentPanel ap)
341 addAlignmentPanel(ap, false);
346 * initalise the alignframe from the underlying viewport data and the
351 if (!Jalview.isHeadlessMode())
353 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
356 avc = new jalview.controller.AlignViewController(this, viewport,
358 if (viewport.getAlignmentConservationAnnotation() == null)
360 // BLOSUM62Colour.setEnabled(false);
361 conservationMenuItem.setEnabled(false);
362 modifyConservation.setEnabled(false);
363 // PIDColour.setEnabled(false);
364 // abovePIDThreshold.setEnabled(false);
365 // modifyPID.setEnabled(false);
368 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
371 if (sortby.equals("Id"))
373 sortIDMenuItem_actionPerformed(null);
375 else if (sortby.equals("Pairwise Identity"))
377 sortPairwiseMenuItem_actionPerformed(null);
381 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
383 setMenusFromViewport(viewport);
384 buildSortByAnnotationScoresMenu();
385 calculateTree.addActionListener(new ActionListener()
389 public void actionPerformed(ActionEvent e)
396 if (Desktop.desktop != null)
398 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
399 addServiceListeners();
403 if (viewport.getWrapAlignment())
405 wrapMenuItem_actionPerformed(null);
408 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
410 this.overviewMenuItem_actionPerformed(null);
415 final List<AlignmentPanel> selviews = new ArrayList<>();
416 final List<AlignmentPanel> origview = new ArrayList<>();
417 final String menuLabel = MessageManager
418 .getString("label.copy_format_from");
419 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
420 new ViewSetProvider()
424 public AlignmentPanel[] getAllAlignmentPanels()
427 origview.add(alignPanel);
428 // make an array of all alignment panels except for this one
429 List<AlignmentPanel> aps = new ArrayList<>(
430 Arrays.asList(Desktop.getAlignmentPanels(null)));
431 aps.remove(AlignFrame.this.alignPanel);
432 return aps.toArray(new AlignmentPanel[aps.size()]);
434 }, selviews, new ItemListener()
438 public void itemStateChanged(ItemEvent e)
440 if (origview.size() > 0)
442 final AlignmentPanel ap = origview.get(0);
445 * Copy the ViewStyle of the selected panel to 'this one'.
446 * Don't change value of 'scaleProteinAsCdna' unless copying
449 ViewStyleI vs = selviews.get(0).getAlignViewport()
451 boolean fromSplitFrame = selviews.get(0)
452 .getAlignViewport().getCodingComplement() != null;
455 vs.setScaleProteinAsCdna(ap.getAlignViewport()
456 .getViewStyle().isScaleProteinAsCdna());
458 ap.getAlignViewport().setViewStyle(vs);
461 * Also rescale ViewStyle of SplitFrame complement if there is
462 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
463 * the whole ViewStyle (allow cDNA protein to have different
466 AlignViewportI complement = ap.getAlignViewport()
467 .getCodingComplement();
468 if (complement != null && vs.isScaleProteinAsCdna())
470 AlignFrame af = Desktop.getAlignFrameFor(complement);
471 ((SplitFrame) af.getSplitViewContainer())
473 af.setMenusForViewport();
477 ap.setSelected(true);
478 ap.alignFrame.setMenusForViewport();
483 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
484 .indexOf("devel") > -1
485 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
486 .indexOf("test") > -1)
488 formatMenu.add(vsel);
490 addFocusListener(new FocusAdapter()
493 public void focusGained(FocusEvent e)
495 Jalview.setCurrentAlignFrame(AlignFrame.this);
502 * Change the filename and format for the alignment, and enable the 'reload'
503 * button functionality.
510 public void setFileName(String file, FileFormatI format)
513 setFileFormat(format);
514 reload.setEnabled(true);
518 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
521 void addKeyListener()
523 addKeyListener(new KeyAdapter()
526 public void keyPressed(KeyEvent evt)
528 if (viewport.cursorMode
529 && ((evt.getKeyCode() >= KeyEvent.VK_0
530 && evt.getKeyCode() <= KeyEvent.VK_9)
531 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
532 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
533 && Character.isDigit(evt.getKeyChar()))
535 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
538 switch (evt.getKeyCode())
541 case 27: // escape key
542 deselectAllSequenceMenuItem_actionPerformed(null);
546 case KeyEvent.VK_DOWN:
547 if (evt.isAltDown() || !viewport.cursorMode)
549 moveSelectedSequences(false);
551 if (viewport.cursorMode)
553 alignPanel.getSeqPanel().moveCursor(0, 1);
558 if (evt.isAltDown() || !viewport.cursorMode)
560 moveSelectedSequences(true);
562 if (viewport.cursorMode)
564 alignPanel.getSeqPanel().moveCursor(0, -1);
569 case KeyEvent.VK_LEFT:
570 if (evt.isAltDown() || !viewport.cursorMode)
572 slideSequences(false,
573 alignPanel.getSeqPanel().getKeyboardNo1());
577 alignPanel.getSeqPanel().moveCursor(-1, 0);
582 case KeyEvent.VK_RIGHT:
583 if (evt.isAltDown() || !viewport.cursorMode)
585 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
589 alignPanel.getSeqPanel().moveCursor(1, 0);
593 case KeyEvent.VK_SPACE:
594 if (viewport.cursorMode)
596 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
597 || evt.isShiftDown() || evt.isAltDown());
601 // case KeyEvent.VK_A:
602 // if (viewport.cursorMode)
604 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
605 // //System.out.println("A");
609 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
610 * System.out.println("closing bracket"); } break;
612 case KeyEvent.VK_DELETE:
613 case KeyEvent.VK_BACK_SPACE:
614 if (!viewport.cursorMode)
616 cut_actionPerformed(null);
620 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
621 || evt.isShiftDown() || evt.isAltDown());
627 if (viewport.cursorMode)
629 alignPanel.getSeqPanel().setCursorRow();
633 if (viewport.cursorMode && !evt.isControlDown())
635 alignPanel.getSeqPanel().setCursorColumn();
639 if (viewport.cursorMode)
641 alignPanel.getSeqPanel().setCursorPosition();
645 case KeyEvent.VK_ENTER:
646 case KeyEvent.VK_COMMA:
647 if (viewport.cursorMode)
649 alignPanel.getSeqPanel().setCursorRowAndColumn();
654 if (viewport.cursorMode)
656 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
660 if (viewport.cursorMode)
662 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
667 viewport.cursorMode = !viewport.cursorMode;
668 statusBar.setText(MessageManager
669 .formatMessage("label.keyboard_editing_mode", new String[]
670 { (viewport.cursorMode ? "on" : "off") }));
671 if (viewport.cursorMode)
673 ViewportRanges ranges = viewport.getRanges();
674 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
676 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
679 alignPanel.getSeqPanel().seqCanvas.repaint();
685 Help.showHelpWindow();
686 } catch (Exception ex)
688 ex.printStackTrace();
693 boolean toggleSeqs = !evt.isControlDown();
694 boolean toggleCols = !evt.isShiftDown();
695 toggleHiddenRegions(toggleSeqs, toggleCols);
700 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
701 boolean modifyExisting = true; // always modify, don't clear
702 // evt.isShiftDown();
703 boolean invertHighlighted = evt.isAltDown();
704 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
708 case KeyEvent.VK_PAGE_UP:
709 viewport.getRanges().pageUp();
711 case KeyEvent.VK_PAGE_DOWN:
712 viewport.getRanges().pageDown();
718 public void keyReleased(KeyEvent evt)
720 switch (evt.getKeyCode())
722 case KeyEvent.VK_LEFT:
723 if (evt.isAltDown() || !viewport.cursorMode)
725 viewport.firePropertyChange("alignment", null,
726 viewport.getAlignment().getSequences());
730 case KeyEvent.VK_RIGHT:
731 if (evt.isAltDown() || !viewport.cursorMode)
733 viewport.firePropertyChange("alignment", null,
734 viewport.getAlignment().getSequences());
742 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
744 ap.alignFrame = this;
745 avc = new jalview.controller.AlignViewController(this, viewport,
750 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
752 int aSize = alignPanels.size();
754 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
756 if (aSize == 1 && ap.av.getViewName() == null)
758 this.getContentPane().add(ap, BorderLayout.CENTER);
764 setInitialTabVisible();
767 expandViews.setEnabled(true);
768 gatherViews.setEnabled(true);
769 tabbedPane.addTab(ap.av.getViewName(), ap);
771 ap.setVisible(false);
776 if (ap.av.isPadGaps())
778 ap.av.getAlignment().padGaps();
780 ap.av.updateConservation(ap);
781 ap.av.updateConsensus(ap);
782 ap.av.updateStrucConsensus(ap);
783 ap.av.initInformationWorker(ap);
787 public void setInitialTabVisible()
789 expandViews.setEnabled(true);
790 gatherViews.setEnabled(true);
791 tabbedPane.setVisible(true);
792 AlignmentPanel first = alignPanels.get(0);
793 tabbedPane.addTab(first.av.getViewName(), first);
794 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
797 public AlignViewport getViewport()
802 /* Set up intrinsic listeners for dynamically generated GUI bits. */
803 private void addServiceListeners()
805 final java.beans.PropertyChangeListener thisListener;
806 Desktop.instance.addJalviewPropertyChangeListener("services",
807 thisListener = new java.beans.PropertyChangeListener()
810 public void propertyChange(PropertyChangeEvent evt)
812 // // System.out.println("Discoverer property change.");
813 // if (evt.getPropertyName().equals("services"))
815 SwingUtilities.invokeLater(new Runnable()
822 "Rebuild WS Menu for service change");
823 BuildWebServiceMenu();
830 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
833 public void internalFrameClosed(
834 javax.swing.event.InternalFrameEvent evt)
836 // System.out.println("deregistering discoverer listener");
837 Desktop.instance.removeJalviewPropertyChangeListener("services",
839 closeMenuItem_actionPerformed(true);
842 // Finally, build the menu once to get current service state
843 new Thread(new Runnable()
848 BuildWebServiceMenu();
854 * Configure menu items that vary according to whether the alignment is
855 * nucleotide or protein
857 public void setGUINucleotide()
859 AlignmentI al = getViewport().getAlignment();
860 boolean nucleotide = al.isNucleotide();
862 loadVcf.setVisible(nucleotide);
863 showTranslation.setVisible(nucleotide);
864 showReverse.setVisible(nucleotide);
865 showReverseComplement.setVisible(nucleotide);
866 conservationMenuItem.setEnabled(!nucleotide);
868 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
869 showGroupConservation.setEnabled(!nucleotide);
871 showComplementMenuItem
872 .setText(nucleotide ? MessageManager.getString("label.protein")
873 : MessageManager.getString("label.nucleotide"));
877 * set up menus for the current viewport. This may be called after any
878 * operation that affects the data in the current view (selection changed,
879 * etc) to update the menus to reflect the new state.
882 public void setMenusForViewport()
884 setMenusFromViewport(viewport);
888 * Need to call this method when tabs are selected for multiple views, or when
889 * loading from Jalview2XML.java
894 public void setMenusFromViewport(AlignViewport av)
896 padGapsMenuitem.setSelected(av.isPadGaps());
897 colourTextMenuItem.setSelected(av.isShowColourText());
898 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
899 modifyPID.setEnabled(abovePIDThreshold.isSelected());
900 conservationMenuItem.setSelected(av.getConservationSelected());
901 modifyConservation.setEnabled(conservationMenuItem.isSelected());
902 seqLimits.setSelected(av.getShowJVSuffix());
903 idRightAlign.setSelected(av.isRightAlignIds());
904 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
905 renderGapsMenuItem.setSelected(av.isRenderGaps());
906 wrapMenuItem.setSelected(av.getWrapAlignment());
907 scaleAbove.setVisible(av.getWrapAlignment());
908 scaleLeft.setVisible(av.getWrapAlignment());
909 scaleRight.setVisible(av.getWrapAlignment());
910 annotationPanelMenuItem.setState(av.isShowAnnotation());
912 * Show/hide annotations only enabled if annotation panel is shown
914 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
915 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
916 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
917 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
918 viewBoxesMenuItem.setSelected(av.getShowBoxes());
919 viewTextMenuItem.setSelected(av.getShowText());
920 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
921 showGroupConsensus.setSelected(av.isShowGroupConsensus());
922 showGroupConservation.setSelected(av.isShowGroupConservation());
923 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
924 showSequenceLogo.setSelected(av.isShowSequenceLogo());
925 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
926 showInformationHistogram.setSelected(av.isShowInformationHistogram());
927 showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
928 normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
930 ColourMenuHelper.setColourSelected(colourMenu,
931 av.getGlobalColourScheme());
933 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
934 hiddenMarkers.setState(av.getShowHiddenMarkers());
935 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
936 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
937 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
938 autoCalculate.setSelected(av.autoCalculateConsensus);
939 sortByTree.setSelected(av.sortByTree);
940 listenToViewSelections.setSelected(av.followSelection);
942 showProducts.setEnabled(canShowProducts());
943 setGroovyEnabled(Desktop.getGroovyConsole() != null);
949 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
953 public void setGroovyEnabled(boolean b)
955 runGroovy.setEnabled(b);
958 private IProgressIndicator progressBar;
963 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
966 public void setProgressBar(String message, long id)
968 progressBar.setProgressBar(message, id);
972 public void registerHandler(final long id,
973 final IProgressIndicatorHandler handler)
975 progressBar.registerHandler(id, handler);
980 * @return true if any progress bars are still active
983 public boolean operationInProgress()
985 return progressBar.operationInProgress();
989 * Sets the text of the status bar. Note that setting a null or empty value
990 * will cause the status bar to be hidden, with possibly undesirable flicker
991 * of the screen layout.
994 public void setStatus(String text)
996 statusBar.setText(text == null || text.isEmpty() ? " " : text);
1000 * Added so Castor Mapping file can obtain Jalview Version
1002 public String getVersion()
1004 return jalview.bin.Cache.getProperty("VERSION");
1007 public FeatureRenderer getFeatureRenderer()
1009 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1013 public void fetchSequence_actionPerformed(ActionEvent e)
1015 new jalview.gui.SequenceFetcher(this);
1019 public void addFromFile_actionPerformed(ActionEvent e)
1021 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1025 public void hmmBuild_actionPerformed(boolean withDefaults)
1027 if (!alignmentIsSufficient(1))
1033 * get default parameters, and optionally show a dialog
1034 * to allow them to be modified
1036 ParamDatastoreI store = HMMERParamStore.forBuild(viewport);
1037 List<ArgumentI> args = store.getServiceParameters();
1041 WsParamSetI set = new HMMERPreset();
1042 WsJobParameters params = new WsJobParameters(store, set, args);
1043 if (params.showRunDialog())
1045 args = params.getJobParams();
1049 return; // user cancelled
1052 new Thread(new HMMBuild(this, args)).start();
1056 public void hmmAlign_actionPerformed(boolean withDefaults)
1058 if (!(checkForHMM() && alignmentIsSufficient(2)))
1064 * get default parameters, and optionally show a dialog
1065 * to allow them to be modified
1067 ParamDatastoreI store = HMMERParamStore.forAlign(viewport);
1068 List<ArgumentI> args = store.getServiceParameters();
1072 WsParamSetI set = new HMMERPreset();
1073 WsJobParameters params = new WsJobParameters(store, set, args);
1074 if (params.showRunDialog())
1076 args = params.getJobParams();
1080 return; // user cancelled
1083 new Thread(new HMMAlign(this, args)).start();
1087 public void hmmSearch_actionPerformed(boolean withDefaults)
1095 * get default parameters, and (if requested) show
1096 * dialog to allow modification
1098 ParamDatastoreI store = HMMERParamStore.forSearch(viewport);
1099 List<ArgumentI> args = store.getServiceParameters();
1103 WsParamSetI set = new HMMERPreset();
1104 WsJobParameters params = new WsJobParameters(store, set, args);
1105 if (params.showRunDialog())
1107 args = params.getJobParams();
1111 return; // user cancelled
1114 new Thread(new HMMSearch(this, args)).start();
1115 alignPanel.repaint();
1119 public void jackhmmer_actionPerformed(boolean withDefaults)
1123 * get default parameters, and (if requested) show
1124 * dialog to allow modification
1127 ParamDatastoreI store = HMMERParamStore.forJackhmmer(viewport);
1128 List<ArgumentI> args = store.getServiceParameters();
1132 WsParamSetI set = new HMMERPreset();
1133 WsJobParameters params = new WsJobParameters(store, set, args);
1134 if (params.showRunDialog())
1136 args = params.getJobParams();
1140 return; // user cancelled
1143 new Thread(new JackHMMER(this, args)).start();
1144 alignPanel.repaint();
1149 * Checks if the alignment has at least one hidden Markov model, if not shows
1150 * a dialog advising to run hmmbuild or load an HMM profile
1154 private boolean checkForHMM()
1156 if (viewport.getAlignment().getHmmSequences().isEmpty())
1158 JOptionPane.showMessageDialog(this,
1159 MessageManager.getString("warn.no_hmm"));
1166 protected void filterByEValue_actionPerformed()
1168 viewport.filterByEvalue(inputDouble("Enter E-Value Cutoff"));
1172 protected void filterByScore_actionPerformed()
1174 viewport.filterByScore(inputDouble("Enter Bit Score Threshold"));
1177 private double inputDouble(String message)
1181 while(d == null || d <= 0)
1183 str = JOptionPane.showInputDialog(this.alignPanel, message);
1186 d = Double.valueOf(str);
1188 catch (NumberFormatException e)
1196 * Checks if the alignment contains the required number of sequences.
1201 public boolean alignmentIsSufficient(int required)
1203 if (getViewport().getSequenceSelection().length < required)
1205 JOptionPane.showMessageDialog(this,
1206 MessageManager.getString("label.not_enough_sequences"));
1213 * Opens a file browser and adds the selected file, if in Fasta, Stockholm or
1214 * Pfam format, to the list held under preference key "HMMSEARCH_DBS" (as a
1215 * comma-separated list)
1218 public void addDatabase_actionPerformed() throws IOException
1220 if (Cache.getProperty(Preferences.HMMSEARCH_DBS) == null)
1222 Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
1225 String path = openFileChooser(false);
1226 if (path != null && new File(path).exists())
1228 IdentifyFile identifier = new IdentifyFile();
1229 FileFormatI format = identifier.identify(path, DataSourceType.FILE);
1230 if (format == FileFormat.Fasta || format == FileFormat.Stockholm
1231 || format == FileFormat.Pfam)
1233 String currentDbPaths = Cache
1234 .getProperty(Preferences.HMMSEARCH_DBS);
1235 currentDbPaths += Preferences.COMMA + path;
1236 Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
1240 JOptionPane.showMessageDialog(this,
1241 MessageManager.getString("warn.invalid_format"));
1247 * Opens a file chooser, optionally restricted to selecting folders
1248 * (directories) only. Answers the path to the selected file or folder, or
1249 * null if none is chosen.
1254 protected String openFileChooser(boolean forFolder)
1256 // TODO duplicates GPreferences method - relocate to JalviewFileChooser?
1257 String choice = null;
1258 JFileChooser chooser = new JFileChooser();
1261 chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
1263 chooser.setDialogTitle(
1264 MessageManager.getString("label.open_local_file"));
1265 chooser.setToolTipText(MessageManager.getString("action.open"));
1267 int value = chooser.showOpenDialog(this);
1269 if (value == JFileChooser.APPROVE_OPTION)
1271 choice = chooser.getSelectedFile().getPath();
1277 public void reload_actionPerformed(ActionEvent e)
1279 if (fileName != null)
1281 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1282 // originating file's format
1283 // TODO: work out how to recover feature settings for correct view(s) when
1284 // file is reloaded.
1285 if (FileFormat.Jalview.equals(currentFileFormat))
1287 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1288 for (int i = 0; i < frames.length; i++)
1290 if (frames[i] instanceof AlignFrame && frames[i] != this
1291 && ((AlignFrame) frames[i]).fileName != null
1292 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1296 frames[i].setSelected(true);
1297 Desktop.instance.closeAssociatedWindows();
1298 } catch (java.beans.PropertyVetoException ex)
1304 Desktop.instance.closeAssociatedWindows();
1306 FileLoader loader = new FileLoader();
1307 DataSourceType protocol = fileName.startsWith("http:")
1308 ? DataSourceType.URL
1309 : DataSourceType.FILE;
1310 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1314 Rectangle bounds = this.getBounds();
1316 FileLoader loader = new FileLoader();
1317 DataSourceType protocol = fileName.startsWith("http:")
1318 ? DataSourceType.URL
1319 : DataSourceType.FILE;
1320 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1321 protocol, currentFileFormat);
1323 newframe.setBounds(bounds);
1324 if (featureSettings != null && featureSettings.isShowing())
1326 final Rectangle fspos = featureSettings.frame.getBounds();
1327 // TODO: need a 'show feature settings' function that takes bounds -
1328 // need to refactor Desktop.addFrame
1329 newframe.featureSettings_actionPerformed(null);
1330 final FeatureSettings nfs = newframe.featureSettings;
1331 SwingUtilities.invokeLater(new Runnable()
1336 nfs.frame.setBounds(fspos);
1339 this.featureSettings.close();
1340 this.featureSettings = null;
1342 this.closeMenuItem_actionPerformed(true);
1348 public void addFromText_actionPerformed(ActionEvent e)
1351 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1355 public void addFromURL_actionPerformed(ActionEvent e)
1357 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1361 public void save_actionPerformed(ActionEvent e)
1363 if (fileName == null || (currentFileFormat == null)
1364 || fileName.startsWith("http"))
1366 saveAs_actionPerformed(null);
1370 saveAlignment(fileName, currentFileFormat);
1381 public void saveAs_actionPerformed(ActionEvent e)
1383 String format = currentFileFormat == null ? null
1384 : currentFileFormat.getName();
1385 JalviewFileChooser chooser = JalviewFileChooser
1386 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1388 chooser.setFileView(new JalviewFileView());
1389 chooser.setDialogTitle(
1390 MessageManager.getString("label.save_alignment_to_file"));
1391 chooser.setToolTipText(MessageManager.getString("action.save"));
1393 int value = chooser.showSaveDialog(this);
1395 if (value == JalviewFileChooser.APPROVE_OPTION)
1397 currentFileFormat = chooser.getSelectedFormat();
1398 while (currentFileFormat == null)
1400 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1401 MessageManager.getString(
1402 "label.select_file_format_before_saving"),
1403 MessageManager.getString("label.file_format_not_specified"),
1404 JvOptionPane.WARNING_MESSAGE);
1405 currentFileFormat = chooser.getSelectedFormat();
1406 value = chooser.showSaveDialog(this);
1407 if (value != JalviewFileChooser.APPROVE_OPTION)
1413 fileName = chooser.getSelectedFile().getPath();
1415 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1417 Cache.setProperty("LAST_DIRECTORY", fileName);
1418 saveAlignment(fileName, currentFileFormat);
1422 public boolean saveAlignment(String file, FileFormatI format)
1424 boolean success = true;
1426 if (FileFormat.Jalview.equals(format))
1428 String shortName = title;
1430 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1432 shortName = shortName.substring(
1433 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1436 success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1439 statusBar.setText(MessageManager.formatMessage(
1440 "label.successfully_saved_to_file_in_format", new Object[]
1441 { fileName, format }));
1446 AlignmentExportData exportData = getAlignmentForExport(format,
1448 if (exportData.getSettings().isCancelled())
1452 FormatAdapter f = new FormatAdapter(alignPanel,
1453 exportData.getSettings());
1454 String output = f.formatSequences(format, exportData.getAlignment(), // class
1458 // occur in the distant future
1459 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1460 f.getCacheSuffixDefault(format),
1461 viewport.getAlignment().getHiddenColumns());
1469 // create backupfiles object and get new temp filename destination
1470 BackupFiles backupfiles = new BackupFiles(file);
1474 PrintWriter out = new PrintWriter(
1475 new FileWriter(backupfiles.getTempFilePath()));
1479 this.setTitle(file);
1480 statusBar.setText(MessageManager.formatMessage(
1481 "label.successfully_saved_to_file_in_format", new Object[]
1482 { fileName, format.getName() }));
1483 } catch (Exception ex)
1486 ex.printStackTrace();
1489 backupfiles.setWriteSuccess(success);
1490 // do the backup file roll and rename the temp file to actual file
1491 success = backupfiles.rollBackupsAndRenameTempFile();
1498 JvOptionPane.showInternalMessageDialog(this, MessageManager
1499 .formatMessage("label.couldnt_save_file", new Object[]
1501 MessageManager.getString("label.error_saving_file"),
1502 JvOptionPane.WARNING_MESSAGE);
1508 private void warningMessage(String warning, String title)
1510 if (new jalview.util.Platform().isHeadless())
1512 System.err.println("Warning: " + title + "\nWarning: " + warning);
1517 JvOptionPane.showInternalMessageDialog(this, warning, title,
1518 JvOptionPane.WARNING_MESSAGE);
1530 protected void outputText_actionPerformed(ActionEvent e)
1532 FileFormatI fileFormat = FileFormats.getInstance()
1533 .forName(e.getActionCommand());
1534 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1536 if (exportData.getSettings().isCancelled())
1540 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1541 cap.setForInput(null);
1544 FileFormatI format = fileFormat;
1545 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1546 .formatSequences(format, exportData.getAlignment(),
1547 exportData.getOmitHidden(),
1548 exportData.getStartEndPostions(),
1549 viewport.getAlignment().getHiddenColumns()));
1550 Desktop.addInternalFrame(cap, MessageManager
1551 .formatMessage("label.alignment_output_command", new Object[]
1552 { e.getActionCommand() }), 600, 500);
1553 } catch (OutOfMemoryError oom)
1555 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1562 public static AlignmentExportData getAlignmentForExport(
1563 FileFormatI format, AlignViewportI viewport,
1564 AlignExportSettingI exportSettings)
1566 AlignmentI alignmentToExport = null;
1567 AlignExportSettingI settings = exportSettings;
1568 String[] omitHidden = null;
1570 HiddenSequences hiddenSeqs = viewport.getAlignment()
1571 .getHiddenSequences();
1573 alignmentToExport = viewport.getAlignment();
1575 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1576 if (settings == null)
1578 settings = new AlignExportSettings(hasHiddenSeqs,
1579 viewport.hasHiddenColumns(), format);
1581 // settings.isExportAnnotations();
1583 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1585 omitHidden = viewport.getViewAsString(false,
1586 settings.isExportHiddenSequences());
1589 int[] alignmentStartEnd = new int[2];
1590 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1592 alignmentToExport = hiddenSeqs.getFullAlignment();
1596 alignmentToExport = viewport.getAlignment();
1598 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1599 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1600 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1601 omitHidden, alignmentStartEnd, settings);
1612 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1614 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1615 htmlSVG.exportHTML(null);
1619 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1621 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1622 bjs.exportHTML(null);
1625 public void createImageMap(File file, String image)
1627 alignPanel.makePNGImageMap(file, image);
1637 public void createPNG(File f)
1639 alignPanel.makePNG(f);
1649 public void createEPS(File f)
1651 alignPanel.makeEPS(f);
1655 public void createSVG(File f)
1657 alignPanel.makeSVG(f);
1661 public void pageSetup_actionPerformed(ActionEvent e)
1663 PrinterJob printJob = PrinterJob.getPrinterJob();
1664 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1674 public void printMenuItem_actionPerformed(ActionEvent e)
1676 // Putting in a thread avoids Swing painting problems
1677 PrintThread thread = new PrintThread(alignPanel);
1682 public void exportFeatures_actionPerformed(ActionEvent e)
1684 new AnnotationExporter(alignPanel).exportFeatures();
1688 public void exportAnnotations_actionPerformed(ActionEvent e)
1690 new AnnotationExporter(alignPanel).exportAnnotations();
1694 public void associatedData_actionPerformed(ActionEvent e)
1695 throws IOException, InterruptedException
1697 // Pick the tree file
1698 JalviewFileChooser chooser = new JalviewFileChooser(
1699 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1700 chooser.setFileView(new JalviewFileView());
1701 chooser.setDialogTitle(
1702 MessageManager.getString("label.load_jalview_annotations"));
1703 chooser.setToolTipText(
1704 MessageManager.getString("label.load_jalview_annotations"));
1706 int value = chooser.showOpenDialog(null);
1708 if (value == JalviewFileChooser.APPROVE_OPTION)
1710 String choice = chooser.getSelectedFile().getPath();
1711 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1712 loadJalviewDataFile(choice, null, null, null);
1718 * Close the current view or all views in the alignment frame. If the frame
1719 * only contains one view then the alignment will be removed from memory.
1721 * @param closeAllTabs
1724 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1726 if (alignPanels != null && alignPanels.size() < 2)
1728 closeAllTabs = true;
1733 if (alignPanels != null)
1737 if (this.isClosed())
1739 // really close all the windows - otherwise wait till
1740 // setClosed(true) is called
1741 for (int i = 0; i < alignPanels.size(); i++)
1743 AlignmentPanel ap = alignPanels.get(i);
1750 closeView(alignPanel);
1757 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1758 * be called recursively, with the frame now in 'closed' state
1760 this.setClosed(true);
1762 } catch (Exception ex)
1764 ex.printStackTrace();
1769 * Close the specified panel and close up tabs appropriately.
1771 * @param panelToClose
1773 public void closeView(AlignmentPanel panelToClose)
1775 int index = tabbedPane.getSelectedIndex();
1776 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1777 alignPanels.remove(panelToClose);
1778 panelToClose.closePanel();
1779 panelToClose = null;
1781 tabbedPane.removeTabAt(closedindex);
1782 tabbedPane.validate();
1784 if (index > closedindex || index == tabbedPane.getTabCount())
1786 // modify currently selected tab index if necessary.
1790 this.tabSelectionChanged(index);
1796 void updateEditMenuBar()
1799 if (viewport.getHistoryList().size() > 0)
1801 undoMenuItem.setEnabled(true);
1802 CommandI command = viewport.getHistoryList().peek();
1803 undoMenuItem.setText(MessageManager
1804 .formatMessage("label.undo_command", new Object[]
1805 { command.getDescription() }));
1809 undoMenuItem.setEnabled(false);
1810 undoMenuItem.setText(MessageManager.getString("action.undo"));
1813 if (viewport.getRedoList().size() > 0)
1815 redoMenuItem.setEnabled(true);
1817 CommandI command = viewport.getRedoList().peek();
1818 redoMenuItem.setText(MessageManager
1819 .formatMessage("label.redo_command", new Object[]
1820 { command.getDescription() }));
1824 redoMenuItem.setEnabled(false);
1825 redoMenuItem.setText(MessageManager.getString("action.redo"));
1830 public void addHistoryItem(CommandI command)
1832 if (command.getSize() > 0)
1834 viewport.addToHistoryList(command);
1835 viewport.clearRedoList();
1836 updateEditMenuBar();
1837 viewport.updateHiddenColumns();
1838 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1839 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1840 // viewport.getColumnSelection()
1841 // .getHiddenColumns().size() > 0);
1847 * @return alignment objects for all views
1849 AlignmentI[] getViewAlignments()
1851 if (alignPanels != null)
1853 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1855 for (AlignmentPanel ap : alignPanels)
1857 als[i++] = ap.av.getAlignment();
1861 if (viewport != null)
1863 return new AlignmentI[] { viewport.getAlignment() };
1875 protected void undoMenuItem_actionPerformed(ActionEvent e)
1877 if (viewport.getHistoryList().isEmpty())
1881 CommandI command = viewport.getHistoryList().pop();
1882 viewport.addToRedoList(command);
1883 command.undoCommand(getViewAlignments());
1885 AlignmentViewport originalSource = getOriginatingSource(command);
1886 updateEditMenuBar();
1888 if (originalSource != null)
1890 if (originalSource != viewport)
1893 "Implementation worry: mismatch of viewport origin for undo");
1895 originalSource.updateHiddenColumns();
1896 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1898 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1899 // viewport.getColumnSelection()
1900 // .getHiddenColumns().size() > 0);
1901 originalSource.firePropertyChange("alignment", null,
1902 originalSource.getAlignment().getSequences());
1913 protected void redoMenuItem_actionPerformed(ActionEvent e)
1915 if (viewport.getRedoList().size() < 1)
1920 CommandI command = viewport.getRedoList().pop();
1921 viewport.addToHistoryList(command);
1922 command.doCommand(getViewAlignments());
1924 AlignmentViewport originalSource = getOriginatingSource(command);
1925 updateEditMenuBar();
1927 if (originalSource != null)
1930 if (originalSource != viewport)
1933 "Implementation worry: mismatch of viewport origin for redo");
1935 originalSource.updateHiddenColumns();
1936 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1938 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1939 // viewport.getColumnSelection()
1940 // .getHiddenColumns().size() > 0);
1941 originalSource.firePropertyChange("alignment", null,
1942 originalSource.getAlignment().getSequences());
1946 AlignmentViewport getOriginatingSource(CommandI command)
1948 AlignmentViewport originalSource = null;
1949 // For sequence removal and addition, we need to fire
1950 // the property change event FROM the viewport where the
1951 // original alignment was altered
1952 AlignmentI al = null;
1953 if (command instanceof EditCommand)
1955 EditCommand editCommand = (EditCommand) command;
1956 al = editCommand.getAlignment();
1957 List<Component> comps = PaintRefresher.components
1958 .get(viewport.getSequenceSetId());
1960 for (Component comp : comps)
1962 if (comp instanceof AlignmentPanel)
1964 if (al == ((AlignmentPanel) comp).av.getAlignment())
1966 originalSource = ((AlignmentPanel) comp).av;
1973 if (originalSource == null)
1975 // The original view is closed, we must validate
1976 // the current view against the closed view first
1979 PaintRefresher.validateSequences(al, viewport.getAlignment());
1982 originalSource = viewport;
1985 return originalSource;
1994 public void moveSelectedSequences(boolean up)
1996 SequenceGroup sg = viewport.getSelectionGroup();
2002 viewport.getAlignment().moveSelectedSequencesByOne(sg,
2003 viewport.getHiddenRepSequences(), up);
2004 alignPanel.paintAlignment(true, false);
2007 synchronized void slideSequences(boolean right, int size)
2009 List<SequenceI> sg = new ArrayList<>();
2010 if (viewport.cursorMode)
2012 sg.add(viewport.getAlignment()
2013 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
2015 else if (viewport.getSelectionGroup() != null
2016 && viewport.getSelectionGroup().getSize() != viewport
2017 .getAlignment().getHeight())
2019 sg = viewport.getSelectionGroup()
2020 .getSequences(viewport.getHiddenRepSequences());
2028 List<SequenceI> invertGroup = new ArrayList<>();
2030 for (SequenceI seq : viewport.getAlignment().getSequences())
2032 if (!sg.contains(seq))
2034 invertGroup.add(seq);
2038 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
2040 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
2041 for (int i = 0; i < invertGroup.size(); i++)
2043 seqs2[i] = invertGroup.get(i);
2046 SlideSequencesCommand ssc;
2049 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
2050 viewport.getGapCharacter());
2054 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
2055 viewport.getGapCharacter());
2058 int groupAdjustment = 0;
2059 if (ssc.getGapsInsertedBegin() && right)
2061 if (viewport.cursorMode)
2063 alignPanel.getSeqPanel().moveCursor(size, 0);
2067 groupAdjustment = size;
2070 else if (!ssc.getGapsInsertedBegin() && !right)
2072 if (viewport.cursorMode)
2074 alignPanel.getSeqPanel().moveCursor(-size, 0);
2078 groupAdjustment = -size;
2082 if (groupAdjustment != 0)
2084 viewport.getSelectionGroup().setStartRes(
2085 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
2086 viewport.getSelectionGroup().setEndRes(
2087 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
2091 * just extend the last slide command if compatible; but not if in
2092 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
2094 boolean appendHistoryItem = false;
2095 Deque<CommandI> historyList = viewport.getHistoryList();
2096 boolean inSplitFrame = getSplitViewContainer() != null;
2097 if (!inSplitFrame && historyList != null && historyList.size() > 0
2098 && historyList.peek() instanceof SlideSequencesCommand)
2100 appendHistoryItem = ssc.appendSlideCommand(
2101 (SlideSequencesCommand) historyList.peek());
2104 if (!appendHistoryItem)
2106 addHistoryItem(ssc);
2119 protected void copy_actionPerformed(ActionEvent e)
2121 if (viewport.getSelectionGroup() == null)
2125 // TODO: preserve the ordering of displayed alignment annotation in any
2126 // internal paste (particularly sequence associated annotation)
2127 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
2128 String[] omitHidden = null;
2130 if (viewport.hasHiddenColumns())
2132 omitHidden = viewport.getViewAsString(true);
2135 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2136 seqs, omitHidden, null);
2138 StringSelection ss = new StringSelection(output);
2142 jalview.gui.Desktop.internalCopy = true;
2143 // Its really worth setting the clipboard contents
2144 // to empty before setting the large StringSelection!!
2145 Toolkit.getDefaultToolkit().getSystemClipboard()
2146 .setContents(new StringSelection(""), null);
2148 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2150 } catch (OutOfMemoryError er)
2152 new OOMWarning("copying region", er);
2156 HiddenColumns hiddenColumns = null;
2157 if (viewport.hasHiddenColumns())
2159 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2160 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2162 // create new HiddenColumns object with copy of hidden regions
2163 // between startRes and endRes, offset by startRes
2164 hiddenColumns = new HiddenColumns(
2165 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
2166 hiddenCutoff, hiddenOffset);
2169 Desktop.jalviewClipboard = new Object[] { seqs,
2170 viewport.getAlignment().getDataset(), hiddenColumns };
2171 statusBar.setText(MessageManager.formatMessage(
2172 "label.copied_sequences_to_clipboard", new Object[]
2173 { Integer.valueOf(seqs.length).toString() }));
2181 * @throws InterruptedException
2182 * @throws IOException
2185 protected void pasteNew_actionPerformed(ActionEvent e)
2186 throws IOException, InterruptedException
2196 * @throws InterruptedException
2197 * @throws IOException
2200 protected void pasteThis_actionPerformed(ActionEvent e)
2201 throws IOException, InterruptedException
2207 * Paste contents of Jalview clipboard
2209 * @param newAlignment
2210 * true to paste to a new alignment, otherwise add to this.
2211 * @throws InterruptedException
2212 * @throws IOException
2214 void paste(boolean newAlignment) throws IOException, InterruptedException
2216 boolean externalPaste = true;
2219 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2220 Transferable contents = c.getContents(this);
2222 if (contents == null)
2231 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2232 if (str.length() < 1)
2237 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2239 } catch (OutOfMemoryError er)
2241 new OOMWarning("Out of memory pasting sequences!!", er);
2245 SequenceI[] sequences;
2246 boolean annotationAdded = false;
2247 AlignmentI alignment = null;
2249 if (Desktop.jalviewClipboard != null)
2251 // The clipboard was filled from within Jalview, we must use the
2253 // And dataset from the copied alignment
2254 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2255 // be doubly sure that we create *new* sequence objects.
2256 sequences = new SequenceI[newseq.length];
2257 for (int i = 0; i < newseq.length; i++)
2259 sequences[i] = new Sequence(newseq[i]);
2261 alignment = new Alignment(sequences);
2262 externalPaste = false;
2266 // parse the clipboard as an alignment.
2267 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2269 sequences = alignment.getSequencesArray();
2273 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2279 if (Desktop.jalviewClipboard != null)
2281 // dataset is inherited
2282 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2286 // new dataset is constructed
2287 alignment.setDataset(null);
2289 alwidth = alignment.getWidth() + 1;
2293 AlignmentI pastedal = alignment; // preserve pasted alignment object
2294 // Add pasted sequences and dataset into existing alignment.
2295 alignment = viewport.getAlignment();
2296 alwidth = alignment.getWidth() + 1;
2297 // decide if we need to import sequences from an existing dataset
2298 boolean importDs = Desktop.jalviewClipboard != null
2299 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2300 // importDs==true instructs us to copy over new dataset sequences from
2301 // an existing alignment
2302 Vector newDs = (importDs) ? new Vector() : null; // used to create
2303 // minimum dataset set
2305 for (int i = 0; i < sequences.length; i++)
2309 newDs.addElement(null);
2311 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2313 if (importDs && ds != null)
2315 if (!newDs.contains(ds))
2317 newDs.setElementAt(ds, i);
2318 ds = new Sequence(ds);
2319 // update with new dataset sequence
2320 sequences[i].setDatasetSequence(ds);
2324 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2329 // copy and derive new dataset sequence
2330 sequences[i] = sequences[i].deriveSequence();
2331 alignment.getDataset()
2332 .addSequence(sequences[i].getDatasetSequence());
2333 // TODO: avoid creation of duplicate dataset sequences with a
2334 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2336 alignment.addSequence(sequences[i]); // merges dataset
2340 newDs.clear(); // tidy up
2342 if (alignment.getAlignmentAnnotation() != null)
2344 for (AlignmentAnnotation alan : alignment
2345 .getAlignmentAnnotation())
2347 if (alan.graphGroup > fgroup)
2349 fgroup = alan.graphGroup;
2353 if (pastedal.getAlignmentAnnotation() != null)
2355 // Add any annotation attached to alignment.
2356 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2357 for (int i = 0; i < alann.length; i++)
2359 annotationAdded = true;
2360 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2362 AlignmentAnnotation newann = new AlignmentAnnotation(
2364 if (newann.graphGroup > -1)
2366 if (newGraphGroups.size() <= newann.graphGroup
2367 || newGraphGroups.get(newann.graphGroup) == null)
2369 for (int q = newGraphGroups
2370 .size(); q <= newann.graphGroup; q++)
2372 newGraphGroups.add(q, null);
2374 newGraphGroups.set(newann.graphGroup,
2375 Integer.valueOf(++fgroup));
2377 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2381 newann.padAnnotation(alwidth);
2382 alignment.addAnnotation(newann);
2392 addHistoryItem(new EditCommand(
2393 MessageManager.getString("label.add_sequences"),
2394 Action.PASTE, sequences, 0, alignment.getWidth(),
2397 // Add any annotations attached to sequences
2398 for (int i = 0; i < sequences.length; i++)
2400 if (sequences[i].getAnnotation() != null)
2402 AlignmentAnnotation newann;
2403 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2405 annotationAdded = true;
2406 newann = sequences[i].getAnnotation()[a];
2407 newann.adjustForAlignment();
2408 newann.padAnnotation(alwidth);
2409 if (newann.graphGroup > -1)
2411 if (newann.graphGroup > -1)
2413 if (newGraphGroups.size() <= newann.graphGroup
2414 || newGraphGroups.get(newann.graphGroup) == null)
2416 for (int q = newGraphGroups
2417 .size(); q <= newann.graphGroup; q++)
2419 newGraphGroups.add(q, null);
2421 newGraphGroups.set(newann.graphGroup,
2422 Integer.valueOf(++fgroup));
2424 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2428 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2432 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2440 // propagate alignment changed.
2441 viewport.getRanges().setEndSeq(alignment.getHeight());
2442 if (annotationAdded)
2444 // Duplicate sequence annotation in all views.
2445 AlignmentI[] alview = this.getViewAlignments();
2446 for (int i = 0; i < sequences.length; i++)
2448 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2453 for (int avnum = 0; avnum < alview.length; avnum++)
2455 if (alview[avnum] != alignment)
2457 // duplicate in a view other than the one with input focus
2458 int avwidth = alview[avnum].getWidth() + 1;
2459 // this relies on sann being preserved after we
2460 // modify the sequence's annotation array for each duplication
2461 for (int a = 0; a < sann.length; a++)
2463 AlignmentAnnotation newann = new AlignmentAnnotation(
2465 sequences[i].addAlignmentAnnotation(newann);
2466 newann.padAnnotation(avwidth);
2467 alview[avnum].addAnnotation(newann); // annotation was
2468 // duplicated earlier
2469 // TODO JAL-1145 graphGroups are not updated for sequence
2470 // annotation added to several views. This may cause
2472 alview[avnum].setAnnotationIndex(newann, a);
2477 buildSortByAnnotationScoresMenu();
2479 viewport.firePropertyChange("alignment", null,
2480 alignment.getSequences());
2481 if (alignPanels != null)
2483 for (AlignmentPanel ap : alignPanels)
2485 ap.validateAnnotationDimensions(false);
2490 alignPanel.validateAnnotationDimensions(false);
2496 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2498 String newtitle = new String("Copied sequences");
2500 if (Desktop.jalviewClipboard != null
2501 && Desktop.jalviewClipboard[2] != null)
2503 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2504 af.viewport.setHiddenColumns(hc);
2507 // >>>This is a fix for the moment, until a better solution is
2509 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2510 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2511 .getFeatureRenderer());
2513 // TODO: maintain provenance of an alignment, rather than just make the
2514 // title a concatenation of operations.
2517 if (title.startsWith("Copied sequences"))
2523 newtitle = newtitle.concat("- from " + title);
2528 newtitle = new String("Pasted sequences");
2531 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2536 } catch (Exception ex)
2538 ex.printStackTrace();
2539 System.out.println("Exception whilst pasting: " + ex);
2540 // could be anything being pasted in here
2545 protected void expand_newalign(ActionEvent e)
2549 AlignmentI alignment = AlignmentUtils
2550 .expandContext(getViewport().getAlignment(), -1);
2551 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2553 String newtitle = new String("Flanking alignment");
2555 if (Desktop.jalviewClipboard != null
2556 && Desktop.jalviewClipboard[2] != null)
2558 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2559 af.viewport.setHiddenColumns(hc);
2562 // >>>This is a fix for the moment, until a better solution is
2564 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2565 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2566 .getFeatureRenderer());
2568 // TODO: maintain provenance of an alignment, rather than just make the
2569 // title a concatenation of operations.
2571 if (title.startsWith("Copied sequences"))
2577 newtitle = newtitle.concat("- from " + title);
2581 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2583 } catch (Exception ex)
2585 ex.printStackTrace();
2586 System.out.println("Exception whilst pasting: " + ex);
2587 // could be anything being pasted in here
2588 } catch (OutOfMemoryError oom)
2590 new OOMWarning("Viewing flanking region of alignment", oom);
2601 protected void cut_actionPerformed(ActionEvent e)
2603 copy_actionPerformed(null);
2604 delete_actionPerformed(null);
2614 protected void delete_actionPerformed(ActionEvent evt)
2617 SequenceGroup sg = viewport.getSelectionGroup();
2624 * If the cut affects all sequences, warn, remove highlighted columns
2626 if (sg.getSize() == viewport.getAlignment().getHeight())
2628 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2629 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2630 if (isEntireAlignWidth)
2632 int confirm = JvOptionPane.showConfirmDialog(this,
2633 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2634 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2635 JvOptionPane.OK_CANCEL_OPTION);
2637 if (confirm == JvOptionPane.CANCEL_OPTION
2638 || confirm == JvOptionPane.CLOSED_OPTION)
2643 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2644 sg.getEndRes() + 1);
2646 SequenceI[] cut = sg.getSequences()
2647 .toArray(new SequenceI[sg.getSize()]);
2649 addHistoryItem(new EditCommand(
2650 MessageManager.getString("label.cut_sequences"), Action.CUT,
2651 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2652 viewport.getAlignment()));
2654 viewport.setSelectionGroup(null);
2655 viewport.sendSelection();
2656 viewport.getAlignment().deleteGroup(sg);
2658 viewport.firePropertyChange("alignment", null,
2659 viewport.getAlignment().getSequences());
2660 if (viewport.getAlignment().getHeight() < 1)
2664 this.setClosed(true);
2665 } catch (Exception ex)
2678 protected void deleteGroups_actionPerformed(ActionEvent e)
2680 if (avc.deleteGroups())
2682 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2683 alignPanel.updateAnnotation();
2684 alignPanel.paintAlignment(true, true);
2695 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2697 SequenceGroup sg = new SequenceGroup(
2698 viewport.getAlignment().getSequences());
2700 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2701 viewport.setSelectionGroup(sg);
2702 viewport.isSelectionGroupChanged(true);
2703 viewport.sendSelection();
2704 // JAL-2034 - should delegate to
2705 // alignPanel to decide if overview needs
2707 alignPanel.paintAlignment(false, false);
2708 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2718 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2720 if (viewport.cursorMode)
2722 alignPanel.getSeqPanel().keyboardNo1 = null;
2723 alignPanel.getSeqPanel().keyboardNo2 = null;
2725 viewport.setSelectionGroup(null);
2726 viewport.getColumnSelection().clear();
2727 viewport.setSelectionGroup(null);
2728 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2729 // JAL-2034 - should delegate to
2730 // alignPanel to decide if overview needs
2732 alignPanel.paintAlignment(false, false);
2733 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2734 viewport.sendSelection();
2744 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2746 SequenceGroup sg = viewport.getSelectionGroup();
2750 selectAllSequenceMenuItem_actionPerformed(null);
2755 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2757 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2759 // JAL-2034 - should delegate to
2760 // alignPanel to decide if overview needs
2763 alignPanel.paintAlignment(true, false);
2764 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2765 viewport.sendSelection();
2769 public void invertColSel_actionPerformed(ActionEvent e)
2771 viewport.invertColumnSelection();
2772 alignPanel.paintAlignment(true, false);
2773 viewport.sendSelection();
2783 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2785 trimAlignment(true);
2795 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2797 trimAlignment(false);
2800 void trimAlignment(boolean trimLeft)
2802 ColumnSelection colSel = viewport.getColumnSelection();
2805 if (!colSel.isEmpty())
2809 column = colSel.getMin();
2813 column = colSel.getMax();
2817 if (viewport.getSelectionGroup() != null)
2819 seqs = viewport.getSelectionGroup()
2820 .getSequencesAsArray(viewport.getHiddenRepSequences());
2824 seqs = viewport.getAlignment().getSequencesArray();
2827 TrimRegionCommand trimRegion;
2830 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2831 column, viewport.getAlignment());
2832 viewport.getRanges().setStartRes(0);
2836 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2837 column, viewport.getAlignment());
2840 statusBar.setText(MessageManager
2841 .formatMessage("label.removed_columns", new String[]
2842 { Integer.valueOf(trimRegion.getSize()).toString() }));
2844 addHistoryItem(trimRegion);
2846 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2848 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2849 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2851 viewport.getAlignment().deleteGroup(sg);
2855 viewport.firePropertyChange("alignment", null,
2856 viewport.getAlignment().getSequences());
2867 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2869 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2872 if (viewport.getSelectionGroup() != null)
2874 seqs = viewport.getSelectionGroup()
2875 .getSequencesAsArray(viewport.getHiddenRepSequences());
2876 start = viewport.getSelectionGroup().getStartRes();
2877 end = viewport.getSelectionGroup().getEndRes();
2881 seqs = viewport.getAlignment().getSequencesArray();
2884 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2885 "Remove Gapped Columns", seqs, start, end,
2886 viewport.getAlignment());
2888 addHistoryItem(removeGapCols);
2890 statusBar.setText(MessageManager
2891 .formatMessage("label.removed_empty_columns", new Object[]
2892 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2894 // This is to maintain viewport position on first residue
2895 // of first sequence
2896 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2897 ViewportRanges ranges = viewport.getRanges();
2898 int startRes = seq.findPosition(ranges.getStartRes());
2899 // ShiftList shifts;
2900 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2901 // edit.alColumnChanges=shifts.getInverse();
2902 // if (viewport.hasHiddenColumns)
2903 // viewport.getColumnSelection().compensateForEdits(shifts);
2904 ranges.setStartRes(seq.findIndex(startRes) - 1);
2905 viewport.firePropertyChange("alignment", null,
2906 viewport.getAlignment().getSequences());
2917 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2919 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2922 if (viewport.getSelectionGroup() != null)
2924 seqs = viewport.getSelectionGroup()
2925 .getSequencesAsArray(viewport.getHiddenRepSequences());
2926 start = viewport.getSelectionGroup().getStartRes();
2927 end = viewport.getSelectionGroup().getEndRes();
2931 seqs = viewport.getAlignment().getSequencesArray();
2934 // This is to maintain viewport position on first residue
2935 // of first sequence
2936 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2937 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2939 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2940 viewport.getAlignment()));
2942 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2944 viewport.firePropertyChange("alignment", null,
2945 viewport.getAlignment().getSequences());
2956 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2958 viewport.setPadGaps(padGapsMenuitem.isSelected());
2959 viewport.firePropertyChange("alignment", null,
2960 viewport.getAlignment().getSequences());
2970 public void findMenuItem_actionPerformed(ActionEvent e)
2976 * Create a new view of the current alignment.
2979 public void newView_actionPerformed(ActionEvent e)
2981 newView(null, true);
2985 * Creates and shows a new view of the current alignment.
2988 * title of newly created view; if null, one will be generated
2989 * @param copyAnnotation
2990 * if true then duplicate all annnotation, groups and settings
2991 * @return new alignment panel, already displayed.
2993 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2996 * Create a new AlignmentPanel (with its own, new Viewport)
2998 AlignmentPanel newap = new jalview.project.Jalview2XML()
2999 .copyAlignPanel(alignPanel);
3000 if (!copyAnnotation)
3003 * remove all groups and annotation except for the automatic stuff
3005 newap.av.getAlignment().deleteAllGroups();
3006 newap.av.getAlignment().deleteAllAnnotations(false);
3009 newap.av.setGatherViewsHere(false);
3011 if (viewport.getViewName() == null)
3013 viewport.setViewName(MessageManager
3014 .getString("label.view_name_original"));
3018 * Views share the same edits undo and redo stacks
3020 newap.av.setHistoryList(viewport.getHistoryList());
3021 newap.av.setRedoList(viewport.getRedoList());
3024 * copy any visualisation settings that are not saved in the project
3026 newap.av.setColourAppliesToAllGroups(
3027 viewport.getColourAppliesToAllGroups());
3030 * Views share the same mappings; need to deregister any new mappings
3031 * created by copyAlignPanel, and register the new reference to the shared
3034 newap.av.replaceMappings(viewport.getAlignment());
3037 * start up cDNA consensus (if applicable) now mappings are in place
3039 if (newap.av.initComplementConsensus())
3041 newap.refresh(true); // adjust layout of annotations
3044 newap.av.setViewName(getNewViewName(viewTitle));
3046 addAlignmentPanel(newap, true);
3047 newap.alignmentChanged();
3049 if (alignPanels.size() == 2)
3051 viewport.setGatherViewsHere(true);
3053 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
3058 * Make a new name for the view, ensuring it is unique within the current
3059 * sequenceSetId. (This used to be essential for Jalview Project archives, but
3060 * these now use viewId. Unique view names are still desirable for usability.)
3065 protected String getNewViewName(String viewTitle)
3067 int index = Desktop.getViewCount(viewport.getSequenceSetId());
3068 boolean addFirstIndex = false;
3069 if (viewTitle == null || viewTitle.trim().length() == 0)
3071 viewTitle = MessageManager.getString("action.view");
3072 addFirstIndex = true;
3076 index = 1;// we count from 1 if given a specific name
3078 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
3080 List<Component> comps = PaintRefresher.components
3081 .get(viewport.getSequenceSetId());
3083 List<String> existingNames = getExistingViewNames(comps);
3085 while (existingNames.contains(newViewName))
3087 newViewName = viewTitle + " " + (++index);
3093 * Returns a list of distinct view names found in the given list of
3094 * components. View names are held on the viewport of an AlignmentPanel.
3099 protected List<String> getExistingViewNames(List<Component> comps)
3101 List<String> existingNames = new ArrayList<>();
3102 for (Component comp : comps)
3104 if (comp instanceof AlignmentPanel)
3106 AlignmentPanel ap = (AlignmentPanel) comp;
3107 if (!existingNames.contains(ap.av.getViewName()))
3109 existingNames.add(ap.av.getViewName());
3113 return existingNames;
3117 * Explode tabbed views into separate windows.
3120 public void expandViews_actionPerformed(ActionEvent e)
3122 Desktop.explodeViews(this);
3126 * Gather views in separate windows back into a tabbed presentation.
3129 public void gatherViews_actionPerformed(ActionEvent e)
3131 Desktop.instance.gatherViews(this);
3141 public void font_actionPerformed(ActionEvent e)
3143 new FontChooser(alignPanel);
3153 protected void seqLimit_actionPerformed(ActionEvent e)
3155 viewport.setShowJVSuffix(seqLimits.isSelected());
3157 alignPanel.getIdPanel().getIdCanvas()
3158 .setPreferredSize(alignPanel.calculateIdWidth());
3159 alignPanel.paintAlignment(true, false);
3163 public void idRightAlign_actionPerformed(ActionEvent e)
3165 viewport.setRightAlignIds(idRightAlign.isSelected());
3166 alignPanel.paintAlignment(false, false);
3170 public void centreColumnLabels_actionPerformed(ActionEvent e)
3172 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3173 alignPanel.paintAlignment(false, false);
3179 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3182 protected void followHighlight_actionPerformed()
3185 * Set the 'follow' flag on the Viewport (and scroll to position if now
3188 final boolean state = this.followHighlightMenuItem.getState();
3189 viewport.setFollowHighlight(state);
3192 alignPanel.scrollToPosition(viewport.getSearchResults());
3203 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3205 viewport.setColourText(colourTextMenuItem.isSelected());
3206 alignPanel.paintAlignment(false, false);
3216 public void wrapMenuItem_actionPerformed(ActionEvent e)
3218 scaleAbove.setVisible(wrapMenuItem.isSelected());
3219 scaleLeft.setVisible(wrapMenuItem.isSelected());
3220 scaleRight.setVisible(wrapMenuItem.isSelected());
3221 viewport.setWrapAlignment(wrapMenuItem.isSelected());
3222 alignPanel.updateLayout();
3226 public void showAllSeqs_actionPerformed(ActionEvent e)
3228 viewport.showAllHiddenSeqs();
3232 public void showAllColumns_actionPerformed(ActionEvent e)
3234 viewport.showAllHiddenColumns();
3235 alignPanel.paintAlignment(true, true);
3236 viewport.sendSelection();
3240 public void hideSelSequences_actionPerformed(ActionEvent e)
3242 viewport.hideAllSelectedSeqs();
3246 * called by key handler and the hide all/show all menu items
3251 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3254 boolean hide = false;
3255 SequenceGroup sg = viewport.getSelectionGroup();
3256 if (!toggleSeqs && !toggleCols)
3258 // Hide everything by the current selection - this is a hack - we do the
3259 // invert and then hide
3260 // first check that there will be visible columns after the invert.
3261 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3262 && sg.getStartRes() <= sg.getEndRes()))
3264 // now invert the sequence set, if required - empty selection implies
3265 // that no hiding is required.
3268 invertSequenceMenuItem_actionPerformed(null);
3269 sg = viewport.getSelectionGroup();
3273 viewport.expandColSelection(sg, true);
3274 // finally invert the column selection and get the new sequence
3276 invertColSel_actionPerformed(null);
3283 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3285 hideSelSequences_actionPerformed(null);
3288 else if (!(toggleCols && viewport.hasSelectedColumns()))
3290 showAllSeqs_actionPerformed(null);
3296 if (viewport.hasSelectedColumns())
3298 hideSelColumns_actionPerformed(null);
3301 viewport.setSelectionGroup(sg);
3306 showAllColumns_actionPerformed(null);
3315 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3316 * event.ActionEvent)
3319 public void hideAllButSelection_actionPerformed(ActionEvent e)
3321 toggleHiddenRegions(false, false);
3322 viewport.sendSelection();
3329 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3333 public void hideAllSelection_actionPerformed(ActionEvent e)
3335 SequenceGroup sg = viewport.getSelectionGroup();
3336 viewport.expandColSelection(sg, false);
3337 viewport.hideAllSelectedSeqs();
3338 viewport.hideSelectedColumns();
3339 alignPanel.updateLayout();
3340 alignPanel.paintAlignment(true, true);
3341 viewport.sendSelection();
3348 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3352 public void showAllhidden_actionPerformed(ActionEvent e)
3354 viewport.showAllHiddenColumns();
3355 viewport.showAllHiddenSeqs();
3356 alignPanel.paintAlignment(true, true);
3357 viewport.sendSelection();
3361 public void hideSelColumns_actionPerformed(ActionEvent e)
3363 viewport.hideSelectedColumns();
3364 alignPanel.updateLayout();
3365 alignPanel.paintAlignment(true, true);
3366 viewport.sendSelection();
3370 public void hiddenMarkers_actionPerformed(ActionEvent e)
3372 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3383 protected void scaleAbove_actionPerformed(ActionEvent e)
3385 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3386 alignPanel.updateLayout();
3387 alignPanel.paintAlignment(true, false);
3397 protected void scaleLeft_actionPerformed(ActionEvent e)
3399 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3400 alignPanel.updateLayout();
3401 alignPanel.paintAlignment(true, false);
3411 protected void scaleRight_actionPerformed(ActionEvent e)
3413 viewport.setScaleRightWrapped(scaleRight.isSelected());
3414 alignPanel.updateLayout();
3415 alignPanel.paintAlignment(true, false);
3425 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3427 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3428 alignPanel.paintAlignment(false, false);
3438 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3440 viewport.setShowText(viewTextMenuItem.isSelected());
3441 alignPanel.paintAlignment(false, false);
3451 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3453 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3454 alignPanel.paintAlignment(false, false);
3457 public FeatureSettings featureSettings;
3460 public FeatureSettingsControllerI getFeatureSettingsUI()
3462 return featureSettings;
3466 public void featureSettings_actionPerformed(ActionEvent e)
3468 if (featureSettings != null)
3470 featureSettings.close();
3471 featureSettings = null;
3473 if (!showSeqFeatures.isSelected())
3475 // make sure features are actually displayed
3476 showSeqFeatures.setSelected(true);
3477 showSeqFeatures_actionPerformed(null);
3479 featureSettings = new FeatureSettings(this);
3483 * Set or clear 'Show Sequence Features'
3489 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3491 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3492 alignPanel.paintAlignment(true, true);
3496 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3497 * the annotations panel as a whole.
3499 * The options to show/hide all annotations should be enabled when the panel
3500 * is shown, and disabled when the panel is hidden.
3505 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3507 final boolean setVisible = annotationPanelMenuItem.isSelected();
3508 viewport.setShowAnnotation(setVisible);
3509 this.showAllSeqAnnotations.setEnabled(setVisible);
3510 this.hideAllSeqAnnotations.setEnabled(setVisible);
3511 this.showAllAlAnnotations.setEnabled(setVisible);
3512 this.hideAllAlAnnotations.setEnabled(setVisible);
3513 alignPanel.updateLayout();
3517 public void alignmentProperties()
3519 JEditorPane editPane = new JEditorPane("text/html", "");
3520 editPane.setEditable(false);
3521 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3524 MessageManager.formatMessage("label.html_content", new Object[]
3525 { contents.toString() }));
3526 JInternalFrame frame = new JInternalFrame();
3527 frame.getContentPane().add(new JScrollPane(editPane));
3529 Desktop.addInternalFrame(frame, MessageManager
3530 .formatMessage("label.alignment_properties", new Object[]
3531 { getTitle() }), 500, 400);
3541 public void overviewMenuItem_actionPerformed(ActionEvent e)
3543 if (alignPanel.overviewPanel != null)
3548 JInternalFrame frame = new JInternalFrame();
3549 final OverviewPanel overview = new OverviewPanel(alignPanel);
3550 frame.setContentPane(overview);
3551 Desktop.addInternalFrame(frame, MessageManager
3552 .formatMessage("label.overview_params", new Object[]
3553 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3556 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3557 frame.addInternalFrameListener(
3558 new javax.swing.event.InternalFrameAdapter()
3561 public void internalFrameClosed(
3562 javax.swing.event.InternalFrameEvent evt)
3565 alignPanel.setOverviewPanel(null);
3568 if (getKeyListeners().length > 0)
3570 frame.addKeyListener(getKeyListeners()[0]);
3573 alignPanel.setOverviewPanel(overview);
3577 public void textColour_actionPerformed()
3579 new TextColourChooser().chooseColour(alignPanel, null);
3583 * public void covariationColour_actionPerformed() {
3585 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3589 public void annotationColour_actionPerformed()
3591 new AnnotationColourChooser(viewport, alignPanel);
3595 public void annotationColumn_actionPerformed(ActionEvent e)
3597 new AnnotationColumnChooser(viewport, alignPanel);
3601 * Action on the user checking or unchecking the option to apply the selected
3602 * colour scheme to all groups. If unchecked, groups may have their own
3603 * independent colour schemes.
3608 public void applyToAllGroups_actionPerformed(boolean selected)
3610 viewport.setColourAppliesToAllGroups(selected);
3614 * Action on user selecting a colour from the colour menu
3617 * the name (not the menu item label!) of the colour scheme
3620 public void changeColour_actionPerformed(String name)
3623 * 'User Defined' opens a panel to configure or load a
3624 * user-defined colour scheme
3626 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3628 new UserDefinedColours(alignPanel);
3633 * otherwise set the chosen colour scheme (or null for 'None')
3635 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3637 viewport.getAlignment(), viewport.getHiddenRepSequences());
3642 * Actions on setting or changing the alignment colour scheme
3647 public void changeColour(ColourSchemeI cs)
3649 // TODO: pull up to controller method
3650 ColourMenuHelper.setColourSelected(colourMenu, cs);
3652 viewport.setGlobalColourScheme(cs);
3654 alignPanel.paintAlignment(true, true);
3658 * Show the PID threshold slider panel
3661 protected void modifyPID_actionPerformed()
3663 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3664 alignPanel.getViewName());
3665 SliderPanel.showPIDSlider();
3669 * Show the Conservation slider panel
3672 protected void modifyConservation_actionPerformed()
3674 SliderPanel.setConservationSlider(alignPanel,
3675 viewport.getResidueShading(), alignPanel.getViewName());
3676 SliderPanel.showConservationSlider();
3680 * Action on selecting or deselecting (Colour) By Conservation
3683 public void conservationMenuItem_actionPerformed(boolean selected)
3685 modifyConservation.setEnabled(selected);
3686 viewport.setConservationSelected(selected);
3687 viewport.getResidueShading().setConservationApplied(selected);
3689 changeColour(viewport.getGlobalColourScheme());
3692 modifyConservation_actionPerformed();
3696 SliderPanel.hideConservationSlider();
3701 * Action on selecting or deselecting (Colour) Above PID Threshold
3704 public void abovePIDThreshold_actionPerformed(boolean selected)
3706 modifyPID.setEnabled(selected);
3707 viewport.setAbovePIDThreshold(selected);
3710 viewport.getResidueShading().setThreshold(0,
3711 viewport.isIgnoreGapsConsensus());
3714 changeColour(viewport.getGlobalColourScheme());
3717 modifyPID_actionPerformed();
3721 SliderPanel.hidePIDSlider();
3732 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3734 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3735 AlignmentSorter.sortByPID(viewport.getAlignment(),
3736 viewport.getAlignment().getSequenceAt(0));
3737 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3738 viewport.getAlignment()));
3739 alignPanel.paintAlignment(true, false);
3749 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3751 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3752 AlignmentSorter.sortByID(viewport.getAlignment());
3754 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3755 alignPanel.paintAlignment(true, false);
3765 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3767 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3768 AlignmentSorter.sortByLength(viewport.getAlignment());
3769 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3770 viewport.getAlignment()));
3771 alignPanel.paintAlignment(true, false);
3781 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3783 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3784 AlignmentSorter.sortByGroup(viewport.getAlignment());
3785 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3786 viewport.getAlignment()));
3788 alignPanel.paintAlignment(true, false);
3792 public void sortEValueMenuItem_actionPerformed(ActionEvent e)
3794 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3795 AlignmentSorter.sortByEValue(viewport.getAlignment());
3796 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3797 viewport.getAlignment()));
3798 alignPanel.paintAlignment(true, false);
3803 public void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
3805 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3806 AlignmentSorter.sortByBitScore(viewport.getAlignment());
3807 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3808 viewport.getAlignment()));
3809 alignPanel.paintAlignment(true, false);
3820 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3822 new RedundancyPanel(alignPanel, this);
3832 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3834 if ((viewport.getSelectionGroup() == null)
3835 || (viewport.getSelectionGroup().getSize() < 2))
3837 JvOptionPane.showInternalMessageDialog(this,
3838 MessageManager.getString(
3839 "label.you_must_select_least_two_sequences"),
3840 MessageManager.getString("label.invalid_selection"),
3841 JvOptionPane.WARNING_MESSAGE);
3845 JInternalFrame frame = new JInternalFrame();
3846 frame.setContentPane(new PairwiseAlignPanel(viewport));
3847 Desktop.addInternalFrame(frame,
3848 MessageManager.getString("action.pairwise_alignment"), 600,
3854 public void autoCalculate_actionPerformed(ActionEvent e)
3856 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3857 if (viewport.autoCalculateConsensus)
3859 viewport.firePropertyChange("alignment", null,
3860 viewport.getAlignment().getSequences());
3865 public void sortByTreeOption_actionPerformed(ActionEvent e)
3867 viewport.sortByTree = sortByTree.isSelected();
3871 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3873 viewport.followSelection = listenToViewSelections.isSelected();
3877 * Constructs a tree panel and adds it to the desktop
3880 * tree type (NJ or AV)
3882 * name of score model used to compute the tree
3884 * parameters for the distance or similarity calculation
3886 void newTreePanel(String type, String modelName,
3887 SimilarityParamsI options)
3889 String frameTitle = "";
3892 boolean onSelection = false;
3893 if (viewport.getSelectionGroup() != null
3894 && viewport.getSelectionGroup().getSize() > 0)
3896 SequenceGroup sg = viewport.getSelectionGroup();
3898 /* Decide if the selection is a column region */
3899 for (SequenceI _s : sg.getSequences())
3901 if (_s.getLength() < sg.getEndRes())
3903 JvOptionPane.showMessageDialog(Desktop.desktop,
3904 MessageManager.getString(
3905 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3906 MessageManager.getString(
3907 "label.sequences_selection_not_aligned"),
3908 JvOptionPane.WARNING_MESSAGE);
3917 if (viewport.getAlignment().getHeight() < 2)
3923 tp = new TreePanel(alignPanel, type, modelName, options);
3924 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3926 frameTitle += " from ";
3928 if (viewport.getViewName() != null)
3930 frameTitle += viewport.getViewName() + " of ";
3933 frameTitle += this.title;
3935 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3946 public void addSortByOrderMenuItem(String title,
3947 final AlignmentOrder order)
3949 final JMenuItem item = new JMenuItem(MessageManager
3950 .formatMessage("action.by_title_param", new Object[]
3953 item.addActionListener(new java.awt.event.ActionListener()
3956 public void actionPerformed(ActionEvent e)
3958 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3960 // TODO: JBPNote - have to map order entries to curent SequenceI
3962 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3964 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3965 viewport.getAlignment()));
3967 alignPanel.paintAlignment(true, false);
3973 * Add a new sort by annotation score menu item
3976 * the menu to add the option to
3978 * the label used to retrieve scores for each sequence on the
3981 public void addSortByAnnotScoreMenuItem(JMenu sort,
3982 final String scoreLabel)
3984 final JMenuItem item = new JMenuItem(scoreLabel);
3986 item.addActionListener(new java.awt.event.ActionListener()
3989 public void actionPerformed(ActionEvent e)
3991 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3992 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3993 viewport.getAlignment());// ,viewport.getSelectionGroup());
3994 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3995 viewport.getAlignment()));
3996 alignPanel.paintAlignment(true, false);
4002 * last hash for alignment's annotation array - used to minimise cost of
4005 protected int _annotationScoreVectorHash;
4008 * search the alignment and rebuild the sort by annotation score submenu the
4009 * last alignment annotation vector hash is stored to minimize cost of
4010 * rebuilding in subsequence calls.
4014 public void buildSortByAnnotationScoresMenu()
4016 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4021 if (viewport.getAlignment().getAlignmentAnnotation()
4022 .hashCode() == _annotationScoreVectorHash)
4027 sortByAnnotScore.removeAll();
4028 Set<String> scoreSorts = new HashSet<>();
4029 for (SequenceI sqa : viewport.getAlignment().getSequences())
4031 AlignmentAnnotation[] anns = sqa.getAnnotation();
4032 for (int i = 0; anns != null && i < anns.length; i++)
4034 AlignmentAnnotation aa = anns[i];
4035 if (aa != null && aa.hasScore() && aa.sequenceRef != null)
4037 scoreSorts.add(aa.label);
4041 for (String label : scoreSorts)
4043 addSortByAnnotScoreMenuItem(sortByAnnotScore, label);
4045 sortByAnnotScore.setVisible(!scoreSorts.isEmpty());
4047 _annotationScoreVectorHash = viewport.getAlignment()
4048 .getAlignmentAnnotation().hashCode();
4052 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4053 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4054 * call. Listeners are added to remove the menu item when the treePanel is
4055 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4059 public void buildTreeSortMenu()
4061 sortByTreeMenu.removeAll();
4063 List<Component> comps = PaintRefresher.components
4064 .get(viewport.getSequenceSetId());
4065 List<TreePanel> treePanels = new ArrayList<>();
4066 for (Component comp : comps)
4068 if (comp instanceof TreePanel)
4070 treePanels.add((TreePanel) comp);
4074 if (treePanels.size() < 1)
4076 sortByTreeMenu.setVisible(false);
4080 sortByTreeMenu.setVisible(true);
4082 for (final TreePanel tp : treePanels)
4084 final JMenuItem item = new JMenuItem(tp.getTitle());
4085 item.addActionListener(new java.awt.event.ActionListener()
4088 public void actionPerformed(ActionEvent e)
4090 tp.sortByTree_actionPerformed();
4091 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4096 sortByTreeMenu.add(item);
4100 public boolean sortBy(AlignmentOrder alorder, String undoname)
4102 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4103 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4104 if (undoname != null)
4106 addHistoryItem(new OrderCommand(undoname, oldOrder,
4107 viewport.getAlignment()));
4109 alignPanel.paintAlignment(true, false);
4114 * Work out whether the whole set of sequences or just the selected set will
4115 * be submitted for multiple alignment.
4118 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4120 // Now, check we have enough sequences
4121 AlignmentView msa = null;
4123 if ((viewport.getSelectionGroup() != null)
4124 && (viewport.getSelectionGroup().getSize() > 1))
4126 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4127 // some common interface!
4129 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4130 * SequenceI[sz = seqs.getSize(false)];
4132 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4133 * seqs.getSequenceAt(i); }
4135 msa = viewport.getAlignmentView(true);
4137 else if (viewport.getSelectionGroup() != null
4138 && viewport.getSelectionGroup().getSize() == 1)
4140 int option = JvOptionPane.showConfirmDialog(this,
4141 MessageManager.getString("warn.oneseq_msainput_selection"),
4142 MessageManager.getString("label.invalid_selection"),
4143 JvOptionPane.OK_CANCEL_OPTION);
4144 if (option == JvOptionPane.OK_OPTION)
4146 msa = viewport.getAlignmentView(false);
4151 msa = viewport.getAlignmentView(false);
4157 * Decides what is submitted to a secondary structure prediction service: the
4158 * first sequence in the alignment, or in the current selection, or, if the
4159 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4160 * region or the whole alignment. (where the first sequence in the set is the
4161 * one that the prediction will be for).
4163 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4165 AlignmentView seqs = null;
4167 if ((viewport.getSelectionGroup() != null)
4168 && (viewport.getSelectionGroup().getSize() > 0))
4170 seqs = viewport.getAlignmentView(true);
4174 seqs = viewport.getAlignmentView(false);
4176 // limit sequences - JBPNote in future - could spawn multiple prediction
4178 // TODO: viewport.getAlignment().isAligned is a global state - the local
4179 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4180 if (!viewport.getAlignment().isAligned(false))
4182 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4183 // TODO: if seqs.getSequences().length>1 then should really have warned
4197 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4199 // Pick the tree file
4200 JalviewFileChooser chooser = new JalviewFileChooser(
4201 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4202 chooser.setFileView(new JalviewFileView());
4203 chooser.setDialogTitle(
4204 MessageManager.getString("label.select_newick_like_tree_file"));
4205 chooser.setToolTipText(
4206 MessageManager.getString("label.load_tree_file"));
4208 int value = chooser.showOpenDialog(null);
4210 if (value == JalviewFileChooser.APPROVE_OPTION)
4212 String filePath = chooser.getSelectedFile().getPath();
4213 Cache.setProperty("LAST_DIRECTORY", filePath);
4214 NewickFile fin = null;
4217 fin = new NewickFile(filePath, DataSourceType.FILE);
4218 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4219 } catch (Exception ex)
4221 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4222 MessageManager.getString("label.problem_reading_tree_file"),
4223 JvOptionPane.WARNING_MESSAGE);
4224 ex.printStackTrace();
4226 if (fin != null && fin.hasWarningMessage())
4228 JvOptionPane.showMessageDialog(Desktop.desktop,
4229 fin.getWarningMessage(),
4231 .getString("label.possible_problem_with_tree_file"),
4232 JvOptionPane.WARNING_MESSAGE);
4237 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4239 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4242 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4243 int h, int x, int y)
4245 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4249 * Add a treeviewer for the tree extracted from a Newick file object to the
4250 * current alignment view
4257 * Associated alignment input data (or null)
4266 * @return TreePanel handle
4268 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4269 AlignmentView input, int w, int h, int x, int y)
4271 TreePanel tp = null;
4277 if (nf.getTree() != null)
4279 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4285 tp.setLocation(x, y);
4288 Desktop.addInternalFrame(tp, treeTitle, w, h);
4290 } catch (Exception ex)
4292 ex.printStackTrace();
4298 private boolean buildingMenu = false;
4301 * Generates menu items and listener event actions for web service clients
4304 public void BuildWebServiceMenu()
4306 while (buildingMenu)
4310 System.err.println("Waiting for building menu to finish.");
4312 } catch (Exception e)
4316 final AlignFrame me = this;
4317 buildingMenu = true;
4318 new Thread(new Runnable()
4323 final List<JMenuItem> legacyItems = new ArrayList<>();
4326 // System.err.println("Building ws menu again "
4327 // + Thread.currentThread());
4328 // TODO: add support for context dependent disabling of services based
4330 // alignment and current selection
4331 // TODO: add additional serviceHandle parameter to specify abstract
4333 // class independently of AbstractName
4334 // TODO: add in rediscovery GUI function to restart discoverer
4335 // TODO: group services by location as well as function and/or
4337 // object broker mechanism.
4338 final Vector<JMenu> wsmenu = new Vector<>();
4339 final IProgressIndicator af = me;
4342 * do not i18n these strings - they are hard-coded in class
4343 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4344 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4346 final JMenu msawsmenu = new JMenu("Alignment");
4347 final JMenu secstrmenu = new JMenu(
4348 "Secondary Structure Prediction");
4349 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4350 final JMenu analymenu = new JMenu("Analysis");
4351 final JMenu dismenu = new JMenu("Protein Disorder");
4352 // JAL-940 - only show secondary structure prediction services from
4353 // the legacy server
4354 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4356 Discoverer.services != null && (Discoverer.services.size() > 0))
4358 // TODO: refactor to allow list of AbstractName/Handler bindings to
4360 // stored or retrieved from elsewhere
4361 // No MSAWS used any more:
4362 // Vector msaws = null; // (Vector)
4363 // Discoverer.services.get("MsaWS");
4364 Vector secstrpr = (Vector) Discoverer.services
4366 if (secstrpr != null)
4368 // Add any secondary structure prediction services
4369 for (int i = 0, j = secstrpr.size(); i < j; i++)
4371 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4373 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4374 .getServiceClient(sh);
4375 int p = secstrmenu.getItemCount();
4376 impl.attachWSMenuEntry(secstrmenu, me);
4377 int q = secstrmenu.getItemCount();
4378 for (int litm = p; litm < q; litm++)
4380 legacyItems.add(secstrmenu.getItem(litm));
4386 // Add all submenus in the order they should appear on the web
4388 wsmenu.add(msawsmenu);
4389 wsmenu.add(secstrmenu);
4390 wsmenu.add(dismenu);
4391 wsmenu.add(analymenu);
4392 // No search services yet
4393 // wsmenu.add(seqsrchmenu);
4395 javax.swing.SwingUtilities.invokeLater(new Runnable()
4402 webService.removeAll();
4403 // first, add discovered services onto the webservices menu
4404 if (wsmenu.size() > 0)
4406 for (int i = 0, j = wsmenu.size(); i < j; i++)
4408 webService.add(wsmenu.get(i));
4413 webService.add(me.webServiceNoServices);
4415 // TODO: move into separate menu builder class.
4416 boolean new_sspred = false;
4417 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4419 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4420 if (jws2servs != null)
4422 if (jws2servs.hasServices())
4424 jws2servs.attachWSMenuEntry(webService, me);
4425 for (Jws2Instance sv : jws2servs.getServices())
4427 if (sv.getName().toLowerCase().contains("jpred"))
4429 for (JMenuItem jmi : legacyItems)
4431 jmi.setVisible(false);
4437 if (jws2servs.isRunning())
4439 JMenuItem tm = new JMenuItem(
4440 "Still discovering JABA Services");
4441 tm.setEnabled(false);
4446 build_urlServiceMenu(me.webService);
4449 // TODO Mateusz - follow pattern for adding web service
4450 // JMenuItems for slivka-based services
4452 SlivkaWSDiscoverer slivkaDiscoverer = SlivkaWSDiscoverer.getInstance();
4453 slivkaDiscoverer.attachWSMenuEntry(webService, me);
4456 build_fetchdbmenu(webService);
4457 for (JMenu item : wsmenu)
4459 if (item.getItemCount() == 0)
4461 item.setEnabled(false);
4465 item.setEnabled(true);
4468 } catch (Exception e)
4471 "Exception during web service menu building process.",
4476 } catch (Exception e)
4479 buildingMenu = false;
4486 * construct any groupURL type service menu entries.
4490 private void build_urlServiceMenu(JMenu webService)
4492 // TODO: remove this code when 2.7 is released
4493 // DEBUG - alignmentView
4495 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4496 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4498 * @Override public void actionPerformed(ActionEvent e) {
4499 * jalview.datamodel.AlignmentView
4500 * .testSelectionViews(af.viewport.getAlignment(),
4501 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4503 * }); webService.add(testAlView);
4505 // TODO: refactor to RestClient discoverer and merge menu entries for
4506 // rest-style services with other types of analysis/calculation service
4507 // SHmmr test client - still being implemented.
4508 // DEBUG - alignmentView
4510 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4513 client.attachWSMenuEntry(
4514 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4520 * Searches the alignment sequences for xRefs and builds the Show
4521 * Cross-References menu (formerly called Show Products), with database
4522 * sources for which cross-references are found (protein sources for a
4523 * nucleotide alignment and vice versa)
4525 * @return true if Show Cross-references menu should be enabled
4527 public boolean canShowProducts()
4529 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4530 AlignmentI dataset = viewport.getAlignment().getDataset();
4532 showProducts.removeAll();
4533 final boolean dna = viewport.getAlignment().isNucleotide();
4535 if (seqs == null || seqs.length == 0)
4537 // nothing to see here.
4541 boolean showp = false;
4544 List<String> ptypes = new CrossRef(seqs, dataset)
4545 .findXrefSourcesForSequences(dna);
4547 for (final String source : ptypes)
4550 final AlignFrame af = this;
4551 JMenuItem xtype = new JMenuItem(source);
4552 xtype.addActionListener(new ActionListener()
4555 public void actionPerformed(ActionEvent e)
4557 showProductsFor(af.viewport.getSequenceSelection(), dna,
4561 showProducts.add(xtype);
4563 showProducts.setVisible(showp);
4564 showProducts.setEnabled(showp);
4565 } catch (Exception e)
4568 "canShowProducts threw an exception - please report to help@jalview.org",
4576 * Finds and displays cross-references for the selected sequences (protein
4577 * products for nucleotide sequences, dna coding sequences for peptides).
4580 * the sequences to show cross-references for
4582 * true if from a nucleotide alignment (so showing proteins)
4584 * the database to show cross-references for
4586 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4587 final String source)
4589 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4594 * Construct and display a new frame containing the translation of this
4595 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4598 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4600 AlignmentI al = null;
4603 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4605 al = dna.translateCdna(codeTable);
4606 } catch (Exception ex)
4608 jalview.bin.Cache.log.error(
4609 "Exception during translation. Please report this !", ex);
4610 final String msg = MessageManager.getString(
4611 "label.error_when_translating_sequences_submit_bug_report");
4612 final String errorTitle = MessageManager
4613 .getString("label.implementation_error")
4614 + MessageManager.getString("label.translation_failed");
4615 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4616 JvOptionPane.ERROR_MESSAGE);
4619 if (al == null || al.getHeight() == 0)
4621 final String msg = MessageManager.getString(
4622 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4623 final String errorTitle = MessageManager
4624 .getString("label.translation_failed");
4625 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4626 JvOptionPane.WARNING_MESSAGE);
4630 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4631 af.setFileFormat(this.currentFileFormat);
4632 final String newTitle = MessageManager
4633 .formatMessage("label.translation_of_params", new Object[]
4634 { this.getTitle(), codeTable.getId() });
4635 af.setTitle(newTitle);
4636 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4638 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4639 viewport.openSplitFrame(af, new Alignment(seqs));
4643 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4650 * Set the file format
4654 public void setFileFormat(FileFormatI format)
4656 this.currentFileFormat = format;
4660 * Try to load a features file onto the alignment.
4663 * contents or path to retrieve file
4665 * access mode of file (see jalview.io.AlignFile)
4666 * @return true if features file was parsed correctly.
4668 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4670 return avc.parseFeaturesFile(file, sourceType,
4671 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4676 public void refreshFeatureUI(boolean enableIfNecessary)
4678 // note - currently this is only still here rather than in the controller
4679 // because of the featureSettings hard reference that is yet to be
4681 if (enableIfNecessary)
4683 viewport.setShowSequenceFeatures(true);
4684 showSeqFeatures.setSelected(true);
4690 public void dragEnter(DropTargetDragEvent evt)
4695 public void dragExit(DropTargetEvent evt)
4700 public void dragOver(DropTargetDragEvent evt)
4705 public void dropActionChanged(DropTargetDragEvent evt)
4710 public void drop(DropTargetDropEvent evt)
4712 // JAL-1552 - acceptDrop required before getTransferable call for
4713 // Java's Transferable for native dnd
4714 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4715 Transferable t = evt.getTransferable();
4716 final AlignFrame thisaf = this;
4717 final List<String> files = new ArrayList<>();
4718 List<DataSourceType> protocols = new ArrayList<>();
4722 Desktop.transferFromDropTarget(files, protocols, evt, t);
4723 } catch (Exception e)
4725 e.printStackTrace();
4729 new Thread(new Runnable()
4736 // check to see if any of these files have names matching sequences
4739 SequenceIdMatcher idm = new SequenceIdMatcher(
4740 viewport.getAlignment().getSequencesArray());
4742 * Object[] { String,SequenceI}
4744 ArrayList<Object[]> filesmatched = new ArrayList<>();
4745 ArrayList<String> filesnotmatched = new ArrayList<>();
4746 for (int i = 0; i < files.size(); i++)
4748 String file = files.get(i).toString();
4750 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4751 if (protocol == DataSourceType.FILE)
4753 File fl = new File(file);
4754 pdbfn = fl.getName();
4756 else if (protocol == DataSourceType.URL)
4758 URL url = new URL(file);
4759 pdbfn = url.getFile();
4761 if (pdbfn.length() > 0)
4763 // attempt to find a match in the alignment
4764 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4765 int l = 0, c = pdbfn.indexOf(".");
4766 while (mtch == null && c != -1)
4771 } while ((c = pdbfn.indexOf(".", l)) > l);
4774 pdbfn = pdbfn.substring(0, l);
4776 mtch = idm.findAllIdMatches(pdbfn);
4780 FileFormatI type = null;
4783 type = new IdentifyFile().identify(file, protocol);
4784 } catch (Exception ex)
4788 if (type != null && type.isStructureFile())
4790 filesmatched.add(new Object[] { file, protocol, mtch });
4794 // File wasn't named like one of the sequences or wasn't a PDB
4796 filesnotmatched.add(file);
4800 if (filesmatched.size() > 0)
4802 boolean autoAssociate = Cache
4803 .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4806 String msg = MessageManager.formatMessage(
4807 "label.automatically_associate_structure_files_with_sequences_same_name",
4809 { Integer.valueOf(filesmatched.size())
4811 String ttl = MessageManager.getString(
4812 "label.automatically_associate_structure_files_by_name");
4813 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4814 ttl, JvOptionPane.YES_NO_OPTION);
4815 autoAssociate = choice == JvOptionPane.YES_OPTION;
4819 for (Object[] fm : filesmatched)
4821 // try and associate
4822 // TODO: may want to set a standard ID naming formalism for
4823 // associating PDB files which have no IDs.
4824 for (SequenceI toassoc : (SequenceI[]) fm[2])
4826 PDBEntry pe = new AssociatePdbFileWithSeq()
4827 .associatePdbWithSeq((String) fm[0],
4828 (DataSourceType) fm[1], toassoc, false,
4832 System.err.println("Associated file : "
4833 + ((String) fm[0]) + " with "
4834 + toassoc.getDisplayId(true));
4838 // TODO: do we need to update overview ? only if features are
4840 alignPanel.paintAlignment(true, false);
4846 * add declined structures as sequences
4848 for (Object[] o : filesmatched)
4850 filesnotmatched.add((String) o[0]);
4854 if (filesnotmatched.size() > 0)
4856 if (assocfiles > 0 && (Cache.getDefault(
4857 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4858 || JvOptionPane.showConfirmDialog(thisaf,
4859 "<html>" + MessageManager.formatMessage(
4860 "label.ignore_unmatched_dropped_files_info",
4863 filesnotmatched.size())
4866 MessageManager.getString(
4867 "label.ignore_unmatched_dropped_files"),
4868 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4872 for (String fn : filesnotmatched)
4874 loadJalviewDataFile(fn, null, null, null);
4878 } catch (Exception ex)
4880 ex.printStackTrace();
4888 * Attempt to load a "dropped" file or URL string, by testing in turn for
4890 * <li>an Annotation file</li>
4891 * <li>a JNet file</li>
4892 * <li>a features file</li>
4893 * <li>else try to interpret as an alignment file</li>
4897 * either a filename or a URL string.
4898 * @throws InterruptedException
4899 * @throws IOException
4901 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4902 FileFormatI format, SequenceI assocSeq)
4906 if (sourceType == null)
4908 sourceType = FormatAdapter.checkProtocol(file);
4910 // if the file isn't identified, or not positively identified as some
4911 // other filetype (PFAM is default unidentified alignment file type) then
4912 // try to parse as annotation.
4913 boolean isAnnotation = (format == null
4914 || FileFormat.Pfam.equals(format))
4915 ? new AnnotationFile().annotateAlignmentView(viewport,
4921 // first see if its a T-COFFEE score file
4922 TCoffeeScoreFile tcf = null;
4925 tcf = new TCoffeeScoreFile(file, sourceType);
4928 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4932 new TCoffeeColourScheme(viewport.getAlignment()));
4933 isAnnotation = true;
4934 statusBar.setText(MessageManager.getString(
4935 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4939 // some problem - if no warning its probable that the ID matching
4940 // process didn't work
4941 JvOptionPane.showMessageDialog(Desktop.desktop,
4942 tcf.getWarningMessage() == null
4943 ? MessageManager.getString(
4944 "label.check_file_matches_sequence_ids_alignment")
4945 : tcf.getWarningMessage(),
4946 MessageManager.getString(
4947 "label.problem_reading_tcoffee_score_file"),
4948 JvOptionPane.WARNING_MESSAGE);
4955 } catch (Exception x)
4958 "Exception when processing data source as T-COFFEE score file",
4964 // try to see if its a JNet 'concise' style annotation file *before*
4966 // try to parse it as a features file
4969 format = new IdentifyFile().identify(file, sourceType);
4971 if (FileFormat.ScoreMatrix == format)
4973 ScoreMatrixFile sm = new ScoreMatrixFile(
4974 new FileParse(file, sourceType));
4976 // todo: i18n this message
4977 statusBar.setText(MessageManager.formatMessage(
4978 "label.successfully_loaded_matrix",
4979 sm.getMatrixName()));
4981 else if (FileFormat.Jnet.equals(format))
4983 JPredFile predictions = new JPredFile(file, sourceType);
4984 new JnetAnnotationMaker();
4985 JnetAnnotationMaker.add_annotation(predictions,
4986 viewport.getAlignment(), 0, false);
4987 viewport.getAlignment().setupJPredAlignment();
4988 isAnnotation = true;
4990 // else if (IdentifyFile.FeaturesFile.equals(format))
4991 else if (FileFormat.Features.equals(format))
4993 if (parseFeaturesFile(file, sourceType))
4995 alignPanel.paintAlignment(true, true);
5000 new FileLoader().LoadFile(viewport, file, sourceType, format);
5006 alignPanel.adjustAnnotationHeight();
5007 viewport.updateSequenceIdColours();
5008 buildSortByAnnotationScoresMenu();
5009 alignPanel.paintAlignment(true, true);
5011 } catch (Exception ex)
5013 ex.printStackTrace();
5014 } catch (OutOfMemoryError oom)
5019 } catch (Exception x)
5024 + (sourceType != null
5025 ? (sourceType == DataSourceType.PASTE
5027 : "using " + sourceType + " from "
5031 ? "(parsing as '" + format + "' file)"
5033 oom, Desktop.desktop);
5038 * Method invoked by the ChangeListener on the tabbed pane, in other words
5039 * when a different tabbed pane is selected by the user or programmatically.
5042 public void tabSelectionChanged(int index)
5046 alignPanel = alignPanels.get(index);
5047 viewport = alignPanel.av;
5048 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5049 setMenusFromViewport(viewport);
5053 * 'focus' any colour slider that is open to the selected viewport
5055 if (viewport.getConservationSelected())
5057 SliderPanel.setConservationSlider(alignPanel,
5058 viewport.getResidueShading(), alignPanel.getViewName());
5062 SliderPanel.hideConservationSlider();
5064 if (viewport.getAbovePIDThreshold())
5066 SliderPanel.setPIDSliderSource(alignPanel,
5067 viewport.getResidueShading(), alignPanel.getViewName());
5071 SliderPanel.hidePIDSlider();
5075 * If there is a frame linked to this one in a SplitPane, switch it to the
5076 * same view tab index. No infinite recursion of calls should happen, since
5077 * tabSelectionChanged() should not get invoked on setting the selected
5078 * index to an unchanged value. Guard against setting an invalid index
5079 * before the new view peer tab has been created.
5081 final AlignViewportI peer = viewport.getCodingComplement();
5084 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
5085 .getAlignPanel().alignFrame;
5086 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5088 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5094 * On right mouse click on view tab, prompt for and set new view name.
5097 public void tabbedPane_mousePressed(MouseEvent e)
5099 if (e.isPopupTrigger())
5101 String msg = MessageManager.getString("label.enter_view_name");
5102 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
5103 JvOptionPane.QUESTION_MESSAGE);
5107 viewport.setViewName(reply);
5108 // TODO warn if reply is in getExistingViewNames()?
5109 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5114 public AlignViewport getCurrentView()
5120 * Open the dialog for regex description parsing.
5123 protected void extractScores_actionPerformed(ActionEvent e)
5125 ParseProperties pp = new jalview.analysis.ParseProperties(
5126 viewport.getAlignment());
5127 // TODO: verify regex and introduce GUI dialog for version 2.5
5128 // if (pp.getScoresFromDescription("col", "score column ",
5129 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5131 if (pp.getScoresFromDescription("description column",
5132 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5134 buildSortByAnnotationScoresMenu();
5142 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5146 protected void showDbRefs_actionPerformed(ActionEvent e)
5148 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5154 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5158 protected void showNpFeats_actionPerformed(ActionEvent e)
5160 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5164 * find the viewport amongst the tabs in this alignment frame and close that
5169 public boolean closeView(AlignViewportI av)
5173 this.closeMenuItem_actionPerformed(false);
5176 Component[] comp = tabbedPane.getComponents();
5177 for (int i = 0; comp != null && i < comp.length; i++)
5179 if (comp[i] instanceof AlignmentPanel)
5181 if (((AlignmentPanel) comp[i]).av == av)
5184 closeView((AlignmentPanel) comp[i]);
5192 protected void build_fetchdbmenu(JMenu webService)
5194 // Temporary hack - DBRef Fetcher always top level ws entry.
5195 // TODO We probably want to store a sequence database checklist in
5196 // preferences and have checkboxes.. rather than individual sources selected
5198 final JMenu rfetch = new JMenu(
5199 MessageManager.getString("action.fetch_db_references"));
5200 rfetch.setToolTipText(MessageManager.getString(
5201 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5202 webService.add(rfetch);
5204 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5205 MessageManager.getString("option.trim_retrieved_seqs"));
5206 trimrs.setToolTipText(
5207 MessageManager.getString("label.trim_retrieved_sequences"));
5209 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5210 trimrs.addActionListener(new ActionListener()
5213 public void actionPerformed(ActionEvent e)
5215 trimrs.setSelected(trimrs.isSelected());
5216 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5217 Boolean.valueOf(trimrs.isSelected()).toString());
5221 JMenuItem fetchr = new JMenuItem(
5222 MessageManager.getString("label.standard_databases"));
5223 fetchr.setToolTipText(
5224 MessageManager.getString("label.fetch_embl_uniprot"));
5225 fetchr.addActionListener(new ActionListener()
5229 public void actionPerformed(ActionEvent e)
5231 new Thread(new Runnable()
5236 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5237 .getAlignment().isNucleotide();
5238 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5239 alignPanel.av.getSequenceSelection(),
5240 alignPanel.alignFrame, null,
5241 alignPanel.alignFrame.featureSettings, isNucleotide);
5242 dbRefFetcher.addListener(new FetchFinishedListenerI()
5245 public void finished()
5248 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5249 .getFeatureSettingsModels())
5252 alignPanel.av.mergeFeaturesStyle(srcSettings);
5254 AlignFrame.this.setMenusForViewport();
5257 dbRefFetcher.fetchDBRefs(false);
5265 final AlignFrame me = this;
5266 new Thread(new Runnable()
5271 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5272 .getSequenceFetcherSingleton(me);
5273 javax.swing.SwingUtilities.invokeLater(new Runnable()
5278 String[] dbclasses = sf.getOrderedSupportedSources();
5279 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5280 // jalview.util.QuickSort.sort(otherdb, otherdb);
5281 List<DbSourceProxy> otherdb;
5282 JMenu dfetch = new JMenu();
5283 JMenu ifetch = new JMenu();
5284 JMenuItem fetchr = null;
5285 int comp = 0, icomp = 0, mcomp = 15;
5286 String mname = null;
5288 for (String dbclass : dbclasses)
5290 otherdb = sf.getSourceProxy(dbclass);
5291 // add a single entry for this class, or submenu allowing 'fetch
5293 if (otherdb == null || otherdb.size() < 1)
5297 // List<DbSourceProxy> dbs=otherdb;
5298 // otherdb=new ArrayList<DbSourceProxy>();
5299 // for (DbSourceProxy db:dbs)
5301 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5305 mname = "From " + dbclass;
5307 if (otherdb.size() == 1)
5309 final DbSourceProxy[] dassource = otherdb
5310 .toArray(new DbSourceProxy[0]);
5311 DbSourceProxy src = otherdb.get(0);
5312 fetchr = new JMenuItem(src.getDbSource());
5313 fetchr.addActionListener(new ActionListener()
5317 public void actionPerformed(ActionEvent e)
5319 new Thread(new Runnable()
5325 boolean isNucleotide = alignPanel.alignFrame
5326 .getViewport().getAlignment()
5328 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5329 alignPanel.av.getSequenceSelection(),
5330 alignPanel.alignFrame, dassource,
5331 alignPanel.alignFrame.featureSettings,
5334 .addListener(new FetchFinishedListenerI()
5337 public void finished()
5339 FeatureSettingsModelI srcSettings = dassource[0]
5340 .getFeatureColourScheme();
5341 alignPanel.av.mergeFeaturesStyle(
5343 AlignFrame.this.setMenusForViewport();
5346 dbRefFetcher.fetchDBRefs(false);
5352 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5353 MessageManager.formatMessage(
5354 "label.fetch_retrieve_from", new Object[]
5355 { src.getDbName() })));
5361 final DbSourceProxy[] dassource = otherdb
5362 .toArray(new DbSourceProxy[0]);
5364 DbSourceProxy src = otherdb.get(0);
5365 fetchr = new JMenuItem(MessageManager
5366 .formatMessage("label.fetch_all_param", new Object[]
5367 { src.getDbSource() }));
5368 fetchr.addActionListener(new ActionListener()
5371 public void actionPerformed(ActionEvent e)
5373 new Thread(new Runnable()
5379 boolean isNucleotide = alignPanel.alignFrame
5380 .getViewport().getAlignment()
5382 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5383 alignPanel.av.getSequenceSelection(),
5384 alignPanel.alignFrame, dassource,
5385 alignPanel.alignFrame.featureSettings,
5388 .addListener(new FetchFinishedListenerI()
5391 public void finished()
5393 AlignFrame.this.setMenusForViewport();
5396 dbRefFetcher.fetchDBRefs(false);
5402 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5403 MessageManager.formatMessage(
5404 "label.fetch_retrieve_from_all_sources",
5406 { Integer.valueOf(otherdb.size())
5408 src.getDbSource(), src.getDbName() })));
5411 // and then build the rest of the individual menus
5412 ifetch = new JMenu(MessageManager.formatMessage(
5413 "label.source_from_db_source", new Object[]
5414 { src.getDbSource() }));
5416 String imname = null;
5418 for (DbSourceProxy sproxy : otherdb)
5420 String dbname = sproxy.getDbName();
5421 String sname = dbname.length() > 5
5422 ? dbname.substring(0, 5) + "..."
5424 String msname = dbname.length() > 10
5425 ? dbname.substring(0, 10) + "..."
5429 imname = MessageManager
5430 .formatMessage("label.from_msname", new Object[]
5433 fetchr = new JMenuItem(msname);
5434 final DbSourceProxy[] dassrc = { sproxy };
5435 fetchr.addActionListener(new ActionListener()
5439 public void actionPerformed(ActionEvent e)
5441 new Thread(new Runnable()
5447 boolean isNucleotide = alignPanel.alignFrame
5448 .getViewport().getAlignment()
5450 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5451 alignPanel.av.getSequenceSelection(),
5452 alignPanel.alignFrame, dassrc,
5453 alignPanel.alignFrame.featureSettings,
5456 .addListener(new FetchFinishedListenerI()
5459 public void finished()
5461 AlignFrame.this.setMenusForViewport();
5464 dbRefFetcher.fetchDBRefs(false);
5470 fetchr.setToolTipText(
5471 "<html>" + MessageManager.formatMessage(
5472 "label.fetch_retrieve_from", new Object[]
5476 if (++icomp >= mcomp || i == (otherdb.size()))
5478 ifetch.setText(MessageManager.formatMessage(
5479 "label.source_to_target", imname, sname));
5481 ifetch = new JMenu();
5489 if (comp >= mcomp || dbi >= (dbclasses.length))
5491 dfetch.setText(MessageManager.formatMessage(
5492 "label.source_to_target", mname, dbclass));
5494 dfetch = new JMenu();
5507 * Left justify the whole alignment.
5510 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5512 AlignmentI al = viewport.getAlignment();
5514 viewport.firePropertyChange("alignment", null, al);
5518 * Right justify the whole alignment.
5521 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5523 AlignmentI al = viewport.getAlignment();
5525 viewport.firePropertyChange("alignment", null, al);
5529 public void setShowSeqFeatures(boolean b)
5531 showSeqFeatures.setSelected(b);
5532 viewport.setShowSequenceFeatures(b);
5539 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5540 * awt.event.ActionEvent)
5543 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5545 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5546 alignPanel.paintAlignment(false, false);
5553 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5557 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5559 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5560 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5568 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5569 * .event.ActionEvent)
5572 protected void showGroupConservation_actionPerformed(ActionEvent e)
5574 viewport.setShowGroupConservation(showGroupConservation.getState());
5575 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5582 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5583 * .event.ActionEvent)
5586 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5588 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5589 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5596 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5597 * .event.ActionEvent)
5600 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5602 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5603 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5607 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5609 showSequenceLogo.setState(true);
5610 viewport.setShowSequenceLogo(true);
5611 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5612 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5616 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5618 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5625 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5626 * .event.ActionEvent)
5629 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5631 if (avc.makeGroupsFromSelection())
5633 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5634 alignPanel.updateAnnotation();
5635 alignPanel.paintAlignment(true,
5636 viewport.needToUpdateStructureViews());
5640 public void clearAlignmentSeqRep()
5642 // TODO refactor alignmentseqrep to controller
5643 if (viewport.getAlignment().hasSeqrep())
5645 viewport.getAlignment().setSeqrep(null);
5646 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5647 alignPanel.updateAnnotation();
5648 alignPanel.paintAlignment(true, true);
5653 protected void createGroup_actionPerformed(ActionEvent e)
5655 if (avc.createGroup())
5657 if (applyAutoAnnotationSettings.isSelected())
5659 alignPanel.updateAnnotation(true, false);
5661 alignPanel.alignmentChanged();
5666 protected void unGroup_actionPerformed(ActionEvent e)
5670 alignPanel.alignmentChanged();
5675 * make the given alignmentPanel the currently selected tab
5677 * @param alignmentPanel
5679 public void setDisplayedView(AlignmentPanel alignmentPanel)
5681 if (!viewport.getSequenceSetId()
5682 .equals(alignmentPanel.av.getSequenceSetId()))
5684 throw new Error(MessageManager.getString(
5685 "error.implementation_error_cannot_show_view_alignment_frame"));
5687 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5688 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5690 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5695 * Action on selection of menu options to Show or Hide annotations.
5698 * @param forSequences
5699 * update sequence-related annotations
5700 * @param forAlignment
5701 * update non-sequence-related annotations
5704 protected void setAnnotationsVisibility(boolean visible,
5705 boolean forSequences, boolean forAlignment)
5707 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5708 .getAlignmentAnnotation();
5713 for (AlignmentAnnotation aa : anns)
5716 * don't display non-positional annotations on an alignment
5718 if (aa.annotations == null)
5722 boolean apply = (aa.sequenceRef == null && forAlignment)
5723 || (aa.sequenceRef != null && forSequences);
5726 aa.visible = visible;
5729 alignPanel.validateAnnotationDimensions(true);
5730 alignPanel.alignmentChanged();
5734 * Store selected annotation sort order for the view and repaint.
5737 protected void sortAnnotations_actionPerformed()
5739 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5741 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5742 alignPanel.paintAlignment(false, false);
5747 * @return alignment panels in this alignment frame
5749 public List<? extends AlignmentViewPanel> getAlignPanels()
5751 // alignPanels is never null
5752 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5757 * Open a new alignment window, with the cDNA associated with this (protein)
5758 * alignment, aligned as is the protein.
5760 protected void viewAsCdna_actionPerformed()
5762 // TODO no longer a menu action - refactor as required
5763 final AlignmentI alignment = getViewport().getAlignment();
5764 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5765 if (mappings == null)
5769 List<SequenceI> cdnaSeqs = new ArrayList<>();
5770 for (SequenceI aaSeq : alignment.getSequences())
5772 for (AlignedCodonFrame acf : mappings)
5774 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5778 * There is a cDNA mapping for this protein sequence - add to new
5779 * alignment. It will share the same dataset sequence as other mapped
5780 * cDNA (no new mappings need to be created).
5782 final Sequence newSeq = new Sequence(dnaSeq);
5783 newSeq.setDatasetSequence(dnaSeq);
5784 cdnaSeqs.add(newSeq);
5788 if (cdnaSeqs.size() == 0)
5790 // show a warning dialog no mapped cDNA
5793 AlignmentI cdna = new Alignment(
5794 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5795 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5796 AlignFrame.DEFAULT_HEIGHT);
5797 cdna.alignAs(alignment);
5798 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5800 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5801 AlignFrame.DEFAULT_HEIGHT);
5805 * Set visibility of dna/protein complement view (available when shown in a
5811 protected void showComplement_actionPerformed(boolean show)
5813 SplitContainerI sf = getSplitViewContainer();
5816 sf.setComplementVisible(this, show);
5821 * Generate the reverse (optionally complemented) of the selected sequences,
5822 * and add them to the alignment
5825 protected void showReverse_actionPerformed(boolean complement)
5827 AlignmentI al = null;
5830 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5831 al = dna.reverseCdna(complement);
5832 viewport.addAlignment(al, "");
5833 addHistoryItem(new EditCommand(
5834 MessageManager.getString("label.add_sequences"), Action.PASTE,
5835 al.getSequencesArray(), 0, al.getWidth(),
5836 viewport.getAlignment()));
5837 } catch (Exception ex)
5839 System.err.println(ex.getMessage());
5845 * Try to run a script in the Groovy console, having first ensured that this
5846 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5847 * be targeted at this alignment.
5850 protected void runGroovy_actionPerformed()
5852 Jalview.setCurrentAlignFrame(this);
5853 groovy.ui.Console console = Desktop.getGroovyConsole();
5854 if (console != null)
5858 console.runScript();
5859 } catch (Exception ex)
5861 System.err.println((ex.toString()));
5862 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5863 MessageManager.getString("label.couldnt_run_groovy_script"),
5864 MessageManager.getString("label.groovy_support_failed"),
5865 JvOptionPane.ERROR_MESSAGE);
5870 System.err.println("Can't run Groovy script as console not found");
5875 * Hides columns containing (or not containing) a specified feature, provided
5876 * that would not leave all columns hidden
5878 * @param featureType
5879 * @param columnsContaining
5882 public boolean hideFeatureColumns(String featureType,
5883 boolean columnsContaining)
5885 boolean notForHiding = avc.markColumnsContainingFeatures(
5886 columnsContaining, false, false, featureType);
5889 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5890 false, featureType))
5892 getViewport().hideSelectedColumns();
5900 protected void selectHighlightedColumns_actionPerformed(
5901 ActionEvent actionEvent)
5903 // include key modifier check in case user selects from menu
5904 avc.markHighlightedColumns(
5905 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5906 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5907 | ActionEvent.CTRL_MASK)) != 0);
5911 * Rebuilds the Colour menu, including any user-defined colours which have
5912 * been loaded either on startup or during the session
5914 public void buildColourMenu()
5916 colourMenu.removeAll();
5918 colourMenu.add(applyToAllGroups);
5919 colourMenu.add(textColour);
5920 colourMenu.addSeparator();
5922 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5923 viewport.getAlignment(), false);
5925 colourMenu.add(annotationColour);
5926 bg.add(annotationColour);
5927 colourMenu.addSeparator();
5928 colourMenu.add(conservationMenuItem);
5929 colourMenu.add(modifyConservation);
5930 colourMenu.add(abovePIDThreshold);
5931 colourMenu.add(modifyPID);
5933 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5934 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5938 * Open a dialog (if not already open) that allows the user to select and
5939 * calculate PCA or Tree analysis
5941 protected void openTreePcaDialog()
5943 if (alignPanel.getCalculationDialog() == null)
5945 new CalculationChooser(AlignFrame.this);
5950 * Sets the status of the HMMER menu
5952 public void updateHMMERStatus()
5954 hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
5958 protected void loadVcf_actionPerformed()
5960 JalviewFileChooser chooser = new JalviewFileChooser(
5961 Cache.getProperty("LAST_DIRECTORY"));
5962 chooser.setFileView(new JalviewFileView());
5963 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5964 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5966 int value = chooser.showOpenDialog(null);
5968 if (value == JalviewFileChooser.APPROVE_OPTION)
5970 String choice = chooser.getSelectedFile().getPath();
5971 Cache.setProperty("LAST_DIRECTORY", choice);
5972 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5973 new VCFLoader(choice).loadVCF(seqs, this);
5979 class PrintThread extends Thread
5983 public PrintThread(AlignmentPanel ap)
5988 static PageFormat pf;
5993 PrinterJob printJob = PrinterJob.getPrinterJob();
5997 printJob.setPrintable(ap, pf);
6001 printJob.setPrintable(ap);
6004 if (printJob.printDialog())
6009 } catch (Exception PrintException)
6011 PrintException.printStackTrace();