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.SplitContainerI;
37 import jalview.api.ViewStyleI;
38 import jalview.api.analysis.SimilarityParamsI;
39 import jalview.bin.Cache;
40 import jalview.bin.Jalview;
41 import jalview.commands.CommandI;
42 import jalview.commands.EditCommand;
43 import jalview.commands.EditCommand.Action;
44 import jalview.commands.OrderCommand;
45 import jalview.commands.RemoveGapColCommand;
46 import jalview.commands.RemoveGapsCommand;
47 import jalview.commands.SlideSequencesCommand;
48 import jalview.commands.TrimRegionCommand;
49 import jalview.datamodel.AlignedCodonFrame;
50 import jalview.datamodel.Alignment;
51 import jalview.datamodel.AlignmentAnnotation;
52 import jalview.datamodel.AlignmentExportData;
53 import jalview.datamodel.AlignmentI;
54 import jalview.datamodel.AlignmentOrder;
55 import jalview.datamodel.AlignmentView;
56 import jalview.datamodel.ColumnSelection;
57 import jalview.datamodel.HiddenColumns;
58 import jalview.datamodel.HiddenSequences;
59 import jalview.datamodel.PDBEntry;
60 import jalview.datamodel.SeqCigar;
61 import jalview.datamodel.Sequence;
62 import jalview.datamodel.SequenceGroup;
63 import jalview.datamodel.SequenceI;
64 import jalview.gui.ColourMenuHelper.ColourChangeListener;
65 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
66 import jalview.hmmer.HMMAlign;
67 import jalview.hmmer.HMMBuild;
68 import jalview.hmmer.HMMERParamStore;
69 import jalview.hmmer.HMMERPreset;
70 import jalview.hmmer.HMMSearch;
71 import jalview.hmmer.HmmerCommand;
72 import jalview.hmmer.JackHMMER;
73 import jalview.io.AlignmentProperties;
74 import jalview.io.AnnotationFile;
75 import jalview.io.BackupFiles;
76 import jalview.io.BioJsHTMLOutput;
77 import jalview.io.DataSourceType;
78 import jalview.io.FileFormat;
79 import jalview.io.FileFormatI;
80 import jalview.io.FileFormats;
81 import jalview.io.FileLoader;
82 import jalview.io.FileParse;
83 import jalview.io.FormatAdapter;
84 import jalview.io.HtmlSvgOutput;
85 import jalview.io.IdentifyFile;
86 import jalview.io.JPredFile;
87 import jalview.io.JalviewFileChooser;
88 import jalview.io.JalviewFileView;
89 import jalview.io.JnetAnnotationMaker;
90 import jalview.io.NewickFile;
91 import jalview.io.ScoreMatrixFile;
92 import jalview.io.TCoffeeScoreFile;
93 import jalview.io.vcf.VCFLoader;
94 import jalview.jbgui.GAlignFrame;
95 import jalview.schemes.ColourSchemeI;
96 import jalview.schemes.ColourSchemes;
97 import jalview.schemes.ResidueColourScheme;
98 import jalview.schemes.TCoffeeColourScheme;
99 import jalview.util.MessageManager;
100 import jalview.viewmodel.AlignmentViewport;
101 import jalview.viewmodel.ViewportRanges;
102 import jalview.ws.DBRefFetcher;
103 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
104 import jalview.ws.jws1.Discoverer;
105 import jalview.ws.jws2.Jws2Discoverer;
106 import jalview.ws.jws2.jabaws2.Jws2Instance;
107 import jalview.ws.params.ArgumentI;
108 import jalview.ws.params.ParamDatastoreI;
109 import jalview.ws.params.WsParamSetI;
110 import jalview.ws.seqfetcher.DbSourceProxy;
112 import java.awt.BorderLayout;
113 import java.awt.Component;
114 import java.awt.Rectangle;
115 import java.awt.Toolkit;
116 import java.awt.datatransfer.Clipboard;
117 import java.awt.datatransfer.DataFlavor;
118 import java.awt.datatransfer.StringSelection;
119 import java.awt.datatransfer.Transferable;
120 import java.awt.dnd.DnDConstants;
121 import java.awt.dnd.DropTargetDragEvent;
122 import java.awt.dnd.DropTargetDropEvent;
123 import java.awt.dnd.DropTargetEvent;
124 import java.awt.dnd.DropTargetListener;
125 import java.awt.event.ActionEvent;
126 import java.awt.event.ActionListener;
127 import java.awt.event.FocusAdapter;
128 import java.awt.event.FocusEvent;
129 import java.awt.event.ItemEvent;
130 import java.awt.event.ItemListener;
131 import java.awt.event.KeyAdapter;
132 import java.awt.event.KeyEvent;
133 import java.awt.event.MouseEvent;
134 import java.awt.print.PageFormat;
135 import java.awt.print.PrinterJob;
136 import java.beans.PropertyChangeEvent;
138 import java.io.FileWriter;
139 import java.io.IOException;
140 import java.io.PrintWriter;
142 import java.util.ArrayList;
143 import java.util.Arrays;
144 import java.util.Deque;
145 import java.util.HashSet;
146 import java.util.List;
147 import java.util.Set;
148 import java.util.Vector;
150 import javax.swing.ButtonGroup;
151 import javax.swing.JCheckBoxMenuItem;
152 import javax.swing.JEditorPane;
153 import javax.swing.JFileChooser;
154 import javax.swing.JInternalFrame;
155 import javax.swing.JLayeredPane;
156 import javax.swing.JMenu;
157 import javax.swing.JMenuItem;
158 import javax.swing.JOptionPane;
159 import javax.swing.JScrollPane;
160 import javax.swing.SwingUtilities;
166 * @version $Revision$
168 public class AlignFrame extends GAlignFrame implements DropTargetListener,
169 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
171 public static final int DEFAULT_WIDTH = 700;
173 public static final int DEFAULT_HEIGHT = 500;
176 * The currently displayed panel (selected tabbed view if more than one)
178 public AlignmentPanel alignPanel;
180 AlignViewport viewport;
182 public AlignViewControllerI avc;
184 List<AlignmentPanel> alignPanels = new ArrayList<>();
187 * Last format used to load or save alignments in this window
189 FileFormatI currentFileFormat = null;
192 * Current filename for this alignment
194 String fileName = null;
198 * Creates a new AlignFrame object with specific width and height.
204 public AlignFrame(AlignmentI al, int width, int height)
206 this(al, null, width, height);
210 * Creates a new AlignFrame object with specific width, height and
216 * @param sequenceSetId
218 public AlignFrame(AlignmentI al, int width, int height,
219 String sequenceSetId)
221 this(al, null, width, height, sequenceSetId);
225 * Creates a new AlignFrame object with specific width, height and
231 * @param sequenceSetId
234 public AlignFrame(AlignmentI al, int width, int height,
235 String sequenceSetId, String viewId)
237 this(al, null, width, height, sequenceSetId, viewId);
241 * new alignment window with hidden columns
245 * @param hiddenColumns
246 * ColumnSelection or null
248 * Width of alignment frame
252 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
255 this(al, hiddenColumns, width, height, null);
259 * Create alignment frame for al with hiddenColumns, a specific width and
260 * height, and specific sequenceId
263 * @param hiddenColumns
266 * @param sequenceSetId
269 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
270 int height, String sequenceSetId)
272 this(al, hiddenColumns, width, height, sequenceSetId, null);
276 * Create alignment frame for al with hiddenColumns, a specific width and
277 * height, and specific sequenceId
280 * @param hiddenColumns
283 * @param sequenceSetId
288 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
289 int height, String sequenceSetId, String viewId)
291 setSize(width, height);
293 if (al.getDataset() == null)
298 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
300 alignPanel = new AlignmentPanel(this, viewport);
302 addAlignmentPanel(alignPanel, true);
306 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
307 HiddenColumns hiddenColumns, int width, int height)
309 setSize(width, height);
311 if (al.getDataset() == null)
316 viewport = new AlignViewport(al, hiddenColumns);
318 if (hiddenSeqs != null && hiddenSeqs.length > 0)
320 viewport.hideSequence(hiddenSeqs);
322 alignPanel = new AlignmentPanel(this, viewport);
323 addAlignmentPanel(alignPanel, true);
328 * Make a new AlignFrame from existing alignmentPanels
335 public AlignFrame(AlignmentPanel ap)
339 addAlignmentPanel(ap, false);
344 * initalise the alignframe from the underlying viewport data and the
349 if (!Jalview.isHeadlessMode())
351 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
354 avc = new jalview.controller.AlignViewController(this, viewport,
356 if (viewport.getAlignmentConservationAnnotation() == null)
358 // BLOSUM62Colour.setEnabled(false);
359 conservationMenuItem.setEnabled(false);
360 modifyConservation.setEnabled(false);
361 // PIDColour.setEnabled(false);
362 // abovePIDThreshold.setEnabled(false);
363 // modifyPID.setEnabled(false);
366 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
369 if (sortby.equals("Id"))
371 sortIDMenuItem_actionPerformed(null);
373 else if (sortby.equals("Pairwise Identity"))
375 sortPairwiseMenuItem_actionPerformed(null);
379 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
381 setMenusFromViewport(viewport);
382 buildSortByAnnotationScoresMenu();
383 calculateTree.addActionListener(new ActionListener()
387 public void actionPerformed(ActionEvent e)
394 if (Desktop.desktop != null)
396 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
397 addServiceListeners();
401 if (viewport.getWrapAlignment())
403 wrapMenuItem_actionPerformed(null);
406 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
408 this.overviewMenuItem_actionPerformed(null);
413 final List<AlignmentPanel> selviews = new ArrayList<>();
414 final List<AlignmentPanel> origview = new ArrayList<>();
415 final String menuLabel = MessageManager
416 .getString("label.copy_format_from");
417 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
418 new ViewSetProvider()
422 public AlignmentPanel[] getAllAlignmentPanels()
425 origview.add(alignPanel);
426 // make an array of all alignment panels except for this one
427 List<AlignmentPanel> aps = new ArrayList<>(
428 Arrays.asList(Desktop.getAlignmentPanels(null)));
429 aps.remove(AlignFrame.this.alignPanel);
430 return aps.toArray(new AlignmentPanel[aps.size()]);
432 }, selviews, new ItemListener()
436 public void itemStateChanged(ItemEvent e)
438 if (origview.size() > 0)
440 final AlignmentPanel ap = origview.get(0);
443 * Copy the ViewStyle of the selected panel to 'this one'.
444 * Don't change value of 'scaleProteinAsCdna' unless copying
447 ViewStyleI vs = selviews.get(0).getAlignViewport()
449 boolean fromSplitFrame = selviews.get(0)
450 .getAlignViewport().getCodingComplement() != null;
453 vs.setScaleProteinAsCdna(ap.getAlignViewport()
454 .getViewStyle().isScaleProteinAsCdna());
456 ap.getAlignViewport().setViewStyle(vs);
459 * Also rescale ViewStyle of SplitFrame complement if there is
460 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
461 * the whole ViewStyle (allow cDNA protein to have different
464 AlignViewportI complement = ap.getAlignViewport()
465 .getCodingComplement();
466 if (complement != null && vs.isScaleProteinAsCdna())
468 AlignFrame af = Desktop.getAlignFrameFor(complement);
469 ((SplitFrame) af.getSplitViewContainer())
471 af.setMenusForViewport();
475 ap.setSelected(true);
476 ap.alignFrame.setMenusForViewport();
481 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
482 .indexOf("devel") > -1
483 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
484 .indexOf("test") > -1)
486 formatMenu.add(vsel);
488 addFocusListener(new FocusAdapter()
491 public void focusGained(FocusEvent e)
493 Jalview.setCurrentAlignFrame(AlignFrame.this);
500 * Change the filename and format for the alignment, and enable the 'reload'
501 * button functionality.
508 public void setFileName(String file, FileFormatI format)
511 setFileFormat(format);
512 reload.setEnabled(true);
516 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
519 void addKeyListener()
521 addKeyListener(new KeyAdapter()
524 public void keyPressed(KeyEvent evt)
526 if (viewport.cursorMode
527 && ((evt.getKeyCode() >= KeyEvent.VK_0
528 && evt.getKeyCode() <= KeyEvent.VK_9)
529 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
530 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
531 && Character.isDigit(evt.getKeyChar()))
533 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
536 switch (evt.getKeyCode())
539 case 27: // escape key
540 deselectAllSequenceMenuItem_actionPerformed(null);
544 case KeyEvent.VK_DOWN:
545 if (evt.isAltDown() || !viewport.cursorMode)
547 moveSelectedSequences(false);
549 if (viewport.cursorMode)
551 alignPanel.getSeqPanel().moveCursor(0, 1);
556 if (evt.isAltDown() || !viewport.cursorMode)
558 moveSelectedSequences(true);
560 if (viewport.cursorMode)
562 alignPanel.getSeqPanel().moveCursor(0, -1);
567 case KeyEvent.VK_LEFT:
568 if (evt.isAltDown() || !viewport.cursorMode)
570 slideSequences(false,
571 alignPanel.getSeqPanel().getKeyboardNo1());
575 alignPanel.getSeqPanel().moveCursor(-1, 0);
580 case KeyEvent.VK_RIGHT:
581 if (evt.isAltDown() || !viewport.cursorMode)
583 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
587 alignPanel.getSeqPanel().moveCursor(1, 0);
591 case KeyEvent.VK_SPACE:
592 if (viewport.cursorMode)
594 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
595 || evt.isShiftDown() || evt.isAltDown());
599 // case KeyEvent.VK_A:
600 // if (viewport.cursorMode)
602 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
603 // //System.out.println("A");
607 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
608 * System.out.println("closing bracket"); } break;
610 case KeyEvent.VK_DELETE:
611 case KeyEvent.VK_BACK_SPACE:
612 if (!viewport.cursorMode)
614 cut_actionPerformed(null);
618 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
619 || evt.isShiftDown() || evt.isAltDown());
625 if (viewport.cursorMode)
627 alignPanel.getSeqPanel().setCursorRow();
631 if (viewport.cursorMode && !evt.isControlDown())
633 alignPanel.getSeqPanel().setCursorColumn();
637 if (viewport.cursorMode)
639 alignPanel.getSeqPanel().setCursorPosition();
643 case KeyEvent.VK_ENTER:
644 case KeyEvent.VK_COMMA:
645 if (viewport.cursorMode)
647 alignPanel.getSeqPanel().setCursorRowAndColumn();
652 if (viewport.cursorMode)
654 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
658 if (viewport.cursorMode)
660 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
665 viewport.cursorMode = !viewport.cursorMode;
666 statusBar.setText(MessageManager
667 .formatMessage("label.keyboard_editing_mode", new String[]
668 { (viewport.cursorMode ? "on" : "off") }));
669 if (viewport.cursorMode)
671 ViewportRanges ranges = viewport.getRanges();
672 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
674 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
677 alignPanel.getSeqPanel().seqCanvas.repaint();
683 Help.showHelpWindow();
684 } catch (Exception ex)
686 ex.printStackTrace();
691 boolean toggleSeqs = !evt.isControlDown();
692 boolean toggleCols = !evt.isShiftDown();
693 toggleHiddenRegions(toggleSeqs, toggleCols);
698 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
699 boolean modifyExisting = true; // always modify, don't clear
700 // evt.isShiftDown();
701 boolean invertHighlighted = evt.isAltDown();
702 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
706 case KeyEvent.VK_PAGE_UP:
707 viewport.getRanges().pageUp();
709 case KeyEvent.VK_PAGE_DOWN:
710 viewport.getRanges().pageDown();
716 public void keyReleased(KeyEvent evt)
718 switch (evt.getKeyCode())
720 case KeyEvent.VK_LEFT:
721 if (evt.isAltDown() || !viewport.cursorMode)
723 viewport.firePropertyChange("alignment", null,
724 viewport.getAlignment().getSequences());
728 case KeyEvent.VK_RIGHT:
729 if (evt.isAltDown() || !viewport.cursorMode)
731 viewport.firePropertyChange("alignment", null,
732 viewport.getAlignment().getSequences());
740 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
742 ap.alignFrame = this;
743 avc = new jalview.controller.AlignViewController(this, viewport,
748 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
750 int aSize = alignPanels.size();
752 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
754 if (aSize == 1 && ap.av.getViewName() == null)
756 this.getContentPane().add(ap, BorderLayout.CENTER);
762 setInitialTabVisible();
765 expandViews.setEnabled(true);
766 gatherViews.setEnabled(true);
767 tabbedPane.addTab(ap.av.getViewName(), ap);
769 ap.setVisible(false);
774 if (ap.av.isPadGaps())
776 ap.av.getAlignment().padGaps();
778 ap.av.updateConservation(ap);
779 ap.av.updateConsensus(ap);
780 ap.av.updateStrucConsensus(ap);
781 ap.av.initInformationWorker(ap);
785 public void setInitialTabVisible()
787 expandViews.setEnabled(true);
788 gatherViews.setEnabled(true);
789 tabbedPane.setVisible(true);
790 AlignmentPanel first = alignPanels.get(0);
791 tabbedPane.addTab(first.av.getViewName(), first);
792 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
795 public AlignViewport getViewport()
800 /* Set up intrinsic listeners for dynamically generated GUI bits. */
801 private void addServiceListeners()
803 final java.beans.PropertyChangeListener thisListener;
804 Desktop.instance.addJalviewPropertyChangeListener("services",
805 thisListener = new java.beans.PropertyChangeListener()
808 public void propertyChange(PropertyChangeEvent evt)
810 // // System.out.println("Discoverer property change.");
811 // if (evt.getPropertyName().equals("services"))
813 SwingUtilities.invokeLater(new Runnable()
820 "Rebuild WS Menu for service change");
821 BuildWebServiceMenu();
828 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
831 public void internalFrameClosed(
832 javax.swing.event.InternalFrameEvent evt)
834 // System.out.println("deregistering discoverer listener");
835 Desktop.instance.removeJalviewPropertyChangeListener("services",
837 closeMenuItem_actionPerformed(true);
840 // Finally, build the menu once to get current service state
841 new Thread(new Runnable()
846 BuildWebServiceMenu();
852 * Configure menu items that vary according to whether the alignment is
853 * nucleotide or protein
855 public void setGUINucleotide()
857 AlignmentI al = getViewport().getAlignment();
858 boolean nucleotide = al.isNucleotide();
860 loadVcf.setVisible(nucleotide);
861 showTranslation.setVisible(nucleotide);
862 showReverse.setVisible(nucleotide);
863 showReverseComplement.setVisible(nucleotide);
864 conservationMenuItem.setEnabled(!nucleotide);
866 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
867 showGroupConservation.setEnabled(!nucleotide);
869 showComplementMenuItem
870 .setText(nucleotide ? MessageManager.getString("label.protein")
871 : MessageManager.getString("label.nucleotide"));
875 * set up menus for the current viewport. This may be called after any
876 * operation that affects the data in the current view (selection changed,
877 * etc) to update the menus to reflect the new state.
880 public void setMenusForViewport()
882 setMenusFromViewport(viewport);
886 * Need to call this method when tabs are selected for multiple views, or when
887 * loading from Jalview2XML.java
892 public void setMenusFromViewport(AlignViewport av)
894 padGapsMenuitem.setSelected(av.isPadGaps());
895 colourTextMenuItem.setSelected(av.isShowColourText());
896 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
897 modifyPID.setEnabled(abovePIDThreshold.isSelected());
898 conservationMenuItem.setSelected(av.getConservationSelected());
899 modifyConservation.setEnabled(conservationMenuItem.isSelected());
900 seqLimits.setSelected(av.getShowJVSuffix());
901 idRightAlign.setSelected(av.isRightAlignIds());
902 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
903 renderGapsMenuItem.setSelected(av.isRenderGaps());
904 wrapMenuItem.setSelected(av.getWrapAlignment());
905 scaleAbove.setVisible(av.getWrapAlignment());
906 scaleLeft.setVisible(av.getWrapAlignment());
907 scaleRight.setVisible(av.getWrapAlignment());
908 annotationPanelMenuItem.setState(av.isShowAnnotation());
910 * Show/hide annotations only enabled if annotation panel is shown
912 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
913 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
914 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
915 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
916 viewBoxesMenuItem.setSelected(av.getShowBoxes());
917 viewTextMenuItem.setSelected(av.getShowText());
918 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
919 showGroupConsensus.setSelected(av.isShowGroupConsensus());
920 showGroupConservation.setSelected(av.isShowGroupConservation());
921 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
922 showSequenceLogo.setSelected(av.isShowSequenceLogo());
923 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
924 showInformationHistogram.setSelected(av.isShowInformationHistogram());
925 showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
926 normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
928 ColourMenuHelper.setColourSelected(colourMenu,
929 av.getGlobalColourScheme());
931 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
932 hiddenMarkers.setState(av.getShowHiddenMarkers());
933 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
934 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
935 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
936 autoCalculate.setSelected(av.autoCalculateConsensus);
937 sortByTree.setSelected(av.sortByTree);
938 listenToViewSelections.setSelected(av.followSelection);
940 showProducts.setEnabled(canShowProducts());
941 setGroovyEnabled(Desktop.getGroovyConsole() != null);
947 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
951 public void setGroovyEnabled(boolean b)
953 runGroovy.setEnabled(b);
956 private IProgressIndicator progressBar;
961 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
964 public void setProgressBar(String message, long id)
966 progressBar.setProgressBar(message, id);
970 public void registerHandler(final long id,
971 final IProgressIndicatorHandler handler)
973 progressBar.registerHandler(id, handler);
978 * @return true if any progress bars are still active
981 public boolean operationInProgress()
983 return progressBar.operationInProgress();
987 * Sets the text of the status bar. Note that setting a null or empty value
988 * will cause the status bar to be hidden, with possibly undesirable flicker
989 * of the screen layout.
992 public void setStatus(String text)
994 statusBar.setText(text == null || text.isEmpty() ? " " : text);
998 * Added so Castor Mapping file can obtain Jalview Version
1000 public String getVersion()
1002 return jalview.bin.Cache.getProperty("VERSION");
1005 public FeatureRenderer getFeatureRenderer()
1007 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1011 public void fetchSequence_actionPerformed(ActionEvent e)
1013 new jalview.gui.SequenceFetcher(this);
1017 public void addFromFile_actionPerformed(ActionEvent e)
1019 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1023 public void hmmBuild_actionPerformed(boolean withDefaults)
1025 if (!alignmentIsSufficient(1))
1031 * get default parameters, and optionally show a dialog
1032 * to allow them to be modified
1034 ParamDatastoreI store = HMMERParamStore.forBuild(viewport);
1035 List<ArgumentI> args = store.getServiceParameters();
1039 WsParamSetI set = new HMMERPreset();
1040 WsJobParameters params = new WsJobParameters(store, set, args);
1041 if (params.showRunDialog())
1043 args = params.getJobParams();
1047 return; // user cancelled
1050 new Thread(new HMMBuild(this, args)).start();
1054 public void hmmAlign_actionPerformed(boolean withDefaults)
1056 if (!(checkForHMM() && alignmentIsSufficient(2)))
1062 * get default parameters, and optionally show a dialog
1063 * to allow them to be modified
1065 ParamDatastoreI store = HMMERParamStore.forAlign(viewport);
1066 List<ArgumentI> args = store.getServiceParameters();
1070 WsParamSetI set = new HMMERPreset();
1071 WsJobParameters params = new WsJobParameters(store, set, args);
1072 if (params.showRunDialog())
1074 args = params.getJobParams();
1078 return; // user cancelled
1081 new Thread(new HMMAlign(this, args)).start();
1085 public void hmmSearch_actionPerformed(boolean withDefaults)
1093 * get default parameters, and (if requested) show
1094 * dialog to allow modification
1096 ParamDatastoreI store = HMMERParamStore.forSearch(viewport);
1097 List<ArgumentI> args = store.getServiceParameters();
1101 WsParamSetI set = new HMMERPreset();
1102 WsJobParameters params = new WsJobParameters(store, set, args);
1103 if (params.showRunDialog())
1105 args = params.getJobParams();
1109 return; // user cancelled
1112 new Thread(new HMMSearch(this, args)).start();
1113 alignPanel.repaint();
1117 public void jackhmmer_actionPerformed(boolean withDefaults)
1121 * get default parameters, and (if requested) show
1122 * dialog to allow modification
1125 ParamDatastoreI store = HMMERParamStore.forJackhmmer(viewport);
1126 List<ArgumentI> args = store.getServiceParameters();
1130 WsParamSetI set = new HMMERPreset();
1131 WsJobParameters params = new WsJobParameters(store, set, args);
1132 if (params.showRunDialog())
1134 args = params.getJobParams();
1138 return; // user cancelled
1141 new Thread(new JackHMMER(this, args)).start();
1142 alignPanel.repaint();
1147 * Checks if the alignment has at least one hidden Markov model, if not shows
1148 * a dialog advising to run hmmbuild or load an HMM profile
1152 private boolean checkForHMM()
1154 if (viewport.getAlignment().getHmmSequences().isEmpty())
1156 JOptionPane.showMessageDialog(this,
1157 MessageManager.getString("warn.no_hmm"));
1164 * Checks if the alignment contains the required number of sequences.
1169 public boolean alignmentIsSufficient(int required)
1171 if (getViewport().getAlignment().getSequences().size() < required)
1173 JOptionPane.showMessageDialog(this,
1174 MessageManager.getString("label.not_enough_sequences"));
1181 * Opens a file browser and adds the selected file, if in Fasta, Stockholm or
1182 * Pfam format, to the list held under preference key "HMMSEARCH_DBS" (as a
1183 * comma-separated list)
1186 public void addDatabase_actionPerformed() throws IOException
1188 if (Cache.getProperty(Preferences.HMMSEARCH_DBS) == null)
1190 Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
1193 String path = openFileChooser(false);
1194 if (path != null && new File(path).exists())
1196 IdentifyFile identifier = new IdentifyFile();
1197 FileFormatI format = identifier.identify(path, DataSourceType.FILE);
1198 if (format == FileFormat.Fasta || format == FileFormat.Stockholm
1199 || format == FileFormat.Pfam)
1201 String currentDbPaths = Cache
1202 .getProperty(Preferences.HMMSEARCH_DBS);
1203 currentDbPaths += Preferences.COMMA + path;
1204 Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
1208 JOptionPane.showMessageDialog(this,
1209 MessageManager.getString("warn.invalid_format"));
1215 * Opens a file chooser, optionally restricted to selecting folders
1216 * (directories) only. Answers the path to the selected file or folder, or
1217 * null if none is chosen.
1222 protected String openFileChooser(boolean forFolder)
1224 // TODO duplicates GPreferences method - relocate to JalviewFileChooser?
1225 String choice = null;
1226 JFileChooser chooser = new JFileChooser();
1229 chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
1231 chooser.setDialogTitle(
1232 MessageManager.getString("label.open_local_file"));
1233 chooser.setToolTipText(MessageManager.getString("action.open"));
1235 int value = chooser.showOpenDialog(this);
1237 if (value == JFileChooser.APPROVE_OPTION)
1239 choice = chooser.getSelectedFile().getPath();
1245 public void reload_actionPerformed(ActionEvent e)
1247 if (fileName != null)
1249 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1250 // originating file's format
1251 // TODO: work out how to recover feature settings for correct view(s) when
1252 // file is reloaded.
1253 if (FileFormat.Jalview.equals(currentFileFormat))
1255 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1256 for (int i = 0; i < frames.length; i++)
1258 if (frames[i] instanceof AlignFrame && frames[i] != this
1259 && ((AlignFrame) frames[i]).fileName != null
1260 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1264 frames[i].setSelected(true);
1265 Desktop.instance.closeAssociatedWindows();
1266 } catch (java.beans.PropertyVetoException ex)
1272 Desktop.instance.closeAssociatedWindows();
1274 FileLoader loader = new FileLoader();
1275 DataSourceType protocol = fileName.startsWith("http:")
1276 ? DataSourceType.URL
1277 : DataSourceType.FILE;
1278 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1282 Rectangle bounds = this.getBounds();
1284 FileLoader loader = new FileLoader();
1285 DataSourceType protocol = fileName.startsWith("http:")
1286 ? DataSourceType.URL
1287 : DataSourceType.FILE;
1288 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1289 protocol, currentFileFormat);
1291 newframe.setBounds(bounds);
1292 if (featureSettings != null && featureSettings.isShowing())
1294 final Rectangle fspos = featureSettings.frame.getBounds();
1295 // TODO: need a 'show feature settings' function that takes bounds -
1296 // need to refactor Desktop.addFrame
1297 newframe.featureSettings_actionPerformed(null);
1298 final FeatureSettings nfs = newframe.featureSettings;
1299 SwingUtilities.invokeLater(new Runnable()
1304 nfs.frame.setBounds(fspos);
1307 this.featureSettings.close();
1308 this.featureSettings = null;
1310 this.closeMenuItem_actionPerformed(true);
1316 public void addFromText_actionPerformed(ActionEvent e)
1319 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1323 public void addFromURL_actionPerformed(ActionEvent e)
1325 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1329 public void save_actionPerformed(ActionEvent e)
1331 if (fileName == null || (currentFileFormat == null)
1332 || fileName.startsWith("http"))
1334 saveAs_actionPerformed(null);
1338 saveAlignment(fileName, currentFileFormat);
1349 public void saveAs_actionPerformed(ActionEvent e)
1351 String format = currentFileFormat == null ? null
1352 : currentFileFormat.getName();
1353 JalviewFileChooser chooser = JalviewFileChooser
1354 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1356 chooser.setFileView(new JalviewFileView());
1357 chooser.setDialogTitle(
1358 MessageManager.getString("label.save_alignment_to_file"));
1359 chooser.setToolTipText(MessageManager.getString("action.save"));
1361 int value = chooser.showSaveDialog(this);
1363 if (value == JalviewFileChooser.APPROVE_OPTION)
1365 currentFileFormat = chooser.getSelectedFormat();
1366 while (currentFileFormat == null)
1368 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1369 MessageManager.getString(
1370 "label.select_file_format_before_saving"),
1371 MessageManager.getString("label.file_format_not_specified"),
1372 JvOptionPane.WARNING_MESSAGE);
1373 currentFileFormat = chooser.getSelectedFormat();
1374 value = chooser.showSaveDialog(this);
1375 if (value != JalviewFileChooser.APPROVE_OPTION)
1381 fileName = chooser.getSelectedFile().getPath();
1383 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1385 Cache.setProperty("LAST_DIRECTORY", fileName);
1386 saveAlignment(fileName, currentFileFormat);
1390 public boolean saveAlignment(String file, FileFormatI format)
1392 boolean success = true;
1394 if (FileFormat.Jalview.equals(format))
1396 String shortName = title;
1398 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1400 shortName = shortName.substring(
1401 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1404 success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1407 statusBar.setText(MessageManager.formatMessage(
1408 "label.successfully_saved_to_file_in_format", new Object[]
1409 { fileName, format }));
1414 AlignmentExportData exportData = getAlignmentForExport(format,
1416 if (exportData.getSettings().isCancelled())
1420 FormatAdapter f = new FormatAdapter(alignPanel,
1421 exportData.getSettings());
1422 String output = f.formatSequences(format, exportData.getAlignment(), // class
1426 // occur in the distant future
1427 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1428 f.getCacheSuffixDefault(format),
1429 viewport.getAlignment().getHiddenColumns());
1437 // create backupfiles object and get new temp filename destination
1438 BackupFiles backupfiles = new BackupFiles(file);
1442 PrintWriter out = new PrintWriter(
1443 new FileWriter(backupfiles.getTempFilePath()));
1447 this.setTitle(file);
1448 statusBar.setText(MessageManager.formatMessage(
1449 "label.successfully_saved_to_file_in_format", new Object[]
1450 { fileName, format.getName() }));
1451 } catch (Exception ex)
1454 ex.printStackTrace();
1457 backupfiles.setWriteSuccess(success);
1458 // do the backup file roll and rename the temp file to actual file
1459 success = backupfiles.rollBackupsAndRenameTempFile();
1466 JvOptionPane.showInternalMessageDialog(this, MessageManager
1467 .formatMessage("label.couldnt_save_file", new Object[]
1469 MessageManager.getString("label.error_saving_file"),
1470 JvOptionPane.WARNING_MESSAGE);
1476 private void warningMessage(String warning, String title)
1478 if (new jalview.util.Platform().isHeadless())
1480 System.err.println("Warning: " + title + "\nWarning: " + warning);
1485 JvOptionPane.showInternalMessageDialog(this, warning, title,
1486 JvOptionPane.WARNING_MESSAGE);
1498 protected void outputText_actionPerformed(ActionEvent e)
1500 FileFormatI fileFormat = FileFormats.getInstance()
1501 .forName(e.getActionCommand());
1502 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1504 if (exportData.getSettings().isCancelled())
1508 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1509 cap.setForInput(null);
1512 FileFormatI format = fileFormat;
1513 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1514 .formatSequences(format, exportData.getAlignment(),
1515 exportData.getOmitHidden(),
1516 exportData.getStartEndPostions(),
1517 viewport.getAlignment().getHiddenColumns()));
1518 Desktop.addInternalFrame(cap, MessageManager
1519 .formatMessage("label.alignment_output_command", new Object[]
1520 { e.getActionCommand() }), 600, 500);
1521 } catch (OutOfMemoryError oom)
1523 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1530 public static AlignmentExportData getAlignmentForExport(
1531 FileFormatI format, AlignViewportI viewport,
1532 AlignExportSettingI exportSettings)
1534 AlignmentI alignmentToExport = null;
1535 AlignExportSettingI settings = exportSettings;
1536 String[] omitHidden = null;
1538 HiddenSequences hiddenSeqs = viewport.getAlignment()
1539 .getHiddenSequences();
1541 alignmentToExport = viewport.getAlignment();
1543 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1544 if (settings == null)
1546 settings = new AlignExportSettings(hasHiddenSeqs,
1547 viewport.hasHiddenColumns(), format);
1549 // settings.isExportAnnotations();
1551 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1553 omitHidden = viewport.getViewAsString(false,
1554 settings.isExportHiddenSequences());
1557 int[] alignmentStartEnd = new int[2];
1558 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1560 alignmentToExport = hiddenSeqs.getFullAlignment();
1564 alignmentToExport = viewport.getAlignment();
1566 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1567 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1568 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1569 omitHidden, alignmentStartEnd, settings);
1580 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1582 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1583 htmlSVG.exportHTML(null);
1587 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1589 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1590 bjs.exportHTML(null);
1593 public void createImageMap(File file, String image)
1595 alignPanel.makePNGImageMap(file, image);
1605 public void createPNG(File f)
1607 alignPanel.makePNG(f);
1617 public void createEPS(File f)
1619 alignPanel.makeEPS(f);
1623 public void createSVG(File f)
1625 alignPanel.makeSVG(f);
1629 public void pageSetup_actionPerformed(ActionEvent e)
1631 PrinterJob printJob = PrinterJob.getPrinterJob();
1632 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1642 public void printMenuItem_actionPerformed(ActionEvent e)
1644 // Putting in a thread avoids Swing painting problems
1645 PrintThread thread = new PrintThread(alignPanel);
1650 public void exportFeatures_actionPerformed(ActionEvent e)
1652 new AnnotationExporter(alignPanel).exportFeatures();
1656 public void exportAnnotations_actionPerformed(ActionEvent e)
1658 new AnnotationExporter(alignPanel).exportAnnotations();
1662 public void associatedData_actionPerformed(ActionEvent e)
1663 throws IOException, InterruptedException
1665 // Pick the tree file
1666 JalviewFileChooser chooser = new JalviewFileChooser(
1667 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1668 chooser.setFileView(new JalviewFileView());
1669 chooser.setDialogTitle(
1670 MessageManager.getString("label.load_jalview_annotations"));
1671 chooser.setToolTipText(
1672 MessageManager.getString("label.load_jalview_annotations"));
1674 int value = chooser.showOpenDialog(null);
1676 if (value == JalviewFileChooser.APPROVE_OPTION)
1678 String choice = chooser.getSelectedFile().getPath();
1679 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1680 loadJalviewDataFile(choice, null, null, null);
1686 * Close the current view or all views in the alignment frame. If the frame
1687 * only contains one view then the alignment will be removed from memory.
1689 * @param closeAllTabs
1692 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1694 if (alignPanels != null && alignPanels.size() < 2)
1696 closeAllTabs = true;
1701 if (alignPanels != null)
1705 if (this.isClosed())
1707 // really close all the windows - otherwise wait till
1708 // setClosed(true) is called
1709 for (int i = 0; i < alignPanels.size(); i++)
1711 AlignmentPanel ap = alignPanels.get(i);
1718 closeView(alignPanel);
1725 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1726 * be called recursively, with the frame now in 'closed' state
1728 this.setClosed(true);
1730 } catch (Exception ex)
1732 ex.printStackTrace();
1737 * Close the specified panel and close up tabs appropriately.
1739 * @param panelToClose
1741 public void closeView(AlignmentPanel panelToClose)
1743 int index = tabbedPane.getSelectedIndex();
1744 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1745 alignPanels.remove(panelToClose);
1746 panelToClose.closePanel();
1747 panelToClose = null;
1749 tabbedPane.removeTabAt(closedindex);
1750 tabbedPane.validate();
1752 if (index > closedindex || index == tabbedPane.getTabCount())
1754 // modify currently selected tab index if necessary.
1758 this.tabSelectionChanged(index);
1764 void updateEditMenuBar()
1767 if (viewport.getHistoryList().size() > 0)
1769 undoMenuItem.setEnabled(true);
1770 CommandI command = viewport.getHistoryList().peek();
1771 undoMenuItem.setText(MessageManager
1772 .formatMessage("label.undo_command", new Object[]
1773 { command.getDescription() }));
1777 undoMenuItem.setEnabled(false);
1778 undoMenuItem.setText(MessageManager.getString("action.undo"));
1781 if (viewport.getRedoList().size() > 0)
1783 redoMenuItem.setEnabled(true);
1785 CommandI command = viewport.getRedoList().peek();
1786 redoMenuItem.setText(MessageManager
1787 .formatMessage("label.redo_command", new Object[]
1788 { command.getDescription() }));
1792 redoMenuItem.setEnabled(false);
1793 redoMenuItem.setText(MessageManager.getString("action.redo"));
1798 public void addHistoryItem(CommandI command)
1800 if (command.getSize() > 0)
1802 viewport.addToHistoryList(command);
1803 viewport.clearRedoList();
1804 updateEditMenuBar();
1805 viewport.updateHiddenColumns();
1806 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1807 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1808 // viewport.getColumnSelection()
1809 // .getHiddenColumns().size() > 0);
1815 * @return alignment objects for all views
1817 AlignmentI[] getViewAlignments()
1819 if (alignPanels != null)
1821 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1823 for (AlignmentPanel ap : alignPanels)
1825 als[i++] = ap.av.getAlignment();
1829 if (viewport != null)
1831 return new AlignmentI[] { viewport.getAlignment() };
1843 protected void undoMenuItem_actionPerformed(ActionEvent e)
1845 if (viewport.getHistoryList().isEmpty())
1849 CommandI command = viewport.getHistoryList().pop();
1850 viewport.addToRedoList(command);
1851 command.undoCommand(getViewAlignments());
1853 AlignmentViewport originalSource = getOriginatingSource(command);
1854 updateEditMenuBar();
1856 if (originalSource != null)
1858 if (originalSource != viewport)
1861 "Implementation worry: mismatch of viewport origin for undo");
1863 originalSource.updateHiddenColumns();
1864 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1866 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1867 // viewport.getColumnSelection()
1868 // .getHiddenColumns().size() > 0);
1869 originalSource.firePropertyChange("alignment", null,
1870 originalSource.getAlignment().getSequences());
1881 protected void redoMenuItem_actionPerformed(ActionEvent e)
1883 if (viewport.getRedoList().size() < 1)
1888 CommandI command = viewport.getRedoList().pop();
1889 viewport.addToHistoryList(command);
1890 command.doCommand(getViewAlignments());
1892 AlignmentViewport originalSource = getOriginatingSource(command);
1893 updateEditMenuBar();
1895 if (originalSource != null)
1898 if (originalSource != viewport)
1901 "Implementation worry: mismatch of viewport origin for redo");
1903 originalSource.updateHiddenColumns();
1904 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1906 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1907 // viewport.getColumnSelection()
1908 // .getHiddenColumns().size() > 0);
1909 originalSource.firePropertyChange("alignment", null,
1910 originalSource.getAlignment().getSequences());
1914 AlignmentViewport getOriginatingSource(CommandI command)
1916 AlignmentViewport originalSource = null;
1917 // For sequence removal and addition, we need to fire
1918 // the property change event FROM the viewport where the
1919 // original alignment was altered
1920 AlignmentI al = null;
1921 if (command instanceof EditCommand)
1923 EditCommand editCommand = (EditCommand) command;
1924 al = editCommand.getAlignment();
1925 List<Component> comps = PaintRefresher.components
1926 .get(viewport.getSequenceSetId());
1928 for (Component comp : comps)
1930 if (comp instanceof AlignmentPanel)
1932 if (al == ((AlignmentPanel) comp).av.getAlignment())
1934 originalSource = ((AlignmentPanel) comp).av;
1941 if (originalSource == null)
1943 // The original view is closed, we must validate
1944 // the current view against the closed view first
1947 PaintRefresher.validateSequences(al, viewport.getAlignment());
1950 originalSource = viewport;
1953 return originalSource;
1962 public void moveSelectedSequences(boolean up)
1964 SequenceGroup sg = viewport.getSelectionGroup();
1970 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1971 viewport.getHiddenRepSequences(), up);
1972 alignPanel.paintAlignment(true, false);
1975 synchronized void slideSequences(boolean right, int size)
1977 List<SequenceI> sg = new ArrayList<>();
1978 if (viewport.cursorMode)
1980 sg.add(viewport.getAlignment()
1981 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1983 else if (viewport.getSelectionGroup() != null
1984 && viewport.getSelectionGroup().getSize() != viewport
1985 .getAlignment().getHeight())
1987 sg = viewport.getSelectionGroup()
1988 .getSequences(viewport.getHiddenRepSequences());
1996 List<SequenceI> invertGroup = new ArrayList<>();
1998 for (SequenceI seq : viewport.getAlignment().getSequences())
2000 if (!sg.contains(seq))
2002 invertGroup.add(seq);
2006 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
2008 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
2009 for (int i = 0; i < invertGroup.size(); i++)
2011 seqs2[i] = invertGroup.get(i);
2014 SlideSequencesCommand ssc;
2017 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
2018 viewport.getGapCharacter());
2022 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
2023 viewport.getGapCharacter());
2026 int groupAdjustment = 0;
2027 if (ssc.getGapsInsertedBegin() && right)
2029 if (viewport.cursorMode)
2031 alignPanel.getSeqPanel().moveCursor(size, 0);
2035 groupAdjustment = size;
2038 else if (!ssc.getGapsInsertedBegin() && !right)
2040 if (viewport.cursorMode)
2042 alignPanel.getSeqPanel().moveCursor(-size, 0);
2046 groupAdjustment = -size;
2050 if (groupAdjustment != 0)
2052 viewport.getSelectionGroup().setStartRes(
2053 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
2054 viewport.getSelectionGroup().setEndRes(
2055 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
2059 * just extend the last slide command if compatible; but not if in
2060 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
2062 boolean appendHistoryItem = false;
2063 Deque<CommandI> historyList = viewport.getHistoryList();
2064 boolean inSplitFrame = getSplitViewContainer() != null;
2065 if (!inSplitFrame && historyList != null && historyList.size() > 0
2066 && historyList.peek() instanceof SlideSequencesCommand)
2068 appendHistoryItem = ssc.appendSlideCommand(
2069 (SlideSequencesCommand) historyList.peek());
2072 if (!appendHistoryItem)
2074 addHistoryItem(ssc);
2087 protected void copy_actionPerformed(ActionEvent e)
2089 if (viewport.getSelectionGroup() == null)
2093 // TODO: preserve the ordering of displayed alignment annotation in any
2094 // internal paste (particularly sequence associated annotation)
2095 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
2096 String[] omitHidden = null;
2098 if (viewport.hasHiddenColumns())
2100 omitHidden = viewport.getViewAsString(true);
2103 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2104 seqs, omitHidden, null);
2106 StringSelection ss = new StringSelection(output);
2110 jalview.gui.Desktop.internalCopy = true;
2111 // Its really worth setting the clipboard contents
2112 // to empty before setting the large StringSelection!!
2113 Toolkit.getDefaultToolkit().getSystemClipboard()
2114 .setContents(new StringSelection(""), null);
2116 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2118 } catch (OutOfMemoryError er)
2120 new OOMWarning("copying region", er);
2124 HiddenColumns hiddenColumns = null;
2125 if (viewport.hasHiddenColumns())
2127 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2128 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2130 // create new HiddenColumns object with copy of hidden regions
2131 // between startRes and endRes, offset by startRes
2132 hiddenColumns = new HiddenColumns(
2133 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
2134 hiddenCutoff, hiddenOffset);
2137 Desktop.jalviewClipboard = new Object[] { seqs,
2138 viewport.getAlignment().getDataset(), hiddenColumns };
2139 statusBar.setText(MessageManager.formatMessage(
2140 "label.copied_sequences_to_clipboard", new Object[]
2141 { Integer.valueOf(seqs.length).toString() }));
2149 * @throws InterruptedException
2150 * @throws IOException
2153 protected void pasteNew_actionPerformed(ActionEvent e)
2154 throws IOException, InterruptedException
2164 * @throws InterruptedException
2165 * @throws IOException
2168 protected void pasteThis_actionPerformed(ActionEvent e)
2169 throws IOException, InterruptedException
2175 * Paste contents of Jalview clipboard
2177 * @param newAlignment
2178 * true to paste to a new alignment, otherwise add to this.
2179 * @throws InterruptedException
2180 * @throws IOException
2182 void paste(boolean newAlignment) throws IOException, InterruptedException
2184 boolean externalPaste = true;
2187 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2188 Transferable contents = c.getContents(this);
2190 if (contents == null)
2199 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2200 if (str.length() < 1)
2205 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2207 } catch (OutOfMemoryError er)
2209 new OOMWarning("Out of memory pasting sequences!!", er);
2213 SequenceI[] sequences;
2214 boolean annotationAdded = false;
2215 AlignmentI alignment = null;
2217 if (Desktop.jalviewClipboard != null)
2219 // The clipboard was filled from within Jalview, we must use the
2221 // And dataset from the copied alignment
2222 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2223 // be doubly sure that we create *new* sequence objects.
2224 sequences = new SequenceI[newseq.length];
2225 for (int i = 0; i < newseq.length; i++)
2227 sequences[i] = new Sequence(newseq[i]);
2229 alignment = new Alignment(sequences);
2230 externalPaste = false;
2234 // parse the clipboard as an alignment.
2235 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2237 sequences = alignment.getSequencesArray();
2241 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2247 if (Desktop.jalviewClipboard != null)
2249 // dataset is inherited
2250 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2254 // new dataset is constructed
2255 alignment.setDataset(null);
2257 alwidth = alignment.getWidth() + 1;
2261 AlignmentI pastedal = alignment; // preserve pasted alignment object
2262 // Add pasted sequences and dataset into existing alignment.
2263 alignment = viewport.getAlignment();
2264 alwidth = alignment.getWidth() + 1;
2265 // decide if we need to import sequences from an existing dataset
2266 boolean importDs = Desktop.jalviewClipboard != null
2267 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2268 // importDs==true instructs us to copy over new dataset sequences from
2269 // an existing alignment
2270 Vector newDs = (importDs) ? new Vector() : null; // used to create
2271 // minimum dataset set
2273 for (int i = 0; i < sequences.length; i++)
2277 newDs.addElement(null);
2279 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2281 if (importDs && ds != null)
2283 if (!newDs.contains(ds))
2285 newDs.setElementAt(ds, i);
2286 ds = new Sequence(ds);
2287 // update with new dataset sequence
2288 sequences[i].setDatasetSequence(ds);
2292 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2297 // copy and derive new dataset sequence
2298 sequences[i] = sequences[i].deriveSequence();
2299 alignment.getDataset()
2300 .addSequence(sequences[i].getDatasetSequence());
2301 // TODO: avoid creation of duplicate dataset sequences with a
2302 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2304 alignment.addSequence(sequences[i]); // merges dataset
2308 newDs.clear(); // tidy up
2310 if (alignment.getAlignmentAnnotation() != null)
2312 for (AlignmentAnnotation alan : alignment
2313 .getAlignmentAnnotation())
2315 if (alan.graphGroup > fgroup)
2317 fgroup = alan.graphGroup;
2321 if (pastedal.getAlignmentAnnotation() != null)
2323 // Add any annotation attached to alignment.
2324 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2325 for (int i = 0; i < alann.length; i++)
2327 annotationAdded = true;
2328 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2330 AlignmentAnnotation newann = new AlignmentAnnotation(
2332 if (newann.graphGroup > -1)
2334 if (newGraphGroups.size() <= newann.graphGroup
2335 || newGraphGroups.get(newann.graphGroup) == null)
2337 for (int q = newGraphGroups
2338 .size(); q <= newann.graphGroup; q++)
2340 newGraphGroups.add(q, null);
2342 newGraphGroups.set(newann.graphGroup,
2343 Integer.valueOf(++fgroup));
2345 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2349 newann.padAnnotation(alwidth);
2350 alignment.addAnnotation(newann);
2360 addHistoryItem(new EditCommand(
2361 MessageManager.getString("label.add_sequences"),
2362 Action.PASTE, sequences, 0, alignment.getWidth(),
2365 // Add any annotations attached to sequences
2366 for (int i = 0; i < sequences.length; i++)
2368 if (sequences[i].getAnnotation() != null)
2370 AlignmentAnnotation newann;
2371 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2373 annotationAdded = true;
2374 newann = sequences[i].getAnnotation()[a];
2375 newann.adjustForAlignment();
2376 newann.padAnnotation(alwidth);
2377 if (newann.graphGroup > -1)
2379 if (newann.graphGroup > -1)
2381 if (newGraphGroups.size() <= newann.graphGroup
2382 || newGraphGroups.get(newann.graphGroup) == null)
2384 for (int q = newGraphGroups
2385 .size(); q <= newann.graphGroup; q++)
2387 newGraphGroups.add(q, null);
2389 newGraphGroups.set(newann.graphGroup,
2390 Integer.valueOf(++fgroup));
2392 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2396 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2400 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2408 // propagate alignment changed.
2409 viewport.getRanges().setEndSeq(alignment.getHeight());
2410 if (annotationAdded)
2412 // Duplicate sequence annotation in all views.
2413 AlignmentI[] alview = this.getViewAlignments();
2414 for (int i = 0; i < sequences.length; i++)
2416 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2421 for (int avnum = 0; avnum < alview.length; avnum++)
2423 if (alview[avnum] != alignment)
2425 // duplicate in a view other than the one with input focus
2426 int avwidth = alview[avnum].getWidth() + 1;
2427 // this relies on sann being preserved after we
2428 // modify the sequence's annotation array for each duplication
2429 for (int a = 0; a < sann.length; a++)
2431 AlignmentAnnotation newann = new AlignmentAnnotation(
2433 sequences[i].addAlignmentAnnotation(newann);
2434 newann.padAnnotation(avwidth);
2435 alview[avnum].addAnnotation(newann); // annotation was
2436 // duplicated earlier
2437 // TODO JAL-1145 graphGroups are not updated for sequence
2438 // annotation added to several views. This may cause
2440 alview[avnum].setAnnotationIndex(newann, a);
2445 buildSortByAnnotationScoresMenu();
2447 viewport.firePropertyChange("alignment", null,
2448 alignment.getSequences());
2449 if (alignPanels != null)
2451 for (AlignmentPanel ap : alignPanels)
2453 ap.validateAnnotationDimensions(false);
2458 alignPanel.validateAnnotationDimensions(false);
2464 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2466 String newtitle = new String("Copied sequences");
2468 if (Desktop.jalviewClipboard != null
2469 && Desktop.jalviewClipboard[2] != null)
2471 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2472 af.viewport.setHiddenColumns(hc);
2475 // >>>This is a fix for the moment, until a better solution is
2477 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2478 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2479 .getFeatureRenderer());
2481 // TODO: maintain provenance of an alignment, rather than just make the
2482 // title a concatenation of operations.
2485 if (title.startsWith("Copied sequences"))
2491 newtitle = newtitle.concat("- from " + title);
2496 newtitle = new String("Pasted sequences");
2499 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2504 } catch (Exception ex)
2506 ex.printStackTrace();
2507 System.out.println("Exception whilst pasting: " + ex);
2508 // could be anything being pasted in here
2513 protected void expand_newalign(ActionEvent e)
2517 AlignmentI alignment = AlignmentUtils
2518 .expandContext(getViewport().getAlignment(), -1);
2519 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2521 String newtitle = new String("Flanking alignment");
2523 if (Desktop.jalviewClipboard != null
2524 && Desktop.jalviewClipboard[2] != null)
2526 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2527 af.viewport.setHiddenColumns(hc);
2530 // >>>This is a fix for the moment, until a better solution is
2532 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2533 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2534 .getFeatureRenderer());
2536 // TODO: maintain provenance of an alignment, rather than just make the
2537 // title a concatenation of operations.
2539 if (title.startsWith("Copied sequences"))
2545 newtitle = newtitle.concat("- from " + title);
2549 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2551 } catch (Exception ex)
2553 ex.printStackTrace();
2554 System.out.println("Exception whilst pasting: " + ex);
2555 // could be anything being pasted in here
2556 } catch (OutOfMemoryError oom)
2558 new OOMWarning("Viewing flanking region of alignment", oom);
2569 protected void cut_actionPerformed(ActionEvent e)
2571 copy_actionPerformed(null);
2572 delete_actionPerformed(null);
2582 protected void delete_actionPerformed(ActionEvent evt)
2585 SequenceGroup sg = viewport.getSelectionGroup();
2592 * If the cut affects all sequences, warn, remove highlighted columns
2594 if (sg.getSize() == viewport.getAlignment().getHeight())
2596 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2597 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2598 if (isEntireAlignWidth)
2600 int confirm = JvOptionPane.showConfirmDialog(this,
2601 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2602 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2603 JvOptionPane.OK_CANCEL_OPTION);
2605 if (confirm == JvOptionPane.CANCEL_OPTION
2606 || confirm == JvOptionPane.CLOSED_OPTION)
2611 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2612 sg.getEndRes() + 1);
2614 SequenceI[] cut = sg.getSequences()
2615 .toArray(new SequenceI[sg.getSize()]);
2617 addHistoryItem(new EditCommand(
2618 MessageManager.getString("label.cut_sequences"), Action.CUT,
2619 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2620 viewport.getAlignment()));
2622 viewport.setSelectionGroup(null);
2623 viewport.sendSelection();
2624 viewport.getAlignment().deleteGroup(sg);
2626 viewport.firePropertyChange("alignment", null,
2627 viewport.getAlignment().getSequences());
2628 if (viewport.getAlignment().getHeight() < 1)
2632 this.setClosed(true);
2633 } catch (Exception ex)
2646 protected void deleteGroups_actionPerformed(ActionEvent e)
2648 if (avc.deleteGroups())
2650 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2651 alignPanel.updateAnnotation();
2652 alignPanel.paintAlignment(true, true);
2663 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2665 SequenceGroup sg = new SequenceGroup(
2666 viewport.getAlignment().getSequences());
2668 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2669 viewport.setSelectionGroup(sg);
2670 viewport.isSelectionGroupChanged(true);
2671 viewport.sendSelection();
2672 // JAL-2034 - should delegate to
2673 // alignPanel to decide if overview needs
2675 alignPanel.paintAlignment(false, false);
2676 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2686 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2688 if (viewport.cursorMode)
2690 alignPanel.getSeqPanel().keyboardNo1 = null;
2691 alignPanel.getSeqPanel().keyboardNo2 = null;
2693 viewport.setSelectionGroup(null);
2694 viewport.getColumnSelection().clear();
2695 viewport.setSelectionGroup(null);
2696 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2697 // JAL-2034 - should delegate to
2698 // alignPanel to decide if overview needs
2700 alignPanel.paintAlignment(false, false);
2701 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2702 viewport.sendSelection();
2712 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2714 SequenceGroup sg = viewport.getSelectionGroup();
2718 selectAllSequenceMenuItem_actionPerformed(null);
2723 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2725 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2727 // JAL-2034 - should delegate to
2728 // alignPanel to decide if overview needs
2731 alignPanel.paintAlignment(true, false);
2732 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2733 viewport.sendSelection();
2737 public void invertColSel_actionPerformed(ActionEvent e)
2739 viewport.invertColumnSelection();
2740 alignPanel.paintAlignment(true, false);
2741 viewport.sendSelection();
2751 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2753 trimAlignment(true);
2763 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2765 trimAlignment(false);
2768 void trimAlignment(boolean trimLeft)
2770 ColumnSelection colSel = viewport.getColumnSelection();
2773 if (!colSel.isEmpty())
2777 column = colSel.getMin();
2781 column = colSel.getMax();
2785 if (viewport.getSelectionGroup() != null)
2787 seqs = viewport.getSelectionGroup()
2788 .getSequencesAsArray(viewport.getHiddenRepSequences());
2792 seqs = viewport.getAlignment().getSequencesArray();
2795 TrimRegionCommand trimRegion;
2798 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2799 column, viewport.getAlignment());
2800 viewport.getRanges().setStartRes(0);
2804 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2805 column, viewport.getAlignment());
2808 statusBar.setText(MessageManager
2809 .formatMessage("label.removed_columns", new String[]
2810 { Integer.valueOf(trimRegion.getSize()).toString() }));
2812 addHistoryItem(trimRegion);
2814 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2816 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2817 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2819 viewport.getAlignment().deleteGroup(sg);
2823 viewport.firePropertyChange("alignment", null,
2824 viewport.getAlignment().getSequences());
2835 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2837 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2840 if (viewport.getSelectionGroup() != null)
2842 seqs = viewport.getSelectionGroup()
2843 .getSequencesAsArray(viewport.getHiddenRepSequences());
2844 start = viewport.getSelectionGroup().getStartRes();
2845 end = viewport.getSelectionGroup().getEndRes();
2849 seqs = viewport.getAlignment().getSequencesArray();
2852 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2853 "Remove Gapped Columns", seqs, start, end,
2854 viewport.getAlignment());
2856 addHistoryItem(removeGapCols);
2858 statusBar.setText(MessageManager
2859 .formatMessage("label.removed_empty_columns", new Object[]
2860 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2862 // This is to maintain viewport position on first residue
2863 // of first sequence
2864 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2865 ViewportRanges ranges = viewport.getRanges();
2866 int startRes = seq.findPosition(ranges.getStartRes());
2867 // ShiftList shifts;
2868 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2869 // edit.alColumnChanges=shifts.getInverse();
2870 // if (viewport.hasHiddenColumns)
2871 // viewport.getColumnSelection().compensateForEdits(shifts);
2872 ranges.setStartRes(seq.findIndex(startRes) - 1);
2873 viewport.firePropertyChange("alignment", null,
2874 viewport.getAlignment().getSequences());
2885 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2887 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2890 if (viewport.getSelectionGroup() != null)
2892 seqs = viewport.getSelectionGroup()
2893 .getSequencesAsArray(viewport.getHiddenRepSequences());
2894 start = viewport.getSelectionGroup().getStartRes();
2895 end = viewport.getSelectionGroup().getEndRes();
2899 seqs = viewport.getAlignment().getSequencesArray();
2902 // This is to maintain viewport position on first residue
2903 // of first sequence
2904 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2905 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2907 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2908 viewport.getAlignment()));
2910 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2912 viewport.firePropertyChange("alignment", null,
2913 viewport.getAlignment().getSequences());
2924 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2926 viewport.setPadGaps(padGapsMenuitem.isSelected());
2927 viewport.firePropertyChange("alignment", null,
2928 viewport.getAlignment().getSequences());
2938 public void findMenuItem_actionPerformed(ActionEvent e)
2944 * Create a new view of the current alignment.
2947 public void newView_actionPerformed(ActionEvent e)
2949 newView(null, true);
2953 * Creates and shows a new view of the current alignment.
2956 * title of newly created view; if null, one will be generated
2957 * @param copyAnnotation
2958 * if true then duplicate all annnotation, groups and settings
2959 * @return new alignment panel, already displayed.
2961 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2964 * Create a new AlignmentPanel (with its own, new Viewport)
2966 AlignmentPanel newap = new jalview.project.Jalview2XML()
2967 .copyAlignPanel(alignPanel);
2968 if (!copyAnnotation)
2971 * remove all groups and annotation except for the automatic stuff
2973 newap.av.getAlignment().deleteAllGroups();
2974 newap.av.getAlignment().deleteAllAnnotations(false);
2977 newap.av.setGatherViewsHere(false);
2979 if (viewport.getViewName() == null)
2981 viewport.setViewName(MessageManager
2982 .getString("label.view_name_original"));
2986 * Views share the same edits undo and redo stacks
2988 newap.av.setHistoryList(viewport.getHistoryList());
2989 newap.av.setRedoList(viewport.getRedoList());
2992 * copy any visualisation settings that are not saved in the project
2994 newap.av.setColourAppliesToAllGroups(
2995 viewport.getColourAppliesToAllGroups());
2998 * Views share the same mappings; need to deregister any new mappings
2999 * created by copyAlignPanel, and register the new reference to the shared
3002 newap.av.replaceMappings(viewport.getAlignment());
3005 * start up cDNA consensus (if applicable) now mappings are in place
3007 if (newap.av.initComplementConsensus())
3009 newap.refresh(true); // adjust layout of annotations
3012 newap.av.setViewName(getNewViewName(viewTitle));
3014 addAlignmentPanel(newap, true);
3015 newap.alignmentChanged();
3017 if (alignPanels.size() == 2)
3019 viewport.setGatherViewsHere(true);
3021 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
3026 * Make a new name for the view, ensuring it is unique within the current
3027 * sequenceSetId. (This used to be essential for Jalview Project archives, but
3028 * these now use viewId. Unique view names are still desirable for usability.)
3033 protected String getNewViewName(String viewTitle)
3035 int index = Desktop.getViewCount(viewport.getSequenceSetId());
3036 boolean addFirstIndex = false;
3037 if (viewTitle == null || viewTitle.trim().length() == 0)
3039 viewTitle = MessageManager.getString("action.view");
3040 addFirstIndex = true;
3044 index = 1;// we count from 1 if given a specific name
3046 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
3048 List<Component> comps = PaintRefresher.components
3049 .get(viewport.getSequenceSetId());
3051 List<String> existingNames = getExistingViewNames(comps);
3053 while (existingNames.contains(newViewName))
3055 newViewName = viewTitle + " " + (++index);
3061 * Returns a list of distinct view names found in the given list of
3062 * components. View names are held on the viewport of an AlignmentPanel.
3067 protected List<String> getExistingViewNames(List<Component> comps)
3069 List<String> existingNames = new ArrayList<>();
3070 for (Component comp : comps)
3072 if (comp instanceof AlignmentPanel)
3074 AlignmentPanel ap = (AlignmentPanel) comp;
3075 if (!existingNames.contains(ap.av.getViewName()))
3077 existingNames.add(ap.av.getViewName());
3081 return existingNames;
3085 * Explode tabbed views into separate windows.
3088 public void expandViews_actionPerformed(ActionEvent e)
3090 Desktop.explodeViews(this);
3094 * Gather views in separate windows back into a tabbed presentation.
3097 public void gatherViews_actionPerformed(ActionEvent e)
3099 Desktop.instance.gatherViews(this);
3109 public void font_actionPerformed(ActionEvent e)
3111 new FontChooser(alignPanel);
3121 protected void seqLimit_actionPerformed(ActionEvent e)
3123 viewport.setShowJVSuffix(seqLimits.isSelected());
3125 alignPanel.getIdPanel().getIdCanvas()
3126 .setPreferredSize(alignPanel.calculateIdWidth());
3127 alignPanel.paintAlignment(true, false);
3131 public void idRightAlign_actionPerformed(ActionEvent e)
3133 viewport.setRightAlignIds(idRightAlign.isSelected());
3134 alignPanel.paintAlignment(false, false);
3138 public void centreColumnLabels_actionPerformed(ActionEvent e)
3140 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3141 alignPanel.paintAlignment(false, false);
3147 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3150 protected void followHighlight_actionPerformed()
3153 * Set the 'follow' flag on the Viewport (and scroll to position if now
3156 final boolean state = this.followHighlightMenuItem.getState();
3157 viewport.setFollowHighlight(state);
3160 alignPanel.scrollToPosition(viewport.getSearchResults());
3171 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3173 viewport.setColourText(colourTextMenuItem.isSelected());
3174 alignPanel.paintAlignment(false, false);
3184 public void wrapMenuItem_actionPerformed(ActionEvent e)
3186 scaleAbove.setVisible(wrapMenuItem.isSelected());
3187 scaleLeft.setVisible(wrapMenuItem.isSelected());
3188 scaleRight.setVisible(wrapMenuItem.isSelected());
3189 viewport.setWrapAlignment(wrapMenuItem.isSelected());
3190 alignPanel.updateLayout();
3194 public void showAllSeqs_actionPerformed(ActionEvent e)
3196 viewport.showAllHiddenSeqs();
3200 public void showAllColumns_actionPerformed(ActionEvent e)
3202 viewport.showAllHiddenColumns();
3203 alignPanel.paintAlignment(true, true);
3204 viewport.sendSelection();
3208 public void hideSelSequences_actionPerformed(ActionEvent e)
3210 viewport.hideAllSelectedSeqs();
3214 * called by key handler and the hide all/show all menu items
3219 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3222 boolean hide = false;
3223 SequenceGroup sg = viewport.getSelectionGroup();
3224 if (!toggleSeqs && !toggleCols)
3226 // Hide everything by the current selection - this is a hack - we do the
3227 // invert and then hide
3228 // first check that there will be visible columns after the invert.
3229 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3230 && sg.getStartRes() <= sg.getEndRes()))
3232 // now invert the sequence set, if required - empty selection implies
3233 // that no hiding is required.
3236 invertSequenceMenuItem_actionPerformed(null);
3237 sg = viewport.getSelectionGroup();
3241 viewport.expandColSelection(sg, true);
3242 // finally invert the column selection and get the new sequence
3244 invertColSel_actionPerformed(null);
3251 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3253 hideSelSequences_actionPerformed(null);
3256 else if (!(toggleCols && viewport.hasSelectedColumns()))
3258 showAllSeqs_actionPerformed(null);
3264 if (viewport.hasSelectedColumns())
3266 hideSelColumns_actionPerformed(null);
3269 viewport.setSelectionGroup(sg);
3274 showAllColumns_actionPerformed(null);
3283 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3284 * event.ActionEvent)
3287 public void hideAllButSelection_actionPerformed(ActionEvent e)
3289 toggleHiddenRegions(false, false);
3290 viewport.sendSelection();
3297 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3301 public void hideAllSelection_actionPerformed(ActionEvent e)
3303 SequenceGroup sg = viewport.getSelectionGroup();
3304 viewport.expandColSelection(sg, false);
3305 viewport.hideAllSelectedSeqs();
3306 viewport.hideSelectedColumns();
3307 alignPanel.updateLayout();
3308 alignPanel.paintAlignment(true, true);
3309 viewport.sendSelection();
3316 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3320 public void showAllhidden_actionPerformed(ActionEvent e)
3322 viewport.showAllHiddenColumns();
3323 viewport.showAllHiddenSeqs();
3324 alignPanel.paintAlignment(true, true);
3325 viewport.sendSelection();
3329 public void hideSelColumns_actionPerformed(ActionEvent e)
3331 viewport.hideSelectedColumns();
3332 alignPanel.updateLayout();
3333 alignPanel.paintAlignment(true, true);
3334 viewport.sendSelection();
3338 public void hiddenMarkers_actionPerformed(ActionEvent e)
3340 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3351 protected void scaleAbove_actionPerformed(ActionEvent e)
3353 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3354 alignPanel.updateLayout();
3355 alignPanel.paintAlignment(true, false);
3365 protected void scaleLeft_actionPerformed(ActionEvent e)
3367 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3368 alignPanel.updateLayout();
3369 alignPanel.paintAlignment(true, false);
3379 protected void scaleRight_actionPerformed(ActionEvent e)
3381 viewport.setScaleRightWrapped(scaleRight.isSelected());
3382 alignPanel.updateLayout();
3383 alignPanel.paintAlignment(true, false);
3393 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3395 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3396 alignPanel.paintAlignment(false, false);
3406 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3408 viewport.setShowText(viewTextMenuItem.isSelected());
3409 alignPanel.paintAlignment(false, false);
3419 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3421 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3422 alignPanel.paintAlignment(false, false);
3425 public FeatureSettings featureSettings;
3428 public FeatureSettingsControllerI getFeatureSettingsUI()
3430 return featureSettings;
3434 public void featureSettings_actionPerformed(ActionEvent e)
3436 if (featureSettings != null)
3438 featureSettings.close();
3439 featureSettings = null;
3441 if (!showSeqFeatures.isSelected())
3443 // make sure features are actually displayed
3444 showSeqFeatures.setSelected(true);
3445 showSeqFeatures_actionPerformed(null);
3447 featureSettings = new FeatureSettings(this);
3451 * Set or clear 'Show Sequence Features'
3457 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3459 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3460 alignPanel.paintAlignment(true, true);
3464 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3465 * the annotations panel as a whole.
3467 * The options to show/hide all annotations should be enabled when the panel
3468 * is shown, and disabled when the panel is hidden.
3473 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3475 final boolean setVisible = annotationPanelMenuItem.isSelected();
3476 viewport.setShowAnnotation(setVisible);
3477 this.showAllSeqAnnotations.setEnabled(setVisible);
3478 this.hideAllSeqAnnotations.setEnabled(setVisible);
3479 this.showAllAlAnnotations.setEnabled(setVisible);
3480 this.hideAllAlAnnotations.setEnabled(setVisible);
3481 alignPanel.updateLayout();
3485 public void alignmentProperties()
3487 JEditorPane editPane = new JEditorPane("text/html", "");
3488 editPane.setEditable(false);
3489 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3492 MessageManager.formatMessage("label.html_content", new Object[]
3493 { contents.toString() }));
3494 JInternalFrame frame = new JInternalFrame();
3495 frame.getContentPane().add(new JScrollPane(editPane));
3497 Desktop.addInternalFrame(frame, MessageManager
3498 .formatMessage("label.alignment_properties", new Object[]
3499 { getTitle() }), 500, 400);
3509 public void overviewMenuItem_actionPerformed(ActionEvent e)
3511 if (alignPanel.overviewPanel != null)
3516 JInternalFrame frame = new JInternalFrame();
3517 final OverviewPanel overview = new OverviewPanel(alignPanel);
3518 frame.setContentPane(overview);
3519 Desktop.addInternalFrame(frame, MessageManager
3520 .formatMessage("label.overview_params", new Object[]
3521 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3524 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3525 frame.addInternalFrameListener(
3526 new javax.swing.event.InternalFrameAdapter()
3529 public void internalFrameClosed(
3530 javax.swing.event.InternalFrameEvent evt)
3533 alignPanel.setOverviewPanel(null);
3536 if (getKeyListeners().length > 0)
3538 frame.addKeyListener(getKeyListeners()[0]);
3541 alignPanel.setOverviewPanel(overview);
3545 public void textColour_actionPerformed()
3547 new TextColourChooser().chooseColour(alignPanel, null);
3551 * public void covariationColour_actionPerformed() {
3553 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3557 public void annotationColour_actionPerformed()
3559 new AnnotationColourChooser(viewport, alignPanel);
3563 public void annotationColumn_actionPerformed(ActionEvent e)
3565 new AnnotationColumnChooser(viewport, alignPanel);
3569 * Action on the user checking or unchecking the option to apply the selected
3570 * colour scheme to all groups. If unchecked, groups may have their own
3571 * independent colour schemes.
3576 public void applyToAllGroups_actionPerformed(boolean selected)
3578 viewport.setColourAppliesToAllGroups(selected);
3582 * Action on user selecting a colour from the colour menu
3585 * the name (not the menu item label!) of the colour scheme
3588 public void changeColour_actionPerformed(String name)
3591 * 'User Defined' opens a panel to configure or load a
3592 * user-defined colour scheme
3594 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3596 new UserDefinedColours(alignPanel);
3601 * otherwise set the chosen colour scheme (or null for 'None')
3603 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3605 viewport.getAlignment(), viewport.getHiddenRepSequences());
3610 * Actions on setting or changing the alignment colour scheme
3615 public void changeColour(ColourSchemeI cs)
3617 // TODO: pull up to controller method
3618 ColourMenuHelper.setColourSelected(colourMenu, cs);
3620 viewport.setGlobalColourScheme(cs);
3622 alignPanel.paintAlignment(true, true);
3626 * Show the PID threshold slider panel
3629 protected void modifyPID_actionPerformed()
3631 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3632 alignPanel.getViewName());
3633 SliderPanel.showPIDSlider();
3637 * Show the Conservation slider panel
3640 protected void modifyConservation_actionPerformed()
3642 SliderPanel.setConservationSlider(alignPanel,
3643 viewport.getResidueShading(), alignPanel.getViewName());
3644 SliderPanel.showConservationSlider();
3648 * Action on selecting or deselecting (Colour) By Conservation
3651 public void conservationMenuItem_actionPerformed(boolean selected)
3653 modifyConservation.setEnabled(selected);
3654 viewport.setConservationSelected(selected);
3655 viewport.getResidueShading().setConservationApplied(selected);
3657 changeColour(viewport.getGlobalColourScheme());
3660 modifyConservation_actionPerformed();
3664 SliderPanel.hideConservationSlider();
3669 * Action on selecting or deselecting (Colour) Above PID Threshold
3672 public void abovePIDThreshold_actionPerformed(boolean selected)
3674 modifyPID.setEnabled(selected);
3675 viewport.setAbovePIDThreshold(selected);
3678 viewport.getResidueShading().setThreshold(0,
3679 viewport.isIgnoreGapsConsensus());
3682 changeColour(viewport.getGlobalColourScheme());
3685 modifyPID_actionPerformed();
3689 SliderPanel.hidePIDSlider();
3700 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3702 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3703 AlignmentSorter.sortByPID(viewport.getAlignment(),
3704 viewport.getAlignment().getSequenceAt(0));
3705 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3706 viewport.getAlignment()));
3707 alignPanel.paintAlignment(true, false);
3717 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3719 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3720 AlignmentSorter.sortByID(viewport.getAlignment());
3722 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3723 alignPanel.paintAlignment(true, false);
3733 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3735 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3736 AlignmentSorter.sortByLength(viewport.getAlignment());
3737 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3738 viewport.getAlignment()));
3739 alignPanel.paintAlignment(true, false);
3749 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3751 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3752 AlignmentSorter.sortByGroup(viewport.getAlignment());
3753 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3754 viewport.getAlignment()));
3756 alignPanel.paintAlignment(true, false);
3766 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3768 new RedundancyPanel(alignPanel, this);
3778 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3780 if ((viewport.getSelectionGroup() == null)
3781 || (viewport.getSelectionGroup().getSize() < 2))
3783 JvOptionPane.showInternalMessageDialog(this,
3784 MessageManager.getString(
3785 "label.you_must_select_least_two_sequences"),
3786 MessageManager.getString("label.invalid_selection"),
3787 JvOptionPane.WARNING_MESSAGE);
3791 JInternalFrame frame = new JInternalFrame();
3792 frame.setContentPane(new PairwiseAlignPanel(viewport));
3793 Desktop.addInternalFrame(frame,
3794 MessageManager.getString("action.pairwise_alignment"), 600,
3800 public void autoCalculate_actionPerformed(ActionEvent e)
3802 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3803 if (viewport.autoCalculateConsensus)
3805 viewport.firePropertyChange("alignment", null,
3806 viewport.getAlignment().getSequences());
3811 public void sortByTreeOption_actionPerformed(ActionEvent e)
3813 viewport.sortByTree = sortByTree.isSelected();
3817 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3819 viewport.followSelection = listenToViewSelections.isSelected();
3823 * Constructs a tree panel and adds it to the desktop
3826 * tree type (NJ or AV)
3828 * name of score model used to compute the tree
3830 * parameters for the distance or similarity calculation
3832 void newTreePanel(String type, String modelName,
3833 SimilarityParamsI options)
3835 String frameTitle = "";
3838 boolean onSelection = false;
3839 if (viewport.getSelectionGroup() != null
3840 && viewport.getSelectionGroup().getSize() > 0)
3842 SequenceGroup sg = viewport.getSelectionGroup();
3844 /* Decide if the selection is a column region */
3845 for (SequenceI _s : sg.getSequences())
3847 if (_s.getLength() < sg.getEndRes())
3849 JvOptionPane.showMessageDialog(Desktop.desktop,
3850 MessageManager.getString(
3851 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3852 MessageManager.getString(
3853 "label.sequences_selection_not_aligned"),
3854 JvOptionPane.WARNING_MESSAGE);
3863 if (viewport.getAlignment().getHeight() < 2)
3869 tp = new TreePanel(alignPanel, type, modelName, options);
3870 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3872 frameTitle += " from ";
3874 if (viewport.getViewName() != null)
3876 frameTitle += viewport.getViewName() + " of ";
3879 frameTitle += this.title;
3881 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3892 public void addSortByOrderMenuItem(String title,
3893 final AlignmentOrder order)
3895 final JMenuItem item = new JMenuItem(MessageManager
3896 .formatMessage("action.by_title_param", new Object[]
3899 item.addActionListener(new java.awt.event.ActionListener()
3902 public void actionPerformed(ActionEvent e)
3904 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3906 // TODO: JBPNote - have to map order entries to curent SequenceI
3908 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3910 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3911 viewport.getAlignment()));
3913 alignPanel.paintAlignment(true, false);
3919 * Add a new sort by annotation score menu item
3922 * the menu to add the option to
3924 * the label used to retrieve scores for each sequence on the
3927 public void addSortByAnnotScoreMenuItem(JMenu sort,
3928 final String scoreLabel)
3930 final JMenuItem item = new JMenuItem(scoreLabel);
3932 item.addActionListener(new java.awt.event.ActionListener()
3935 public void actionPerformed(ActionEvent e)
3937 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3938 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3939 viewport.getAlignment());// ,viewport.getSelectionGroup());
3940 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3941 viewport.getAlignment()));
3942 alignPanel.paintAlignment(true, false);
3948 * last hash for alignment's annotation array - used to minimise cost of
3951 protected int _annotationScoreVectorHash;
3954 * search the alignment and rebuild the sort by annotation score submenu the
3955 * last alignment annotation vector hash is stored to minimize cost of
3956 * rebuilding in subsequence calls.
3960 public void buildSortByAnnotationScoresMenu()
3962 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3967 if (viewport.getAlignment().getAlignmentAnnotation()
3968 .hashCode() == _annotationScoreVectorHash)
3973 sortByAnnotScore.removeAll();
3974 Set<String> scoreSorts = new HashSet<>();
3975 for (SequenceI sqa : viewport.getAlignment().getSequences())
3977 AlignmentAnnotation[] anns = sqa.getAnnotation();
3978 for (int i = 0; anns != null && i < anns.length; i++)
3980 AlignmentAnnotation aa = anns[i];
3981 if (aa != null && aa.hasScore() && aa.sequenceRef != null)
3983 scoreSorts.add(aa.label);
3987 for (String label : scoreSorts)
3989 addSortByAnnotScoreMenuItem(sortByAnnotScore, label);
3991 sortByAnnotScore.setVisible(!scoreSorts.isEmpty());
3993 _annotationScoreVectorHash = viewport.getAlignment()
3994 .getAlignmentAnnotation().hashCode();
3998 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3999 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4000 * call. Listeners are added to remove the menu item when the treePanel is
4001 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4005 public void buildTreeSortMenu()
4007 sortByTreeMenu.removeAll();
4009 List<Component> comps = PaintRefresher.components
4010 .get(viewport.getSequenceSetId());
4011 List<TreePanel> treePanels = new ArrayList<>();
4012 for (Component comp : comps)
4014 if (comp instanceof TreePanel)
4016 treePanels.add((TreePanel) comp);
4020 if (treePanels.size() < 1)
4022 sortByTreeMenu.setVisible(false);
4026 sortByTreeMenu.setVisible(true);
4028 for (final TreePanel tp : treePanels)
4030 final JMenuItem item = new JMenuItem(tp.getTitle());
4031 item.addActionListener(new java.awt.event.ActionListener()
4034 public void actionPerformed(ActionEvent e)
4036 tp.sortByTree_actionPerformed();
4037 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4042 sortByTreeMenu.add(item);
4046 public boolean sortBy(AlignmentOrder alorder, String undoname)
4048 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4049 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4050 if (undoname != null)
4052 addHistoryItem(new OrderCommand(undoname, oldOrder,
4053 viewport.getAlignment()));
4055 alignPanel.paintAlignment(true, false);
4060 * Work out whether the whole set of sequences or just the selected set will
4061 * be submitted for multiple alignment.
4064 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4066 // Now, check we have enough sequences
4067 AlignmentView msa = null;
4069 if ((viewport.getSelectionGroup() != null)
4070 && (viewport.getSelectionGroup().getSize() > 1))
4072 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4073 // some common interface!
4075 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4076 * SequenceI[sz = seqs.getSize(false)];
4078 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4079 * seqs.getSequenceAt(i); }
4081 msa = viewport.getAlignmentView(true);
4083 else if (viewport.getSelectionGroup() != null
4084 && viewport.getSelectionGroup().getSize() == 1)
4086 int option = JvOptionPane.showConfirmDialog(this,
4087 MessageManager.getString("warn.oneseq_msainput_selection"),
4088 MessageManager.getString("label.invalid_selection"),
4089 JvOptionPane.OK_CANCEL_OPTION);
4090 if (option == JvOptionPane.OK_OPTION)
4092 msa = viewport.getAlignmentView(false);
4097 msa = viewport.getAlignmentView(false);
4103 * Decides what is submitted to a secondary structure prediction service: the
4104 * first sequence in the alignment, or in the current selection, or, if the
4105 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4106 * region or the whole alignment. (where the first sequence in the set is the
4107 * one that the prediction will be for).
4109 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4111 AlignmentView seqs = null;
4113 if ((viewport.getSelectionGroup() != null)
4114 && (viewport.getSelectionGroup().getSize() > 0))
4116 seqs = viewport.getAlignmentView(true);
4120 seqs = viewport.getAlignmentView(false);
4122 // limit sequences - JBPNote in future - could spawn multiple prediction
4124 // TODO: viewport.getAlignment().isAligned is a global state - the local
4125 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4126 if (!viewport.getAlignment().isAligned(false))
4128 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4129 // TODO: if seqs.getSequences().length>1 then should really have warned
4143 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4145 // Pick the tree file
4146 JalviewFileChooser chooser = new JalviewFileChooser(
4147 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4148 chooser.setFileView(new JalviewFileView());
4149 chooser.setDialogTitle(
4150 MessageManager.getString("label.select_newick_like_tree_file"));
4151 chooser.setToolTipText(
4152 MessageManager.getString("label.load_tree_file"));
4154 int value = chooser.showOpenDialog(null);
4156 if (value == JalviewFileChooser.APPROVE_OPTION)
4158 String filePath = chooser.getSelectedFile().getPath();
4159 Cache.setProperty("LAST_DIRECTORY", filePath);
4160 NewickFile fin = null;
4163 fin = new NewickFile(filePath, DataSourceType.FILE);
4164 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4165 } catch (Exception ex)
4167 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4168 MessageManager.getString("label.problem_reading_tree_file"),
4169 JvOptionPane.WARNING_MESSAGE);
4170 ex.printStackTrace();
4172 if (fin != null && fin.hasWarningMessage())
4174 JvOptionPane.showMessageDialog(Desktop.desktop,
4175 fin.getWarningMessage(),
4177 .getString("label.possible_problem_with_tree_file"),
4178 JvOptionPane.WARNING_MESSAGE);
4183 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4185 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4188 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4189 int h, int x, int y)
4191 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4195 * Add a treeviewer for the tree extracted from a Newick file object to the
4196 * current alignment view
4203 * Associated alignment input data (or null)
4212 * @return TreePanel handle
4214 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4215 AlignmentView input, int w, int h, int x, int y)
4217 TreePanel tp = null;
4223 if (nf.getTree() != null)
4225 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4231 tp.setLocation(x, y);
4234 Desktop.addInternalFrame(tp, treeTitle, w, h);
4236 } catch (Exception ex)
4238 ex.printStackTrace();
4244 private boolean buildingMenu = false;
4247 * Generates menu items and listener event actions for web service clients
4250 public void BuildWebServiceMenu()
4252 while (buildingMenu)
4256 System.err.println("Waiting for building menu to finish.");
4258 } catch (Exception e)
4262 final AlignFrame me = this;
4263 buildingMenu = true;
4264 new Thread(new Runnable()
4269 final List<JMenuItem> legacyItems = new ArrayList<>();
4272 // System.err.println("Building ws menu again "
4273 // + Thread.currentThread());
4274 // TODO: add support for context dependent disabling of services based
4276 // alignment and current selection
4277 // TODO: add additional serviceHandle parameter to specify abstract
4279 // class independently of AbstractName
4280 // TODO: add in rediscovery GUI function to restart discoverer
4281 // TODO: group services by location as well as function and/or
4283 // object broker mechanism.
4284 final Vector<JMenu> wsmenu = new Vector<>();
4285 final IProgressIndicator af = me;
4288 * do not i18n these strings - they are hard-coded in class
4289 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4290 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4292 final JMenu msawsmenu = new JMenu("Alignment");
4293 final JMenu secstrmenu = new JMenu(
4294 "Secondary Structure Prediction");
4295 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4296 final JMenu analymenu = new JMenu("Analysis");
4297 final JMenu dismenu = new JMenu("Protein Disorder");
4298 // JAL-940 - only show secondary structure prediction services from
4299 // the legacy server
4300 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4302 Discoverer.services != null && (Discoverer.services.size() > 0))
4304 // TODO: refactor to allow list of AbstractName/Handler bindings to
4306 // stored or retrieved from elsewhere
4307 // No MSAWS used any more:
4308 // Vector msaws = null; // (Vector)
4309 // Discoverer.services.get("MsaWS");
4310 Vector secstrpr = (Vector) Discoverer.services
4312 if (secstrpr != null)
4314 // Add any secondary structure prediction services
4315 for (int i = 0, j = secstrpr.size(); i < j; i++)
4317 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4319 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4320 .getServiceClient(sh);
4321 int p = secstrmenu.getItemCount();
4322 impl.attachWSMenuEntry(secstrmenu, me);
4323 int q = secstrmenu.getItemCount();
4324 for (int litm = p; litm < q; litm++)
4326 legacyItems.add(secstrmenu.getItem(litm));
4332 // Add all submenus in the order they should appear on the web
4334 wsmenu.add(msawsmenu);
4335 wsmenu.add(secstrmenu);
4336 wsmenu.add(dismenu);
4337 wsmenu.add(analymenu);
4338 // No search services yet
4339 // wsmenu.add(seqsrchmenu);
4341 javax.swing.SwingUtilities.invokeLater(new Runnable()
4348 webService.removeAll();
4349 // first, add discovered services onto the webservices menu
4350 if (wsmenu.size() > 0)
4352 for (int i = 0, j = wsmenu.size(); i < j; i++)
4354 webService.add(wsmenu.get(i));
4359 webService.add(me.webServiceNoServices);
4361 // TODO: move into separate menu builder class.
4362 boolean new_sspred = false;
4363 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4365 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4366 if (jws2servs != null)
4368 if (jws2servs.hasServices())
4370 jws2servs.attachWSMenuEntry(webService, me);
4371 for (Jws2Instance sv : jws2servs.getServices())
4373 if (sv.description.toLowerCase().contains("jpred"))
4375 for (JMenuItem jmi : legacyItems)
4377 jmi.setVisible(false);
4383 if (jws2servs.isRunning())
4385 JMenuItem tm = new JMenuItem(
4386 "Still discovering JABA Services");
4387 tm.setEnabled(false);
4392 build_urlServiceMenu(me.webService);
4393 build_fetchdbmenu(webService);
4394 for (JMenu item : wsmenu)
4396 if (item.getItemCount() == 0)
4398 item.setEnabled(false);
4402 item.setEnabled(true);
4405 } catch (Exception e)
4408 "Exception during web service menu building process.",
4413 } catch (Exception e)
4416 buildingMenu = false;
4423 * construct any groupURL type service menu entries.
4427 private void build_urlServiceMenu(JMenu webService)
4429 // TODO: remove this code when 2.7 is released
4430 // DEBUG - alignmentView
4432 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4433 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4435 * @Override public void actionPerformed(ActionEvent e) {
4436 * jalview.datamodel.AlignmentView
4437 * .testSelectionViews(af.viewport.getAlignment(),
4438 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4440 * }); webService.add(testAlView);
4442 // TODO: refactor to RestClient discoverer and merge menu entries for
4443 // rest-style services with other types of analysis/calculation service
4444 // SHmmr test client - still being implemented.
4445 // DEBUG - alignmentView
4447 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4450 client.attachWSMenuEntry(
4451 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4457 * Searches the alignment sequences for xRefs and builds the Show
4458 * Cross-References menu (formerly called Show Products), with database
4459 * sources for which cross-references are found (protein sources for a
4460 * nucleotide alignment and vice versa)
4462 * @return true if Show Cross-references menu should be enabled
4464 public boolean canShowProducts()
4466 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4467 AlignmentI dataset = viewport.getAlignment().getDataset();
4469 showProducts.removeAll();
4470 final boolean dna = viewport.getAlignment().isNucleotide();
4472 if (seqs == null || seqs.length == 0)
4474 // nothing to see here.
4478 boolean showp = false;
4481 List<String> ptypes = new CrossRef(seqs, dataset)
4482 .findXrefSourcesForSequences(dna);
4484 for (final String source : ptypes)
4487 final AlignFrame af = this;
4488 JMenuItem xtype = new JMenuItem(source);
4489 xtype.addActionListener(new ActionListener()
4492 public void actionPerformed(ActionEvent e)
4494 showProductsFor(af.viewport.getSequenceSelection(), dna,
4498 showProducts.add(xtype);
4500 showProducts.setVisible(showp);
4501 showProducts.setEnabled(showp);
4502 } catch (Exception e)
4505 "canShowProducts threw an exception - please report to help@jalview.org",
4513 * Finds and displays cross-references for the selected sequences (protein
4514 * products for nucleotide sequences, dna coding sequences for peptides).
4517 * the sequences to show cross-references for
4519 * true if from a nucleotide alignment (so showing proteins)
4521 * the database to show cross-references for
4523 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4524 final String source)
4526 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4531 * Construct and display a new frame containing the translation of this
4532 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4535 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4537 AlignmentI al = null;
4540 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4542 al = dna.translateCdna(codeTable);
4543 } catch (Exception ex)
4545 jalview.bin.Cache.log.error(
4546 "Exception during translation. Please report this !", ex);
4547 final String msg = MessageManager.getString(
4548 "label.error_when_translating_sequences_submit_bug_report");
4549 final String errorTitle = MessageManager
4550 .getString("label.implementation_error")
4551 + MessageManager.getString("label.translation_failed");
4552 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4553 JvOptionPane.ERROR_MESSAGE);
4556 if (al == null || al.getHeight() == 0)
4558 final String msg = MessageManager.getString(
4559 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4560 final String errorTitle = MessageManager
4561 .getString("label.translation_failed");
4562 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4563 JvOptionPane.WARNING_MESSAGE);
4567 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4568 af.setFileFormat(this.currentFileFormat);
4569 final String newTitle = MessageManager
4570 .formatMessage("label.translation_of_params", new Object[]
4571 { this.getTitle(), codeTable.getId() });
4572 af.setTitle(newTitle);
4573 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4575 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4576 viewport.openSplitFrame(af, new Alignment(seqs));
4580 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4587 * Set the file format
4591 public void setFileFormat(FileFormatI format)
4593 this.currentFileFormat = format;
4597 * Try to load a features file onto the alignment.
4600 * contents or path to retrieve file
4602 * access mode of file (see jalview.io.AlignFile)
4603 * @return true if features file was parsed correctly.
4605 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4607 return avc.parseFeaturesFile(file, sourceType,
4608 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4613 public void refreshFeatureUI(boolean enableIfNecessary)
4615 // note - currently this is only still here rather than in the controller
4616 // because of the featureSettings hard reference that is yet to be
4618 if (enableIfNecessary)
4620 viewport.setShowSequenceFeatures(true);
4621 showSeqFeatures.setSelected(true);
4627 public void dragEnter(DropTargetDragEvent evt)
4632 public void dragExit(DropTargetEvent evt)
4637 public void dragOver(DropTargetDragEvent evt)
4642 public void dropActionChanged(DropTargetDragEvent evt)
4647 public void drop(DropTargetDropEvent evt)
4649 // JAL-1552 - acceptDrop required before getTransferable call for
4650 // Java's Transferable for native dnd
4651 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4652 Transferable t = evt.getTransferable();
4653 final AlignFrame thisaf = this;
4654 final List<String> files = new ArrayList<>();
4655 List<DataSourceType> protocols = new ArrayList<>();
4659 Desktop.transferFromDropTarget(files, protocols, evt, t);
4660 } catch (Exception e)
4662 e.printStackTrace();
4666 new Thread(new Runnable()
4673 // check to see if any of these files have names matching sequences
4676 SequenceIdMatcher idm = new SequenceIdMatcher(
4677 viewport.getAlignment().getSequencesArray());
4679 * Object[] { String,SequenceI}
4681 ArrayList<Object[]> filesmatched = new ArrayList<>();
4682 ArrayList<String> filesnotmatched = new ArrayList<>();
4683 for (int i = 0; i < files.size(); i++)
4685 String file = files.get(i).toString();
4687 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4688 if (protocol == DataSourceType.FILE)
4690 File fl = new File(file);
4691 pdbfn = fl.getName();
4693 else if (protocol == DataSourceType.URL)
4695 URL url = new URL(file);
4696 pdbfn = url.getFile();
4698 if (pdbfn.length() > 0)
4700 // attempt to find a match in the alignment
4701 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4702 int l = 0, c = pdbfn.indexOf(".");
4703 while (mtch == null && c != -1)
4708 } while ((c = pdbfn.indexOf(".", l)) > l);
4711 pdbfn = pdbfn.substring(0, l);
4713 mtch = idm.findAllIdMatches(pdbfn);
4717 FileFormatI type = null;
4720 type = new IdentifyFile().identify(file, protocol);
4721 } catch (Exception ex)
4725 if (type != null && type.isStructureFile())
4727 filesmatched.add(new Object[] { file, protocol, mtch });
4731 // File wasn't named like one of the sequences or wasn't a PDB
4733 filesnotmatched.add(file);
4737 if (filesmatched.size() > 0)
4739 boolean autoAssociate = Cache
4740 .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4743 String msg = MessageManager.formatMessage(
4744 "label.automatically_associate_structure_files_with_sequences_same_name",
4746 { Integer.valueOf(filesmatched.size())
4748 String ttl = MessageManager.getString(
4749 "label.automatically_associate_structure_files_by_name");
4750 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4751 ttl, JvOptionPane.YES_NO_OPTION);
4752 autoAssociate = choice == JvOptionPane.YES_OPTION;
4756 for (Object[] fm : filesmatched)
4758 // try and associate
4759 // TODO: may want to set a standard ID naming formalism for
4760 // associating PDB files which have no IDs.
4761 for (SequenceI toassoc : (SequenceI[]) fm[2])
4763 PDBEntry pe = new AssociatePdbFileWithSeq()
4764 .associatePdbWithSeq((String) fm[0],
4765 (DataSourceType) fm[1], toassoc, false,
4769 System.err.println("Associated file : "
4770 + ((String) fm[0]) + " with "
4771 + toassoc.getDisplayId(true));
4775 // TODO: do we need to update overview ? only if features are
4777 alignPanel.paintAlignment(true, false);
4783 * add declined structures as sequences
4785 for (Object[] o : filesmatched)
4787 filesnotmatched.add((String) o[0]);
4791 if (filesnotmatched.size() > 0)
4793 if (assocfiles > 0 && (Cache.getDefault(
4794 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4795 || JvOptionPane.showConfirmDialog(thisaf,
4796 "<html>" + MessageManager.formatMessage(
4797 "label.ignore_unmatched_dropped_files_info",
4800 filesnotmatched.size())
4803 MessageManager.getString(
4804 "label.ignore_unmatched_dropped_files"),
4805 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4809 for (String fn : filesnotmatched)
4811 loadJalviewDataFile(fn, null, null, null);
4815 } catch (Exception ex)
4817 ex.printStackTrace();
4825 * Attempt to load a "dropped" file or URL string, by testing in turn for
4827 * <li>an Annotation file</li>
4828 * <li>a JNet file</li>
4829 * <li>a features file</li>
4830 * <li>else try to interpret as an alignment file</li>
4834 * either a filename or a URL string.
4835 * @throws InterruptedException
4836 * @throws IOException
4838 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4839 FileFormatI format, SequenceI assocSeq)
4843 if (sourceType == null)
4845 sourceType = FormatAdapter.checkProtocol(file);
4847 // if the file isn't identified, or not positively identified as some
4848 // other filetype (PFAM is default unidentified alignment file type) then
4849 // try to parse as annotation.
4850 boolean isAnnotation = (format == null
4851 || FileFormat.Pfam.equals(format))
4852 ? new AnnotationFile().annotateAlignmentView(viewport,
4858 // first see if its a T-COFFEE score file
4859 TCoffeeScoreFile tcf = null;
4862 tcf = new TCoffeeScoreFile(file, sourceType);
4865 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4869 new TCoffeeColourScheme(viewport.getAlignment()));
4870 isAnnotation = true;
4871 statusBar.setText(MessageManager.getString(
4872 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4876 // some problem - if no warning its probable that the ID matching
4877 // process didn't work
4878 JvOptionPane.showMessageDialog(Desktop.desktop,
4879 tcf.getWarningMessage() == null
4880 ? MessageManager.getString(
4881 "label.check_file_matches_sequence_ids_alignment")
4882 : tcf.getWarningMessage(),
4883 MessageManager.getString(
4884 "label.problem_reading_tcoffee_score_file"),
4885 JvOptionPane.WARNING_MESSAGE);
4892 } catch (Exception x)
4895 "Exception when processing data source as T-COFFEE score file",
4901 // try to see if its a JNet 'concise' style annotation file *before*
4903 // try to parse it as a features file
4906 format = new IdentifyFile().identify(file, sourceType);
4908 if (FileFormat.ScoreMatrix == format)
4910 ScoreMatrixFile sm = new ScoreMatrixFile(
4911 new FileParse(file, sourceType));
4913 // todo: i18n this message
4914 statusBar.setText(MessageManager.formatMessage(
4915 "label.successfully_loaded_matrix",
4916 sm.getMatrixName()));
4918 else if (FileFormat.Jnet.equals(format))
4920 JPredFile predictions = new JPredFile(file, sourceType);
4921 new JnetAnnotationMaker();
4922 JnetAnnotationMaker.add_annotation(predictions,
4923 viewport.getAlignment(), 0, false);
4924 viewport.getAlignment().setupJPredAlignment();
4925 isAnnotation = true;
4927 // else if (IdentifyFile.FeaturesFile.equals(format))
4928 else if (FileFormat.Features.equals(format))
4930 if (parseFeaturesFile(file, sourceType))
4932 alignPanel.paintAlignment(true, true);
4937 new FileLoader().LoadFile(viewport, file, sourceType, format);
4943 alignPanel.adjustAnnotationHeight();
4944 viewport.updateSequenceIdColours();
4945 buildSortByAnnotationScoresMenu();
4946 alignPanel.paintAlignment(true, true);
4948 } catch (Exception ex)
4950 ex.printStackTrace();
4951 } catch (OutOfMemoryError oom)
4956 } catch (Exception x)
4961 + (sourceType != null
4962 ? (sourceType == DataSourceType.PASTE
4964 : "using " + sourceType + " from "
4968 ? "(parsing as '" + format + "' file)"
4970 oom, Desktop.desktop);
4975 * Method invoked by the ChangeListener on the tabbed pane, in other words
4976 * when a different tabbed pane is selected by the user or programmatically.
4979 public void tabSelectionChanged(int index)
4983 alignPanel = alignPanels.get(index);
4984 viewport = alignPanel.av;
4985 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4986 setMenusFromViewport(viewport);
4990 * 'focus' any colour slider that is open to the selected viewport
4992 if (viewport.getConservationSelected())
4994 SliderPanel.setConservationSlider(alignPanel,
4995 viewport.getResidueShading(), alignPanel.getViewName());
4999 SliderPanel.hideConservationSlider();
5001 if (viewport.getAbovePIDThreshold())
5003 SliderPanel.setPIDSliderSource(alignPanel,
5004 viewport.getResidueShading(), alignPanel.getViewName());
5008 SliderPanel.hidePIDSlider();
5012 * If there is a frame linked to this one in a SplitPane, switch it to the
5013 * same view tab index. No infinite recursion of calls should happen, since
5014 * tabSelectionChanged() should not get invoked on setting the selected
5015 * index to an unchanged value. Guard against setting an invalid index
5016 * before the new view peer tab has been created.
5018 final AlignViewportI peer = viewport.getCodingComplement();
5021 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
5022 .getAlignPanel().alignFrame;
5023 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5025 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5031 * On right mouse click on view tab, prompt for and set new view name.
5034 public void tabbedPane_mousePressed(MouseEvent e)
5036 if (e.isPopupTrigger())
5038 String msg = MessageManager.getString("label.enter_view_name");
5039 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
5040 JvOptionPane.QUESTION_MESSAGE);
5044 viewport.setViewName(reply);
5045 // TODO warn if reply is in getExistingViewNames()?
5046 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5051 public AlignViewport getCurrentView()
5057 * Open the dialog for regex description parsing.
5060 protected void extractScores_actionPerformed(ActionEvent e)
5062 ParseProperties pp = new jalview.analysis.ParseProperties(
5063 viewport.getAlignment());
5064 // TODO: verify regex and introduce GUI dialog for version 2.5
5065 // if (pp.getScoresFromDescription("col", "score column ",
5066 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5068 if (pp.getScoresFromDescription("description column",
5069 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5071 buildSortByAnnotationScoresMenu();
5079 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5083 protected void showDbRefs_actionPerformed(ActionEvent e)
5085 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5091 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5095 protected void showNpFeats_actionPerformed(ActionEvent e)
5097 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5101 * find the viewport amongst the tabs in this alignment frame and close that
5106 public boolean closeView(AlignViewportI av)
5110 this.closeMenuItem_actionPerformed(false);
5113 Component[] comp = tabbedPane.getComponents();
5114 for (int i = 0; comp != null && i < comp.length; i++)
5116 if (comp[i] instanceof AlignmentPanel)
5118 if (((AlignmentPanel) comp[i]).av == av)
5121 closeView((AlignmentPanel) comp[i]);
5129 protected void build_fetchdbmenu(JMenu webService)
5131 // Temporary hack - DBRef Fetcher always top level ws entry.
5132 // TODO We probably want to store a sequence database checklist in
5133 // preferences and have checkboxes.. rather than individual sources selected
5135 final JMenu rfetch = new JMenu(
5136 MessageManager.getString("action.fetch_db_references"));
5137 rfetch.setToolTipText(MessageManager.getString(
5138 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5139 webService.add(rfetch);
5141 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5142 MessageManager.getString("option.trim_retrieved_seqs"));
5143 trimrs.setToolTipText(
5144 MessageManager.getString("label.trim_retrieved_sequences"));
5146 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5147 trimrs.addActionListener(new ActionListener()
5150 public void actionPerformed(ActionEvent e)
5152 trimrs.setSelected(trimrs.isSelected());
5153 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5154 Boolean.valueOf(trimrs.isSelected()).toString());
5158 JMenuItem fetchr = new JMenuItem(
5159 MessageManager.getString("label.standard_databases"));
5160 fetchr.setToolTipText(
5161 MessageManager.getString("label.fetch_embl_uniprot"));
5162 fetchr.addActionListener(new ActionListener()
5166 public void actionPerformed(ActionEvent e)
5168 new Thread(new Runnable()
5173 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5174 .getAlignment().isNucleotide();
5175 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5176 alignPanel.av.getSequenceSelection(),
5177 alignPanel.alignFrame, null,
5178 alignPanel.alignFrame.featureSettings, isNucleotide);
5179 dbRefFetcher.addListener(new FetchFinishedListenerI()
5182 public void finished()
5184 AlignFrame.this.setMenusForViewport();
5187 dbRefFetcher.fetchDBRefs(false);
5195 final AlignFrame me = this;
5196 new Thread(new Runnable()
5201 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5202 .getSequenceFetcherSingleton(me);
5203 javax.swing.SwingUtilities.invokeLater(new Runnable()
5208 String[] dbclasses = sf.getOrderedSupportedSources();
5209 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5210 // jalview.util.QuickSort.sort(otherdb, otherdb);
5211 List<DbSourceProxy> otherdb;
5212 JMenu dfetch = new JMenu();
5213 JMenu ifetch = new JMenu();
5214 JMenuItem fetchr = null;
5215 int comp = 0, icomp = 0, mcomp = 15;
5216 String mname = null;
5218 for (String dbclass : dbclasses)
5220 otherdb = sf.getSourceProxy(dbclass);
5221 // add a single entry for this class, or submenu allowing 'fetch
5223 if (otherdb == null || otherdb.size() < 1)
5227 // List<DbSourceProxy> dbs=otherdb;
5228 // otherdb=new ArrayList<DbSourceProxy>();
5229 // for (DbSourceProxy db:dbs)
5231 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5235 mname = "From " + dbclass;
5237 if (otherdb.size() == 1)
5239 final DbSourceProxy[] dassource = otherdb
5240 .toArray(new DbSourceProxy[0]);
5241 DbSourceProxy src = otherdb.get(0);
5242 fetchr = new JMenuItem(src.getDbSource());
5243 fetchr.addActionListener(new ActionListener()
5247 public void actionPerformed(ActionEvent e)
5249 new Thread(new Runnable()
5255 boolean isNucleotide = alignPanel.alignFrame
5256 .getViewport().getAlignment()
5258 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5259 alignPanel.av.getSequenceSelection(),
5260 alignPanel.alignFrame, dassource,
5261 alignPanel.alignFrame.featureSettings,
5264 .addListener(new FetchFinishedListenerI()
5267 public void finished()
5269 AlignFrame.this.setMenusForViewport();
5272 dbRefFetcher.fetchDBRefs(false);
5278 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5279 MessageManager.formatMessage(
5280 "label.fetch_retrieve_from", new Object[]
5281 { src.getDbName() })));
5287 final DbSourceProxy[] dassource = otherdb
5288 .toArray(new DbSourceProxy[0]);
5290 DbSourceProxy src = otherdb.get(0);
5291 fetchr = new JMenuItem(MessageManager
5292 .formatMessage("label.fetch_all_param", new Object[]
5293 { src.getDbSource() }));
5294 fetchr.addActionListener(new ActionListener()
5297 public void actionPerformed(ActionEvent e)
5299 new Thread(new Runnable()
5305 boolean isNucleotide = alignPanel.alignFrame
5306 .getViewport().getAlignment()
5308 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5309 alignPanel.av.getSequenceSelection(),
5310 alignPanel.alignFrame, dassource,
5311 alignPanel.alignFrame.featureSettings,
5314 .addListener(new FetchFinishedListenerI()
5317 public void finished()
5319 AlignFrame.this.setMenusForViewport();
5322 dbRefFetcher.fetchDBRefs(false);
5328 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5329 MessageManager.formatMessage(
5330 "label.fetch_retrieve_from_all_sources",
5332 { Integer.valueOf(otherdb.size())
5334 src.getDbSource(), src.getDbName() })));
5337 // and then build the rest of the individual menus
5338 ifetch = new JMenu(MessageManager.formatMessage(
5339 "label.source_from_db_source", new Object[]
5340 { src.getDbSource() }));
5342 String imname = null;
5344 for (DbSourceProxy sproxy : otherdb)
5346 String dbname = sproxy.getDbName();
5347 String sname = dbname.length() > 5
5348 ? dbname.substring(0, 5) + "..."
5350 String msname = dbname.length() > 10
5351 ? dbname.substring(0, 10) + "..."
5355 imname = MessageManager
5356 .formatMessage("label.from_msname", new Object[]
5359 fetchr = new JMenuItem(msname);
5360 final DbSourceProxy[] dassrc = { sproxy };
5361 fetchr.addActionListener(new ActionListener()
5365 public void actionPerformed(ActionEvent e)
5367 new Thread(new Runnable()
5373 boolean isNucleotide = alignPanel.alignFrame
5374 .getViewport().getAlignment()
5376 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5377 alignPanel.av.getSequenceSelection(),
5378 alignPanel.alignFrame, dassrc,
5379 alignPanel.alignFrame.featureSettings,
5382 .addListener(new FetchFinishedListenerI()
5385 public void finished()
5387 AlignFrame.this.setMenusForViewport();
5390 dbRefFetcher.fetchDBRefs(false);
5396 fetchr.setToolTipText(
5397 "<html>" + MessageManager.formatMessage(
5398 "label.fetch_retrieve_from", new Object[]
5402 if (++icomp >= mcomp || i == (otherdb.size()))
5404 ifetch.setText(MessageManager.formatMessage(
5405 "label.source_to_target", imname, sname));
5407 ifetch = new JMenu();
5415 if (comp >= mcomp || dbi >= (dbclasses.length))
5417 dfetch.setText(MessageManager.formatMessage(
5418 "label.source_to_target", mname, dbclass));
5420 dfetch = new JMenu();
5433 * Left justify the whole alignment.
5436 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5438 AlignmentI al = viewport.getAlignment();
5440 viewport.firePropertyChange("alignment", null, al);
5444 * Right justify the whole alignment.
5447 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5449 AlignmentI al = viewport.getAlignment();
5451 viewport.firePropertyChange("alignment", null, al);
5455 public void setShowSeqFeatures(boolean b)
5457 showSeqFeatures.setSelected(b);
5458 viewport.setShowSequenceFeatures(b);
5465 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5466 * awt.event.ActionEvent)
5469 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5471 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5472 alignPanel.paintAlignment(false, false);
5479 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5483 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5485 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5486 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5494 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5495 * .event.ActionEvent)
5498 protected void showGroupConservation_actionPerformed(ActionEvent e)
5500 viewport.setShowGroupConservation(showGroupConservation.getState());
5501 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5508 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5509 * .event.ActionEvent)
5512 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5514 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5515 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5522 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5523 * .event.ActionEvent)
5526 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5528 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5529 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5533 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5535 showSequenceLogo.setState(true);
5536 viewport.setShowSequenceLogo(true);
5537 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5538 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5542 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5544 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5551 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5552 * .event.ActionEvent)
5555 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5557 if (avc.makeGroupsFromSelection())
5559 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5560 alignPanel.updateAnnotation();
5561 alignPanel.paintAlignment(true,
5562 viewport.needToUpdateStructureViews());
5566 public void clearAlignmentSeqRep()
5568 // TODO refactor alignmentseqrep to controller
5569 if (viewport.getAlignment().hasSeqrep())
5571 viewport.getAlignment().setSeqrep(null);
5572 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5573 alignPanel.updateAnnotation();
5574 alignPanel.paintAlignment(true, true);
5579 protected void createGroup_actionPerformed(ActionEvent e)
5581 if (avc.createGroup())
5583 if (applyAutoAnnotationSettings.isSelected())
5585 alignPanel.updateAnnotation(true, false);
5587 alignPanel.alignmentChanged();
5592 protected void unGroup_actionPerformed(ActionEvent e)
5596 alignPanel.alignmentChanged();
5601 * make the given alignmentPanel the currently selected tab
5603 * @param alignmentPanel
5605 public void setDisplayedView(AlignmentPanel alignmentPanel)
5607 if (!viewport.getSequenceSetId()
5608 .equals(alignmentPanel.av.getSequenceSetId()))
5610 throw new Error(MessageManager.getString(
5611 "error.implementation_error_cannot_show_view_alignment_frame"));
5613 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5614 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5616 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5621 * Action on selection of menu options to Show or Hide annotations.
5624 * @param forSequences
5625 * update sequence-related annotations
5626 * @param forAlignment
5627 * update non-sequence-related annotations
5630 protected void setAnnotationsVisibility(boolean visible,
5631 boolean forSequences, boolean forAlignment)
5633 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5634 .getAlignmentAnnotation();
5639 for (AlignmentAnnotation aa : anns)
5642 * don't display non-positional annotations on an alignment
5644 if (aa.annotations == null)
5648 boolean apply = (aa.sequenceRef == null && forAlignment)
5649 || (aa.sequenceRef != null && forSequences);
5652 aa.visible = visible;
5655 alignPanel.validateAnnotationDimensions(true);
5656 alignPanel.alignmentChanged();
5660 * Store selected annotation sort order for the view and repaint.
5663 protected void sortAnnotations_actionPerformed()
5665 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5667 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5668 alignPanel.paintAlignment(false, false);
5673 * @return alignment panels in this alignment frame
5675 public List<? extends AlignmentViewPanel> getAlignPanels()
5677 // alignPanels is never null
5678 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5683 * Open a new alignment window, with the cDNA associated with this (protein)
5684 * alignment, aligned as is the protein.
5686 protected void viewAsCdna_actionPerformed()
5688 // TODO no longer a menu action - refactor as required
5689 final AlignmentI alignment = getViewport().getAlignment();
5690 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5691 if (mappings == null)
5695 List<SequenceI> cdnaSeqs = new ArrayList<>();
5696 for (SequenceI aaSeq : alignment.getSequences())
5698 for (AlignedCodonFrame acf : mappings)
5700 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5704 * There is a cDNA mapping for this protein sequence - add to new
5705 * alignment. It will share the same dataset sequence as other mapped
5706 * cDNA (no new mappings need to be created).
5708 final Sequence newSeq = new Sequence(dnaSeq);
5709 newSeq.setDatasetSequence(dnaSeq);
5710 cdnaSeqs.add(newSeq);
5714 if (cdnaSeqs.size() == 0)
5716 // show a warning dialog no mapped cDNA
5719 AlignmentI cdna = new Alignment(
5720 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5721 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5722 AlignFrame.DEFAULT_HEIGHT);
5723 cdna.alignAs(alignment);
5724 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5726 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5727 AlignFrame.DEFAULT_HEIGHT);
5731 * Set visibility of dna/protein complement view (available when shown in a
5737 protected void showComplement_actionPerformed(boolean show)
5739 SplitContainerI sf = getSplitViewContainer();
5742 sf.setComplementVisible(this, show);
5747 * Generate the reverse (optionally complemented) of the selected sequences,
5748 * and add them to the alignment
5751 protected void showReverse_actionPerformed(boolean complement)
5753 AlignmentI al = null;
5756 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5757 al = dna.reverseCdna(complement);
5758 viewport.addAlignment(al, "");
5759 addHistoryItem(new EditCommand(
5760 MessageManager.getString("label.add_sequences"), Action.PASTE,
5761 al.getSequencesArray(), 0, al.getWidth(),
5762 viewport.getAlignment()));
5763 } catch (Exception ex)
5765 System.err.println(ex.getMessage());
5771 * Try to run a script in the Groovy console, having first ensured that this
5772 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5773 * be targeted at this alignment.
5776 protected void runGroovy_actionPerformed()
5778 Jalview.setCurrentAlignFrame(this);
5779 groovy.ui.Console console = Desktop.getGroovyConsole();
5780 if (console != null)
5784 console.runScript();
5785 } catch (Exception ex)
5787 System.err.println((ex.toString()));
5788 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5789 MessageManager.getString("label.couldnt_run_groovy_script"),
5790 MessageManager.getString("label.groovy_support_failed"),
5791 JvOptionPane.ERROR_MESSAGE);
5796 System.err.println("Can't run Groovy script as console not found");
5801 * Hides columns containing (or not containing) a specified feature, provided
5802 * that would not leave all columns hidden
5804 * @param featureType
5805 * @param columnsContaining
5808 public boolean hideFeatureColumns(String featureType,
5809 boolean columnsContaining)
5811 boolean notForHiding = avc.markColumnsContainingFeatures(
5812 columnsContaining, false, false, featureType);
5815 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5816 false, featureType))
5818 getViewport().hideSelectedColumns();
5826 protected void selectHighlightedColumns_actionPerformed(
5827 ActionEvent actionEvent)
5829 // include key modifier check in case user selects from menu
5830 avc.markHighlightedColumns(
5831 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5832 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5833 | ActionEvent.CTRL_MASK)) != 0);
5837 * Rebuilds the Colour menu, including any user-defined colours which have
5838 * been loaded either on startup or during the session
5840 public void buildColourMenu()
5842 colourMenu.removeAll();
5844 colourMenu.add(applyToAllGroups);
5845 colourMenu.add(textColour);
5846 colourMenu.addSeparator();
5848 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5849 viewport.getAlignment(), false);
5851 colourMenu.add(annotationColour);
5852 bg.add(annotationColour);
5853 colourMenu.addSeparator();
5854 colourMenu.add(conservationMenuItem);
5855 colourMenu.add(modifyConservation);
5856 colourMenu.add(abovePIDThreshold);
5857 colourMenu.add(modifyPID);
5859 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5860 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5864 * Open a dialog (if not already open) that allows the user to select and
5865 * calculate PCA or Tree analysis
5867 protected void openTreePcaDialog()
5869 if (alignPanel.getCalculationDialog() == null)
5871 new CalculationChooser(AlignFrame.this);
5876 * Sets the status of the HMMER menu
5878 public void updateHMMERStatus()
5880 hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
5884 protected void loadVcf_actionPerformed()
5886 JalviewFileChooser chooser = new JalviewFileChooser(
5887 Cache.getProperty("LAST_DIRECTORY"));
5888 chooser.setFileView(new JalviewFileView());
5889 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5890 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5892 int value = chooser.showOpenDialog(null);
5894 if (value == JalviewFileChooser.APPROVE_OPTION)
5896 String choice = chooser.getSelectedFile().getPath();
5897 Cache.setProperty("LAST_DIRECTORY", choice);
5898 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5899 new VCFLoader(choice).loadVCF(seqs, this);
5905 class PrintThread extends Thread
5909 public PrintThread(AlignmentPanel ap)
5914 static PageFormat pf;
5919 PrinterJob printJob = PrinterJob.getPrinterJob();
5923 printJob.setPrintable(ap, pf);
5927 printJob.setPrintable(ap);
5930 if (printJob.printDialog())
5935 } catch (Exception PrintException)
5937 PrintException.printStackTrace();