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.io.AlignmentProperties;
73 import jalview.io.AnnotationFile;
74 import jalview.io.BackupFiles;
75 import jalview.io.BioJsHTMLOutput;
76 import jalview.io.DataSourceType;
77 import jalview.io.FileFormat;
78 import jalview.io.FileFormatI;
79 import jalview.io.FileFormats;
80 import jalview.io.FileLoader;
81 import jalview.io.FileParse;
82 import jalview.io.FormatAdapter;
83 import jalview.io.HtmlSvgOutput;
84 import jalview.io.IdentifyFile;
85 import jalview.io.JPredFile;
86 import jalview.io.JalviewFileChooser;
87 import jalview.io.JalviewFileView;
88 import jalview.io.JnetAnnotationMaker;
89 import jalview.io.NewickFile;
90 import jalview.io.ScoreMatrixFile;
91 import jalview.io.TCoffeeScoreFile;
92 import jalview.io.vcf.VCFLoader;
93 import jalview.jbgui.GAlignFrame;
94 import jalview.schemes.ColourSchemeI;
95 import jalview.schemes.ColourSchemes;
96 import jalview.schemes.ResidueColourScheme;
97 import jalview.schemes.TCoffeeColourScheme;
98 import jalview.util.MessageManager;
99 import jalview.viewmodel.AlignmentViewport;
100 import jalview.viewmodel.ViewportRanges;
101 import jalview.ws.DBRefFetcher;
102 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
103 import jalview.ws.jws1.Discoverer;
104 import jalview.ws.jws2.Jws2Discoverer;
105 import jalview.ws.jws2.jabaws2.Jws2Instance;
106 import jalview.ws.params.ArgumentI;
107 import jalview.ws.params.ParamDatastoreI;
108 import jalview.ws.params.WsParamSetI;
109 import jalview.ws.seqfetcher.DbSourceProxy;
111 import java.awt.BorderLayout;
112 import java.awt.Component;
113 import java.awt.Rectangle;
114 import java.awt.Toolkit;
115 import java.awt.datatransfer.Clipboard;
116 import java.awt.datatransfer.DataFlavor;
117 import java.awt.datatransfer.StringSelection;
118 import java.awt.datatransfer.Transferable;
119 import java.awt.dnd.DnDConstants;
120 import java.awt.dnd.DropTargetDragEvent;
121 import java.awt.dnd.DropTargetDropEvent;
122 import java.awt.dnd.DropTargetEvent;
123 import java.awt.dnd.DropTargetListener;
124 import java.awt.event.ActionEvent;
125 import java.awt.event.ActionListener;
126 import java.awt.event.FocusAdapter;
127 import java.awt.event.FocusEvent;
128 import java.awt.event.ItemEvent;
129 import java.awt.event.ItemListener;
130 import java.awt.event.KeyAdapter;
131 import java.awt.event.KeyEvent;
132 import java.awt.event.MouseEvent;
133 import java.awt.print.PageFormat;
134 import java.awt.print.PrinterJob;
135 import java.beans.PropertyChangeEvent;
137 import java.io.FileWriter;
138 import java.io.IOException;
139 import java.io.PrintWriter;
141 import java.util.ArrayList;
142 import java.util.Arrays;
143 import java.util.Deque;
144 import java.util.HashSet;
145 import java.util.List;
146 import java.util.Set;
147 import java.util.Vector;
149 import javax.swing.ButtonGroup;
150 import javax.swing.JCheckBoxMenuItem;
151 import javax.swing.JEditorPane;
152 import javax.swing.JFileChooser;
153 import javax.swing.JInternalFrame;
154 import javax.swing.JLayeredPane;
155 import javax.swing.JMenu;
156 import javax.swing.JMenuItem;
157 import javax.swing.JOptionPane;
158 import javax.swing.JScrollPane;
159 import javax.swing.SwingUtilities;
165 * @version $Revision$
167 public class AlignFrame extends GAlignFrame implements DropTargetListener,
168 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
170 public static final int DEFAULT_WIDTH = 700;
172 public static final int DEFAULT_HEIGHT = 500;
175 * The currently displayed panel (selected tabbed view if more than one)
177 public AlignmentPanel alignPanel;
179 AlignViewport viewport;
181 public AlignViewControllerI avc;
183 List<AlignmentPanel> alignPanels = new ArrayList<>();
186 * Last format used to load or save alignments in this window
188 FileFormatI currentFileFormat = null;
191 * Current filename for this alignment
193 String fileName = null;
197 * Creates a new AlignFrame object with specific width and height.
203 public AlignFrame(AlignmentI al, int width, int height)
205 this(al, null, width, height);
209 * Creates a new AlignFrame object with specific width, height and
215 * @param sequenceSetId
217 public AlignFrame(AlignmentI al, int width, int height,
218 String sequenceSetId)
220 this(al, null, width, height, sequenceSetId);
224 * Creates a new AlignFrame object with specific width, height and
230 * @param sequenceSetId
233 public AlignFrame(AlignmentI al, int width, int height,
234 String sequenceSetId, String viewId)
236 this(al, null, width, height, sequenceSetId, viewId);
240 * new alignment window with hidden columns
244 * @param hiddenColumns
245 * ColumnSelection or null
247 * Width of alignment frame
251 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
254 this(al, hiddenColumns, width, height, null);
258 * Create alignment frame for al with hiddenColumns, a specific width and
259 * height, and specific sequenceId
262 * @param hiddenColumns
265 * @param sequenceSetId
268 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
269 int height, String sequenceSetId)
271 this(al, hiddenColumns, width, height, sequenceSetId, null);
275 * Create alignment frame for al with hiddenColumns, a specific width and
276 * height, and specific sequenceId
279 * @param hiddenColumns
282 * @param sequenceSetId
287 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
288 int height, String sequenceSetId, String viewId)
290 setSize(width, height);
292 if (al.getDataset() == null)
297 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
299 alignPanel = new AlignmentPanel(this, viewport);
301 addAlignmentPanel(alignPanel, true);
305 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
306 HiddenColumns hiddenColumns, int width, int height)
308 setSize(width, height);
310 if (al.getDataset() == null)
315 viewport = new AlignViewport(al, hiddenColumns);
317 if (hiddenSeqs != null && hiddenSeqs.length > 0)
319 viewport.hideSequence(hiddenSeqs);
321 alignPanel = new AlignmentPanel(this, viewport);
322 addAlignmentPanel(alignPanel, true);
327 * Make a new AlignFrame from existing alignmentPanels
334 public AlignFrame(AlignmentPanel ap)
338 addAlignmentPanel(ap, false);
343 * initalise the alignframe from the underlying viewport data and the
348 if (!Jalview.isHeadlessMode())
350 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
353 avc = new jalview.controller.AlignViewController(this, viewport,
355 if (viewport.getAlignmentConservationAnnotation() == null)
357 // BLOSUM62Colour.setEnabled(false);
358 conservationMenuItem.setEnabled(false);
359 modifyConservation.setEnabled(false);
360 // PIDColour.setEnabled(false);
361 // abovePIDThreshold.setEnabled(false);
362 // modifyPID.setEnabled(false);
365 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
368 if (sortby.equals("Id"))
370 sortIDMenuItem_actionPerformed(null);
372 else if (sortby.equals("Pairwise Identity"))
374 sortPairwiseMenuItem_actionPerformed(null);
378 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
380 setMenusFromViewport(viewport);
381 buildSortByAnnotationScoresMenu();
382 calculateTree.addActionListener(new ActionListener()
386 public void actionPerformed(ActionEvent e)
393 if (Desktop.desktop != null)
395 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
396 addServiceListeners();
400 if (viewport.getWrapAlignment())
402 wrapMenuItem_actionPerformed(null);
405 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
407 this.overviewMenuItem_actionPerformed(null);
412 final List<AlignmentPanel> selviews = new ArrayList<>();
413 final List<AlignmentPanel> origview = new ArrayList<>();
414 final String menuLabel = MessageManager
415 .getString("label.copy_format_from");
416 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
417 new ViewSetProvider()
421 public AlignmentPanel[] getAllAlignmentPanels()
424 origview.add(alignPanel);
425 // make an array of all alignment panels except for this one
426 List<AlignmentPanel> aps = new ArrayList<>(
427 Arrays.asList(Desktop.getAlignmentPanels(null)));
428 aps.remove(AlignFrame.this.alignPanel);
429 return aps.toArray(new AlignmentPanel[aps.size()]);
431 }, selviews, new ItemListener()
435 public void itemStateChanged(ItemEvent e)
437 if (origview.size() > 0)
439 final AlignmentPanel ap = origview.get(0);
442 * Copy the ViewStyle of the selected panel to 'this one'.
443 * Don't change value of 'scaleProteinAsCdna' unless copying
446 ViewStyleI vs = selviews.get(0).getAlignViewport()
448 boolean fromSplitFrame = selviews.get(0)
449 .getAlignViewport().getCodingComplement() != null;
452 vs.setScaleProteinAsCdna(ap.getAlignViewport()
453 .getViewStyle().isScaleProteinAsCdna());
455 ap.getAlignViewport().setViewStyle(vs);
458 * Also rescale ViewStyle of SplitFrame complement if there is
459 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
460 * the whole ViewStyle (allow cDNA protein to have different
463 AlignViewportI complement = ap.getAlignViewport()
464 .getCodingComplement();
465 if (complement != null && vs.isScaleProteinAsCdna())
467 AlignFrame af = Desktop.getAlignFrameFor(complement);
468 ((SplitFrame) af.getSplitViewContainer())
470 af.setMenusForViewport();
474 ap.setSelected(true);
475 ap.alignFrame.setMenusForViewport();
480 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
481 .indexOf("devel") > -1
482 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
483 .indexOf("test") > -1)
485 formatMenu.add(vsel);
487 addFocusListener(new FocusAdapter()
490 public void focusGained(FocusEvent e)
492 Jalview.setCurrentAlignFrame(AlignFrame.this);
499 * Change the filename and format for the alignment, and enable the 'reload'
500 * button functionality.
507 public void setFileName(String file, FileFormatI format)
510 setFileFormat(format);
511 reload.setEnabled(true);
515 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
518 void addKeyListener()
520 addKeyListener(new KeyAdapter()
523 public void keyPressed(KeyEvent evt)
525 if (viewport.cursorMode
526 && ((evt.getKeyCode() >= KeyEvent.VK_0
527 && evt.getKeyCode() <= KeyEvent.VK_9)
528 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
529 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
530 && Character.isDigit(evt.getKeyChar()))
532 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
535 switch (evt.getKeyCode())
538 case 27: // escape key
539 deselectAllSequenceMenuItem_actionPerformed(null);
543 case KeyEvent.VK_DOWN:
544 if (evt.isAltDown() || !viewport.cursorMode)
546 moveSelectedSequences(false);
548 if (viewport.cursorMode)
550 alignPanel.getSeqPanel().moveCursor(0, 1);
555 if (evt.isAltDown() || !viewport.cursorMode)
557 moveSelectedSequences(true);
559 if (viewport.cursorMode)
561 alignPanel.getSeqPanel().moveCursor(0, -1);
566 case KeyEvent.VK_LEFT:
567 if (evt.isAltDown() || !viewport.cursorMode)
569 slideSequences(false,
570 alignPanel.getSeqPanel().getKeyboardNo1());
574 alignPanel.getSeqPanel().moveCursor(-1, 0);
579 case KeyEvent.VK_RIGHT:
580 if (evt.isAltDown() || !viewport.cursorMode)
582 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
586 alignPanel.getSeqPanel().moveCursor(1, 0);
590 case KeyEvent.VK_SPACE:
591 if (viewport.cursorMode)
593 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
594 || evt.isShiftDown() || evt.isAltDown());
598 // case KeyEvent.VK_A:
599 // if (viewport.cursorMode)
601 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
602 // //System.out.println("A");
606 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
607 * System.out.println("closing bracket"); } break;
609 case KeyEvent.VK_DELETE:
610 case KeyEvent.VK_BACK_SPACE:
611 if (!viewport.cursorMode)
613 cut_actionPerformed(null);
617 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
618 || evt.isShiftDown() || evt.isAltDown());
624 if (viewport.cursorMode)
626 alignPanel.getSeqPanel().setCursorRow();
630 if (viewport.cursorMode && !evt.isControlDown())
632 alignPanel.getSeqPanel().setCursorColumn();
636 if (viewport.cursorMode)
638 alignPanel.getSeqPanel().setCursorPosition();
642 case KeyEvent.VK_ENTER:
643 case KeyEvent.VK_COMMA:
644 if (viewport.cursorMode)
646 alignPanel.getSeqPanel().setCursorRowAndColumn();
651 if (viewport.cursorMode)
653 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
657 if (viewport.cursorMode)
659 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
664 viewport.cursorMode = !viewport.cursorMode;
665 statusBar.setText(MessageManager
666 .formatMessage("label.keyboard_editing_mode", new String[]
667 { (viewport.cursorMode ? "on" : "off") }));
668 if (viewport.cursorMode)
670 ViewportRanges ranges = viewport.getRanges();
671 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
673 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
676 alignPanel.getSeqPanel().seqCanvas.repaint();
682 Help.showHelpWindow();
683 } catch (Exception ex)
685 ex.printStackTrace();
690 boolean toggleSeqs = !evt.isControlDown();
691 boolean toggleCols = !evt.isShiftDown();
692 toggleHiddenRegions(toggleSeqs, toggleCols);
697 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
698 boolean modifyExisting = true; // always modify, don't clear
699 // evt.isShiftDown();
700 boolean invertHighlighted = evt.isAltDown();
701 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
705 case KeyEvent.VK_PAGE_UP:
706 viewport.getRanges().pageUp();
708 case KeyEvent.VK_PAGE_DOWN:
709 viewport.getRanges().pageDown();
715 public void keyReleased(KeyEvent evt)
717 switch (evt.getKeyCode())
719 case KeyEvent.VK_LEFT:
720 if (evt.isAltDown() || !viewport.cursorMode)
722 viewport.firePropertyChange("alignment", null,
723 viewport.getAlignment().getSequences());
727 case KeyEvent.VK_RIGHT:
728 if (evt.isAltDown() || !viewport.cursorMode)
730 viewport.firePropertyChange("alignment", null,
731 viewport.getAlignment().getSequences());
739 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
741 ap.alignFrame = this;
742 avc = new jalview.controller.AlignViewController(this, viewport,
747 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
749 int aSize = alignPanels.size();
751 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
753 if (aSize == 1 && ap.av.getViewName() == null)
755 this.getContentPane().add(ap, BorderLayout.CENTER);
761 setInitialTabVisible();
764 expandViews.setEnabled(true);
765 gatherViews.setEnabled(true);
766 tabbedPane.addTab(ap.av.getViewName(), ap);
768 ap.setVisible(false);
773 if (ap.av.isPadGaps())
775 ap.av.getAlignment().padGaps();
777 ap.av.updateConservation(ap);
778 ap.av.updateConsensus(ap);
779 ap.av.updateStrucConsensus(ap);
780 ap.av.initInformationWorker(ap);
784 public void setInitialTabVisible()
786 expandViews.setEnabled(true);
787 gatherViews.setEnabled(true);
788 tabbedPane.setVisible(true);
789 AlignmentPanel first = alignPanels.get(0);
790 tabbedPane.addTab(first.av.getViewName(), first);
791 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
794 public AlignViewport getViewport()
799 /* Set up intrinsic listeners for dynamically generated GUI bits. */
800 private void addServiceListeners()
802 final java.beans.PropertyChangeListener thisListener;
803 Desktop.instance.addJalviewPropertyChangeListener("services",
804 thisListener = new java.beans.PropertyChangeListener()
807 public void propertyChange(PropertyChangeEvent evt)
809 // // System.out.println("Discoverer property change.");
810 // if (evt.getPropertyName().equals("services"))
812 SwingUtilities.invokeLater(new Runnable()
819 "Rebuild WS Menu for service change");
820 BuildWebServiceMenu();
827 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
830 public void internalFrameClosed(
831 javax.swing.event.InternalFrameEvent evt)
833 // System.out.println("deregistering discoverer listener");
834 Desktop.instance.removeJalviewPropertyChangeListener("services",
836 closeMenuItem_actionPerformed(true);
839 // Finally, build the menu once to get current service state
840 new Thread(new Runnable()
845 BuildWebServiceMenu();
851 * Configure menu items that vary according to whether the alignment is
852 * nucleotide or protein
854 public void setGUINucleotide()
856 AlignmentI al = getViewport().getAlignment();
857 boolean nucleotide = al.isNucleotide();
859 loadVcf.setVisible(nucleotide);
860 showTranslation.setVisible(nucleotide);
861 showReverse.setVisible(nucleotide);
862 showReverseComplement.setVisible(nucleotide);
863 conservationMenuItem.setEnabled(!nucleotide);
865 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
866 showGroupConservation.setEnabled(!nucleotide);
868 showComplementMenuItem
869 .setText(nucleotide ? MessageManager.getString("label.protein")
870 : MessageManager.getString("label.nucleotide"));
874 * set up menus for the current viewport. This may be called after any
875 * operation that affects the data in the current view (selection changed,
876 * etc) to update the menus to reflect the new state.
879 public void setMenusForViewport()
881 setMenusFromViewport(viewport);
885 * Need to call this method when tabs are selected for multiple views, or when
886 * loading from Jalview2XML.java
891 public void setMenusFromViewport(AlignViewport av)
893 padGapsMenuitem.setSelected(av.isPadGaps());
894 colourTextMenuItem.setSelected(av.isShowColourText());
895 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
896 modifyPID.setEnabled(abovePIDThreshold.isSelected());
897 conservationMenuItem.setSelected(av.getConservationSelected());
898 modifyConservation.setEnabled(conservationMenuItem.isSelected());
899 seqLimits.setSelected(av.getShowJVSuffix());
900 idRightAlign.setSelected(av.isRightAlignIds());
901 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
902 renderGapsMenuItem.setSelected(av.isRenderGaps());
903 wrapMenuItem.setSelected(av.getWrapAlignment());
904 scaleAbove.setVisible(av.getWrapAlignment());
905 scaleLeft.setVisible(av.getWrapAlignment());
906 scaleRight.setVisible(av.getWrapAlignment());
907 annotationPanelMenuItem.setState(av.isShowAnnotation());
909 * Show/hide annotations only enabled if annotation panel is shown
911 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
912 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
913 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
914 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
915 viewBoxesMenuItem.setSelected(av.getShowBoxes());
916 viewTextMenuItem.setSelected(av.getShowText());
917 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
918 showGroupConsensus.setSelected(av.isShowGroupConsensus());
919 showGroupConservation.setSelected(av.isShowGroupConservation());
920 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
921 showSequenceLogo.setSelected(av.isShowSequenceLogo());
922 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
923 showInformationHistogram.setSelected(av.isShowInformationHistogram());
924 showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
925 normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
927 ColourMenuHelper.setColourSelected(colourMenu,
928 av.getGlobalColourScheme());
930 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
931 hiddenMarkers.setState(av.getShowHiddenMarkers());
932 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
933 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
934 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
935 autoCalculate.setSelected(av.autoCalculateConsensus);
936 sortByTree.setSelected(av.sortByTree);
937 listenToViewSelections.setSelected(av.followSelection);
939 showProducts.setEnabled(canShowProducts());
940 setGroovyEnabled(Desktop.getGroovyConsole() != null);
946 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
950 public void setGroovyEnabled(boolean b)
952 runGroovy.setEnabled(b);
955 private IProgressIndicator progressBar;
960 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
963 public void setProgressBar(String message, long id)
965 progressBar.setProgressBar(message, id);
969 public void registerHandler(final long id,
970 final IProgressIndicatorHandler handler)
972 progressBar.registerHandler(id, handler);
977 * @return true if any progress bars are still active
980 public boolean operationInProgress()
982 return progressBar.operationInProgress();
986 * Sets the text of the status bar. Note that setting a null or empty value
987 * will cause the status bar to be hidden, with possibly undesirable flicker
988 * of the screen layout.
991 public void setStatus(String text)
993 statusBar.setText(text == null || text.isEmpty() ? " " : text);
997 * Added so Castor Mapping file can obtain Jalview Version
999 public String getVersion()
1001 return jalview.bin.Cache.getProperty("VERSION");
1004 public FeatureRenderer getFeatureRenderer()
1006 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1010 public void fetchSequence_actionPerformed(ActionEvent e)
1012 new jalview.gui.SequenceFetcher(this);
1016 public void addFromFile_actionPerformed(ActionEvent e)
1018 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1022 public void hmmBuild_actionPerformed(boolean withDefaults)
1024 if (!alignmentIsSufficient(1))
1030 * get default parameters, and optionally show a dialog
1031 * to allow them to be modified
1033 ParamDatastoreI store = HMMERParamStore.forBuild(viewport);
1034 List<ArgumentI> args = store.getServiceParameters();
1038 WsParamSetI set = new HMMERPreset();
1039 WsJobParameters params = new WsJobParameters(store, set, args);
1040 if (params.showRunDialog())
1042 args = params.getJobParams();
1046 return; // user cancelled
1049 new Thread(new HMMBuild(this, args)).start();
1053 public void hmmAlign_actionPerformed(boolean withDefaults)
1055 if (!(checkForHMM() && alignmentIsSufficient(2)))
1061 * get default parameters, and optionally show a dialog
1062 * to allow them to be modified
1064 ParamDatastoreI store = HMMERParamStore.forAlign(viewport);
1065 List<ArgumentI> args = store.getServiceParameters();
1069 WsParamSetI set = new HMMERPreset();
1070 WsJobParameters params = new WsJobParameters(store, set, args);
1071 if (params.showRunDialog())
1073 args = params.getJobParams();
1077 return; // user cancelled
1080 new Thread(new HMMAlign(this, args)).start();
1084 public void hmmSearch_actionPerformed(boolean withDefaults)
1092 * get default parameters, and (if requested) show
1093 * dialog to allow modification
1095 ParamDatastoreI store = HMMERParamStore.forSearch(viewport);
1096 List<ArgumentI> args = store.getServiceParameters();
1100 WsParamSetI set = new HMMERPreset();
1101 WsJobParameters params = new WsJobParameters(store, set, args);
1102 if (params.showRunDialog())
1104 args = params.getJobParams();
1108 return; // user cancelled
1111 new Thread(new HMMSearch(this, args)).start();
1112 alignPanel.repaint();
1116 * Checks if the alignment has at least one hidden Markov model, if not shows
1117 * a dialog advising to run hmmbuild or load an HMM profile
1121 private boolean checkForHMM()
1123 if (viewport.getAlignment().getHmmSequences().isEmpty())
1125 JOptionPane.showMessageDialog(this,
1126 MessageManager.getString("warn.no_hmm"));
1133 * Checks if the alignment contains the required number of sequences.
1138 public boolean alignmentIsSufficient(int required)
1140 if (getViewport().getAlignment().getSequences().size() < required)
1142 JOptionPane.showMessageDialog(this,
1143 MessageManager.getString("label.not_enough_sequences"));
1150 * Opens a file browser and adds the selected file, if in Fasta, Stockholm or
1151 * Pfam format, to the list held under preference key "HMMSEARCH_DBS" (as a
1152 * comma-separated list)
1155 public void addDatabase_actionPerformed() throws IOException
1157 if (Cache.getProperty(Preferences.HMMSEARCH_DBS) == null)
1159 Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
1162 String path = openFileChooser(false);
1163 if (path != null && new File(path).exists())
1165 IdentifyFile identifier = new IdentifyFile();
1166 FileFormatI format = identifier.identify(path, DataSourceType.FILE);
1167 if (format == FileFormat.Fasta || format == FileFormat.Stockholm
1168 || format == FileFormat.Pfam)
1170 String currentDbPaths = Cache
1171 .getProperty(Preferences.HMMSEARCH_DBS);
1172 currentDbPaths += Preferences.COMMA + path;
1173 Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
1177 JOptionPane.showMessageDialog(this,
1178 MessageManager.getString("warn.invalid_format"));
1184 * Opens a file chooser, optionally restricted to selecting folders
1185 * (directories) only. Answers the path to the selected file or folder, or
1186 * null if none is chosen.
1191 protected String openFileChooser(boolean forFolder)
1193 // TODO duplicates GPreferences method - relocate to JalviewFileChooser?
1194 String choice = null;
1195 JFileChooser chooser = new JFileChooser();
1198 chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
1200 chooser.setDialogTitle(
1201 MessageManager.getString("label.open_local_file"));
1202 chooser.setToolTipText(MessageManager.getString("action.open"));
1204 int value = chooser.showOpenDialog(this);
1206 if (value == JFileChooser.APPROVE_OPTION)
1208 choice = chooser.getSelectedFile().getPath();
1214 public void reload_actionPerformed(ActionEvent e)
1216 if (fileName != null)
1218 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1219 // originating file's format
1220 // TODO: work out how to recover feature settings for correct view(s) when
1221 // file is reloaded.
1222 if (FileFormat.Jalview.equals(currentFileFormat))
1224 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1225 for (int i = 0; i < frames.length; i++)
1227 if (frames[i] instanceof AlignFrame && frames[i] != this
1228 && ((AlignFrame) frames[i]).fileName != null
1229 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1233 frames[i].setSelected(true);
1234 Desktop.instance.closeAssociatedWindows();
1235 } catch (java.beans.PropertyVetoException ex)
1241 Desktop.instance.closeAssociatedWindows();
1243 FileLoader loader = new FileLoader();
1244 DataSourceType protocol = fileName.startsWith("http:")
1245 ? DataSourceType.URL
1246 : DataSourceType.FILE;
1247 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1251 Rectangle bounds = this.getBounds();
1253 FileLoader loader = new FileLoader();
1254 DataSourceType protocol = fileName.startsWith("http:")
1255 ? DataSourceType.URL
1256 : DataSourceType.FILE;
1257 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1258 protocol, currentFileFormat);
1260 newframe.setBounds(bounds);
1261 if (featureSettings != null && featureSettings.isShowing())
1263 final Rectangle fspos = featureSettings.frame.getBounds();
1264 // TODO: need a 'show feature settings' function that takes bounds -
1265 // need to refactor Desktop.addFrame
1266 newframe.featureSettings_actionPerformed(null);
1267 final FeatureSettings nfs = newframe.featureSettings;
1268 SwingUtilities.invokeLater(new Runnable()
1273 nfs.frame.setBounds(fspos);
1276 this.featureSettings.close();
1277 this.featureSettings = null;
1279 this.closeMenuItem_actionPerformed(true);
1285 public void addFromText_actionPerformed(ActionEvent e)
1288 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1292 public void addFromURL_actionPerformed(ActionEvent e)
1294 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1298 public void save_actionPerformed(ActionEvent e)
1300 if (fileName == null || (currentFileFormat == null)
1301 || fileName.startsWith("http"))
1303 saveAs_actionPerformed(null);
1307 saveAlignment(fileName, currentFileFormat);
1318 public void saveAs_actionPerformed(ActionEvent e)
1320 String format = currentFileFormat == null ? null
1321 : currentFileFormat.getName();
1322 JalviewFileChooser chooser = JalviewFileChooser
1323 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1325 chooser.setFileView(new JalviewFileView());
1326 chooser.setDialogTitle(
1327 MessageManager.getString("label.save_alignment_to_file"));
1328 chooser.setToolTipText(MessageManager.getString("action.save"));
1330 int value = chooser.showSaveDialog(this);
1332 if (value == JalviewFileChooser.APPROVE_OPTION)
1334 currentFileFormat = chooser.getSelectedFormat();
1335 while (currentFileFormat == null)
1337 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1338 MessageManager.getString(
1339 "label.select_file_format_before_saving"),
1340 MessageManager.getString("label.file_format_not_specified"),
1341 JvOptionPane.WARNING_MESSAGE);
1342 currentFileFormat = chooser.getSelectedFormat();
1343 value = chooser.showSaveDialog(this);
1344 if (value != JalviewFileChooser.APPROVE_OPTION)
1350 fileName = chooser.getSelectedFile().getPath();
1352 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1354 Cache.setProperty("LAST_DIRECTORY", fileName);
1355 saveAlignment(fileName, currentFileFormat);
1359 public boolean saveAlignment(String file, FileFormatI format)
1361 boolean success = true;
1363 if (FileFormat.Jalview.equals(format))
1365 String shortName = title;
1367 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1369 shortName = shortName.substring(
1370 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1373 success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1376 statusBar.setText(MessageManager.formatMessage(
1377 "label.successfully_saved_to_file_in_format", new Object[]
1378 { fileName, format }));
1383 AlignmentExportData exportData = getAlignmentForExport(format,
1385 if (exportData.getSettings().isCancelled())
1389 FormatAdapter f = new FormatAdapter(alignPanel,
1390 exportData.getSettings());
1391 String output = f.formatSequences(format, exportData.getAlignment(), // class
1395 // occur in the distant future
1396 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1397 f.getCacheSuffixDefault(format),
1398 viewport.getAlignment().getHiddenColumns());
1406 // create backupfiles object and get new temp filename destination
1407 BackupFiles backupfiles = new BackupFiles(file);
1411 PrintWriter out = new PrintWriter(
1412 new FileWriter(backupfiles.getTempFilePath()));
1416 this.setTitle(file);
1417 statusBar.setText(MessageManager.formatMessage(
1418 "label.successfully_saved_to_file_in_format", new Object[]
1419 { fileName, format.getName() }));
1420 } catch (Exception ex)
1423 ex.printStackTrace();
1426 backupfiles.setWriteSuccess(success);
1427 // do the backup file roll and rename the temp file to actual file
1428 success = backupfiles.rollBackupsAndRenameTempFile();
1435 JvOptionPane.showInternalMessageDialog(this, MessageManager
1436 .formatMessage("label.couldnt_save_file", new Object[]
1438 MessageManager.getString("label.error_saving_file"),
1439 JvOptionPane.WARNING_MESSAGE);
1445 private void warningMessage(String warning, String title)
1447 if (new jalview.util.Platform().isHeadless())
1449 System.err.println("Warning: " + title + "\nWarning: " + warning);
1454 JvOptionPane.showInternalMessageDialog(this, warning, title,
1455 JvOptionPane.WARNING_MESSAGE);
1467 protected void outputText_actionPerformed(ActionEvent e)
1469 FileFormatI fileFormat = FileFormats.getInstance()
1470 .forName(e.getActionCommand());
1471 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1473 if (exportData.getSettings().isCancelled())
1477 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1478 cap.setForInput(null);
1481 FileFormatI format = fileFormat;
1482 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1483 .formatSequences(format, exportData.getAlignment(),
1484 exportData.getOmitHidden(),
1485 exportData.getStartEndPostions(),
1486 viewport.getAlignment().getHiddenColumns()));
1487 Desktop.addInternalFrame(cap, MessageManager
1488 .formatMessage("label.alignment_output_command", new Object[]
1489 { e.getActionCommand() }), 600, 500);
1490 } catch (OutOfMemoryError oom)
1492 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1499 public static AlignmentExportData getAlignmentForExport(
1500 FileFormatI format, AlignViewportI viewport,
1501 AlignExportSettingI exportSettings)
1503 AlignmentI alignmentToExport = null;
1504 AlignExportSettingI settings = exportSettings;
1505 String[] omitHidden = null;
1507 HiddenSequences hiddenSeqs = viewport.getAlignment()
1508 .getHiddenSequences();
1510 alignmentToExport = viewport.getAlignment();
1512 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1513 if (settings == null)
1515 settings = new AlignExportSettings(hasHiddenSeqs,
1516 viewport.hasHiddenColumns(), format);
1518 // settings.isExportAnnotations();
1520 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1522 omitHidden = viewport.getViewAsString(false,
1523 settings.isExportHiddenSequences());
1526 int[] alignmentStartEnd = new int[2];
1527 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1529 alignmentToExport = hiddenSeqs.getFullAlignment();
1533 alignmentToExport = viewport.getAlignment();
1535 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1536 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1537 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1538 omitHidden, alignmentStartEnd, settings);
1549 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1551 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1552 htmlSVG.exportHTML(null);
1556 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1558 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1559 bjs.exportHTML(null);
1562 public void createImageMap(File file, String image)
1564 alignPanel.makePNGImageMap(file, image);
1574 public void createPNG(File f)
1576 alignPanel.makePNG(f);
1586 public void createEPS(File f)
1588 alignPanel.makeEPS(f);
1592 public void createSVG(File f)
1594 alignPanel.makeSVG(f);
1598 public void pageSetup_actionPerformed(ActionEvent e)
1600 PrinterJob printJob = PrinterJob.getPrinterJob();
1601 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1611 public void printMenuItem_actionPerformed(ActionEvent e)
1613 // Putting in a thread avoids Swing painting problems
1614 PrintThread thread = new PrintThread(alignPanel);
1619 public void exportFeatures_actionPerformed(ActionEvent e)
1621 new AnnotationExporter(alignPanel).exportFeatures();
1625 public void exportAnnotations_actionPerformed(ActionEvent e)
1627 new AnnotationExporter(alignPanel).exportAnnotations();
1631 public void associatedData_actionPerformed(ActionEvent e)
1632 throws IOException, InterruptedException
1634 // Pick the tree file
1635 JalviewFileChooser chooser = new JalviewFileChooser(
1636 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1637 chooser.setFileView(new JalviewFileView());
1638 chooser.setDialogTitle(
1639 MessageManager.getString("label.load_jalview_annotations"));
1640 chooser.setToolTipText(
1641 MessageManager.getString("label.load_jalview_annotations"));
1643 int value = chooser.showOpenDialog(null);
1645 if (value == JalviewFileChooser.APPROVE_OPTION)
1647 String choice = chooser.getSelectedFile().getPath();
1648 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1649 loadJalviewDataFile(choice, null, null, null);
1655 * Close the current view or all views in the alignment frame. If the frame
1656 * only contains one view then the alignment will be removed from memory.
1658 * @param closeAllTabs
1661 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1663 if (alignPanels != null && alignPanels.size() < 2)
1665 closeAllTabs = true;
1670 if (alignPanels != null)
1674 if (this.isClosed())
1676 // really close all the windows - otherwise wait till
1677 // setClosed(true) is called
1678 for (int i = 0; i < alignPanels.size(); i++)
1680 AlignmentPanel ap = alignPanels.get(i);
1687 closeView(alignPanel);
1694 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1695 * be called recursively, with the frame now in 'closed' state
1697 this.setClosed(true);
1699 } catch (Exception ex)
1701 ex.printStackTrace();
1706 * Close the specified panel and close up tabs appropriately.
1708 * @param panelToClose
1710 public void closeView(AlignmentPanel panelToClose)
1712 int index = tabbedPane.getSelectedIndex();
1713 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1714 alignPanels.remove(panelToClose);
1715 panelToClose.closePanel();
1716 panelToClose = null;
1718 tabbedPane.removeTabAt(closedindex);
1719 tabbedPane.validate();
1721 if (index > closedindex || index == tabbedPane.getTabCount())
1723 // modify currently selected tab index if necessary.
1727 this.tabSelectionChanged(index);
1733 void updateEditMenuBar()
1736 if (viewport.getHistoryList().size() > 0)
1738 undoMenuItem.setEnabled(true);
1739 CommandI command = viewport.getHistoryList().peek();
1740 undoMenuItem.setText(MessageManager
1741 .formatMessage("label.undo_command", new Object[]
1742 { command.getDescription() }));
1746 undoMenuItem.setEnabled(false);
1747 undoMenuItem.setText(MessageManager.getString("action.undo"));
1750 if (viewport.getRedoList().size() > 0)
1752 redoMenuItem.setEnabled(true);
1754 CommandI command = viewport.getRedoList().peek();
1755 redoMenuItem.setText(MessageManager
1756 .formatMessage("label.redo_command", new Object[]
1757 { command.getDescription() }));
1761 redoMenuItem.setEnabled(false);
1762 redoMenuItem.setText(MessageManager.getString("action.redo"));
1767 public void addHistoryItem(CommandI command)
1769 if (command.getSize() > 0)
1771 viewport.addToHistoryList(command);
1772 viewport.clearRedoList();
1773 updateEditMenuBar();
1774 viewport.updateHiddenColumns();
1775 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1776 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1777 // viewport.getColumnSelection()
1778 // .getHiddenColumns().size() > 0);
1784 * @return alignment objects for all views
1786 AlignmentI[] getViewAlignments()
1788 if (alignPanels != null)
1790 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1792 for (AlignmentPanel ap : alignPanels)
1794 als[i++] = ap.av.getAlignment();
1798 if (viewport != null)
1800 return new AlignmentI[] { viewport.getAlignment() };
1812 protected void undoMenuItem_actionPerformed(ActionEvent e)
1814 if (viewport.getHistoryList().isEmpty())
1818 CommandI command = viewport.getHistoryList().pop();
1819 viewport.addToRedoList(command);
1820 command.undoCommand(getViewAlignments());
1822 AlignmentViewport originalSource = getOriginatingSource(command);
1823 updateEditMenuBar();
1825 if (originalSource != null)
1827 if (originalSource != viewport)
1830 "Implementation worry: mismatch of viewport origin for undo");
1832 originalSource.updateHiddenColumns();
1833 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1835 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1836 // viewport.getColumnSelection()
1837 // .getHiddenColumns().size() > 0);
1838 originalSource.firePropertyChange("alignment", null,
1839 originalSource.getAlignment().getSequences());
1850 protected void redoMenuItem_actionPerformed(ActionEvent e)
1852 if (viewport.getRedoList().size() < 1)
1857 CommandI command = viewport.getRedoList().pop();
1858 viewport.addToHistoryList(command);
1859 command.doCommand(getViewAlignments());
1861 AlignmentViewport originalSource = getOriginatingSource(command);
1862 updateEditMenuBar();
1864 if (originalSource != null)
1867 if (originalSource != viewport)
1870 "Implementation worry: mismatch of viewport origin for redo");
1872 originalSource.updateHiddenColumns();
1873 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1875 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1876 // viewport.getColumnSelection()
1877 // .getHiddenColumns().size() > 0);
1878 originalSource.firePropertyChange("alignment", null,
1879 originalSource.getAlignment().getSequences());
1883 AlignmentViewport getOriginatingSource(CommandI command)
1885 AlignmentViewport originalSource = null;
1886 // For sequence removal and addition, we need to fire
1887 // the property change event FROM the viewport where the
1888 // original alignment was altered
1889 AlignmentI al = null;
1890 if (command instanceof EditCommand)
1892 EditCommand editCommand = (EditCommand) command;
1893 al = editCommand.getAlignment();
1894 List<Component> comps = PaintRefresher.components
1895 .get(viewport.getSequenceSetId());
1897 for (Component comp : comps)
1899 if (comp instanceof AlignmentPanel)
1901 if (al == ((AlignmentPanel) comp).av.getAlignment())
1903 originalSource = ((AlignmentPanel) comp).av;
1910 if (originalSource == null)
1912 // The original view is closed, we must validate
1913 // the current view against the closed view first
1916 PaintRefresher.validateSequences(al, viewport.getAlignment());
1919 originalSource = viewport;
1922 return originalSource;
1931 public void moveSelectedSequences(boolean up)
1933 SequenceGroup sg = viewport.getSelectionGroup();
1939 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1940 viewport.getHiddenRepSequences(), up);
1941 alignPanel.paintAlignment(true, false);
1944 synchronized void slideSequences(boolean right, int size)
1946 List<SequenceI> sg = new ArrayList<>();
1947 if (viewport.cursorMode)
1949 sg.add(viewport.getAlignment()
1950 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1952 else if (viewport.getSelectionGroup() != null
1953 && viewport.getSelectionGroup().getSize() != viewport
1954 .getAlignment().getHeight())
1956 sg = viewport.getSelectionGroup()
1957 .getSequences(viewport.getHiddenRepSequences());
1965 List<SequenceI> invertGroup = new ArrayList<>();
1967 for (SequenceI seq : viewport.getAlignment().getSequences())
1969 if (!sg.contains(seq))
1971 invertGroup.add(seq);
1975 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1977 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1978 for (int i = 0; i < invertGroup.size(); i++)
1980 seqs2[i] = invertGroup.get(i);
1983 SlideSequencesCommand ssc;
1986 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1987 viewport.getGapCharacter());
1991 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1992 viewport.getGapCharacter());
1995 int groupAdjustment = 0;
1996 if (ssc.getGapsInsertedBegin() && right)
1998 if (viewport.cursorMode)
2000 alignPanel.getSeqPanel().moveCursor(size, 0);
2004 groupAdjustment = size;
2007 else if (!ssc.getGapsInsertedBegin() && !right)
2009 if (viewport.cursorMode)
2011 alignPanel.getSeqPanel().moveCursor(-size, 0);
2015 groupAdjustment = -size;
2019 if (groupAdjustment != 0)
2021 viewport.getSelectionGroup().setStartRes(
2022 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
2023 viewport.getSelectionGroup().setEndRes(
2024 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
2028 * just extend the last slide command if compatible; but not if in
2029 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
2031 boolean appendHistoryItem = false;
2032 Deque<CommandI> historyList = viewport.getHistoryList();
2033 boolean inSplitFrame = getSplitViewContainer() != null;
2034 if (!inSplitFrame && historyList != null && historyList.size() > 0
2035 && historyList.peek() instanceof SlideSequencesCommand)
2037 appendHistoryItem = ssc.appendSlideCommand(
2038 (SlideSequencesCommand) historyList.peek());
2041 if (!appendHistoryItem)
2043 addHistoryItem(ssc);
2056 protected void copy_actionPerformed(ActionEvent e)
2058 if (viewport.getSelectionGroup() == null)
2062 // TODO: preserve the ordering of displayed alignment annotation in any
2063 // internal paste (particularly sequence associated annotation)
2064 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
2065 String[] omitHidden = null;
2067 if (viewport.hasHiddenColumns())
2069 omitHidden = viewport.getViewAsString(true);
2072 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2073 seqs, omitHidden, null);
2075 StringSelection ss = new StringSelection(output);
2079 jalview.gui.Desktop.internalCopy = true;
2080 // Its really worth setting the clipboard contents
2081 // to empty before setting the large StringSelection!!
2082 Toolkit.getDefaultToolkit().getSystemClipboard()
2083 .setContents(new StringSelection(""), null);
2085 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2087 } catch (OutOfMemoryError er)
2089 new OOMWarning("copying region", er);
2093 HiddenColumns hiddenColumns = null;
2094 if (viewport.hasHiddenColumns())
2096 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2097 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2099 // create new HiddenColumns object with copy of hidden regions
2100 // between startRes and endRes, offset by startRes
2101 hiddenColumns = new HiddenColumns(
2102 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
2103 hiddenCutoff, hiddenOffset);
2106 Desktop.jalviewClipboard = new Object[] { seqs,
2107 viewport.getAlignment().getDataset(), hiddenColumns };
2108 statusBar.setText(MessageManager.formatMessage(
2109 "label.copied_sequences_to_clipboard", new Object[]
2110 { Integer.valueOf(seqs.length).toString() }));
2118 * @throws InterruptedException
2119 * @throws IOException
2122 protected void pasteNew_actionPerformed(ActionEvent e)
2123 throws IOException, InterruptedException
2133 * @throws InterruptedException
2134 * @throws IOException
2137 protected void pasteThis_actionPerformed(ActionEvent e)
2138 throws IOException, InterruptedException
2144 * Paste contents of Jalview clipboard
2146 * @param newAlignment
2147 * true to paste to a new alignment, otherwise add to this.
2148 * @throws InterruptedException
2149 * @throws IOException
2151 void paste(boolean newAlignment) throws IOException, InterruptedException
2153 boolean externalPaste = true;
2156 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2157 Transferable contents = c.getContents(this);
2159 if (contents == null)
2168 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2169 if (str.length() < 1)
2174 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2176 } catch (OutOfMemoryError er)
2178 new OOMWarning("Out of memory pasting sequences!!", er);
2182 SequenceI[] sequences;
2183 boolean annotationAdded = false;
2184 AlignmentI alignment = null;
2186 if (Desktop.jalviewClipboard != null)
2188 // The clipboard was filled from within Jalview, we must use the
2190 // And dataset from the copied alignment
2191 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2192 // be doubly sure that we create *new* sequence objects.
2193 sequences = new SequenceI[newseq.length];
2194 for (int i = 0; i < newseq.length; i++)
2196 sequences[i] = new Sequence(newseq[i]);
2198 alignment = new Alignment(sequences);
2199 externalPaste = false;
2203 // parse the clipboard as an alignment.
2204 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2206 sequences = alignment.getSequencesArray();
2210 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2216 if (Desktop.jalviewClipboard != null)
2218 // dataset is inherited
2219 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2223 // new dataset is constructed
2224 alignment.setDataset(null);
2226 alwidth = alignment.getWidth() + 1;
2230 AlignmentI pastedal = alignment; // preserve pasted alignment object
2231 // Add pasted sequences and dataset into existing alignment.
2232 alignment = viewport.getAlignment();
2233 alwidth = alignment.getWidth() + 1;
2234 // decide if we need to import sequences from an existing dataset
2235 boolean importDs = Desktop.jalviewClipboard != null
2236 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2237 // importDs==true instructs us to copy over new dataset sequences from
2238 // an existing alignment
2239 Vector newDs = (importDs) ? new Vector() : null; // used to create
2240 // minimum dataset set
2242 for (int i = 0; i < sequences.length; i++)
2246 newDs.addElement(null);
2248 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2250 if (importDs && ds != null)
2252 if (!newDs.contains(ds))
2254 newDs.setElementAt(ds, i);
2255 ds = new Sequence(ds);
2256 // update with new dataset sequence
2257 sequences[i].setDatasetSequence(ds);
2261 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2266 // copy and derive new dataset sequence
2267 sequences[i] = sequences[i].deriveSequence();
2268 alignment.getDataset()
2269 .addSequence(sequences[i].getDatasetSequence());
2270 // TODO: avoid creation of duplicate dataset sequences with a
2271 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2273 alignment.addSequence(sequences[i]); // merges dataset
2277 newDs.clear(); // tidy up
2279 if (alignment.getAlignmentAnnotation() != null)
2281 for (AlignmentAnnotation alan : alignment
2282 .getAlignmentAnnotation())
2284 if (alan.graphGroup > fgroup)
2286 fgroup = alan.graphGroup;
2290 if (pastedal.getAlignmentAnnotation() != null)
2292 // Add any annotation attached to alignment.
2293 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2294 for (int i = 0; i < alann.length; i++)
2296 annotationAdded = true;
2297 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2299 AlignmentAnnotation newann = new AlignmentAnnotation(
2301 if (newann.graphGroup > -1)
2303 if (newGraphGroups.size() <= newann.graphGroup
2304 || newGraphGroups.get(newann.graphGroup) == null)
2306 for (int q = newGraphGroups
2307 .size(); q <= newann.graphGroup; q++)
2309 newGraphGroups.add(q, null);
2311 newGraphGroups.set(newann.graphGroup,
2312 Integer.valueOf(++fgroup));
2314 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2318 newann.padAnnotation(alwidth);
2319 alignment.addAnnotation(newann);
2329 addHistoryItem(new EditCommand(
2330 MessageManager.getString("label.add_sequences"),
2331 Action.PASTE, sequences, 0, alignment.getWidth(),
2334 // Add any annotations attached to sequences
2335 for (int i = 0; i < sequences.length; i++)
2337 if (sequences[i].getAnnotation() != null)
2339 AlignmentAnnotation newann;
2340 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2342 annotationAdded = true;
2343 newann = sequences[i].getAnnotation()[a];
2344 newann.adjustForAlignment();
2345 newann.padAnnotation(alwidth);
2346 if (newann.graphGroup > -1)
2348 if (newann.graphGroup > -1)
2350 if (newGraphGroups.size() <= newann.graphGroup
2351 || newGraphGroups.get(newann.graphGroup) == null)
2353 for (int q = newGraphGroups
2354 .size(); q <= newann.graphGroup; q++)
2356 newGraphGroups.add(q, null);
2358 newGraphGroups.set(newann.graphGroup,
2359 Integer.valueOf(++fgroup));
2361 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2365 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2369 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2377 // propagate alignment changed.
2378 viewport.getRanges().setEndSeq(alignment.getHeight());
2379 if (annotationAdded)
2381 // Duplicate sequence annotation in all views.
2382 AlignmentI[] alview = this.getViewAlignments();
2383 for (int i = 0; i < sequences.length; i++)
2385 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2390 for (int avnum = 0; avnum < alview.length; avnum++)
2392 if (alview[avnum] != alignment)
2394 // duplicate in a view other than the one with input focus
2395 int avwidth = alview[avnum].getWidth() + 1;
2396 // this relies on sann being preserved after we
2397 // modify the sequence's annotation array for each duplication
2398 for (int a = 0; a < sann.length; a++)
2400 AlignmentAnnotation newann = new AlignmentAnnotation(
2402 sequences[i].addAlignmentAnnotation(newann);
2403 newann.padAnnotation(avwidth);
2404 alview[avnum].addAnnotation(newann); // annotation was
2405 // duplicated earlier
2406 // TODO JAL-1145 graphGroups are not updated for sequence
2407 // annotation added to several views. This may cause
2409 alview[avnum].setAnnotationIndex(newann, a);
2414 buildSortByAnnotationScoresMenu();
2416 viewport.firePropertyChange("alignment", null,
2417 alignment.getSequences());
2418 if (alignPanels != null)
2420 for (AlignmentPanel ap : alignPanels)
2422 ap.validateAnnotationDimensions(false);
2427 alignPanel.validateAnnotationDimensions(false);
2433 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2435 String newtitle = new String("Copied sequences");
2437 if (Desktop.jalviewClipboard != null
2438 && Desktop.jalviewClipboard[2] != null)
2440 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2441 af.viewport.setHiddenColumns(hc);
2444 // >>>This is a fix for the moment, until a better solution is
2446 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2447 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2448 .getFeatureRenderer());
2450 // TODO: maintain provenance of an alignment, rather than just make the
2451 // title a concatenation of operations.
2454 if (title.startsWith("Copied sequences"))
2460 newtitle = newtitle.concat("- from " + title);
2465 newtitle = new String("Pasted sequences");
2468 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2473 } catch (Exception ex)
2475 ex.printStackTrace();
2476 System.out.println("Exception whilst pasting: " + ex);
2477 // could be anything being pasted in here
2482 protected void expand_newalign(ActionEvent e)
2486 AlignmentI alignment = AlignmentUtils
2487 .expandContext(getViewport().getAlignment(), -1);
2488 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2490 String newtitle = new String("Flanking alignment");
2492 if (Desktop.jalviewClipboard != null
2493 && Desktop.jalviewClipboard[2] != null)
2495 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2496 af.viewport.setHiddenColumns(hc);
2499 // >>>This is a fix for the moment, until a better solution is
2501 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2502 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2503 .getFeatureRenderer());
2505 // TODO: maintain provenance of an alignment, rather than just make the
2506 // title a concatenation of operations.
2508 if (title.startsWith("Copied sequences"))
2514 newtitle = newtitle.concat("- from " + title);
2518 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2520 } catch (Exception ex)
2522 ex.printStackTrace();
2523 System.out.println("Exception whilst pasting: " + ex);
2524 // could be anything being pasted in here
2525 } catch (OutOfMemoryError oom)
2527 new OOMWarning("Viewing flanking region of alignment", oom);
2538 protected void cut_actionPerformed(ActionEvent e)
2540 copy_actionPerformed(null);
2541 delete_actionPerformed(null);
2551 protected void delete_actionPerformed(ActionEvent evt)
2554 SequenceGroup sg = viewport.getSelectionGroup();
2561 * If the cut affects all sequences, warn, remove highlighted columns
2563 if (sg.getSize() == viewport.getAlignment().getHeight())
2565 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2566 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2567 if (isEntireAlignWidth)
2569 int confirm = JvOptionPane.showConfirmDialog(this,
2570 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2571 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2572 JvOptionPane.OK_CANCEL_OPTION);
2574 if (confirm == JvOptionPane.CANCEL_OPTION
2575 || confirm == JvOptionPane.CLOSED_OPTION)
2580 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2581 sg.getEndRes() + 1);
2583 SequenceI[] cut = sg.getSequences()
2584 .toArray(new SequenceI[sg.getSize()]);
2586 addHistoryItem(new EditCommand(
2587 MessageManager.getString("label.cut_sequences"), Action.CUT,
2588 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2589 viewport.getAlignment()));
2591 viewport.setSelectionGroup(null);
2592 viewport.sendSelection();
2593 viewport.getAlignment().deleteGroup(sg);
2595 viewport.firePropertyChange("alignment", null,
2596 viewport.getAlignment().getSequences());
2597 if (viewport.getAlignment().getHeight() < 1)
2601 this.setClosed(true);
2602 } catch (Exception ex)
2615 protected void deleteGroups_actionPerformed(ActionEvent e)
2617 if (avc.deleteGroups())
2619 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2620 alignPanel.updateAnnotation();
2621 alignPanel.paintAlignment(true, true);
2632 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2634 SequenceGroup sg = new SequenceGroup(
2635 viewport.getAlignment().getSequences());
2637 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2638 viewport.setSelectionGroup(sg);
2639 viewport.isSelectionGroupChanged(true);
2640 viewport.sendSelection();
2641 // JAL-2034 - should delegate to
2642 // alignPanel to decide if overview needs
2644 alignPanel.paintAlignment(false, false);
2645 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2655 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2657 if (viewport.cursorMode)
2659 alignPanel.getSeqPanel().keyboardNo1 = null;
2660 alignPanel.getSeqPanel().keyboardNo2 = null;
2662 viewport.setSelectionGroup(null);
2663 viewport.getColumnSelection().clear();
2664 viewport.setSelectionGroup(null);
2665 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2666 // JAL-2034 - should delegate to
2667 // alignPanel to decide if overview needs
2669 alignPanel.paintAlignment(false, false);
2670 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2671 viewport.sendSelection();
2681 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2683 SequenceGroup sg = viewport.getSelectionGroup();
2687 selectAllSequenceMenuItem_actionPerformed(null);
2692 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2694 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2696 // JAL-2034 - should delegate to
2697 // alignPanel to decide if overview needs
2700 alignPanel.paintAlignment(true, false);
2701 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2702 viewport.sendSelection();
2706 public void invertColSel_actionPerformed(ActionEvent e)
2708 viewport.invertColumnSelection();
2709 alignPanel.paintAlignment(true, false);
2710 viewport.sendSelection();
2720 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2722 trimAlignment(true);
2732 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2734 trimAlignment(false);
2737 void trimAlignment(boolean trimLeft)
2739 ColumnSelection colSel = viewport.getColumnSelection();
2742 if (!colSel.isEmpty())
2746 column = colSel.getMin();
2750 column = colSel.getMax();
2754 if (viewport.getSelectionGroup() != null)
2756 seqs = viewport.getSelectionGroup()
2757 .getSequencesAsArray(viewport.getHiddenRepSequences());
2761 seqs = viewport.getAlignment().getSequencesArray();
2764 TrimRegionCommand trimRegion;
2767 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2768 column, viewport.getAlignment());
2769 viewport.getRanges().setStartRes(0);
2773 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2774 column, viewport.getAlignment());
2777 statusBar.setText(MessageManager
2778 .formatMessage("label.removed_columns", new String[]
2779 { Integer.valueOf(trimRegion.getSize()).toString() }));
2781 addHistoryItem(trimRegion);
2783 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2785 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2786 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2788 viewport.getAlignment().deleteGroup(sg);
2792 viewport.firePropertyChange("alignment", null,
2793 viewport.getAlignment().getSequences());
2804 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2806 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2809 if (viewport.getSelectionGroup() != null)
2811 seqs = viewport.getSelectionGroup()
2812 .getSequencesAsArray(viewport.getHiddenRepSequences());
2813 start = viewport.getSelectionGroup().getStartRes();
2814 end = viewport.getSelectionGroup().getEndRes();
2818 seqs = viewport.getAlignment().getSequencesArray();
2821 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2822 "Remove Gapped Columns", seqs, start, end,
2823 viewport.getAlignment());
2825 addHistoryItem(removeGapCols);
2827 statusBar.setText(MessageManager
2828 .formatMessage("label.removed_empty_columns", new Object[]
2829 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2831 // This is to maintain viewport position on first residue
2832 // of first sequence
2833 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2834 ViewportRanges ranges = viewport.getRanges();
2835 int startRes = seq.findPosition(ranges.getStartRes());
2836 // ShiftList shifts;
2837 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2838 // edit.alColumnChanges=shifts.getInverse();
2839 // if (viewport.hasHiddenColumns)
2840 // viewport.getColumnSelection().compensateForEdits(shifts);
2841 ranges.setStartRes(seq.findIndex(startRes) - 1);
2842 viewport.firePropertyChange("alignment", null,
2843 viewport.getAlignment().getSequences());
2854 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2856 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2859 if (viewport.getSelectionGroup() != null)
2861 seqs = viewport.getSelectionGroup()
2862 .getSequencesAsArray(viewport.getHiddenRepSequences());
2863 start = viewport.getSelectionGroup().getStartRes();
2864 end = viewport.getSelectionGroup().getEndRes();
2868 seqs = viewport.getAlignment().getSequencesArray();
2871 // This is to maintain viewport position on first residue
2872 // of first sequence
2873 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2874 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2876 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2877 viewport.getAlignment()));
2879 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2881 viewport.firePropertyChange("alignment", null,
2882 viewport.getAlignment().getSequences());
2893 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2895 viewport.setPadGaps(padGapsMenuitem.isSelected());
2896 viewport.firePropertyChange("alignment", null,
2897 viewport.getAlignment().getSequences());
2907 public void findMenuItem_actionPerformed(ActionEvent e)
2913 * Create a new view of the current alignment.
2916 public void newView_actionPerformed(ActionEvent e)
2918 newView(null, true);
2922 * Creates and shows a new view of the current alignment.
2925 * title of newly created view; if null, one will be generated
2926 * @param copyAnnotation
2927 * if true then duplicate all annnotation, groups and settings
2928 * @return new alignment panel, already displayed.
2930 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2933 * Create a new AlignmentPanel (with its own, new Viewport)
2935 AlignmentPanel newap = new jalview.project.Jalview2XML()
2936 .copyAlignPanel(alignPanel);
2937 if (!copyAnnotation)
2940 * remove all groups and annotation except for the automatic stuff
2942 newap.av.getAlignment().deleteAllGroups();
2943 newap.av.getAlignment().deleteAllAnnotations(false);
2946 newap.av.setGatherViewsHere(false);
2948 if (viewport.getViewName() == null)
2950 viewport.setViewName(MessageManager
2951 .getString("label.view_name_original"));
2955 * Views share the same edits undo and redo stacks
2957 newap.av.setHistoryList(viewport.getHistoryList());
2958 newap.av.setRedoList(viewport.getRedoList());
2961 * copy any visualisation settings that are not saved in the project
2963 newap.av.setColourAppliesToAllGroups(
2964 viewport.getColourAppliesToAllGroups());
2967 * Views share the same mappings; need to deregister any new mappings
2968 * created by copyAlignPanel, and register the new reference to the shared
2971 newap.av.replaceMappings(viewport.getAlignment());
2974 * start up cDNA consensus (if applicable) now mappings are in place
2976 if (newap.av.initComplementConsensus())
2978 newap.refresh(true); // adjust layout of annotations
2981 newap.av.setViewName(getNewViewName(viewTitle));
2983 addAlignmentPanel(newap, true);
2984 newap.alignmentChanged();
2986 if (alignPanels.size() == 2)
2988 viewport.setGatherViewsHere(true);
2990 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2995 * Make a new name for the view, ensuring it is unique within the current
2996 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2997 * these now use viewId. Unique view names are still desirable for usability.)
3002 protected String getNewViewName(String viewTitle)
3004 int index = Desktop.getViewCount(viewport.getSequenceSetId());
3005 boolean addFirstIndex = false;
3006 if (viewTitle == null || viewTitle.trim().length() == 0)
3008 viewTitle = MessageManager.getString("action.view");
3009 addFirstIndex = true;
3013 index = 1;// we count from 1 if given a specific name
3015 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
3017 List<Component> comps = PaintRefresher.components
3018 .get(viewport.getSequenceSetId());
3020 List<String> existingNames = getExistingViewNames(comps);
3022 while (existingNames.contains(newViewName))
3024 newViewName = viewTitle + " " + (++index);
3030 * Returns a list of distinct view names found in the given list of
3031 * components. View names are held on the viewport of an AlignmentPanel.
3036 protected List<String> getExistingViewNames(List<Component> comps)
3038 List<String> existingNames = new ArrayList<>();
3039 for (Component comp : comps)
3041 if (comp instanceof AlignmentPanel)
3043 AlignmentPanel ap = (AlignmentPanel) comp;
3044 if (!existingNames.contains(ap.av.getViewName()))
3046 existingNames.add(ap.av.getViewName());
3050 return existingNames;
3054 * Explode tabbed views into separate windows.
3057 public void expandViews_actionPerformed(ActionEvent e)
3059 Desktop.explodeViews(this);
3063 * Gather views in separate windows back into a tabbed presentation.
3066 public void gatherViews_actionPerformed(ActionEvent e)
3068 Desktop.instance.gatherViews(this);
3078 public void font_actionPerformed(ActionEvent e)
3080 new FontChooser(alignPanel);
3090 protected void seqLimit_actionPerformed(ActionEvent e)
3092 viewport.setShowJVSuffix(seqLimits.isSelected());
3094 alignPanel.getIdPanel().getIdCanvas()
3095 .setPreferredSize(alignPanel.calculateIdWidth());
3096 alignPanel.paintAlignment(true, false);
3100 public void idRightAlign_actionPerformed(ActionEvent e)
3102 viewport.setRightAlignIds(idRightAlign.isSelected());
3103 alignPanel.paintAlignment(false, false);
3107 public void centreColumnLabels_actionPerformed(ActionEvent e)
3109 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3110 alignPanel.paintAlignment(false, false);
3116 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3119 protected void followHighlight_actionPerformed()
3122 * Set the 'follow' flag on the Viewport (and scroll to position if now
3125 final boolean state = this.followHighlightMenuItem.getState();
3126 viewport.setFollowHighlight(state);
3129 alignPanel.scrollToPosition(viewport.getSearchResults());
3140 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3142 viewport.setColourText(colourTextMenuItem.isSelected());
3143 alignPanel.paintAlignment(false, false);
3153 public void wrapMenuItem_actionPerformed(ActionEvent e)
3155 scaleAbove.setVisible(wrapMenuItem.isSelected());
3156 scaleLeft.setVisible(wrapMenuItem.isSelected());
3157 scaleRight.setVisible(wrapMenuItem.isSelected());
3158 viewport.setWrapAlignment(wrapMenuItem.isSelected());
3159 alignPanel.updateLayout();
3163 public void showAllSeqs_actionPerformed(ActionEvent e)
3165 viewport.showAllHiddenSeqs();
3169 public void showAllColumns_actionPerformed(ActionEvent e)
3171 viewport.showAllHiddenColumns();
3172 alignPanel.paintAlignment(true, true);
3173 viewport.sendSelection();
3177 public void hideSelSequences_actionPerformed(ActionEvent e)
3179 viewport.hideAllSelectedSeqs();
3183 * called by key handler and the hide all/show all menu items
3188 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3191 boolean hide = false;
3192 SequenceGroup sg = viewport.getSelectionGroup();
3193 if (!toggleSeqs && !toggleCols)
3195 // Hide everything by the current selection - this is a hack - we do the
3196 // invert and then hide
3197 // first check that there will be visible columns after the invert.
3198 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3199 && sg.getStartRes() <= sg.getEndRes()))
3201 // now invert the sequence set, if required - empty selection implies
3202 // that no hiding is required.
3205 invertSequenceMenuItem_actionPerformed(null);
3206 sg = viewport.getSelectionGroup();
3210 viewport.expandColSelection(sg, true);
3211 // finally invert the column selection and get the new sequence
3213 invertColSel_actionPerformed(null);
3220 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3222 hideSelSequences_actionPerformed(null);
3225 else if (!(toggleCols && viewport.hasSelectedColumns()))
3227 showAllSeqs_actionPerformed(null);
3233 if (viewport.hasSelectedColumns())
3235 hideSelColumns_actionPerformed(null);
3238 viewport.setSelectionGroup(sg);
3243 showAllColumns_actionPerformed(null);
3252 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3253 * event.ActionEvent)
3256 public void hideAllButSelection_actionPerformed(ActionEvent e)
3258 toggleHiddenRegions(false, false);
3259 viewport.sendSelection();
3266 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3270 public void hideAllSelection_actionPerformed(ActionEvent e)
3272 SequenceGroup sg = viewport.getSelectionGroup();
3273 viewport.expandColSelection(sg, false);
3274 viewport.hideAllSelectedSeqs();
3275 viewport.hideSelectedColumns();
3276 alignPanel.updateLayout();
3277 alignPanel.paintAlignment(true, true);
3278 viewport.sendSelection();
3285 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3289 public void showAllhidden_actionPerformed(ActionEvent e)
3291 viewport.showAllHiddenColumns();
3292 viewport.showAllHiddenSeqs();
3293 alignPanel.paintAlignment(true, true);
3294 viewport.sendSelection();
3298 public void hideSelColumns_actionPerformed(ActionEvent e)
3300 viewport.hideSelectedColumns();
3301 alignPanel.updateLayout();
3302 alignPanel.paintAlignment(true, true);
3303 viewport.sendSelection();
3307 public void hiddenMarkers_actionPerformed(ActionEvent e)
3309 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3320 protected void scaleAbove_actionPerformed(ActionEvent e)
3322 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3323 alignPanel.updateLayout();
3324 alignPanel.paintAlignment(true, false);
3334 protected void scaleLeft_actionPerformed(ActionEvent e)
3336 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3337 alignPanel.updateLayout();
3338 alignPanel.paintAlignment(true, false);
3348 protected void scaleRight_actionPerformed(ActionEvent e)
3350 viewport.setScaleRightWrapped(scaleRight.isSelected());
3351 alignPanel.updateLayout();
3352 alignPanel.paintAlignment(true, false);
3362 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3364 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3365 alignPanel.paintAlignment(false, false);
3375 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3377 viewport.setShowText(viewTextMenuItem.isSelected());
3378 alignPanel.paintAlignment(false, false);
3388 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3390 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3391 alignPanel.paintAlignment(false, false);
3394 public FeatureSettings featureSettings;
3397 public FeatureSettingsControllerI getFeatureSettingsUI()
3399 return featureSettings;
3403 public void featureSettings_actionPerformed(ActionEvent e)
3405 if (featureSettings != null)
3407 featureSettings.close();
3408 featureSettings = null;
3410 if (!showSeqFeatures.isSelected())
3412 // make sure features are actually displayed
3413 showSeqFeatures.setSelected(true);
3414 showSeqFeatures_actionPerformed(null);
3416 featureSettings = new FeatureSettings(this);
3420 * Set or clear 'Show Sequence Features'
3426 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3428 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3429 alignPanel.paintAlignment(true, true);
3433 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3434 * the annotations panel as a whole.
3436 * The options to show/hide all annotations should be enabled when the panel
3437 * is shown, and disabled when the panel is hidden.
3442 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3444 final boolean setVisible = annotationPanelMenuItem.isSelected();
3445 viewport.setShowAnnotation(setVisible);
3446 this.showAllSeqAnnotations.setEnabled(setVisible);
3447 this.hideAllSeqAnnotations.setEnabled(setVisible);
3448 this.showAllAlAnnotations.setEnabled(setVisible);
3449 this.hideAllAlAnnotations.setEnabled(setVisible);
3450 alignPanel.updateLayout();
3454 public void alignmentProperties()
3456 JEditorPane editPane = new JEditorPane("text/html", "");
3457 editPane.setEditable(false);
3458 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3461 MessageManager.formatMessage("label.html_content", new Object[]
3462 { contents.toString() }));
3463 JInternalFrame frame = new JInternalFrame();
3464 frame.getContentPane().add(new JScrollPane(editPane));
3466 Desktop.addInternalFrame(frame, MessageManager
3467 .formatMessage("label.alignment_properties", new Object[]
3468 { getTitle() }), 500, 400);
3478 public void overviewMenuItem_actionPerformed(ActionEvent e)
3480 if (alignPanel.overviewPanel != null)
3485 JInternalFrame frame = new JInternalFrame();
3486 final OverviewPanel overview = new OverviewPanel(alignPanel);
3487 frame.setContentPane(overview);
3488 Desktop.addInternalFrame(frame, MessageManager
3489 .formatMessage("label.overview_params", new Object[]
3490 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3493 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3494 frame.addInternalFrameListener(
3495 new javax.swing.event.InternalFrameAdapter()
3498 public void internalFrameClosed(
3499 javax.swing.event.InternalFrameEvent evt)
3502 alignPanel.setOverviewPanel(null);
3505 if (getKeyListeners().length > 0)
3507 frame.addKeyListener(getKeyListeners()[0]);
3510 alignPanel.setOverviewPanel(overview);
3514 public void textColour_actionPerformed()
3516 new TextColourChooser().chooseColour(alignPanel, null);
3520 * public void covariationColour_actionPerformed() {
3522 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3526 public void annotationColour_actionPerformed()
3528 new AnnotationColourChooser(viewport, alignPanel);
3532 public void annotationColumn_actionPerformed(ActionEvent e)
3534 new AnnotationColumnChooser(viewport, alignPanel);
3538 * Action on the user checking or unchecking the option to apply the selected
3539 * colour scheme to all groups. If unchecked, groups may have their own
3540 * independent colour schemes.
3545 public void applyToAllGroups_actionPerformed(boolean selected)
3547 viewport.setColourAppliesToAllGroups(selected);
3551 * Action on user selecting a colour from the colour menu
3554 * the name (not the menu item label!) of the colour scheme
3557 public void changeColour_actionPerformed(String name)
3560 * 'User Defined' opens a panel to configure or load a
3561 * user-defined colour scheme
3563 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3565 new UserDefinedColours(alignPanel);
3570 * otherwise set the chosen colour scheme (or null for 'None')
3572 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3574 viewport.getAlignment(), viewport.getHiddenRepSequences());
3579 * Actions on setting or changing the alignment colour scheme
3584 public void changeColour(ColourSchemeI cs)
3586 // TODO: pull up to controller method
3587 ColourMenuHelper.setColourSelected(colourMenu, cs);
3589 viewport.setGlobalColourScheme(cs);
3591 alignPanel.paintAlignment(true, true);
3595 * Show the PID threshold slider panel
3598 protected void modifyPID_actionPerformed()
3600 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3601 alignPanel.getViewName());
3602 SliderPanel.showPIDSlider();
3606 * Show the Conservation slider panel
3609 protected void modifyConservation_actionPerformed()
3611 SliderPanel.setConservationSlider(alignPanel,
3612 viewport.getResidueShading(), alignPanel.getViewName());
3613 SliderPanel.showConservationSlider();
3617 * Action on selecting or deselecting (Colour) By Conservation
3620 public void conservationMenuItem_actionPerformed(boolean selected)
3622 modifyConservation.setEnabled(selected);
3623 viewport.setConservationSelected(selected);
3624 viewport.getResidueShading().setConservationApplied(selected);
3626 changeColour(viewport.getGlobalColourScheme());
3629 modifyConservation_actionPerformed();
3633 SliderPanel.hideConservationSlider();
3638 * Action on selecting or deselecting (Colour) Above PID Threshold
3641 public void abovePIDThreshold_actionPerformed(boolean selected)
3643 modifyPID.setEnabled(selected);
3644 viewport.setAbovePIDThreshold(selected);
3647 viewport.getResidueShading().setThreshold(0,
3648 viewport.isIgnoreGapsConsensus());
3651 changeColour(viewport.getGlobalColourScheme());
3654 modifyPID_actionPerformed();
3658 SliderPanel.hidePIDSlider();
3669 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3671 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3672 AlignmentSorter.sortByPID(viewport.getAlignment(),
3673 viewport.getAlignment().getSequenceAt(0));
3674 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3675 viewport.getAlignment()));
3676 alignPanel.paintAlignment(true, false);
3686 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3688 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3689 AlignmentSorter.sortByID(viewport.getAlignment());
3691 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3692 alignPanel.paintAlignment(true, false);
3702 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3704 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3705 AlignmentSorter.sortByLength(viewport.getAlignment());
3706 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3707 viewport.getAlignment()));
3708 alignPanel.paintAlignment(true, false);
3718 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3720 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3721 AlignmentSorter.sortByGroup(viewport.getAlignment());
3722 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3723 viewport.getAlignment()));
3725 alignPanel.paintAlignment(true, false);
3735 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3737 new RedundancyPanel(alignPanel, this);
3747 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3749 if ((viewport.getSelectionGroup() == null)
3750 || (viewport.getSelectionGroup().getSize() < 2))
3752 JvOptionPane.showInternalMessageDialog(this,
3753 MessageManager.getString(
3754 "label.you_must_select_least_two_sequences"),
3755 MessageManager.getString("label.invalid_selection"),
3756 JvOptionPane.WARNING_MESSAGE);
3760 JInternalFrame frame = new JInternalFrame();
3761 frame.setContentPane(new PairwiseAlignPanel(viewport));
3762 Desktop.addInternalFrame(frame,
3763 MessageManager.getString("action.pairwise_alignment"), 600,
3769 public void autoCalculate_actionPerformed(ActionEvent e)
3771 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3772 if (viewport.autoCalculateConsensus)
3774 viewport.firePropertyChange("alignment", null,
3775 viewport.getAlignment().getSequences());
3780 public void sortByTreeOption_actionPerformed(ActionEvent e)
3782 viewport.sortByTree = sortByTree.isSelected();
3786 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3788 viewport.followSelection = listenToViewSelections.isSelected();
3792 * Constructs a tree panel and adds it to the desktop
3795 * tree type (NJ or AV)
3797 * name of score model used to compute the tree
3799 * parameters for the distance or similarity calculation
3801 void newTreePanel(String type, String modelName,
3802 SimilarityParamsI options)
3804 String frameTitle = "";
3807 boolean onSelection = false;
3808 if (viewport.getSelectionGroup() != null
3809 && viewport.getSelectionGroup().getSize() > 0)
3811 SequenceGroup sg = viewport.getSelectionGroup();
3813 /* Decide if the selection is a column region */
3814 for (SequenceI _s : sg.getSequences())
3816 if (_s.getLength() < sg.getEndRes())
3818 JvOptionPane.showMessageDialog(Desktop.desktop,
3819 MessageManager.getString(
3820 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3821 MessageManager.getString(
3822 "label.sequences_selection_not_aligned"),
3823 JvOptionPane.WARNING_MESSAGE);
3832 if (viewport.getAlignment().getHeight() < 2)
3838 tp = new TreePanel(alignPanel, type, modelName, options);
3839 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3841 frameTitle += " from ";
3843 if (viewport.getViewName() != null)
3845 frameTitle += viewport.getViewName() + " of ";
3848 frameTitle += this.title;
3850 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3861 public void addSortByOrderMenuItem(String title,
3862 final AlignmentOrder order)
3864 final JMenuItem item = new JMenuItem(MessageManager
3865 .formatMessage("action.by_title_param", new Object[]
3868 item.addActionListener(new java.awt.event.ActionListener()
3871 public void actionPerformed(ActionEvent e)
3873 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3875 // TODO: JBPNote - have to map order entries to curent SequenceI
3877 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3879 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3880 viewport.getAlignment()));
3882 alignPanel.paintAlignment(true, false);
3888 * Add a new sort by annotation score menu item
3891 * the menu to add the option to
3893 * the label used to retrieve scores for each sequence on the
3896 public void addSortByAnnotScoreMenuItem(JMenu sort,
3897 final String scoreLabel)
3899 final JMenuItem item = new JMenuItem(scoreLabel);
3901 item.addActionListener(new java.awt.event.ActionListener()
3904 public void actionPerformed(ActionEvent e)
3906 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3907 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3908 viewport.getAlignment());// ,viewport.getSelectionGroup());
3909 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3910 viewport.getAlignment()));
3911 alignPanel.paintAlignment(true, false);
3917 * last hash for alignment's annotation array - used to minimise cost of
3920 protected int _annotationScoreVectorHash;
3923 * search the alignment and rebuild the sort by annotation score submenu the
3924 * last alignment annotation vector hash is stored to minimize cost of
3925 * rebuilding in subsequence calls.
3929 public void buildSortByAnnotationScoresMenu()
3931 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3936 if (viewport.getAlignment().getAlignmentAnnotation()
3937 .hashCode() == _annotationScoreVectorHash)
3942 sortByAnnotScore.removeAll();
3943 Set<String> scoreSorts = new HashSet<>();
3944 for (SequenceI sqa : viewport.getAlignment().getSequences())
3946 AlignmentAnnotation[] anns = sqa.getAnnotation();
3947 for (int i = 0; anns != null && i < anns.length; i++)
3949 AlignmentAnnotation aa = anns[i];
3950 if (aa != null && aa.hasScore() && aa.sequenceRef != null)
3952 scoreSorts.add(aa.label);
3956 for (String label : scoreSorts)
3958 addSortByAnnotScoreMenuItem(sortByAnnotScore, label);
3960 sortByAnnotScore.setVisible(!scoreSorts.isEmpty());
3962 _annotationScoreVectorHash = viewport.getAlignment()
3963 .getAlignmentAnnotation().hashCode();
3967 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3968 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3969 * call. Listeners are added to remove the menu item when the treePanel is
3970 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3974 public void buildTreeSortMenu()
3976 sortByTreeMenu.removeAll();
3978 List<Component> comps = PaintRefresher.components
3979 .get(viewport.getSequenceSetId());
3980 List<TreePanel> treePanels = new ArrayList<>();
3981 for (Component comp : comps)
3983 if (comp instanceof TreePanel)
3985 treePanels.add((TreePanel) comp);
3989 if (treePanels.size() < 1)
3991 sortByTreeMenu.setVisible(false);
3995 sortByTreeMenu.setVisible(true);
3997 for (final TreePanel tp : treePanels)
3999 final JMenuItem item = new JMenuItem(tp.getTitle());
4000 item.addActionListener(new java.awt.event.ActionListener()
4003 public void actionPerformed(ActionEvent e)
4005 tp.sortByTree_actionPerformed();
4006 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4011 sortByTreeMenu.add(item);
4015 public boolean sortBy(AlignmentOrder alorder, String undoname)
4017 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4018 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4019 if (undoname != null)
4021 addHistoryItem(new OrderCommand(undoname, oldOrder,
4022 viewport.getAlignment()));
4024 alignPanel.paintAlignment(true, false);
4029 * Work out whether the whole set of sequences or just the selected set will
4030 * be submitted for multiple alignment.
4033 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4035 // Now, check we have enough sequences
4036 AlignmentView msa = null;
4038 if ((viewport.getSelectionGroup() != null)
4039 && (viewport.getSelectionGroup().getSize() > 1))
4041 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4042 // some common interface!
4044 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4045 * SequenceI[sz = seqs.getSize(false)];
4047 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4048 * seqs.getSequenceAt(i); }
4050 msa = viewport.getAlignmentView(true);
4052 else if (viewport.getSelectionGroup() != null
4053 && viewport.getSelectionGroup().getSize() == 1)
4055 int option = JvOptionPane.showConfirmDialog(this,
4056 MessageManager.getString("warn.oneseq_msainput_selection"),
4057 MessageManager.getString("label.invalid_selection"),
4058 JvOptionPane.OK_CANCEL_OPTION);
4059 if (option == JvOptionPane.OK_OPTION)
4061 msa = viewport.getAlignmentView(false);
4066 msa = viewport.getAlignmentView(false);
4072 * Decides what is submitted to a secondary structure prediction service: the
4073 * first sequence in the alignment, or in the current selection, or, if the
4074 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4075 * region or the whole alignment. (where the first sequence in the set is the
4076 * one that the prediction will be for).
4078 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4080 AlignmentView seqs = null;
4082 if ((viewport.getSelectionGroup() != null)
4083 && (viewport.getSelectionGroup().getSize() > 0))
4085 seqs = viewport.getAlignmentView(true);
4089 seqs = viewport.getAlignmentView(false);
4091 // limit sequences - JBPNote in future - could spawn multiple prediction
4093 // TODO: viewport.getAlignment().isAligned is a global state - the local
4094 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4095 if (!viewport.getAlignment().isAligned(false))
4097 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4098 // TODO: if seqs.getSequences().length>1 then should really have warned
4112 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4114 // Pick the tree file
4115 JalviewFileChooser chooser = new JalviewFileChooser(
4116 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4117 chooser.setFileView(new JalviewFileView());
4118 chooser.setDialogTitle(
4119 MessageManager.getString("label.select_newick_like_tree_file"));
4120 chooser.setToolTipText(
4121 MessageManager.getString("label.load_tree_file"));
4123 int value = chooser.showOpenDialog(null);
4125 if (value == JalviewFileChooser.APPROVE_OPTION)
4127 String filePath = chooser.getSelectedFile().getPath();
4128 Cache.setProperty("LAST_DIRECTORY", filePath);
4129 NewickFile fin = null;
4132 fin = new NewickFile(filePath, DataSourceType.FILE);
4133 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4134 } catch (Exception ex)
4136 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4137 MessageManager.getString("label.problem_reading_tree_file"),
4138 JvOptionPane.WARNING_MESSAGE);
4139 ex.printStackTrace();
4141 if (fin != null && fin.hasWarningMessage())
4143 JvOptionPane.showMessageDialog(Desktop.desktop,
4144 fin.getWarningMessage(),
4146 .getString("label.possible_problem_with_tree_file"),
4147 JvOptionPane.WARNING_MESSAGE);
4152 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4154 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4157 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4158 int h, int x, int y)
4160 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4164 * Add a treeviewer for the tree extracted from a Newick file object to the
4165 * current alignment view
4172 * Associated alignment input data (or null)
4181 * @return TreePanel handle
4183 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4184 AlignmentView input, int w, int h, int x, int y)
4186 TreePanel tp = null;
4192 if (nf.getTree() != null)
4194 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4200 tp.setLocation(x, y);
4203 Desktop.addInternalFrame(tp, treeTitle, w, h);
4205 } catch (Exception ex)
4207 ex.printStackTrace();
4213 private boolean buildingMenu = false;
4216 * Generates menu items and listener event actions for web service clients
4219 public void BuildWebServiceMenu()
4221 while (buildingMenu)
4225 System.err.println("Waiting for building menu to finish.");
4227 } catch (Exception e)
4231 final AlignFrame me = this;
4232 buildingMenu = true;
4233 new Thread(new Runnable()
4238 final List<JMenuItem> legacyItems = new ArrayList<>();
4241 // System.err.println("Building ws menu again "
4242 // + Thread.currentThread());
4243 // TODO: add support for context dependent disabling of services based
4245 // alignment and current selection
4246 // TODO: add additional serviceHandle parameter to specify abstract
4248 // class independently of AbstractName
4249 // TODO: add in rediscovery GUI function to restart discoverer
4250 // TODO: group services by location as well as function and/or
4252 // object broker mechanism.
4253 final Vector<JMenu> wsmenu = new Vector<>();
4254 final IProgressIndicator af = me;
4257 * do not i18n these strings - they are hard-coded in class
4258 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4259 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4261 final JMenu msawsmenu = new JMenu("Alignment");
4262 final JMenu secstrmenu = new JMenu(
4263 "Secondary Structure Prediction");
4264 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4265 final JMenu analymenu = new JMenu("Analysis");
4266 final JMenu dismenu = new JMenu("Protein Disorder");
4267 // JAL-940 - only show secondary structure prediction services from
4268 // the legacy server
4269 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4271 Discoverer.services != null && (Discoverer.services.size() > 0))
4273 // TODO: refactor to allow list of AbstractName/Handler bindings to
4275 // stored or retrieved from elsewhere
4276 // No MSAWS used any more:
4277 // Vector msaws = null; // (Vector)
4278 // Discoverer.services.get("MsaWS");
4279 Vector secstrpr = (Vector) Discoverer.services
4281 if (secstrpr != null)
4283 // Add any secondary structure prediction services
4284 for (int i = 0, j = secstrpr.size(); i < j; i++)
4286 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4288 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4289 .getServiceClient(sh);
4290 int p = secstrmenu.getItemCount();
4291 impl.attachWSMenuEntry(secstrmenu, me);
4292 int q = secstrmenu.getItemCount();
4293 for (int litm = p; litm < q; litm++)
4295 legacyItems.add(secstrmenu.getItem(litm));
4301 // Add all submenus in the order they should appear on the web
4303 wsmenu.add(msawsmenu);
4304 wsmenu.add(secstrmenu);
4305 wsmenu.add(dismenu);
4306 wsmenu.add(analymenu);
4307 // No search services yet
4308 // wsmenu.add(seqsrchmenu);
4310 javax.swing.SwingUtilities.invokeLater(new Runnable()
4317 webService.removeAll();
4318 // first, add discovered services onto the webservices menu
4319 if (wsmenu.size() > 0)
4321 for (int i = 0, j = wsmenu.size(); i < j; i++)
4323 webService.add(wsmenu.get(i));
4328 webService.add(me.webServiceNoServices);
4330 // TODO: move into separate menu builder class.
4331 boolean new_sspred = false;
4332 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4334 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4335 if (jws2servs != null)
4337 if (jws2servs.hasServices())
4339 jws2servs.attachWSMenuEntry(webService, me);
4340 for (Jws2Instance sv : jws2servs.getServices())
4342 if (sv.description.toLowerCase().contains("jpred"))
4344 for (JMenuItem jmi : legacyItems)
4346 jmi.setVisible(false);
4352 if (jws2servs.isRunning())
4354 JMenuItem tm = new JMenuItem(
4355 "Still discovering JABA Services");
4356 tm.setEnabled(false);
4361 build_urlServiceMenu(me.webService);
4362 build_fetchdbmenu(webService);
4363 for (JMenu item : wsmenu)
4365 if (item.getItemCount() == 0)
4367 item.setEnabled(false);
4371 item.setEnabled(true);
4374 } catch (Exception e)
4377 "Exception during web service menu building process.",
4382 } catch (Exception e)
4385 buildingMenu = false;
4392 * construct any groupURL type service menu entries.
4396 private void build_urlServiceMenu(JMenu webService)
4398 // TODO: remove this code when 2.7 is released
4399 // DEBUG - alignmentView
4401 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4402 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4404 * @Override public void actionPerformed(ActionEvent e) {
4405 * jalview.datamodel.AlignmentView
4406 * .testSelectionViews(af.viewport.getAlignment(),
4407 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4409 * }); webService.add(testAlView);
4411 // TODO: refactor to RestClient discoverer and merge menu entries for
4412 // rest-style services with other types of analysis/calculation service
4413 // SHmmr test client - still being implemented.
4414 // DEBUG - alignmentView
4416 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4419 client.attachWSMenuEntry(
4420 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4426 * Searches the alignment sequences for xRefs and builds the Show
4427 * Cross-References menu (formerly called Show Products), with database
4428 * sources for which cross-references are found (protein sources for a
4429 * nucleotide alignment and vice versa)
4431 * @return true if Show Cross-references menu should be enabled
4433 public boolean canShowProducts()
4435 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4436 AlignmentI dataset = viewport.getAlignment().getDataset();
4438 showProducts.removeAll();
4439 final boolean dna = viewport.getAlignment().isNucleotide();
4441 if (seqs == null || seqs.length == 0)
4443 // nothing to see here.
4447 boolean showp = false;
4450 List<String> ptypes = new CrossRef(seqs, dataset)
4451 .findXrefSourcesForSequences(dna);
4453 for (final String source : ptypes)
4456 final AlignFrame af = this;
4457 JMenuItem xtype = new JMenuItem(source);
4458 xtype.addActionListener(new ActionListener()
4461 public void actionPerformed(ActionEvent e)
4463 showProductsFor(af.viewport.getSequenceSelection(), dna,
4467 showProducts.add(xtype);
4469 showProducts.setVisible(showp);
4470 showProducts.setEnabled(showp);
4471 } catch (Exception e)
4474 "canShowProducts threw an exception - please report to help@jalview.org",
4482 * Finds and displays cross-references for the selected sequences (protein
4483 * products for nucleotide sequences, dna coding sequences for peptides).
4486 * the sequences to show cross-references for
4488 * true if from a nucleotide alignment (so showing proteins)
4490 * the database to show cross-references for
4492 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4493 final String source)
4495 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4500 * Construct and display a new frame containing the translation of this
4501 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4504 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4506 AlignmentI al = null;
4509 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4511 al = dna.translateCdna(codeTable);
4512 } catch (Exception ex)
4514 jalview.bin.Cache.log.error(
4515 "Exception during translation. Please report this !", ex);
4516 final String msg = MessageManager.getString(
4517 "label.error_when_translating_sequences_submit_bug_report");
4518 final String errorTitle = MessageManager
4519 .getString("label.implementation_error")
4520 + MessageManager.getString("label.translation_failed");
4521 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4522 JvOptionPane.ERROR_MESSAGE);
4525 if (al == null || al.getHeight() == 0)
4527 final String msg = MessageManager.getString(
4528 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4529 final String errorTitle = MessageManager
4530 .getString("label.translation_failed");
4531 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4532 JvOptionPane.WARNING_MESSAGE);
4536 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4537 af.setFileFormat(this.currentFileFormat);
4538 final String newTitle = MessageManager
4539 .formatMessage("label.translation_of_params", new Object[]
4540 { this.getTitle(), codeTable.getId() });
4541 af.setTitle(newTitle);
4542 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4544 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4545 viewport.openSplitFrame(af, new Alignment(seqs));
4549 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4556 * Set the file format
4560 public void setFileFormat(FileFormatI format)
4562 this.currentFileFormat = format;
4566 * Try to load a features file onto the alignment.
4569 * contents or path to retrieve file
4571 * access mode of file (see jalview.io.AlignFile)
4572 * @return true if features file was parsed correctly.
4574 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4576 return avc.parseFeaturesFile(file, sourceType,
4577 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4582 public void refreshFeatureUI(boolean enableIfNecessary)
4584 // note - currently this is only still here rather than in the controller
4585 // because of the featureSettings hard reference that is yet to be
4587 if (enableIfNecessary)
4589 viewport.setShowSequenceFeatures(true);
4590 showSeqFeatures.setSelected(true);
4596 public void dragEnter(DropTargetDragEvent evt)
4601 public void dragExit(DropTargetEvent evt)
4606 public void dragOver(DropTargetDragEvent evt)
4611 public void dropActionChanged(DropTargetDragEvent evt)
4616 public void drop(DropTargetDropEvent evt)
4618 // JAL-1552 - acceptDrop required before getTransferable call for
4619 // Java's Transferable for native dnd
4620 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4621 Transferable t = evt.getTransferable();
4622 final AlignFrame thisaf = this;
4623 final List<String> files = new ArrayList<>();
4624 List<DataSourceType> protocols = new ArrayList<>();
4628 Desktop.transferFromDropTarget(files, protocols, evt, t);
4629 } catch (Exception e)
4631 e.printStackTrace();
4635 new Thread(new Runnable()
4642 // check to see if any of these files have names matching sequences
4645 SequenceIdMatcher idm = new SequenceIdMatcher(
4646 viewport.getAlignment().getSequencesArray());
4648 * Object[] { String,SequenceI}
4650 ArrayList<Object[]> filesmatched = new ArrayList<>();
4651 ArrayList<String> filesnotmatched = new ArrayList<>();
4652 for (int i = 0; i < files.size(); i++)
4654 String file = files.get(i).toString();
4656 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4657 if (protocol == DataSourceType.FILE)
4659 File fl = new File(file);
4660 pdbfn = fl.getName();
4662 else if (protocol == DataSourceType.URL)
4664 URL url = new URL(file);
4665 pdbfn = url.getFile();
4667 if (pdbfn.length() > 0)
4669 // attempt to find a match in the alignment
4670 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4671 int l = 0, c = pdbfn.indexOf(".");
4672 while (mtch == null && c != -1)
4677 } while ((c = pdbfn.indexOf(".", l)) > l);
4680 pdbfn = pdbfn.substring(0, l);
4682 mtch = idm.findAllIdMatches(pdbfn);
4686 FileFormatI type = null;
4689 type = new IdentifyFile().identify(file, protocol);
4690 } catch (Exception ex)
4694 if (type != null && type.isStructureFile())
4696 filesmatched.add(new Object[] { file, protocol, mtch });
4700 // File wasn't named like one of the sequences or wasn't a PDB
4702 filesnotmatched.add(file);
4706 if (filesmatched.size() > 0)
4708 boolean autoAssociate = Cache
4709 .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4712 String msg = MessageManager.formatMessage(
4713 "label.automatically_associate_structure_files_with_sequences_same_name",
4715 { Integer.valueOf(filesmatched.size())
4717 String ttl = MessageManager.getString(
4718 "label.automatically_associate_structure_files_by_name");
4719 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4720 ttl, JvOptionPane.YES_NO_OPTION);
4721 autoAssociate = choice == JvOptionPane.YES_OPTION;
4725 for (Object[] fm : filesmatched)
4727 // try and associate
4728 // TODO: may want to set a standard ID naming formalism for
4729 // associating PDB files which have no IDs.
4730 for (SequenceI toassoc : (SequenceI[]) fm[2])
4732 PDBEntry pe = new AssociatePdbFileWithSeq()
4733 .associatePdbWithSeq((String) fm[0],
4734 (DataSourceType) fm[1], toassoc, false,
4738 System.err.println("Associated file : "
4739 + ((String) fm[0]) + " with "
4740 + toassoc.getDisplayId(true));
4744 // TODO: do we need to update overview ? only if features are
4746 alignPanel.paintAlignment(true, false);
4752 * add declined structures as sequences
4754 for (Object[] o : filesmatched)
4756 filesnotmatched.add((String) o[0]);
4760 if (filesnotmatched.size() > 0)
4762 if (assocfiles > 0 && (Cache.getDefault(
4763 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4764 || JvOptionPane.showConfirmDialog(thisaf,
4765 "<html>" + MessageManager.formatMessage(
4766 "label.ignore_unmatched_dropped_files_info",
4769 filesnotmatched.size())
4772 MessageManager.getString(
4773 "label.ignore_unmatched_dropped_files"),
4774 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4778 for (String fn : filesnotmatched)
4780 loadJalviewDataFile(fn, null, null, null);
4784 } catch (Exception ex)
4786 ex.printStackTrace();
4794 * Attempt to load a "dropped" file or URL string, by testing in turn for
4796 * <li>an Annotation file</li>
4797 * <li>a JNet file</li>
4798 * <li>a features file</li>
4799 * <li>else try to interpret as an alignment file</li>
4803 * either a filename or a URL string.
4804 * @throws InterruptedException
4805 * @throws IOException
4807 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4808 FileFormatI format, SequenceI assocSeq)
4812 if (sourceType == null)
4814 sourceType = FormatAdapter.checkProtocol(file);
4816 // if the file isn't identified, or not positively identified as some
4817 // other filetype (PFAM is default unidentified alignment file type) then
4818 // try to parse as annotation.
4819 boolean isAnnotation = (format == null
4820 || FileFormat.Pfam.equals(format))
4821 ? new AnnotationFile().annotateAlignmentView(viewport,
4827 // first see if its a T-COFFEE score file
4828 TCoffeeScoreFile tcf = null;
4831 tcf = new TCoffeeScoreFile(file, sourceType);
4834 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4838 new TCoffeeColourScheme(viewport.getAlignment()));
4839 isAnnotation = true;
4840 statusBar.setText(MessageManager.getString(
4841 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4845 // some problem - if no warning its probable that the ID matching
4846 // process didn't work
4847 JvOptionPane.showMessageDialog(Desktop.desktop,
4848 tcf.getWarningMessage() == null
4849 ? MessageManager.getString(
4850 "label.check_file_matches_sequence_ids_alignment")
4851 : tcf.getWarningMessage(),
4852 MessageManager.getString(
4853 "label.problem_reading_tcoffee_score_file"),
4854 JvOptionPane.WARNING_MESSAGE);
4861 } catch (Exception x)
4864 "Exception when processing data source as T-COFFEE score file",
4870 // try to see if its a JNet 'concise' style annotation file *before*
4872 // try to parse it as a features file
4875 format = new IdentifyFile().identify(file, sourceType);
4877 if (FileFormat.ScoreMatrix == format)
4879 ScoreMatrixFile sm = new ScoreMatrixFile(
4880 new FileParse(file, sourceType));
4882 // todo: i18n this message
4883 statusBar.setText(MessageManager.formatMessage(
4884 "label.successfully_loaded_matrix",
4885 sm.getMatrixName()));
4887 else if (FileFormat.Jnet.equals(format))
4889 JPredFile predictions = new JPredFile(file, sourceType);
4890 new JnetAnnotationMaker();
4891 JnetAnnotationMaker.add_annotation(predictions,
4892 viewport.getAlignment(), 0, false);
4893 viewport.getAlignment().setupJPredAlignment();
4894 isAnnotation = true;
4896 // else if (IdentifyFile.FeaturesFile.equals(format))
4897 else if (FileFormat.Features.equals(format))
4899 if (parseFeaturesFile(file, sourceType))
4901 alignPanel.paintAlignment(true, true);
4906 new FileLoader().LoadFile(viewport, file, sourceType, format);
4912 alignPanel.adjustAnnotationHeight();
4913 viewport.updateSequenceIdColours();
4914 buildSortByAnnotationScoresMenu();
4915 alignPanel.paintAlignment(true, true);
4917 } catch (Exception ex)
4919 ex.printStackTrace();
4920 } catch (OutOfMemoryError oom)
4925 } catch (Exception x)
4930 + (sourceType != null
4931 ? (sourceType == DataSourceType.PASTE
4933 : "using " + sourceType + " from "
4937 ? "(parsing as '" + format + "' file)"
4939 oom, Desktop.desktop);
4944 * Method invoked by the ChangeListener on the tabbed pane, in other words
4945 * when a different tabbed pane is selected by the user or programmatically.
4948 public void tabSelectionChanged(int index)
4952 alignPanel = alignPanels.get(index);
4953 viewport = alignPanel.av;
4954 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4955 setMenusFromViewport(viewport);
4959 * 'focus' any colour slider that is open to the selected viewport
4961 if (viewport.getConservationSelected())
4963 SliderPanel.setConservationSlider(alignPanel,
4964 viewport.getResidueShading(), alignPanel.getViewName());
4968 SliderPanel.hideConservationSlider();
4970 if (viewport.getAbovePIDThreshold())
4972 SliderPanel.setPIDSliderSource(alignPanel,
4973 viewport.getResidueShading(), alignPanel.getViewName());
4977 SliderPanel.hidePIDSlider();
4981 * If there is a frame linked to this one in a SplitPane, switch it to the
4982 * same view tab index. No infinite recursion of calls should happen, since
4983 * tabSelectionChanged() should not get invoked on setting the selected
4984 * index to an unchanged value. Guard against setting an invalid index
4985 * before the new view peer tab has been created.
4987 final AlignViewportI peer = viewport.getCodingComplement();
4990 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4991 .getAlignPanel().alignFrame;
4992 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4994 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5000 * On right mouse click on view tab, prompt for and set new view name.
5003 public void tabbedPane_mousePressed(MouseEvent e)
5005 if (e.isPopupTrigger())
5007 String msg = MessageManager.getString("label.enter_view_name");
5008 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
5009 JvOptionPane.QUESTION_MESSAGE);
5013 viewport.setViewName(reply);
5014 // TODO warn if reply is in getExistingViewNames()?
5015 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5020 public AlignViewport getCurrentView()
5026 * Open the dialog for regex description parsing.
5029 protected void extractScores_actionPerformed(ActionEvent e)
5031 ParseProperties pp = new jalview.analysis.ParseProperties(
5032 viewport.getAlignment());
5033 // TODO: verify regex and introduce GUI dialog for version 2.5
5034 // if (pp.getScoresFromDescription("col", "score column ",
5035 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5037 if (pp.getScoresFromDescription("description column",
5038 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5040 buildSortByAnnotationScoresMenu();
5048 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5052 protected void showDbRefs_actionPerformed(ActionEvent e)
5054 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5060 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5064 protected void showNpFeats_actionPerformed(ActionEvent e)
5066 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5070 * find the viewport amongst the tabs in this alignment frame and close that
5075 public boolean closeView(AlignViewportI av)
5079 this.closeMenuItem_actionPerformed(false);
5082 Component[] comp = tabbedPane.getComponents();
5083 for (int i = 0; comp != null && i < comp.length; i++)
5085 if (comp[i] instanceof AlignmentPanel)
5087 if (((AlignmentPanel) comp[i]).av == av)
5090 closeView((AlignmentPanel) comp[i]);
5098 protected void build_fetchdbmenu(JMenu webService)
5100 // Temporary hack - DBRef Fetcher always top level ws entry.
5101 // TODO We probably want to store a sequence database checklist in
5102 // preferences and have checkboxes.. rather than individual sources selected
5104 final JMenu rfetch = new JMenu(
5105 MessageManager.getString("action.fetch_db_references"));
5106 rfetch.setToolTipText(MessageManager.getString(
5107 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5108 webService.add(rfetch);
5110 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5111 MessageManager.getString("option.trim_retrieved_seqs"));
5112 trimrs.setToolTipText(
5113 MessageManager.getString("label.trim_retrieved_sequences"));
5115 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5116 trimrs.addActionListener(new ActionListener()
5119 public void actionPerformed(ActionEvent e)
5121 trimrs.setSelected(trimrs.isSelected());
5122 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5123 Boolean.valueOf(trimrs.isSelected()).toString());
5127 JMenuItem fetchr = new JMenuItem(
5128 MessageManager.getString("label.standard_databases"));
5129 fetchr.setToolTipText(
5130 MessageManager.getString("label.fetch_embl_uniprot"));
5131 fetchr.addActionListener(new ActionListener()
5135 public void actionPerformed(ActionEvent e)
5137 new Thread(new Runnable()
5142 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5143 .getAlignment().isNucleotide();
5144 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5145 alignPanel.av.getSequenceSelection(),
5146 alignPanel.alignFrame, null,
5147 alignPanel.alignFrame.featureSettings, isNucleotide);
5148 dbRefFetcher.addListener(new FetchFinishedListenerI()
5151 public void finished()
5153 AlignFrame.this.setMenusForViewport();
5156 dbRefFetcher.fetchDBRefs(false);
5164 final AlignFrame me = this;
5165 new Thread(new Runnable()
5170 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5171 .getSequenceFetcherSingleton(me);
5172 javax.swing.SwingUtilities.invokeLater(new Runnable()
5177 String[] dbclasses = sf.getOrderedSupportedSources();
5178 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5179 // jalview.util.QuickSort.sort(otherdb, otherdb);
5180 List<DbSourceProxy> otherdb;
5181 JMenu dfetch = new JMenu();
5182 JMenu ifetch = new JMenu();
5183 JMenuItem fetchr = null;
5184 int comp = 0, icomp = 0, mcomp = 15;
5185 String mname = null;
5187 for (String dbclass : dbclasses)
5189 otherdb = sf.getSourceProxy(dbclass);
5190 // add a single entry for this class, or submenu allowing 'fetch
5192 if (otherdb == null || otherdb.size() < 1)
5196 // List<DbSourceProxy> dbs=otherdb;
5197 // otherdb=new ArrayList<DbSourceProxy>();
5198 // for (DbSourceProxy db:dbs)
5200 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5204 mname = "From " + dbclass;
5206 if (otherdb.size() == 1)
5208 final DbSourceProxy[] dassource = otherdb
5209 .toArray(new DbSourceProxy[0]);
5210 DbSourceProxy src = otherdb.get(0);
5211 fetchr = new JMenuItem(src.getDbSource());
5212 fetchr.addActionListener(new ActionListener()
5216 public void actionPerformed(ActionEvent e)
5218 new Thread(new Runnable()
5224 boolean isNucleotide = alignPanel.alignFrame
5225 .getViewport().getAlignment()
5227 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5228 alignPanel.av.getSequenceSelection(),
5229 alignPanel.alignFrame, dassource,
5230 alignPanel.alignFrame.featureSettings,
5233 .addListener(new FetchFinishedListenerI()
5236 public void finished()
5238 AlignFrame.this.setMenusForViewport();
5241 dbRefFetcher.fetchDBRefs(false);
5247 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5248 MessageManager.formatMessage(
5249 "label.fetch_retrieve_from", new Object[]
5250 { src.getDbName() })));
5256 final DbSourceProxy[] dassource = otherdb
5257 .toArray(new DbSourceProxy[0]);
5259 DbSourceProxy src = otherdb.get(0);
5260 fetchr = new JMenuItem(MessageManager
5261 .formatMessage("label.fetch_all_param", new Object[]
5262 { src.getDbSource() }));
5263 fetchr.addActionListener(new ActionListener()
5266 public void actionPerformed(ActionEvent e)
5268 new Thread(new Runnable()
5274 boolean isNucleotide = alignPanel.alignFrame
5275 .getViewport().getAlignment()
5277 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5278 alignPanel.av.getSequenceSelection(),
5279 alignPanel.alignFrame, dassource,
5280 alignPanel.alignFrame.featureSettings,
5283 .addListener(new FetchFinishedListenerI()
5286 public void finished()
5288 AlignFrame.this.setMenusForViewport();
5291 dbRefFetcher.fetchDBRefs(false);
5297 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5298 MessageManager.formatMessage(
5299 "label.fetch_retrieve_from_all_sources",
5301 { Integer.valueOf(otherdb.size())
5303 src.getDbSource(), src.getDbName() })));
5306 // and then build the rest of the individual menus
5307 ifetch = new JMenu(MessageManager.formatMessage(
5308 "label.source_from_db_source", new Object[]
5309 { src.getDbSource() }));
5311 String imname = null;
5313 for (DbSourceProxy sproxy : otherdb)
5315 String dbname = sproxy.getDbName();
5316 String sname = dbname.length() > 5
5317 ? dbname.substring(0, 5) + "..."
5319 String msname = dbname.length() > 10
5320 ? dbname.substring(0, 10) + "..."
5324 imname = MessageManager
5325 .formatMessage("label.from_msname", new Object[]
5328 fetchr = new JMenuItem(msname);
5329 final DbSourceProxy[] dassrc = { sproxy };
5330 fetchr.addActionListener(new ActionListener()
5334 public void actionPerformed(ActionEvent e)
5336 new Thread(new Runnable()
5342 boolean isNucleotide = alignPanel.alignFrame
5343 .getViewport().getAlignment()
5345 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5346 alignPanel.av.getSequenceSelection(),
5347 alignPanel.alignFrame, dassrc,
5348 alignPanel.alignFrame.featureSettings,
5351 .addListener(new FetchFinishedListenerI()
5354 public void finished()
5356 AlignFrame.this.setMenusForViewport();
5359 dbRefFetcher.fetchDBRefs(false);
5365 fetchr.setToolTipText(
5366 "<html>" + MessageManager.formatMessage(
5367 "label.fetch_retrieve_from", new Object[]
5371 if (++icomp >= mcomp || i == (otherdb.size()))
5373 ifetch.setText(MessageManager.formatMessage(
5374 "label.source_to_target", imname, sname));
5376 ifetch = new JMenu();
5384 if (comp >= mcomp || dbi >= (dbclasses.length))
5386 dfetch.setText(MessageManager.formatMessage(
5387 "label.source_to_target", mname, dbclass));
5389 dfetch = new JMenu();
5402 * Left justify the whole alignment.
5405 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5407 AlignmentI al = viewport.getAlignment();
5409 viewport.firePropertyChange("alignment", null, al);
5413 * Right justify the whole alignment.
5416 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5418 AlignmentI al = viewport.getAlignment();
5420 viewport.firePropertyChange("alignment", null, al);
5424 public void setShowSeqFeatures(boolean b)
5426 showSeqFeatures.setSelected(b);
5427 viewport.setShowSequenceFeatures(b);
5434 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5435 * awt.event.ActionEvent)
5438 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5440 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5441 alignPanel.paintAlignment(false, false);
5448 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5452 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5454 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5455 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5463 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5464 * .event.ActionEvent)
5467 protected void showGroupConservation_actionPerformed(ActionEvent e)
5469 viewport.setShowGroupConservation(showGroupConservation.getState());
5470 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5477 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5478 * .event.ActionEvent)
5481 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5483 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5484 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5491 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5492 * .event.ActionEvent)
5495 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5497 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5498 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5502 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5504 showSequenceLogo.setState(true);
5505 viewport.setShowSequenceLogo(true);
5506 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5507 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5511 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5513 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5520 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5521 * .event.ActionEvent)
5524 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5526 if (avc.makeGroupsFromSelection())
5528 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5529 alignPanel.updateAnnotation();
5530 alignPanel.paintAlignment(true,
5531 viewport.needToUpdateStructureViews());
5535 public void clearAlignmentSeqRep()
5537 // TODO refactor alignmentseqrep to controller
5538 if (viewport.getAlignment().hasSeqrep())
5540 viewport.getAlignment().setSeqrep(null);
5541 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5542 alignPanel.updateAnnotation();
5543 alignPanel.paintAlignment(true, true);
5548 protected void createGroup_actionPerformed(ActionEvent e)
5550 if (avc.createGroup())
5552 if (applyAutoAnnotationSettings.isSelected())
5554 alignPanel.updateAnnotation(true, false);
5556 alignPanel.alignmentChanged();
5561 protected void unGroup_actionPerformed(ActionEvent e)
5565 alignPanel.alignmentChanged();
5570 * make the given alignmentPanel the currently selected tab
5572 * @param alignmentPanel
5574 public void setDisplayedView(AlignmentPanel alignmentPanel)
5576 if (!viewport.getSequenceSetId()
5577 .equals(alignmentPanel.av.getSequenceSetId()))
5579 throw new Error(MessageManager.getString(
5580 "error.implementation_error_cannot_show_view_alignment_frame"));
5582 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5583 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5585 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5590 * Action on selection of menu options to Show or Hide annotations.
5593 * @param forSequences
5594 * update sequence-related annotations
5595 * @param forAlignment
5596 * update non-sequence-related annotations
5599 protected void setAnnotationsVisibility(boolean visible,
5600 boolean forSequences, boolean forAlignment)
5602 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5603 .getAlignmentAnnotation();
5608 for (AlignmentAnnotation aa : anns)
5611 * don't display non-positional annotations on an alignment
5613 if (aa.annotations == null)
5617 boolean apply = (aa.sequenceRef == null && forAlignment)
5618 || (aa.sequenceRef != null && forSequences);
5621 aa.visible = visible;
5624 alignPanel.validateAnnotationDimensions(true);
5625 alignPanel.alignmentChanged();
5629 * Store selected annotation sort order for the view and repaint.
5632 protected void sortAnnotations_actionPerformed()
5634 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5636 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5637 alignPanel.paintAlignment(false, false);
5642 * @return alignment panels in this alignment frame
5644 public List<? extends AlignmentViewPanel> getAlignPanels()
5646 // alignPanels is never null
5647 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5652 * Open a new alignment window, with the cDNA associated with this (protein)
5653 * alignment, aligned as is the protein.
5655 protected void viewAsCdna_actionPerformed()
5657 // TODO no longer a menu action - refactor as required
5658 final AlignmentI alignment = getViewport().getAlignment();
5659 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5660 if (mappings == null)
5664 List<SequenceI> cdnaSeqs = new ArrayList<>();
5665 for (SequenceI aaSeq : alignment.getSequences())
5667 for (AlignedCodonFrame acf : mappings)
5669 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5673 * There is a cDNA mapping for this protein sequence - add to new
5674 * alignment. It will share the same dataset sequence as other mapped
5675 * cDNA (no new mappings need to be created).
5677 final Sequence newSeq = new Sequence(dnaSeq);
5678 newSeq.setDatasetSequence(dnaSeq);
5679 cdnaSeqs.add(newSeq);
5683 if (cdnaSeqs.size() == 0)
5685 // show a warning dialog no mapped cDNA
5688 AlignmentI cdna = new Alignment(
5689 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5690 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5691 AlignFrame.DEFAULT_HEIGHT);
5692 cdna.alignAs(alignment);
5693 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5695 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5696 AlignFrame.DEFAULT_HEIGHT);
5700 * Set visibility of dna/protein complement view (available when shown in a
5706 protected void showComplement_actionPerformed(boolean show)
5708 SplitContainerI sf = getSplitViewContainer();
5711 sf.setComplementVisible(this, show);
5716 * Generate the reverse (optionally complemented) of the selected sequences,
5717 * and add them to the alignment
5720 protected void showReverse_actionPerformed(boolean complement)
5722 AlignmentI al = null;
5725 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5726 al = dna.reverseCdna(complement);
5727 viewport.addAlignment(al, "");
5728 addHistoryItem(new EditCommand(
5729 MessageManager.getString("label.add_sequences"), Action.PASTE,
5730 al.getSequencesArray(), 0, al.getWidth(),
5731 viewport.getAlignment()));
5732 } catch (Exception ex)
5734 System.err.println(ex.getMessage());
5740 * Try to run a script in the Groovy console, having first ensured that this
5741 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5742 * be targeted at this alignment.
5745 protected void runGroovy_actionPerformed()
5747 Jalview.setCurrentAlignFrame(this);
5748 groovy.ui.Console console = Desktop.getGroovyConsole();
5749 if (console != null)
5753 console.runScript();
5754 } catch (Exception ex)
5756 System.err.println((ex.toString()));
5757 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5758 MessageManager.getString("label.couldnt_run_groovy_script"),
5759 MessageManager.getString("label.groovy_support_failed"),
5760 JvOptionPane.ERROR_MESSAGE);
5765 System.err.println("Can't run Groovy script as console not found");
5770 * Hides columns containing (or not containing) a specified feature, provided
5771 * that would not leave all columns hidden
5773 * @param featureType
5774 * @param columnsContaining
5777 public boolean hideFeatureColumns(String featureType,
5778 boolean columnsContaining)
5780 boolean notForHiding = avc.markColumnsContainingFeatures(
5781 columnsContaining, false, false, featureType);
5784 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5785 false, featureType))
5787 getViewport().hideSelectedColumns();
5795 protected void selectHighlightedColumns_actionPerformed(
5796 ActionEvent actionEvent)
5798 // include key modifier check in case user selects from menu
5799 avc.markHighlightedColumns(
5800 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5801 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5802 | ActionEvent.CTRL_MASK)) != 0);
5806 * Rebuilds the Colour menu, including any user-defined colours which have
5807 * been loaded either on startup or during the session
5809 public void buildColourMenu()
5811 colourMenu.removeAll();
5813 colourMenu.add(applyToAllGroups);
5814 colourMenu.add(textColour);
5815 colourMenu.addSeparator();
5817 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5818 viewport.getAlignment(), false);
5820 colourMenu.add(annotationColour);
5821 bg.add(annotationColour);
5822 colourMenu.addSeparator();
5823 colourMenu.add(conservationMenuItem);
5824 colourMenu.add(modifyConservation);
5825 colourMenu.add(abovePIDThreshold);
5826 colourMenu.add(modifyPID);
5828 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5829 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5833 * Open a dialog (if not already open) that allows the user to select and
5834 * calculate PCA or Tree analysis
5836 protected void openTreePcaDialog()
5838 if (alignPanel.getCalculationDialog() == null)
5840 new CalculationChooser(AlignFrame.this);
5845 * Sets the status of the HMMER menu
5847 public void updateHMMERStatus()
5849 hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
5853 protected void loadVcf_actionPerformed()
5855 JalviewFileChooser chooser = new JalviewFileChooser(
5856 Cache.getProperty("LAST_DIRECTORY"));
5857 chooser.setFileView(new JalviewFileView());
5858 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5859 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5861 int value = chooser.showOpenDialog(null);
5863 if (value == JalviewFileChooser.APPROVE_OPTION)
5865 String choice = chooser.getSelectedFile().getPath();
5866 Cache.setProperty("LAST_DIRECTORY", choice);
5867 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5868 new VCFLoader(choice).loadVCF(seqs, this);
5874 class PrintThread extends Thread
5878 public PrintThread(AlignmentPanel ap)
5883 static PageFormat pf;
5888 PrinterJob printJob = PrinterJob.getPrinterJob();
5892 printJob.setPrintable(ap, pf);
5896 printJob.setPrintable(ap);
5899 if (printJob.printDialog())
5904 } catch (Exception PrintException)
5906 PrintException.printStackTrace();