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.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingsI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.SimilarityParamsI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignExportSettingsAdapter;
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.PDBEntry;
59 import jalview.datamodel.SeqCigar;
60 import jalview.datamodel.Sequence;
61 import jalview.datamodel.SequenceGroup;
62 import jalview.datamodel.SequenceI;
63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.DataSourceType;
69 import jalview.io.FileFormat;
70 import jalview.io.FileFormatI;
71 import jalview.io.FileFormats;
72 import jalview.io.FileLoader;
73 import jalview.io.FileParse;
74 import jalview.io.FormatAdapter;
75 import jalview.io.HtmlSvgOutput;
76 import jalview.io.IdentifyFile;
77 import jalview.io.JPredFile;
78 import jalview.io.JalviewFileChooser;
79 import jalview.io.JalviewFileView;
80 import jalview.io.JnetAnnotationMaker;
81 import jalview.io.NewickFile;
82 import jalview.io.ScoreMatrixFile;
83 import jalview.io.TCoffeeScoreFile;
84 import jalview.io.vcf.VCFLoader;
85 import jalview.jbgui.GAlignFrame;
86 import jalview.schemes.ColourSchemeI;
87 import jalview.schemes.ColourSchemes;
88 import jalview.schemes.ResidueColourScheme;
89 import jalview.schemes.TCoffeeColourScheme;
90 import jalview.util.ImageMaker.TYPE;
91 import jalview.util.MessageManager;
92 import jalview.util.Platform;
93 import jalview.viewmodel.AlignmentViewport;
94 import jalview.viewmodel.ViewportRanges;
95 import jalview.ws.DBRefFetcher;
96 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
97 import jalview.ws.jws1.Discoverer;
98 import jalview.ws.jws2.Jws2Discoverer;
99 import jalview.ws.jws2.jabaws2.Jws2Instance;
100 import jalview.ws.seqfetcher.DbSourceProxy;
102 import java.awt.BorderLayout;
103 import java.awt.Color;
104 import java.awt.Component;
105 import java.awt.Rectangle;
106 import java.awt.Toolkit;
107 import java.awt.datatransfer.Clipboard;
108 import java.awt.datatransfer.DataFlavor;
109 import java.awt.datatransfer.StringSelection;
110 import java.awt.datatransfer.Transferable;
111 import java.awt.dnd.DnDConstants;
112 import java.awt.dnd.DropTargetDragEvent;
113 import java.awt.dnd.DropTargetDropEvent;
114 import java.awt.dnd.DropTargetEvent;
115 import java.awt.dnd.DropTargetListener;
116 import java.awt.event.ActionEvent;
117 import java.awt.event.ActionListener;
118 import java.awt.event.FocusAdapter;
119 import java.awt.event.FocusEvent;
120 import java.awt.event.ItemEvent;
121 import java.awt.event.ItemListener;
122 import java.awt.event.KeyAdapter;
123 import java.awt.event.KeyEvent;
124 import java.awt.event.MouseEvent;
125 import java.awt.print.PageFormat;
126 import java.awt.print.PrinterJob;
127 import java.beans.PropertyChangeEvent;
129 import java.io.FileWriter;
130 import java.io.PrintWriter;
132 import java.util.ArrayList;
133 import java.util.Arrays;
134 import java.util.Deque;
135 import java.util.Enumeration;
136 import java.util.Hashtable;
137 import java.util.List;
138 import java.util.Vector;
140 import javax.swing.JCheckBoxMenuItem;
141 import javax.swing.JComponent;
142 import javax.swing.JEditorPane;
143 import javax.swing.JInternalFrame;
144 import javax.swing.JLabel;
145 import javax.swing.JLayeredPane;
146 import javax.swing.JMenu;
147 import javax.swing.JMenuItem;
148 import javax.swing.JPanel;
149 import javax.swing.JScrollPane;
150 import javax.swing.SwingUtilities;
156 * @version $Revision$
158 public class AlignFrame extends GAlignFrame implements DropTargetListener,
159 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
162 public static final int DEFAULT_WIDTH = 700;
164 public static final int DEFAULT_HEIGHT = 500;
167 * The currently displayed panel (selected tabbed view if more than one)
169 public AlignmentPanel alignPanel;
171 AlignViewport viewport;
173 public AlignViewControllerI avc;
175 List<AlignmentPanel> alignPanels = new ArrayList<>();
178 * Last format used to load or save alignments in this window
180 FileFormatI currentFileFormat = null;
183 * Current filename for this alignment
185 String fileName = null;
190 * Creates a new AlignFrame object with specific width and height.
196 public AlignFrame(AlignmentI al, int width, int height)
198 this(al, null, width, height);
202 * Creates a new AlignFrame object with specific width, height and
208 * @param sequenceSetId
210 public AlignFrame(AlignmentI al, int width, int height,
211 String sequenceSetId)
213 this(al, null, width, height, sequenceSetId);
217 * Creates a new AlignFrame object with specific width, height and
223 * @param sequenceSetId
226 public AlignFrame(AlignmentI al, int width, int height,
227 String sequenceSetId, String viewId)
229 this(al, null, width, height, sequenceSetId, viewId);
233 * new alignment window with hidden columns
237 * @param hiddenColumns
238 * ColumnSelection or null
240 * Width of alignment frame
244 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
247 this(al, hiddenColumns, width, height, null);
251 * Create alignment frame for al with hiddenColumns, a specific width and
252 * height, and specific sequenceId
255 * @param hiddenColumns
258 * @param sequenceSetId
261 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
262 int height, String sequenceSetId)
264 this(al, hiddenColumns, width, height, sequenceSetId, null);
268 * Create alignment frame for al with hiddenColumns, a specific width and
269 * height, and specific sequenceId
272 * @param hiddenColumns
275 * @param sequenceSetId
280 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
281 int height, String sequenceSetId, String viewId)
283 setSize(width, height);
285 if (al.getDataset() == null)
290 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
292 alignPanel = new AlignmentPanel(this, viewport);
294 addAlignmentPanel(alignPanel, true);
298 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
299 HiddenColumns hiddenColumns, int width, int height)
301 setSize(width, height);
303 if (al.getDataset() == null)
308 viewport = new AlignViewport(al, hiddenColumns);
310 if (hiddenSeqs != null && hiddenSeqs.length > 0)
312 viewport.hideSequence(hiddenSeqs);
314 alignPanel = new AlignmentPanel(this, viewport);
315 addAlignmentPanel(alignPanel, true);
320 * Make a new AlignFrame from existing alignmentPanels
327 public AlignFrame(AlignmentPanel ap)
331 addAlignmentPanel(ap, false);
336 * initalise the alignframe from the underlying viewport data and the
341 // setBackground(Color.white); // BH 2019
343 if (!Jalview.isHeadlessMode())
345 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
348 avc = new jalview.controller.AlignViewController(this, viewport,
350 if (viewport.getAlignmentConservationAnnotation() == null)
352 // BLOSUM62Colour.setEnabled(false);
353 conservationMenuItem.setEnabled(false);
354 modifyConservation.setEnabled(false);
355 // PIDColour.setEnabled(false);
356 // abovePIDThreshold.setEnabled(false);
357 // modifyPID.setEnabled(false);
360 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
363 if (sortby.equals("Id"))
365 sortIDMenuItem_actionPerformed(null);
367 else if (sortby.equals("Pairwise Identity"))
369 sortPairwiseMenuItem_actionPerformed(null);
373 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
375 setMenusFromViewport(viewport);
376 buildSortByAnnotationScoresMenu();
377 calculateTree.addActionListener(new ActionListener()
381 public void actionPerformed(ActionEvent e)
388 if (Desktop.desktop != null)
390 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
392 * BH 2018 ignore service listeners
398 addServiceListeners();
403 if (viewport.getWrapAlignment())
405 wrapMenuItem_actionPerformed(null);
408 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
410 this.overviewMenuItem_actionPerformed(null);
415 final List<AlignmentPanel> selviews = new ArrayList<>();
416 final List<AlignmentPanel> origview = new ArrayList<>();
417 final String menuLabel = MessageManager
418 .getString("label.copy_format_from");
419 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
420 new ViewSetProvider()
424 public AlignmentPanel[] getAllAlignmentPanels()
427 origview.add(alignPanel);
428 // make an array of all alignment panels except for this one
429 List<AlignmentPanel> aps = new ArrayList<>(
430 Arrays.asList(Desktop.getAlignmentPanels(null)));
431 aps.remove(AlignFrame.this.alignPanel);
432 return aps.toArray(new AlignmentPanel[aps.size()]);
434 }, selviews, new ItemListener()
438 public void itemStateChanged(ItemEvent e)
440 if (origview.size() > 0)
442 final AlignmentPanel ap = origview.get(0);
445 * Copy the ViewStyle of the selected panel to 'this one'.
446 * Don't change value of 'scaleProteinAsCdna' unless copying
449 ViewStyleI vs = selviews.get(0).getAlignViewport()
451 boolean fromSplitFrame = selviews.get(0)
452 .getAlignViewport().getCodingComplement() != null;
455 vs.setScaleProteinAsCdna(ap.getAlignViewport()
456 .getViewStyle().isScaleProteinAsCdna());
458 ap.getAlignViewport().setViewStyle(vs);
461 * Also rescale ViewStyle of SplitFrame complement if there is
462 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
463 * the whole ViewStyle (allow cDNA protein to have different
466 AlignViewportI complement = ap.getAlignViewport()
467 .getCodingComplement();
468 if (complement != null && vs.isScaleProteinAsCdna())
470 AlignFrame af = Desktop.getAlignFrameFor(complement);
471 ((SplitFrame) af.getSplitViewContainer())
473 af.setMenusForViewport();
477 ap.setSelected(true);
478 ap.alignFrame.setMenusForViewport();
483 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
484 .indexOf("devel") > -1
485 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
486 .indexOf("test") > -1)
488 formatMenu.add(vsel);
490 addFocusListener(new FocusAdapter()
493 public void focusGained(FocusEvent e)
495 Jalview.setCurrentAlignFrame(AlignFrame.this);
502 * Change the filename and format for the alignment, and enable the 'reload'
503 * button functionality.
510 public void setFileName(String file, FileFormatI format)
513 setFileFormat(format);
514 reload.setEnabled(true);
518 * JavaScript will have this, maybe others. More dependable than a file name
519 * and maintains a reference to the actual bytes loaded.
523 public void setFileObject(File file)
525 this.fileObject = file;
529 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
532 void addKeyListener()
534 addKeyListener(new KeyAdapter()
537 public void keyPressed(KeyEvent evt)
539 if (viewport.cursorMode
540 && ((evt.getKeyCode() >= KeyEvent.VK_0
541 && evt.getKeyCode() <= KeyEvent.VK_9)
542 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
543 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
544 && Character.isDigit(evt.getKeyChar()))
546 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
549 switch (evt.getKeyCode())
552 case 27: // escape key
553 deselectAllSequenceMenuItem_actionPerformed(null);
557 case KeyEvent.VK_DOWN:
558 if (evt.isAltDown() || !viewport.cursorMode)
560 moveSelectedSequences(false);
562 if (viewport.cursorMode)
564 alignPanel.getSeqPanel().moveCursor(0, 1);
569 if (evt.isAltDown() || !viewport.cursorMode)
571 moveSelectedSequences(true);
573 if (viewport.cursorMode)
575 alignPanel.getSeqPanel().moveCursor(0, -1);
580 case KeyEvent.VK_LEFT:
581 if (evt.isAltDown() || !viewport.cursorMode)
583 slideSequences(false,
584 alignPanel.getSeqPanel().getKeyboardNo1());
588 alignPanel.getSeqPanel().moveCursor(-1, 0);
593 case KeyEvent.VK_RIGHT:
594 if (evt.isAltDown() || !viewport.cursorMode)
596 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
600 alignPanel.getSeqPanel().moveCursor(1, 0);
604 case KeyEvent.VK_SPACE:
605 if (viewport.cursorMode)
607 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
608 || evt.isShiftDown() || evt.isAltDown());
612 // case KeyEvent.VK_A:
613 // if (viewport.cursorMode)
615 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
616 // //System.out.println("A");
620 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
621 * System.out.println("closing bracket"); } break;
623 case KeyEvent.VK_DELETE:
624 case KeyEvent.VK_BACK_SPACE:
625 if (!viewport.cursorMode)
627 cut_actionPerformed(null);
631 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
632 || evt.isShiftDown() || evt.isAltDown());
638 if (viewport.cursorMode)
640 alignPanel.getSeqPanel().setCursorRow();
644 if (viewport.cursorMode && !evt.isControlDown())
646 alignPanel.getSeqPanel().setCursorColumn();
650 if (viewport.cursorMode)
652 alignPanel.getSeqPanel().setCursorPosition();
656 case KeyEvent.VK_ENTER:
657 case KeyEvent.VK_COMMA:
658 if (viewport.cursorMode)
660 alignPanel.getSeqPanel().setCursorRowAndColumn();
665 if (viewport.cursorMode)
667 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
671 if (viewport.cursorMode)
673 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
678 viewport.cursorMode = !viewport.cursorMode;
679 setStatus(MessageManager
680 .formatMessage("label.keyboard_editing_mode", new String[]
681 { (viewport.cursorMode ? "on" : "off") }));
682 if (viewport.cursorMode)
684 ViewportRanges ranges = viewport.getRanges();
685 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
687 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
690 alignPanel.getSeqPanel().seqCanvas.repaint();
696 Help.showHelpWindow();
697 } catch (Exception ex)
699 ex.printStackTrace();
704 boolean toggleSeqs = !evt.isControlDown();
705 boolean toggleCols = !evt.isShiftDown();
706 toggleHiddenRegions(toggleSeqs, toggleCols);
711 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
712 boolean modifyExisting = true; // always modify, don't clear
713 // evt.isShiftDown();
714 boolean invertHighlighted = evt.isAltDown();
715 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
719 case KeyEvent.VK_PAGE_UP:
720 viewport.getRanges().pageUp();
722 case KeyEvent.VK_PAGE_DOWN:
723 viewport.getRanges().pageDown();
729 public void keyReleased(KeyEvent evt)
731 switch (evt.getKeyCode())
733 case KeyEvent.VK_LEFT:
734 if (evt.isAltDown() || !viewport.cursorMode)
736 viewport.firePropertyChange("alignment", null,
737 viewport.getAlignment().getSequences());
741 case KeyEvent.VK_RIGHT:
742 if (evt.isAltDown() || !viewport.cursorMode)
744 viewport.firePropertyChange("alignment", null,
745 viewport.getAlignment().getSequences());
753 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
755 ap.alignFrame = this;
756 avc = new jalview.controller.AlignViewController(this, viewport,
761 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
763 int aSize = alignPanels.size();
765 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
767 if (aSize == 1 && ap.av.getViewName() == null)
769 this.getContentPane().add(ap, BorderLayout.CENTER);
775 setInitialTabVisible();
778 expandViews.setEnabled(true);
779 gatherViews.setEnabled(true);
780 tabbedPane.addTab(ap.av.getViewName(), ap);
782 ap.setVisible(false);
787 if (ap.av.isPadGaps())
789 ap.av.getAlignment().padGaps();
791 ap.av.updateConservation(ap);
792 ap.av.updateConsensus(ap);
793 ap.av.updateStrucConsensus(ap);
797 public void setInitialTabVisible()
799 expandViews.setEnabled(true);
800 gatherViews.setEnabled(true);
801 tabbedPane.setVisible(true);
802 AlignmentPanel first = alignPanels.get(0);
803 tabbedPane.addTab(first.av.getViewName(), first);
804 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
807 public AlignViewport getViewport()
812 /* Set up intrinsic listeners for dynamically generated GUI bits. */
813 private void addServiceListeners()
815 final java.beans.PropertyChangeListener thisListener;
816 Desktop.instance.addJalviewPropertyChangeListener("services",
817 thisListener = new java.beans.PropertyChangeListener()
820 public void propertyChange(PropertyChangeEvent evt)
822 // // System.out.println("Discoverer property change.");
823 // if (evt.getPropertyName().equals("services"))
825 SwingUtilities.invokeLater(new Runnable()
832 "Rebuild WS Menu for service change");
833 BuildWebServiceMenu();
840 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
843 public void internalFrameClosed(
844 javax.swing.event.InternalFrameEvent evt)
846 // System.out.println("deregistering discoverer listener");
847 Desktop.instance.removeJalviewPropertyChangeListener("services",
849 closeMenuItem_actionPerformed(true);
852 // Finally, build the menu once to get current service state
853 new Thread(new Runnable()
858 BuildWebServiceMenu();
864 * Configure menu items that vary according to whether the alignment is
865 * nucleotide or protein
867 public void setGUINucleotide()
869 AlignmentI al = getViewport().getAlignment();
870 boolean nucleotide = al.isNucleotide();
872 loadVcf.setVisible(nucleotide);
873 showTranslation.setVisible(nucleotide);
874 showReverse.setVisible(nucleotide);
875 showReverseComplement.setVisible(nucleotide);
876 conservationMenuItem.setEnabled(!nucleotide);
878 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
879 showGroupConservation.setEnabled(!nucleotide);
881 showComplementMenuItem
882 .setText(nucleotide ? MessageManager.getString("label.protein")
883 : MessageManager.getString("label.nucleotide"));
887 * set up menus for the current viewport. This may be called after any
888 * operation that affects the data in the current view (selection changed,
889 * etc) to update the menus to reflect the new state.
892 public void setMenusForViewport()
894 setMenusFromViewport(viewport);
898 * Need to call this method when tabs are selected for multiple views, or when
899 * loading from Jalview2XML.java
904 public void setMenusFromViewport(AlignViewport av)
906 padGapsMenuitem.setSelected(av.isPadGaps());
907 colourTextMenuItem.setSelected(av.isShowColourText());
908 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
909 modifyPID.setEnabled(abovePIDThreshold.isSelected());
910 conservationMenuItem.setSelected(av.getConservationSelected());
911 modifyConservation.setEnabled(conservationMenuItem.isSelected());
912 seqLimits.setSelected(av.getShowJVSuffix());
913 idRightAlign.setSelected(av.isRightAlignIds());
914 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
915 renderGapsMenuItem.setSelected(av.isRenderGaps());
916 wrapMenuItem.setSelected(av.getWrapAlignment());
917 scaleAbove.setVisible(av.getWrapAlignment());
918 scaleLeft.setVisible(av.getWrapAlignment());
919 scaleRight.setVisible(av.getWrapAlignment());
920 annotationPanelMenuItem.setState(av.isShowAnnotation());
922 * Show/hide annotations only enabled if annotation panel is shown
924 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
925 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
926 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
927 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
928 viewBoxesMenuItem.setSelected(av.getShowBoxes());
929 viewTextMenuItem.setSelected(av.getShowText());
930 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
931 showGroupConsensus.setSelected(av.isShowGroupConsensus());
932 showGroupConservation.setSelected(av.isShowGroupConservation());
933 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
934 showSequenceLogo.setSelected(av.isShowSequenceLogo());
935 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
937 ColourMenuHelper.setColourSelected(colourMenu,
938 av.getGlobalColourScheme());
940 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
941 hiddenMarkers.setState(av.getShowHiddenMarkers());
942 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
943 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
944 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
945 autoCalculate.setSelected(av.autoCalculateConsensus);
946 sortByTree.setSelected(av.sortByTree);
947 listenToViewSelections.setSelected(av.followSelection);
949 showProducts.setEnabled(canShowProducts());
950 setGroovyEnabled(Desktop.getGroovyConsole() != null);
956 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
960 public void setGroovyEnabled(boolean b)
962 runGroovy.setEnabled(b);
965 private IProgressIndicator progressBar;
970 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
973 public void setProgressBar(String message, long id)
975 progressBar.setProgressBar(message, id);
979 public void registerHandler(final long id,
980 final IProgressIndicatorHandler handler)
982 progressBar.registerHandler(id, handler);
987 * @return true if any progress bars are still active
990 public boolean operationInProgress()
992 return progressBar.operationInProgress();
996 public void setStatus(String text)
998 // BH note: If text width and height are 0, then the layout manager
999 // will dispense of it and change the frame height.
1000 // In JavaScript, we use \u00A0 -- unicode "non-breaking space"
1001 // which is the unicode encoding of
1003 statusBar.setText(text == null || text.isEmpty() ? " " : text);
1007 * Added so Castor Mapping file can obtain Jalview Version
1009 public String getVersion()
1011 return jalview.bin.Cache.getProperty("VERSION");
1014 public FeatureRenderer getFeatureRenderer()
1016 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1020 public void fetchSequence_actionPerformed()
1022 new SequenceFetcher(this);
1026 public void addFromFile_actionPerformed(ActionEvent e)
1028 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1032 public void reload_actionPerformed(ActionEvent e)
1034 if (fileName != null)
1036 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1037 // originating file's format
1038 // TODO: work out how to recover feature settings for correct view(s) when
1039 // file is reloaded.
1040 if (FileFormat.Jalview.equals(currentFileFormat))
1042 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1043 for (int i = 0; i < frames.length; i++)
1045 if (frames[i] instanceof AlignFrame && frames[i] != this
1046 && ((AlignFrame) frames[i]).fileName != null
1047 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1051 frames[i].setSelected(true);
1052 Desktop.instance.closeAssociatedWindows();
1053 } catch (java.beans.PropertyVetoException ex)
1059 Desktop.instance.closeAssociatedWindows();
1061 FileLoader loader = new FileLoader();
1062 DataSourceType protocol = fileName.startsWith("http:")
1063 ? DataSourceType.URL
1064 : DataSourceType.FILE;
1065 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1069 Rectangle bounds = this.getBounds();
1071 FileLoader loader = new FileLoader();
1073 AlignFrame newframe = null;
1075 if (fileObject == null)
1078 DataSourceType protocol = (fileName.startsWith("http:")
1079 ? DataSourceType.URL
1080 : DataSourceType.FILE);
1081 newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1086 newframe = loader.LoadFileWaitTillLoaded(fileObject,
1087 DataSourceType.FILE, currentFileFormat);
1090 newframe.setBounds(bounds);
1091 if (featureSettings != null && featureSettings.isShowing())
1093 final Rectangle fspos = featureSettings.frame.getBounds();
1094 // TODO: need a 'show feature settings' function that takes bounds -
1095 // need to refactor Desktop.addFrame
1096 newframe.featureSettings_actionPerformed(null);
1097 final FeatureSettings nfs = newframe.featureSettings;
1098 SwingUtilities.invokeLater(new Runnable()
1103 nfs.frame.setBounds(fspos);
1106 this.featureSettings.close();
1107 this.featureSettings = null;
1109 this.closeMenuItem_actionPerformed(true);
1115 public void addFromText_actionPerformed(ActionEvent e)
1118 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1122 public void addFromURL_actionPerformed(ActionEvent e)
1124 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1128 public void save_actionPerformed(ActionEvent e)
1130 if (fileName == null || (currentFileFormat == null)
1131 || fileName.startsWith("http"))
1133 saveAs_actionPerformed();
1137 saveAlignment(fileName, currentFileFormat);
1142 * Saves the alignment to a file with a name chosen by the user, if necessary
1143 * warning if a file would be overwritten
1146 public void saveAs_actionPerformed()
1148 String format = currentFileFormat == null ? null
1149 : currentFileFormat.getName();
1150 JalviewFileChooser chooser = JalviewFileChooser
1151 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1153 chooser.setFileView(new JalviewFileView());
1154 chooser.setDialogTitle(
1155 MessageManager.getString("label.save_alignment_to_file"));
1156 chooser.setToolTipText(MessageManager.getString("action.save"));
1158 int value = chooser.showSaveDialog(this);
1160 if (value != JalviewFileChooser.APPROVE_OPTION)
1164 currentFileFormat = chooser.getSelectedFormat();
1165 // todo is this (2005) test now obsolete - value is never null?
1166 while (currentFileFormat == null)
1168 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1170 .getString("label.select_file_format_before_saving"),
1171 MessageManager.getString("label.file_format_not_specified"),
1172 JvOptionPane.WARNING_MESSAGE);
1173 currentFileFormat = chooser.getSelectedFormat();
1174 value = chooser.showSaveDialog(this);
1175 if (value != JalviewFileChooser.APPROVE_OPTION)
1181 fileName = chooser.getSelectedFile().getPath();
1183 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1184 Cache.setProperty("LAST_DIRECTORY", fileName);
1185 saveAlignment(fileName, currentFileFormat);
1188 boolean lastSaveSuccessful = false;
1190 FileFormatI lastFormatSaved;
1192 String lastFilenameSaved;
1195 * Raise a dialog or status message for the last call to saveAlignment.
1197 * @return true if last call to saveAlignment(file, format) was successful.
1199 public boolean isSaveAlignmentSuccessful()
1202 if (!lastSaveSuccessful)
1204 JvOptionPane.showInternalMessageDialog(this, MessageManager
1205 .formatMessage("label.couldnt_save_file", new Object[]
1206 { lastFilenameSaved }),
1207 MessageManager.getString("label.error_saving_file"),
1208 JvOptionPane.WARNING_MESSAGE);
1213 setStatus(MessageManager.formatMessage(
1214 "label.successfully_saved_to_file_in_format", new Object[]
1215 { lastFilenameSaved, lastFormatSaved }));
1218 return lastSaveSuccessful;
1222 * Saves the alignment to the specified file path, in the specified format,
1223 * which may be an alignment format, or Jalview project format. If the
1224 * alignment has hidden regions, or the format is one capable of including
1225 * non-sequence data (features, annotations, groups), then the user may be
1226 * prompted to specify what to include in the output.
1231 public void saveAlignment(String file, FileFormatI format)
1233 lastSaveSuccessful = false;
1234 lastFilenameSaved = file;
1235 lastFormatSaved = format;
1237 if (FileFormat.Jalview.equals(format))
1239 String shortName = title;
1240 if (shortName.indexOf(File.separatorChar) > -1)
1242 shortName = shortName.substring(
1243 shortName.lastIndexOf(File.separatorChar) + 1);
1245 lastSaveSuccessful = new jalview.project.Jalview2XML().saveAlignment(this, file,
1248 statusBar.setText(MessageManager.formatMessage(
1249 "label.successfully_saved_to_file_in_format", new Object[]
1250 { fileName, format }));
1255 AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1256 Runnable cancelAction = new Runnable()
1261 lastSaveSuccessful = false;
1264 Runnable outputAction = new Runnable()
1269 // todo defer this to inside formatSequences (or later)
1270 AlignmentExportData exportData = viewport
1271 .getAlignExportData(options);
1272 String output = new FormatAdapter(alignPanel, options)
1273 .formatSequences(format, exportData.getAlignment(),
1274 exportData.getOmitHidden(),
1275 exportData.getStartEndPostions(),
1276 viewport.getAlignment().getHiddenColumns());
1279 lastSaveSuccessful = false;
1285 PrintWriter out = new PrintWriter(new FileWriter(file));
1288 AlignFrame.this.setTitle(file);
1289 setStatus(MessageManager.formatMessage(
1290 "label.successfully_saved_to_file_in_format",
1292 { fileName, format.getName() }));
1293 } catch (Exception ex)
1295 lastSaveSuccessful = false;
1296 ex.printStackTrace();
1303 * show dialog with export options if applicable; else just do it
1305 if (AlignExportOptions.isNeeded(viewport, format))
1307 AlignExportOptions choices = new AlignExportOptions(
1308 alignPanel.getAlignViewport(), format, options);
1309 choices.setResponseAction(0, outputAction);
1310 choices.setResponseAction(1, cancelAction);
1311 choices.showDialog();
1320 * Outputs the alignment to textbox in the requested format, if necessary
1321 * first prompting the user for whether to include hidden regions or
1324 * @param fileFormatName
1327 protected void outputText_actionPerformed(String fileFormatName)
1329 FileFormatI fileFormat = FileFormats.getInstance()
1330 .forName(fileFormatName);
1331 AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1332 Runnable outputAction = new Runnable()
1337 // todo defer this to inside formatSequences (or later)
1338 AlignmentExportData exportData = viewport
1339 .getAlignExportData(options);
1340 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1341 cap.setForInput(null);
1344 FileFormatI format = fileFormat;
1345 cap.setText(new FormatAdapter(alignPanel, options)
1346 .formatSequences(format, exportData.getAlignment(),
1347 exportData.getOmitHidden(),
1348 exportData.getStartEndPostions(),
1349 viewport.getAlignment().getHiddenColumns()));
1350 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1351 "label.alignment_output_command", new Object[]
1352 { fileFormat.getName() }), 600, 500);
1353 } catch (OutOfMemoryError oom)
1355 new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1363 * show dialog with export options if applicable; else just do it
1365 if (AlignExportOptions.isNeeded(viewport, fileFormat))
1367 AlignExportOptions choices = new AlignExportOptions(
1368 alignPanel.getAlignViewport(), fileFormat, options);
1369 choices.setResponseAction(0, outputAction);
1370 choices.showDialog();
1385 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1387 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1388 htmlSVG.exportHTML(null);
1392 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1394 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1395 bjs.exportHTML(null);
1398 public void createImageMap(File file, String image)
1400 alignPanel.makePNGImageMap(file, image);
1404 * Creates a PNG image of the alignment and writes it to the given file. If
1405 * the file is null, the user is prompted to choose a file.
1410 public void createPNG(File f)
1412 alignPanel.makeAlignmentImage(TYPE.PNG, f);
1416 * Creates an EPS image of the alignment and writes it to the given file. If
1417 * the file is null, the user is prompted to choose a file.
1422 public void createEPS(File f)
1424 alignPanel.makeAlignmentImage(TYPE.EPS, f);
1428 * Creates an SVG image of the alignment and writes it to the given file. If
1429 * the file is null, the user is prompted to choose a file.
1434 public void createSVG(File f)
1436 alignPanel.makeAlignmentImage(TYPE.SVG, f);
1440 public void pageSetup_actionPerformed(ActionEvent e)
1442 PrinterJob printJob = PrinterJob.getPrinterJob();
1443 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1453 public void printMenuItem_actionPerformed(ActionEvent e)
1455 // Putting in a thread avoids Swing painting problems
1456 PrintThread thread = new PrintThread(alignPanel);
1461 public void exportFeatures_actionPerformed(ActionEvent e)
1463 new AnnotationExporter(alignPanel).exportFeatures();
1467 public void exportAnnotations_actionPerformed(ActionEvent e)
1469 new AnnotationExporter(alignPanel).exportAnnotations();
1473 public void associatedData_actionPerformed(ActionEvent e)
1475 final JalviewFileChooser chooser = new JalviewFileChooser(
1476 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1477 chooser.setFileView(new JalviewFileView());
1478 chooser.setDialogTitle(
1479 MessageManager.getString("label.load_jalview_annotations"));
1480 chooser.setToolTipText(
1481 MessageManager.getString("label.load_jalview_annotations"));
1482 chooser.setResponseHandler(0, new Runnable()
1487 String choice = chooser.getSelectedFile().getPath();
1488 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1489 loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1493 chooser.showOpenDialog(this);
1497 * Close the current view or all views in the alignment frame. If the frame
1498 * only contains one view then the alignment will be removed from memory.
1500 * @param closeAllTabs
1503 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1505 if (alignPanels != null && alignPanels.size() < 2)
1507 closeAllTabs = true;
1512 if (alignPanels != null)
1516 if (this.isClosed())
1518 // really close all the windows - otherwise wait till
1519 // setClosed(true) is called
1520 for (int i = 0; i < alignPanels.size(); i++)
1522 AlignmentPanel ap = alignPanels.get(i);
1529 closeView(alignPanel);
1536 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1537 * be called recursively, with the frame now in 'closed' state
1539 this.setClosed(true);
1541 } catch (Exception ex)
1543 ex.printStackTrace();
1548 * Close the specified panel and close up tabs appropriately.
1550 * @param panelToClose
1552 public void closeView(AlignmentPanel panelToClose)
1554 int index = tabbedPane.getSelectedIndex();
1555 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1556 alignPanels.remove(panelToClose);
1557 panelToClose.closePanel();
1558 panelToClose = null;
1560 tabbedPane.removeTabAt(closedindex);
1561 tabbedPane.validate();
1563 if (index > closedindex || index == tabbedPane.getTabCount())
1565 // modify currently selected tab index if necessary.
1569 this.tabSelectionChanged(index);
1575 void updateEditMenuBar()
1578 if (viewport.getHistoryList().size() > 0)
1580 undoMenuItem.setEnabled(true);
1581 CommandI command = viewport.getHistoryList().peek();
1582 undoMenuItem.setText(MessageManager
1583 .formatMessage("label.undo_command", new Object[]
1584 { command.getDescription() }));
1588 undoMenuItem.setEnabled(false);
1589 undoMenuItem.setText(MessageManager.getString("action.undo"));
1592 if (viewport.getRedoList().size() > 0)
1594 redoMenuItem.setEnabled(true);
1596 CommandI command = viewport.getRedoList().peek();
1597 redoMenuItem.setText(MessageManager
1598 .formatMessage("label.redo_command", new Object[]
1599 { command.getDescription() }));
1603 redoMenuItem.setEnabled(false);
1604 redoMenuItem.setText(MessageManager.getString("action.redo"));
1609 public void addHistoryItem(CommandI command)
1611 if (command.getSize() > 0)
1613 viewport.addToHistoryList(command);
1614 viewport.clearRedoList();
1615 updateEditMenuBar();
1616 viewport.updateHiddenColumns();
1617 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1618 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1619 // viewport.getColumnSelection()
1620 // .getHiddenColumns().size() > 0);
1626 * @return alignment objects for all views
1628 AlignmentI[] getViewAlignments()
1630 if (alignPanels != null)
1632 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1634 for (AlignmentPanel ap : alignPanels)
1636 als[i++] = ap.av.getAlignment();
1640 if (viewport != null)
1642 return new AlignmentI[] { viewport.getAlignment() };
1654 protected void undoMenuItem_actionPerformed(ActionEvent e)
1656 if (viewport.getHistoryList().isEmpty())
1660 CommandI command = viewport.getHistoryList().pop();
1661 viewport.addToRedoList(command);
1662 command.undoCommand(getViewAlignments());
1664 AlignmentViewport originalSource = getOriginatingSource(command);
1665 updateEditMenuBar();
1667 if (originalSource != null)
1669 if (originalSource != viewport)
1672 "Implementation worry: mismatch of viewport origin for undo");
1674 originalSource.updateHiddenColumns();
1675 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1677 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1678 // viewport.getColumnSelection()
1679 // .getHiddenColumns().size() > 0);
1680 originalSource.firePropertyChange("alignment", null,
1681 originalSource.getAlignment().getSequences());
1692 protected void redoMenuItem_actionPerformed(ActionEvent e)
1694 if (viewport.getRedoList().size() < 1)
1699 CommandI command = viewport.getRedoList().pop();
1700 viewport.addToHistoryList(command);
1701 command.doCommand(getViewAlignments());
1703 AlignmentViewport originalSource = getOriginatingSource(command);
1704 updateEditMenuBar();
1706 if (originalSource != null)
1709 if (originalSource != viewport)
1712 "Implementation worry: mismatch of viewport origin for redo");
1714 originalSource.updateHiddenColumns();
1715 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1717 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1718 // viewport.getColumnSelection()
1719 // .getHiddenColumns().size() > 0);
1720 originalSource.firePropertyChange("alignment", null,
1721 originalSource.getAlignment().getSequences());
1725 AlignmentViewport getOriginatingSource(CommandI command)
1727 AlignmentViewport originalSource = null;
1728 // For sequence removal and addition, we need to fire
1729 // the property change event FROM the viewport where the
1730 // original alignment was altered
1731 AlignmentI al = null;
1732 if (command instanceof EditCommand)
1734 EditCommand editCommand = (EditCommand) command;
1735 al = editCommand.getAlignment();
1736 List<Component> comps = PaintRefresher.components
1737 .get(viewport.getSequenceSetId());
1739 for (Component comp : comps)
1741 if (comp instanceof AlignmentPanel)
1743 if (al == ((AlignmentPanel) comp).av.getAlignment())
1745 originalSource = ((AlignmentPanel) comp).av;
1752 if (originalSource == null)
1754 // The original view is closed, we must validate
1755 // the current view against the closed view first
1758 PaintRefresher.validateSequences(al, viewport.getAlignment());
1761 originalSource = viewport;
1764 return originalSource;
1773 public void moveSelectedSequences(boolean up)
1775 SequenceGroup sg = viewport.getSelectionGroup();
1781 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1782 viewport.getHiddenRepSequences(), up);
1783 alignPanel.paintAlignment(true, false);
1786 synchronized void slideSequences(boolean right, int size)
1788 List<SequenceI> sg = new ArrayList<>();
1789 if (viewport.cursorMode)
1791 sg.add(viewport.getAlignment()
1792 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1794 else if (viewport.getSelectionGroup() != null
1795 && viewport.getSelectionGroup().getSize() != viewport
1796 .getAlignment().getHeight())
1798 sg = viewport.getSelectionGroup()
1799 .getSequences(viewport.getHiddenRepSequences());
1807 List<SequenceI> invertGroup = new ArrayList<>();
1809 for (SequenceI seq : viewport.getAlignment().getSequences())
1811 if (!sg.contains(seq))
1813 invertGroup.add(seq);
1817 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1819 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1820 for (int i = 0; i < invertGroup.size(); i++)
1822 seqs2[i] = invertGroup.get(i);
1825 SlideSequencesCommand ssc;
1828 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1829 viewport.getGapCharacter());
1833 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1834 viewport.getGapCharacter());
1837 int groupAdjustment = 0;
1838 if (ssc.getGapsInsertedBegin() && right)
1840 if (viewport.cursorMode)
1842 alignPanel.getSeqPanel().moveCursor(size, 0);
1846 groupAdjustment = size;
1849 else if (!ssc.getGapsInsertedBegin() && !right)
1851 if (viewport.cursorMode)
1853 alignPanel.getSeqPanel().moveCursor(-size, 0);
1857 groupAdjustment = -size;
1861 if (groupAdjustment != 0)
1863 viewport.getSelectionGroup().setStartRes(
1864 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1865 viewport.getSelectionGroup().setEndRes(
1866 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1870 * just extend the last slide command if compatible; but not if in
1871 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1873 boolean appendHistoryItem = false;
1874 Deque<CommandI> historyList = viewport.getHistoryList();
1875 boolean inSplitFrame = getSplitViewContainer() != null;
1876 if (!inSplitFrame && historyList != null && historyList.size() > 0
1877 && historyList.peek() instanceof SlideSequencesCommand)
1879 appendHistoryItem = ssc.appendSlideCommand(
1880 (SlideSequencesCommand) historyList.peek());
1883 if (!appendHistoryItem)
1885 addHistoryItem(ssc);
1898 protected void copy_actionPerformed(ActionEvent e)
1900 if (viewport.getSelectionGroup() == null)
1904 // TODO: preserve the ordering of displayed alignment annotation in any
1905 // internal paste (particularly sequence associated annotation)
1906 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1907 String[] omitHidden = null;
1909 if (viewport.hasHiddenColumns())
1911 omitHidden = viewport.getViewAsString(true);
1914 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1915 seqs, omitHidden, null);
1917 StringSelection ss = new StringSelection(output);
1921 jalview.gui.Desktop.internalCopy = true;
1922 // Its really worth setting the clipboard contents
1923 // to empty before setting the large StringSelection!!
1924 Toolkit.getDefaultToolkit().getSystemClipboard()
1925 .setContents(new StringSelection(""), null);
1927 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1929 } catch (OutOfMemoryError er)
1931 new OOMWarning("copying region", er);
1935 HiddenColumns hiddenColumns = null;
1936 if (viewport.hasHiddenColumns())
1938 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1939 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1941 // create new HiddenColumns object with copy of hidden regions
1942 // between startRes and endRes, offset by startRes
1943 hiddenColumns = new HiddenColumns(
1944 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1945 hiddenCutoff, hiddenOffset);
1948 Desktop.jalviewClipboard = new Object[] { seqs,
1949 viewport.getAlignment().getDataset(), hiddenColumns };
1950 setStatus(MessageManager.formatMessage(
1951 "label.copied_sequences_to_clipboard", new Object[]
1952 { Integer.valueOf(seqs.length).toString() }));
1962 protected void pasteNew_actionPerformed(ActionEvent e)
1974 protected void pasteThis_actionPerformed(ActionEvent e)
1980 * Paste contents of Jalview clipboard
1982 * @param newAlignment
1983 * true to paste to a new alignment, otherwise add to this.
1985 void paste(boolean newAlignment)
1987 boolean externalPaste = true;
1990 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1991 Transferable contents = c.getContents(this);
1993 if (contents == null)
2002 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2003 if (str.length() < 1)
2008 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2010 } catch (OutOfMemoryError er)
2012 new OOMWarning("Out of memory pasting sequences!!", er);
2016 SequenceI[] sequences;
2017 boolean annotationAdded = false;
2018 AlignmentI alignment = null;
2020 if (Desktop.jalviewClipboard != null)
2022 // The clipboard was filled from within Jalview, we must use the
2024 // And dataset from the copied alignment
2025 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2026 // be doubly sure that we create *new* sequence objects.
2027 sequences = new SequenceI[newseq.length];
2028 for (int i = 0; i < newseq.length; i++)
2030 sequences[i] = new Sequence(newseq[i]);
2032 alignment = new Alignment(sequences);
2033 externalPaste = false;
2037 // parse the clipboard as an alignment.
2038 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2040 sequences = alignment.getSequencesArray();
2044 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2050 if (Desktop.jalviewClipboard != null)
2052 // dataset is inherited
2053 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2057 // new dataset is constructed
2058 alignment.setDataset(null);
2060 alwidth = alignment.getWidth() + 1;
2064 AlignmentI pastedal = alignment; // preserve pasted alignment object
2065 // Add pasted sequences and dataset into existing alignment.
2066 alignment = viewport.getAlignment();
2067 alwidth = alignment.getWidth() + 1;
2068 // decide if we need to import sequences from an existing dataset
2069 boolean importDs = Desktop.jalviewClipboard != null
2070 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2071 // importDs==true instructs us to copy over new dataset sequences from
2072 // an existing alignment
2073 Vector newDs = (importDs) ? new Vector() : null; // used to create
2074 // minimum dataset set
2076 for (int i = 0; i < sequences.length; i++)
2080 newDs.addElement(null);
2082 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2084 if (importDs && ds != null)
2086 if (!newDs.contains(ds))
2088 newDs.setElementAt(ds, i);
2089 ds = new Sequence(ds);
2090 // update with new dataset sequence
2091 sequences[i].setDatasetSequence(ds);
2095 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2100 // copy and derive new dataset sequence
2101 sequences[i] = sequences[i].deriveSequence();
2102 alignment.getDataset()
2103 .addSequence(sequences[i].getDatasetSequence());
2104 // TODO: avoid creation of duplicate dataset sequences with a
2105 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2107 alignment.addSequence(sequences[i]); // merges dataset
2111 newDs.clear(); // tidy up
2113 if (alignment.getAlignmentAnnotation() != null)
2115 for (AlignmentAnnotation alan : alignment
2116 .getAlignmentAnnotation())
2118 if (alan.graphGroup > fgroup)
2120 fgroup = alan.graphGroup;
2124 if (pastedal.getAlignmentAnnotation() != null)
2126 // Add any annotation attached to alignment.
2127 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2128 for (int i = 0; i < alann.length; i++)
2130 annotationAdded = true;
2131 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2133 AlignmentAnnotation newann = new AlignmentAnnotation(
2135 if (newann.graphGroup > -1)
2137 if (newGraphGroups.size() <= newann.graphGroup
2138 || newGraphGroups.get(newann.graphGroup) == null)
2140 for (int q = newGraphGroups
2141 .size(); q <= newann.graphGroup; q++)
2143 newGraphGroups.add(q, null);
2145 newGraphGroups.set(newann.graphGroup,
2146 new Integer(++fgroup));
2148 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2152 newann.padAnnotation(alwidth);
2153 alignment.addAnnotation(newann);
2163 addHistoryItem(new EditCommand(
2164 MessageManager.getString("label.add_sequences"),
2165 Action.PASTE, sequences, 0, alignment.getWidth(),
2168 // Add any annotations attached to sequences
2169 for (int i = 0; i < sequences.length; i++)
2171 if (sequences[i].getAnnotation() != null)
2173 AlignmentAnnotation newann;
2174 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2176 annotationAdded = true;
2177 newann = sequences[i].getAnnotation()[a];
2178 newann.adjustForAlignment();
2179 newann.padAnnotation(alwidth);
2180 if (newann.graphGroup > -1)
2182 if (newann.graphGroup > -1)
2184 if (newGraphGroups.size() <= newann.graphGroup
2185 || newGraphGroups.get(newann.graphGroup) == null)
2187 for (int q = newGraphGroups
2188 .size(); q <= newann.graphGroup; q++)
2190 newGraphGroups.add(q, null);
2192 newGraphGroups.set(newann.graphGroup,
2193 new Integer(++fgroup));
2195 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2199 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2203 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2211 // propagate alignment changed.
2212 viewport.getRanges().setEndSeq(alignment.getHeight());
2213 if (annotationAdded)
2215 // Duplicate sequence annotation in all views.
2216 AlignmentI[] alview = this.getViewAlignments();
2217 for (int i = 0; i < sequences.length; i++)
2219 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2224 for (int avnum = 0; avnum < alview.length; avnum++)
2226 if (alview[avnum] != alignment)
2228 // duplicate in a view other than the one with input focus
2229 int avwidth = alview[avnum].getWidth() + 1;
2230 // this relies on sann being preserved after we
2231 // modify the sequence's annotation array for each duplication
2232 for (int a = 0; a < sann.length; a++)
2234 AlignmentAnnotation newann = new AlignmentAnnotation(
2236 sequences[i].addAlignmentAnnotation(newann);
2237 newann.padAnnotation(avwidth);
2238 alview[avnum].addAnnotation(newann); // annotation was
2239 // duplicated earlier
2240 // TODO JAL-1145 graphGroups are not updated for sequence
2241 // annotation added to several views. This may cause
2243 alview[avnum].setAnnotationIndex(newann, a);
2248 buildSortByAnnotationScoresMenu();
2250 viewport.firePropertyChange("alignment", null,
2251 alignment.getSequences());
2252 if (alignPanels != null)
2254 for (AlignmentPanel ap : alignPanels)
2256 ap.validateAnnotationDimensions(false);
2261 alignPanel.validateAnnotationDimensions(false);
2267 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2269 String newtitle = new String("Copied sequences");
2271 if (Desktop.jalviewClipboard != null
2272 && Desktop.jalviewClipboard[2] != null)
2274 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2275 af.viewport.setHiddenColumns(hc);
2278 // >>>This is a fix for the moment, until a better solution is
2280 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2281 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2282 .getFeatureRenderer());
2284 // TODO: maintain provenance of an alignment, rather than just make the
2285 // title a concatenation of operations.
2288 if (title.startsWith("Copied sequences"))
2294 newtitle = newtitle.concat("- from " + title);
2299 newtitle = new String("Pasted sequences");
2302 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2307 } catch (Exception ex)
2309 ex.printStackTrace();
2310 System.out.println("Exception whilst pasting: " + ex);
2311 // could be anything being pasted in here
2317 protected void expand_newalign(ActionEvent e)
2321 AlignmentI alignment = AlignmentUtils
2322 .expandContext(getViewport().getAlignment(), -1);
2323 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2325 String newtitle = new String("Flanking alignment");
2327 if (Desktop.jalviewClipboard != null
2328 && Desktop.jalviewClipboard[2] != null)
2330 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2331 af.viewport.setHiddenColumns(hc);
2334 // >>>This is a fix for the moment, until a better solution is
2336 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2337 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2338 .getFeatureRenderer());
2340 // TODO: maintain provenance of an alignment, rather than just make the
2341 // title a concatenation of operations.
2343 if (title.startsWith("Copied sequences"))
2349 newtitle = newtitle.concat("- from " + title);
2353 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2355 } catch (Exception ex)
2357 ex.printStackTrace();
2358 System.out.println("Exception whilst pasting: " + ex);
2359 // could be anything being pasted in here
2360 } catch (OutOfMemoryError oom)
2362 new OOMWarning("Viewing flanking region of alignment", oom);
2373 protected void cut_actionPerformed(ActionEvent e)
2375 copy_actionPerformed(null);
2376 delete_actionPerformed(null);
2386 protected void delete_actionPerformed(ActionEvent evt)
2389 SequenceGroup sg = viewport.getSelectionGroup();
2396 * If the cut affects all sequences, warn, remove highlighted columns
2398 if (sg.getSize() == viewport.getAlignment().getHeight())
2400 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2401 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2402 if (isEntireAlignWidth)
2404 int confirm = JvOptionPane.showConfirmDialog(this,
2405 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2406 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2407 JvOptionPane.OK_CANCEL_OPTION);
2409 if (confirm == JvOptionPane.CANCEL_OPTION
2410 || confirm == JvOptionPane.CLOSED_OPTION)
2415 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2416 sg.getEndRes() + 1);
2418 SequenceI[] cut = sg.getSequences()
2419 .toArray(new SequenceI[sg.getSize()]);
2421 addHistoryItem(new EditCommand(
2422 MessageManager.getString("label.cut_sequences"), Action.CUT,
2423 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2424 viewport.getAlignment()));
2426 viewport.setSelectionGroup(null);
2427 viewport.sendSelection();
2428 viewport.getAlignment().deleteGroup(sg);
2430 viewport.firePropertyChange("alignment", null,
2431 viewport.getAlignment().getSequences());
2432 if (viewport.getAlignment().getHeight() < 1)
2436 this.setClosed(true);
2437 } catch (Exception ex)
2450 protected void deleteGroups_actionPerformed(ActionEvent e)
2452 if (avc.deleteGroups())
2454 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2455 alignPanel.updateAnnotation();
2456 alignPanel.paintAlignment(true, true);
2467 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2469 SequenceGroup sg = new SequenceGroup();
2471 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2473 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2476 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2477 viewport.setSelectionGroup(sg);
2478 viewport.sendSelection();
2479 // JAL-2034 - should delegate to
2480 // alignPanel to decide if overview needs
2482 alignPanel.paintAlignment(false, false);
2483 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2493 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2495 if (viewport.cursorMode)
2497 alignPanel.getSeqPanel().keyboardNo1 = null;
2498 alignPanel.getSeqPanel().keyboardNo2 = null;
2500 viewport.setSelectionGroup(null);
2501 viewport.getColumnSelection().clear();
2502 viewport.setSelectionGroup(null);
2503 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2504 // JAL-2034 - should delegate to
2505 // alignPanel to decide if overview needs
2507 alignPanel.paintAlignment(false, false);
2508 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2509 viewport.sendSelection();
2519 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2521 SequenceGroup sg = viewport.getSelectionGroup();
2525 selectAllSequenceMenuItem_actionPerformed(null);
2530 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2532 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2534 // JAL-2034 - should delegate to
2535 // alignPanel to decide if overview needs
2538 alignPanel.paintAlignment(true, false);
2539 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2540 viewport.sendSelection();
2544 public void invertColSel_actionPerformed(ActionEvent e)
2546 viewport.invertColumnSelection();
2547 alignPanel.paintAlignment(true, false);
2548 viewport.sendSelection();
2558 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2560 trimAlignment(true);
2570 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2572 trimAlignment(false);
2575 void trimAlignment(boolean trimLeft)
2577 ColumnSelection colSel = viewport.getColumnSelection();
2580 if (!colSel.isEmpty())
2584 column = colSel.getMin();
2588 column = colSel.getMax();
2592 if (viewport.getSelectionGroup() != null)
2594 seqs = viewport.getSelectionGroup()
2595 .getSequencesAsArray(viewport.getHiddenRepSequences());
2599 seqs = viewport.getAlignment().getSequencesArray();
2602 TrimRegionCommand trimRegion;
2605 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2606 column, viewport.getAlignment());
2607 viewport.getRanges().setStartRes(0);
2611 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2612 column, viewport.getAlignment());
2615 setStatus(MessageManager
2616 .formatMessage("label.removed_columns", new String[]
2617 { Integer.valueOf(trimRegion.getSize()).toString() }));
2619 addHistoryItem(trimRegion);
2621 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2623 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2624 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2626 viewport.getAlignment().deleteGroup(sg);
2630 viewport.firePropertyChange("alignment", null,
2631 viewport.getAlignment().getSequences());
2642 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2644 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2647 if (viewport.getSelectionGroup() != null)
2649 seqs = viewport.getSelectionGroup()
2650 .getSequencesAsArray(viewport.getHiddenRepSequences());
2651 start = viewport.getSelectionGroup().getStartRes();
2652 end = viewport.getSelectionGroup().getEndRes();
2656 seqs = viewport.getAlignment().getSequencesArray();
2659 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2660 "Remove Gapped Columns", seqs, start, end,
2661 viewport.getAlignment());
2663 addHistoryItem(removeGapCols);
2665 setStatus(MessageManager
2666 .formatMessage("label.removed_empty_columns", new Object[]
2667 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2669 // This is to maintain viewport position on first residue
2670 // of first sequence
2671 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2672 ViewportRanges ranges = viewport.getRanges();
2673 int startRes = seq.findPosition(ranges.getStartRes());
2674 // ShiftList shifts;
2675 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2676 // edit.alColumnChanges=shifts.getInverse();
2677 // if (viewport.hasHiddenColumns)
2678 // viewport.getColumnSelection().compensateForEdits(shifts);
2679 ranges.setStartRes(seq.findIndex(startRes) - 1);
2680 viewport.firePropertyChange("alignment", null,
2681 viewport.getAlignment().getSequences());
2692 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2694 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2697 if (viewport.getSelectionGroup() != null)
2699 seqs = viewport.getSelectionGroup()
2700 .getSequencesAsArray(viewport.getHiddenRepSequences());
2701 start = viewport.getSelectionGroup().getStartRes();
2702 end = viewport.getSelectionGroup().getEndRes();
2706 seqs = viewport.getAlignment().getSequencesArray();
2709 // This is to maintain viewport position on first residue
2710 // of first sequence
2711 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2712 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2714 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2715 viewport.getAlignment()));
2717 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2719 viewport.firePropertyChange("alignment", null,
2720 viewport.getAlignment().getSequences());
2731 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2733 viewport.setPadGaps(padGapsMenuitem.isSelected());
2734 viewport.firePropertyChange("alignment", null,
2735 viewport.getAlignment().getSequences());
2745 public void findMenuItem_actionPerformed(ActionEvent e)
2751 * Create a new view of the current alignment.
2754 public void newView_actionPerformed(ActionEvent e)
2756 newView(null, true);
2760 * Creates and shows a new view of the current alignment.
2763 * title of newly created view; if null, one will be generated
2764 * @param copyAnnotation
2765 * if true then duplicate all annnotation, groups and settings
2766 * @return new alignment panel, already displayed.
2768 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2771 * Create a new AlignmentPanel (with its own, new Viewport)
2773 AlignmentPanel newap = new jalview.project.Jalview2XML()
2774 .copyAlignPanel(alignPanel);
2775 if (!copyAnnotation)
2778 * remove all groups and annotation except for the automatic stuff
2780 newap.av.getAlignment().deleteAllGroups();
2781 newap.av.getAlignment().deleteAllAnnotations(false);
2784 newap.av.setGatherViewsHere(false);
2786 if (viewport.getViewName() == null)
2788 viewport.setViewName(MessageManager
2789 .getString("label.view_name_original"));
2793 * Views share the same edits undo and redo stacks
2795 newap.av.setHistoryList(viewport.getHistoryList());
2796 newap.av.setRedoList(viewport.getRedoList());
2799 * Views share the same mappings; need to deregister any new mappings
2800 * created by copyAlignPanel, and register the new reference to the shared
2803 newap.av.replaceMappings(viewport.getAlignment());
2806 * start up cDNA consensus (if applicable) now mappings are in place
2808 if (newap.av.initComplementConsensus())
2810 newap.refresh(true); // adjust layout of annotations
2813 newap.av.setViewName(getNewViewName(viewTitle));
2815 addAlignmentPanel(newap, true);
2816 newap.alignmentChanged();
2818 if (alignPanels.size() == 2)
2820 viewport.setGatherViewsHere(true);
2822 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2827 * Make a new name for the view, ensuring it is unique within the current
2828 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2829 * these now use viewId. Unique view names are still desirable for usability.)
2834 protected String getNewViewName(String viewTitle)
2836 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2837 boolean addFirstIndex = false;
2838 if (viewTitle == null || viewTitle.trim().length() == 0)
2840 viewTitle = MessageManager.getString("action.view");
2841 addFirstIndex = true;
2845 index = 1;// we count from 1 if given a specific name
2847 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2849 List<Component> comps = PaintRefresher.components
2850 .get(viewport.getSequenceSetId());
2852 List<String> existingNames = getExistingViewNames(comps);
2854 while (existingNames.contains(newViewName))
2856 newViewName = viewTitle + " " + (++index);
2862 * Returns a list of distinct view names found in the given list of
2863 * components. View names are held on the viewport of an AlignmentPanel.
2868 protected List<String> getExistingViewNames(List<Component> comps)
2870 List<String> existingNames = new ArrayList<>();
2871 for (Component comp : comps)
2873 if (comp instanceof AlignmentPanel)
2875 AlignmentPanel ap = (AlignmentPanel) comp;
2876 if (!existingNames.contains(ap.av.getViewName()))
2878 existingNames.add(ap.av.getViewName());
2882 return existingNames;
2886 * Explode tabbed views into separate windows.
2889 public void expandViews_actionPerformed(ActionEvent e)
2891 Desktop.explodeViews(this);
2895 * Gather views in separate windows back into a tabbed presentation.
2898 public void gatherViews_actionPerformed(ActionEvent e)
2900 Desktop.instance.gatherViews(this);
2910 public void font_actionPerformed(ActionEvent e)
2912 new FontChooser(alignPanel);
2922 protected void seqLimit_actionPerformed(ActionEvent e)
2924 viewport.setShowJVSuffix(seqLimits.isSelected());
2926 alignPanel.getIdPanel().getIdCanvas()
2927 .setPreferredSize(alignPanel.calculateIdWidth());
2928 alignPanel.paintAlignment(true, false);
2932 public void idRightAlign_actionPerformed(ActionEvent e)
2934 viewport.setRightAlignIds(idRightAlign.isSelected());
2935 alignPanel.paintAlignment(false, false);
2939 public void centreColumnLabels_actionPerformed(ActionEvent e)
2941 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2942 alignPanel.paintAlignment(false, false);
2948 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2951 protected void followHighlight_actionPerformed()
2954 * Set the 'follow' flag on the Viewport (and scroll to position if now
2957 final boolean state = this.followHighlightMenuItem.getState();
2958 viewport.setFollowHighlight(state);
2961 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2972 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2974 viewport.setColourText(colourTextMenuItem.isSelected());
2975 alignPanel.paintAlignment(false, false);
2985 public void wrapMenuItem_actionPerformed(ActionEvent e)
2987 scaleAbove.setVisible(wrapMenuItem.isSelected());
2988 scaleLeft.setVisible(wrapMenuItem.isSelected());
2989 scaleRight.setVisible(wrapMenuItem.isSelected());
2990 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2991 alignPanel.updateLayout();
2995 public void showAllSeqs_actionPerformed(ActionEvent e)
2997 viewport.showAllHiddenSeqs();
3001 public void showAllColumns_actionPerformed(ActionEvent e)
3003 viewport.showAllHiddenColumns();
3004 alignPanel.paintAlignment(true, true);
3005 viewport.sendSelection();
3009 public void hideSelSequences_actionPerformed(ActionEvent e)
3011 viewport.hideAllSelectedSeqs();
3015 * called by key handler and the hide all/show all menu items
3020 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3023 boolean hide = false;
3024 SequenceGroup sg = viewport.getSelectionGroup();
3025 if (!toggleSeqs && !toggleCols)
3027 // Hide everything by the current selection - this is a hack - we do the
3028 // invert and then hide
3029 // first check that there will be visible columns after the invert.
3030 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3031 && sg.getStartRes() <= sg.getEndRes()))
3033 // now invert the sequence set, if required - empty selection implies
3034 // that no hiding is required.
3037 invertSequenceMenuItem_actionPerformed(null);
3038 sg = viewport.getSelectionGroup();
3042 viewport.expandColSelection(sg, true);
3043 // finally invert the column selection and get the new sequence
3045 invertColSel_actionPerformed(null);
3052 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3054 hideSelSequences_actionPerformed(null);
3057 else if (!(toggleCols && viewport.hasSelectedColumns()))
3059 showAllSeqs_actionPerformed(null);
3065 if (viewport.hasSelectedColumns())
3067 hideSelColumns_actionPerformed(null);
3070 viewport.setSelectionGroup(sg);
3075 showAllColumns_actionPerformed(null);
3084 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3085 * event.ActionEvent)
3088 public void hideAllButSelection_actionPerformed(ActionEvent e)
3090 toggleHiddenRegions(false, false);
3091 viewport.sendSelection();
3098 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3102 public void hideAllSelection_actionPerformed(ActionEvent e)
3104 SequenceGroup sg = viewport.getSelectionGroup();
3105 viewport.expandColSelection(sg, false);
3106 viewport.hideAllSelectedSeqs();
3107 viewport.hideSelectedColumns();
3108 alignPanel.paintAlignment(true, true);
3109 viewport.sendSelection();
3116 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3120 public void showAllhidden_actionPerformed(ActionEvent e)
3122 viewport.showAllHiddenColumns();
3123 viewport.showAllHiddenSeqs();
3124 alignPanel.paintAlignment(true, true);
3125 viewport.sendSelection();
3129 public void hideSelColumns_actionPerformed(ActionEvent e)
3131 viewport.hideSelectedColumns();
3132 alignPanel.paintAlignment(true, true);
3133 viewport.sendSelection();
3137 public void hiddenMarkers_actionPerformed(ActionEvent e)
3139 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3150 protected void scaleAbove_actionPerformed(ActionEvent e)
3152 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3153 // TODO: do we actually need to update overview for scale above change ?
3154 alignPanel.paintAlignment(true, false);
3164 protected void scaleLeft_actionPerformed(ActionEvent e)
3166 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3167 alignPanel.paintAlignment(true, false);
3177 protected void scaleRight_actionPerformed(ActionEvent e)
3179 viewport.setScaleRightWrapped(scaleRight.isSelected());
3180 alignPanel.paintAlignment(true, false);
3190 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3192 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3193 alignPanel.paintAlignment(false, false);
3203 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3205 viewport.setShowText(viewTextMenuItem.isSelected());
3206 alignPanel.paintAlignment(false, false);
3216 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3218 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3219 alignPanel.paintAlignment(false, false);
3222 public FeatureSettings featureSettings;
3225 public FeatureSettingsControllerI getFeatureSettingsUI()
3227 return featureSettings;
3231 public void featureSettings_actionPerformed(ActionEvent e)
3233 if (featureSettings != null)
3235 featureSettings.close();
3236 featureSettings = null;
3238 if (!showSeqFeatures.isSelected())
3240 // make sure features are actually displayed
3241 showSeqFeatures.setSelected(true);
3242 showSeqFeatures_actionPerformed(null);
3244 featureSettings = new FeatureSettings(this);
3248 * Set or clear 'Show Sequence Features'
3254 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3256 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3257 alignPanel.paintAlignment(true, true);
3261 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3262 * the annotations panel as a whole.
3264 * The options to show/hide all annotations should be enabled when the panel
3265 * is shown, and disabled when the panel is hidden.
3270 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3272 final boolean setVisible = annotationPanelMenuItem.isSelected();
3273 viewport.setShowAnnotation(setVisible);
3274 this.showAllSeqAnnotations.setEnabled(setVisible);
3275 this.hideAllSeqAnnotations.setEnabled(setVisible);
3276 this.showAllAlAnnotations.setEnabled(setVisible);
3277 this.hideAllAlAnnotations.setEnabled(setVisible);
3278 alignPanel.updateLayout();
3282 public void alignmentProperties()
3285 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3288 String content = MessageManager.formatMessage("label.html_content",
3290 { contents.toString() });
3293 if (Platform.isJS())
3295 JLabel textLabel = new JLabel();
3296 textLabel.setText(content);
3297 textLabel.setBackground(Color.WHITE);
3299 pane = new JPanel(new BorderLayout());
3300 ((JPanel) pane).setOpaque(true);
3301 pane.setBackground(Color.WHITE);
3302 ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3306 JEditorPane editPane = new JEditorPane("text/html", "");
3307 editPane.setEditable(false);
3308 editPane.setText(content);
3312 JInternalFrame frame = new JInternalFrame();
3314 frame.getContentPane().add(new JScrollPane(pane));
3316 Desktop.addInternalFrame(frame, MessageManager
3317 .formatMessage("label.alignment_properties", new Object[]
3318 { getTitle() }), 500, 400);
3328 public void overviewMenuItem_actionPerformed(ActionEvent e)
3330 if (alignPanel.overviewPanel != null)
3335 JInternalFrame frame = new JInternalFrame();
3336 final OverviewPanel overview = new OverviewPanel(alignPanel);
3337 frame.setContentPane(overview);
3338 Desktop.addInternalFrame(frame, MessageManager
3339 .formatMessage("label.overview_params", new Object[]
3340 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3343 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3344 frame.addInternalFrameListener(
3345 new javax.swing.event.InternalFrameAdapter()
3348 public void internalFrameClosed(
3349 javax.swing.event.InternalFrameEvent evt)
3352 alignPanel.setOverviewPanel(null);
3355 if (getKeyListeners().length > 0)
3357 frame.addKeyListener(getKeyListeners()[0]);
3360 alignPanel.setOverviewPanel(overview);
3364 public void textColour_actionPerformed()
3366 new TextColourChooser().chooseColour(alignPanel, null);
3370 * public void covariationColour_actionPerformed() {
3372 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3376 public void annotationColour_actionPerformed()
3378 new AnnotationColourChooser(viewport, alignPanel);
3382 public void annotationColumn_actionPerformed(ActionEvent e)
3384 new AnnotationColumnChooser(viewport, alignPanel);
3388 * Action on the user checking or unchecking the option to apply the selected
3389 * colour scheme to all groups. If unchecked, groups may have their own
3390 * independent colour schemes.
3395 public void applyToAllGroups_actionPerformed(boolean selected)
3397 viewport.setColourAppliesToAllGroups(selected);
3401 * Action on user selecting a colour from the colour menu
3404 * the name (not the menu item label!) of the colour scheme
3407 public void changeColour_actionPerformed(String name)
3410 * 'User Defined' opens a panel to configure or load a
3411 * user-defined colour scheme
3413 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3415 new UserDefinedColours(alignPanel);
3420 * otherwise set the chosen colour scheme (or null for 'None')
3422 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3423 viewport.getAlignment(), viewport.getHiddenRepSequences());
3428 * Actions on setting or changing the alignment colour scheme
3433 public void changeColour(ColourSchemeI cs)
3435 // TODO: pull up to controller method
3436 ColourMenuHelper.setColourSelected(colourMenu, cs);
3438 viewport.setGlobalColourScheme(cs);
3440 alignPanel.paintAlignment(true, true);
3444 * Show the PID threshold slider panel
3447 protected void modifyPID_actionPerformed()
3449 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3450 alignPanel.getViewName());
3451 SliderPanel.showPIDSlider();
3455 * Show the Conservation slider panel
3458 protected void modifyConservation_actionPerformed()
3460 SliderPanel.setConservationSlider(alignPanel,
3461 viewport.getResidueShading(), alignPanel.getViewName());
3462 SliderPanel.showConservationSlider();
3466 * Action on selecting or deselecting (Colour) By Conservation
3469 public void conservationMenuItem_actionPerformed(boolean selected)
3471 modifyConservation.setEnabled(selected);
3472 viewport.setConservationSelected(selected);
3473 viewport.getResidueShading().setConservationApplied(selected);
3475 changeColour(viewport.getGlobalColourScheme());
3478 modifyConservation_actionPerformed();
3482 SliderPanel.hideConservationSlider();
3487 * Action on selecting or deselecting (Colour) Above PID Threshold
3490 public void abovePIDThreshold_actionPerformed(boolean selected)
3492 modifyPID.setEnabled(selected);
3493 viewport.setAbovePIDThreshold(selected);
3496 viewport.getResidueShading().setThreshold(0,
3497 viewport.isIgnoreGapsConsensus());
3500 changeColour(viewport.getGlobalColourScheme());
3503 modifyPID_actionPerformed();
3507 SliderPanel.hidePIDSlider();
3518 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3520 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3521 AlignmentSorter.sortByPID(viewport.getAlignment(),
3522 viewport.getAlignment().getSequenceAt(0));
3523 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3524 viewport.getAlignment()));
3525 alignPanel.paintAlignment(true, false);
3535 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3537 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3538 AlignmentSorter.sortByID(viewport.getAlignment());
3540 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3541 alignPanel.paintAlignment(true, false);
3551 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3553 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3554 AlignmentSorter.sortByLength(viewport.getAlignment());
3555 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3556 viewport.getAlignment()));
3557 alignPanel.paintAlignment(true, false);
3567 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3569 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3570 AlignmentSorter.sortByGroup(viewport.getAlignment());
3571 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3572 viewport.getAlignment()));
3574 alignPanel.paintAlignment(true, false);
3584 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3586 new RedundancyPanel(alignPanel, this);
3596 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3598 if ((viewport.getSelectionGroup() == null)
3599 || (viewport.getSelectionGroup().getSize() < 2))
3601 JvOptionPane.showInternalMessageDialog(this,
3602 MessageManager.getString(
3603 "label.you_must_select_least_two_sequences"),
3604 MessageManager.getString("label.invalid_selection"),
3605 JvOptionPane.WARNING_MESSAGE);
3609 JInternalFrame frame = new JInternalFrame();
3610 frame.setContentPane(new PairwiseAlignPanel(viewport));
3611 Desktop.addInternalFrame(frame,
3612 MessageManager.getString("action.pairwise_alignment"), 600,
3618 public void autoCalculate_actionPerformed(ActionEvent e)
3620 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3621 if (viewport.autoCalculateConsensus)
3623 viewport.firePropertyChange("alignment", null,
3624 viewport.getAlignment().getSequences());
3629 public void sortByTreeOption_actionPerformed(ActionEvent e)
3631 viewport.sortByTree = sortByTree.isSelected();
3635 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3637 viewport.followSelection = listenToViewSelections.isSelected();
3641 * Constructs a tree panel and adds it to the desktop
3644 * tree type (NJ or AV)
3646 * name of score model used to compute the tree
3648 * parameters for the distance or similarity calculation
3650 void newTreePanel(String type, String modelName,
3651 SimilarityParamsI options)
3653 String frameTitle = "";
3656 boolean onSelection = false;
3657 if (viewport.getSelectionGroup() != null
3658 && viewport.getSelectionGroup().getSize() > 0)
3660 SequenceGroup sg = viewport.getSelectionGroup();
3662 /* Decide if the selection is a column region */
3663 for (SequenceI _s : sg.getSequences())
3665 if (_s.getLength() < sg.getEndRes())
3667 JvOptionPane.showMessageDialog(Desktop.desktop,
3668 MessageManager.getString(
3669 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3670 MessageManager.getString(
3671 "label.sequences_selection_not_aligned"),
3672 JvOptionPane.WARNING_MESSAGE);
3681 if (viewport.getAlignment().getHeight() < 2)
3687 tp = new TreePanel(alignPanel, type, modelName, options);
3688 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3690 frameTitle += " from ";
3692 if (viewport.getViewName() != null)
3694 frameTitle += viewport.getViewName() + " of ";
3697 frameTitle += this.title;
3699 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3710 public void addSortByOrderMenuItem(String title,
3711 final AlignmentOrder order)
3713 final JMenuItem item = new JMenuItem(MessageManager
3714 .formatMessage("action.by_title_param", new Object[]
3717 item.addActionListener(new java.awt.event.ActionListener()
3720 public void actionPerformed(ActionEvent e)
3722 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3724 // TODO: JBPNote - have to map order entries to curent SequenceI
3726 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3728 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3729 viewport.getAlignment()));
3731 alignPanel.paintAlignment(true, false);
3737 * Add a new sort by annotation score menu item
3740 * the menu to add the option to
3742 * the label used to retrieve scores for each sequence on the
3745 public void addSortByAnnotScoreMenuItem(JMenu sort,
3746 final String scoreLabel)
3748 final JMenuItem item = new JMenuItem(scoreLabel);
3750 item.addActionListener(new java.awt.event.ActionListener()
3753 public void actionPerformed(ActionEvent e)
3755 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3756 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3757 viewport.getAlignment());// ,viewport.getSelectionGroup());
3758 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3759 viewport.getAlignment()));
3760 alignPanel.paintAlignment(true, false);
3766 * last hash for alignment's annotation array - used to minimise cost of
3769 protected int _annotationScoreVectorHash;
3772 * search the alignment and rebuild the sort by annotation score submenu the
3773 * last alignment annotation vector hash is stored to minimize cost of
3774 * rebuilding in subsequence calls.
3778 public void buildSortByAnnotationScoresMenu()
3780 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3785 if (viewport.getAlignment().getAlignmentAnnotation()
3786 .hashCode() != _annotationScoreVectorHash)
3788 sortByAnnotScore.removeAll();
3789 // almost certainly a quicker way to do this - but we keep it simple
3790 Hashtable scoreSorts = new Hashtable();
3791 AlignmentAnnotation aann[];
3792 for (SequenceI sqa : viewport.getAlignment().getSequences())
3794 aann = sqa.getAnnotation();
3795 for (int i = 0; aann != null && i < aann.length; i++)
3797 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3799 scoreSorts.put(aann[i].label, aann[i].label);
3803 Enumeration labels = scoreSorts.keys();
3804 while (labels.hasMoreElements())
3806 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3807 (String) labels.nextElement());
3809 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3812 _annotationScoreVectorHash = viewport.getAlignment()
3813 .getAlignmentAnnotation().hashCode();
3818 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3819 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3820 * call. Listeners are added to remove the menu item when the treePanel is
3821 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3825 public void buildTreeSortMenu()
3827 sortByTreeMenu.removeAll();
3829 List<Component> comps = PaintRefresher.components
3830 .get(viewport.getSequenceSetId());
3831 List<TreePanel> treePanels = new ArrayList<>();
3832 for (Component comp : comps)
3834 if (comp instanceof TreePanel)
3836 treePanels.add((TreePanel) comp);
3840 if (treePanels.size() < 1)
3842 sortByTreeMenu.setVisible(false);
3846 sortByTreeMenu.setVisible(true);
3848 for (final TreePanel tp : treePanels)
3850 final JMenuItem item = new JMenuItem(tp.getTitle());
3851 item.addActionListener(new java.awt.event.ActionListener()
3854 public void actionPerformed(ActionEvent e)
3856 tp.sortByTree_actionPerformed();
3857 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3862 sortByTreeMenu.add(item);
3866 public boolean sortBy(AlignmentOrder alorder, String undoname)
3868 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3869 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3870 if (undoname != null)
3872 addHistoryItem(new OrderCommand(undoname, oldOrder,
3873 viewport.getAlignment()));
3875 alignPanel.paintAlignment(true, false);
3880 * Work out whether the whole set of sequences or just the selected set will
3881 * be submitted for multiple alignment.
3884 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3886 // Now, check we have enough sequences
3887 AlignmentView msa = null;
3889 if ((viewport.getSelectionGroup() != null)
3890 && (viewport.getSelectionGroup().getSize() > 1))
3892 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3893 // some common interface!
3895 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3896 * SequenceI[sz = seqs.getSize(false)];
3898 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3899 * seqs.getSequenceAt(i); }
3901 msa = viewport.getAlignmentView(true);
3903 else if (viewport.getSelectionGroup() != null
3904 && viewport.getSelectionGroup().getSize() == 1)
3906 int option = JvOptionPane.showConfirmDialog(this,
3907 MessageManager.getString("warn.oneseq_msainput_selection"),
3908 MessageManager.getString("label.invalid_selection"),
3909 JvOptionPane.OK_CANCEL_OPTION);
3910 if (option == JvOptionPane.OK_OPTION)
3912 msa = viewport.getAlignmentView(false);
3917 msa = viewport.getAlignmentView(false);
3923 * Decides what is submitted to a secondary structure prediction service: the
3924 * first sequence in the alignment, or in the current selection, or, if the
3925 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3926 * region or the whole alignment. (where the first sequence in the set is the
3927 * one that the prediction will be for).
3929 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3931 AlignmentView seqs = null;
3933 if ((viewport.getSelectionGroup() != null)
3934 && (viewport.getSelectionGroup().getSize() > 0))
3936 seqs = viewport.getAlignmentView(true);
3940 seqs = viewport.getAlignmentView(false);
3942 // limit sequences - JBPNote in future - could spawn multiple prediction
3944 // TODO: viewport.getAlignment().isAligned is a global state - the local
3945 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3946 if (!viewport.getAlignment().isAligned(false))
3948 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3949 // TODO: if seqs.getSequences().length>1 then should really have warned
3963 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3965 // Pick the tree file
3966 JalviewFileChooser chooser = new JalviewFileChooser(
3967 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3968 chooser.setFileView(new JalviewFileView());
3969 chooser.setDialogTitle(
3970 MessageManager.getString("label.select_newick_like_tree_file"));
3971 chooser.setToolTipText(
3972 MessageManager.getString("label.load_tree_file"));
3974 chooser.setResponseHandler(0,new Runnable()
3979 String filePath = chooser.getSelectedFile().getPath();
3980 Cache.setProperty("LAST_DIRECTORY", filePath);
3981 NewickFile fin = null;
3984 fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
3985 DataSourceType.FILE));
3986 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3987 } catch (Exception ex)
3989 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3991 .getString("label.problem_reading_tree_file"),
3992 JvOptionPane.WARNING_MESSAGE);
3993 ex.printStackTrace();
3995 if (fin != null && fin.hasWarningMessage())
3997 JvOptionPane.showMessageDialog(Desktop.desktop,
3998 fin.getWarningMessage(),
3999 MessageManager.getString(
4000 "label.possible_problem_with_tree_file"),
4001 JvOptionPane.WARNING_MESSAGE);
4005 chooser.showOpenDialog(this);
4008 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4010 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4013 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4014 int h, int x, int y)
4016 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4020 * Add a treeviewer for the tree extracted from a Newick file object to the
4021 * current alignment view
4028 * Associated alignment input data (or null)
4037 * @return TreePanel handle
4039 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4040 AlignmentView input, int w, int h, int x, int y)
4042 TreePanel tp = null;
4048 if (nf.getTree() != null)
4050 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4056 tp.setLocation(x, y);
4059 Desktop.addInternalFrame(tp, treeTitle, w, h);
4061 } catch (Exception ex)
4063 ex.printStackTrace();
4069 private boolean buildingMenu = false;
4072 * Generates menu items and listener event actions for web service clients
4075 public void BuildWebServiceMenu()
4077 while (buildingMenu)
4081 System.err.println("Waiting for building menu to finish.");
4083 } catch (Exception e)
4087 final AlignFrame me = this;
4088 buildingMenu = true;
4089 new Thread(new Runnable()
4094 final List<JMenuItem> legacyItems = new ArrayList<>();
4097 // System.err.println("Building ws menu again "
4098 // + Thread.currentThread());
4099 // TODO: add support for context dependent disabling of services based
4101 // alignment and current selection
4102 // TODO: add additional serviceHandle parameter to specify abstract
4104 // class independently of AbstractName
4105 // TODO: add in rediscovery GUI function to restart discoverer
4106 // TODO: group services by location as well as function and/or
4108 // object broker mechanism.
4109 final Vector<JMenu> wsmenu = new Vector<>();
4110 final IProgressIndicator af = me;
4113 * do not i18n these strings - they are hard-coded in class
4114 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4115 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4117 final JMenu msawsmenu = new JMenu("Alignment");
4118 final JMenu secstrmenu = new JMenu(
4119 "Secondary Structure Prediction");
4120 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4121 final JMenu analymenu = new JMenu("Analysis");
4122 final JMenu dismenu = new JMenu("Protein Disorder");
4123 // JAL-940 - only show secondary structure prediction services from
4124 // the legacy server
4125 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4127 Discoverer.services != null && (Discoverer.services.size() > 0))
4129 // TODO: refactor to allow list of AbstractName/Handler bindings to
4131 // stored or retrieved from elsewhere
4132 // No MSAWS used any more:
4133 // Vector msaws = null; // (Vector)
4134 // Discoverer.services.get("MsaWS");
4135 Vector secstrpr = (Vector) Discoverer.services
4137 if (secstrpr != null)
4139 // Add any secondary structure prediction services
4140 for (int i = 0, j = secstrpr.size(); i < j; i++)
4142 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4144 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4145 .getServiceClient(sh);
4146 int p = secstrmenu.getItemCount();
4147 impl.attachWSMenuEntry(secstrmenu, me);
4148 int q = secstrmenu.getItemCount();
4149 for (int litm = p; litm < q; litm++)
4151 legacyItems.add(secstrmenu.getItem(litm));
4157 // Add all submenus in the order they should appear on the web
4159 wsmenu.add(msawsmenu);
4160 wsmenu.add(secstrmenu);
4161 wsmenu.add(dismenu);
4162 wsmenu.add(analymenu);
4163 // No search services yet
4164 // wsmenu.add(seqsrchmenu);
4166 javax.swing.SwingUtilities.invokeLater(new Runnable()
4173 webService.removeAll();
4174 // first, add discovered services onto the webservices menu
4175 if (wsmenu.size() > 0)
4177 for (int i = 0, j = wsmenu.size(); i < j; i++)
4179 webService.add(wsmenu.get(i));
4184 webService.add(me.webServiceNoServices);
4186 // TODO: move into separate menu builder class.
4187 boolean new_sspred = false;
4188 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4190 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4191 if (jws2servs != null)
4193 if (jws2servs.hasServices())
4195 jws2servs.attachWSMenuEntry(webService, me);
4196 for (Jws2Instance sv : jws2servs.getServices())
4198 if (sv.description.toLowerCase().contains("jpred"))
4200 for (JMenuItem jmi : legacyItems)
4202 jmi.setVisible(false);
4208 if (jws2servs.isRunning())
4210 JMenuItem tm = new JMenuItem(
4211 "Still discovering JABA Services");
4212 tm.setEnabled(false);
4217 build_urlServiceMenu(me.webService);
4218 build_fetchdbmenu(webService);
4219 for (JMenu item : wsmenu)
4221 if (item.getItemCount() == 0)
4223 item.setEnabled(false);
4227 item.setEnabled(true);
4230 } catch (Exception e)
4233 "Exception during web service menu building process.",
4238 } catch (Exception e)
4241 buildingMenu = false;
4248 * construct any groupURL type service menu entries.
4252 private void build_urlServiceMenu(JMenu webService)
4254 // TODO: remove this code when 2.7 is released
4255 // DEBUG - alignmentView
4257 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4258 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4260 * @Override public void actionPerformed(ActionEvent e) {
4261 * jalview.datamodel.AlignmentView
4262 * .testSelectionViews(af.viewport.getAlignment(),
4263 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4265 * }); webService.add(testAlView);
4267 // TODO: refactor to RestClient discoverer and merge menu entries for
4268 // rest-style services with other types of analysis/calculation service
4269 // SHmmr test client - still being implemented.
4270 // DEBUG - alignmentView
4272 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4275 client.attachWSMenuEntry(
4276 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4282 * Searches the alignment sequences for xRefs and builds the Show
4283 * Cross-References menu (formerly called Show Products), with database
4284 * sources for which cross-references are found (protein sources for a
4285 * nucleotide alignment and vice versa)
4287 * @return true if Show Cross-references menu should be enabled
4289 public boolean canShowProducts()
4291 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4292 AlignmentI dataset = viewport.getAlignment().getDataset();
4294 showProducts.removeAll();
4295 final boolean dna = viewport.getAlignment().isNucleotide();
4297 if (seqs == null || seqs.length == 0)
4299 // nothing to see here.
4303 boolean showp = false;
4306 List<String> ptypes = new CrossRef(seqs, dataset)
4307 .findXrefSourcesForSequences(dna);
4309 for (final String source : ptypes)
4312 final AlignFrame af = this;
4313 JMenuItem xtype = new JMenuItem(source);
4314 xtype.addActionListener(new ActionListener()
4317 public void actionPerformed(ActionEvent e)
4319 showProductsFor(af.viewport.getSequenceSelection(), dna,
4323 showProducts.add(xtype);
4325 showProducts.setVisible(showp);
4326 showProducts.setEnabled(showp);
4327 } catch (Exception e)
4330 "canShowProducts threw an exception - please report to help@jalview.org",
4338 * Finds and displays cross-references for the selected sequences (protein
4339 * products for nucleotide sequences, dna coding sequences for peptides).
4342 * the sequences to show cross-references for
4344 * true if from a nucleotide alignment (so showing proteins)
4346 * the database to show cross-references for
4348 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4349 final String source)
4351 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4356 * Construct and display a new frame containing the translation of this
4357 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4360 public void showTranslation_actionPerformed(ActionEvent e)
4362 AlignmentI al = null;
4365 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4367 al = dna.translateCdna();
4368 } catch (Exception ex)
4370 jalview.bin.Cache.log.error(
4371 "Exception during translation. Please report this !", ex);
4372 final String msg = MessageManager.getString(
4373 "label.error_when_translating_sequences_submit_bug_report");
4374 final String errorTitle = MessageManager
4375 .getString("label.implementation_error")
4376 + MessageManager.getString("label.translation_failed");
4377 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4378 JvOptionPane.ERROR_MESSAGE);
4381 if (al == null || al.getHeight() == 0)
4383 final String msg = MessageManager.getString(
4384 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4385 final String errorTitle = MessageManager
4386 .getString("label.translation_failed");
4387 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4388 JvOptionPane.WARNING_MESSAGE);
4392 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4393 af.setFileFormat(this.currentFileFormat);
4394 final String newTitle = MessageManager
4395 .formatMessage("label.translation_of_params", new Object[]
4396 { this.getTitle() });
4397 af.setTitle(newTitle);
4398 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4400 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4401 viewport.openSplitFrame(af, new Alignment(seqs));
4405 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4412 * Set the file format
4416 public void setFileFormat(FileFormatI format)
4418 this.currentFileFormat = format;
4422 * Try to load a features file onto the alignment.
4425 * contents or path to retrieve file or a File object
4427 * access mode of file (see jalview.io.AlignFile)
4428 * @return true if features file was parsed correctly.
4430 public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4433 return avc.parseFeaturesFile(file, sourceType,
4434 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4439 public void refreshFeatureUI(boolean enableIfNecessary)
4441 // note - currently this is only still here rather than in the controller
4442 // because of the featureSettings hard reference that is yet to be
4444 if (enableIfNecessary)
4446 viewport.setShowSequenceFeatures(true);
4447 showSeqFeatures.setSelected(true);
4453 public void dragEnter(DropTargetDragEvent evt)
4458 public void dragExit(DropTargetEvent evt)
4463 public void dragOver(DropTargetDragEvent evt)
4468 public void dropActionChanged(DropTargetDragEvent evt)
4473 public void drop(DropTargetDropEvent evt)
4475 // JAL-1552 - acceptDrop required before getTransferable call for
4476 // Java's Transferable for native dnd
4477 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4478 Transferable t = evt.getTransferable();
4480 final AlignFrame thisaf = this;
4481 final List<Object> files = new ArrayList<>();
4482 List<DataSourceType> protocols = new ArrayList<>();
4486 Desktop.transferFromDropTarget(files, protocols, evt, t);
4487 } catch (Exception e)
4489 e.printStackTrace();
4493 new Thread(new Runnable()
4500 // check to see if any of these files have names matching sequences
4503 SequenceIdMatcher idm = new SequenceIdMatcher(
4504 viewport.getAlignment().getSequencesArray());
4506 * Object[] { String,SequenceI}
4508 ArrayList<Object[]> filesmatched = new ArrayList<>();
4509 ArrayList<Object> filesnotmatched = new ArrayList<>();
4510 for (int i = 0; i < files.size(); i++)
4513 Object file = files.get(i);
4514 String fileName = file.toString();
4516 DataSourceType protocol = (file instanceof File
4517 ? DataSourceType.FILE
4518 : FormatAdapter.checkProtocol(fileName));
4519 if (protocol == DataSourceType.FILE)
4521 File fl = (file instanceof File ? (File) file
4522 : new File(fileName));
4523 pdbfn = fl.getName();
4525 else if (protocol == DataSourceType.URL)
4527 URL url = new URL(fileName);
4528 pdbfn = url.getFile();
4530 if (pdbfn.length() > 0)
4532 // attempt to find a match in the alignment
4533 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4534 int l = 0, c = pdbfn.indexOf(".");
4535 while (mtch == null && c != -1)
4540 } while ((c = pdbfn.indexOf(".", l)) > l);
4543 pdbfn = pdbfn.substring(0, l);
4545 mtch = idm.findAllIdMatches(pdbfn);
4552 type = new IdentifyFile().identify(file, protocol);
4553 } catch (Exception ex)
4557 if (type != null && type.isStructureFile())
4559 filesmatched.add(new Object[] { file, protocol, mtch });
4563 // File wasn't named like one of the sequences or wasn't a PDB
4565 filesnotmatched.add(file);
4569 if (filesmatched.size() > 0)
4571 boolean autoAssociate = Cache
4572 .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4575 String msg = MessageManager.formatMessage(
4576 "label.automatically_associate_structure_files_with_sequences_same_name",
4578 { Integer.valueOf(filesmatched.size())
4580 String ttl = MessageManager.getString(
4581 "label.automatically_associate_structure_files_by_name");
4582 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4583 ttl, JvOptionPane.YES_NO_OPTION);
4584 autoAssociate = choice == JvOptionPane.YES_OPTION;
4588 for (Object[] fm : filesmatched)
4590 // try and associate
4591 // TODO: may want to set a standard ID naming formalism for
4592 // associating PDB files which have no IDs.
4593 for (SequenceI toassoc : (SequenceI[]) fm[2])
4595 PDBEntry pe = new AssociatePdbFileWithSeq()
4596 .associatePdbWithSeq(fm[0].toString(),
4597 (DataSourceType) fm[1], toassoc, false,
4601 System.err.println("Associated file : "
4602 + (fm[0].toString()) + " with "
4603 + toassoc.getDisplayId(true));
4607 // TODO: do we need to update overview ? only if features are
4609 alignPanel.paintAlignment(true, false);
4615 * add declined structures as sequences
4617 for (Object[] o : filesmatched)
4619 filesnotmatched.add(o[0]);
4623 if (filesnotmatched.size() > 0)
4625 if (assocfiles > 0 && (Cache.getDefault(
4626 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4627 || JvOptionPane.showConfirmDialog(thisaf,
4628 "<html>" + MessageManager.formatMessage(
4629 "label.ignore_unmatched_dropped_files_info",
4632 filesnotmatched.size())
4635 MessageManager.getString(
4636 "label.ignore_unmatched_dropped_files"),
4637 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4641 for (Object fn : filesnotmatched)
4643 loadJalviewDataFile(fn, null, null, null);
4647 } catch (Exception ex)
4649 ex.printStackTrace();
4657 * Attempt to load a "dropped" file or URL string, by testing in turn for
4659 * <li>an Annotation file</li>
4660 * <li>a JNet file</li>
4661 * <li>a features file</li>
4662 * <li>else try to interpret as an alignment file</li>
4666 * either a filename or a URL string.
4668 public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4669 FileFormatI format, SequenceI assocSeq)
4671 // BH 2018 was String file
4674 if (sourceType == null)
4676 sourceType = FormatAdapter.checkProtocol(file);
4678 // if the file isn't identified, or not positively identified as some
4679 // other filetype (PFAM is default unidentified alignment file type) then
4680 // try to parse as annotation.
4681 boolean isAnnotation = (format == null
4682 || FileFormat.Pfam.equals(format))
4683 ? new AnnotationFile().annotateAlignmentView(viewport,
4689 // first see if its a T-COFFEE score file
4690 TCoffeeScoreFile tcf = null;
4693 tcf = new TCoffeeScoreFile(file, sourceType);
4696 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4700 new TCoffeeColourScheme(viewport.getAlignment()));
4701 isAnnotation = true;
4702 setStatus(MessageManager.getString(
4703 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4707 // some problem - if no warning its probable that the ID matching
4708 // process didn't work
4709 JvOptionPane.showMessageDialog(Desktop.desktop,
4710 tcf.getWarningMessage() == null
4711 ? MessageManager.getString(
4712 "label.check_file_matches_sequence_ids_alignment")
4713 : tcf.getWarningMessage(),
4714 MessageManager.getString(
4715 "label.problem_reading_tcoffee_score_file"),
4716 JvOptionPane.WARNING_MESSAGE);
4723 } catch (Exception x)
4726 "Exception when processing data source as T-COFFEE score file",
4732 // try to see if its a JNet 'concise' style annotation file *before*
4734 // try to parse it as a features file
4737 format = new IdentifyFile().identify(file, sourceType);
4739 if (FileFormat.ScoreMatrix == format)
4741 ScoreMatrixFile sm = new ScoreMatrixFile(
4742 new FileParse(file, sourceType));
4744 // todo: i18n this message
4745 setStatus(MessageManager.formatMessage(
4746 "label.successfully_loaded_matrix",
4747 sm.getMatrixName()));
4749 else if (FileFormat.Jnet.equals(format))
4751 JPredFile predictions = new JPredFile(file, sourceType);
4752 new JnetAnnotationMaker();
4753 JnetAnnotationMaker.add_annotation(predictions,
4754 viewport.getAlignment(), 0, false);
4755 viewport.getAlignment().setupJPredAlignment();
4756 isAnnotation = true;
4758 // else if (IdentifyFile.FeaturesFile.equals(format))
4759 else if (FileFormat.Features.equals(format))
4761 if (parseFeaturesFile(file, sourceType))
4763 alignPanel.paintAlignment(true, true);
4768 new FileLoader().LoadFile(viewport, file, sourceType, format);
4775 alignPanel.adjustAnnotationHeight();
4776 viewport.updateSequenceIdColours();
4777 buildSortByAnnotationScoresMenu();
4778 alignPanel.paintAlignment(true, true);
4780 } catch (Exception ex)
4782 ex.printStackTrace();
4783 } catch (OutOfMemoryError oom)
4788 } catch (Exception x)
4793 + (sourceType != null
4794 ? (sourceType == DataSourceType.PASTE
4796 : "using " + sourceType + " from "
4800 ? "(parsing as '" + format + "' file)"
4802 oom, Desktop.desktop);
4807 * Method invoked by the ChangeListener on the tabbed pane, in other words
4808 * when a different tabbed pane is selected by the user or programmatically.
4811 public void tabSelectionChanged(int index)
4815 alignPanel = alignPanels.get(index);
4816 viewport = alignPanel.av;
4817 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4818 setMenusFromViewport(viewport);
4822 * 'focus' any colour slider that is open to the selected viewport
4824 if (viewport.getConservationSelected())
4826 SliderPanel.setConservationSlider(alignPanel,
4827 viewport.getResidueShading(), alignPanel.getViewName());
4831 SliderPanel.hideConservationSlider();
4833 if (viewport.getAbovePIDThreshold())
4835 SliderPanel.setPIDSliderSource(alignPanel,
4836 viewport.getResidueShading(), alignPanel.getViewName());
4840 SliderPanel.hidePIDSlider();
4844 * If there is a frame linked to this one in a SplitPane, switch it to the
4845 * same view tab index. No infinite recursion of calls should happen, since
4846 * tabSelectionChanged() should not get invoked on setting the selected
4847 * index to an unchanged value. Guard against setting an invalid index
4848 * before the new view peer tab has been created.
4850 final AlignViewportI peer = viewport.getCodingComplement();
4853 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4854 .getAlignPanel().alignFrame;
4855 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4857 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4863 * On right mouse click on view tab, prompt for and set new view name.
4866 public void tabbedPane_mousePressed(MouseEvent e)
4868 if (e.isPopupTrigger())
4870 String msg = MessageManager.getString("label.enter_view_name");
4871 String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
4872 String reply = JvOptionPane.showInputDialog(msg, ttl);
4876 viewport.setViewName(reply);
4877 // TODO warn if reply is in getExistingViewNames()?
4878 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4883 public AlignViewport getCurrentView()
4889 * Open the dialog for regex description parsing.
4892 protected void extractScores_actionPerformed(ActionEvent e)
4894 ParseProperties pp = new jalview.analysis.ParseProperties(
4895 viewport.getAlignment());
4896 // TODO: verify regex and introduce GUI dialog for version 2.5
4897 // if (pp.getScoresFromDescription("col", "score column ",
4898 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4900 if (pp.getScoresFromDescription("description column",
4901 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4903 buildSortByAnnotationScoresMenu();
4911 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4915 protected void showDbRefs_actionPerformed(ActionEvent e)
4917 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4923 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4927 protected void showNpFeats_actionPerformed(ActionEvent e)
4929 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4933 * find the viewport amongst the tabs in this alignment frame and close that
4938 public boolean closeView(AlignViewportI av)
4942 this.closeMenuItem_actionPerformed(false);
4945 Component[] comp = tabbedPane.getComponents();
4946 for (int i = 0; comp != null && i < comp.length; i++)
4948 if (comp[i] instanceof AlignmentPanel)
4950 if (((AlignmentPanel) comp[i]).av == av)
4953 closeView((AlignmentPanel) comp[i]);
4961 protected void build_fetchdbmenu(JMenu webService)
4963 // Temporary hack - DBRef Fetcher always top level ws entry.
4964 // TODO We probably want to store a sequence database checklist in
4965 // preferences and have checkboxes.. rather than individual sources selected
4967 final JMenu rfetch = new JMenu(
4968 MessageManager.getString("action.fetch_db_references"));
4969 rfetch.setToolTipText(MessageManager.getString(
4970 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4971 webService.add(rfetch);
4973 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4974 MessageManager.getString("option.trim_retrieved_seqs"));
4975 trimrs.setToolTipText(
4976 MessageManager.getString("label.trim_retrieved_sequences"));
4978 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4979 trimrs.addActionListener(new ActionListener()
4982 public void actionPerformed(ActionEvent e)
4984 trimrs.setSelected(trimrs.isSelected());
4985 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4986 Boolean.valueOf(trimrs.isSelected()).toString());
4990 JMenuItem fetchr = new JMenuItem(
4991 MessageManager.getString("label.standard_databases"));
4992 fetchr.setToolTipText(
4993 MessageManager.getString("label.fetch_embl_uniprot"));
4994 fetchr.addActionListener(new ActionListener()
4998 public void actionPerformed(ActionEvent e)
5000 new Thread(new Runnable()
5005 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5006 .getAlignment().isNucleotide();
5007 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5008 alignPanel.av.getSequenceSelection(),
5009 alignPanel.alignFrame, null,
5010 alignPanel.alignFrame.featureSettings, isNucleotide);
5011 dbRefFetcher.addListener(new FetchFinishedListenerI()
5014 public void finished()
5016 AlignFrame.this.setMenusForViewport();
5019 dbRefFetcher.fetchDBRefs(false);
5027 new Thread(new Runnable()
5032 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5033 .getSequenceFetcherSingleton();
5034 javax.swing.SwingUtilities.invokeLater(new Runnable()
5039 String[] dbclasses = sf.getNonAlignmentSources();
5040 List<DbSourceProxy> otherdb;
5041 JMenu dfetch = new JMenu();
5042 JMenu ifetch = new JMenu();
5043 JMenuItem fetchr = null;
5044 int comp = 0, icomp = 0, mcomp = 15;
5045 String mname = null;
5047 for (String dbclass : dbclasses)
5049 otherdb = sf.getSourceProxy(dbclass);
5050 // add a single entry for this class, or submenu allowing 'fetch
5052 if (otherdb == null || otherdb.size() < 1)
5058 mname = "From " + dbclass;
5060 if (otherdb.size() == 1)
5062 final DbSourceProxy[] dassource = otherdb
5063 .toArray(new DbSourceProxy[0]);
5064 DbSourceProxy src = otherdb.get(0);
5065 fetchr = new JMenuItem(src.getDbSource());
5066 fetchr.addActionListener(new ActionListener()
5070 public void actionPerformed(ActionEvent e)
5072 new Thread(new Runnable()
5078 boolean isNucleotide = alignPanel.alignFrame
5079 .getViewport().getAlignment()
5081 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5082 alignPanel.av.getSequenceSelection(),
5083 alignPanel.alignFrame, dassource,
5084 alignPanel.alignFrame.featureSettings,
5087 .addListener(new FetchFinishedListenerI()
5090 public void finished()
5092 AlignFrame.this.setMenusForViewport();
5095 dbRefFetcher.fetchDBRefs(false);
5101 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5102 MessageManager.formatMessage(
5103 "label.fetch_retrieve_from", new Object[]
5104 { src.getDbName() })));
5110 final DbSourceProxy[] dassource = otherdb
5111 .toArray(new DbSourceProxy[0]);
5113 DbSourceProxy src = otherdb.get(0);
5114 fetchr = new JMenuItem(MessageManager
5115 .formatMessage("label.fetch_all_param", new Object[]
5116 { src.getDbSource() }));
5117 fetchr.addActionListener(new ActionListener()
5120 public void actionPerformed(ActionEvent e)
5122 new Thread(new Runnable()
5128 boolean isNucleotide = alignPanel.alignFrame
5129 .getViewport().getAlignment()
5131 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5132 alignPanel.av.getSequenceSelection(),
5133 alignPanel.alignFrame, dassource,
5134 alignPanel.alignFrame.featureSettings,
5137 .addListener(new FetchFinishedListenerI()
5140 public void finished()
5142 AlignFrame.this.setMenusForViewport();
5145 dbRefFetcher.fetchDBRefs(false);
5151 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5152 MessageManager.formatMessage(
5153 "label.fetch_retrieve_from_all_sources",
5155 { Integer.valueOf(otherdb.size())
5157 src.getDbSource(), src.getDbName() })));
5160 // and then build the rest of the individual menus
5161 ifetch = new JMenu(MessageManager.formatMessage(
5162 "label.source_from_db_source", new Object[]
5163 { src.getDbSource() }));
5165 String imname = null;
5167 for (DbSourceProxy sproxy : otherdb)
5169 String dbname = sproxy.getDbName();
5170 String sname = dbname.length() > 5
5171 ? dbname.substring(0, 5) + "..."
5173 String msname = dbname.length() > 10
5174 ? dbname.substring(0, 10) + "..."
5178 imname = MessageManager
5179 .formatMessage("label.from_msname", new Object[]
5182 fetchr = new JMenuItem(msname);
5183 final DbSourceProxy[] dassrc = { sproxy };
5184 fetchr.addActionListener(new ActionListener()
5188 public void actionPerformed(ActionEvent e)
5190 new Thread(new Runnable()
5196 boolean isNucleotide = alignPanel.alignFrame
5197 .getViewport().getAlignment()
5199 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5200 alignPanel.av.getSequenceSelection(),
5201 alignPanel.alignFrame, dassrc,
5202 alignPanel.alignFrame.featureSettings,
5205 .addListener(new FetchFinishedListenerI()
5208 public void finished()
5210 AlignFrame.this.setMenusForViewport();
5213 dbRefFetcher.fetchDBRefs(false);
5219 fetchr.setToolTipText(
5220 "<html>" + MessageManager.formatMessage(
5221 "label.fetch_retrieve_from", new Object[]
5225 if (++icomp >= mcomp || i == (otherdb.size()))
5227 ifetch.setText(MessageManager.formatMessage(
5228 "label.source_to_target", imname, sname));
5230 ifetch = new JMenu();
5238 if (comp >= mcomp || dbi >= (dbclasses.length))
5240 dfetch.setText(MessageManager.formatMessage(
5241 "label.source_to_target", mname, dbclass));
5243 dfetch = new JMenu();
5256 * Left justify the whole alignment.
5259 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5261 AlignmentI al = viewport.getAlignment();
5263 viewport.firePropertyChange("alignment", null, al);
5267 * Right justify the whole alignment.
5270 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5272 AlignmentI al = viewport.getAlignment();
5274 viewport.firePropertyChange("alignment", null, al);
5278 public void setShowSeqFeatures(boolean b)
5280 showSeqFeatures.setSelected(b);
5281 viewport.setShowSequenceFeatures(b);
5288 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5289 * awt.event.ActionEvent)
5292 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5294 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5295 alignPanel.paintAlignment(false, false);
5302 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5306 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5308 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5309 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5317 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5318 * .event.ActionEvent)
5321 protected void showGroupConservation_actionPerformed(ActionEvent e)
5323 viewport.setShowGroupConservation(showGroupConservation.getState());
5324 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5331 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5332 * .event.ActionEvent)
5335 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5337 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5338 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5345 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5346 * .event.ActionEvent)
5349 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5351 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5352 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5356 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5358 showSequenceLogo.setState(true);
5359 viewport.setShowSequenceLogo(true);
5360 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5361 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5365 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5367 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5374 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5375 * .event.ActionEvent)
5378 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5380 if (avc.makeGroupsFromSelection())
5382 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5383 alignPanel.updateAnnotation();
5384 alignPanel.paintAlignment(true, true);
5388 public void clearAlignmentSeqRep()
5390 // TODO refactor alignmentseqrep to controller
5391 if (viewport.getAlignment().hasSeqrep())
5393 viewport.getAlignment().setSeqrep(null);
5394 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5395 alignPanel.updateAnnotation();
5396 alignPanel.paintAlignment(true, true);
5401 protected void createGroup_actionPerformed(ActionEvent e)
5403 if (avc.createGroup())
5405 if (applyAutoAnnotationSettings.isSelected())
5407 alignPanel.updateAnnotation(true, false);
5409 alignPanel.alignmentChanged();
5414 protected void unGroup_actionPerformed(ActionEvent e)
5418 alignPanel.alignmentChanged();
5423 * make the given alignmentPanel the currently selected tab
5425 * @param alignmentPanel
5427 public void setDisplayedView(AlignmentPanel alignmentPanel)
5429 if (!viewport.getSequenceSetId()
5430 .equals(alignmentPanel.av.getSequenceSetId()))
5432 throw new Error(MessageManager.getString(
5433 "error.implementation_error_cannot_show_view_alignment_frame"));
5435 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5436 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5438 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5443 * Action on selection of menu options to Show or Hide annotations.
5446 * @param forSequences
5447 * update sequence-related annotations
5448 * @param forAlignment
5449 * update non-sequence-related annotations
5452 protected void setAnnotationsVisibility(boolean visible,
5453 boolean forSequences, boolean forAlignment)
5455 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5456 .getAlignmentAnnotation();
5461 for (AlignmentAnnotation aa : anns)
5464 * don't display non-positional annotations on an alignment
5466 if (aa.annotations == null)
5470 boolean apply = (aa.sequenceRef == null && forAlignment)
5471 || (aa.sequenceRef != null && forSequences);
5474 aa.visible = visible;
5477 alignPanel.validateAnnotationDimensions(true);
5478 alignPanel.alignmentChanged();
5482 * Store selected annotation sort order for the view and repaint.
5485 protected void sortAnnotations_actionPerformed()
5487 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5489 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5490 alignPanel.paintAlignment(false, false);
5495 * @return alignment panels in this alignment frame
5497 public List<? extends AlignmentViewPanel> getAlignPanels()
5499 // alignPanels is never null
5500 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5505 * Open a new alignment window, with the cDNA associated with this (protein)
5506 * alignment, aligned as is the protein.
5508 protected void viewAsCdna_actionPerformed()
5510 // TODO no longer a menu action - refactor as required
5511 final AlignmentI alignment = getViewport().getAlignment();
5512 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5513 if (mappings == null)
5517 List<SequenceI> cdnaSeqs = new ArrayList<>();
5518 for (SequenceI aaSeq : alignment.getSequences())
5520 for (AlignedCodonFrame acf : mappings)
5522 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5526 * There is a cDNA mapping for this protein sequence - add to new
5527 * alignment. It will share the same dataset sequence as other mapped
5528 * cDNA (no new mappings need to be created).
5530 final Sequence newSeq = new Sequence(dnaSeq);
5531 newSeq.setDatasetSequence(dnaSeq);
5532 cdnaSeqs.add(newSeq);
5536 if (cdnaSeqs.size() == 0)
5538 // show a warning dialog no mapped cDNA
5541 AlignmentI cdna = new Alignment(
5542 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5543 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5544 AlignFrame.DEFAULT_HEIGHT);
5545 cdna.alignAs(alignment);
5546 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5548 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5549 AlignFrame.DEFAULT_HEIGHT);
5553 * Set visibility of dna/protein complement view (available when shown in a
5559 protected void showComplement_actionPerformed(boolean show)
5561 SplitContainerI sf = getSplitViewContainer();
5564 sf.setComplementVisible(this, show);
5569 * Generate the reverse (optionally complemented) of the selected sequences,
5570 * and add them to the alignment
5573 protected void showReverse_actionPerformed(boolean complement)
5575 AlignmentI al = null;
5578 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5579 al = dna.reverseCdna(complement);
5580 viewport.addAlignment(al, "");
5581 addHistoryItem(new EditCommand(
5582 MessageManager.getString("label.add_sequences"), Action.PASTE,
5583 al.getSequencesArray(), 0, al.getWidth(),
5584 viewport.getAlignment()));
5585 } catch (Exception ex)
5587 System.err.println(ex.getMessage());
5593 * Try to run a script in the Groovy console, having first ensured that this
5594 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5595 * be targeted at this alignment.
5598 protected void runGroovy_actionPerformed()
5600 Jalview.setCurrentAlignFrame(this);
5601 groovy.ui.Console console = Desktop.getGroovyConsole();
5602 if (console != null)
5606 console.runScript();
5607 } catch (Exception ex)
5609 System.err.println((ex.toString()));
5610 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5611 MessageManager.getString("label.couldnt_run_groovy_script"),
5612 MessageManager.getString("label.groovy_support_failed"),
5613 JvOptionPane.ERROR_MESSAGE);
5618 System.err.println("Can't run Groovy script as console not found");
5623 * Hides columns containing (or not containing) a specified feature, provided
5624 * that would not leave all columns hidden
5626 * @param featureType
5627 * @param columnsContaining
5630 public boolean hideFeatureColumns(String featureType,
5631 boolean columnsContaining)
5633 boolean notForHiding = avc.markColumnsContainingFeatures(
5634 columnsContaining, false, false, featureType);
5637 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5638 false, featureType))
5640 getViewport().hideSelectedColumns();
5648 protected void selectHighlightedColumns_actionPerformed(
5649 ActionEvent actionEvent)
5651 // include key modifier check in case user selects from menu
5652 avc.markHighlightedColumns(
5653 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5654 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5655 | ActionEvent.CTRL_MASK)) != 0);
5659 * Rebuilds the Colour menu, including any user-defined colours which have
5660 * been loaded either on startup or during the session
5662 public void buildColourMenu()
5664 colourMenu.removeAll();
5666 colourMenu.add(applyToAllGroups);
5667 colourMenu.add(textColour);
5668 colourMenu.addSeparator();
5670 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5673 colourMenu.addSeparator();
5674 colourMenu.add(conservationMenuItem);
5675 colourMenu.add(modifyConservation);
5676 colourMenu.add(abovePIDThreshold);
5677 colourMenu.add(modifyPID);
5678 colourMenu.add(annotationColour);
5680 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5681 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5685 * Open a dialog (if not already open) that allows the user to select and
5686 * calculate PCA or Tree analysis
5688 protected void openTreePcaDialog()
5690 if (alignPanel.getCalculationDialog() == null)
5692 new CalculationChooser(AlignFrame.this);
5697 protected void loadVcf_actionPerformed()
5699 JalviewFileChooser chooser = new JalviewFileChooser(
5700 Cache.getProperty("LAST_DIRECTORY"));
5701 chooser.setFileView(new JalviewFileView());
5702 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5703 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5704 final AlignFrame us = this;
5705 chooser.setResponseHandler(0, new Runnable()
5710 String choice = chooser.getSelectedFile().getPath();
5711 Cache.setProperty("LAST_DIRECTORY", choice);
5712 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5713 new VCFLoader(choice).loadVCF(seqs, us);
5716 chooser.showOpenDialog(null);
5722 class PrintThread extends Thread
5726 public PrintThread(AlignmentPanel ap)
5731 static PageFormat pf;
5736 PrinterJob printJob = PrinterJob.getPrinterJob();
5740 printJob.setPrintable(ap, pf);
5744 printJob.setPrintable(ap);
5747 if (printJob.printDialog())
5752 } catch (Exception PrintException)
5754 PrintException.printStackTrace();