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 java.util.Locale;
25 import java.awt.BorderLayout;
26 import java.awt.Color;
27 import java.awt.Component;
28 import java.awt.Rectangle;
29 import java.awt.Toolkit;
30 import java.awt.datatransfer.Clipboard;
31 import java.awt.datatransfer.DataFlavor;
32 import java.awt.datatransfer.StringSelection;
33 import java.awt.datatransfer.Transferable;
34 import java.awt.dnd.DnDConstants;
35 import java.awt.dnd.DropTargetDragEvent;
36 import java.awt.dnd.DropTargetDropEvent;
37 import java.awt.dnd.DropTargetEvent;
38 import java.awt.dnd.DropTargetListener;
39 import java.awt.event.ActionEvent;
40 import java.awt.event.ActionListener;
41 import java.awt.event.FocusAdapter;
42 import java.awt.event.FocusEvent;
43 import java.awt.event.ItemEvent;
44 import java.awt.event.ItemListener;
45 import java.awt.event.KeyAdapter;
46 import java.awt.event.KeyEvent;
47 import java.awt.event.MouseEvent;
48 import java.awt.print.PageFormat;
49 import java.awt.print.PrinterJob;
50 import java.beans.PropertyChangeEvent;
52 import java.io.FileWriter;
53 import java.io.IOException;
54 import java.io.PrintWriter;
56 import java.util.ArrayList;
57 import java.util.Arrays;
58 import java.util.Deque;
59 import java.util.Enumeration;
60 import java.util.Hashtable;
61 import java.util.List;
62 import java.util.Vector;
64 import javax.swing.ButtonGroup;
65 import javax.swing.JCheckBoxMenuItem;
66 import javax.swing.JComponent;
67 import javax.swing.JEditorPane;
68 import javax.swing.JInternalFrame;
69 import javax.swing.JLabel;
70 import javax.swing.JLayeredPane;
71 import javax.swing.JMenu;
72 import javax.swing.JMenuItem;
73 import javax.swing.JPanel;
74 import javax.swing.JScrollPane;
75 import javax.swing.SwingUtilities;
77 import ext.vamsas.ServiceHandle;
78 import jalview.analysis.AlignmentSorter;
79 import jalview.analysis.AlignmentUtils;
80 import jalview.analysis.CrossRef;
81 import jalview.analysis.Dna;
82 import jalview.analysis.GeneticCodeI;
83 import jalview.analysis.ParseProperties;
84 import jalview.analysis.SequenceIdMatcher;
85 import jalview.api.AlignExportSettingsI;
86 import jalview.api.AlignViewControllerGuiI;
87 import jalview.api.AlignViewControllerI;
88 import jalview.api.AlignViewportI;
89 import jalview.api.AlignmentViewPanel;
90 import jalview.api.FeatureSettingsControllerI;
91 import jalview.api.FeatureSettingsModelI;
92 import jalview.api.SplitContainerI;
93 import jalview.api.ViewStyleI;
94 import jalview.api.analysis.SimilarityParamsI;
95 import jalview.bin.Cache;
96 import jalview.bin.Console;
97 import jalview.bin.Jalview;
98 import jalview.commands.CommandI;
99 import jalview.commands.EditCommand;
100 import jalview.commands.EditCommand.Action;
101 import jalview.commands.OrderCommand;
102 import jalview.commands.RemoveGapColCommand;
103 import jalview.commands.RemoveGapsCommand;
104 import jalview.commands.SlideSequencesCommand;
105 import jalview.commands.TrimRegionCommand;
106 import jalview.datamodel.AlignExportSettingsAdapter;
107 import jalview.datamodel.AlignedCodonFrame;
108 import jalview.datamodel.Alignment;
109 import jalview.datamodel.AlignmentAnnotation;
110 import jalview.datamodel.AlignmentExportData;
111 import jalview.datamodel.AlignmentI;
112 import jalview.datamodel.AlignmentOrder;
113 import jalview.datamodel.AlignmentView;
114 import jalview.datamodel.ColumnSelection;
115 import jalview.datamodel.HiddenColumns;
116 import jalview.datamodel.PDBEntry;
117 import jalview.datamodel.SeqCigar;
118 import jalview.datamodel.Sequence;
119 import jalview.datamodel.SequenceGroup;
120 import jalview.datamodel.SequenceI;
121 import jalview.gui.ColourMenuHelper.ColourChangeListener;
122 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
123 import jalview.io.AlignmentProperties;
124 import jalview.io.AnnotationFile;
125 import jalview.io.BackupFiles;
126 import jalview.io.BioJsHTMLOutput;
127 import jalview.io.DataSourceType;
128 import jalview.io.FileFormat;
129 import jalview.io.FileFormatI;
130 import jalview.io.FileFormats;
131 import jalview.io.FileLoader;
132 import jalview.io.FileParse;
133 import jalview.io.FormatAdapter;
134 import jalview.io.HtmlSvgOutput;
135 import jalview.io.IdentifyFile;
136 import jalview.io.JPredFile;
137 import jalview.io.JalviewFileChooser;
138 import jalview.io.JalviewFileView;
139 import jalview.io.JnetAnnotationMaker;
140 import jalview.io.NewickFile;
141 import jalview.io.ScoreMatrixFile;
142 import jalview.io.TCoffeeScoreFile;
143 import jalview.io.vcf.VCFLoader;
144 import jalview.jbgui.GAlignFrame;
145 import jalview.project.Jalview2XML;
146 import jalview.schemes.ColourSchemeI;
147 import jalview.schemes.ColourSchemes;
148 import jalview.schemes.ResidueColourScheme;
149 import jalview.schemes.TCoffeeColourScheme;
150 import jalview.util.HttpUtils;
151 import jalview.util.ImageMaker.TYPE;
152 import jalview.util.MessageManager;
153 import jalview.util.Platform;
154 import jalview.viewmodel.AlignmentViewport;
155 import jalview.viewmodel.ViewportRanges;
156 import jalview.ws.DBRefFetcher;
157 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
158 import jalview.ws.jws1.Discoverer;
159 import jalview.ws.jws2.Jws2Discoverer;
160 import jalview.ws.jws2.jabaws2.Jws2Instance;
161 import jalview.ws.seqfetcher.DbSourceProxy;
167 * @version $Revision$
169 @SuppressWarnings("serial")
170 public class AlignFrame extends GAlignFrame implements DropTargetListener,
171 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
174 public static final int DEFAULT_WIDTH = 700;
176 public static final int DEFAULT_HEIGHT = 500;
179 * The currently displayed panel (selected tabbed view if more than one)
181 public AlignmentPanel alignPanel;
183 AlignViewport viewport;
185 public AlignViewControllerI avc;
187 List<AlignmentPanel> alignPanels = new ArrayList<>();
190 * Last format used to load or save alignments in this window
192 FileFormatI currentFileFormat = null;
195 * Current filename for this alignment
197 String fileName = null;
202 * Creates a new AlignFrame object with specific width and height.
208 public AlignFrame(AlignmentI al, int width, int height)
210 this(al, null, width, height);
214 * Creates a new AlignFrame object with specific width, height and
220 * @param sequenceSetId
222 public AlignFrame(AlignmentI al, int width, int height,
223 String sequenceSetId)
225 this(al, null, width, height, sequenceSetId);
229 * Creates a new AlignFrame object with specific width, height and
235 * @param sequenceSetId
238 public AlignFrame(AlignmentI al, int width, int height,
239 String sequenceSetId, String viewId)
241 this(al, null, width, height, sequenceSetId, viewId);
245 * new alignment window with hidden columns
249 * @param hiddenColumns
250 * ColumnSelection or null
252 * Width of alignment frame
256 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
259 this(al, hiddenColumns, width, height, null);
263 * Create alignment frame for al with hiddenColumns, a specific width and
264 * height, and specific sequenceId
267 * @param hiddenColumns
270 * @param sequenceSetId
273 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
274 int height, String sequenceSetId)
276 this(al, hiddenColumns, width, height, sequenceSetId, null);
280 * Create alignment frame for al with hiddenColumns, a specific width and
281 * height, and specific sequenceId
284 * @param hiddenColumns
287 * @param sequenceSetId
292 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
293 int height, String sequenceSetId, String viewId)
295 setSize(width, height);
297 if (al.getDataset() == null)
302 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
304 alignPanel = new AlignmentPanel(this, viewport);
306 addAlignmentPanel(alignPanel, true);
310 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
311 HiddenColumns hiddenColumns, int width, int height)
313 setSize(width, height);
315 if (al.getDataset() == null)
320 viewport = new AlignViewport(al, hiddenColumns);
322 if (hiddenSeqs != null && hiddenSeqs.length > 0)
324 viewport.hideSequence(hiddenSeqs);
326 alignPanel = new AlignmentPanel(this, viewport);
327 addAlignmentPanel(alignPanel, true);
332 * Make a new AlignFrame from existing alignmentPanels
339 public AlignFrame(AlignmentPanel ap)
343 addAlignmentPanel(ap, false);
348 * initalise the alignframe from the underlying viewport data and the
353 // setBackground(Color.white); // BH 2019
355 if (!Jalview.isHeadlessMode())
357 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
360 avc = new jalview.controller.AlignViewController(this, viewport,
362 if (viewport.getAlignmentConservationAnnotation() == null)
364 // BLOSUM62Colour.setEnabled(false);
365 conservationMenuItem.setEnabled(false);
366 modifyConservation.setEnabled(false);
367 // PIDColour.setEnabled(false);
368 // abovePIDThreshold.setEnabled(false);
369 // modifyPID.setEnabled(false);
372 String sortby = Cache.getDefault("SORT_ALIGNMENT",
375 if (sortby.equals("Id"))
377 sortIDMenuItem_actionPerformed(null);
379 else if (sortby.equals("Pairwise Identity"))
381 sortPairwiseMenuItem_actionPerformed(null);
385 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
387 setMenusFromViewport(viewport);
388 buildSortByAnnotationScoresMenu();
389 calculateTree.addActionListener(new ActionListener()
393 public void actionPerformed(ActionEvent e)
400 if (Desktop.desktop != null)
402 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
403 if (!Platform.isJS())
405 addServiceListeners();
410 if (viewport.getWrapAlignment())
412 wrapMenuItem_actionPerformed(null);
415 if (Cache.getDefault("SHOW_OVERVIEW", false))
417 this.overviewMenuItem_actionPerformed(null);
422 final List<AlignmentViewPanel> selviews = new ArrayList<>();
423 final List<AlignmentPanel> origview = new ArrayList<>();
424 final String menuLabel = MessageManager
425 .getString("label.copy_format_from");
426 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
427 new ViewSetProvider()
431 public AlignmentPanel[] getAllAlignmentPanels()
434 origview.add(alignPanel);
435 // make an array of all alignment panels except for this one
436 List<AlignmentPanel> aps = new ArrayList<>(
437 Arrays.asList(Desktop.getAlignmentPanels(null)));
438 aps.remove(AlignFrame.this.alignPanel);
439 return aps.toArray(new AlignmentPanel[aps.size()]);
441 }, selviews, new ItemListener()
445 public void itemStateChanged(ItemEvent e)
447 if (origview.size() > 0)
449 final AlignmentPanel ap = origview.get(0);
452 * Copy the ViewStyle of the selected panel to 'this one'.
453 * Don't change value of 'scaleProteinAsCdna' unless copying
456 ViewStyleI vs = selviews.get(0).getAlignViewport()
458 boolean fromSplitFrame = selviews.get(0)
459 .getAlignViewport().getCodingComplement() != null;
462 vs.setScaleProteinAsCdna(ap.getAlignViewport()
463 .getViewStyle().isScaleProteinAsCdna());
465 ap.getAlignViewport().setViewStyle(vs);
468 * Also rescale ViewStyle of SplitFrame complement if there is
469 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
470 * the whole ViewStyle (allow cDNA protein to have different
473 AlignViewportI complement = ap.getAlignViewport()
474 .getCodingComplement();
475 if (complement != null && vs.isScaleProteinAsCdna())
477 AlignFrame af = Desktop.getAlignFrameFor(complement);
478 ((SplitFrame) af.getSplitViewContainer())
480 af.setMenusForViewport();
484 ap.setSelected(true);
485 ap.alignFrame.setMenusForViewport();
490 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
491 .indexOf("devel") > -1
492 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
493 .indexOf("test") > -1)
495 formatMenu.add(vsel);
497 addFocusListener(new FocusAdapter()
500 public void focusGained(FocusEvent e)
502 Jalview.setCurrentAlignFrame(AlignFrame.this);
509 * Change the filename and format for the alignment, and enable the 'reload'
510 * button functionality.
517 public void setFileName(String file, FileFormatI format)
520 setFileFormat(format);
521 reload.setEnabled(true);
525 * JavaScript will have this, maybe others. More dependable than a file name
526 * and maintains a reference to the actual bytes loaded.
530 public void setFileObject(File file)
532 this.fileObject = file;
536 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
539 void addKeyListener()
541 addKeyListener(new KeyAdapter()
544 public void keyPressed(KeyEvent evt)
546 if (viewport.cursorMode
547 && ((evt.getKeyCode() >= KeyEvent.VK_0
548 && evt.getKeyCode() <= KeyEvent.VK_9)
549 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
550 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
551 && Character.isDigit(evt.getKeyChar()))
553 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
556 switch (evt.getKeyCode())
559 case 27: // escape key
560 deselectAllSequenceMenuItem_actionPerformed(null);
564 case KeyEvent.VK_DOWN:
565 if (evt.isAltDown() || !viewport.cursorMode)
567 moveSelectedSequences(false);
569 if (viewport.cursorMode)
571 alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
576 if (evt.isAltDown() || !viewport.cursorMode)
578 moveSelectedSequences(true);
580 if (viewport.cursorMode)
582 alignPanel.getSeqPanel().moveCursor(0, -1,evt.isShiftDown());
587 case KeyEvent.VK_LEFT:
588 if (evt.isAltDown() || !viewport.cursorMode)
590 slideSequences(false,
591 alignPanel.getSeqPanel().getKeyboardNo1());
595 alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
600 case KeyEvent.VK_RIGHT:
601 if (evt.isAltDown() || !viewport.cursorMode)
603 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
607 alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
611 case KeyEvent.VK_SPACE:
612 if (viewport.cursorMode)
614 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
615 || evt.isShiftDown() || evt.isAltDown());
619 // case KeyEvent.VK_A:
620 // if (viewport.cursorMode)
622 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
623 // //System.out.println("A");
627 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
628 * System.out.println("closing bracket"); } break;
630 case KeyEvent.VK_DELETE:
631 case KeyEvent.VK_BACK_SPACE:
632 if (!viewport.cursorMode)
634 cut_actionPerformed();
638 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
639 || evt.isShiftDown() || evt.isAltDown());
645 if (viewport.cursorMode)
647 alignPanel.getSeqPanel().setCursorRow();
651 if (viewport.cursorMode && !evt.isControlDown())
653 alignPanel.getSeqPanel().setCursorColumn();
657 if (viewport.cursorMode)
659 alignPanel.getSeqPanel().setCursorPosition();
663 case KeyEvent.VK_ENTER:
664 case KeyEvent.VK_COMMA:
665 if (viewport.cursorMode)
667 alignPanel.getSeqPanel().setCursorRowAndColumn();
672 if (viewport.cursorMode)
674 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
678 if (viewport.cursorMode)
680 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
685 viewport.cursorMode = !viewport.cursorMode;
686 setStatus(MessageManager
687 .formatMessage("label.keyboard_editing_mode", new String[]
688 { (viewport.cursorMode ? "on" : "off") }));
689 if (viewport.cursorMode)
691 ViewportRanges ranges = viewport.getRanges();
692 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
694 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
697 alignPanel.getSeqPanel().seqCanvas.repaint();
703 Help.showHelpWindow();
704 } catch (Exception ex)
706 ex.printStackTrace();
711 boolean toggleSeqs = !evt.isControlDown();
712 boolean toggleCols = !evt.isShiftDown();
713 toggleHiddenRegions(toggleSeqs, toggleCols);
718 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
719 boolean modifyExisting = true; // always modify, don't clear
720 // evt.isShiftDown();
721 boolean invertHighlighted = evt.isAltDown();
722 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
726 case KeyEvent.VK_PAGE_UP:
727 viewport.getRanges().pageUp();
729 case KeyEvent.VK_PAGE_DOWN:
730 viewport.getRanges().pageDown();
736 public void keyReleased(KeyEvent evt)
738 switch (evt.getKeyCode())
740 case KeyEvent.VK_LEFT:
741 if (evt.isAltDown() || !viewport.cursorMode)
743 viewport.firePropertyChange("alignment", null,
744 viewport.getAlignment().getSequences());
748 case KeyEvent.VK_RIGHT:
749 if (evt.isAltDown() || !viewport.cursorMode)
751 viewport.firePropertyChange("alignment", null,
752 viewport.getAlignment().getSequences());
760 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
762 ap.alignFrame = this;
763 avc = new jalview.controller.AlignViewController(this, viewport,
768 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
770 int aSize = alignPanels.size();
772 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
774 if (aSize == 1 && ap.av.getViewName() == null)
776 this.getContentPane().add(ap, BorderLayout.CENTER);
782 setInitialTabVisible();
785 expandViews.setEnabled(true);
786 gatherViews.setEnabled(true);
787 tabbedPane.addTab(ap.av.getViewName(), ap);
789 ap.setVisible(false);
794 if (ap.av.isPadGaps())
796 ap.av.getAlignment().padGaps();
798 ap.av.updateConservation(ap);
799 ap.av.updateConsensus(ap);
800 ap.av.updateStrucConsensus(ap);
804 public void setInitialTabVisible()
806 expandViews.setEnabled(true);
807 gatherViews.setEnabled(true);
808 tabbedPane.setVisible(true);
809 AlignmentPanel first = alignPanels.get(0);
810 tabbedPane.addTab(first.av.getViewName(), first);
811 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
814 public AlignViewport getViewport()
819 /* Set up intrinsic listeners for dynamically generated GUI bits. */
820 private void addServiceListeners()
822 final java.beans.PropertyChangeListener thisListener;
823 Desktop.instance.addJalviewPropertyChangeListener("services",
824 thisListener = new java.beans.PropertyChangeListener()
827 public void propertyChange(PropertyChangeEvent evt)
829 // // System.out.println("Discoverer property change.");
830 // if (evt.getPropertyName().equals("services"))
832 SwingUtilities.invokeLater(new Runnable()
839 "Rebuild WS Menu for service change");
840 BuildWebServiceMenu();
847 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
850 public void internalFrameClosed(
851 javax.swing.event.InternalFrameEvent evt)
853 // System.out.println("deregistering discoverer listener");
854 Desktop.instance.removeJalviewPropertyChangeListener("services",
856 closeMenuItem_actionPerformed(true);
859 // Finally, build the menu once to get current service state
860 new Thread(new Runnable()
865 BuildWebServiceMenu();
871 * Configure menu items that vary according to whether the alignment is
872 * nucleotide or protein
874 public void setGUINucleotide()
876 AlignmentI al = getViewport().getAlignment();
877 boolean nucleotide = al.isNucleotide();
879 loadVcf.setVisible(nucleotide);
880 showTranslation.setVisible(nucleotide);
881 showReverse.setVisible(nucleotide);
882 showReverseComplement.setVisible(nucleotide);
883 conservationMenuItem.setEnabled(!nucleotide);
885 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
886 showGroupConservation.setEnabled(!nucleotide);
888 showComplementMenuItem
889 .setText(nucleotide ? MessageManager.getString("label.protein")
890 : MessageManager.getString("label.nucleotide"));
894 * set up menus for the current viewport. This may be called after any
895 * operation that affects the data in the current view (selection changed,
896 * etc) to update the menus to reflect the new state.
899 public void setMenusForViewport()
901 setMenusFromViewport(viewport);
905 * Need to call this method when tabs are selected for multiple views, or when
906 * loading from Jalview2XML.java
911 public void setMenusFromViewport(AlignViewport av)
913 padGapsMenuitem.setSelected(av.isPadGaps());
914 colourTextMenuItem.setSelected(av.isShowColourText());
915 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
916 modifyPID.setEnabled(abovePIDThreshold.isSelected());
917 conservationMenuItem.setSelected(av.getConservationSelected());
918 modifyConservation.setEnabled(conservationMenuItem.isSelected());
919 seqLimits.setSelected(av.getShowJVSuffix());
920 idRightAlign.setSelected(av.isRightAlignIds());
921 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
922 renderGapsMenuItem.setSelected(av.isRenderGaps());
923 wrapMenuItem.setSelected(av.getWrapAlignment());
924 scaleAbove.setVisible(av.getWrapAlignment());
925 scaleLeft.setVisible(av.getWrapAlignment());
926 scaleRight.setVisible(av.getWrapAlignment());
927 annotationPanelMenuItem.setState(av.isShowAnnotation());
929 * Show/hide annotations only enabled if annotation panel is shown
931 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
932 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
933 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
934 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
935 viewBoxesMenuItem.setSelected(av.getShowBoxes());
936 viewTextMenuItem.setSelected(av.getShowText());
937 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
938 showGroupConsensus.setSelected(av.isShowGroupConsensus());
939 showGroupConservation.setSelected(av.isShowGroupConservation());
940 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
941 showSequenceLogo.setSelected(av.isShowSequenceLogo());
942 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
944 ColourMenuHelper.setColourSelected(colourMenu,
945 av.getGlobalColourScheme());
947 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
948 hiddenMarkers.setState(av.getShowHiddenMarkers());
949 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
950 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
951 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
952 autoCalculate.setSelected(av.autoCalculateConsensus);
953 sortByTree.setSelected(av.sortByTree);
954 listenToViewSelections.setSelected(av.followSelection);
956 showProducts.setEnabled(canShowProducts());
957 setGroovyEnabled(Desktop.getGroovyConsole() != null);
963 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
967 public void setGroovyEnabled(boolean b)
969 runGroovy.setEnabled(b);
972 private IProgressIndicator progressBar;
977 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
980 public void setProgressBar(String message, long id)
982 progressBar.setProgressBar(message, id);
986 public void registerHandler(final long id,
987 final IProgressIndicatorHandler handler)
989 progressBar.registerHandler(id, handler);
994 * @return true if any progress bars are still active
997 public boolean operationInProgress()
999 return progressBar.operationInProgress();
1003 * Sets the text of the status bar. Note that setting a null or empty value
1004 * will cause the status bar to be hidden, with possibly undesirable flicker
1005 * of the screen layout.
1008 public void setStatus(String text)
1010 statusBar.setText(text == null || text.isEmpty() ? " " : text);
1014 * Added so Castor Mapping file can obtain Jalview Version
1016 public String getVersion()
1018 return Cache.getProperty("VERSION");
1021 public FeatureRenderer getFeatureRenderer()
1023 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1027 public void fetchSequence_actionPerformed()
1029 new SequenceFetcher(this);
1033 public void addFromFile_actionPerformed(ActionEvent e)
1035 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1039 public void reload_actionPerformed(ActionEvent e)
1041 if (fileName != null)
1043 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1044 // originating file's format
1045 // TODO: work out how to recover feature settings for correct view(s) when
1046 // file is reloaded.
1047 if (FileFormat.Jalview.equals(currentFileFormat))
1049 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1050 for (int i = 0; i < frames.length; i++)
1052 if (frames[i] instanceof AlignFrame && frames[i] != this
1053 && ((AlignFrame) frames[i]).fileName != null
1054 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1058 frames[i].setSelected(true);
1059 Desktop.instance.closeAssociatedWindows();
1060 } catch (java.beans.PropertyVetoException ex)
1066 Desktop.instance.closeAssociatedWindows();
1068 FileLoader loader = new FileLoader();
1069 DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
1070 ? DataSourceType.URL
1071 : DataSourceType.FILE;
1072 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1076 Rectangle bounds = this.getBounds();
1078 FileLoader loader = new FileLoader();
1080 AlignFrame newframe = null;
1082 if (fileObject == null)
1085 DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(
1086 fileName) ? DataSourceType.URL : DataSourceType.FILE;
1087 newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1092 newframe = loader.LoadFileWaitTillLoaded(fileObject,
1093 DataSourceType.FILE, currentFileFormat);
1096 newframe.setBounds(bounds);
1097 if (featureSettings != null && featureSettings.isShowing())
1099 final Rectangle fspos = featureSettings.frame.getBounds();
1100 // TODO: need a 'show feature settings' function that takes bounds -
1101 // need to refactor Desktop.addFrame
1102 newframe.featureSettings_actionPerformed(null);
1103 final FeatureSettings nfs = newframe.featureSettings;
1104 SwingUtilities.invokeLater(new Runnable()
1109 nfs.frame.setBounds(fspos);
1112 this.featureSettings.close();
1113 this.featureSettings = null;
1115 this.closeMenuItem_actionPerformed(true);
1121 public void addFromText_actionPerformed(ActionEvent e)
1124 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1128 public void addFromURL_actionPerformed(ActionEvent e)
1130 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1134 public void save_actionPerformed(ActionEvent e)
1136 if (fileName == null || (currentFileFormat == null)
1137 || HttpUtils.startsWithHttpOrHttps(fileName))
1139 saveAs_actionPerformed();
1143 saveAlignment(fileName, currentFileFormat);
1148 * Saves the alignment to a file with a name chosen by the user, if necessary
1149 * warning if a file would be overwritten
1152 public void saveAs_actionPerformed()
1154 String format = currentFileFormat == null ? null
1155 : currentFileFormat.getName();
1156 JalviewFileChooser chooser = JalviewFileChooser
1157 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1159 chooser.setFileView(new JalviewFileView());
1160 chooser.setDialogTitle(
1161 MessageManager.getString("label.save_alignment_to_file"));
1162 chooser.setToolTipText(MessageManager.getString("action.save"));
1164 int value = chooser.showSaveDialog(this);
1166 if (value != JalviewFileChooser.APPROVE_OPTION)
1170 currentFileFormat = chooser.getSelectedFormat();
1171 // todo is this (2005) test now obsolete - value is never null?
1172 while (currentFileFormat == null)
1174 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1176 .getString("label.select_file_format_before_saving"),
1177 MessageManager.getString("label.file_format_not_specified"),
1178 JvOptionPane.WARNING_MESSAGE);
1179 currentFileFormat = chooser.getSelectedFormat();
1180 value = chooser.showSaveDialog(this);
1181 if (value != JalviewFileChooser.APPROVE_OPTION)
1187 fileName = chooser.getSelectedFile().getPath();
1189 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1190 Cache.setProperty("LAST_DIRECTORY", fileName);
1191 saveAlignment(fileName, currentFileFormat);
1194 boolean lastSaveSuccessful = false;
1196 FileFormatI lastFormatSaved;
1198 String lastFilenameSaved;
1201 * Raise a dialog or status message for the last call to saveAlignment.
1203 * @return true if last call to saveAlignment(file, format) was successful.
1205 public boolean isSaveAlignmentSuccessful()
1208 if (!lastSaveSuccessful)
1210 if (!Platform.isHeadless())
1212 JvOptionPane.showInternalMessageDialog(this, MessageManager
1213 .formatMessage("label.couldnt_save_file", new Object[]
1214 { lastFilenameSaved }),
1215 MessageManager.getString("label.error_saving_file"),
1216 JvOptionPane.WARNING_MESSAGE);
1220 Console.error(MessageManager
1221 .formatMessage("label.couldnt_save_file", new Object[]
1222 { lastFilenameSaved }));
1228 setStatus(MessageManager.formatMessage(
1229 "label.successfully_saved_to_file_in_format", new Object[]
1230 { lastFilenameSaved, lastFormatSaved }));
1233 return lastSaveSuccessful;
1237 * Saves the alignment to the specified file path, in the specified format,
1238 * which may be an alignment format, or Jalview project format. If the
1239 * alignment has hidden regions, or the format is one capable of including
1240 * non-sequence data (features, annotations, groups), then the user may be
1241 * prompted to specify what to include in the output.
1246 public void saveAlignment(String file, FileFormatI format)
1248 lastSaveSuccessful = true;
1249 lastFilenameSaved = file;
1250 lastFormatSaved = format;
1252 if (FileFormat.Jalview.equals(format))
1254 String shortName = title;
1255 if (shortName.indexOf(File.separatorChar) > -1)
1257 shortName = shortName
1258 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
1260 lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
1263 statusBar.setText(MessageManager.formatMessage(
1264 "label.successfully_saved_to_file_in_format", new Object[]
1270 AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1271 Runnable cancelAction = new Runnable()
1276 lastSaveSuccessful = false;
1279 Runnable outputAction = new Runnable()
1284 // todo defer this to inside formatSequences (or later)
1285 AlignmentExportData exportData = viewport
1286 .getAlignExportData(options);
1287 String output = new FormatAdapter(alignPanel, options)
1288 .formatSequences(format, exportData.getAlignment(),
1289 exportData.getOmitHidden(),
1290 exportData.getStartEndPostions(),
1291 viewport.getAlignment().getHiddenColumns());
1294 lastSaveSuccessful = false;
1298 // create backupfiles object and get new temp filename destination
1299 boolean doBackup = BackupFiles.getEnabled();
1300 BackupFiles backupfiles = null;
1304 "ALIGNFRAME making backupfiles object for " + file);
1305 backupfiles = new BackupFiles(file);
1309 String tempFilePath = doBackup ? backupfiles.getTempFilePath()
1311 Console.trace("ALIGNFRAME setting PrintWriter");
1312 PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
1314 if (backupfiles != null)
1316 Console.trace("ALIGNFRAME about to write to temp file "
1317 + backupfiles.getTempFilePath());
1321 Console.trace("ALIGNFRAME about to close file");
1323 Console.trace("ALIGNFRAME closed file");
1324 AlignFrame.this.setTitle(file);
1325 statusBar.setText(MessageManager.formatMessage(
1326 "label.successfully_saved_to_file_in_format",
1328 { fileName, format.getName() }));
1329 lastSaveSuccessful = true;
1330 } catch (IOException e)
1332 lastSaveSuccessful = false;
1334 "ALIGNFRAME Something happened writing the temp file");
1335 Console.error(e.getMessage());
1336 Console.debug(Cache.getStackTraceString(e));
1337 } catch (Exception ex)
1339 lastSaveSuccessful = false;
1341 "ALIGNFRAME Something unexpected happened writing the temp file");
1342 Console.error(ex.getMessage());
1343 Console.debug(Cache.getStackTraceString(ex));
1348 backupfiles.setWriteSuccess(lastSaveSuccessful);
1349 Console.debug("ALIGNFRAME writing temp file was "
1350 + (lastSaveSuccessful ? "" : "NOT ") + "successful");
1351 // do the backup file roll and rename the temp file to actual file
1353 "ALIGNFRAME about to rollBackupsAndRenameTempFile");
1354 lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1356 "ALIGNFRAME performed rollBackupsAndRenameTempFile "
1357 + (lastSaveSuccessful ? "" : "un")
1365 * show dialog with export options if applicable; else just do it
1367 if (AlignExportOptions.isNeeded(viewport, format))
1369 AlignExportOptions choices = new AlignExportOptions(
1370 alignPanel.getAlignViewport(), format, options);
1371 choices.setResponseAction(0, outputAction);
1372 choices.setResponseAction(1, cancelAction);
1373 choices.showDialog();
1382 * Outputs the alignment to textbox in the requested format, if necessary
1383 * first prompting the user for whether to include hidden regions or
1386 * @param fileFormatName
1389 protected void outputText_actionPerformed(String fileFormatName)
1391 FileFormatI fileFormat = FileFormats.getInstance()
1392 .forName(fileFormatName);
1393 AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1394 Runnable outputAction = new Runnable()
1399 // todo defer this to inside formatSequences (or later)
1400 AlignmentExportData exportData = viewport
1401 .getAlignExportData(options);
1402 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1403 cap.setForInput(null);
1406 FileFormatI format = fileFormat;
1407 cap.setText(new FormatAdapter(alignPanel, options)
1408 .formatSequences(format, exportData.getAlignment(),
1409 exportData.getOmitHidden(),
1410 exportData.getStartEndPostions(),
1411 viewport.getAlignment().getHiddenColumns()));
1412 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1413 "label.alignment_output_command", new Object[]
1414 { fileFormat.getName() }), 600, 500);
1415 } catch (OutOfMemoryError oom)
1417 new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1425 * show dialog with export options if applicable; else just do it
1427 if (AlignExportOptions.isNeeded(viewport, fileFormat))
1429 AlignExportOptions choices = new AlignExportOptions(
1430 alignPanel.getAlignViewport(), fileFormat, options);
1431 choices.setResponseAction(0, outputAction);
1432 choices.showDialog();
1447 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1449 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1450 htmlSVG.exportHTML(null);
1454 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1456 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1457 bjs.exportHTML(null);
1460 public void createImageMap(File file, String image)
1462 alignPanel.makePNGImageMap(file, image);
1466 * Creates a PNG image of the alignment and writes it to the given file. If
1467 * the file is null, the user is prompted to choose a file.
1472 public void createPNG(File f)
1474 alignPanel.makeAlignmentImage(TYPE.PNG, f);
1478 * Creates an EPS image of the alignment and writes it to the given file. If
1479 * the file is null, the user is prompted to choose a file.
1484 public void createEPS(File f)
1486 alignPanel.makeAlignmentImage(TYPE.EPS, f);
1490 * Creates an SVG image of the alignment and writes it to the given file. If
1491 * the file is null, the user is prompted to choose a file.
1496 public void createSVG(File f)
1498 alignPanel.makeAlignmentImage(TYPE.SVG, f);
1502 public void pageSetup_actionPerformed(ActionEvent e)
1504 PrinterJob printJob = PrinterJob.getPrinterJob();
1505 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1515 public void printMenuItem_actionPerformed(ActionEvent e)
1517 // Putting in a thread avoids Swing painting problems
1518 PrintThread thread = new PrintThread(alignPanel);
1523 public void exportFeatures_actionPerformed(ActionEvent e)
1525 new AnnotationExporter(alignPanel).exportFeatures();
1529 public void exportAnnotations_actionPerformed(ActionEvent e)
1531 new AnnotationExporter(alignPanel).exportAnnotations();
1535 public void associatedData_actionPerformed(ActionEvent e)
1537 final JalviewFileChooser chooser = new JalviewFileChooser(
1538 Cache.getProperty("LAST_DIRECTORY"));
1539 chooser.setFileView(new JalviewFileView());
1540 String tooltip = MessageManager
1541 .getString("label.load_jalview_annotations");
1542 chooser.setDialogTitle(tooltip);
1543 chooser.setToolTipText(tooltip);
1544 chooser.setResponseHandler(0, new Runnable()
1549 String choice = chooser.getSelectedFile().getPath();
1550 Cache.setProperty("LAST_DIRECTORY", choice);
1551 loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1555 chooser.showOpenDialog(this);
1559 * Close the current view or all views in the alignment frame. If the frame
1560 * only contains one view then the alignment will be removed from memory.
1562 * @param closeAllTabs
1565 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1567 if (alignPanels != null && alignPanels.size() < 2)
1569 closeAllTabs = true;
1574 if (alignPanels != null)
1578 if (this.isClosed())
1580 // really close all the windows - otherwise wait till
1581 // setClosed(true) is called
1582 for (int i = 0; i < alignPanels.size(); i++)
1584 AlignmentPanel ap = alignPanels.get(i);
1591 closeView(alignPanel);
1596 if (featureSettings != null && featureSettings.isOpen())
1598 featureSettings.close();
1599 featureSettings = null;
1602 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1603 * be called recursively, with the frame now in 'closed' state
1605 this.setClosed(true);
1607 } catch (Exception ex)
1609 ex.printStackTrace();
1614 * Close the specified panel and close up tabs appropriately.
1616 * @param panelToClose
1618 public void closeView(AlignmentPanel panelToClose)
1620 int index = tabbedPane.getSelectedIndex();
1621 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1622 alignPanels.remove(panelToClose);
1623 panelToClose.closePanel();
1624 panelToClose = null;
1626 tabbedPane.removeTabAt(closedindex);
1627 tabbedPane.validate();
1629 if (index > closedindex || index == tabbedPane.getTabCount())
1631 // modify currently selected tab index if necessary.
1635 this.tabSelectionChanged(index);
1641 void updateEditMenuBar()
1644 if (viewport.getHistoryList().size() > 0)
1646 undoMenuItem.setEnabled(true);
1647 CommandI command = viewport.getHistoryList().peek();
1648 undoMenuItem.setText(MessageManager
1649 .formatMessage("label.undo_command", new Object[]
1650 { command.getDescription() }));
1654 undoMenuItem.setEnabled(false);
1655 undoMenuItem.setText(MessageManager.getString("action.undo"));
1658 if (viewport.getRedoList().size() > 0)
1660 redoMenuItem.setEnabled(true);
1662 CommandI command = viewport.getRedoList().peek();
1663 redoMenuItem.setText(MessageManager
1664 .formatMessage("label.redo_command", new Object[]
1665 { command.getDescription() }));
1669 redoMenuItem.setEnabled(false);
1670 redoMenuItem.setText(MessageManager.getString("action.redo"));
1675 public void addHistoryItem(CommandI command)
1677 if (command.getSize() > 0)
1679 viewport.addToHistoryList(command);
1680 viewport.clearRedoList();
1681 updateEditMenuBar();
1682 viewport.updateHiddenColumns();
1683 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1684 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1685 // viewport.getColumnSelection()
1686 // .getHiddenColumns().size() > 0);
1692 * @return alignment objects for all views
1694 AlignmentI[] getViewAlignments()
1696 if (alignPanels != null)
1698 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1700 for (AlignmentPanel ap : alignPanels)
1702 als[i++] = ap.av.getAlignment();
1706 if (viewport != null)
1708 return new AlignmentI[] { viewport.getAlignment() };
1720 protected void undoMenuItem_actionPerformed(ActionEvent e)
1722 if (viewport.getHistoryList().isEmpty())
1726 CommandI command = viewport.getHistoryList().pop();
1727 viewport.addToRedoList(command);
1728 command.undoCommand(getViewAlignments());
1730 AlignmentViewport originalSource = getOriginatingSource(command);
1731 updateEditMenuBar();
1733 if (originalSource != null)
1735 if (originalSource != viewport)
1738 "Implementation worry: mismatch of viewport origin for undo");
1740 originalSource.updateHiddenColumns();
1741 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1743 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1744 // viewport.getColumnSelection()
1745 // .getHiddenColumns().size() > 0);
1746 originalSource.firePropertyChange("alignment", null,
1747 originalSource.getAlignment().getSequences());
1758 protected void redoMenuItem_actionPerformed(ActionEvent e)
1760 if (viewport.getRedoList().size() < 1)
1765 CommandI command = viewport.getRedoList().pop();
1766 viewport.addToHistoryList(command);
1767 command.doCommand(getViewAlignments());
1769 AlignmentViewport originalSource = getOriginatingSource(command);
1770 updateEditMenuBar();
1772 if (originalSource != null)
1775 if (originalSource != viewport)
1778 "Implementation worry: mismatch of viewport origin for redo");
1780 originalSource.updateHiddenColumns();
1781 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1783 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1784 // viewport.getColumnSelection()
1785 // .getHiddenColumns().size() > 0);
1786 originalSource.firePropertyChange("alignment", null,
1787 originalSource.getAlignment().getSequences());
1791 AlignmentViewport getOriginatingSource(CommandI command)
1793 AlignmentViewport originalSource = null;
1794 // For sequence removal and addition, we need to fire
1795 // the property change event FROM the viewport where the
1796 // original alignment was altered
1797 AlignmentI al = null;
1798 if (command instanceof EditCommand)
1800 EditCommand editCommand = (EditCommand) command;
1801 al = editCommand.getAlignment();
1802 List<Component> comps = PaintRefresher.components
1803 .get(viewport.getSequenceSetId());
1805 for (Component comp : comps)
1807 if (comp instanceof AlignmentPanel)
1809 if (al == ((AlignmentPanel) comp).av.getAlignment())
1811 originalSource = ((AlignmentPanel) comp).av;
1818 if (originalSource == null)
1820 // The original view is closed, we must validate
1821 // the current view against the closed view first
1824 PaintRefresher.validateSequences(al, viewport.getAlignment());
1827 originalSource = viewport;
1830 return originalSource;
1834 * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
1835 * or the sequence under cursor in keyboard mode
1840 public void moveSelectedSequences(boolean up)
1842 SequenceGroup sg = viewport.getSelectionGroup();
1846 if (viewport.cursorMode)
1848 sg = new SequenceGroup();
1849 sg.addSequence(viewport.getAlignment().getSequenceAt(
1850 alignPanel.getSeqPanel().seqCanvas.cursorY), false);
1858 if (sg.getSize() < 1)
1863 // TODO: JAL-3733 - add an event to the undo buffer for this !
1865 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1866 viewport.getHiddenRepSequences(), up);
1867 alignPanel.paintAlignment(true, false);
1870 synchronized void slideSequences(boolean right, int size)
1872 List<SequenceI> sg = new ArrayList<>();
1873 if (viewport.cursorMode)
1875 sg.add(viewport.getAlignment()
1876 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1878 else if (viewport.getSelectionGroup() != null
1879 && viewport.getSelectionGroup().getSize() != viewport
1880 .getAlignment().getHeight())
1882 sg = viewport.getSelectionGroup()
1883 .getSequences(viewport.getHiddenRepSequences());
1891 List<SequenceI> invertGroup = new ArrayList<>();
1893 for (SequenceI seq : viewport.getAlignment().getSequences())
1895 if (!sg.contains(seq))
1897 invertGroup.add(seq);
1901 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1903 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1904 for (int i = 0; i < invertGroup.size(); i++)
1906 seqs2[i] = invertGroup.get(i);
1909 SlideSequencesCommand ssc;
1912 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1913 viewport.getGapCharacter());
1917 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1918 viewport.getGapCharacter());
1921 int groupAdjustment = 0;
1922 if (ssc.getGapsInsertedBegin() && right)
1924 if (viewport.cursorMode)
1926 alignPanel.getSeqPanel().moveCursor(size, 0);
1930 groupAdjustment = size;
1933 else if (!ssc.getGapsInsertedBegin() && !right)
1935 if (viewport.cursorMode)
1937 alignPanel.getSeqPanel().moveCursor(-size, 0);
1941 groupAdjustment = -size;
1945 if (groupAdjustment != 0)
1947 viewport.getSelectionGroup().setStartRes(
1948 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1949 viewport.getSelectionGroup().setEndRes(
1950 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1954 * just extend the last slide command if compatible; but not if in
1955 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1957 boolean appendHistoryItem = false;
1958 Deque<CommandI> historyList = viewport.getHistoryList();
1959 boolean inSplitFrame = getSplitViewContainer() != null;
1960 if (!inSplitFrame && historyList != null && historyList.size() > 0
1961 && historyList.peek() instanceof SlideSequencesCommand)
1963 appendHistoryItem = ssc.appendSlideCommand(
1964 (SlideSequencesCommand) historyList.peek());
1967 if (!appendHistoryItem)
1969 addHistoryItem(ssc);
1982 protected void copy_actionPerformed()
1984 if (viewport.getSelectionGroup() == null)
1988 // TODO: preserve the ordering of displayed alignment annotation in any
1989 // internal paste (particularly sequence associated annotation)
1990 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1991 String[] omitHidden = null;
1993 if (viewport.hasHiddenColumns())
1995 omitHidden = viewport.getViewAsString(true);
1998 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1999 seqs, omitHidden, null);
2001 StringSelection ss = new StringSelection(output);
2005 jalview.gui.Desktop.internalCopy = true;
2006 // Its really worth setting the clipboard contents
2007 // to empty before setting the large StringSelection!!
2008 Toolkit.getDefaultToolkit().getSystemClipboard()
2009 .setContents(new StringSelection(""), null);
2011 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2013 } catch (OutOfMemoryError er)
2015 new OOMWarning("copying region", er);
2019 HiddenColumns hiddenColumns = null;
2020 if (viewport.hasHiddenColumns())
2022 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2023 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2025 // create new HiddenColumns object with copy of hidden regions
2026 // between startRes and endRes, offset by startRes
2027 hiddenColumns = new HiddenColumns(
2028 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
2029 hiddenCutoff, hiddenOffset);
2032 Desktop.jalviewClipboard = new Object[] { seqs,
2033 viewport.getAlignment().getDataset(), hiddenColumns };
2034 setStatus(MessageManager.formatMessage(
2035 "label.copied_sequences_to_clipboard", new Object[]
2036 { Integer.valueOf(seqs.length).toString() }));
2046 protected void pasteNew_actionPerformed(ActionEvent e)
2058 protected void pasteThis_actionPerformed(ActionEvent e)
2064 * Paste contents of Jalview clipboard
2066 * @param newAlignment
2067 * true to paste to a new alignment, otherwise add to this.
2069 void paste(boolean newAlignment)
2071 boolean externalPaste = true;
2074 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2075 Transferable contents = c.getContents(this);
2077 if (contents == null)
2086 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2087 if (str.length() < 1)
2092 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2094 } catch (OutOfMemoryError er)
2096 new OOMWarning("Out of memory pasting sequences!!", er);
2100 SequenceI[] sequences;
2101 boolean annotationAdded = false;
2102 AlignmentI alignment = null;
2104 if (Desktop.jalviewClipboard != null)
2106 // The clipboard was filled from within Jalview, we must use the
2108 // And dataset from the copied alignment
2109 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2110 // be doubly sure that we create *new* sequence objects.
2111 sequences = new SequenceI[newseq.length];
2112 for (int i = 0; i < newseq.length; i++)
2114 sequences[i] = new Sequence(newseq[i]);
2116 alignment = new Alignment(sequences);
2117 externalPaste = false;
2121 // parse the clipboard as an alignment.
2122 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2124 sequences = alignment.getSequencesArray();
2128 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2134 if (Desktop.jalviewClipboard != null)
2136 // dataset is inherited
2137 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2141 // new dataset is constructed
2142 alignment.setDataset(null);
2144 alwidth = alignment.getWidth() + 1;
2148 AlignmentI pastedal = alignment; // preserve pasted alignment object
2149 // Add pasted sequences and dataset into existing alignment.
2150 alignment = viewport.getAlignment();
2151 alwidth = alignment.getWidth() + 1;
2152 // decide if we need to import sequences from an existing dataset
2153 boolean importDs = Desktop.jalviewClipboard != null
2154 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2155 // importDs==true instructs us to copy over new dataset sequences from
2156 // an existing alignment
2157 Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
2159 // minimum dataset set
2161 for (int i = 0; i < sequences.length; i++)
2165 newDs.addElement(null);
2167 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2169 if (importDs && ds != null)
2171 if (!newDs.contains(ds))
2173 newDs.setElementAt(ds, i);
2174 ds = new Sequence(ds);
2175 // update with new dataset sequence
2176 sequences[i].setDatasetSequence(ds);
2180 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2185 // copy and derive new dataset sequence
2186 sequences[i] = sequences[i].deriveSequence();
2187 alignment.getDataset()
2188 .addSequence(sequences[i].getDatasetSequence());
2189 // TODO: avoid creation of duplicate dataset sequences with a
2190 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2192 alignment.addSequence(sequences[i]); // merges dataset
2196 newDs.clear(); // tidy up
2198 if (alignment.getAlignmentAnnotation() != null)
2200 for (AlignmentAnnotation alan : alignment
2201 .getAlignmentAnnotation())
2203 if (alan.graphGroup > fgroup)
2205 fgroup = alan.graphGroup;
2209 if (pastedal.getAlignmentAnnotation() != null)
2211 // Add any annotation attached to alignment.
2212 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2213 for (int i = 0; i < alann.length; i++)
2215 annotationAdded = true;
2216 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2218 AlignmentAnnotation newann = new AlignmentAnnotation(
2220 if (newann.graphGroup > -1)
2222 if (newGraphGroups.size() <= newann.graphGroup
2223 || newGraphGroups.get(newann.graphGroup) == null)
2225 for (int q = newGraphGroups
2226 .size(); q <= newann.graphGroup; q++)
2228 newGraphGroups.add(q, null);
2230 newGraphGroups.set(newann.graphGroup,
2231 Integer.valueOf(++fgroup));
2233 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2237 newann.padAnnotation(alwidth);
2238 alignment.addAnnotation(newann);
2248 addHistoryItem(new EditCommand(
2249 MessageManager.getString("label.add_sequences"),
2250 Action.PASTE, sequences, 0, alignment.getWidth(),
2253 // Add any annotations attached to sequences
2254 for (int i = 0; i < sequences.length; i++)
2256 if (sequences[i].getAnnotation() != null)
2258 AlignmentAnnotation newann;
2259 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2261 annotationAdded = true;
2262 newann = sequences[i].getAnnotation()[a];
2263 newann.adjustForAlignment();
2264 newann.padAnnotation(alwidth);
2265 if (newann.graphGroup > -1)
2267 if (newann.graphGroup > -1)
2269 if (newGraphGroups.size() <= newann.graphGroup
2270 || newGraphGroups.get(newann.graphGroup) == null)
2272 for (int q = newGraphGroups
2273 .size(); q <= newann.graphGroup; q++)
2275 newGraphGroups.add(q, null);
2277 newGraphGroups.set(newann.graphGroup,
2278 Integer.valueOf(++fgroup));
2280 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2284 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2288 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2296 // propagate alignment changed.
2297 viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
2298 if (annotationAdded)
2300 // Duplicate sequence annotation in all views.
2301 AlignmentI[] alview = this.getViewAlignments();
2302 for (int i = 0; i < sequences.length; i++)
2304 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2309 for (int avnum = 0; avnum < alview.length; avnum++)
2311 if (alview[avnum] != alignment)
2313 // duplicate in a view other than the one with input focus
2314 int avwidth = alview[avnum].getWidth() + 1;
2315 // this relies on sann being preserved after we
2316 // modify the sequence's annotation array for each duplication
2317 for (int a = 0; a < sann.length; a++)
2319 AlignmentAnnotation newann = new AlignmentAnnotation(
2321 sequences[i].addAlignmentAnnotation(newann);
2322 newann.padAnnotation(avwidth);
2323 alview[avnum].addAnnotation(newann); // annotation was
2324 // duplicated earlier
2325 // TODO JAL-1145 graphGroups are not updated for sequence
2326 // annotation added to several views. This may cause
2328 alview[avnum].setAnnotationIndex(newann, a);
2333 buildSortByAnnotationScoresMenu();
2335 viewport.firePropertyChange("alignment", null,
2336 alignment.getSequences());
2337 if (alignPanels != null)
2339 for (AlignmentPanel ap : alignPanels)
2341 ap.validateAnnotationDimensions(false);
2346 alignPanel.validateAnnotationDimensions(false);
2352 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2354 String newtitle = new String("Copied sequences");
2356 if (Desktop.jalviewClipboard != null
2357 && Desktop.jalviewClipboard[2] != null)
2359 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2360 af.viewport.setHiddenColumns(hc);
2363 // >>>This is a fix for the moment, until a better solution is
2365 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2366 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2367 .getFeatureRenderer());
2369 // TODO: maintain provenance of an alignment, rather than just make the
2370 // title a concatenation of operations.
2373 if (title.startsWith("Copied sequences"))
2379 newtitle = newtitle.concat("- from " + title);
2384 newtitle = new String("Pasted sequences");
2387 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2392 } catch (Exception ex)
2394 ex.printStackTrace();
2395 System.out.println("Exception whilst pasting: " + ex);
2396 // could be anything being pasted in here
2402 protected void expand_newalign(ActionEvent e)
2406 AlignmentI alignment = AlignmentUtils
2407 .expandContext(getViewport().getAlignment(), -1);
2408 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2410 String newtitle = new String("Flanking alignment");
2412 if (Desktop.jalviewClipboard != null
2413 && Desktop.jalviewClipboard[2] != null)
2415 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2416 af.viewport.setHiddenColumns(hc);
2419 // >>>This is a fix for the moment, until a better solution is
2421 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2422 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2423 .getFeatureRenderer());
2425 // TODO: maintain provenance of an alignment, rather than just make the
2426 // title a concatenation of operations.
2428 if (title.startsWith("Copied sequences"))
2434 newtitle = newtitle.concat("- from " + title);
2438 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2440 } catch (Exception ex)
2442 ex.printStackTrace();
2443 System.out.println("Exception whilst pasting: " + ex);
2444 // could be anything being pasted in here
2445 } catch (OutOfMemoryError oom)
2447 new OOMWarning("Viewing flanking region of alignment", oom);
2452 * Action Cut (delete and copy) the selected region
2455 protected void cut_actionPerformed()
2457 copy_actionPerformed();
2458 delete_actionPerformed();
2462 * Performs menu option to Delete the currently selected region
2465 protected void delete_actionPerformed()
2468 SequenceGroup sg = viewport.getSelectionGroup();
2474 Runnable okAction = new Runnable()
2479 SequenceI[] cut = sg.getSequences()
2480 .toArray(new SequenceI[sg.getSize()]);
2482 addHistoryItem(new EditCommand(
2483 MessageManager.getString("label.cut_sequences"), Action.CUT,
2484 cut, sg.getStartRes(),
2485 sg.getEndRes() - sg.getStartRes() + 1,
2486 viewport.getAlignment()));
2488 viewport.setSelectionGroup(null);
2489 viewport.sendSelection();
2490 viewport.getAlignment().deleteGroup(sg);
2492 viewport.firePropertyChange("alignment", null,
2493 viewport.getAlignment().getSequences());
2494 if (viewport.getAlignment().getHeight() < 1)
2498 AlignFrame.this.setClosed(true);
2499 } catch (Exception ex)
2507 * If the cut affects all sequences, prompt for confirmation
2509 boolean wholeHeight = sg.getSize() == viewport.getAlignment()
2511 boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2512 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2513 if (wholeHeight && wholeWidth)
2515 JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2516 dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2517 Object[] options = new Object[] {
2518 MessageManager.getString("action.ok"),
2519 MessageManager.getString("action.cancel") };
2520 dialog.showDialog(MessageManager.getString("warn.delete_all"),
2521 MessageManager.getString("label.delete_all"),
2522 JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2523 options, options[0]);
2538 protected void deleteGroups_actionPerformed(ActionEvent e)
2540 if (avc.deleteGroups())
2542 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2543 alignPanel.updateAnnotation();
2544 alignPanel.paintAlignment(true, true);
2555 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2557 SequenceGroup sg = new SequenceGroup(
2558 viewport.getAlignment().getSequences());
2560 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2561 viewport.setSelectionGroup(sg);
2562 viewport.isSelectionGroupChanged(true);
2563 viewport.sendSelection();
2564 // JAL-2034 - should delegate to
2565 // alignPanel to decide if overview needs
2567 alignPanel.paintAlignment(false, false);
2568 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2578 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2580 if (viewport.cursorMode)
2582 alignPanel.getSeqPanel().keyboardNo1 = null;
2583 alignPanel.getSeqPanel().keyboardNo2 = null;
2585 viewport.setSelectionGroup(null);
2586 viewport.getColumnSelection().clear();
2587 viewport.setSearchResults(null);
2588 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2589 // JAL-2034 - should delegate to
2590 // alignPanel to decide if overview needs
2592 alignPanel.paintAlignment(false, false);
2593 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2594 viewport.sendSelection();
2604 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2606 SequenceGroup sg = viewport.getSelectionGroup();
2610 selectAllSequenceMenuItem_actionPerformed(null);
2615 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2617 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2619 // JAL-2034 - should delegate to
2620 // alignPanel to decide if overview needs
2623 alignPanel.paintAlignment(true, false);
2624 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2625 viewport.sendSelection();
2629 public void invertColSel_actionPerformed(ActionEvent e)
2631 viewport.invertColumnSelection();
2632 alignPanel.paintAlignment(true, false);
2633 viewport.sendSelection();
2643 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2645 trimAlignment(true);
2655 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2657 trimAlignment(false);
2660 void trimAlignment(boolean trimLeft)
2662 ColumnSelection colSel = viewport.getColumnSelection();
2665 if (!colSel.isEmpty())
2669 column = colSel.getMin();
2673 column = colSel.getMax();
2677 if (viewport.getSelectionGroup() != null)
2679 seqs = viewport.getSelectionGroup()
2680 .getSequencesAsArray(viewport.getHiddenRepSequences());
2684 seqs = viewport.getAlignment().getSequencesArray();
2687 TrimRegionCommand trimRegion;
2690 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2691 column, viewport.getAlignment());
2692 viewport.getRanges().setStartRes(0);
2696 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2697 column, viewport.getAlignment());
2700 setStatus(MessageManager.formatMessage("label.removed_columns",
2702 { Integer.valueOf(trimRegion.getSize()).toString() }));
2704 addHistoryItem(trimRegion);
2706 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2708 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2709 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2711 viewport.getAlignment().deleteGroup(sg);
2715 viewport.firePropertyChange("alignment", null,
2716 viewport.getAlignment().getSequences());
2727 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2729 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2732 if (viewport.getSelectionGroup() != null)
2734 seqs = viewport.getSelectionGroup()
2735 .getSequencesAsArray(viewport.getHiddenRepSequences());
2736 start = viewport.getSelectionGroup().getStartRes();
2737 end = viewport.getSelectionGroup().getEndRes();
2741 seqs = viewport.getAlignment().getSequencesArray();
2744 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2745 "Remove Gapped Columns", seqs, start, end,
2746 viewport.getAlignment());
2748 addHistoryItem(removeGapCols);
2750 setStatus(MessageManager.formatMessage("label.removed_empty_columns",
2752 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2754 // This is to maintain viewport position on first residue
2755 // of first sequence
2756 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2757 ViewportRanges ranges = viewport.getRanges();
2758 int startRes = seq.findPosition(ranges.getStartRes());
2759 // ShiftList shifts;
2760 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2761 // edit.alColumnChanges=shifts.getInverse();
2762 // if (viewport.hasHiddenColumns)
2763 // viewport.getColumnSelection().compensateForEdits(shifts);
2764 ranges.setStartRes(seq.findIndex(startRes) - 1);
2765 viewport.firePropertyChange("alignment", null,
2766 viewport.getAlignment().getSequences());
2777 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2779 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2782 if (viewport.getSelectionGroup() != null)
2784 seqs = viewport.getSelectionGroup()
2785 .getSequencesAsArray(viewport.getHiddenRepSequences());
2786 start = viewport.getSelectionGroup().getStartRes();
2787 end = viewport.getSelectionGroup().getEndRes();
2791 seqs = viewport.getAlignment().getSequencesArray();
2794 // This is to maintain viewport position on first residue
2795 // of first sequence
2796 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2797 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2799 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2800 viewport.getAlignment()));
2802 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2804 viewport.firePropertyChange("alignment", null,
2805 viewport.getAlignment().getSequences());
2816 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2818 viewport.setPadGaps(padGapsMenuitem.isSelected());
2819 viewport.firePropertyChange("alignment", null,
2820 viewport.getAlignment().getSequences());
2824 * Opens a Finder dialog
2829 public void findMenuItem_actionPerformed(ActionEvent e)
2831 new Finder(alignPanel, false, null);
2835 * Create a new view of the current alignment.
2838 public void newView_actionPerformed(ActionEvent e)
2840 newView(null, true);
2844 * Creates and shows a new view of the current alignment.
2847 * title of newly created view; if null, one will be generated
2848 * @param copyAnnotation
2849 * if true then duplicate all annnotation, groups and settings
2850 * @return new alignment panel, already displayed.
2852 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2855 * Create a new AlignmentPanel (with its own, new Viewport)
2857 AlignmentPanel newap = new jalview.project.Jalview2XML()
2858 .copyAlignPanel(alignPanel);
2859 if (!copyAnnotation)
2862 * remove all groups and annotation except for the automatic stuff
2864 newap.av.getAlignment().deleteAllGroups();
2865 newap.av.getAlignment().deleteAllAnnotations(false);
2868 newap.av.setGatherViewsHere(false);
2870 if (viewport.getViewName() == null)
2872 viewport.setViewName(
2873 MessageManager.getString("label.view_name_original"));
2877 * Views share the same edits undo and redo stacks
2879 newap.av.setHistoryList(viewport.getHistoryList());
2880 newap.av.setRedoList(viewport.getRedoList());
2883 * copy any visualisation settings that are not saved in the project
2885 newap.av.setColourAppliesToAllGroups(
2886 viewport.getColourAppliesToAllGroups());
2889 * Views share the same mappings; need to deregister any new mappings
2890 * created by copyAlignPanel, and register the new reference to the shared
2893 newap.av.replaceMappings(viewport.getAlignment());
2896 * start up cDNA consensus (if applicable) now mappings are in place
2898 if (newap.av.initComplementConsensus())
2900 newap.refresh(true); // adjust layout of annotations
2903 newap.av.setViewName(getNewViewName(viewTitle));
2905 addAlignmentPanel(newap, true);
2906 newap.alignmentChanged();
2908 if (alignPanels.size() == 2)
2910 viewport.setGatherViewsHere(true);
2912 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2917 * Make a new name for the view, ensuring it is unique within the current
2918 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2919 * these now use viewId. Unique view names are still desirable for usability.)
2924 protected String getNewViewName(String viewTitle)
2926 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2927 boolean addFirstIndex = false;
2928 if (viewTitle == null || viewTitle.trim().length() == 0)
2930 viewTitle = MessageManager.getString("action.view");
2931 addFirstIndex = true;
2935 index = 1;// we count from 1 if given a specific name
2937 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2939 List<Component> comps = PaintRefresher.components
2940 .get(viewport.getSequenceSetId());
2942 List<String> existingNames = getExistingViewNames(comps);
2944 while (existingNames.contains(newViewName))
2946 newViewName = viewTitle + " " + (++index);
2952 * Returns a list of distinct view names found in the given list of
2953 * components. View names are held on the viewport of an AlignmentPanel.
2958 protected List<String> getExistingViewNames(List<Component> comps)
2960 List<String> existingNames = new ArrayList<>();
2961 for (Component comp : comps)
2963 if (comp instanceof AlignmentPanel)
2965 AlignmentPanel ap = (AlignmentPanel) comp;
2966 if (!existingNames.contains(ap.av.getViewName()))
2968 existingNames.add(ap.av.getViewName());
2972 return existingNames;
2976 * Explode tabbed views into separate windows.
2979 public void expandViews_actionPerformed(ActionEvent e)
2981 Desktop.explodeViews(this);
2985 * Gather views in separate windows back into a tabbed presentation.
2988 public void gatherViews_actionPerformed(ActionEvent e)
2990 Desktop.instance.gatherViews(this);
3000 public void font_actionPerformed(ActionEvent e)
3002 new FontChooser(alignPanel);
3012 protected void seqLimit_actionPerformed(ActionEvent e)
3014 viewport.setShowJVSuffix(seqLimits.isSelected());
3016 alignPanel.getIdPanel().getIdCanvas()
3017 .setPreferredSize(alignPanel.calculateIdWidth());
3018 alignPanel.paintAlignment(true, false);
3022 public void idRightAlign_actionPerformed(ActionEvent e)
3024 viewport.setRightAlignIds(idRightAlign.isSelected());
3025 alignPanel.paintAlignment(false, false);
3029 public void centreColumnLabels_actionPerformed(ActionEvent e)
3031 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3032 alignPanel.paintAlignment(false, false);
3038 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3041 protected void followHighlight_actionPerformed()
3044 * Set the 'follow' flag on the Viewport (and scroll to position if now
3047 final boolean state = this.followHighlightMenuItem.getState();
3048 viewport.setFollowHighlight(state);
3051 alignPanel.scrollToPosition(viewport.getSearchResults());
3062 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3064 viewport.setColourText(colourTextMenuItem.isSelected());
3065 alignPanel.paintAlignment(false, false);
3075 public void wrapMenuItem_actionPerformed(ActionEvent e)
3077 scaleAbove.setVisible(wrapMenuItem.isSelected());
3078 scaleLeft.setVisible(wrapMenuItem.isSelected());
3079 scaleRight.setVisible(wrapMenuItem.isSelected());
3080 viewport.setWrapAlignment(wrapMenuItem.isSelected());
3081 alignPanel.updateLayout();
3085 public void showAllSeqs_actionPerformed(ActionEvent e)
3087 viewport.showAllHiddenSeqs();
3091 public void showAllColumns_actionPerformed(ActionEvent e)
3093 viewport.showAllHiddenColumns();
3094 alignPanel.paintAlignment(true, true);
3095 viewport.sendSelection();
3099 public void hideSelSequences_actionPerformed(ActionEvent e)
3101 viewport.hideAllSelectedSeqs();
3105 * called by key handler and the hide all/show all menu items
3110 protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3113 boolean hide = false;
3114 SequenceGroup sg = viewport.getSelectionGroup();
3115 if (!toggleSeqs && !toggleCols)
3117 // Hide everything by the current selection - this is a hack - we do the
3118 // invert and then hide
3119 // first check that there will be visible columns after the invert.
3120 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3121 && sg.getStartRes() <= sg.getEndRes()))
3123 // now invert the sequence set, if required - empty selection implies
3124 // that no hiding is required.
3127 invertSequenceMenuItem_actionPerformed(null);
3128 sg = viewport.getSelectionGroup();
3132 viewport.expandColSelection(sg, true);
3133 // finally invert the column selection and get the new sequence
3135 invertColSel_actionPerformed(null);
3142 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3144 hideSelSequences_actionPerformed(null);
3147 else if (!(toggleCols && viewport.hasSelectedColumns()))
3149 showAllSeqs_actionPerformed(null);
3155 if (viewport.hasSelectedColumns())
3157 hideSelColumns_actionPerformed(null);
3160 viewport.setSelectionGroup(sg);
3165 showAllColumns_actionPerformed(null);
3174 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3175 * event.ActionEvent)
3178 public void hideAllButSelection_actionPerformed(ActionEvent e)
3180 toggleHiddenRegions(false, false);
3181 viewport.sendSelection();
3188 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3192 public void hideAllSelection_actionPerformed(ActionEvent e)
3194 SequenceGroup sg = viewport.getSelectionGroup();
3195 viewport.expandColSelection(sg, false);
3196 viewport.hideAllSelectedSeqs();
3197 viewport.hideSelectedColumns();
3198 alignPanel.updateLayout();
3199 alignPanel.paintAlignment(true, true);
3200 viewport.sendSelection();
3207 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3211 public void showAllhidden_actionPerformed(ActionEvent e)
3213 viewport.showAllHiddenColumns();
3214 viewport.showAllHiddenSeqs();
3215 alignPanel.paintAlignment(true, true);
3216 viewport.sendSelection();
3220 public void hideSelColumns_actionPerformed(ActionEvent e)
3222 viewport.hideSelectedColumns();
3223 alignPanel.updateLayout();
3224 alignPanel.paintAlignment(true, true);
3225 viewport.sendSelection();
3229 public void hiddenMarkers_actionPerformed(ActionEvent e)
3231 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3242 protected void scaleAbove_actionPerformed(ActionEvent e)
3244 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3245 alignPanel.updateLayout();
3246 alignPanel.paintAlignment(true, false);
3256 protected void scaleLeft_actionPerformed(ActionEvent e)
3258 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3259 alignPanel.updateLayout();
3260 alignPanel.paintAlignment(true, false);
3270 protected void scaleRight_actionPerformed(ActionEvent e)
3272 viewport.setScaleRightWrapped(scaleRight.isSelected());
3273 alignPanel.updateLayout();
3274 alignPanel.paintAlignment(true, false);
3284 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3286 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3287 alignPanel.paintAlignment(false, false);
3297 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3299 viewport.setShowText(viewTextMenuItem.isSelected());
3300 alignPanel.paintAlignment(false, false);
3310 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3312 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3313 alignPanel.paintAlignment(false, false);
3316 public FeatureSettings featureSettings;
3319 public FeatureSettingsControllerI getFeatureSettingsUI()
3321 return featureSettings;
3325 public void featureSettings_actionPerformed(ActionEvent e)
3327 showFeatureSettingsUI();
3331 public FeatureSettingsControllerI showFeatureSettingsUI()
3333 if (featureSettings != null)
3335 featureSettings.closeOldSettings();
3336 featureSettings = null;
3338 if (!showSeqFeatures.isSelected())
3340 // make sure features are actually displayed
3341 showSeqFeatures.setSelected(true);
3342 showSeqFeatures_actionPerformed(null);
3344 featureSettings = new FeatureSettings(this);
3345 return featureSettings;
3349 * Set or clear 'Show Sequence Features'
3355 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3357 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3358 alignPanel.paintAlignment(true, true);
3362 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3363 * the annotations panel as a whole.
3365 * The options to show/hide all annotations should be enabled when the panel
3366 * is shown, and disabled when the panel is hidden.
3371 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3373 final boolean setVisible = annotationPanelMenuItem.isSelected();
3374 viewport.setShowAnnotation(setVisible);
3375 this.showAllSeqAnnotations.setEnabled(setVisible);
3376 this.hideAllSeqAnnotations.setEnabled(setVisible);
3377 this.showAllAlAnnotations.setEnabled(setVisible);
3378 this.hideAllAlAnnotations.setEnabled(setVisible);
3379 alignPanel.updateLayout();
3383 public void alignmentProperties()
3386 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3389 String content = MessageManager.formatMessage("label.html_content",
3391 { contents.toString() });
3394 if (Platform.isJS())
3396 JLabel textLabel = new JLabel();
3397 textLabel.setText(content);
3398 textLabel.setBackground(Color.WHITE);
3400 pane = new JPanel(new BorderLayout());
3401 ((JPanel) pane).setOpaque(true);
3402 pane.setBackground(Color.WHITE);
3403 ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3412 JEditorPane editPane = new JEditorPane("text/html", "");
3413 editPane.setEditable(false);
3414 editPane.setText(content);
3418 JInternalFrame frame = new JInternalFrame();
3420 frame.getContentPane().add(new JScrollPane(pane));
3422 Desktop.addInternalFrame(frame, MessageManager
3423 .formatMessage("label.alignment_properties", new Object[]
3424 { getTitle() }), 500, 400);
3434 public void overviewMenuItem_actionPerformed(ActionEvent e)
3436 if (alignPanel.overviewPanel != null)
3441 JInternalFrame frame = new JInternalFrame();
3442 final OverviewPanel overview = new OverviewPanel(alignPanel);
3443 frame.setContentPane(overview);
3444 Desktop.addInternalFrame(frame, MessageManager
3445 .formatMessage("label.overview_params", new Object[]
3446 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3449 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3450 frame.addInternalFrameListener(
3451 new javax.swing.event.InternalFrameAdapter()
3454 public void internalFrameClosed(
3455 javax.swing.event.InternalFrameEvent evt)
3458 alignPanel.setOverviewPanel(null);
3461 if (getKeyListeners().length > 0)
3463 frame.addKeyListener(getKeyListeners()[0]);
3466 alignPanel.setOverviewPanel(overview);
3470 public void textColour_actionPerformed()
3472 new TextColourChooser().chooseColour(alignPanel, null);
3476 * public void covariationColour_actionPerformed() {
3478 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3482 public void annotationColour_actionPerformed()
3484 new AnnotationColourChooser(viewport, alignPanel);
3488 public void annotationColumn_actionPerformed(ActionEvent e)
3490 new AnnotationColumnChooser(viewport, alignPanel);
3494 * Action on the user checking or unchecking the option to apply the selected
3495 * colour scheme to all groups. If unchecked, groups may have their own
3496 * independent colour schemes.
3501 public void applyToAllGroups_actionPerformed(boolean selected)
3503 viewport.setColourAppliesToAllGroups(selected);
3507 * Action on user selecting a colour from the colour menu
3510 * the name (not the menu item label!) of the colour scheme
3513 public void changeColour_actionPerformed(String name)
3516 * 'User Defined' opens a panel to configure or load a
3517 * user-defined colour scheme
3519 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3521 new UserDefinedColours(alignPanel);
3526 * otherwise set the chosen colour scheme (or null for 'None')
3528 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3529 viewport, viewport.getAlignment(),
3530 viewport.getHiddenRepSequences());
3535 * Actions on setting or changing the alignment colour scheme
3540 public void changeColour(ColourSchemeI cs)
3542 // TODO: pull up to controller method
3543 ColourMenuHelper.setColourSelected(colourMenu, cs);
3545 viewport.setGlobalColourScheme(cs);
3547 alignPanel.paintAlignment(true, true);
3551 * Show the PID threshold slider panel
3554 protected void modifyPID_actionPerformed()
3556 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3557 alignPanel.getViewName());
3558 SliderPanel.showPIDSlider();
3562 * Show the Conservation slider panel
3565 protected void modifyConservation_actionPerformed()
3567 SliderPanel.setConservationSlider(alignPanel,
3568 viewport.getResidueShading(), alignPanel.getViewName());
3569 SliderPanel.showConservationSlider();
3573 * Action on selecting or deselecting (Colour) By Conservation
3576 public void conservationMenuItem_actionPerformed(boolean selected)
3578 modifyConservation.setEnabled(selected);
3579 viewport.setConservationSelected(selected);
3580 viewport.getResidueShading().setConservationApplied(selected);
3582 changeColour(viewport.getGlobalColourScheme());
3585 modifyConservation_actionPerformed();
3589 SliderPanel.hideConservationSlider();
3594 * Action on selecting or deselecting (Colour) Above PID Threshold
3597 public void abovePIDThreshold_actionPerformed(boolean selected)
3599 modifyPID.setEnabled(selected);
3600 viewport.setAbovePIDThreshold(selected);
3603 viewport.getResidueShading().setThreshold(0,
3604 viewport.isIgnoreGapsConsensus());
3607 changeColour(viewport.getGlobalColourScheme());
3610 modifyPID_actionPerformed();
3614 SliderPanel.hidePIDSlider();
3625 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3627 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3628 AlignmentSorter.sortByPID(viewport.getAlignment(),
3629 viewport.getAlignment().getSequenceAt(0));
3630 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3631 viewport.getAlignment()));
3632 alignPanel.paintAlignment(true, false);
3642 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3644 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3645 AlignmentSorter.sortByID(viewport.getAlignment());
3647 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3648 alignPanel.paintAlignment(true, false);
3658 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3660 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3661 AlignmentSorter.sortByLength(viewport.getAlignment());
3662 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3663 viewport.getAlignment()));
3664 alignPanel.paintAlignment(true, false);
3674 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3676 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3677 AlignmentSorter.sortByGroup(viewport.getAlignment());
3678 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3679 viewport.getAlignment()));
3681 alignPanel.paintAlignment(true, false);
3691 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3693 new RedundancyPanel(alignPanel, this);
3703 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3705 if ((viewport.getSelectionGroup() == null)
3706 || (viewport.getSelectionGroup().getSize() < 2))
3708 JvOptionPane.showInternalMessageDialog(this,
3709 MessageManager.getString(
3710 "label.you_must_select_least_two_sequences"),
3711 MessageManager.getString("label.invalid_selection"),
3712 JvOptionPane.WARNING_MESSAGE);
3716 JInternalFrame frame = new JInternalFrame();
3717 frame.setContentPane(new PairwiseAlignPanel(viewport));
3718 Desktop.addInternalFrame(frame,
3719 MessageManager.getString("action.pairwise_alignment"), 600,
3725 public void autoCalculate_actionPerformed(ActionEvent e)
3727 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3728 if (viewport.autoCalculateConsensus)
3730 viewport.firePropertyChange("alignment", null,
3731 viewport.getAlignment().getSequences());
3736 public void sortByTreeOption_actionPerformed(ActionEvent e)
3738 viewport.sortByTree = sortByTree.isSelected();
3742 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3744 viewport.followSelection = listenToViewSelections.isSelected();
3748 * Constructs a tree panel and adds it to the desktop
3751 * tree type (NJ or AV)
3753 * name of score model used to compute the tree
3755 * parameters for the distance or similarity calculation
3757 void newTreePanel(String type, String modelName,
3758 SimilarityParamsI options)
3760 String frameTitle = "";
3763 boolean onSelection = false;
3764 if (viewport.getSelectionGroup() != null
3765 && viewport.getSelectionGroup().getSize() > 0)
3767 SequenceGroup sg = viewport.getSelectionGroup();
3769 /* Decide if the selection is a column region */
3770 for (SequenceI _s : sg.getSequences())
3772 if (_s.getLength() < sg.getEndRes())
3774 JvOptionPane.showMessageDialog(Desktop.desktop,
3775 MessageManager.getString(
3776 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3777 MessageManager.getString(
3778 "label.sequences_selection_not_aligned"),
3779 JvOptionPane.WARNING_MESSAGE);
3788 if (viewport.getAlignment().getHeight() < 2)
3794 tp = new TreePanel(alignPanel, type, modelName, options);
3795 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3797 frameTitle += " from ";
3799 if (viewport.getViewName() != null)
3801 frameTitle += viewport.getViewName() + " of ";
3804 frameTitle += this.title;
3806 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3817 public void addSortByOrderMenuItem(String title,
3818 final AlignmentOrder order)
3820 final JMenuItem item = new JMenuItem(MessageManager
3821 .formatMessage("action.by_title_param", new Object[]
3824 item.addActionListener(new java.awt.event.ActionListener()
3827 public void actionPerformed(ActionEvent e)
3829 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3831 // TODO: JBPNote - have to map order entries to curent SequenceI
3833 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3835 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3836 viewport.getAlignment()));
3838 alignPanel.paintAlignment(true, false);
3844 * Add a new sort by annotation score menu item
3847 * the menu to add the option to
3849 * the label used to retrieve scores for each sequence on the
3852 public void addSortByAnnotScoreMenuItem(JMenu sort,
3853 final String scoreLabel)
3855 final JMenuItem item = new JMenuItem(scoreLabel);
3857 item.addActionListener(new java.awt.event.ActionListener()
3860 public void actionPerformed(ActionEvent e)
3862 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3863 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3864 viewport.getAlignment());// ,viewport.getSelectionGroup());
3865 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3866 viewport.getAlignment()));
3867 alignPanel.paintAlignment(true, false);
3873 * last hash for alignment's annotation array - used to minimise cost of
3876 protected int _annotationScoreVectorHash;
3879 * search the alignment and rebuild the sort by annotation score submenu the
3880 * last alignment annotation vector hash is stored to minimize cost of
3881 * rebuilding in subsequence calls.
3885 public void buildSortByAnnotationScoresMenu()
3887 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3892 if (viewport.getAlignment().getAlignmentAnnotation()
3893 .hashCode() != _annotationScoreVectorHash)
3895 sortByAnnotScore.removeAll();
3896 // almost certainly a quicker way to do this - but we keep it simple
3897 Hashtable<String, String> scoreSorts = new Hashtable<>();
3898 AlignmentAnnotation aann[];
3899 for (SequenceI sqa : viewport.getAlignment().getSequences())
3901 aann = sqa.getAnnotation();
3902 for (int i = 0; aann != null && i < aann.length; i++)
3904 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3906 scoreSorts.put(aann[i].label, aann[i].label);
3910 Enumeration<String> labels = scoreSorts.keys();
3911 while (labels.hasMoreElements())
3913 addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement());
3915 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3918 _annotationScoreVectorHash = viewport.getAlignment()
3919 .getAlignmentAnnotation().hashCode();
3924 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3925 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3926 * call. Listeners are added to remove the menu item when the treePanel is
3927 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3931 public void buildTreeSortMenu()
3933 sortByTreeMenu.removeAll();
3935 List<Component> comps = PaintRefresher.components
3936 .get(viewport.getSequenceSetId());
3937 List<TreePanel> treePanels = new ArrayList<>();
3938 for (Component comp : comps)
3940 if (comp instanceof TreePanel)
3942 treePanels.add((TreePanel) comp);
3946 if (treePanels.size() < 1)
3948 sortByTreeMenu.setVisible(false);
3952 sortByTreeMenu.setVisible(true);
3954 for (final TreePanel tp : treePanels)
3956 final JMenuItem item = new JMenuItem(tp.getTitle());
3957 item.addActionListener(new java.awt.event.ActionListener()
3960 public void actionPerformed(ActionEvent e)
3962 tp.sortByTree_actionPerformed();
3963 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3968 sortByTreeMenu.add(item);
3972 public boolean sortBy(AlignmentOrder alorder, String undoname)
3974 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3975 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3976 if (undoname != null)
3978 addHistoryItem(new OrderCommand(undoname, oldOrder,
3979 viewport.getAlignment()));
3981 alignPanel.paintAlignment(true, false);
3986 * Work out whether the whole set of sequences or just the selected set will
3987 * be submitted for multiple alignment.
3990 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3992 // Now, check we have enough sequences
3993 AlignmentView msa = null;
3995 if ((viewport.getSelectionGroup() != null)
3996 && (viewport.getSelectionGroup().getSize() > 1))
3998 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3999 // some common interface!
4001 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4002 * SequenceI[sz = seqs.getSize(false)];
4004 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4005 * seqs.getSequenceAt(i); }
4007 msa = viewport.getAlignmentView(true);
4009 else if (viewport.getSelectionGroup() != null
4010 && viewport.getSelectionGroup().getSize() == 1)
4012 int option = JvOptionPane.showConfirmDialog(this,
4013 MessageManager.getString("warn.oneseq_msainput_selection"),
4014 MessageManager.getString("label.invalid_selection"),
4015 JvOptionPane.OK_CANCEL_OPTION);
4016 if (option == JvOptionPane.OK_OPTION)
4018 msa = viewport.getAlignmentView(false);
4023 msa = viewport.getAlignmentView(false);
4029 * Decides what is submitted to a secondary structure prediction service: the
4030 * first sequence in the alignment, or in the current selection, or, if the
4031 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4032 * region or the whole alignment. (where the first sequence in the set is the
4033 * one that the prediction will be for).
4035 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4037 AlignmentView seqs = null;
4039 if ((viewport.getSelectionGroup() != null)
4040 && (viewport.getSelectionGroup().getSize() > 0))
4042 seqs = viewport.getAlignmentView(true);
4046 seqs = viewport.getAlignmentView(false);
4048 // limit sequences - JBPNote in future - could spawn multiple prediction
4050 // TODO: viewport.getAlignment().isAligned is a global state - the local
4051 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4052 if (!viewport.getAlignment().isAligned(false))
4054 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4055 // TODO: if seqs.getSequences().length>1 then should really have warned
4069 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4071 // Pick the tree file
4072 JalviewFileChooser chooser = new JalviewFileChooser(
4073 Cache.getProperty("LAST_DIRECTORY"));
4074 chooser.setFileView(new JalviewFileView());
4075 chooser.setDialogTitle(
4076 MessageManager.getString("label.select_newick_like_tree_file"));
4077 chooser.setToolTipText(
4078 MessageManager.getString("label.load_tree_file"));
4080 chooser.setResponseHandler(0, new Runnable()
4085 String filePath = chooser.getSelectedFile().getPath();
4086 Cache.setProperty("LAST_DIRECTORY", filePath);
4087 NewickFile fin = null;
4090 fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4091 DataSourceType.FILE));
4092 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4093 } catch (Exception ex)
4095 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4097 .getString("label.problem_reading_tree_file"),
4098 JvOptionPane.WARNING_MESSAGE);
4099 ex.printStackTrace();
4101 if (fin != null && fin.hasWarningMessage())
4103 JvOptionPane.showMessageDialog(Desktop.desktop,
4104 fin.getWarningMessage(),
4105 MessageManager.getString(
4106 "label.possible_problem_with_tree_file"),
4107 JvOptionPane.WARNING_MESSAGE);
4111 chooser.showOpenDialog(this);
4114 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4116 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4119 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4120 int h, int x, int y)
4122 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4126 * Add a treeviewer for the tree extracted from a Newick file object to the
4127 * current alignment view
4134 * Associated alignment input data (or null)
4143 * @return TreePanel handle
4145 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4146 AlignmentView input, int w, int h, int x, int y)
4148 TreePanel tp = null;
4154 if (nf.getTree() != null)
4156 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4162 tp.setLocation(x, y);
4165 Desktop.addInternalFrame(tp, treeTitle, w, h);
4167 } catch (Exception ex)
4169 ex.printStackTrace();
4175 private boolean buildingMenu = false;
4178 * Generates menu items and listener event actions for web service clients
4181 public void BuildWebServiceMenu()
4183 while (buildingMenu)
4187 System.err.println("Waiting for building menu to finish.");
4189 } catch (Exception e)
4193 final AlignFrame me = this;
4194 buildingMenu = true;
4195 new Thread(new Runnable()
4200 final List<JMenuItem> legacyItems = new ArrayList<>();
4203 // System.err.println("Building ws menu again "
4204 // + Thread.currentThread());
4205 // TODO: add support for context dependent disabling of services based
4207 // alignment and current selection
4208 // TODO: add additional serviceHandle parameter to specify abstract
4210 // class independently of AbstractName
4211 // TODO: add in rediscovery GUI function to restart discoverer
4212 // TODO: group services by location as well as function and/or
4214 // object broker mechanism.
4215 final Vector<JMenu> wsmenu = new Vector<>();
4216 final IProgressIndicator af = me;
4219 * do not i18n these strings - they are hard-coded in class
4220 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4221 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4223 final JMenu msawsmenu = new JMenu("Alignment");
4224 final JMenu secstrmenu = new JMenu(
4225 "Secondary Structure Prediction");
4226 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4227 final JMenu analymenu = new JMenu("Analysis");
4228 final JMenu dismenu = new JMenu("Protein Disorder");
4229 // JAL-940 - only show secondary structure prediction services from
4230 // the legacy server
4231 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4233 Discoverer.services != null && (Discoverer.services.size() > 0))
4235 // TODO: refactor to allow list of AbstractName/Handler bindings to
4237 // stored or retrieved from elsewhere
4238 // No MSAWS used any more:
4239 // Vector msaws = null; // (Vector)
4240 // Discoverer.services.get("MsaWS");
4241 Vector<ServiceHandle> secstrpr = Discoverer.services
4243 if (secstrpr != null)
4245 // Add any secondary structure prediction services
4246 for (int i = 0, j = secstrpr.size(); i < j; i++)
4248 final ext.vamsas.ServiceHandle sh = secstrpr.get(i);
4249 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4250 .getServiceClient(sh);
4251 int p = secstrmenu.getItemCount();
4252 impl.attachWSMenuEntry(secstrmenu, me);
4253 int q = secstrmenu.getItemCount();
4254 for (int litm = p; litm < q; litm++)
4256 legacyItems.add(secstrmenu.getItem(litm));
4262 // Add all submenus in the order they should appear on the web
4264 wsmenu.add(msawsmenu);
4265 wsmenu.add(secstrmenu);
4266 wsmenu.add(dismenu);
4267 wsmenu.add(analymenu);
4268 // No search services yet
4269 // wsmenu.add(seqsrchmenu);
4271 javax.swing.SwingUtilities.invokeLater(new Runnable()
4278 webService.removeAll();
4279 // first, add discovered services onto the webservices menu
4280 if (wsmenu.size() > 0)
4282 for (int i = 0, j = wsmenu.size(); i < j; i++)
4284 webService.add(wsmenu.get(i));
4289 webService.add(me.webServiceNoServices);
4291 // TODO: move into separate menu builder class.
4293 // logic for 2.11.1.4 is
4294 // always look to see if there is a discover. if there isn't
4295 // we can't show any Jws2 services
4296 // if there are services available, show them - regardless of
4297 // the 'show JWS2 preference'
4298 // if the discoverer is running then say so
4299 // otherwise offer to trigger discovery if 'show JWS2' is not
4301 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4302 if (jws2servs != null)
4304 if (jws2servs.hasServices())
4306 jws2servs.attachWSMenuEntry(webService, me);
4307 for (Jws2Instance sv : jws2servs.getServices())
4309 if (sv.description.toLowerCase(Locale.ROOT).contains("jpred"))
4311 for (JMenuItem jmi : legacyItems)
4313 jmi.setVisible(false);
4319 if (jws2servs.isRunning())
4321 JMenuItem tm = new JMenuItem(
4322 "Still discovering JABA Services");
4323 tm.setEnabled(false);
4326 else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true))
4328 JMenuItem enableJws2 = new JMenuItem(
4329 "Discover Web Services");
4330 enableJws2.setToolTipText(
4331 "Select to start JABA Web Service discovery (or enable option in Web Service preferences)");
4332 enableJws2.setEnabled(true);
4333 enableJws2.addActionListener(new ActionListener()
4337 public void actionPerformed(ActionEvent e)
4339 // start service discoverer, but ignore preference
4340 Desktop.instance.startServiceDiscovery(false,
4344 webService.add(enableJws2);
4348 build_urlServiceMenu(me.webService);
4349 build_fetchdbmenu(webService);
4350 for (JMenu item : wsmenu)
4352 if (item.getItemCount() == 0)
4354 item.setEnabled(false);
4358 item.setEnabled(true);
4361 } catch (Exception e)
4364 "Exception during web service menu building process.",
4369 } catch (Exception e)
4372 buildingMenu = false;
4379 * construct any groupURL type service menu entries.
4383 protected void build_urlServiceMenu(JMenu webService)
4385 // TODO: remove this code when 2.7 is released
4386 // DEBUG - alignmentView
4388 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4389 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4391 * @Override public void actionPerformed(ActionEvent e) {
4392 * jalview.datamodel.AlignmentView
4393 * .testSelectionViews(af.viewport.getAlignment(),
4394 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4396 * }); webService.add(testAlView);
4398 // TODO: refactor to RestClient discoverer and merge menu entries for
4399 // rest-style services with other types of analysis/calculation service
4400 // SHmmr test client - still being implemented.
4401 // DEBUG - alignmentView
4403 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4406 client.attachWSMenuEntry(
4407 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4413 * Searches the alignment sequences for xRefs and builds the Show
4414 * Cross-References menu (formerly called Show Products), with database
4415 * sources for which cross-references are found (protein sources for a
4416 * nucleotide alignment and vice versa)
4418 * @return true if Show Cross-references menu should be enabled
4420 public boolean canShowProducts()
4422 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4423 AlignmentI dataset = viewport.getAlignment().getDataset();
4425 showProducts.removeAll();
4426 final boolean dna = viewport.getAlignment().isNucleotide();
4428 if (seqs == null || seqs.length == 0)
4430 // nothing to see here.
4434 boolean showp = false;
4437 List<String> ptypes = new CrossRef(seqs, dataset)
4438 .findXrefSourcesForSequences(dna);
4440 for (final String source : ptypes)
4443 final AlignFrame af = this;
4444 JMenuItem xtype = new JMenuItem(source);
4445 xtype.addActionListener(new ActionListener()
4448 public void actionPerformed(ActionEvent e)
4450 showProductsFor(af.viewport.getSequenceSelection(), dna,
4454 showProducts.add(xtype);
4456 showProducts.setVisible(showp);
4457 showProducts.setEnabled(showp);
4458 } catch (Exception e)
4461 "canShowProducts threw an exception - please report to help@jalview.org",
4469 * Finds and displays cross-references for the selected sequences (protein
4470 * products for nucleotide sequences, dna coding sequences for peptides).
4473 * the sequences to show cross-references for
4475 * true if from a nucleotide alignment (so showing proteins)
4477 * the database to show cross-references for
4479 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4480 final String source)
4482 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4487 * Construct and display a new frame containing the translation of this
4488 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4491 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4493 AlignmentI al = null;
4496 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4498 al = dna.translateCdna(codeTable);
4499 } catch (Exception ex)
4502 "Exception during translation. Please report this !", ex);
4503 final String msg = MessageManager.getString(
4504 "label.error_when_translating_sequences_submit_bug_report");
4505 final String errorTitle = MessageManager
4506 .getString("label.implementation_error")
4507 + MessageManager.getString("label.translation_failed");
4508 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4509 JvOptionPane.ERROR_MESSAGE);
4512 if (al == null || al.getHeight() == 0)
4514 final String msg = MessageManager.getString(
4515 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4516 final String errorTitle = MessageManager
4517 .getString("label.translation_failed");
4518 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4519 JvOptionPane.WARNING_MESSAGE);
4523 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4524 af.setFileFormat(this.currentFileFormat);
4525 final String newTitle = MessageManager
4526 .formatMessage("label.translation_of_params", new Object[]
4527 { this.getTitle(), codeTable.getId() });
4528 af.setTitle(newTitle);
4529 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4531 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4532 viewport.openSplitFrame(af, new Alignment(seqs));
4536 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4543 * Set the file format
4547 public void setFileFormat(FileFormatI format)
4549 this.currentFileFormat = format;
4553 * Try to load a features file onto the alignment.
4556 * contents or path to retrieve file or a File object
4558 * access mode of file (see jalview.io.AlignFile)
4559 * @return true if features file was parsed correctly.
4561 public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4564 return avc.parseFeaturesFile(file, sourceType,
4565 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4570 public void refreshFeatureUI(boolean enableIfNecessary)
4572 // note - currently this is only still here rather than in the controller
4573 // because of the featureSettings hard reference that is yet to be
4575 if (enableIfNecessary)
4577 viewport.setShowSequenceFeatures(true);
4578 showSeqFeatures.setSelected(true);
4584 public void dragEnter(DropTargetDragEvent evt)
4589 public void dragExit(DropTargetEvent evt)
4594 public void dragOver(DropTargetDragEvent evt)
4599 public void dropActionChanged(DropTargetDragEvent evt)
4604 public void drop(DropTargetDropEvent evt)
4606 // JAL-1552 - acceptDrop required before getTransferable call for
4607 // Java's Transferable for native dnd
4608 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4609 Transferable t = evt.getTransferable();
4611 final AlignFrame thisaf = this;
4612 final List<Object> files = new ArrayList<>();
4613 List<DataSourceType> protocols = new ArrayList<>();
4617 Desktop.transferFromDropTarget(files, protocols, evt, t);
4618 } catch (Exception e)
4620 e.printStackTrace();
4624 new Thread(new Runnable()
4631 // check to see if any of these files have names matching sequences
4634 SequenceIdMatcher idm = new SequenceIdMatcher(
4635 viewport.getAlignment().getSequencesArray());
4637 * Object[] { String,SequenceI}
4639 ArrayList<Object[]> filesmatched = new ArrayList<>();
4640 ArrayList<Object> filesnotmatched = new ArrayList<>();
4641 for (int i = 0; i < files.size(); i++)
4644 Object file = files.get(i);
4645 String fileName = file.toString();
4647 DataSourceType protocol = (file instanceof File
4648 ? DataSourceType.FILE
4649 : FormatAdapter.checkProtocol(fileName));
4650 if (protocol == DataSourceType.FILE)
4653 if (file instanceof File)
4656 Platform.cacheFileData(fl);
4660 fl = new File(fileName);
4662 pdbfn = fl.getName();
4664 else if (protocol == DataSourceType.URL)
4666 URL url = new URL(fileName);
4667 pdbfn = url.getFile();
4669 if (pdbfn.length() > 0)
4671 // attempt to find a match in the alignment
4672 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4673 int l = 0, c = pdbfn.indexOf(".");
4674 while (mtch == null && c != -1)
4679 } while ((c = pdbfn.indexOf(".", l)) > l);
4682 pdbfn = pdbfn.substring(0, l);
4684 mtch = idm.findAllIdMatches(pdbfn);
4691 type = new IdentifyFile().identify(file, protocol);
4692 } catch (Exception ex)
4696 if (type != null && type.isStructureFile())
4698 filesmatched.add(new Object[] { file, protocol, mtch });
4702 // File wasn't named like one of the sequences or wasn't a PDB
4704 filesnotmatched.add(file);
4708 if (filesmatched.size() > 0)
4710 boolean autoAssociate = Cache
4711 .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4714 String msg = MessageManager.formatMessage(
4715 "label.automatically_associate_structure_files_with_sequences_same_name",
4717 { Integer.valueOf(filesmatched.size())
4719 String ttl = MessageManager.getString(
4720 "label.automatically_associate_structure_files_by_name");
4721 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4722 ttl, JvOptionPane.YES_NO_OPTION);
4723 autoAssociate = choice == JvOptionPane.YES_OPTION;
4727 for (Object[] fm : filesmatched)
4729 // try and associate
4730 // TODO: may want to set a standard ID naming formalism for
4731 // associating PDB files which have no IDs.
4732 for (SequenceI toassoc : (SequenceI[]) fm[2])
4734 PDBEntry pe = new AssociatePdbFileWithSeq()
4735 .associatePdbWithSeq(fm[0].toString(),
4736 (DataSourceType) fm[1], toassoc, false,
4740 System.err.println("Associated file : "
4741 + (fm[0].toString()) + " with "
4742 + toassoc.getDisplayId(true));
4746 // TODO: do we need to update overview ? only if features are
4748 alignPanel.paintAlignment(true, false);
4754 * add declined structures as sequences
4756 for (Object[] o : filesmatched)
4758 filesnotmatched.add(o[0]);
4762 if (filesnotmatched.size() > 0)
4764 if (assocfiles > 0 && (Cache.getDefault(
4765 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4766 || JvOptionPane.showConfirmDialog(thisaf,
4767 "<html>" + MessageManager.formatMessage(
4768 "label.ignore_unmatched_dropped_files_info",
4771 filesnotmatched.size())
4774 MessageManager.getString(
4775 "label.ignore_unmatched_dropped_files"),
4776 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4780 for (Object fn : filesnotmatched)
4782 loadJalviewDataFile(fn, null, null, null);
4786 } catch (Exception ex)
4788 ex.printStackTrace();
4796 * Attempt to load a "dropped" file or URL string, by testing in turn for
4798 * <li>an Annotation file</li>
4799 * <li>a JNet file</li>
4800 * <li>a features file</li>
4801 * <li>else try to interpret as an alignment file</li>
4805 * either a filename or a URL string.
4807 public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4808 FileFormatI format, SequenceI assocSeq)
4810 // BH 2018 was String file
4813 if (sourceType == null)
4815 sourceType = FormatAdapter.checkProtocol(file);
4817 // if the file isn't identified, or not positively identified as some
4818 // other filetype (PFAM is default unidentified alignment file type) then
4819 // try to parse as annotation.
4820 boolean isAnnotation = (format == null
4821 || FileFormat.Pfam.equals(format))
4822 ? new AnnotationFile().annotateAlignmentView(viewport,
4828 // first see if its a T-COFFEE score file
4829 TCoffeeScoreFile tcf = null;
4832 tcf = new TCoffeeScoreFile(file, sourceType);
4835 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4839 new TCoffeeColourScheme(viewport.getAlignment()));
4840 isAnnotation = true;
4841 setStatus(MessageManager.getString(
4842 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4846 // some problem - if no warning its probable that the ID matching
4847 // process didn't work
4848 JvOptionPane.showMessageDialog(Desktop.desktop,
4849 tcf.getWarningMessage() == null
4850 ? MessageManager.getString(
4851 "label.check_file_matches_sequence_ids_alignment")
4852 : tcf.getWarningMessage(),
4853 MessageManager.getString(
4854 "label.problem_reading_tcoffee_score_file"),
4855 JvOptionPane.WARNING_MESSAGE);
4862 } catch (Exception x)
4865 "Exception when processing data source as T-COFFEE score file",
4871 // try to see if its a JNet 'concise' style annotation file *before*
4873 // try to parse it as a features file
4876 format = new IdentifyFile().identify(file, sourceType);
4878 if (FileFormat.ScoreMatrix == format)
4880 ScoreMatrixFile sm = new ScoreMatrixFile(
4881 new FileParse(file, sourceType));
4883 // todo: i18n this message
4884 setStatus(MessageManager.formatMessage(
4885 "label.successfully_loaded_matrix",
4886 sm.getMatrixName()));
4888 else if (FileFormat.Jnet.equals(format))
4890 JPredFile predictions = new JPredFile(file, sourceType);
4891 new JnetAnnotationMaker();
4892 JnetAnnotationMaker.add_annotation(predictions,
4893 viewport.getAlignment(), 0, false);
4894 viewport.getAlignment().setupJPredAlignment();
4895 isAnnotation = true;
4897 // else if (IdentifyFile.FeaturesFile.equals(format))
4898 else if (FileFormat.Features.equals(format))
4900 if (parseFeaturesFile(file, sourceType))
4902 SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4903 if (splitFrame != null)
4905 splitFrame.repaint();
4909 alignPanel.paintAlignment(true, true);
4915 new FileLoader().LoadFile(viewport, file, sourceType, format);
4922 alignPanel.adjustAnnotationHeight();
4923 viewport.updateSequenceIdColours();
4924 buildSortByAnnotationScoresMenu();
4925 alignPanel.paintAlignment(true, true);
4927 } catch (Exception ex)
4929 ex.printStackTrace();
4930 } catch (OutOfMemoryError oom)
4935 } catch (Exception x)
4940 + (sourceType != null
4941 ? (sourceType == DataSourceType.PASTE
4943 : "using " + sourceType + " from "
4947 ? "(parsing as '" + format + "' file)"
4949 oom, Desktop.desktop);
4954 * Method invoked by the ChangeListener on the tabbed pane, in other words
4955 * when a different tabbed pane is selected by the user or programmatically.
4958 public void tabSelectionChanged(int index)
4962 alignPanel = alignPanels.get(index);
4963 viewport = alignPanel.av;
4964 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4965 setMenusFromViewport(viewport);
4966 if (featureSettings != null && featureSettings.isOpen()
4967 && featureSettings.fr.getViewport() != viewport)
4969 if (viewport.isShowSequenceFeatures())
4971 // refresh the featureSettings to reflect UI change
4972 showFeatureSettingsUI();
4976 // close feature settings for this view.
4977 featureSettings.close();
4984 * 'focus' any colour slider that is open to the selected viewport
4986 if (viewport.getConservationSelected())
4988 SliderPanel.setConservationSlider(alignPanel,
4989 viewport.getResidueShading(), alignPanel.getViewName());
4993 SliderPanel.hideConservationSlider();
4995 if (viewport.getAbovePIDThreshold())
4997 SliderPanel.setPIDSliderSource(alignPanel,
4998 viewport.getResidueShading(), alignPanel.getViewName());
5002 SliderPanel.hidePIDSlider();
5006 * If there is a frame linked to this one in a SplitPane, switch it to the
5007 * same view tab index. No infinite recursion of calls should happen, since
5008 * tabSelectionChanged() should not get invoked on setting the selected
5009 * index to an unchanged value. Guard against setting an invalid index
5010 * before the new view peer tab has been created.
5012 final AlignViewportI peer = viewport.getCodingComplement();
5015 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
5016 .getAlignPanel().alignFrame;
5017 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5019 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5025 * On right mouse click on view tab, prompt for and set new view name.
5028 public void tabbedPane_mousePressed(MouseEvent e)
5030 if (e.isPopupTrigger())
5032 String msg = MessageManager.getString("label.enter_view_name");
5033 String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
5034 String reply = JvOptionPane.showInputDialog(msg, ttl);
5038 viewport.setViewName(reply);
5039 // TODO warn if reply is in getExistingViewNames()?
5040 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5045 public AlignViewport getCurrentView()
5051 * Open the dialog for regex description parsing.
5054 protected void extractScores_actionPerformed(ActionEvent e)
5056 ParseProperties pp = new jalview.analysis.ParseProperties(
5057 viewport.getAlignment());
5058 // TODO: verify regex and introduce GUI dialog for version 2.5
5059 // if (pp.getScoresFromDescription("col", "score column ",
5060 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5062 if (pp.getScoresFromDescription("description column",
5063 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5065 buildSortByAnnotationScoresMenu();
5073 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5077 protected void showDbRefs_actionPerformed(ActionEvent e)
5079 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5085 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5089 protected void showNpFeats_actionPerformed(ActionEvent e)
5091 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5095 * find the viewport amongst the tabs in this alignment frame and close that
5100 public boolean closeView(AlignViewportI av)
5104 this.closeMenuItem_actionPerformed(false);
5107 Component[] comp = tabbedPane.getComponents();
5108 for (int i = 0; comp != null && i < comp.length; i++)
5110 if (comp[i] instanceof AlignmentPanel)
5112 if (((AlignmentPanel) comp[i]).av == av)
5115 closeView((AlignmentPanel) comp[i]);
5123 protected void build_fetchdbmenu(JMenu webService)
5125 // Temporary hack - DBRef Fetcher always top level ws entry.
5126 // TODO We probably want to store a sequence database checklist in
5127 // preferences and have checkboxes.. rather than individual sources selected
5129 final JMenu rfetch = new JMenu(
5130 MessageManager.getString("action.fetch_db_references"));
5131 rfetch.setToolTipText(MessageManager.getString(
5132 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5133 webService.add(rfetch);
5135 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5136 MessageManager.getString("option.trim_retrieved_seqs"));
5137 trimrs.setToolTipText(
5138 MessageManager.getString("label.trim_retrieved_sequences"));
5140 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5141 trimrs.addActionListener(new ActionListener()
5144 public void actionPerformed(ActionEvent e)
5146 trimrs.setSelected(trimrs.isSelected());
5147 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5148 Boolean.valueOf(trimrs.isSelected()).toString());
5152 JMenuItem fetchr = new JMenuItem(
5153 MessageManager.getString("label.standard_databases"));
5154 fetchr.setToolTipText(
5155 MessageManager.getString("label.fetch_embl_uniprot"));
5156 fetchr.addActionListener(new ActionListener()
5160 public void actionPerformed(ActionEvent e)
5162 new Thread(new Runnable()
5167 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5168 .getAlignment().isNucleotide();
5169 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5170 alignPanel.av.getSequenceSelection(),
5171 alignPanel.alignFrame, null,
5172 alignPanel.alignFrame.featureSettings, isNucleotide);
5173 dbRefFetcher.addListener(new FetchFinishedListenerI()
5176 public void finished()
5179 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5180 .getFeatureSettingsModels())
5183 alignPanel.av.mergeFeaturesStyle(srcSettings);
5185 AlignFrame.this.setMenusForViewport();
5188 dbRefFetcher.fetchDBRefs(false);
5196 new Thread(new Runnable()
5201 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5202 .getSequenceFetcherSingleton();
5203 javax.swing.SwingUtilities.invokeLater(new Runnable()
5208 String[] dbclasses = sf.getNonAlignmentSources();
5209 List<DbSourceProxy> otherdb;
5210 JMenu dfetch = new JMenu();
5211 JMenu ifetch = new JMenu();
5212 JMenuItem fetchr = null;
5213 int comp = 0, icomp = 0, mcomp = 15;
5214 String mname = null;
5216 for (String dbclass : dbclasses)
5218 otherdb = sf.getSourceProxy(dbclass);
5219 // add a single entry for this class, or submenu allowing 'fetch
5221 if (otherdb == null || otherdb.size() < 1)
5227 mname = "From " + dbclass;
5229 if (otherdb.size() == 1)
5231 final DbSourceProxy[] dassource = otherdb
5232 .toArray(new DbSourceProxy[0]);
5233 DbSourceProxy src = otherdb.get(0);
5234 fetchr = new JMenuItem(src.getDbSource());
5235 fetchr.addActionListener(new ActionListener()
5239 public void actionPerformed(ActionEvent e)
5241 new Thread(new Runnable()
5247 boolean isNucleotide = alignPanel.alignFrame
5248 .getViewport().getAlignment()
5250 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5251 alignPanel.av.getSequenceSelection(),
5252 alignPanel.alignFrame, dassource,
5253 alignPanel.alignFrame.featureSettings,
5256 .addListener(new FetchFinishedListenerI()
5259 public void finished()
5261 FeatureSettingsModelI srcSettings = dassource[0]
5262 .getFeatureColourScheme();
5263 alignPanel.av.mergeFeaturesStyle(
5265 AlignFrame.this.setMenusForViewport();
5268 dbRefFetcher.fetchDBRefs(false);
5274 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5275 MessageManager.formatMessage(
5276 "label.fetch_retrieve_from", new Object[]
5277 { src.getDbName() })));
5283 final DbSourceProxy[] dassource = otherdb
5284 .toArray(new DbSourceProxy[0]);
5286 DbSourceProxy src = otherdb.get(0);
5287 fetchr = new JMenuItem(MessageManager
5288 .formatMessage("label.fetch_all_param", new Object[]
5289 { src.getDbSource() }));
5290 fetchr.addActionListener(new ActionListener()
5293 public void actionPerformed(ActionEvent e)
5295 new Thread(new Runnable()
5301 boolean isNucleotide = alignPanel.alignFrame
5302 .getViewport().getAlignment()
5304 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5305 alignPanel.av.getSequenceSelection(),
5306 alignPanel.alignFrame, dassource,
5307 alignPanel.alignFrame.featureSettings,
5310 .addListener(new FetchFinishedListenerI()
5313 public void finished()
5315 AlignFrame.this.setMenusForViewport();
5318 dbRefFetcher.fetchDBRefs(false);
5324 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5325 MessageManager.formatMessage(
5326 "label.fetch_retrieve_from_all_sources",
5328 { Integer.valueOf(otherdb.size())
5330 src.getDbSource(), src.getDbName() })));
5333 // and then build the rest of the individual menus
5334 ifetch = new JMenu(MessageManager.formatMessage(
5335 "label.source_from_db_source", new Object[]
5336 { src.getDbSource() }));
5338 String imname = null;
5340 for (DbSourceProxy sproxy : otherdb)
5342 String dbname = sproxy.getDbName();
5343 String sname = dbname.length() > 5
5344 ? dbname.substring(0, 5) + "..."
5346 String msname = dbname.length() > 10
5347 ? dbname.substring(0, 10) + "..."
5351 imname = MessageManager
5352 .formatMessage("label.from_msname", new Object[]
5355 fetchr = new JMenuItem(msname);
5356 final DbSourceProxy[] dassrc = { sproxy };
5357 fetchr.addActionListener(new ActionListener()
5361 public void actionPerformed(ActionEvent e)
5363 new Thread(new Runnable()
5369 boolean isNucleotide = alignPanel.alignFrame
5370 .getViewport().getAlignment()
5372 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5373 alignPanel.av.getSequenceSelection(),
5374 alignPanel.alignFrame, dassrc,
5375 alignPanel.alignFrame.featureSettings,
5378 .addListener(new FetchFinishedListenerI()
5381 public void finished()
5383 AlignFrame.this.setMenusForViewport();
5386 dbRefFetcher.fetchDBRefs(false);
5392 fetchr.setToolTipText(
5393 "<html>" + MessageManager.formatMessage(
5394 "label.fetch_retrieve_from", new Object[]
5398 if (++icomp >= mcomp || i == (otherdb.size()))
5400 ifetch.setText(MessageManager.formatMessage(
5401 "label.source_to_target", imname, sname));
5403 ifetch = new JMenu();
5411 if (comp >= mcomp || dbi >= (dbclasses.length))
5413 dfetch.setText(MessageManager.formatMessage(
5414 "label.source_to_target", mname, dbclass));
5416 dfetch = new JMenu();
5429 * Left justify the whole alignment.
5432 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5434 AlignmentI al = viewport.getAlignment();
5436 viewport.firePropertyChange("alignment", null, al);
5440 * Right justify the whole alignment.
5443 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5445 AlignmentI al = viewport.getAlignment();
5447 viewport.firePropertyChange("alignment", null, al);
5451 public void setShowSeqFeatures(boolean b)
5453 showSeqFeatures.setSelected(b);
5454 viewport.setShowSequenceFeatures(b);
5461 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5462 * awt.event.ActionEvent)
5465 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5467 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5468 alignPanel.paintAlignment(false, false);
5475 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5479 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5481 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5482 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5490 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5491 * .event.ActionEvent)
5494 protected void showGroupConservation_actionPerformed(ActionEvent e)
5496 viewport.setShowGroupConservation(showGroupConservation.getState());
5497 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5504 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5505 * .event.ActionEvent)
5508 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5510 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5511 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5518 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5519 * .event.ActionEvent)
5522 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5524 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5525 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5529 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5531 showSequenceLogo.setState(true);
5532 viewport.setShowSequenceLogo(true);
5533 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5534 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5538 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5540 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5547 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5548 * .event.ActionEvent)
5551 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5553 if (avc.makeGroupsFromSelection())
5555 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5556 alignPanel.updateAnnotation();
5557 alignPanel.paintAlignment(true,
5558 viewport.needToUpdateStructureViews());
5562 public void clearAlignmentSeqRep()
5564 // TODO refactor alignmentseqrep to controller
5565 if (viewport.getAlignment().hasSeqrep())
5567 viewport.getAlignment().setSeqrep(null);
5568 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5569 alignPanel.updateAnnotation();
5570 alignPanel.paintAlignment(true, true);
5575 protected void createGroup_actionPerformed(ActionEvent e)
5577 if (avc.createGroup())
5579 if (applyAutoAnnotationSettings.isSelected())
5581 alignPanel.updateAnnotation(true, false);
5583 alignPanel.alignmentChanged();
5588 protected void unGroup_actionPerformed(ActionEvent e)
5592 alignPanel.alignmentChanged();
5597 * make the given alignmentPanel the currently selected tab
5599 * @param alignmentPanel
5601 public void setDisplayedView(AlignmentPanel alignmentPanel)
5603 if (!viewport.getSequenceSetId()
5604 .equals(alignmentPanel.av.getSequenceSetId()))
5606 throw new Error(MessageManager.getString(
5607 "error.implementation_error_cannot_show_view_alignment_frame"));
5609 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5610 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5612 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5617 * Action on selection of menu options to Show or Hide annotations.
5620 * @param forSequences
5621 * update sequence-related annotations
5622 * @param forAlignment
5623 * update non-sequence-related annotations
5626 protected void setAnnotationsVisibility(boolean visible,
5627 boolean forSequences, boolean forAlignment)
5629 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5630 .getAlignmentAnnotation();
5635 for (AlignmentAnnotation aa : anns)
5638 * don't display non-positional annotations on an alignment
5640 if (aa.annotations == null)
5644 boolean apply = (aa.sequenceRef == null && forAlignment)
5645 || (aa.sequenceRef != null && forSequences);
5648 aa.visible = visible;
5651 alignPanel.validateAnnotationDimensions(true);
5652 alignPanel.alignmentChanged();
5656 * Store selected annotation sort order for the view and repaint.
5659 protected void sortAnnotations_actionPerformed()
5661 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5663 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5664 alignPanel.paintAlignment(false, false);
5669 * @return alignment panels in this alignment frame
5671 public List<? extends AlignmentViewPanel> getAlignPanels()
5673 // alignPanels is never null
5674 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5679 * Open a new alignment window, with the cDNA associated with this (protein)
5680 * alignment, aligned as is the protein.
5682 protected void viewAsCdna_actionPerformed()
5684 // TODO no longer a menu action - refactor as required
5685 final AlignmentI alignment = getViewport().getAlignment();
5686 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5687 if (mappings == null)
5691 List<SequenceI> cdnaSeqs = new ArrayList<>();
5692 for (SequenceI aaSeq : alignment.getSequences())
5694 for (AlignedCodonFrame acf : mappings)
5696 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5700 * There is a cDNA mapping for this protein sequence - add to new
5701 * alignment. It will share the same dataset sequence as other mapped
5702 * cDNA (no new mappings need to be created).
5704 final Sequence newSeq = new Sequence(dnaSeq);
5705 newSeq.setDatasetSequence(dnaSeq);
5706 cdnaSeqs.add(newSeq);
5710 if (cdnaSeqs.size() == 0)
5712 // show a warning dialog no mapped cDNA
5715 AlignmentI cdna = new Alignment(
5716 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5717 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5718 AlignFrame.DEFAULT_HEIGHT);
5719 cdna.alignAs(alignment);
5720 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5722 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5723 AlignFrame.DEFAULT_HEIGHT);
5727 * Set visibility of dna/protein complement view (available when shown in a
5733 protected void showComplement_actionPerformed(boolean show)
5735 SplitContainerI sf = getSplitViewContainer();
5738 sf.setComplementVisible(this, show);
5743 * Generate the reverse (optionally complemented) of the selected sequences,
5744 * and add them to the alignment
5747 protected void showReverse_actionPerformed(boolean complement)
5749 AlignmentI al = null;
5752 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5753 al = dna.reverseCdna(complement);
5754 viewport.addAlignment(al, "");
5755 addHistoryItem(new EditCommand(
5756 MessageManager.getString("label.add_sequences"), Action.PASTE,
5757 al.getSequencesArray(), 0, al.getWidth(),
5758 viewport.getAlignment()));
5759 } catch (Exception ex)
5761 System.err.println(ex.getMessage());
5767 * Try to run a script in the Groovy console, having first ensured that this
5768 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5769 * be targeted at this alignment.
5772 protected void runGroovy_actionPerformed()
5774 Jalview.setCurrentAlignFrame(this);
5775 groovy.ui.Console console = Desktop.getGroovyConsole();
5776 if (console != null)
5780 console.runScript();
5781 } catch (Exception ex)
5783 System.err.println((ex.toString()));
5784 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5785 MessageManager.getString("label.couldnt_run_groovy_script"),
5786 MessageManager.getString("label.groovy_support_failed"),
5787 JvOptionPane.ERROR_MESSAGE);
5792 System.err.println("Can't run Groovy script as console not found");
5797 * Hides columns containing (or not containing) a specified feature, provided
5798 * that would not leave all columns hidden
5800 * @param featureType
5801 * @param columnsContaining
5804 public boolean hideFeatureColumns(String featureType,
5805 boolean columnsContaining)
5807 boolean notForHiding = avc.markColumnsContainingFeatures(
5808 columnsContaining, false, false, featureType);
5811 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5812 false, featureType))
5814 getViewport().hideSelectedColumns();
5822 protected void selectHighlightedColumns_actionPerformed(
5823 ActionEvent actionEvent)
5825 // include key modifier check in case user selects from menu
5826 avc.markHighlightedColumns(
5827 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5828 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5829 | ActionEvent.CTRL_MASK)) != 0);
5833 * Rebuilds the Colour menu, including any user-defined colours which have
5834 * been loaded either on startup or during the session
5836 public void buildColourMenu()
5838 colourMenu.removeAll();
5840 colourMenu.add(applyToAllGroups);
5841 colourMenu.add(textColour);
5842 colourMenu.addSeparator();
5844 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5845 viewport.getAlignment(), false);
5847 colourMenu.add(annotationColour);
5848 bg.add(annotationColour);
5849 colourMenu.addSeparator();
5850 colourMenu.add(conservationMenuItem);
5851 colourMenu.add(modifyConservation);
5852 colourMenu.add(abovePIDThreshold);
5853 colourMenu.add(modifyPID);
5855 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5856 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5860 * Open a dialog (if not already open) that allows the user to select and
5861 * calculate PCA or Tree analysis
5863 protected void openTreePcaDialog()
5865 if (alignPanel.getCalculationDialog() == null)
5867 new CalculationChooser(AlignFrame.this);
5872 protected void loadVcf_actionPerformed()
5874 JalviewFileChooser chooser = new JalviewFileChooser(
5875 Cache.getProperty("LAST_DIRECTORY"));
5876 chooser.setFileView(new JalviewFileView());
5877 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5878 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5879 final AlignFrame us = this;
5880 chooser.setResponseHandler(0, new Runnable()
5885 String choice = chooser.getSelectedFile().getPath();
5886 Cache.setProperty("LAST_DIRECTORY", choice);
5887 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5888 new VCFLoader(choice).loadVCF(seqs, us);
5891 chooser.showOpenDialog(null);
5895 private Rectangle lastFeatureSettingsBounds = null;
5898 public void setFeatureSettingsGeometry(Rectangle bounds)
5900 lastFeatureSettingsBounds = bounds;
5904 public Rectangle getFeatureSettingsGeometry()
5906 return lastFeatureSettingsBounds;
5910 class PrintThread extends Thread
5914 public PrintThread(AlignmentPanel ap)
5919 static PageFormat pf;
5924 PrinterJob printJob = PrinterJob.getPrinterJob();
5928 printJob.setPrintable(ap, pf);
5932 printJob.setPrintable(ap);
5935 if (printJob.printDialog())
5940 } catch (Exception PrintException)
5942 PrintException.printStackTrace();