2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.SimilarityParamsI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenColumns;
57 import jalview.datamodel.HiddenSequences;
58 import jalview.datamodel.PDBEntry;
59 import jalview.datamodel.SeqCigar;
60 import jalview.datamodel.Sequence;
61 import jalview.datamodel.SequenceGroup;
62 import jalview.datamodel.SequenceI;
63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.DataSourceType;
69 import jalview.io.FileFormat;
70 import jalview.io.FileFormatI;
71 import jalview.io.FileFormats;
72 import jalview.io.FileLoader;
73 import jalview.io.FileParse;
74 import jalview.io.FormatAdapter;
75 import jalview.io.HtmlSvgOutput;
76 import jalview.io.IdentifyFile;
77 import jalview.io.JPredFile;
78 import jalview.io.JalviewFileChooser;
79 import jalview.io.JalviewFileView;
80 import jalview.io.JnetAnnotationMaker;
81 import jalview.io.NewickFile;
82 import jalview.io.ScoreMatrixFile;
83 import jalview.io.TCoffeeScoreFile;
84 import jalview.jbgui.GAlignFrame;
85 import jalview.schemes.ColourSchemeI;
86 import jalview.schemes.ColourSchemes;
87 import jalview.schemes.ResidueColourScheme;
88 import jalview.schemes.TCoffeeColourScheme;
89 import jalview.util.MessageManager;
90 import jalview.viewmodel.AlignmentViewport;
91 import jalview.viewmodel.ViewportRanges;
92 import jalview.ws.DBRefFetcher;
93 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
94 import jalview.ws.jws1.Discoverer;
95 import jalview.ws.jws2.Jws2Discoverer;
96 import jalview.ws.jws2.jabaws2.Jws2Instance;
97 import jalview.ws.seqfetcher.DbSourceProxy;
99 import java.awt.BorderLayout;
100 import java.awt.Component;
101 import java.awt.Rectangle;
102 import java.awt.Toolkit;
103 import java.awt.datatransfer.Clipboard;
104 import java.awt.datatransfer.DataFlavor;
105 import java.awt.datatransfer.StringSelection;
106 import java.awt.datatransfer.Transferable;
107 import java.awt.dnd.DnDConstants;
108 import java.awt.dnd.DropTargetDragEvent;
109 import java.awt.dnd.DropTargetDropEvent;
110 import java.awt.dnd.DropTargetEvent;
111 import java.awt.dnd.DropTargetListener;
112 import java.awt.event.ActionEvent;
113 import java.awt.event.ActionListener;
114 import java.awt.event.FocusAdapter;
115 import java.awt.event.FocusEvent;
116 import java.awt.event.ItemEvent;
117 import java.awt.event.ItemListener;
118 import java.awt.event.KeyAdapter;
119 import java.awt.event.KeyEvent;
120 import java.awt.event.MouseEvent;
121 import java.awt.print.PageFormat;
122 import java.awt.print.PrinterJob;
123 import java.beans.PropertyChangeEvent;
125 import java.io.FileWriter;
126 import java.io.PrintWriter;
128 import java.util.ArrayList;
129 import java.util.Arrays;
130 import java.util.Deque;
131 import java.util.Enumeration;
132 import java.util.Hashtable;
133 import java.util.List;
134 import java.util.Vector;
136 import javax.swing.JCheckBoxMenuItem;
137 import javax.swing.JEditorPane;
138 import javax.swing.JInternalFrame;
139 import javax.swing.JLayeredPane;
140 import javax.swing.JMenu;
141 import javax.swing.JMenuItem;
142 import javax.swing.JScrollPane;
143 import javax.swing.SwingUtilities;
149 * @version $Revision$
151 public class AlignFrame extends GAlignFrame implements DropTargetListener,
152 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
155 public static final int DEFAULT_WIDTH = 700;
157 public static final int DEFAULT_HEIGHT = 500;
160 * The currently displayed panel (selected tabbed view if more than one)
162 public AlignmentPanel alignPanel;
164 AlignViewport viewport;
166 ViewportRanges vpRanges;
168 public AlignViewControllerI avc;
170 List<AlignmentPanel> alignPanels = new ArrayList<>();
173 * Last format used to load or save alignments in this window
175 FileFormatI currentFileFormat = null;
178 * Current filename for this alignment
180 String fileName = null;
183 * Creates a new AlignFrame object with specific width and height.
189 public AlignFrame(AlignmentI al, int width, int height)
191 this(al, null, width, height);
195 * Creates a new AlignFrame object with specific width, height and
201 * @param sequenceSetId
203 public AlignFrame(AlignmentI al, int width, int height,
204 String sequenceSetId)
206 this(al, null, width, height, sequenceSetId);
210 * Creates a new AlignFrame object with specific width, height and
216 * @param sequenceSetId
219 public AlignFrame(AlignmentI al, int width, int height,
220 String sequenceSetId, String viewId)
222 this(al, null, width, height, sequenceSetId, viewId);
226 * new alignment window with hidden columns
230 * @param hiddenColumns
231 * ColumnSelection or null
233 * Width of alignment frame
237 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
240 this(al, hiddenColumns, width, height, null);
244 * Create alignment frame for al with hiddenColumns, a specific width and
245 * height, and specific sequenceId
248 * @param hiddenColumns
251 * @param sequenceSetId
254 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
255 int height, String sequenceSetId)
257 this(al, hiddenColumns, width, height, sequenceSetId, null);
261 * Create alignment frame for al with hiddenColumns, a specific width and
262 * height, and specific sequenceId
265 * @param hiddenColumns
268 * @param sequenceSetId
273 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
274 int height, String sequenceSetId, String viewId)
276 setSize(width, height);
278 if (al.getDataset() == null)
283 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
285 alignPanel = new AlignmentPanel(this, viewport);
287 addAlignmentPanel(alignPanel, true);
291 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
292 HiddenColumns hiddenColumns, int width, int height)
294 setSize(width, height);
296 if (al.getDataset() == null)
301 viewport = new AlignViewport(al, hiddenColumns);
303 if (hiddenSeqs != null && hiddenSeqs.length > 0)
305 viewport.hideSequence(hiddenSeqs);
307 alignPanel = new AlignmentPanel(this, viewport);
308 addAlignmentPanel(alignPanel, true);
313 * Make a new AlignFrame from existing alignmentPanels
320 public AlignFrame(AlignmentPanel ap)
324 addAlignmentPanel(ap, false);
329 * initalise the alignframe from the underlying viewport data and the
334 if (!Jalview.isHeadlessMode())
336 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
339 vpRanges = viewport.getRanges();
340 avc = new jalview.controller.AlignViewController(this, viewport,
342 if (viewport.getAlignmentConservationAnnotation() == null)
344 // BLOSUM62Colour.setEnabled(false);
345 conservationMenuItem.setEnabled(false);
346 modifyConservation.setEnabled(false);
347 // PIDColour.setEnabled(false);
348 // abovePIDThreshold.setEnabled(false);
349 // modifyPID.setEnabled(false);
352 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
355 if (sortby.equals("Id"))
357 sortIDMenuItem_actionPerformed(null);
359 else if (sortby.equals("Pairwise Identity"))
361 sortPairwiseMenuItem_actionPerformed(null);
365 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
367 setMenusFromViewport(viewport);
368 buildSortByAnnotationScoresMenu();
369 calculateTree.addActionListener(new ActionListener()
373 public void actionPerformed(ActionEvent e)
380 if (Desktop.desktop != null)
382 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
383 addServiceListeners();
387 if (viewport.getWrapAlignment())
389 wrapMenuItem_actionPerformed(null);
392 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
394 this.overviewMenuItem_actionPerformed(null);
399 final List<AlignmentPanel> selviews = new ArrayList<>();
400 final List<AlignmentPanel> origview = new ArrayList<>();
401 final String menuLabel = MessageManager
402 .getString("label.copy_format_from");
403 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
404 new ViewSetProvider()
408 public AlignmentPanel[] getAllAlignmentPanels()
411 origview.add(alignPanel);
412 // make an array of all alignment panels except for this one
413 List<AlignmentPanel> aps = new ArrayList<>(
414 Arrays.asList(Desktop.getAlignmentPanels(null)));
415 aps.remove(AlignFrame.this.alignPanel);
416 return aps.toArray(new AlignmentPanel[aps.size()]);
418 }, selviews, new ItemListener()
422 public void itemStateChanged(ItemEvent e)
424 if (origview.size() > 0)
426 final AlignmentPanel ap = origview.get(0);
429 * Copy the ViewStyle of the selected panel to 'this one'.
430 * Don't change value of 'scaleProteinAsCdna' unless copying
433 ViewStyleI vs = selviews.get(0).getAlignViewport()
435 boolean fromSplitFrame = selviews.get(0)
436 .getAlignViewport().getCodingComplement() != null;
439 vs.setScaleProteinAsCdna(ap.getAlignViewport()
440 .getViewStyle().isScaleProteinAsCdna());
442 ap.getAlignViewport().setViewStyle(vs);
445 * Also rescale ViewStyle of SplitFrame complement if there is
446 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
447 * the whole ViewStyle (allow cDNA protein to have different
450 AlignViewportI complement = ap.getAlignViewport()
451 .getCodingComplement();
452 if (complement != null && vs.isScaleProteinAsCdna())
454 AlignFrame af = Desktop.getAlignFrameFor(complement);
455 ((SplitFrame) af.getSplitViewContainer())
457 af.setMenusForViewport();
461 ap.setSelected(true);
462 ap.alignFrame.setMenusForViewport();
467 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
468 .indexOf("devel") > -1
469 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
470 .indexOf("test") > -1)
472 formatMenu.add(vsel);
474 addFocusListener(new FocusAdapter()
477 public void focusGained(FocusEvent e)
479 Jalview.setCurrentAlignFrame(AlignFrame.this);
486 * Change the filename and format for the alignment, and enable the 'reload'
487 * button functionality.
494 public void setFileName(String file, FileFormatI format)
497 setFileFormat(format);
498 reload.setEnabled(true);
502 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
505 void addKeyListener()
507 addKeyListener(new KeyAdapter()
510 public void keyPressed(KeyEvent evt)
512 if (viewport.cursorMode
513 && ((evt.getKeyCode() >= KeyEvent.VK_0
514 && evt.getKeyCode() <= KeyEvent.VK_9)
515 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
516 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
517 && Character.isDigit(evt.getKeyChar()))
519 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
522 switch (evt.getKeyCode())
525 case 27: // escape key
526 deselectAllSequenceMenuItem_actionPerformed(null);
530 case KeyEvent.VK_DOWN:
531 if (evt.isAltDown() || !viewport.cursorMode)
533 moveSelectedSequences(false);
535 if (viewport.cursorMode)
537 alignPanel.getSeqPanel().moveCursor(0, 1);
542 if (evt.isAltDown() || !viewport.cursorMode)
544 moveSelectedSequences(true);
546 if (viewport.cursorMode)
548 alignPanel.getSeqPanel().moveCursor(0, -1);
553 case KeyEvent.VK_LEFT:
554 if (evt.isAltDown() || !viewport.cursorMode)
556 slideSequences(false,
557 alignPanel.getSeqPanel().getKeyboardNo1());
561 alignPanel.getSeqPanel().moveCursor(-1, 0);
566 case KeyEvent.VK_RIGHT:
567 if (evt.isAltDown() || !viewport.cursorMode)
569 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
573 alignPanel.getSeqPanel().moveCursor(1, 0);
577 case KeyEvent.VK_SPACE:
578 if (viewport.cursorMode)
580 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
581 || evt.isShiftDown() || evt.isAltDown());
585 // case KeyEvent.VK_A:
586 // if (viewport.cursorMode)
588 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
589 // //System.out.println("A");
593 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
594 * System.out.println("closing bracket"); } break;
596 case KeyEvent.VK_DELETE:
597 case KeyEvent.VK_BACK_SPACE:
598 if (!viewport.cursorMode)
600 cut_actionPerformed(null);
604 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
605 || evt.isShiftDown() || evt.isAltDown());
611 if (viewport.cursorMode)
613 alignPanel.getSeqPanel().setCursorRow();
617 if (viewport.cursorMode && !evt.isControlDown())
619 alignPanel.getSeqPanel().setCursorColumn();
623 if (viewport.cursorMode)
625 alignPanel.getSeqPanel().setCursorPosition();
629 case KeyEvent.VK_ENTER:
630 case KeyEvent.VK_COMMA:
631 if (viewport.cursorMode)
633 alignPanel.getSeqPanel().setCursorRowAndColumn();
638 if (viewport.cursorMode)
640 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
644 if (viewport.cursorMode)
646 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
651 viewport.cursorMode = !viewport.cursorMode;
652 statusBar.setText(MessageManager
653 .formatMessage("label.keyboard_editing_mode", new String[]
654 { (viewport.cursorMode ? "on" : "off") }));
655 if (viewport.cursorMode)
657 alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
659 alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
662 alignPanel.getSeqPanel().seqCanvas.repaint();
668 Help.showHelpWindow();
669 } catch (Exception ex)
671 ex.printStackTrace();
676 boolean toggleSeqs = !evt.isControlDown();
677 boolean toggleCols = !evt.isShiftDown();
678 toggleHiddenRegions(toggleSeqs, toggleCols);
683 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
684 boolean modifyExisting = true; // always modify, don't clear
685 // evt.isShiftDown();
686 boolean invertHighlighted = evt.isAltDown();
687 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
691 case KeyEvent.VK_PAGE_UP:
694 case KeyEvent.VK_PAGE_DOWN:
701 public void keyReleased(KeyEvent evt)
703 switch (evt.getKeyCode())
705 case KeyEvent.VK_LEFT:
706 if (evt.isAltDown() || !viewport.cursorMode)
708 viewport.firePropertyChange("alignment", null,
709 viewport.getAlignment().getSequences());
713 case KeyEvent.VK_RIGHT:
714 if (evt.isAltDown() || !viewport.cursorMode)
716 viewport.firePropertyChange("alignment", null,
717 viewport.getAlignment().getSequences());
725 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
727 ap.alignFrame = this;
728 avc = new jalview.controller.AlignViewController(this, viewport,
733 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
735 int aSize = alignPanels.size();
737 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
739 if (aSize == 1 && ap.av.viewName == null)
741 this.getContentPane().add(ap, BorderLayout.CENTER);
747 setInitialTabVisible();
750 expandViews.setEnabled(true);
751 gatherViews.setEnabled(true);
752 tabbedPane.addTab(ap.av.viewName, ap);
754 ap.setVisible(false);
759 if (ap.av.isPadGaps())
761 ap.av.getAlignment().padGaps();
763 ap.av.updateConservation(ap);
764 ap.av.updateConsensus(ap);
765 ap.av.updateStrucConsensus(ap);
769 public void setInitialTabVisible()
771 expandViews.setEnabled(true);
772 gatherViews.setEnabled(true);
773 tabbedPane.setVisible(true);
774 AlignmentPanel first = alignPanels.get(0);
775 tabbedPane.addTab(first.av.viewName, first);
776 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
779 public AlignViewport getViewport()
784 /* Set up intrinsic listeners for dynamically generated GUI bits. */
785 private void addServiceListeners()
787 final java.beans.PropertyChangeListener thisListener;
788 Desktop.instance.addJalviewPropertyChangeListener("services",
789 thisListener = new java.beans.PropertyChangeListener()
792 public void propertyChange(PropertyChangeEvent evt)
794 // // System.out.println("Discoverer property change.");
795 // if (evt.getPropertyName().equals("services"))
797 SwingUtilities.invokeLater(new Runnable()
804 "Rebuild WS Menu for service change");
805 BuildWebServiceMenu();
812 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
815 public void internalFrameClosed(
816 javax.swing.event.InternalFrameEvent evt)
818 // System.out.println("deregistering discoverer listener");
819 Desktop.instance.removeJalviewPropertyChangeListener("services",
821 closeMenuItem_actionPerformed(true);
824 // Finally, build the menu once to get current service state
825 new Thread(new Runnable()
830 BuildWebServiceMenu();
836 * Configure menu items that vary according to whether the alignment is
837 * nucleotide or protein
839 public void setGUINucleotide()
841 AlignmentI al = getViewport().getAlignment();
842 boolean nucleotide = al.isNucleotide();
844 showTranslation.setVisible(nucleotide);
845 showReverse.setVisible(nucleotide);
846 showReverseComplement.setVisible(nucleotide);
847 conservationMenuItem.setEnabled(!nucleotide);
849 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
850 showGroupConservation.setEnabled(!nucleotide);
852 showComplementMenuItem
853 .setText(nucleotide ? MessageManager.getString("label.protein")
854 : MessageManager.getString("label.nucleotide"));
858 * set up menus for the current viewport. This may be called after any
859 * operation that affects the data in the current view (selection changed,
860 * etc) to update the menus to reflect the new state.
863 public void setMenusForViewport()
865 setMenusFromViewport(viewport);
869 * Need to call this method when tabs are selected for multiple views, or when
870 * loading from Jalview2XML.java
875 void setMenusFromViewport(AlignViewport av)
877 padGapsMenuitem.setSelected(av.isPadGaps());
878 colourTextMenuItem.setSelected(av.isShowColourText());
879 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
880 modifyPID.setEnabled(abovePIDThreshold.isSelected());
881 conservationMenuItem.setSelected(av.getConservationSelected());
882 modifyConservation.setEnabled(conservationMenuItem.isSelected());
883 seqLimits.setSelected(av.getShowJVSuffix());
884 idRightAlign.setSelected(av.isRightAlignIds());
885 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
886 renderGapsMenuItem.setSelected(av.isRenderGaps());
887 wrapMenuItem.setSelected(av.getWrapAlignment());
888 scaleAbove.setVisible(av.getWrapAlignment());
889 scaleLeft.setVisible(av.getWrapAlignment());
890 scaleRight.setVisible(av.getWrapAlignment());
891 annotationPanelMenuItem.setState(av.isShowAnnotation());
893 * Show/hide annotations only enabled if annotation panel is shown
895 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
896 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
897 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
898 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
899 viewBoxesMenuItem.setSelected(av.getShowBoxes());
900 viewTextMenuItem.setSelected(av.getShowText());
901 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
902 showGroupConsensus.setSelected(av.isShowGroupConsensus());
903 showGroupConservation.setSelected(av.isShowGroupConservation());
904 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
905 showSequenceLogo.setSelected(av.isShowSequenceLogo());
906 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
908 ColourMenuHelper.setColourSelected(colourMenu,
909 av.getGlobalColourScheme());
911 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
912 hiddenMarkers.setState(av.getShowHiddenMarkers());
913 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
914 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
915 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
916 autoCalculate.setSelected(av.autoCalculateConsensus);
917 sortByTree.setSelected(av.sortByTree);
918 listenToViewSelections.setSelected(av.followSelection);
920 showProducts.setEnabled(canShowProducts());
921 setGroovyEnabled(Desktop.getGroovyConsole() != null);
927 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
931 public void setGroovyEnabled(boolean b)
933 runGroovy.setEnabled(b);
936 private IProgressIndicator progressBar;
941 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
944 public void setProgressBar(String message, long id)
946 progressBar.setProgressBar(message, id);
950 public void registerHandler(final long id,
951 final IProgressIndicatorHandler handler)
953 progressBar.registerHandler(id, handler);
958 * @return true if any progress bars are still active
961 public boolean operationInProgress()
963 return progressBar.operationInProgress();
967 public void setStatus(String text)
969 statusBar.setText(text);
973 * Added so Castor Mapping file can obtain Jalview Version
975 public String getVersion()
977 return jalview.bin.Cache.getProperty("VERSION");
980 public FeatureRenderer getFeatureRenderer()
982 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
986 public void fetchSequence_actionPerformed(ActionEvent e)
988 new jalview.gui.SequenceFetcher(this);
992 public void addFromFile_actionPerformed(ActionEvent e)
994 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
998 public void reload_actionPerformed(ActionEvent e)
1000 if (fileName != null)
1002 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1003 // originating file's format
1004 // TODO: work out how to recover feature settings for correct view(s) when
1005 // file is reloaded.
1006 if (FileFormat.Jalview.equals(currentFileFormat))
1008 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1009 for (int i = 0; i < frames.length; i++)
1011 if (frames[i] instanceof AlignFrame && frames[i] != this
1012 && ((AlignFrame) frames[i]).fileName != null
1013 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1017 frames[i].setSelected(true);
1018 Desktop.instance.closeAssociatedWindows();
1019 } catch (java.beans.PropertyVetoException ex)
1025 Desktop.instance.closeAssociatedWindows();
1027 FileLoader loader = new FileLoader();
1028 DataSourceType protocol = fileName.startsWith("http:")
1029 ? DataSourceType.URL
1030 : DataSourceType.FILE;
1031 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1035 Rectangle bounds = this.getBounds();
1037 FileLoader loader = new FileLoader();
1038 DataSourceType protocol = fileName.startsWith("http:")
1039 ? DataSourceType.URL
1040 : DataSourceType.FILE;
1041 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1042 protocol, currentFileFormat);
1044 newframe.setBounds(bounds);
1045 if (featureSettings != null && featureSettings.isShowing())
1047 final Rectangle fspos = featureSettings.frame.getBounds();
1048 // TODO: need a 'show feature settings' function that takes bounds -
1049 // need to refactor Desktop.addFrame
1050 newframe.featureSettings_actionPerformed(null);
1051 final FeatureSettings nfs = newframe.featureSettings;
1052 SwingUtilities.invokeLater(new Runnable()
1057 nfs.frame.setBounds(fspos);
1060 this.featureSettings.close();
1061 this.featureSettings = null;
1063 this.closeMenuItem_actionPerformed(true);
1069 public void addFromText_actionPerformed(ActionEvent e)
1072 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1076 public void addFromURL_actionPerformed(ActionEvent e)
1078 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1082 public void save_actionPerformed(ActionEvent e)
1084 if (fileName == null || (currentFileFormat == null)
1085 || fileName.startsWith("http"))
1087 saveAs_actionPerformed(null);
1091 saveAlignment(fileName, currentFileFormat);
1102 public void saveAs_actionPerformed(ActionEvent e)
1104 String format = currentFileFormat == null ? null
1105 : currentFileFormat.getName();
1106 JalviewFileChooser chooser = JalviewFileChooser
1107 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1109 chooser.setFileView(new JalviewFileView());
1110 chooser.setDialogTitle(
1111 MessageManager.getString("label.save_alignment_to_file"));
1112 chooser.setToolTipText(MessageManager.getString("action.save"));
1114 int value = chooser.showSaveDialog(this);
1116 if (value == JalviewFileChooser.APPROVE_OPTION)
1118 currentFileFormat = chooser.getSelectedFormat();
1119 while (currentFileFormat == null)
1121 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1122 MessageManager.getString(
1123 "label.select_file_format_before_saving"),
1124 MessageManager.getString("label.file_format_not_specified"),
1125 JvOptionPane.WARNING_MESSAGE);
1126 currentFileFormat = chooser.getSelectedFormat();
1127 value = chooser.showSaveDialog(this);
1128 if (value != JalviewFileChooser.APPROVE_OPTION)
1134 fileName = chooser.getSelectedFile().getPath();
1136 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1138 Cache.setProperty("LAST_DIRECTORY", fileName);
1139 saveAlignment(fileName, currentFileFormat);
1143 public boolean saveAlignment(String file, FileFormatI format)
1145 boolean success = true;
1147 if (FileFormat.Jalview.equals(format))
1149 String shortName = title;
1151 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1153 shortName = shortName.substring(
1154 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1157 success = new Jalview2XML().saveAlignment(this, file, shortName);
1159 statusBar.setText(MessageManager.formatMessage(
1160 "label.successfully_saved_to_file_in_format", new Object[]
1161 { fileName, format }));
1166 AlignmentExportData exportData = getAlignmentForExport(format,
1168 if (exportData.getSettings().isCancelled())
1172 FormatAdapter f = new FormatAdapter(alignPanel,
1173 exportData.getSettings());
1174 String output = f.formatSequences(format, exportData.getAlignment(), // class
1178 // occur in the distant future
1179 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1180 f.getCacheSuffixDefault(format),
1181 viewport.getAlignment().getHiddenColumns());
1191 PrintWriter out = new PrintWriter(new FileWriter(file));
1195 this.setTitle(file);
1196 statusBar.setText(MessageManager.formatMessage(
1197 "label.successfully_saved_to_file_in_format", new Object[]
1198 { fileName, format.getName() }));
1199 } catch (Exception ex)
1202 ex.printStackTrace();
1209 JvOptionPane.showInternalMessageDialog(this, MessageManager
1210 .formatMessage("label.couldnt_save_file", new Object[]
1212 MessageManager.getString("label.error_saving_file"),
1213 JvOptionPane.WARNING_MESSAGE);
1219 private void warningMessage(String warning, String title)
1221 if (new jalview.util.Platform().isHeadless())
1223 System.err.println("Warning: " + title + "\nWarning: " + warning);
1228 JvOptionPane.showInternalMessageDialog(this, warning, title,
1229 JvOptionPane.WARNING_MESSAGE);
1241 protected void outputText_actionPerformed(ActionEvent e)
1243 FileFormatI fileFormat = FileFormats.getInstance()
1244 .forName(e.getActionCommand());
1245 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1247 if (exportData.getSettings().isCancelled())
1251 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1252 cap.setForInput(null);
1255 FileFormatI format = fileFormat;
1256 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1257 .formatSequences(format, exportData.getAlignment(),
1258 exportData.getOmitHidden(),
1259 exportData.getStartEndPostions(),
1260 viewport.getAlignment().getHiddenColumns()));
1261 Desktop.addInternalFrame(cap, MessageManager
1262 .formatMessage("label.alignment_output_command", new Object[]
1263 { e.getActionCommand() }), 600, 500);
1264 } catch (OutOfMemoryError oom)
1266 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1273 public static AlignmentExportData getAlignmentForExport(
1274 FileFormatI format, AlignViewportI viewport,
1275 AlignExportSettingI exportSettings)
1277 AlignmentI alignmentToExport = null;
1278 AlignExportSettingI settings = exportSettings;
1279 String[] omitHidden = null;
1281 HiddenSequences hiddenSeqs = viewport.getAlignment()
1282 .getHiddenSequences();
1284 alignmentToExport = viewport.getAlignment();
1286 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1287 if (settings == null)
1289 settings = new AlignExportSettings(hasHiddenSeqs,
1290 viewport.hasHiddenColumns(), format);
1292 // settings.isExportAnnotations();
1294 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1296 omitHidden = viewport.getViewAsString(false,
1297 settings.isExportHiddenSequences());
1300 int[] alignmentStartEnd = new int[2];
1301 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1303 alignmentToExport = hiddenSeqs.getFullAlignment();
1307 alignmentToExport = viewport.getAlignment();
1309 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1310 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1311 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1312 omitHidden, alignmentStartEnd, settings);
1323 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1325 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1326 htmlSVG.exportHTML(null);
1330 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1332 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1333 bjs.exportHTML(null);
1336 public void createImageMap(File file, String image)
1338 alignPanel.makePNGImageMap(file, image);
1348 public void createPNG(File f)
1350 alignPanel.makePNG(f);
1360 public void createEPS(File f)
1362 alignPanel.makeEPS(f);
1366 public void createSVG(File f)
1368 alignPanel.makeSVG(f);
1372 public void pageSetup_actionPerformed(ActionEvent e)
1374 PrinterJob printJob = PrinterJob.getPrinterJob();
1375 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1385 public void printMenuItem_actionPerformed(ActionEvent e)
1387 // Putting in a thread avoids Swing painting problems
1388 PrintThread thread = new PrintThread(alignPanel);
1393 public void exportFeatures_actionPerformed(ActionEvent e)
1395 new AnnotationExporter().exportFeatures(alignPanel);
1399 public void exportAnnotations_actionPerformed(ActionEvent e)
1401 new AnnotationExporter().exportAnnotations(alignPanel);
1405 public void associatedData_actionPerformed(ActionEvent e)
1407 // Pick the tree file
1408 JalviewFileChooser chooser = new JalviewFileChooser(
1409 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1410 chooser.setFileView(new JalviewFileView());
1411 chooser.setDialogTitle(
1412 MessageManager.getString("label.load_jalview_annotations"));
1413 chooser.setToolTipText(
1414 MessageManager.getString("label.load_jalview_annotations"));
1416 int value = chooser.showOpenDialog(null);
1418 if (value == JalviewFileChooser.APPROVE_OPTION)
1420 String choice = chooser.getSelectedFile().getPath();
1421 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1422 loadJalviewDataFile(choice, null, null, null);
1428 * Close the current view or all views in the alignment frame. If the frame
1429 * only contains one view then the alignment will be removed from memory.
1431 * @param closeAllTabs
1434 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1436 if (alignPanels != null && alignPanels.size() < 2)
1438 closeAllTabs = true;
1443 if (alignPanels != null)
1447 if (this.isClosed())
1449 // really close all the windows - otherwise wait till
1450 // setClosed(true) is called
1451 for (int i = 0; i < alignPanels.size(); i++)
1453 AlignmentPanel ap = alignPanels.get(i);
1460 closeView(alignPanel);
1467 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1468 * be called recursively, with the frame now in 'closed' state
1470 this.setClosed(true);
1472 } catch (Exception ex)
1474 ex.printStackTrace();
1479 * Close the specified panel and close up tabs appropriately.
1481 * @param panelToClose
1483 public void closeView(AlignmentPanel panelToClose)
1485 int index = tabbedPane.getSelectedIndex();
1486 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1487 alignPanels.remove(panelToClose);
1488 panelToClose.closePanel();
1489 panelToClose = null;
1491 tabbedPane.removeTabAt(closedindex);
1492 tabbedPane.validate();
1494 if (index > closedindex || index == tabbedPane.getTabCount())
1496 // modify currently selected tab index if necessary.
1500 this.tabSelectionChanged(index);
1506 void updateEditMenuBar()
1509 if (viewport.getHistoryList().size() > 0)
1511 undoMenuItem.setEnabled(true);
1512 CommandI command = viewport.getHistoryList().peek();
1513 undoMenuItem.setText(MessageManager
1514 .formatMessage("label.undo_command", new Object[]
1515 { command.getDescription() }));
1519 undoMenuItem.setEnabled(false);
1520 undoMenuItem.setText(MessageManager.getString("action.undo"));
1523 if (viewport.getRedoList().size() > 0)
1525 redoMenuItem.setEnabled(true);
1527 CommandI command = viewport.getRedoList().peek();
1528 redoMenuItem.setText(MessageManager
1529 .formatMessage("label.redo_command", new Object[]
1530 { command.getDescription() }));
1534 redoMenuItem.setEnabled(false);
1535 redoMenuItem.setText(MessageManager.getString("action.redo"));
1540 public void addHistoryItem(CommandI command)
1542 if (command.getSize() > 0)
1544 viewport.addToHistoryList(command);
1545 viewport.clearRedoList();
1546 updateEditMenuBar();
1547 viewport.updateHiddenColumns();
1548 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1549 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1550 // viewport.getColumnSelection()
1551 // .getHiddenColumns().size() > 0);
1557 * @return alignment objects for all views
1559 AlignmentI[] getViewAlignments()
1561 if (alignPanels != null)
1563 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1565 for (AlignmentPanel ap : alignPanels)
1567 als[i++] = ap.av.getAlignment();
1571 if (viewport != null)
1573 return new AlignmentI[] { viewport.getAlignment() };
1585 protected void undoMenuItem_actionPerformed(ActionEvent e)
1587 if (viewport.getHistoryList().isEmpty())
1591 CommandI command = viewport.getHistoryList().pop();
1592 viewport.addToRedoList(command);
1593 command.undoCommand(getViewAlignments());
1595 AlignmentViewport originalSource = getOriginatingSource(command);
1596 updateEditMenuBar();
1598 if (originalSource != null)
1600 if (originalSource != viewport)
1603 "Implementation worry: mismatch of viewport origin for undo");
1605 originalSource.updateHiddenColumns();
1606 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1608 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1609 // viewport.getColumnSelection()
1610 // .getHiddenColumns().size() > 0);
1611 originalSource.firePropertyChange("alignment", null,
1612 originalSource.getAlignment().getSequences());
1623 protected void redoMenuItem_actionPerformed(ActionEvent e)
1625 if (viewport.getRedoList().size() < 1)
1630 CommandI command = viewport.getRedoList().pop();
1631 viewport.addToHistoryList(command);
1632 command.doCommand(getViewAlignments());
1634 AlignmentViewport originalSource = getOriginatingSource(command);
1635 updateEditMenuBar();
1637 if (originalSource != null)
1640 if (originalSource != viewport)
1643 "Implementation worry: mismatch of viewport origin for redo");
1645 originalSource.updateHiddenColumns();
1646 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1648 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1649 // viewport.getColumnSelection()
1650 // .getHiddenColumns().size() > 0);
1651 originalSource.firePropertyChange("alignment", null,
1652 originalSource.getAlignment().getSequences());
1656 AlignmentViewport getOriginatingSource(CommandI command)
1658 AlignmentViewport originalSource = null;
1659 // For sequence removal and addition, we need to fire
1660 // the property change event FROM the viewport where the
1661 // original alignment was altered
1662 AlignmentI al = null;
1663 if (command instanceof EditCommand)
1665 EditCommand editCommand = (EditCommand) command;
1666 al = editCommand.getAlignment();
1667 List<Component> comps = PaintRefresher.components
1668 .get(viewport.getSequenceSetId());
1670 for (Component comp : comps)
1672 if (comp instanceof AlignmentPanel)
1674 if (al == ((AlignmentPanel) comp).av.getAlignment())
1676 originalSource = ((AlignmentPanel) comp).av;
1683 if (originalSource == null)
1685 // The original view is closed, we must validate
1686 // the current view against the closed view first
1689 PaintRefresher.validateSequences(al, viewport.getAlignment());
1692 originalSource = viewport;
1695 return originalSource;
1704 public void moveSelectedSequences(boolean up)
1706 SequenceGroup sg = viewport.getSelectionGroup();
1712 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1713 viewport.getHiddenRepSequences(), up);
1714 alignPanel.paintAlignment(true);
1717 synchronized void slideSequences(boolean right, int size)
1719 List<SequenceI> sg = new ArrayList<>();
1720 if (viewport.cursorMode)
1722 sg.add(viewport.getAlignment()
1723 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1725 else if (viewport.getSelectionGroup() != null
1726 && viewport.getSelectionGroup().getSize() != viewport
1727 .getAlignment().getHeight())
1729 sg = viewport.getSelectionGroup()
1730 .getSequences(viewport.getHiddenRepSequences());
1738 List<SequenceI> invertGroup = new ArrayList<>();
1740 for (SequenceI seq : viewport.getAlignment().getSequences())
1742 if (!sg.contains(seq))
1744 invertGroup.add(seq);
1748 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1750 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1751 for (int i = 0; i < invertGroup.size(); i++)
1753 seqs2[i] = invertGroup.get(i);
1756 SlideSequencesCommand ssc;
1759 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1760 viewport.getGapCharacter());
1764 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1765 viewport.getGapCharacter());
1768 int groupAdjustment = 0;
1769 if (ssc.getGapsInsertedBegin() && right)
1771 if (viewport.cursorMode)
1773 alignPanel.getSeqPanel().moveCursor(size, 0);
1777 groupAdjustment = size;
1780 else if (!ssc.getGapsInsertedBegin() && !right)
1782 if (viewport.cursorMode)
1784 alignPanel.getSeqPanel().moveCursor(-size, 0);
1788 groupAdjustment = -size;
1792 if (groupAdjustment != 0)
1794 viewport.getSelectionGroup().setStartRes(
1795 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1796 viewport.getSelectionGroup().setEndRes(
1797 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1801 * just extend the last slide command if compatible; but not if in
1802 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1804 boolean appendHistoryItem = false;
1805 Deque<CommandI> historyList = viewport.getHistoryList();
1806 boolean inSplitFrame = getSplitViewContainer() != null;
1807 if (!inSplitFrame && historyList != null && historyList.size() > 0
1808 && historyList.peek() instanceof SlideSequencesCommand)
1810 appendHistoryItem = ssc.appendSlideCommand(
1811 (SlideSequencesCommand) historyList.peek());
1814 if (!appendHistoryItem)
1816 addHistoryItem(ssc);
1829 protected void copy_actionPerformed(ActionEvent e)
1832 if (viewport.getSelectionGroup() == null)
1836 // TODO: preserve the ordering of displayed alignment annotation in any
1837 // internal paste (particularly sequence associated annotation)
1838 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1839 String[] omitHidden = null;
1841 if (viewport.hasHiddenColumns())
1843 omitHidden = viewport.getViewAsString(true);
1846 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1847 seqs, omitHidden, null);
1849 StringSelection ss = new StringSelection(output);
1853 jalview.gui.Desktop.internalCopy = true;
1854 // Its really worth setting the clipboard contents
1855 // to empty before setting the large StringSelection!!
1856 Toolkit.getDefaultToolkit().getSystemClipboard()
1857 .setContents(new StringSelection(""), null);
1859 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1861 } catch (OutOfMemoryError er)
1863 new OOMWarning("copying region", er);
1867 ArrayList<int[]> hiddenColumns = null;
1868 if (viewport.hasHiddenColumns())
1870 hiddenColumns = new ArrayList<>();
1871 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1872 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1873 ArrayList<int[]> hiddenRegions = viewport.getAlignment()
1874 .getHiddenColumns().getHiddenColumnsCopy();
1875 for (int[] region : hiddenRegions)
1877 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1881 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1886 Desktop.jalviewClipboard = new Object[] { seqs,
1887 viewport.getAlignment().getDataset(), hiddenColumns };
1888 statusBar.setText(MessageManager.formatMessage(
1889 "label.copied_sequences_to_clipboard", new Object[]
1890 { Integer.valueOf(seqs.length).toString() }));
1900 protected void pasteNew_actionPerformed(ActionEvent e)
1912 protected void pasteThis_actionPerformed(ActionEvent e)
1918 * Paste contents of Jalview clipboard
1920 * @param newAlignment
1921 * true to paste to a new alignment, otherwise add to this.
1923 void paste(boolean newAlignment)
1925 boolean externalPaste = true;
1928 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1929 Transferable contents = c.getContents(this);
1931 if (contents == null)
1940 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1941 if (str.length() < 1)
1946 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1948 } catch (OutOfMemoryError er)
1950 new OOMWarning("Out of memory pasting sequences!!", er);
1954 SequenceI[] sequences;
1955 boolean annotationAdded = false;
1956 AlignmentI alignment = null;
1958 if (Desktop.jalviewClipboard != null)
1960 // The clipboard was filled from within Jalview, we must use the
1962 // And dataset from the copied alignment
1963 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1964 // be doubly sure that we create *new* sequence objects.
1965 sequences = new SequenceI[newseq.length];
1966 for (int i = 0; i < newseq.length; i++)
1968 sequences[i] = new Sequence(newseq[i]);
1970 alignment = new Alignment(sequences);
1971 externalPaste = false;
1975 // parse the clipboard as an alignment.
1976 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1978 sequences = alignment.getSequencesArray();
1982 ArrayList<Integer> newGraphGroups = new ArrayList<>();
1988 if (Desktop.jalviewClipboard != null)
1990 // dataset is inherited
1991 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1995 // new dataset is constructed
1996 alignment.setDataset(null);
1998 alwidth = alignment.getWidth() + 1;
2002 AlignmentI pastedal = alignment; // preserve pasted alignment object
2003 // Add pasted sequences and dataset into existing alignment.
2004 alignment = viewport.getAlignment();
2005 alwidth = alignment.getWidth() + 1;
2006 // decide if we need to import sequences from an existing dataset
2007 boolean importDs = Desktop.jalviewClipboard != null
2008 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2009 // importDs==true instructs us to copy over new dataset sequences from
2010 // an existing alignment
2011 Vector newDs = (importDs) ? new Vector() : null; // used to create
2012 // minimum dataset set
2014 for (int i = 0; i < sequences.length; i++)
2018 newDs.addElement(null);
2020 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2022 if (importDs && ds != null)
2024 if (!newDs.contains(ds))
2026 newDs.setElementAt(ds, i);
2027 ds = new Sequence(ds);
2028 // update with new dataset sequence
2029 sequences[i].setDatasetSequence(ds);
2033 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2038 // copy and derive new dataset sequence
2039 sequences[i] = sequences[i].deriveSequence();
2040 alignment.getDataset()
2041 .addSequence(sequences[i].getDatasetSequence());
2042 // TODO: avoid creation of duplicate dataset sequences with a
2043 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2045 alignment.addSequence(sequences[i]); // merges dataset
2049 newDs.clear(); // tidy up
2051 if (alignment.getAlignmentAnnotation() != null)
2053 for (AlignmentAnnotation alan : alignment
2054 .getAlignmentAnnotation())
2056 if (alan.graphGroup > fgroup)
2058 fgroup = alan.graphGroup;
2062 if (pastedal.getAlignmentAnnotation() != null)
2064 // Add any annotation attached to alignment.
2065 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2066 for (int i = 0; i < alann.length; i++)
2068 annotationAdded = true;
2069 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2071 AlignmentAnnotation newann = new AlignmentAnnotation(
2073 if (newann.graphGroup > -1)
2075 if (newGraphGroups.size() <= newann.graphGroup
2076 || newGraphGroups.get(newann.graphGroup) == null)
2078 for (int q = newGraphGroups
2079 .size(); q <= newann.graphGroup; q++)
2081 newGraphGroups.add(q, null);
2083 newGraphGroups.set(newann.graphGroup,
2084 new Integer(++fgroup));
2086 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2090 newann.padAnnotation(alwidth);
2091 alignment.addAnnotation(newann);
2101 addHistoryItem(new EditCommand(
2102 MessageManager.getString("label.add_sequences"),
2103 Action.PASTE, sequences, 0, alignment.getWidth(),
2106 // Add any annotations attached to sequences
2107 for (int i = 0; i < sequences.length; i++)
2109 if (sequences[i].getAnnotation() != null)
2111 AlignmentAnnotation newann;
2112 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2114 annotationAdded = true;
2115 newann = sequences[i].getAnnotation()[a];
2116 newann.adjustForAlignment();
2117 newann.padAnnotation(alwidth);
2118 if (newann.graphGroup > -1)
2120 if (newann.graphGroup > -1)
2122 if (newGraphGroups.size() <= newann.graphGroup
2123 || newGraphGroups.get(newann.graphGroup) == null)
2125 for (int q = newGraphGroups
2126 .size(); q <= newann.graphGroup; q++)
2128 newGraphGroups.add(q, null);
2130 newGraphGroups.set(newann.graphGroup,
2131 new Integer(++fgroup));
2133 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2137 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2141 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2149 // propagate alignment changed.
2150 vpRanges.setEndSeq(alignment.getHeight());
2151 if (annotationAdded)
2153 // Duplicate sequence annotation in all views.
2154 AlignmentI[] alview = this.getViewAlignments();
2155 for (int i = 0; i < sequences.length; i++)
2157 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2162 for (int avnum = 0; avnum < alview.length; avnum++)
2164 if (alview[avnum] != alignment)
2166 // duplicate in a view other than the one with input focus
2167 int avwidth = alview[avnum].getWidth() + 1;
2168 // this relies on sann being preserved after we
2169 // modify the sequence's annotation array for each duplication
2170 for (int a = 0; a < sann.length; a++)
2172 AlignmentAnnotation newann = new AlignmentAnnotation(
2174 sequences[i].addAlignmentAnnotation(newann);
2175 newann.padAnnotation(avwidth);
2176 alview[avnum].addAnnotation(newann); // annotation was
2177 // duplicated earlier
2178 // TODO JAL-1145 graphGroups are not updated for sequence
2179 // annotation added to several views. This may cause
2181 alview[avnum].setAnnotationIndex(newann, a);
2186 buildSortByAnnotationScoresMenu();
2188 viewport.firePropertyChange("alignment", null,
2189 alignment.getSequences());
2190 if (alignPanels != null)
2192 for (AlignmentPanel ap : alignPanels)
2194 ap.validateAnnotationDimensions(false);
2199 alignPanel.validateAnnotationDimensions(false);
2205 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2207 String newtitle = new String("Copied sequences");
2209 if (Desktop.jalviewClipboard != null
2210 && Desktop.jalviewClipboard[2] != null)
2212 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2213 for (int[] region : hc)
2215 af.viewport.hideColumns(region[0], region[1]);
2219 // >>>This is a fix for the moment, until a better solution is
2221 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2222 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2223 .getFeatureRenderer());
2225 // TODO: maintain provenance of an alignment, rather than just make the
2226 // title a concatenation of operations.
2229 if (title.startsWith("Copied sequences"))
2235 newtitle = newtitle.concat("- from " + title);
2240 newtitle = new String("Pasted sequences");
2243 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2248 } catch (Exception ex)
2250 ex.printStackTrace();
2251 System.out.println("Exception whilst pasting: " + ex);
2252 // could be anything being pasted in here
2258 protected void expand_newalign(ActionEvent e)
2262 AlignmentI alignment = AlignmentUtils
2263 .expandContext(getViewport().getAlignment(), -1);
2264 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2266 String newtitle = new String("Flanking alignment");
2268 if (Desktop.jalviewClipboard != null
2269 && Desktop.jalviewClipboard[2] != null)
2271 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2272 for (int region[] : hc)
2274 af.viewport.hideColumns(region[0], region[1]);
2278 // >>>This is a fix for the moment, until a better solution is
2280 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2281 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2282 .getFeatureRenderer());
2284 // TODO: maintain provenance of an alignment, rather than just make the
2285 // title a concatenation of operations.
2287 if (title.startsWith("Copied sequences"))
2293 newtitle = newtitle.concat("- from " + title);
2297 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2299 } catch (Exception ex)
2301 ex.printStackTrace();
2302 System.out.println("Exception whilst pasting: " + ex);
2303 // could be anything being pasted in here
2304 } catch (OutOfMemoryError oom)
2306 new OOMWarning("Viewing flanking region of alignment", oom);
2317 protected void cut_actionPerformed(ActionEvent e)
2319 copy_actionPerformed(null);
2320 delete_actionPerformed(null);
2330 protected void delete_actionPerformed(ActionEvent evt)
2333 SequenceGroup sg = viewport.getSelectionGroup();
2340 * If the cut affects all sequences, warn, remove highlighted columns
2342 if (sg.getSize() == viewport.getAlignment().getHeight())
2344 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2345 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2346 if (isEntireAlignWidth)
2348 int confirm = JvOptionPane.showConfirmDialog(this,
2349 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2350 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2351 JvOptionPane.OK_CANCEL_OPTION);
2353 if (confirm == JvOptionPane.CANCEL_OPTION
2354 || confirm == JvOptionPane.CLOSED_OPTION)
2359 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2360 sg.getEndRes() + 1);
2362 SequenceI[] cut = sg.getSequences()
2363 .toArray(new SequenceI[sg.getSize()]);
2365 addHistoryItem(new EditCommand(
2366 MessageManager.getString("label.cut_sequences"), Action.CUT,
2367 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2368 viewport.getAlignment()));
2370 viewport.setSelectionGroup(null);
2371 viewport.sendSelection();
2372 viewport.getAlignment().deleteGroup(sg);
2374 viewport.firePropertyChange("alignment", null,
2375 viewport.getAlignment().getSequences());
2376 if (viewport.getAlignment().getHeight() < 1)
2380 this.setClosed(true);
2381 } catch (Exception ex)
2394 protected void deleteGroups_actionPerformed(ActionEvent e)
2396 if (avc.deleteGroups())
2398 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2399 alignPanel.updateAnnotation();
2400 alignPanel.paintAlignment(true);
2411 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2413 SequenceGroup sg = new SequenceGroup();
2415 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2417 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2420 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2421 viewport.setSelectionGroup(sg);
2422 viewport.sendSelection();
2423 // JAL-2034 - should delegate to
2424 // alignPanel to decide if overview needs
2426 alignPanel.paintAlignment(false);
2427 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2437 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2439 if (viewport.cursorMode)
2441 alignPanel.getSeqPanel().keyboardNo1 = null;
2442 alignPanel.getSeqPanel().keyboardNo2 = null;
2444 viewport.setSelectionGroup(null);
2445 viewport.getColumnSelection().clear();
2446 viewport.setSelectionGroup(null);
2447 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2448 // JAL-2034 - should delegate to
2449 // alignPanel to decide if overview needs
2451 alignPanel.paintAlignment(false);
2452 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2453 viewport.sendSelection();
2463 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2465 SequenceGroup sg = viewport.getSelectionGroup();
2469 selectAllSequenceMenuItem_actionPerformed(null);
2474 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2476 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2478 // JAL-2034 - should delegate to
2479 // alignPanel to decide if overview needs
2482 alignPanel.paintAlignment(true);
2483 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2484 viewport.sendSelection();
2488 public void invertColSel_actionPerformed(ActionEvent e)
2490 viewport.invertColumnSelection();
2491 alignPanel.paintAlignment(true);
2492 viewport.sendSelection();
2502 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2504 trimAlignment(true);
2514 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2516 trimAlignment(false);
2519 void trimAlignment(boolean trimLeft)
2521 ColumnSelection colSel = viewport.getColumnSelection();
2524 if (!colSel.isEmpty())
2528 column = colSel.getMin();
2532 column = colSel.getMax();
2536 if (viewport.getSelectionGroup() != null)
2538 seqs = viewport.getSelectionGroup()
2539 .getSequencesAsArray(viewport.getHiddenRepSequences());
2543 seqs = viewport.getAlignment().getSequencesArray();
2546 TrimRegionCommand trimRegion;
2549 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2550 column, viewport.getAlignment());
2551 vpRanges.setStartRes(0);
2555 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2556 column, viewport.getAlignment());
2559 statusBar.setText(MessageManager
2560 .formatMessage("label.removed_columns", new String[]
2561 { Integer.valueOf(trimRegion.getSize()).toString() }));
2563 addHistoryItem(trimRegion);
2565 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2567 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2568 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2570 viewport.getAlignment().deleteGroup(sg);
2574 viewport.firePropertyChange("alignment", null,
2575 viewport.getAlignment().getSequences());
2586 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2588 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2591 if (viewport.getSelectionGroup() != null)
2593 seqs = viewport.getSelectionGroup()
2594 .getSequencesAsArray(viewport.getHiddenRepSequences());
2595 start = viewport.getSelectionGroup().getStartRes();
2596 end = viewport.getSelectionGroup().getEndRes();
2600 seqs = viewport.getAlignment().getSequencesArray();
2603 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2604 "Remove Gapped Columns", seqs, start, end,
2605 viewport.getAlignment());
2607 addHistoryItem(removeGapCols);
2609 statusBar.setText(MessageManager
2610 .formatMessage("label.removed_empty_columns", new Object[]
2611 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2613 // This is to maintain viewport position on first residue
2614 // of first sequence
2615 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2616 int startRes = seq.findPosition(vpRanges.getStartRes());
2617 // ShiftList shifts;
2618 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2619 // edit.alColumnChanges=shifts.getInverse();
2620 // if (viewport.hasHiddenColumns)
2621 // viewport.getColumnSelection().compensateForEdits(shifts);
2622 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2623 viewport.firePropertyChange("alignment", null,
2624 viewport.getAlignment().getSequences());
2635 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2637 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2640 if (viewport.getSelectionGroup() != null)
2642 seqs = viewport.getSelectionGroup()
2643 .getSequencesAsArray(viewport.getHiddenRepSequences());
2644 start = viewport.getSelectionGroup().getStartRes();
2645 end = viewport.getSelectionGroup().getEndRes();
2649 seqs = viewport.getAlignment().getSequencesArray();
2652 // This is to maintain viewport position on first residue
2653 // of first sequence
2654 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2655 int startRes = seq.findPosition(vpRanges.getStartRes());
2657 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2658 viewport.getAlignment()));
2660 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2662 viewport.firePropertyChange("alignment", null,
2663 viewport.getAlignment().getSequences());
2674 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2676 viewport.setPadGaps(padGapsMenuitem.isSelected());
2677 viewport.firePropertyChange("alignment", null,
2678 viewport.getAlignment().getSequences());
2688 public void findMenuItem_actionPerformed(ActionEvent e)
2694 * Create a new view of the current alignment.
2697 public void newView_actionPerformed(ActionEvent e)
2699 newView(null, true);
2703 * Creates and shows a new view of the current alignment.
2706 * title of newly created view; if null, one will be generated
2707 * @param copyAnnotation
2708 * if true then duplicate all annnotation, groups and settings
2709 * @return new alignment panel, already displayed.
2711 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2714 * Create a new AlignmentPanel (with its own, new Viewport)
2716 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2718 if (!copyAnnotation)
2721 * remove all groups and annotation except for the automatic stuff
2723 newap.av.getAlignment().deleteAllGroups();
2724 newap.av.getAlignment().deleteAllAnnotations(false);
2727 newap.av.setGatherViewsHere(false);
2729 if (viewport.viewName == null)
2731 viewport.viewName = MessageManager
2732 .getString("label.view_name_original");
2736 * Views share the same edits undo and redo stacks
2738 newap.av.setHistoryList(viewport.getHistoryList());
2739 newap.av.setRedoList(viewport.getRedoList());
2742 * Views share the same mappings; need to deregister any new mappings
2743 * created by copyAlignPanel, and register the new reference to the shared
2746 newap.av.replaceMappings(viewport.getAlignment());
2749 * start up cDNA consensus (if applicable) now mappings are in place
2751 if (newap.av.initComplementConsensus())
2753 newap.refresh(true); // adjust layout of annotations
2756 newap.av.viewName = getNewViewName(viewTitle);
2758 addAlignmentPanel(newap, true);
2759 newap.alignmentChanged();
2761 if (alignPanels.size() == 2)
2763 viewport.setGatherViewsHere(true);
2765 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2770 * Make a new name for the view, ensuring it is unique within the current
2771 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2772 * these now use viewId. Unique view names are still desirable for usability.)
2777 protected String getNewViewName(String viewTitle)
2779 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2780 boolean addFirstIndex = false;
2781 if (viewTitle == null || viewTitle.trim().length() == 0)
2783 viewTitle = MessageManager.getString("action.view");
2784 addFirstIndex = true;
2788 index = 1;// we count from 1 if given a specific name
2790 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2792 List<Component> comps = PaintRefresher.components
2793 .get(viewport.getSequenceSetId());
2795 List<String> existingNames = getExistingViewNames(comps);
2797 while (existingNames.contains(newViewName))
2799 newViewName = viewTitle + " " + (++index);
2805 * Returns a list of distinct view names found in the given list of
2806 * components. View names are held on the viewport of an AlignmentPanel.
2811 protected List<String> getExistingViewNames(List<Component> comps)
2813 List<String> existingNames = new ArrayList<>();
2814 for (Component comp : comps)
2816 if (comp instanceof AlignmentPanel)
2818 AlignmentPanel ap = (AlignmentPanel) comp;
2819 if (!existingNames.contains(ap.av.viewName))
2821 existingNames.add(ap.av.viewName);
2825 return existingNames;
2829 * Explode tabbed views into separate windows.
2832 public void expandViews_actionPerformed(ActionEvent e)
2834 Desktop.explodeViews(this);
2838 * Gather views in separate windows back into a tabbed presentation.
2841 public void gatherViews_actionPerformed(ActionEvent e)
2843 Desktop.instance.gatherViews(this);
2853 public void font_actionPerformed(ActionEvent e)
2855 new FontChooser(alignPanel);
2865 protected void seqLimit_actionPerformed(ActionEvent e)
2867 viewport.setShowJVSuffix(seqLimits.isSelected());
2869 alignPanel.getIdPanel().getIdCanvas()
2870 .setPreferredSize(alignPanel.calculateIdWidth());
2871 alignPanel.paintAlignment(true);
2875 public void idRightAlign_actionPerformed(ActionEvent e)
2877 viewport.setRightAlignIds(idRightAlign.isSelected());
2878 alignPanel.paintAlignment(true);
2882 public void centreColumnLabels_actionPerformed(ActionEvent e)
2884 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2885 alignPanel.paintAlignment(true);
2891 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2894 protected void followHighlight_actionPerformed()
2897 * Set the 'follow' flag on the Viewport (and scroll to position if now
2900 final boolean state = this.followHighlightMenuItem.getState();
2901 viewport.setFollowHighlight(state);
2904 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2915 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2917 viewport.setColourText(colourTextMenuItem.isSelected());
2918 alignPanel.paintAlignment(true);
2928 public void wrapMenuItem_actionPerformed(ActionEvent e)
2930 scaleAbove.setVisible(wrapMenuItem.isSelected());
2931 scaleLeft.setVisible(wrapMenuItem.isSelected());
2932 scaleRight.setVisible(wrapMenuItem.isSelected());
2933 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2934 alignPanel.updateLayout();
2938 public void showAllSeqs_actionPerformed(ActionEvent e)
2940 viewport.showAllHiddenSeqs();
2944 public void showAllColumns_actionPerformed(ActionEvent e)
2946 viewport.showAllHiddenColumns();
2947 alignPanel.paintAlignment(true);
2948 viewport.sendSelection();
2952 public void hideSelSequences_actionPerformed(ActionEvent e)
2954 viewport.hideAllSelectedSeqs();
2958 * called by key handler and the hide all/show all menu items
2963 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2966 boolean hide = false;
2967 SequenceGroup sg = viewport.getSelectionGroup();
2968 if (!toggleSeqs && !toggleCols)
2970 // Hide everything by the current selection - this is a hack - we do the
2971 // invert and then hide
2972 // first check that there will be visible columns after the invert.
2973 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2974 && sg.getStartRes() <= sg.getEndRes()))
2976 // now invert the sequence set, if required - empty selection implies
2977 // that no hiding is required.
2980 invertSequenceMenuItem_actionPerformed(null);
2981 sg = viewport.getSelectionGroup();
2985 viewport.expandColSelection(sg, true);
2986 // finally invert the column selection and get the new sequence
2988 invertColSel_actionPerformed(null);
2995 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2997 hideSelSequences_actionPerformed(null);
3000 else if (!(toggleCols && viewport.hasSelectedColumns()))
3002 showAllSeqs_actionPerformed(null);
3008 if (viewport.hasSelectedColumns())
3010 hideSelColumns_actionPerformed(null);
3013 viewport.setSelectionGroup(sg);
3018 showAllColumns_actionPerformed(null);
3027 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3028 * event.ActionEvent)
3031 public void hideAllButSelection_actionPerformed(ActionEvent e)
3033 toggleHiddenRegions(false, false);
3034 viewport.sendSelection();
3041 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3045 public void hideAllSelection_actionPerformed(ActionEvent e)
3047 SequenceGroup sg = viewport.getSelectionGroup();
3048 viewport.expandColSelection(sg, false);
3049 viewport.hideAllSelectedSeqs();
3050 viewport.hideSelectedColumns();
3051 alignPanel.paintAlignment(true);
3052 viewport.sendSelection();
3059 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3063 public void showAllhidden_actionPerformed(ActionEvent e)
3065 viewport.showAllHiddenColumns();
3066 viewport.showAllHiddenSeqs();
3067 alignPanel.paintAlignment(true);
3068 viewport.sendSelection();
3072 public void hideSelColumns_actionPerformed(ActionEvent e)
3074 viewport.hideSelectedColumns();
3075 alignPanel.paintAlignment(true);
3076 viewport.sendSelection();
3080 public void hiddenMarkers_actionPerformed(ActionEvent e)
3082 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3093 protected void scaleAbove_actionPerformed(ActionEvent e)
3095 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3096 alignPanel.paintAlignment(true);
3106 protected void scaleLeft_actionPerformed(ActionEvent e)
3108 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3109 alignPanel.paintAlignment(true);
3119 protected void scaleRight_actionPerformed(ActionEvent e)
3121 viewport.setScaleRightWrapped(scaleRight.isSelected());
3122 alignPanel.paintAlignment(true);
3132 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3134 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3135 alignPanel.paintAlignment(true);
3145 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3147 viewport.setShowText(viewTextMenuItem.isSelected());
3148 alignPanel.paintAlignment(true);
3158 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3160 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3161 alignPanel.paintAlignment(true);
3164 public FeatureSettings featureSettings;
3167 public FeatureSettingsControllerI getFeatureSettingsUI()
3169 return featureSettings;
3173 public void featureSettings_actionPerformed(ActionEvent e)
3175 if (featureSettings != null)
3177 featureSettings.close();
3178 featureSettings = null;
3180 if (!showSeqFeatures.isSelected())
3182 // make sure features are actually displayed
3183 showSeqFeatures.setSelected(true);
3184 showSeqFeatures_actionPerformed(null);
3186 featureSettings = new FeatureSettings(this);
3190 * Set or clear 'Show Sequence Features'
3196 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3198 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3199 alignPanel.paintAlignment(true);
3203 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3204 * the annotations panel as a whole.
3206 * The options to show/hide all annotations should be enabled when the panel
3207 * is shown, and disabled when the panel is hidden.
3212 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3214 final boolean setVisible = annotationPanelMenuItem.isSelected();
3215 viewport.setShowAnnotation(setVisible);
3216 this.showAllSeqAnnotations.setEnabled(setVisible);
3217 this.hideAllSeqAnnotations.setEnabled(setVisible);
3218 this.showAllAlAnnotations.setEnabled(setVisible);
3219 this.hideAllAlAnnotations.setEnabled(setVisible);
3220 alignPanel.updateLayout();
3224 public void alignmentProperties()
3226 JEditorPane editPane = new JEditorPane("text/html", "");
3227 editPane.setEditable(false);
3228 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3231 MessageManager.formatMessage("label.html_content", new Object[]
3232 { contents.toString() }));
3233 JInternalFrame frame = new JInternalFrame();
3234 frame.getContentPane().add(new JScrollPane(editPane));
3236 Desktop.addInternalFrame(frame, MessageManager
3237 .formatMessage("label.alignment_properties", new Object[]
3238 { getTitle() }), 500, 400);
3248 public void overviewMenuItem_actionPerformed(ActionEvent e)
3250 if (alignPanel.overviewPanel != null)
3255 JInternalFrame frame = new JInternalFrame();
3256 final OverviewPanel overview = new OverviewPanel(alignPanel);
3257 frame.setContentPane(overview);
3258 Desktop.addInternalFrame(frame, MessageManager
3259 .formatMessage("label.overview_params", new Object[]
3260 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3263 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3264 frame.addInternalFrameListener(
3265 new javax.swing.event.InternalFrameAdapter()
3268 public void internalFrameClosed(
3269 javax.swing.event.InternalFrameEvent evt)
3272 alignPanel.setOverviewPanel(null);
3276 alignPanel.setOverviewPanel(overview);
3280 public void textColour_actionPerformed()
3282 new TextColourChooser().chooseColour(alignPanel, null);
3286 * public void covariationColour_actionPerformed() {
3288 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3292 public void annotationColour_actionPerformed()
3294 new AnnotationColourChooser(viewport, alignPanel);
3298 public void annotationColumn_actionPerformed(ActionEvent e)
3300 new AnnotationColumnChooser(viewport, alignPanel);
3304 * Action on the user checking or unchecking the option to apply the selected
3305 * colour scheme to all groups. If unchecked, groups may have their own
3306 * independent colour schemes.
3311 public void applyToAllGroups_actionPerformed(boolean selected)
3313 viewport.setColourAppliesToAllGroups(selected);
3317 * Action on user selecting a colour from the colour menu
3320 * the name (not the menu item label!) of the colour scheme
3323 public void changeColour_actionPerformed(String name)
3326 * 'User Defined' opens a panel to configure or load a
3327 * user-defined colour scheme
3329 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3331 new UserDefinedColours(alignPanel);
3336 * otherwise set the chosen colour scheme (or null for 'None')
3338 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3339 viewport.getAlignment(), viewport.getHiddenRepSequences());
3344 * Actions on setting or changing the alignment colour scheme
3349 public void changeColour(ColourSchemeI cs)
3351 // TODO: pull up to controller method
3352 ColourMenuHelper.setColourSelected(colourMenu, cs);
3354 viewport.setGlobalColourScheme(cs);
3356 alignPanel.paintAlignment(true);
3360 * Show the PID threshold slider panel
3363 protected void modifyPID_actionPerformed()
3365 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3366 alignPanel.getViewName());
3367 SliderPanel.showPIDSlider();
3371 * Show the Conservation slider panel
3374 protected void modifyConservation_actionPerformed()
3376 SliderPanel.setConservationSlider(alignPanel,
3377 viewport.getResidueShading(), alignPanel.getViewName());
3378 SliderPanel.showConservationSlider();
3382 * Action on selecting or deselecting (Colour) By Conservation
3385 public void conservationMenuItem_actionPerformed(boolean selected)
3387 modifyConservation.setEnabled(selected);
3388 viewport.setConservationSelected(selected);
3389 viewport.getResidueShading().setConservationApplied(selected);
3391 changeColour(viewport.getGlobalColourScheme());
3394 modifyConservation_actionPerformed();
3398 SliderPanel.hideConservationSlider();
3403 * Action on selecting or deselecting (Colour) Above PID Threshold
3406 public void abovePIDThreshold_actionPerformed(boolean selected)
3408 modifyPID.setEnabled(selected);
3409 viewport.setAbovePIDThreshold(selected);
3412 viewport.getResidueShading().setThreshold(0,
3413 viewport.isIgnoreGapsConsensus());
3416 changeColour(viewport.getGlobalColourScheme());
3419 modifyPID_actionPerformed();
3423 SliderPanel.hidePIDSlider();
3434 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3436 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3437 AlignmentSorter.sortByPID(viewport.getAlignment(),
3438 viewport.getAlignment().getSequenceAt(0));
3439 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3440 viewport.getAlignment()));
3441 alignPanel.paintAlignment(true);
3451 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3453 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3454 AlignmentSorter.sortByID(viewport.getAlignment());
3456 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3457 alignPanel.paintAlignment(true);
3467 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3469 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3470 AlignmentSorter.sortByLength(viewport.getAlignment());
3471 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3472 viewport.getAlignment()));
3473 alignPanel.paintAlignment(true);
3483 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3485 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3486 AlignmentSorter.sortByGroup(viewport.getAlignment());
3487 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3488 viewport.getAlignment()));
3490 alignPanel.paintAlignment(true);
3500 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3502 new RedundancyPanel(alignPanel, this);
3512 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3514 if ((viewport.getSelectionGroup() == null)
3515 || (viewport.getSelectionGroup().getSize() < 2))
3517 JvOptionPane.showInternalMessageDialog(this,
3518 MessageManager.getString(
3519 "label.you_must_select_least_two_sequences"),
3520 MessageManager.getString("label.invalid_selection"),
3521 JvOptionPane.WARNING_MESSAGE);
3525 JInternalFrame frame = new JInternalFrame();
3526 frame.setContentPane(new PairwiseAlignPanel(viewport));
3527 Desktop.addInternalFrame(frame,
3528 MessageManager.getString("action.pairwise_alignment"), 600,
3534 public void autoCalculate_actionPerformed(ActionEvent e)
3536 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3537 if (viewport.autoCalculateConsensus)
3539 viewport.firePropertyChange("alignment", null,
3540 viewport.getAlignment().getSequences());
3545 public void sortByTreeOption_actionPerformed(ActionEvent e)
3547 viewport.sortByTree = sortByTree.isSelected();
3551 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3553 viewport.followSelection = listenToViewSelections.isSelected();
3557 * Constructs a tree panel and adds it to the desktop
3560 * tree type (NJ or AV)
3562 * name of score model used to compute the tree
3564 * parameters for the distance or similarity calculation
3566 void newTreePanel(String type, String modelName,
3567 SimilarityParamsI options)
3569 String frameTitle = "";
3572 boolean onSelection = false;
3573 if (viewport.getSelectionGroup() != null
3574 && viewport.getSelectionGroup().getSize() > 0)
3576 SequenceGroup sg = viewport.getSelectionGroup();
3578 /* Decide if the selection is a column region */
3579 for (SequenceI _s : sg.getSequences())
3581 if (_s.getLength() < sg.getEndRes())
3583 JvOptionPane.showMessageDialog(Desktop.desktop,
3584 MessageManager.getString(
3585 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3586 MessageManager.getString(
3587 "label.sequences_selection_not_aligned"),
3588 JvOptionPane.WARNING_MESSAGE);
3597 if (viewport.getAlignment().getHeight() < 2)
3603 tp = new TreePanel(alignPanel, type, modelName, options);
3604 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3606 frameTitle += " from ";
3608 if (viewport.viewName != null)
3610 frameTitle += viewport.viewName + " of ";
3613 frameTitle += this.title;
3615 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3626 public void addSortByOrderMenuItem(String title,
3627 final AlignmentOrder order)
3629 final JMenuItem item = new JMenuItem(MessageManager
3630 .formatMessage("action.by_title_param", new Object[]
3633 item.addActionListener(new java.awt.event.ActionListener()
3636 public void actionPerformed(ActionEvent e)
3638 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3640 // TODO: JBPNote - have to map order entries to curent SequenceI
3642 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3644 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3645 viewport.getAlignment()));
3647 alignPanel.paintAlignment(true);
3653 * Add a new sort by annotation score menu item
3656 * the menu to add the option to
3658 * the label used to retrieve scores for each sequence on the
3661 public void addSortByAnnotScoreMenuItem(JMenu sort,
3662 final String scoreLabel)
3664 final JMenuItem item = new JMenuItem(scoreLabel);
3666 item.addActionListener(new java.awt.event.ActionListener()
3669 public void actionPerformed(ActionEvent e)
3671 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3672 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3673 viewport.getAlignment());// ,viewport.getSelectionGroup());
3674 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3675 viewport.getAlignment()));
3676 alignPanel.paintAlignment(true);
3682 * last hash for alignment's annotation array - used to minimise cost of
3685 protected int _annotationScoreVectorHash;
3688 * search the alignment and rebuild the sort by annotation score submenu the
3689 * last alignment annotation vector hash is stored to minimize cost of
3690 * rebuilding in subsequence calls.
3694 public void buildSortByAnnotationScoresMenu()
3696 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3701 if (viewport.getAlignment().getAlignmentAnnotation()
3702 .hashCode() != _annotationScoreVectorHash)
3704 sortByAnnotScore.removeAll();
3705 // almost certainly a quicker way to do this - but we keep it simple
3706 Hashtable scoreSorts = new Hashtable();
3707 AlignmentAnnotation aann[];
3708 for (SequenceI sqa : viewport.getAlignment().getSequences())
3710 aann = sqa.getAnnotation();
3711 for (int i = 0; aann != null && i < aann.length; i++)
3713 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3715 scoreSorts.put(aann[i].label, aann[i].label);
3719 Enumeration labels = scoreSorts.keys();
3720 while (labels.hasMoreElements())
3722 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3723 (String) labels.nextElement());
3725 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3728 _annotationScoreVectorHash = viewport.getAlignment()
3729 .getAlignmentAnnotation().hashCode();
3734 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3735 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3736 * call. Listeners are added to remove the menu item when the treePanel is
3737 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3741 public void buildTreeSortMenu()
3743 sortByTreeMenu.removeAll();
3745 List<Component> comps = PaintRefresher.components
3746 .get(viewport.getSequenceSetId());
3747 List<TreePanel> treePanels = new ArrayList<>();
3748 for (Component comp : comps)
3750 if (comp instanceof TreePanel)
3752 treePanels.add((TreePanel) comp);
3756 if (treePanels.size() < 1)
3758 sortByTreeMenu.setVisible(false);
3762 sortByTreeMenu.setVisible(true);
3764 for (final TreePanel tp : treePanels)
3766 final JMenuItem item = new JMenuItem(tp.getTitle());
3767 item.addActionListener(new java.awt.event.ActionListener()
3770 public void actionPerformed(ActionEvent e)
3772 tp.sortByTree_actionPerformed();
3773 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3778 sortByTreeMenu.add(item);
3782 public boolean sortBy(AlignmentOrder alorder, String undoname)
3784 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3785 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3786 if (undoname != null)
3788 addHistoryItem(new OrderCommand(undoname, oldOrder,
3789 viewport.getAlignment()));
3791 alignPanel.paintAlignment(true);
3796 * Work out whether the whole set of sequences or just the selected set will
3797 * be submitted for multiple alignment.
3800 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3802 // Now, check we have enough sequences
3803 AlignmentView msa = null;
3805 if ((viewport.getSelectionGroup() != null)
3806 && (viewport.getSelectionGroup().getSize() > 1))
3808 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3809 // some common interface!
3811 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3812 * SequenceI[sz = seqs.getSize(false)];
3814 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3815 * seqs.getSequenceAt(i); }
3817 msa = viewport.getAlignmentView(true);
3819 else if (viewport.getSelectionGroup() != null
3820 && viewport.getSelectionGroup().getSize() == 1)
3822 int option = JvOptionPane.showConfirmDialog(this,
3823 MessageManager.getString("warn.oneseq_msainput_selection"),
3824 MessageManager.getString("label.invalid_selection"),
3825 JvOptionPane.OK_CANCEL_OPTION);
3826 if (option == JvOptionPane.OK_OPTION)
3828 msa = viewport.getAlignmentView(false);
3833 msa = viewport.getAlignmentView(false);
3839 * Decides what is submitted to a secondary structure prediction service: the
3840 * first sequence in the alignment, or in the current selection, or, if the
3841 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3842 * region or the whole alignment. (where the first sequence in the set is the
3843 * one that the prediction will be for).
3845 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3847 AlignmentView seqs = null;
3849 if ((viewport.getSelectionGroup() != null)
3850 && (viewport.getSelectionGroup().getSize() > 0))
3852 seqs = viewport.getAlignmentView(true);
3856 seqs = viewport.getAlignmentView(false);
3858 // limit sequences - JBPNote in future - could spawn multiple prediction
3860 // TODO: viewport.getAlignment().isAligned is a global state - the local
3861 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3862 if (!viewport.getAlignment().isAligned(false))
3864 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3865 // TODO: if seqs.getSequences().length>1 then should really have warned
3879 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3881 // Pick the tree file
3882 JalviewFileChooser chooser = new JalviewFileChooser(
3883 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3884 chooser.setFileView(new JalviewFileView());
3885 chooser.setDialogTitle(
3886 MessageManager.getString("label.select_newick_like_tree_file"));
3887 chooser.setToolTipText(
3888 MessageManager.getString("label.load_tree_file"));
3890 int value = chooser.showOpenDialog(null);
3892 if (value == JalviewFileChooser.APPROVE_OPTION)
3894 String filePath = chooser.getSelectedFile().getPath();
3895 Cache.setProperty("LAST_DIRECTORY", filePath);
3896 NewickFile fin = null;
3899 fin = new NewickFile(filePath, DataSourceType.FILE);
3900 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3901 } catch (Exception ex)
3903 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3904 MessageManager.getString("label.problem_reading_tree_file"),
3905 JvOptionPane.WARNING_MESSAGE);
3906 ex.printStackTrace();
3908 if (fin != null && fin.hasWarningMessage())
3910 JvOptionPane.showMessageDialog(Desktop.desktop,
3911 fin.getWarningMessage(),
3913 .getString("label.possible_problem_with_tree_file"),
3914 JvOptionPane.WARNING_MESSAGE);
3919 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3921 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3924 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3925 int h, int x, int y)
3927 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3931 * Add a treeviewer for the tree extracted from a Newick file object to the
3932 * current alignment view
3939 * Associated alignment input data (or null)
3948 * @return TreePanel handle
3950 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3951 AlignmentView input, int w, int h, int x, int y)
3953 TreePanel tp = null;
3959 if (nf.getTree() != null)
3961 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3967 tp.setLocation(x, y);
3970 Desktop.addInternalFrame(tp, treeTitle, w, h);
3972 } catch (Exception ex)
3974 ex.printStackTrace();
3980 private boolean buildingMenu = false;
3983 * Generates menu items and listener event actions for web service clients
3986 public void BuildWebServiceMenu()
3988 while (buildingMenu)
3992 System.err.println("Waiting for building menu to finish.");
3994 } catch (Exception e)
3998 final AlignFrame me = this;
3999 buildingMenu = true;
4000 new Thread(new Runnable()
4005 final List<JMenuItem> legacyItems = new ArrayList<>();
4008 // System.err.println("Building ws menu again "
4009 // + Thread.currentThread());
4010 // TODO: add support for context dependent disabling of services based
4012 // alignment and current selection
4013 // TODO: add additional serviceHandle parameter to specify abstract
4015 // class independently of AbstractName
4016 // TODO: add in rediscovery GUI function to restart discoverer
4017 // TODO: group services by location as well as function and/or
4019 // object broker mechanism.
4020 final Vector<JMenu> wsmenu = new Vector<>();
4021 final IProgressIndicator af = me;
4024 * do not i18n these strings - they are hard-coded in class
4025 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4026 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4028 final JMenu msawsmenu = new JMenu("Alignment");
4029 final JMenu secstrmenu = new JMenu(
4030 "Secondary Structure Prediction");
4031 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4032 final JMenu analymenu = new JMenu("Analysis");
4033 final JMenu dismenu = new JMenu("Protein Disorder");
4034 // JAL-940 - only show secondary structure prediction services from
4035 // the legacy server
4036 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4038 Discoverer.services != null && (Discoverer.services.size() > 0))
4040 // TODO: refactor to allow list of AbstractName/Handler bindings to
4042 // stored or retrieved from elsewhere
4043 // No MSAWS used any more:
4044 // Vector msaws = null; // (Vector)
4045 // Discoverer.services.get("MsaWS");
4046 Vector secstrpr = (Vector) Discoverer.services
4048 if (secstrpr != null)
4050 // Add any secondary structure prediction services
4051 for (int i = 0, j = secstrpr.size(); i < j; i++)
4053 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4055 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4056 .getServiceClient(sh);
4057 int p = secstrmenu.getItemCount();
4058 impl.attachWSMenuEntry(secstrmenu, me);
4059 int q = secstrmenu.getItemCount();
4060 for (int litm = p; litm < q; litm++)
4062 legacyItems.add(secstrmenu.getItem(litm));
4068 // Add all submenus in the order they should appear on the web
4070 wsmenu.add(msawsmenu);
4071 wsmenu.add(secstrmenu);
4072 wsmenu.add(dismenu);
4073 wsmenu.add(analymenu);
4074 // No search services yet
4075 // wsmenu.add(seqsrchmenu);
4077 javax.swing.SwingUtilities.invokeLater(new Runnable()
4084 webService.removeAll();
4085 // first, add discovered services onto the webservices menu
4086 if (wsmenu.size() > 0)
4088 for (int i = 0, j = wsmenu.size(); i < j; i++)
4090 webService.add(wsmenu.get(i));
4095 webService.add(me.webServiceNoServices);
4097 // TODO: move into separate menu builder class.
4098 boolean new_sspred = false;
4099 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4101 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4102 if (jws2servs != null)
4104 if (jws2servs.hasServices())
4106 jws2servs.attachWSMenuEntry(webService, me);
4107 for (Jws2Instance sv : jws2servs.getServices())
4109 if (sv.description.toLowerCase().contains("jpred"))
4111 for (JMenuItem jmi : legacyItems)
4113 jmi.setVisible(false);
4119 if (jws2servs.isRunning())
4121 JMenuItem tm = new JMenuItem(
4122 "Still discovering JABA Services");
4123 tm.setEnabled(false);
4128 build_urlServiceMenu(me.webService);
4129 build_fetchdbmenu(webService);
4130 for (JMenu item : wsmenu)
4132 if (item.getItemCount() == 0)
4134 item.setEnabled(false);
4138 item.setEnabled(true);
4141 } catch (Exception e)
4144 "Exception during web service menu building process.",
4149 } catch (Exception e)
4152 buildingMenu = false;
4159 * construct any groupURL type service menu entries.
4163 private void build_urlServiceMenu(JMenu webService)
4165 // TODO: remove this code when 2.7 is released
4166 // DEBUG - alignmentView
4168 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4169 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4171 * @Override public void actionPerformed(ActionEvent e) {
4172 * jalview.datamodel.AlignmentView
4173 * .testSelectionViews(af.viewport.getAlignment(),
4174 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4176 * }); webService.add(testAlView);
4178 // TODO: refactor to RestClient discoverer and merge menu entries for
4179 // rest-style services with other types of analysis/calculation service
4180 // SHmmr test client - still being implemented.
4181 // DEBUG - alignmentView
4183 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4186 client.attachWSMenuEntry(
4187 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4193 * Searches the alignment sequences for xRefs and builds the Show
4194 * Cross-References menu (formerly called Show Products), with database
4195 * sources for which cross-references are found (protein sources for a
4196 * nucleotide alignment and vice versa)
4198 * @return true if Show Cross-references menu should be enabled
4200 public boolean canShowProducts()
4202 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4203 AlignmentI dataset = viewport.getAlignment().getDataset();
4205 showProducts.removeAll();
4206 final boolean dna = viewport.getAlignment().isNucleotide();
4208 if (seqs == null || seqs.length == 0)
4210 // nothing to see here.
4214 boolean showp = false;
4217 List<String> ptypes = new CrossRef(seqs, dataset)
4218 .findXrefSourcesForSequences(dna);
4220 for (final String source : ptypes)
4223 final AlignFrame af = this;
4224 JMenuItem xtype = new JMenuItem(source);
4225 xtype.addActionListener(new ActionListener()
4228 public void actionPerformed(ActionEvent e)
4230 showProductsFor(af.viewport.getSequenceSelection(), dna,
4234 showProducts.add(xtype);
4236 showProducts.setVisible(showp);
4237 showProducts.setEnabled(showp);
4238 } catch (Exception e)
4241 "canShowProducts threw an exception - please report to help@jalview.org",
4249 * Finds and displays cross-references for the selected sequences (protein
4250 * products for nucleotide sequences, dna coding sequences for peptides).
4253 * the sequences to show cross-references for
4255 * true if from a nucleotide alignment (so showing proteins)
4257 * the database to show cross-references for
4259 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4260 final String source)
4262 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4267 * Construct and display a new frame containing the translation of this
4268 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4271 public void showTranslation_actionPerformed(ActionEvent e)
4273 AlignmentI al = null;
4276 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4278 al = dna.translateCdna();
4279 } catch (Exception ex)
4281 jalview.bin.Cache.log.error(
4282 "Exception during translation. Please report this !", ex);
4283 final String msg = MessageManager.getString(
4284 "label.error_when_translating_sequences_submit_bug_report");
4285 final String errorTitle = MessageManager
4286 .getString("label.implementation_error")
4287 + MessageManager.getString("label.translation_failed");
4288 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4289 JvOptionPane.ERROR_MESSAGE);
4292 if (al == null || al.getHeight() == 0)
4294 final String msg = MessageManager.getString(
4295 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4296 final String errorTitle = MessageManager
4297 .getString("label.translation_failed");
4298 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4299 JvOptionPane.WARNING_MESSAGE);
4303 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4304 af.setFileFormat(this.currentFileFormat);
4305 final String newTitle = MessageManager
4306 .formatMessage("label.translation_of_params", new Object[]
4307 { this.getTitle() });
4308 af.setTitle(newTitle);
4309 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4311 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4312 viewport.openSplitFrame(af, new Alignment(seqs));
4316 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4323 * Set the file format
4327 public void setFileFormat(FileFormatI format)
4329 this.currentFileFormat = format;
4333 * Try to load a features file onto the alignment.
4336 * contents or path to retrieve file
4338 * access mode of file (see jalview.io.AlignFile)
4339 * @return true if features file was parsed correctly.
4341 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4343 return avc.parseFeaturesFile(file, sourceType,
4344 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4349 public void refreshFeatureUI(boolean enableIfNecessary)
4351 // note - currently this is only still here rather than in the controller
4352 // because of the featureSettings hard reference that is yet to be
4354 if (enableIfNecessary)
4356 viewport.setShowSequenceFeatures(true);
4357 showSeqFeatures.setSelected(true);
4363 public void dragEnter(DropTargetDragEvent evt)
4368 public void dragExit(DropTargetEvent evt)
4373 public void dragOver(DropTargetDragEvent evt)
4378 public void dropActionChanged(DropTargetDragEvent evt)
4383 public void drop(DropTargetDropEvent evt)
4385 // JAL-1552 - acceptDrop required before getTransferable call for
4386 // Java's Transferable for native dnd
4387 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4388 Transferable t = evt.getTransferable();
4389 final AlignFrame thisaf = this;
4390 final List<String> files = new ArrayList<>();
4391 List<DataSourceType> protocols = new ArrayList<>();
4395 Desktop.transferFromDropTarget(files, protocols, evt, t);
4396 } catch (Exception e)
4398 e.printStackTrace();
4402 new Thread(new Runnable()
4409 // check to see if any of these files have names matching sequences
4412 SequenceIdMatcher idm = new SequenceIdMatcher(
4413 viewport.getAlignment().getSequencesArray());
4415 * Object[] { String,SequenceI}
4417 ArrayList<Object[]> filesmatched = new ArrayList<>();
4418 ArrayList<String> filesnotmatched = new ArrayList<>();
4419 for (int i = 0; i < files.size(); i++)
4421 String file = files.get(i).toString();
4423 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4424 if (protocol == DataSourceType.FILE)
4426 File fl = new File(file);
4427 pdbfn = fl.getName();
4429 else if (protocol == DataSourceType.URL)
4431 URL url = new URL(file);
4432 pdbfn = url.getFile();
4434 if (pdbfn.length() > 0)
4436 // attempt to find a match in the alignment
4437 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4438 int l = 0, c = pdbfn.indexOf(".");
4439 while (mtch == null && c != -1)
4444 } while ((c = pdbfn.indexOf(".", l)) > l);
4447 pdbfn = pdbfn.substring(0, l);
4449 mtch = idm.findAllIdMatches(pdbfn);
4453 FileFormatI type = null;
4456 type = new IdentifyFile().identify(file, protocol);
4457 } catch (Exception ex)
4461 if (type != null && type.isStructureFile())
4463 filesmatched.add(new Object[] { file, protocol, mtch });
4467 // File wasn't named like one of the sequences or wasn't a PDB
4469 filesnotmatched.add(file);
4473 if (filesmatched.size() > 0)
4475 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4476 || JvOptionPane.showConfirmDialog(thisaf,
4477 MessageManager.formatMessage(
4478 "label.automatically_associate_structure_files_with_sequences_same_name",
4480 { Integer.valueOf(filesmatched.size())
4482 MessageManager.getString(
4483 "label.automatically_associate_structure_files_by_name"),
4484 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4487 for (Object[] fm : filesmatched)
4489 // try and associate
4490 // TODO: may want to set a standard ID naming formalism for
4491 // associating PDB files which have no IDs.
4492 for (SequenceI toassoc : (SequenceI[]) fm[2])
4494 PDBEntry pe = new AssociatePdbFileWithSeq()
4495 .associatePdbWithSeq((String) fm[0],
4496 (DataSourceType) fm[1], toassoc, false,
4500 System.err.println("Associated file : "
4501 + ((String) fm[0]) + " with "
4502 + toassoc.getDisplayId(true));
4506 alignPanel.paintAlignment(true);
4510 if (filesnotmatched.size() > 0)
4512 if (assocfiles > 0 && (Cache.getDefault(
4513 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4514 || JvOptionPane.showConfirmDialog(thisaf,
4515 "<html>" + MessageManager.formatMessage(
4516 "label.ignore_unmatched_dropped_files_info",
4519 filesnotmatched.size())
4522 MessageManager.getString(
4523 "label.ignore_unmatched_dropped_files"),
4524 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4528 for (String fn : filesnotmatched)
4530 loadJalviewDataFile(fn, null, null, null);
4534 } catch (Exception ex)
4536 ex.printStackTrace();
4544 * Attempt to load a "dropped" file or URL string, by testing in turn for
4546 * <li>an Annotation file</li>
4547 * <li>a JNet file</li>
4548 * <li>a features file</li>
4549 * <li>else try to interpret as an alignment file</li>
4553 * either a filename or a URL string.
4555 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4556 FileFormatI format, SequenceI assocSeq)
4560 if (sourceType == null)
4562 sourceType = FormatAdapter.checkProtocol(file);
4564 // if the file isn't identified, or not positively identified as some
4565 // other filetype (PFAM is default unidentified alignment file type) then
4566 // try to parse as annotation.
4567 boolean isAnnotation = (format == null
4568 || FileFormat.Pfam.equals(format))
4569 ? new AnnotationFile().annotateAlignmentView(viewport,
4575 // first see if its a T-COFFEE score file
4576 TCoffeeScoreFile tcf = null;
4579 tcf = new TCoffeeScoreFile(file, sourceType);
4582 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4586 new TCoffeeColourScheme(viewport.getAlignment()));
4587 isAnnotation = true;
4588 statusBar.setText(MessageManager.getString(
4589 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4593 // some problem - if no warning its probable that the ID matching
4594 // process didn't work
4595 JvOptionPane.showMessageDialog(Desktop.desktop,
4596 tcf.getWarningMessage() == null
4597 ? MessageManager.getString(
4598 "label.check_file_matches_sequence_ids_alignment")
4599 : tcf.getWarningMessage(),
4600 MessageManager.getString(
4601 "label.problem_reading_tcoffee_score_file"),
4602 JvOptionPane.WARNING_MESSAGE);
4609 } catch (Exception x)
4612 "Exception when processing data source as T-COFFEE score file",
4618 // try to see if its a JNet 'concise' style annotation file *before*
4620 // try to parse it as a features file
4623 format = new IdentifyFile().identify(file, sourceType);
4625 if (FileFormat.ScoreMatrix == format)
4627 ScoreMatrixFile sm = new ScoreMatrixFile(
4628 new FileParse(file, sourceType));
4630 // todo: i18n this message
4631 statusBar.setText(MessageManager.formatMessage(
4632 "label.successfully_loaded_matrix",
4633 sm.getMatrixName()));
4635 else if (FileFormat.Jnet.equals(format))
4637 JPredFile predictions = new JPredFile(file, sourceType);
4638 new JnetAnnotationMaker();
4639 JnetAnnotationMaker.add_annotation(predictions,
4640 viewport.getAlignment(), 0, false);
4641 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4642 viewport.getAlignment().setSeqrep(repseq);
4643 HiddenColumns cs = new HiddenColumns();
4644 cs.hideInsertionsFor(repseq);
4645 viewport.getAlignment().setHiddenColumns(cs);
4646 isAnnotation = true;
4648 // else if (IdentifyFile.FeaturesFile.equals(format))
4649 else if (FileFormat.Features.equals(format))
4651 if (parseFeaturesFile(file, sourceType))
4653 alignPanel.paintAlignment(true);
4658 new FileLoader().LoadFile(viewport, file, sourceType, format);
4665 alignPanel.adjustAnnotationHeight();
4666 viewport.updateSequenceIdColours();
4667 buildSortByAnnotationScoresMenu();
4668 alignPanel.paintAlignment(true);
4670 } catch (Exception ex)
4672 ex.printStackTrace();
4673 } catch (OutOfMemoryError oom)
4678 } catch (Exception x)
4683 + (sourceType != null
4684 ? (sourceType == DataSourceType.PASTE
4686 : "using " + sourceType + " from "
4690 ? "(parsing as '" + format + "' file)"
4692 oom, Desktop.desktop);
4697 * Method invoked by the ChangeListener on the tabbed pane, in other words
4698 * when a different tabbed pane is selected by the user or programmatically.
4701 public void tabSelectionChanged(int index)
4705 alignPanel = alignPanels.get(index);
4706 viewport = alignPanel.av;
4707 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4708 setMenusFromViewport(viewport);
4712 * 'focus' any colour slider that is open to the selected viewport
4714 if (viewport.getConservationSelected())
4716 SliderPanel.setConservationSlider(alignPanel,
4717 viewport.getResidueShading(), alignPanel.getViewName());
4721 SliderPanel.hideConservationSlider();
4723 if (viewport.getAbovePIDThreshold())
4725 SliderPanel.setPIDSliderSource(alignPanel,
4726 viewport.getResidueShading(), alignPanel.getViewName());
4730 SliderPanel.hidePIDSlider();
4734 * If there is a frame linked to this one in a SplitPane, switch it to the
4735 * same view tab index. No infinite recursion of calls should happen, since
4736 * tabSelectionChanged() should not get invoked on setting the selected
4737 * index to an unchanged value. Guard against setting an invalid index
4738 * before the new view peer tab has been created.
4740 final AlignViewportI peer = viewport.getCodingComplement();
4743 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4744 .getAlignPanel().alignFrame;
4745 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4747 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4753 * On right mouse click on view tab, prompt for and set new view name.
4756 public void tabbedPane_mousePressed(MouseEvent e)
4758 if (e.isPopupTrigger())
4760 String msg = MessageManager.getString("label.enter_view_name");
4761 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4762 JvOptionPane.QUESTION_MESSAGE);
4766 viewport.viewName = reply;
4767 // TODO warn if reply is in getExistingViewNames()?
4768 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4773 public AlignViewport getCurrentView()
4779 * Open the dialog for regex description parsing.
4782 protected void extractScores_actionPerformed(ActionEvent e)
4784 ParseProperties pp = new jalview.analysis.ParseProperties(
4785 viewport.getAlignment());
4786 // TODO: verify regex and introduce GUI dialog for version 2.5
4787 // if (pp.getScoresFromDescription("col", "score column ",
4788 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4790 if (pp.getScoresFromDescription("description column",
4791 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4793 buildSortByAnnotationScoresMenu();
4801 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4805 protected void showDbRefs_actionPerformed(ActionEvent e)
4807 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4813 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4817 protected void showNpFeats_actionPerformed(ActionEvent e)
4819 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4823 * find the viewport amongst the tabs in this alignment frame and close that
4828 public boolean closeView(AlignViewportI av)
4832 this.closeMenuItem_actionPerformed(false);
4835 Component[] comp = tabbedPane.getComponents();
4836 for (int i = 0; comp != null && i < comp.length; i++)
4838 if (comp[i] instanceof AlignmentPanel)
4840 if (((AlignmentPanel) comp[i]).av == av)
4843 closeView((AlignmentPanel) comp[i]);
4851 protected void build_fetchdbmenu(JMenu webService)
4853 // Temporary hack - DBRef Fetcher always top level ws entry.
4854 // TODO We probably want to store a sequence database checklist in
4855 // preferences and have checkboxes.. rather than individual sources selected
4857 final JMenu rfetch = new JMenu(
4858 MessageManager.getString("action.fetch_db_references"));
4859 rfetch.setToolTipText(MessageManager.getString(
4860 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4861 webService.add(rfetch);
4863 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4864 MessageManager.getString("option.trim_retrieved_seqs"));
4865 trimrs.setToolTipText(
4866 MessageManager.getString("label.trim_retrieved_sequences"));
4867 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4868 trimrs.addActionListener(new ActionListener()
4871 public void actionPerformed(ActionEvent e)
4873 trimrs.setSelected(trimrs.isSelected());
4874 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4875 Boolean.valueOf(trimrs.isSelected()).toString());
4879 JMenuItem fetchr = new JMenuItem(
4880 MessageManager.getString("label.standard_databases"));
4881 fetchr.setToolTipText(
4882 MessageManager.getString("label.fetch_embl_uniprot"));
4883 fetchr.addActionListener(new ActionListener()
4887 public void actionPerformed(ActionEvent e)
4889 new Thread(new Runnable()
4894 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4895 .getAlignment().isNucleotide();
4896 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4897 alignPanel.av.getSequenceSelection(),
4898 alignPanel.alignFrame, null,
4899 alignPanel.alignFrame.featureSettings, isNucleotide);
4900 dbRefFetcher.addListener(new FetchFinishedListenerI()
4903 public void finished()
4905 AlignFrame.this.setMenusForViewport();
4908 dbRefFetcher.fetchDBRefs(false);
4916 final AlignFrame me = this;
4917 new Thread(new Runnable()
4922 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4923 .getSequenceFetcherSingleton(me);
4924 javax.swing.SwingUtilities.invokeLater(new Runnable()
4929 String[] dbclasses = sf.getOrderedSupportedSources();
4930 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4931 // jalview.util.QuickSort.sort(otherdb, otherdb);
4932 List<DbSourceProxy> otherdb;
4933 JMenu dfetch = new JMenu();
4934 JMenu ifetch = new JMenu();
4935 JMenuItem fetchr = null;
4936 int comp = 0, icomp = 0, mcomp = 15;
4937 String mname = null;
4939 for (String dbclass : dbclasses)
4941 otherdb = sf.getSourceProxy(dbclass);
4942 // add a single entry for this class, or submenu allowing 'fetch
4944 if (otherdb == null || otherdb.size() < 1)
4948 // List<DbSourceProxy> dbs=otherdb;
4949 // otherdb=new ArrayList<DbSourceProxy>();
4950 // for (DbSourceProxy db:dbs)
4952 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4956 mname = "From " + dbclass;
4958 if (otherdb.size() == 1)
4960 final DbSourceProxy[] dassource = otherdb
4961 .toArray(new DbSourceProxy[0]);
4962 DbSourceProxy src = otherdb.get(0);
4963 fetchr = new JMenuItem(src.getDbSource());
4964 fetchr.addActionListener(new ActionListener()
4968 public void actionPerformed(ActionEvent e)
4970 new Thread(new Runnable()
4976 boolean isNucleotide = alignPanel.alignFrame
4977 .getViewport().getAlignment()
4979 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4980 alignPanel.av.getSequenceSelection(),
4981 alignPanel.alignFrame, dassource,
4982 alignPanel.alignFrame.featureSettings,
4985 .addListener(new FetchFinishedListenerI()
4988 public void finished()
4990 AlignFrame.this.setMenusForViewport();
4993 dbRefFetcher.fetchDBRefs(false);
4999 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5000 MessageManager.formatMessage(
5001 "label.fetch_retrieve_from", new Object[]
5002 { src.getDbName() })));
5008 final DbSourceProxy[] dassource = otherdb
5009 .toArray(new DbSourceProxy[0]);
5011 DbSourceProxy src = otherdb.get(0);
5012 fetchr = new JMenuItem(MessageManager
5013 .formatMessage("label.fetch_all_param", new Object[]
5014 { src.getDbSource() }));
5015 fetchr.addActionListener(new ActionListener()
5018 public void actionPerformed(ActionEvent e)
5020 new Thread(new Runnable()
5026 boolean isNucleotide = alignPanel.alignFrame
5027 .getViewport().getAlignment()
5029 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5030 alignPanel.av.getSequenceSelection(),
5031 alignPanel.alignFrame, dassource,
5032 alignPanel.alignFrame.featureSettings,
5035 .addListener(new FetchFinishedListenerI()
5038 public void finished()
5040 AlignFrame.this.setMenusForViewport();
5043 dbRefFetcher.fetchDBRefs(false);
5049 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5050 MessageManager.formatMessage(
5051 "label.fetch_retrieve_from_all_sources",
5053 { Integer.valueOf(otherdb.size())
5055 src.getDbSource(), src.getDbName() })));
5058 // and then build the rest of the individual menus
5059 ifetch = new JMenu(MessageManager.formatMessage(
5060 "label.source_from_db_source", new Object[]
5061 { src.getDbSource() }));
5063 String imname = null;
5065 for (DbSourceProxy sproxy : otherdb)
5067 String dbname = sproxy.getDbName();
5068 String sname = dbname.length() > 5
5069 ? dbname.substring(0, 5) + "..."
5071 String msname = dbname.length() > 10
5072 ? dbname.substring(0, 10) + "..."
5076 imname = MessageManager
5077 .formatMessage("label.from_msname", new Object[]
5080 fetchr = new JMenuItem(msname);
5081 final DbSourceProxy[] dassrc = { sproxy };
5082 fetchr.addActionListener(new ActionListener()
5086 public void actionPerformed(ActionEvent e)
5088 new Thread(new Runnable()
5094 boolean isNucleotide = alignPanel.alignFrame
5095 .getViewport().getAlignment()
5097 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5098 alignPanel.av.getSequenceSelection(),
5099 alignPanel.alignFrame, dassrc,
5100 alignPanel.alignFrame.featureSettings,
5103 .addListener(new FetchFinishedListenerI()
5106 public void finished()
5108 AlignFrame.this.setMenusForViewport();
5111 dbRefFetcher.fetchDBRefs(false);
5117 fetchr.setToolTipText(
5118 "<html>" + MessageManager.formatMessage(
5119 "label.fetch_retrieve_from", new Object[]
5123 if (++icomp >= mcomp || i == (otherdb.size()))
5125 ifetch.setText(MessageManager.formatMessage(
5126 "label.source_to_target", imname, sname));
5128 ifetch = new JMenu();
5136 if (comp >= mcomp || dbi >= (dbclasses.length))
5138 dfetch.setText(MessageManager.formatMessage(
5139 "label.source_to_target", mname, dbclass));
5141 dfetch = new JMenu();
5154 * Left justify the whole alignment.
5157 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5159 AlignmentI al = viewport.getAlignment();
5161 viewport.firePropertyChange("alignment", null, al);
5165 * Right justify the whole alignment.
5168 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5170 AlignmentI al = viewport.getAlignment();
5172 viewport.firePropertyChange("alignment", null, al);
5176 public void setShowSeqFeatures(boolean b)
5178 showSeqFeatures.setSelected(b);
5179 viewport.setShowSequenceFeatures(b);
5186 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5187 * awt.event.ActionEvent)
5190 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5192 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5193 alignPanel.paintAlignment(true);
5200 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5204 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5206 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5207 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5215 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5216 * .event.ActionEvent)
5219 protected void showGroupConservation_actionPerformed(ActionEvent e)
5221 viewport.setShowGroupConservation(showGroupConservation.getState());
5222 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5229 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5230 * .event.ActionEvent)
5233 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5235 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5236 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5243 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5244 * .event.ActionEvent)
5247 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5249 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5250 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5254 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5256 showSequenceLogo.setState(true);
5257 viewport.setShowSequenceLogo(true);
5258 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5259 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5263 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5265 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5272 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5273 * .event.ActionEvent)
5276 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5278 if (avc.makeGroupsFromSelection())
5280 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5281 alignPanel.updateAnnotation();
5282 alignPanel.paintAlignment(true);
5286 public void clearAlignmentSeqRep()
5288 // TODO refactor alignmentseqrep to controller
5289 if (viewport.getAlignment().hasSeqrep())
5291 viewport.getAlignment().setSeqrep(null);
5292 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5293 alignPanel.updateAnnotation();
5294 alignPanel.paintAlignment(true);
5299 protected void createGroup_actionPerformed(ActionEvent e)
5301 if (avc.createGroup())
5303 alignPanel.alignmentChanged();
5308 protected void unGroup_actionPerformed(ActionEvent e)
5312 alignPanel.alignmentChanged();
5317 * make the given alignmentPanel the currently selected tab
5319 * @param alignmentPanel
5321 public void setDisplayedView(AlignmentPanel alignmentPanel)
5323 if (!viewport.getSequenceSetId()
5324 .equals(alignmentPanel.av.getSequenceSetId()))
5326 throw new Error(MessageManager.getString(
5327 "error.implementation_error_cannot_show_view_alignment_frame"));
5329 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5330 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5332 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5337 * Action on selection of menu options to Show or Hide annotations.
5340 * @param forSequences
5341 * update sequence-related annotations
5342 * @param forAlignment
5343 * update non-sequence-related annotations
5346 protected void setAnnotationsVisibility(boolean visible,
5347 boolean forSequences, boolean forAlignment)
5349 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5350 .getAlignmentAnnotation();
5355 for (AlignmentAnnotation aa : anns)
5358 * don't display non-positional annotations on an alignment
5360 if (aa.annotations == null)
5364 boolean apply = (aa.sequenceRef == null && forAlignment)
5365 || (aa.sequenceRef != null && forSequences);
5368 aa.visible = visible;
5371 alignPanel.validateAnnotationDimensions(true);
5372 alignPanel.alignmentChanged();
5376 * Store selected annotation sort order for the view and repaint.
5379 protected void sortAnnotations_actionPerformed()
5381 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5383 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5384 alignPanel.paintAlignment(true);
5389 * @return alignment panels in this alignment frame
5391 public List<? extends AlignmentViewPanel> getAlignPanels()
5393 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5397 * Open a new alignment window, with the cDNA associated with this (protein)
5398 * alignment, aligned as is the protein.
5400 protected void viewAsCdna_actionPerformed()
5402 // TODO no longer a menu action - refactor as required
5403 final AlignmentI alignment = getViewport().getAlignment();
5404 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5405 if (mappings == null)
5409 List<SequenceI> cdnaSeqs = new ArrayList<>();
5410 for (SequenceI aaSeq : alignment.getSequences())
5412 for (AlignedCodonFrame acf : mappings)
5414 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5418 * There is a cDNA mapping for this protein sequence - add to new
5419 * alignment. It will share the same dataset sequence as other mapped
5420 * cDNA (no new mappings need to be created).
5422 final Sequence newSeq = new Sequence(dnaSeq);
5423 newSeq.setDatasetSequence(dnaSeq);
5424 cdnaSeqs.add(newSeq);
5428 if (cdnaSeqs.size() == 0)
5430 // show a warning dialog no mapped cDNA
5433 AlignmentI cdna = new Alignment(
5434 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5435 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5436 AlignFrame.DEFAULT_HEIGHT);
5437 cdna.alignAs(alignment);
5438 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5440 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5441 AlignFrame.DEFAULT_HEIGHT);
5445 * Set visibility of dna/protein complement view (available when shown in a
5451 protected void showComplement_actionPerformed(boolean show)
5453 SplitContainerI sf = getSplitViewContainer();
5456 sf.setComplementVisible(this, show);
5461 * Generate the reverse (optionally complemented) of the selected sequences,
5462 * and add them to the alignment
5465 protected void showReverse_actionPerformed(boolean complement)
5467 AlignmentI al = null;
5470 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5471 al = dna.reverseCdna(complement);
5472 viewport.addAlignment(al, "");
5473 addHistoryItem(new EditCommand(
5474 MessageManager.getString("label.add_sequences"), Action.PASTE,
5475 al.getSequencesArray(), 0, al.getWidth(),
5476 viewport.getAlignment()));
5477 } catch (Exception ex)
5479 System.err.println(ex.getMessage());
5485 * Try to run a script in the Groovy console, having first ensured that this
5486 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5487 * be targeted at this alignment.
5490 protected void runGroovy_actionPerformed()
5492 Jalview.setCurrentAlignFrame(this);
5493 groovy.ui.Console console = Desktop.getGroovyConsole();
5494 if (console != null)
5498 console.runScript();
5499 } catch (Exception ex)
5501 System.err.println((ex.toString()));
5502 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5503 MessageManager.getString("label.couldnt_run_groovy_script"),
5504 MessageManager.getString("label.groovy_support_failed"),
5505 JvOptionPane.ERROR_MESSAGE);
5510 System.err.println("Can't run Groovy script as console not found");
5515 * Hides columns containing (or not containing) a specified feature, provided
5516 * that would not leave all columns hidden
5518 * @param featureType
5519 * @param columnsContaining
5522 public boolean hideFeatureColumns(String featureType,
5523 boolean columnsContaining)
5525 boolean notForHiding = avc.markColumnsContainingFeatures(
5526 columnsContaining, false, false, featureType);
5529 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5530 false, featureType))
5532 getViewport().hideSelectedColumns();
5540 protected void selectHighlightedColumns_actionPerformed(
5541 ActionEvent actionEvent)
5543 // include key modifier check in case user selects from menu
5544 avc.markHighlightedColumns(
5545 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5546 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5547 | ActionEvent.CTRL_MASK)) != 0);
5551 * Rebuilds the Colour menu, including any user-defined colours which have
5552 * been loaded either on startup or during the session
5554 public void buildColourMenu()
5556 colourMenu.removeAll();
5558 colourMenu.add(applyToAllGroups);
5559 colourMenu.add(textColour);
5560 colourMenu.addSeparator();
5562 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5565 colourMenu.addSeparator();
5566 colourMenu.add(conservationMenuItem);
5567 colourMenu.add(modifyConservation);
5568 colourMenu.add(abovePIDThreshold);
5569 colourMenu.add(modifyPID);
5570 colourMenu.add(annotationColour);
5572 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5573 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5577 * Open a dialog (if not already open) that allows the user to select and
5578 * calculate PCA or Tree analysis
5580 protected void openTreePcaDialog()
5582 if (alignPanel.getCalculationDialog() == null)
5584 new CalculationChooser(AlignFrame.this);
5589 class PrintThread extends Thread
5593 public PrintThread(AlignmentPanel ap)
5598 static PageFormat pf;
5603 PrinterJob printJob = PrinterJob.getPrinterJob();
5607 printJob.setPrintable(ap, pf);
5611 printJob.setPrintable(ap);
5614 if (printJob.printDialog())
5619 } catch (Exception PrintException)
5621 PrintException.printStackTrace();