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.JInternalFrame;
138 import javax.swing.JLayeredPane;
139 import javax.swing.JMenu;
140 import javax.swing.JMenuItem;
141 import javax.swing.SwingUtilities;
147 * @version $Revision$
149 public class AlignFrame extends GAlignFrame implements DropTargetListener,
150 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
153 public static final int DEFAULT_WIDTH = 700;
155 public static final int DEFAULT_HEIGHT = 500;
158 * The currently displayed panel (selected tabbed view if more than one)
160 public AlignmentPanel alignPanel;
162 AlignViewport viewport;
164 public AlignViewControllerI avc;
166 List<AlignmentPanel> alignPanels = new ArrayList<>();
169 * Last format used to load or save alignments in this window
171 FileFormatI currentFileFormat = null;
174 * Current filename for this alignment
176 String fileName = null;
179 * Creates a new AlignFrame object with specific width and height.
185 public AlignFrame(AlignmentI al, int width, int height)
187 this(al, null, width, height);
191 * Creates a new AlignFrame object with specific width, height and
197 * @param sequenceSetId
199 public AlignFrame(AlignmentI al, int width, int height,
200 String sequenceSetId)
202 this(al, null, width, height, sequenceSetId);
206 * Creates a new AlignFrame object with specific width, height and
212 * @param sequenceSetId
215 public AlignFrame(AlignmentI al, int width, int height,
216 String sequenceSetId, String viewId)
218 this(al, null, width, height, sequenceSetId, viewId);
222 * new alignment window with hidden columns
226 * @param hiddenColumns
227 * ColumnSelection or null
229 * Width of alignment frame
233 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
236 this(al, hiddenColumns, width, height, null);
240 * Create alignment frame for al with hiddenColumns, a specific width and
241 * height, and specific sequenceId
244 * @param hiddenColumns
247 * @param sequenceSetId
250 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
251 int height, String sequenceSetId)
253 this(al, hiddenColumns, width, height, sequenceSetId, null);
257 * Create alignment frame for al with hiddenColumns, a specific width and
258 * height, and specific sequenceId
261 * @param hiddenColumns
264 * @param sequenceSetId
269 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
270 int height, String sequenceSetId, String viewId)
272 setSize(width, height);
274 if (al.getDataset() == null)
279 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
281 alignPanel = new AlignmentPanel(this, viewport);
283 addAlignmentPanel(alignPanel, true);
287 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
288 HiddenColumns hiddenColumns, int width, int height)
290 setSize(width, height);
292 if (al.getDataset() == null)
297 viewport = new AlignViewport(al, hiddenColumns);
299 if (hiddenSeqs != null && hiddenSeqs.length > 0)
301 viewport.hideSequence(hiddenSeqs);
303 alignPanel = new AlignmentPanel(this, viewport);
304 addAlignmentPanel(alignPanel, true);
309 * Make a new AlignFrame from existing alignmentPanels
316 public AlignFrame(AlignmentPanel ap)
320 addAlignmentPanel(ap, false);
325 * initalise the alignframe from the underlying viewport data and the
330 if (!Jalview.isHeadlessMode())
332 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
335 avc = new jalview.controller.AlignViewController(this, viewport,
337 if (viewport.getAlignmentConservationAnnotation() == null)
339 // BLOSUM62Colour.setEnabled(false);
340 conservationMenuItem.setEnabled(false);
341 modifyConservation.setEnabled(false);
342 // PIDColour.setEnabled(false);
343 // abovePIDThreshold.setEnabled(false);
344 // modifyPID.setEnabled(false);
347 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
350 if (sortby.equals("Id"))
352 sortIDMenuItem_actionPerformed(null);
354 else if (sortby.equals("Pairwise Identity"))
356 sortPairwiseMenuItem_actionPerformed(null);
360 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
362 setMenusFromViewport(viewport);
363 buildSortByAnnotationScoresMenu();
364 calculateTree.addActionListener(new ActionListener()
368 public void actionPerformed(ActionEvent e)
375 if (Desktop.desktop != null)
377 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
378 addServiceListeners();
382 if (viewport.getWrapAlignment())
384 wrapMenuItem_actionPerformed(null);
387 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
389 this.overviewMenuItem_actionPerformed(null);
394 final List<AlignmentPanel> selviews = new ArrayList<>();
395 final List<AlignmentPanel> origview = new ArrayList<>();
396 final String menuLabel = MessageManager
397 .getString("label.copy_format_from");
398 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
399 new ViewSetProvider()
403 public AlignmentPanel[] getAllAlignmentPanels()
406 origview.add(alignPanel);
407 // make an array of all alignment panels except for this one
408 List<AlignmentPanel> aps = new ArrayList<>(
409 Arrays.asList(Desktop.getAlignmentPanels(null)));
410 aps.remove(AlignFrame.this.alignPanel);
411 return aps.toArray(new AlignmentPanel[aps.size()]);
413 }, selviews, new ItemListener()
417 public void itemStateChanged(ItemEvent e)
419 if (origview.size() > 0)
421 final AlignmentPanel ap = origview.get(0);
424 * Copy the ViewStyle of the selected panel to 'this one'.
425 * Don't change value of 'scaleProteinAsCdna' unless copying
428 ViewStyleI vs = selviews.get(0).getAlignViewport()
430 boolean fromSplitFrame = selviews.get(0)
431 .getAlignViewport().getCodingComplement() != null;
434 vs.setScaleProteinAsCdna(ap.getAlignViewport()
435 .getViewStyle().isScaleProteinAsCdna());
437 ap.getAlignViewport().setViewStyle(vs);
440 * Also rescale ViewStyle of SplitFrame complement if there is
441 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
442 * the whole ViewStyle (allow cDNA protein to have different
445 AlignViewportI complement = ap.getAlignViewport()
446 .getCodingComplement();
447 if (complement != null && vs.isScaleProteinAsCdna())
449 AlignFrame af = Desktop.getAlignFrameFor(complement);
450 ((SplitFrame) af.getSplitViewContainer())
452 af.setMenusForViewport();
456 ap.setSelected(true);
457 ap.alignFrame.setMenusForViewport();
462 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
463 .indexOf("devel") > -1
464 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
465 .indexOf("test") > -1)
467 formatMenu.add(vsel);
469 addFocusListener(new FocusAdapter()
472 public void focusGained(FocusEvent e)
474 Jalview.setCurrentAlignFrame(AlignFrame.this);
481 * Change the filename and format for the alignment, and enable the 'reload'
482 * button functionality.
489 public void setFileName(String file, FileFormatI format)
492 setFileFormat(format);
493 reload.setEnabled(true);
497 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
500 void addKeyListener()
502 addKeyListener(new KeyAdapter()
505 public void keyPressed(KeyEvent evt)
507 if (viewport.cursorMode
508 && ((evt.getKeyCode() >= KeyEvent.VK_0
509 && evt.getKeyCode() <= KeyEvent.VK_9)
510 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
511 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
512 && Character.isDigit(evt.getKeyChar()))
514 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
517 switch (evt.getKeyCode())
520 case 27: // escape key
521 deselectAllSequenceMenuItem_actionPerformed(null);
525 case KeyEvent.VK_DOWN:
526 if (evt.isAltDown() || !viewport.cursorMode)
528 moveSelectedSequences(false);
530 if (viewport.cursorMode)
532 alignPanel.getSeqPanel().moveCursor(0, 1);
537 if (evt.isAltDown() || !viewport.cursorMode)
539 moveSelectedSequences(true);
541 if (viewport.cursorMode)
543 alignPanel.getSeqPanel().moveCursor(0, -1);
548 case KeyEvent.VK_LEFT:
549 if (evt.isAltDown() || !viewport.cursorMode)
551 slideSequences(false,
552 alignPanel.getSeqPanel().getKeyboardNo1());
556 alignPanel.getSeqPanel().moveCursor(-1, 0);
561 case KeyEvent.VK_RIGHT:
562 if (evt.isAltDown() || !viewport.cursorMode)
564 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
568 alignPanel.getSeqPanel().moveCursor(1, 0);
572 case KeyEvent.VK_SPACE:
573 if (viewport.cursorMode)
575 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
576 || evt.isShiftDown() || evt.isAltDown());
580 // case KeyEvent.VK_A:
581 // if (viewport.cursorMode)
583 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
584 // //System.out.println("A");
588 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
589 * System.out.println("closing bracket"); } break;
591 case KeyEvent.VK_DELETE:
592 case KeyEvent.VK_BACK_SPACE:
593 if (!viewport.cursorMode)
595 cut_actionPerformed(null);
599 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
600 || evt.isShiftDown() || evt.isAltDown());
606 if (viewport.cursorMode)
608 alignPanel.getSeqPanel().setCursorRow();
612 if (viewport.cursorMode && !evt.isControlDown())
614 alignPanel.getSeqPanel().setCursorColumn();
618 if (viewport.cursorMode)
620 alignPanel.getSeqPanel().setCursorPosition();
624 case KeyEvent.VK_ENTER:
625 case KeyEvent.VK_COMMA:
626 if (viewport.cursorMode)
628 alignPanel.getSeqPanel().setCursorRowAndColumn();
633 if (viewport.cursorMode)
635 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
639 if (viewport.cursorMode)
641 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
646 viewport.cursorMode = !viewport.cursorMode;
647 statusBar.setText(MessageManager
648 .formatMessage("label.keyboard_editing_mode", new String[]
649 { (viewport.cursorMode ? "on" : "off") }));
650 if (viewport.cursorMode)
652 ViewportRanges ranges = viewport.getRanges();
653 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
655 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
658 alignPanel.getSeqPanel().seqCanvas.repaint();
664 Help.showHelpWindow();
665 } catch (Exception ex)
667 ex.printStackTrace();
672 boolean toggleSeqs = !evt.isControlDown();
673 boolean toggleCols = !evt.isShiftDown();
674 toggleHiddenRegions(toggleSeqs, toggleCols);
679 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
680 boolean modifyExisting = true; // always modify, don't clear
681 // evt.isShiftDown();
682 boolean invertHighlighted = evt.isAltDown();
683 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
687 case KeyEvent.VK_PAGE_UP:
688 viewport.getRanges().pageUp();
690 case KeyEvent.VK_PAGE_DOWN:
691 viewport.getRanges().pageDown();
697 public void keyReleased(KeyEvent evt)
699 switch (evt.getKeyCode())
701 case KeyEvent.VK_LEFT:
702 if (evt.isAltDown() || !viewport.cursorMode)
704 viewport.firePropertyChange("alignment", null,
705 viewport.getAlignment().getSequences());
709 case KeyEvent.VK_RIGHT:
710 if (evt.isAltDown() || !viewport.cursorMode)
712 viewport.firePropertyChange("alignment", null,
713 viewport.getAlignment().getSequences());
721 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
723 ap.alignFrame = this;
724 avc = new jalview.controller.AlignViewController(this, viewport,
729 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
731 int aSize = alignPanels.size();
733 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
735 if (aSize == 1 && ap.av.viewName == null)
737 this.getContentPane().add(ap, BorderLayout.CENTER);
743 setInitialTabVisible();
746 expandViews.setEnabled(true);
747 gatherViews.setEnabled(true);
748 tabbedPane.addTab(ap.av.viewName, ap);
750 ap.setVisible(false);
755 if (ap.av.isPadGaps())
757 ap.av.getAlignment().padGaps();
759 ap.av.updateConservation(ap);
760 ap.av.updateConsensus(ap);
761 ap.av.updateStrucConsensus(ap);
765 public void setInitialTabVisible()
767 expandViews.setEnabled(true);
768 gatherViews.setEnabled(true);
769 tabbedPane.setVisible(true);
770 AlignmentPanel first = alignPanels.get(0);
771 tabbedPane.addTab(first.av.viewName, first);
772 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
775 public AlignViewport getViewport()
780 /* Set up intrinsic listeners for dynamically generated GUI bits. */
781 private void addServiceListeners()
783 final java.beans.PropertyChangeListener thisListener;
784 Desktop.instance.addJalviewPropertyChangeListener("services",
785 thisListener = new java.beans.PropertyChangeListener()
788 public void propertyChange(PropertyChangeEvent evt)
790 // // System.out.println("Discoverer property change.");
791 // if (evt.getPropertyName().equals("services"))
793 SwingUtilities.invokeLater(new Runnable()
800 "Rebuild WS Menu for service change");
801 BuildWebServiceMenu();
808 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
811 public void internalFrameClosed(
812 javax.swing.event.InternalFrameEvent evt)
814 // System.out.println("deregistering discoverer listener");
815 Desktop.instance.removeJalviewPropertyChangeListener("services",
817 closeMenuItem_actionPerformed(true);
820 // Finally, build the menu once to get current service state
821 new Thread(new Runnable()
826 BuildWebServiceMenu();
832 * Configure menu items that vary according to whether the alignment is
833 * nucleotide or protein
835 public void setGUINucleotide()
837 AlignmentI al = getViewport().getAlignment();
838 boolean nucleotide = al.isNucleotide();
840 showTranslation.setVisible(nucleotide);
841 showReverse.setVisible(nucleotide);
842 showReverseComplement.setVisible(nucleotide);
843 conservationMenuItem.setEnabled(!nucleotide);
845 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
846 showGroupConservation.setEnabled(!nucleotide);
848 showComplementMenuItem
849 .setText(nucleotide ? MessageManager.getString("label.protein")
850 : MessageManager.getString("label.nucleotide"));
854 * set up menus for the current viewport. This may be called after any
855 * operation that affects the data in the current view (selection changed,
856 * etc) to update the menus to reflect the new state.
859 public void setMenusForViewport()
861 setMenusFromViewport(viewport);
865 * Need to call this method when tabs are selected for multiple views, or when
866 * loading from Jalview2XML.java
871 void setMenusFromViewport(AlignViewport av)
873 padGapsMenuitem.setSelected(av.isPadGaps());
874 colourTextMenuItem.setSelected(av.isShowColourText());
875 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
876 modifyPID.setEnabled(abovePIDThreshold.isSelected());
877 conservationMenuItem.setSelected(av.getConservationSelected());
878 modifyConservation.setEnabled(conservationMenuItem.isSelected());
879 seqLimits.setSelected(av.getShowJVSuffix());
880 idRightAlign.setSelected(av.isRightAlignIds());
881 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
882 renderGapsMenuItem.setSelected(av.isRenderGaps());
883 wrapMenuItem.setSelected(av.getWrapAlignment());
884 scaleAbove.setVisible(av.getWrapAlignment());
885 scaleLeft.setVisible(av.getWrapAlignment());
886 scaleRight.setVisible(av.getWrapAlignment());
887 annotationPanelMenuItem.setState(av.isShowAnnotation());
889 * Show/hide annotations only enabled if annotation panel is shown
891 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
892 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
893 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
894 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
895 viewBoxesMenuItem.setSelected(av.getShowBoxes());
896 viewTextMenuItem.setSelected(av.getShowText());
897 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
898 showGroupConsensus.setSelected(av.isShowGroupConsensus());
899 showGroupConservation.setSelected(av.isShowGroupConservation());
900 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
901 showSequenceLogo.setSelected(av.isShowSequenceLogo());
902 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
904 ColourMenuHelper.setColourSelected(colourMenu,
905 av.getGlobalColourScheme());
907 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
908 hiddenMarkers.setState(av.getShowHiddenMarkers());
909 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
910 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
911 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
912 autoCalculate.setSelected(av.autoCalculateConsensus);
913 sortByTree.setSelected(av.sortByTree);
914 listenToViewSelections.setSelected(av.followSelection);
916 showProducts.setEnabled(canShowProducts());
917 setGroovyEnabled(Desktop.getGroovyConsole() != null);
923 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
927 public void setGroovyEnabled(boolean b)
929 runGroovy.setEnabled(b);
932 private IProgressIndicator progressBar;
937 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
940 public void setProgressBar(String message, long id)
942 progressBar.setProgressBar(message, id);
946 public void registerHandler(final long id,
947 final IProgressIndicatorHandler handler)
949 progressBar.registerHandler(id, handler);
954 * @return true if any progress bars are still active
957 public boolean operationInProgress()
959 return progressBar.operationInProgress();
963 public void setStatus(String text)
965 statusBar.setText(text);
969 * Added so Castor Mapping file can obtain Jalview Version
971 public String getVersion()
973 return jalview.bin.Cache.getProperty("VERSION");
976 public FeatureRenderer getFeatureRenderer()
978 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
982 public void fetchSequence_actionPerformed(ActionEvent e)
984 new jalview.gui.SequenceFetcher(this);
988 public void addFromFile_actionPerformed(ActionEvent e)
990 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
994 public void reload_actionPerformed(ActionEvent e)
996 if (fileName != null)
998 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
999 // originating file's format
1000 // TODO: work out how to recover feature settings for correct view(s) when
1001 // file is reloaded.
1002 if (FileFormat.Jalview.equals(currentFileFormat))
1004 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1005 for (int i = 0; i < frames.length; i++)
1007 if (frames[i] instanceof AlignFrame && frames[i] != this
1008 && ((AlignFrame) frames[i]).fileName != null
1009 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1013 frames[i].setSelected(true);
1014 Desktop.instance.closeAssociatedWindows();
1015 } catch (java.beans.PropertyVetoException ex)
1021 Desktop.instance.closeAssociatedWindows();
1023 FileLoader loader = new FileLoader();
1024 DataSourceType protocol = fileName.startsWith("http:")
1025 ? DataSourceType.URL
1026 : DataSourceType.FILE;
1027 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1031 Rectangle bounds = this.getBounds();
1033 FileLoader loader = new FileLoader();
1034 DataSourceType protocol = fileName.startsWith("http:")
1035 ? DataSourceType.URL
1036 : DataSourceType.FILE;
1037 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1038 protocol, currentFileFormat);
1040 newframe.setBounds(bounds);
1041 if (featureSettings != null && featureSettings.isShowing())
1043 final Rectangle fspos = featureSettings.frame.getBounds();
1044 // TODO: need a 'show feature settings' function that takes bounds -
1045 // need to refactor Desktop.addFrame
1046 newframe.featureSettings_actionPerformed(null);
1047 final FeatureSettings nfs = newframe.featureSettings;
1048 SwingUtilities.invokeLater(new Runnable()
1053 nfs.frame.setBounds(fspos);
1056 this.featureSettings.close();
1057 this.featureSettings = null;
1059 this.closeMenuItem_actionPerformed(true);
1065 public void addFromText_actionPerformed(ActionEvent e)
1068 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1072 public void addFromURL_actionPerformed(ActionEvent e)
1074 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1078 public void save_actionPerformed(ActionEvent e)
1080 if (fileName == null || (currentFileFormat == null)
1081 || fileName.startsWith("http"))
1083 saveAs_actionPerformed(null);
1087 saveAlignment(fileName, currentFileFormat);
1098 public void saveAs_actionPerformed(ActionEvent e)
1100 String format = currentFileFormat == null ? null
1101 : currentFileFormat.getName();
1102 JalviewFileChooser chooser = JalviewFileChooser
1103 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1105 chooser.setFileView(new JalviewFileView());
1106 chooser.setDialogTitle(
1107 MessageManager.getString("label.save_alignment_to_file"));
1108 chooser.setToolTipText(MessageManager.getString("action.save"));
1110 int value = chooser.showSaveDialog(this);
1112 if (value == JalviewFileChooser.APPROVE_OPTION)
1114 currentFileFormat = chooser.getSelectedFormat();
1115 while (currentFileFormat == null)
1117 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1118 MessageManager.getString(
1119 "label.select_file_format_before_saving"),
1120 MessageManager.getString("label.file_format_not_specified"),
1121 JvOptionPane.WARNING_MESSAGE);
1122 currentFileFormat = chooser.getSelectedFormat();
1123 value = chooser.showSaveDialog(this);
1124 if (value != JalviewFileChooser.APPROVE_OPTION)
1130 fileName = chooser.getSelectedFile().getPath();
1132 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1134 Cache.setProperty("LAST_DIRECTORY", fileName);
1135 saveAlignment(fileName, currentFileFormat);
1139 public boolean saveAlignment(String file, FileFormatI format)
1141 boolean success = true;
1143 if (FileFormat.Jalview.equals(format))
1145 String shortName = title;
1147 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1149 shortName = shortName.substring(
1150 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1153 success = new Jalview2XML().saveAlignment(this, file, shortName);
1155 statusBar.setText(MessageManager.formatMessage(
1156 "label.successfully_saved_to_file_in_format", new Object[]
1157 { fileName, format }));
1162 AlignmentExportData exportData = getAlignmentForExport(format,
1164 if (exportData.getSettings().isCancelled())
1168 FormatAdapter f = new FormatAdapter(alignPanel,
1169 exportData.getSettings());
1170 String output = f.formatSequences(format, exportData.getAlignment(), // class
1174 // occur in the distant future
1175 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1176 f.getCacheSuffixDefault(format),
1177 viewport.getAlignment().getHiddenColumns());
1187 PrintWriter out = new PrintWriter(new FileWriter(file));
1191 this.setTitle(file);
1192 statusBar.setText(MessageManager.formatMessage(
1193 "label.successfully_saved_to_file_in_format", new Object[]
1194 { fileName, format.getName() }));
1195 } catch (Exception ex)
1198 ex.printStackTrace();
1205 JvOptionPane.showInternalMessageDialog(this, MessageManager
1206 .formatMessage("label.couldnt_save_file", new Object[]
1208 MessageManager.getString("label.error_saving_file"),
1209 JvOptionPane.WARNING_MESSAGE);
1215 private void warningMessage(String warning, String title)
1217 if (new jalview.util.Platform().isHeadless())
1219 System.err.println("Warning: " + title + "\nWarning: " + warning);
1224 JvOptionPane.showInternalMessageDialog(this, warning, title,
1225 JvOptionPane.WARNING_MESSAGE);
1237 protected void outputText_actionPerformed(ActionEvent e)
1239 FileFormatI fileFormat = FileFormats.getInstance()
1240 .forName(e.getActionCommand());
1241 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1243 if (exportData.getSettings().isCancelled())
1247 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1248 cap.setForInput(null);
1251 FileFormatI format = fileFormat;
1252 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1253 .formatSequences(format, exportData.getAlignment(),
1254 exportData.getOmitHidden(),
1255 exportData.getStartEndPostions(),
1256 viewport.getAlignment().getHiddenColumns()));
1257 Desktop.addInternalFrame(cap, MessageManager
1258 .formatMessage("label.alignment_output_command", new Object[]
1259 { e.getActionCommand() }), 600, 500);
1260 } catch (OutOfMemoryError oom)
1262 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1269 public static AlignmentExportData getAlignmentForExport(
1270 FileFormatI format, AlignViewportI viewport,
1271 AlignExportSettingI exportSettings)
1273 AlignmentI alignmentToExport = null;
1274 AlignExportSettingI settings = exportSettings;
1275 String[] omitHidden = null;
1277 HiddenSequences hiddenSeqs = viewport.getAlignment()
1278 .getHiddenSequences();
1280 alignmentToExport = viewport.getAlignment();
1282 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1283 if (settings == null)
1285 settings = new AlignExportSettings(hasHiddenSeqs,
1286 viewport.hasHiddenColumns(), format);
1288 // settings.isExportAnnotations();
1290 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1292 omitHidden = viewport.getViewAsString(false,
1293 settings.isExportHiddenSequences());
1296 int[] alignmentStartEnd = new int[2];
1297 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1299 alignmentToExport = hiddenSeqs.getFullAlignment();
1303 alignmentToExport = viewport.getAlignment();
1305 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1306 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1307 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1308 omitHidden, alignmentStartEnd, settings);
1319 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1321 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1322 htmlSVG.exportHTML(null);
1326 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1328 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1329 bjs.exportHTML(null);
1332 public void createImageMap(File file, String image)
1334 alignPanel.makePNGImageMap(file, image);
1344 public void createPNG(File f)
1346 alignPanel.makePNG(f);
1356 public void createEPS(File f)
1358 alignPanel.makeEPS(f);
1362 public void createSVG(File f)
1364 alignPanel.makeSVG(f);
1368 public void pageSetup_actionPerformed(ActionEvent e)
1370 PrinterJob printJob = PrinterJob.getPrinterJob();
1371 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1381 public void printMenuItem_actionPerformed(ActionEvent e)
1383 // Putting in a thread avoids Swing painting problems
1384 PrintThread thread = new PrintThread(alignPanel);
1389 public void exportFeatures_actionPerformed(ActionEvent e)
1391 new AnnotationExporter().exportFeatures(alignPanel);
1395 public void exportAnnotations_actionPerformed(ActionEvent e)
1397 new AnnotationExporter().exportAnnotations(alignPanel);
1401 public void associatedData_actionPerformed(ActionEvent e)
1403 // Pick the tree file
1404 JalviewFileChooser chooser = new JalviewFileChooser(
1405 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1406 chooser.setFileView(new JalviewFileView());
1407 chooser.setDialogTitle(
1408 MessageManager.getString("label.load_jalview_annotations"));
1409 chooser.setToolTipText(
1410 MessageManager.getString("label.load_jalview_annotations"));
1412 int value = chooser.showOpenDialog(null);
1414 if (value == JalviewFileChooser.APPROVE_OPTION)
1416 String choice = chooser.getSelectedFile().getPath();
1417 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1418 loadJalviewDataFile(choice, null, null, null);
1424 * Close the current view or all views in the alignment frame. If the frame
1425 * only contains one view then the alignment will be removed from memory.
1427 * @param closeAllTabs
1430 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1432 if (alignPanels != null && alignPanels.size() < 2)
1434 closeAllTabs = true;
1439 if (alignPanels != null)
1443 if (this.isClosed())
1445 // really close all the windows - otherwise wait till
1446 // setClosed(true) is called
1447 for (int i = 0; i < alignPanels.size(); i++)
1449 AlignmentPanel ap = alignPanels.get(i);
1456 closeView(alignPanel);
1463 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1464 * be called recursively, with the frame now in 'closed' state
1466 this.setClosed(true);
1468 } catch (Exception ex)
1470 ex.printStackTrace();
1475 * Close the specified panel and close up tabs appropriately.
1477 * @param panelToClose
1479 public void closeView(AlignmentPanel panelToClose)
1481 int index = tabbedPane.getSelectedIndex();
1482 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1483 alignPanels.remove(panelToClose);
1484 panelToClose.closePanel();
1485 panelToClose = null;
1487 tabbedPane.removeTabAt(closedindex);
1488 tabbedPane.validate();
1490 if (index > closedindex || index == tabbedPane.getTabCount())
1492 // modify currently selected tab index if necessary.
1496 this.tabSelectionChanged(index);
1502 void updateEditMenuBar()
1505 if (viewport.getHistoryList().size() > 0)
1507 undoMenuItem.setEnabled(true);
1508 CommandI command = viewport.getHistoryList().peek();
1509 undoMenuItem.setText(MessageManager
1510 .formatMessage("label.undo_command", new Object[]
1511 { command.getDescription() }));
1515 undoMenuItem.setEnabled(false);
1516 undoMenuItem.setText(MessageManager.getString("action.undo"));
1519 if (viewport.getRedoList().size() > 0)
1521 redoMenuItem.setEnabled(true);
1523 CommandI command = viewport.getRedoList().peek();
1524 redoMenuItem.setText(MessageManager
1525 .formatMessage("label.redo_command", new Object[]
1526 { command.getDescription() }));
1530 redoMenuItem.setEnabled(false);
1531 redoMenuItem.setText(MessageManager.getString("action.redo"));
1536 public void addHistoryItem(CommandI command)
1538 if (command.getSize() > 0)
1540 viewport.addToHistoryList(command);
1541 viewport.clearRedoList();
1542 updateEditMenuBar();
1543 viewport.updateHiddenColumns();
1544 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1545 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1546 // viewport.getColumnSelection()
1547 // .getHiddenColumns().size() > 0);
1553 * @return alignment objects for all views
1555 AlignmentI[] getViewAlignments()
1557 if (alignPanels != null)
1559 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1561 for (AlignmentPanel ap : alignPanels)
1563 als[i++] = ap.av.getAlignment();
1567 if (viewport != null)
1569 return new AlignmentI[] { viewport.getAlignment() };
1581 protected void undoMenuItem_actionPerformed(ActionEvent e)
1583 if (viewport.getHistoryList().isEmpty())
1587 CommandI command = viewport.getHistoryList().pop();
1588 viewport.addToRedoList(command);
1589 command.undoCommand(getViewAlignments());
1591 AlignmentViewport originalSource = getOriginatingSource(command);
1592 updateEditMenuBar();
1594 if (originalSource != null)
1596 if (originalSource != viewport)
1599 "Implementation worry: mismatch of viewport origin for undo");
1601 originalSource.updateHiddenColumns();
1602 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1604 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1605 // viewport.getColumnSelection()
1606 // .getHiddenColumns().size() > 0);
1607 originalSource.firePropertyChange("alignment", null,
1608 originalSource.getAlignment().getSequences());
1619 protected void redoMenuItem_actionPerformed(ActionEvent e)
1621 if (viewport.getRedoList().size() < 1)
1626 CommandI command = viewport.getRedoList().pop();
1627 viewport.addToHistoryList(command);
1628 command.doCommand(getViewAlignments());
1630 AlignmentViewport originalSource = getOriginatingSource(command);
1631 updateEditMenuBar();
1633 if (originalSource != null)
1636 if (originalSource != viewport)
1639 "Implementation worry: mismatch of viewport origin for redo");
1641 originalSource.updateHiddenColumns();
1642 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1644 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1645 // viewport.getColumnSelection()
1646 // .getHiddenColumns().size() > 0);
1647 originalSource.firePropertyChange("alignment", null,
1648 originalSource.getAlignment().getSequences());
1652 AlignmentViewport getOriginatingSource(CommandI command)
1654 AlignmentViewport originalSource = null;
1655 // For sequence removal and addition, we need to fire
1656 // the property change event FROM the viewport where the
1657 // original alignment was altered
1658 AlignmentI al = null;
1659 if (command instanceof EditCommand)
1661 EditCommand editCommand = (EditCommand) command;
1662 al = editCommand.getAlignment();
1663 List<Component> comps = PaintRefresher.components
1664 .get(viewport.getSequenceSetId());
1666 for (Component comp : comps)
1668 if (comp instanceof AlignmentPanel)
1670 if (al == ((AlignmentPanel) comp).av.getAlignment())
1672 originalSource = ((AlignmentPanel) comp).av;
1679 if (originalSource == null)
1681 // The original view is closed, we must validate
1682 // the current view against the closed view first
1685 PaintRefresher.validateSequences(al, viewport.getAlignment());
1688 originalSource = viewport;
1691 return originalSource;
1700 public void moveSelectedSequences(boolean up)
1702 SequenceGroup sg = viewport.getSelectionGroup();
1708 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1709 viewport.getHiddenRepSequences(), up);
1710 alignPanel.paintAlignment(true, false);
1713 synchronized void slideSequences(boolean right, int size)
1715 List<SequenceI> sg = new ArrayList<>();
1716 if (viewport.cursorMode)
1718 sg.add(viewport.getAlignment()
1719 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1721 else if (viewport.getSelectionGroup() != null
1722 && viewport.getSelectionGroup().getSize() != viewport
1723 .getAlignment().getHeight())
1725 sg = viewport.getSelectionGroup()
1726 .getSequences(viewport.getHiddenRepSequences());
1734 List<SequenceI> invertGroup = new ArrayList<>();
1736 for (SequenceI seq : viewport.getAlignment().getSequences())
1738 if (!sg.contains(seq))
1740 invertGroup.add(seq);
1744 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1746 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1747 for (int i = 0; i < invertGroup.size(); i++)
1749 seqs2[i] = invertGroup.get(i);
1752 SlideSequencesCommand ssc;
1755 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1756 viewport.getGapCharacter());
1760 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1761 viewport.getGapCharacter());
1764 int groupAdjustment = 0;
1765 if (ssc.getGapsInsertedBegin() && right)
1767 if (viewport.cursorMode)
1769 alignPanel.getSeqPanel().moveCursor(size, 0);
1773 groupAdjustment = size;
1776 else if (!ssc.getGapsInsertedBegin() && !right)
1778 if (viewport.cursorMode)
1780 alignPanel.getSeqPanel().moveCursor(-size, 0);
1784 groupAdjustment = -size;
1788 if (groupAdjustment != 0)
1790 viewport.getSelectionGroup().setStartRes(
1791 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1792 viewport.getSelectionGroup().setEndRes(
1793 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1797 * just extend the last slide command if compatible; but not if in
1798 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1800 boolean appendHistoryItem = false;
1801 Deque<CommandI> historyList = viewport.getHistoryList();
1802 boolean inSplitFrame = getSplitViewContainer() != null;
1803 if (!inSplitFrame && historyList != null && historyList.size() > 0
1804 && historyList.peek() instanceof SlideSequencesCommand)
1806 appendHistoryItem = ssc.appendSlideCommand(
1807 (SlideSequencesCommand) historyList.peek());
1810 if (!appendHistoryItem)
1812 addHistoryItem(ssc);
1825 protected void copy_actionPerformed(ActionEvent e)
1828 if (viewport.getSelectionGroup() == null)
1832 // TODO: preserve the ordering of displayed alignment annotation in any
1833 // internal paste (particularly sequence associated annotation)
1834 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1835 String[] omitHidden = null;
1837 if (viewport.hasHiddenColumns())
1839 omitHidden = viewport.getViewAsString(true);
1842 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1843 seqs, omitHidden, null);
1845 StringSelection ss = new StringSelection(output);
1849 jalview.gui.Desktop.internalCopy = true;
1850 // Its really worth setting the clipboard contents
1851 // to empty before setting the large StringSelection!!
1852 Toolkit.getDefaultToolkit().getSystemClipboard()
1853 .setContents(new StringSelection(""), null);
1855 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1857 } catch (OutOfMemoryError er)
1859 new OOMWarning("copying region", er);
1863 ArrayList<int[]> hiddenColumns = null;
1864 if (viewport.hasHiddenColumns())
1866 hiddenColumns = new ArrayList<>();
1867 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1868 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1869 ArrayList<int[]> hiddenRegions = viewport.getAlignment()
1870 .getHiddenColumns().getHiddenColumnsCopy();
1871 for (int[] region : hiddenRegions)
1873 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1877 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1882 Desktop.jalviewClipboard = new Object[] { seqs,
1883 viewport.getAlignment().getDataset(), hiddenColumns };
1884 statusBar.setText(MessageManager.formatMessage(
1885 "label.copied_sequences_to_clipboard", new Object[]
1886 { Integer.valueOf(seqs.length).toString() }));
1896 protected void pasteNew_actionPerformed(ActionEvent e)
1908 protected void pasteThis_actionPerformed(ActionEvent e)
1914 * Paste contents of Jalview clipboard
1916 * @param newAlignment
1917 * true to paste to a new alignment, otherwise add to this.
1919 void paste(boolean newAlignment)
1921 boolean externalPaste = true;
1924 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1925 Transferable contents = c.getContents(this);
1927 if (contents == null)
1936 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1937 if (str.length() < 1)
1942 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1944 } catch (OutOfMemoryError er)
1946 new OOMWarning("Out of memory pasting sequences!!", er);
1950 SequenceI[] sequences;
1951 boolean annotationAdded = false;
1952 AlignmentI alignment = null;
1954 if (Desktop.jalviewClipboard != null)
1956 // The clipboard was filled from within Jalview, we must use the
1958 // And dataset from the copied alignment
1959 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1960 // be doubly sure that we create *new* sequence objects.
1961 sequences = new SequenceI[newseq.length];
1962 for (int i = 0; i < newseq.length; i++)
1964 sequences[i] = new Sequence(newseq[i]);
1966 alignment = new Alignment(sequences);
1967 externalPaste = false;
1971 // parse the clipboard as an alignment.
1972 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1974 sequences = alignment.getSequencesArray();
1978 ArrayList<Integer> newGraphGroups = new ArrayList<>();
1984 if (Desktop.jalviewClipboard != null)
1986 // dataset is inherited
1987 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1991 // new dataset is constructed
1992 alignment.setDataset(null);
1994 alwidth = alignment.getWidth() + 1;
1998 AlignmentI pastedal = alignment; // preserve pasted alignment object
1999 // Add pasted sequences and dataset into existing alignment.
2000 alignment = viewport.getAlignment();
2001 alwidth = alignment.getWidth() + 1;
2002 // decide if we need to import sequences from an existing dataset
2003 boolean importDs = Desktop.jalviewClipboard != null
2004 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2005 // importDs==true instructs us to copy over new dataset sequences from
2006 // an existing alignment
2007 Vector newDs = (importDs) ? new Vector() : null; // used to create
2008 // minimum dataset set
2010 for (int i = 0; i < sequences.length; i++)
2014 newDs.addElement(null);
2016 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2018 if (importDs && ds != null)
2020 if (!newDs.contains(ds))
2022 newDs.setElementAt(ds, i);
2023 ds = new Sequence(ds);
2024 // update with new dataset sequence
2025 sequences[i].setDatasetSequence(ds);
2029 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2034 // copy and derive new dataset sequence
2035 sequences[i] = sequences[i].deriveSequence();
2036 alignment.getDataset()
2037 .addSequence(sequences[i].getDatasetSequence());
2038 // TODO: avoid creation of duplicate dataset sequences with a
2039 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2041 alignment.addSequence(sequences[i]); // merges dataset
2045 newDs.clear(); // tidy up
2047 if (alignment.getAlignmentAnnotation() != null)
2049 for (AlignmentAnnotation alan : alignment
2050 .getAlignmentAnnotation())
2052 if (alan.graphGroup > fgroup)
2054 fgroup = alan.graphGroup;
2058 if (pastedal.getAlignmentAnnotation() != null)
2060 // Add any annotation attached to alignment.
2061 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2062 for (int i = 0; i < alann.length; i++)
2064 annotationAdded = true;
2065 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2067 AlignmentAnnotation newann = new AlignmentAnnotation(
2069 if (newann.graphGroup > -1)
2071 if (newGraphGroups.size() <= newann.graphGroup
2072 || newGraphGroups.get(newann.graphGroup) == null)
2074 for (int q = newGraphGroups
2075 .size(); q <= newann.graphGroup; q++)
2077 newGraphGroups.add(q, null);
2079 newGraphGroups.set(newann.graphGroup,
2080 new Integer(++fgroup));
2082 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2086 newann.padAnnotation(alwidth);
2087 alignment.addAnnotation(newann);
2097 addHistoryItem(new EditCommand(
2098 MessageManager.getString("label.add_sequences"),
2099 Action.PASTE, sequences, 0, alignment.getWidth(),
2102 // Add any annotations attached to sequences
2103 for (int i = 0; i < sequences.length; i++)
2105 if (sequences[i].getAnnotation() != null)
2107 AlignmentAnnotation newann;
2108 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2110 annotationAdded = true;
2111 newann = sequences[i].getAnnotation()[a];
2112 newann.adjustForAlignment();
2113 newann.padAnnotation(alwidth);
2114 if (newann.graphGroup > -1)
2116 if (newann.graphGroup > -1)
2118 if (newGraphGroups.size() <= newann.graphGroup
2119 || newGraphGroups.get(newann.graphGroup) == null)
2121 for (int q = newGraphGroups
2122 .size(); q <= newann.graphGroup; q++)
2124 newGraphGroups.add(q, null);
2126 newGraphGroups.set(newann.graphGroup,
2127 new Integer(++fgroup));
2129 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2133 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2137 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2145 // propagate alignment changed.
2146 viewport.getRanges().setEndSeq(alignment.getHeight());
2147 if (annotationAdded)
2149 // Duplicate sequence annotation in all views.
2150 AlignmentI[] alview = this.getViewAlignments();
2151 for (int i = 0; i < sequences.length; i++)
2153 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2158 for (int avnum = 0; avnum < alview.length; avnum++)
2160 if (alview[avnum] != alignment)
2162 // duplicate in a view other than the one with input focus
2163 int avwidth = alview[avnum].getWidth() + 1;
2164 // this relies on sann being preserved after we
2165 // modify the sequence's annotation array for each duplication
2166 for (int a = 0; a < sann.length; a++)
2168 AlignmentAnnotation newann = new AlignmentAnnotation(
2170 sequences[i].addAlignmentAnnotation(newann);
2171 newann.padAnnotation(avwidth);
2172 alview[avnum].addAnnotation(newann); // annotation was
2173 // duplicated earlier
2174 // TODO JAL-1145 graphGroups are not updated for sequence
2175 // annotation added to several views. This may cause
2177 alview[avnum].setAnnotationIndex(newann, a);
2182 buildSortByAnnotationScoresMenu();
2184 viewport.firePropertyChange("alignment", null,
2185 alignment.getSequences());
2186 if (alignPanels != null)
2188 for (AlignmentPanel ap : alignPanels)
2190 ap.validateAnnotationDimensions(false);
2195 alignPanel.validateAnnotationDimensions(false);
2201 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2203 String newtitle = new String("Copied sequences");
2205 if (Desktop.jalviewClipboard != null
2206 && Desktop.jalviewClipboard[2] != null)
2208 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2209 for (int[] region : hc)
2211 af.viewport.hideColumns(region[0], region[1]);
2215 // >>>This is a fix for the moment, until a better solution is
2217 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2218 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2219 .getFeatureRenderer());
2221 // TODO: maintain provenance of an alignment, rather than just make the
2222 // title a concatenation of operations.
2225 if (title.startsWith("Copied sequences"))
2231 newtitle = newtitle.concat("- from " + title);
2236 newtitle = new String("Pasted sequences");
2239 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2244 } catch (Exception ex)
2246 ex.printStackTrace();
2247 System.out.println("Exception whilst pasting: " + ex);
2248 // could be anything being pasted in here
2254 protected void expand_newalign(ActionEvent e)
2258 AlignmentI alignment = AlignmentUtils
2259 .expandContext(getViewport().getAlignment(), -1);
2260 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2262 String newtitle = new String("Flanking alignment");
2264 if (Desktop.jalviewClipboard != null
2265 && Desktop.jalviewClipboard[2] != null)
2267 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2268 for (int region[] : hc)
2270 af.viewport.hideColumns(region[0], region[1]);
2274 // >>>This is a fix for the moment, until a better solution is
2276 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2277 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2278 .getFeatureRenderer());
2280 // TODO: maintain provenance of an alignment, rather than just make the
2281 // title a concatenation of operations.
2283 if (title.startsWith("Copied sequences"))
2289 newtitle = newtitle.concat("- from " + title);
2293 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2295 } catch (Exception ex)
2297 ex.printStackTrace();
2298 System.out.println("Exception whilst pasting: " + ex);
2299 // could be anything being pasted in here
2300 } catch (OutOfMemoryError oom)
2302 new OOMWarning("Viewing flanking region of alignment", oom);
2313 protected void cut_actionPerformed(ActionEvent e)
2315 copy_actionPerformed(null);
2316 delete_actionPerformed(null);
2326 protected void delete_actionPerformed(ActionEvent evt)
2329 SequenceGroup sg = viewport.getSelectionGroup();
2336 * If the cut affects all sequences, warn, remove highlighted columns
2338 if (sg.getSize() == viewport.getAlignment().getHeight())
2340 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2341 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2342 if (isEntireAlignWidth)
2344 int confirm = JvOptionPane.showConfirmDialog(this,
2345 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2346 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2347 JvOptionPane.OK_CANCEL_OPTION);
2349 if (confirm == JvOptionPane.CANCEL_OPTION
2350 || confirm == JvOptionPane.CLOSED_OPTION)
2355 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2356 sg.getEndRes() + 1);
2358 SequenceI[] cut = sg.getSequences()
2359 .toArray(new SequenceI[sg.getSize()]);
2361 addHistoryItem(new EditCommand(
2362 MessageManager.getString("label.cut_sequences"), Action.CUT,
2363 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2364 viewport.getAlignment()));
2366 viewport.setSelectionGroup(null);
2367 viewport.sendSelection();
2368 viewport.getAlignment().deleteGroup(sg);
2370 viewport.firePropertyChange("alignment", null,
2371 viewport.getAlignment().getSequences());
2372 if (viewport.getAlignment().getHeight() < 1)
2376 this.setClosed(true);
2377 } catch (Exception ex)
2390 protected void deleteGroups_actionPerformed(ActionEvent e)
2392 if (avc.deleteGroups())
2394 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2395 alignPanel.updateAnnotation();
2396 alignPanel.paintAlignment(true, true);
2407 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2409 SequenceGroup sg = new SequenceGroup();
2411 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2413 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2416 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2417 viewport.setSelectionGroup(sg);
2418 viewport.sendSelection();
2419 // JAL-2034 - should delegate to
2420 // alignPanel to decide if overview needs
2422 alignPanel.paintAlignment(false, false);
2423 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2433 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2435 if (viewport.cursorMode)
2437 alignPanel.getSeqPanel().keyboardNo1 = null;
2438 alignPanel.getSeqPanel().keyboardNo2 = null;
2440 viewport.setSelectionGroup(null);
2441 viewport.getColumnSelection().clear();
2442 viewport.setSelectionGroup(null);
2443 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2444 // JAL-2034 - should delegate to
2445 // alignPanel to decide if overview needs
2447 alignPanel.paintAlignment(false, false);
2448 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2449 viewport.sendSelection();
2459 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2461 SequenceGroup sg = viewport.getSelectionGroup();
2465 selectAllSequenceMenuItem_actionPerformed(null);
2470 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2472 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2474 // JAL-2034 - should delegate to
2475 // alignPanel to decide if overview needs
2478 alignPanel.paintAlignment(true, false);
2479 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2480 viewport.sendSelection();
2484 public void invertColSel_actionPerformed(ActionEvent e)
2486 viewport.invertColumnSelection();
2487 alignPanel.paintAlignment(true, false);
2488 viewport.sendSelection();
2498 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2500 trimAlignment(true);
2510 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2512 trimAlignment(false);
2515 void trimAlignment(boolean trimLeft)
2517 ColumnSelection colSel = viewport.getColumnSelection();
2520 if (!colSel.isEmpty())
2524 column = colSel.getMin();
2528 column = colSel.getMax();
2532 if (viewport.getSelectionGroup() != null)
2534 seqs = viewport.getSelectionGroup()
2535 .getSequencesAsArray(viewport.getHiddenRepSequences());
2539 seqs = viewport.getAlignment().getSequencesArray();
2542 TrimRegionCommand trimRegion;
2545 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2546 column, viewport.getAlignment());
2547 viewport.getRanges().setStartRes(0);
2551 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2552 column, viewport.getAlignment());
2555 statusBar.setText(MessageManager
2556 .formatMessage("label.removed_columns", new String[]
2557 { Integer.valueOf(trimRegion.getSize()).toString() }));
2559 addHistoryItem(trimRegion);
2561 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2563 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2564 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2566 viewport.getAlignment().deleteGroup(sg);
2570 viewport.firePropertyChange("alignment", null,
2571 viewport.getAlignment().getSequences());
2582 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2584 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2587 if (viewport.getSelectionGroup() != null)
2589 seqs = viewport.getSelectionGroup()
2590 .getSequencesAsArray(viewport.getHiddenRepSequences());
2591 start = viewport.getSelectionGroup().getStartRes();
2592 end = viewport.getSelectionGroup().getEndRes();
2596 seqs = viewport.getAlignment().getSequencesArray();
2599 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2600 "Remove Gapped Columns", seqs, start, end,
2601 viewport.getAlignment());
2603 addHistoryItem(removeGapCols);
2605 statusBar.setText(MessageManager
2606 .formatMessage("label.removed_empty_columns", new Object[]
2607 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2609 // This is to maintain viewport position on first residue
2610 // of first sequence
2611 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2612 ViewportRanges ranges = viewport.getRanges();
2613 int startRes = seq.findPosition(ranges.getStartRes());
2614 // ShiftList shifts;
2615 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2616 // edit.alColumnChanges=shifts.getInverse();
2617 // if (viewport.hasHiddenColumns)
2618 // viewport.getColumnSelection().compensateForEdits(shifts);
2619 ranges.setStartRes(seq.findIndex(startRes) - 1);
2620 viewport.firePropertyChange("alignment", null,
2621 viewport.getAlignment().getSequences());
2632 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2634 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2637 if (viewport.getSelectionGroup() != null)
2639 seqs = viewport.getSelectionGroup()
2640 .getSequencesAsArray(viewport.getHiddenRepSequences());
2641 start = viewport.getSelectionGroup().getStartRes();
2642 end = viewport.getSelectionGroup().getEndRes();
2646 seqs = viewport.getAlignment().getSequencesArray();
2649 // This is to maintain viewport position on first residue
2650 // of first sequence
2651 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2652 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2654 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2655 viewport.getAlignment()));
2657 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2659 viewport.firePropertyChange("alignment", null,
2660 viewport.getAlignment().getSequences());
2671 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2673 viewport.setPadGaps(padGapsMenuitem.isSelected());
2674 viewport.firePropertyChange("alignment", null,
2675 viewport.getAlignment().getSequences());
2685 public void findMenuItem_actionPerformed(ActionEvent e)
2691 * Create a new view of the current alignment.
2694 public void newView_actionPerformed(ActionEvent e)
2696 newView(null, true);
2700 * Creates and shows a new view of the current alignment.
2703 * title of newly created view; if null, one will be generated
2704 * @param copyAnnotation
2705 * if true then duplicate all annnotation, groups and settings
2706 * @return new alignment panel, already displayed.
2708 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2711 * Create a new AlignmentPanel (with its own, new Viewport)
2713 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2714 if (!copyAnnotation)
2717 * remove all groups and annotation except for the automatic stuff
2719 newap.av.getAlignment().deleteAllGroups();
2720 newap.av.getAlignment().deleteAllAnnotations(false);
2723 newap.av.setGatherViewsHere(false);
2725 if (viewport.viewName == null)
2727 viewport.viewName = MessageManager
2728 .getString("label.view_name_original");
2732 * Views share the same edits undo and redo stacks
2734 newap.av.setHistoryList(viewport.getHistoryList());
2735 newap.av.setRedoList(viewport.getRedoList());
2738 * Views share the same mappings; need to deregister any new mappings
2739 * created by copyAlignPanel, and register the new reference to the shared
2742 newap.av.replaceMappings(viewport.getAlignment());
2745 * start up cDNA consensus (if applicable) now mappings are in place
2747 if (newap.av.initComplementConsensus())
2749 newap.refresh(true); // adjust layout of annotations
2752 newap.av.viewName = getNewViewName(viewTitle);
2754 addAlignmentPanel(newap, true);
2755 newap.alignmentChanged();
2757 if (alignPanels.size() == 2)
2759 viewport.setGatherViewsHere(true);
2761 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2766 * Make a new name for the view, ensuring it is unique within the current
2767 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2768 * these now use viewId. Unique view names are still desirable for usability.)
2773 protected String getNewViewName(String viewTitle)
2775 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2776 boolean addFirstIndex = false;
2777 if (viewTitle == null || viewTitle.trim().length() == 0)
2779 viewTitle = MessageManager.getString("action.view");
2780 addFirstIndex = true;
2784 index = 1;// we count from 1 if given a specific name
2786 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2788 List<Component> comps = PaintRefresher.components
2789 .get(viewport.getSequenceSetId());
2791 List<String> existingNames = getExistingViewNames(comps);
2793 while (existingNames.contains(newViewName))
2795 newViewName = viewTitle + " " + (++index);
2801 * Returns a list of distinct view names found in the given list of
2802 * components. View names are held on the viewport of an AlignmentPanel.
2807 protected List<String> getExistingViewNames(List<Component> comps)
2809 List<String> existingNames = new ArrayList<>();
2810 for (Component comp : comps)
2812 if (comp instanceof AlignmentPanel)
2814 AlignmentPanel ap = (AlignmentPanel) comp;
2815 if (!existingNames.contains(ap.av.viewName))
2817 existingNames.add(ap.av.viewName);
2821 return existingNames;
2825 * Explode tabbed views into separate windows.
2828 public void expandViews_actionPerformed(ActionEvent e)
2830 Desktop.explodeViews(this);
2834 * Gather views in separate windows back into a tabbed presentation.
2837 public void gatherViews_actionPerformed(ActionEvent e)
2839 Desktop.instance.gatherViews(this);
2849 public void font_actionPerformed(ActionEvent e)
2851 new FontChooser(alignPanel);
2861 protected void seqLimit_actionPerformed(ActionEvent e)
2863 viewport.setShowJVSuffix(seqLimits.isSelected());
2865 alignPanel.getIdPanel().getIdCanvas()
2866 .setPreferredSize(alignPanel.calculateIdWidth());
2867 alignPanel.paintAlignment(true, false);
2871 public void idRightAlign_actionPerformed(ActionEvent e)
2873 viewport.setRightAlignIds(idRightAlign.isSelected());
2874 alignPanel.paintAlignment(false, false);
2878 public void centreColumnLabels_actionPerformed(ActionEvent e)
2880 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2881 alignPanel.paintAlignment(false, false);
2887 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2890 protected void followHighlight_actionPerformed()
2893 * Set the 'follow' flag on the Viewport (and scroll to position if now
2896 final boolean state = this.followHighlightMenuItem.getState();
2897 viewport.setFollowHighlight(state);
2900 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2911 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2913 viewport.setColourText(colourTextMenuItem.isSelected());
2914 alignPanel.paintAlignment(false, false);
2924 public void wrapMenuItem_actionPerformed(ActionEvent e)
2926 scaleAbove.setVisible(wrapMenuItem.isSelected());
2927 scaleLeft.setVisible(wrapMenuItem.isSelected());
2928 scaleRight.setVisible(wrapMenuItem.isSelected());
2929 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2930 alignPanel.updateLayout();
2934 public void showAllSeqs_actionPerformed(ActionEvent e)
2936 viewport.showAllHiddenSeqs();
2940 public void showAllColumns_actionPerformed(ActionEvent e)
2942 viewport.showAllHiddenColumns();
2943 alignPanel.paintAlignment(true, true);
2944 viewport.sendSelection();
2948 public void hideSelSequences_actionPerformed(ActionEvent e)
2950 viewport.hideAllSelectedSeqs();
2954 * called by key handler and the hide all/show all menu items
2959 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2962 boolean hide = false;
2963 SequenceGroup sg = viewport.getSelectionGroup();
2964 if (!toggleSeqs && !toggleCols)
2966 // Hide everything by the current selection - this is a hack - we do the
2967 // invert and then hide
2968 // first check that there will be visible columns after the invert.
2969 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2970 && sg.getStartRes() <= sg.getEndRes()))
2972 // now invert the sequence set, if required - empty selection implies
2973 // that no hiding is required.
2976 invertSequenceMenuItem_actionPerformed(null);
2977 sg = viewport.getSelectionGroup();
2981 viewport.expandColSelection(sg, true);
2982 // finally invert the column selection and get the new sequence
2984 invertColSel_actionPerformed(null);
2991 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2993 hideSelSequences_actionPerformed(null);
2996 else if (!(toggleCols && viewport.hasSelectedColumns()))
2998 showAllSeqs_actionPerformed(null);
3004 if (viewport.hasSelectedColumns())
3006 hideSelColumns_actionPerformed(null);
3009 viewport.setSelectionGroup(sg);
3014 showAllColumns_actionPerformed(null);
3023 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3024 * event.ActionEvent)
3027 public void hideAllButSelection_actionPerformed(ActionEvent e)
3029 toggleHiddenRegions(false, false);
3030 viewport.sendSelection();
3037 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3041 public void hideAllSelection_actionPerformed(ActionEvent e)
3043 SequenceGroup sg = viewport.getSelectionGroup();
3044 viewport.expandColSelection(sg, false);
3045 viewport.hideAllSelectedSeqs();
3046 viewport.hideSelectedColumns();
3047 alignPanel.paintAlignment(true, true);
3048 viewport.sendSelection();
3055 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3059 public void showAllhidden_actionPerformed(ActionEvent e)
3061 viewport.showAllHiddenColumns();
3062 viewport.showAllHiddenSeqs();
3063 alignPanel.paintAlignment(true, true);
3064 viewport.sendSelection();
3068 public void hideSelColumns_actionPerformed(ActionEvent e)
3070 viewport.hideSelectedColumns();
3071 alignPanel.paintAlignment(true, true);
3072 viewport.sendSelection();
3076 public void hiddenMarkers_actionPerformed(ActionEvent e)
3078 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3089 protected void scaleAbove_actionPerformed(ActionEvent e)
3091 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3092 // TODO: do we actually need to update overview for scale above change ?
3093 alignPanel.paintAlignment(true, false);
3103 protected void scaleLeft_actionPerformed(ActionEvent e)
3105 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3106 alignPanel.paintAlignment(true, false);
3116 protected void scaleRight_actionPerformed(ActionEvent e)
3118 viewport.setScaleRightWrapped(scaleRight.isSelected());
3119 alignPanel.paintAlignment(true, false);
3129 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3131 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3132 alignPanel.paintAlignment(false, false);
3142 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3144 viewport.setShowText(viewTextMenuItem.isSelected());
3145 alignPanel.paintAlignment(false, false);
3155 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3157 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3158 alignPanel.paintAlignment(false, false);
3161 public FeatureSettings featureSettings;
3164 public FeatureSettingsControllerI getFeatureSettingsUI()
3166 return featureSettings;
3170 public void featureSettings_actionPerformed(ActionEvent e)
3172 if (featureSettings != null)
3174 featureSettings.close();
3175 featureSettings = null;
3177 if (!showSeqFeatures.isSelected())
3179 // make sure features are actually displayed
3180 showSeqFeatures.setSelected(true);
3181 showSeqFeatures_actionPerformed(null);
3183 featureSettings = new FeatureSettings(this);
3187 * Set or clear 'Show Sequence Features'
3193 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3195 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3196 alignPanel.paintAlignment(true, true);
3200 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3201 * the annotations panel as a whole.
3203 * The options to show/hide all annotations should be enabled when the panel
3204 * is shown, and disabled when the panel is hidden.
3209 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3211 final boolean setVisible = annotationPanelMenuItem.isSelected();
3212 viewport.setShowAnnotation(setVisible);
3213 this.showAllSeqAnnotations.setEnabled(setVisible);
3214 this.hideAllSeqAnnotations.setEnabled(setVisible);
3215 this.showAllAlAnnotations.setEnabled(setVisible);
3216 this.hideAllAlAnnotations.setEnabled(setVisible);
3217 alignPanel.updateLayout();
3221 public void alignmentProperties()
3223 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
3224 StringBuilder contents = new AlignmentProperties(
3225 viewport.getAlignment())
3227 cap.setText("<html>" + contents.toString() + "</html>");
3229 Desktop.addInternalFrame(cap, MessageManager
3230 .formatMessage("label.alignment_properties", new Object[]
3231 { getTitle() }), 500, 400);
3241 public void overviewMenuItem_actionPerformed(ActionEvent e)
3243 if (alignPanel.overviewPanel != null)
3248 JInternalFrame frame = new JInternalFrame();
3249 final OverviewPanel overview = new OverviewPanel(alignPanel);
3250 frame.setContentPane(overview);
3251 Desktop.addInternalFrame(frame, MessageManager
3252 .formatMessage("label.overview_params", new Object[]
3253 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3256 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3257 frame.addInternalFrameListener(
3258 new javax.swing.event.InternalFrameAdapter()
3261 public void internalFrameClosed(
3262 javax.swing.event.InternalFrameEvent evt)
3265 alignPanel.setOverviewPanel(null);
3269 alignPanel.setOverviewPanel(overview);
3273 public void textColour_actionPerformed()
3275 new TextColourChooser().chooseColour(alignPanel, null);
3279 * public void covariationColour_actionPerformed() {
3281 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3285 public void annotationColour_actionPerformed()
3287 new AnnotationColourChooser(viewport, alignPanel);
3291 public void annotationColumn_actionPerformed(ActionEvent e)
3293 new AnnotationColumnChooser(viewport, alignPanel);
3297 * Action on the user checking or unchecking the option to apply the selected
3298 * colour scheme to all groups. If unchecked, groups may have their own
3299 * independent colour schemes.
3304 public void applyToAllGroups_actionPerformed(boolean selected)
3306 viewport.setColourAppliesToAllGroups(selected);
3310 * Action on user selecting a colour from the colour menu
3313 * the name (not the menu item label!) of the colour scheme
3316 public void changeColour_actionPerformed(String name)
3319 * 'User Defined' opens a panel to configure or load a
3320 * user-defined colour scheme
3322 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3324 new UserDefinedColours(alignPanel);
3329 * otherwise set the chosen colour scheme (or null for 'None')
3331 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3332 viewport.getAlignment(), viewport.getHiddenRepSequences());
3337 * Actions on setting or changing the alignment colour scheme
3342 public void changeColour(ColourSchemeI cs)
3344 // TODO: pull up to controller method
3345 ColourMenuHelper.setColourSelected(colourMenu, cs);
3347 viewport.setGlobalColourScheme(cs);
3349 alignPanel.paintAlignment(true, true);
3353 * Show the PID threshold slider panel
3356 protected void modifyPID_actionPerformed()
3358 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3359 alignPanel.getViewName());
3360 SliderPanel.showPIDSlider();
3364 * Show the Conservation slider panel
3367 protected void modifyConservation_actionPerformed()
3369 SliderPanel.setConservationSlider(alignPanel,
3370 viewport.getResidueShading(), alignPanel.getViewName());
3371 SliderPanel.showConservationSlider();
3375 * Action on selecting or deselecting (Colour) By Conservation
3378 public void conservationMenuItem_actionPerformed(boolean selected)
3380 modifyConservation.setEnabled(selected);
3381 viewport.setConservationSelected(selected);
3382 viewport.getResidueShading().setConservationApplied(selected);
3384 changeColour(viewport.getGlobalColourScheme());
3387 modifyConservation_actionPerformed();
3391 SliderPanel.hideConservationSlider();
3396 * Action on selecting or deselecting (Colour) Above PID Threshold
3399 public void abovePIDThreshold_actionPerformed(boolean selected)
3401 modifyPID.setEnabled(selected);
3402 viewport.setAbovePIDThreshold(selected);
3405 viewport.getResidueShading().setThreshold(0,
3406 viewport.isIgnoreGapsConsensus());
3409 changeColour(viewport.getGlobalColourScheme());
3412 modifyPID_actionPerformed();
3416 SliderPanel.hidePIDSlider();
3427 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3429 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3430 AlignmentSorter.sortByPID(viewport.getAlignment(),
3431 viewport.getAlignment().getSequenceAt(0));
3432 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3433 viewport.getAlignment()));
3434 alignPanel.paintAlignment(true, false);
3444 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3446 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3447 AlignmentSorter.sortByID(viewport.getAlignment());
3449 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3450 alignPanel.paintAlignment(true, false);
3460 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3462 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3463 AlignmentSorter.sortByLength(viewport.getAlignment());
3464 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3465 viewport.getAlignment()));
3466 alignPanel.paintAlignment(true, false);
3476 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3478 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3479 AlignmentSorter.sortByGroup(viewport.getAlignment());
3480 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3481 viewport.getAlignment()));
3483 alignPanel.paintAlignment(true, false);
3493 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3495 new RedundancyPanel(alignPanel, this);
3505 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3507 if ((viewport.getSelectionGroup() == null)
3508 || (viewport.getSelectionGroup().getSize() < 2))
3510 JvOptionPane.showInternalMessageDialog(this,
3511 MessageManager.getString(
3512 "label.you_must_select_least_two_sequences"),
3513 MessageManager.getString("label.invalid_selection"),
3514 JvOptionPane.WARNING_MESSAGE);
3518 JInternalFrame frame = new JInternalFrame();
3519 frame.setContentPane(new PairwiseAlignPanel(viewport));
3520 Desktop.addInternalFrame(frame,
3521 MessageManager.getString("action.pairwise_alignment"), 600,
3527 public void autoCalculate_actionPerformed(ActionEvent e)
3529 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3530 if (viewport.autoCalculateConsensus)
3532 viewport.firePropertyChange("alignment", null,
3533 viewport.getAlignment().getSequences());
3538 public void sortByTreeOption_actionPerformed(ActionEvent e)
3540 viewport.sortByTree = sortByTree.isSelected();
3544 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3546 viewport.followSelection = listenToViewSelections.isSelected();
3550 * Constructs a tree panel and adds it to the desktop
3553 * tree type (NJ or AV)
3555 * name of score model used to compute the tree
3557 * parameters for the distance or similarity calculation
3559 void newTreePanel(String type, String modelName,
3560 SimilarityParamsI options)
3562 String frameTitle = "";
3565 boolean onSelection = false;
3566 if (viewport.getSelectionGroup() != null
3567 && viewport.getSelectionGroup().getSize() > 0)
3569 SequenceGroup sg = viewport.getSelectionGroup();
3571 /* Decide if the selection is a column region */
3572 for (SequenceI _s : sg.getSequences())
3574 if (_s.getLength() < sg.getEndRes())
3576 JvOptionPane.showMessageDialog(Desktop.desktop,
3577 MessageManager.getString(
3578 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3579 MessageManager.getString(
3580 "label.sequences_selection_not_aligned"),
3581 JvOptionPane.WARNING_MESSAGE);
3590 if (viewport.getAlignment().getHeight() < 2)
3596 tp = new TreePanel(alignPanel, type, modelName, options);
3597 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3599 frameTitle += " from ";
3601 if (viewport.viewName != null)
3603 frameTitle += viewport.viewName + " of ";
3606 frameTitle += this.title;
3608 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3619 public void addSortByOrderMenuItem(String title,
3620 final AlignmentOrder order)
3622 final JMenuItem item = new JMenuItem(MessageManager
3623 .formatMessage("action.by_title_param", new Object[]
3626 item.addActionListener(new java.awt.event.ActionListener()
3629 public void actionPerformed(ActionEvent e)
3631 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3633 // TODO: JBPNote - have to map order entries to curent SequenceI
3635 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3637 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3638 viewport.getAlignment()));
3640 alignPanel.paintAlignment(true, false);
3646 * Add a new sort by annotation score menu item
3649 * the menu to add the option to
3651 * the label used to retrieve scores for each sequence on the
3654 public void addSortByAnnotScoreMenuItem(JMenu sort,
3655 final String scoreLabel)
3657 final JMenuItem item = new JMenuItem(scoreLabel);
3659 item.addActionListener(new java.awt.event.ActionListener()
3662 public void actionPerformed(ActionEvent e)
3664 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3665 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3666 viewport.getAlignment());// ,viewport.getSelectionGroup());
3667 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3668 viewport.getAlignment()));
3669 alignPanel.paintAlignment(true, false);
3675 * last hash for alignment's annotation array - used to minimise cost of
3678 protected int _annotationScoreVectorHash;
3681 * search the alignment and rebuild the sort by annotation score submenu the
3682 * last alignment annotation vector hash is stored to minimize cost of
3683 * rebuilding in subsequence calls.
3687 public void buildSortByAnnotationScoresMenu()
3689 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3694 if (viewport.getAlignment().getAlignmentAnnotation()
3695 .hashCode() != _annotationScoreVectorHash)
3697 sortByAnnotScore.removeAll();
3698 // almost certainly a quicker way to do this - but we keep it simple
3699 Hashtable scoreSorts = new Hashtable();
3700 AlignmentAnnotation aann[];
3701 for (SequenceI sqa : viewport.getAlignment().getSequences())
3703 aann = sqa.getAnnotation();
3704 for (int i = 0; aann != null && i < aann.length; i++)
3706 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3708 scoreSorts.put(aann[i].label, aann[i].label);
3712 Enumeration labels = scoreSorts.keys();
3713 while (labels.hasMoreElements())
3715 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3716 (String) labels.nextElement());
3718 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3721 _annotationScoreVectorHash = viewport.getAlignment()
3722 .getAlignmentAnnotation().hashCode();
3727 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3728 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3729 * call. Listeners are added to remove the menu item when the treePanel is
3730 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3734 public void buildTreeSortMenu()
3736 sortByTreeMenu.removeAll();
3738 List<Component> comps = PaintRefresher.components
3739 .get(viewport.getSequenceSetId());
3740 List<TreePanel> treePanels = new ArrayList<>();
3741 for (Component comp : comps)
3743 if (comp instanceof TreePanel)
3745 treePanels.add((TreePanel) comp);
3749 if (treePanels.size() < 1)
3751 sortByTreeMenu.setVisible(false);
3755 sortByTreeMenu.setVisible(true);
3757 for (final TreePanel tp : treePanels)
3759 final JMenuItem item = new JMenuItem(tp.getTitle());
3760 item.addActionListener(new java.awt.event.ActionListener()
3763 public void actionPerformed(ActionEvent e)
3765 tp.sortByTree_actionPerformed();
3766 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3771 sortByTreeMenu.add(item);
3775 public boolean sortBy(AlignmentOrder alorder, String undoname)
3777 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3778 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3779 if (undoname != null)
3781 addHistoryItem(new OrderCommand(undoname, oldOrder,
3782 viewport.getAlignment()));
3784 alignPanel.paintAlignment(true, false);
3789 * Work out whether the whole set of sequences or just the selected set will
3790 * be submitted for multiple alignment.
3793 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3795 // Now, check we have enough sequences
3796 AlignmentView msa = null;
3798 if ((viewport.getSelectionGroup() != null)
3799 && (viewport.getSelectionGroup().getSize() > 1))
3801 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3802 // some common interface!
3804 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3805 * SequenceI[sz = seqs.getSize(false)];
3807 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3808 * seqs.getSequenceAt(i); }
3810 msa = viewport.getAlignmentView(true);
3812 else if (viewport.getSelectionGroup() != null
3813 && viewport.getSelectionGroup().getSize() == 1)
3815 int option = JvOptionPane.showConfirmDialog(this,
3816 MessageManager.getString("warn.oneseq_msainput_selection"),
3817 MessageManager.getString("label.invalid_selection"),
3818 JvOptionPane.OK_CANCEL_OPTION);
3819 if (option == JvOptionPane.OK_OPTION)
3821 msa = viewport.getAlignmentView(false);
3826 msa = viewport.getAlignmentView(false);
3832 * Decides what is submitted to a secondary structure prediction service: the
3833 * first sequence in the alignment, or in the current selection, or, if the
3834 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3835 * region or the whole alignment. (where the first sequence in the set is the
3836 * one that the prediction will be for).
3838 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3840 AlignmentView seqs = null;
3842 if ((viewport.getSelectionGroup() != null)
3843 && (viewport.getSelectionGroup().getSize() > 0))
3845 seqs = viewport.getAlignmentView(true);
3849 seqs = viewport.getAlignmentView(false);
3851 // limit sequences - JBPNote in future - could spawn multiple prediction
3853 // TODO: viewport.getAlignment().isAligned is a global state - the local
3854 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3855 if (!viewport.getAlignment().isAligned(false))
3857 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3858 // TODO: if seqs.getSequences().length>1 then should really have warned
3872 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3874 // Pick the tree file
3875 JalviewFileChooser chooser = new JalviewFileChooser(
3876 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3877 chooser.setFileView(new JalviewFileView());
3878 chooser.setDialogTitle(
3879 MessageManager.getString("label.select_newick_like_tree_file"));
3880 chooser.setToolTipText(
3881 MessageManager.getString("label.load_tree_file"));
3883 int value = chooser.showOpenDialog(null);
3885 if (value == JalviewFileChooser.APPROVE_OPTION)
3887 String filePath = chooser.getSelectedFile().getPath();
3888 Cache.setProperty("LAST_DIRECTORY", filePath);
3889 NewickFile fin = null;
3892 fin = new NewickFile(filePath, DataSourceType.FILE);
3893 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3894 } catch (Exception ex)
3896 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3897 MessageManager.getString("label.problem_reading_tree_file"),
3898 JvOptionPane.WARNING_MESSAGE);
3899 ex.printStackTrace();
3901 if (fin != null && fin.hasWarningMessage())
3903 JvOptionPane.showMessageDialog(Desktop.desktop,
3904 fin.getWarningMessage(),
3906 .getString("label.possible_problem_with_tree_file"),
3907 JvOptionPane.WARNING_MESSAGE);
3912 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3914 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3917 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3918 int h, int x, int y)
3920 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3924 * Add a treeviewer for the tree extracted from a Newick file object to the
3925 * current alignment view
3932 * Associated alignment input data (or null)
3941 * @return TreePanel handle
3943 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3944 AlignmentView input, int w, int h, int x, int y)
3946 TreePanel tp = null;
3952 if (nf.getTree() != null)
3954 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3960 tp.setLocation(x, y);
3963 Desktop.addInternalFrame(tp, treeTitle, w, h);
3965 } catch (Exception ex)
3967 ex.printStackTrace();
3973 private boolean buildingMenu = false;
3976 * Generates menu items and listener event actions for web service clients
3979 public void BuildWebServiceMenu()
3981 while (buildingMenu)
3985 System.err.println("Waiting for building menu to finish.");
3987 } catch (Exception e)
3991 final AlignFrame me = this;
3992 buildingMenu = true;
3993 new Thread(new Runnable()
3998 final List<JMenuItem> legacyItems = new ArrayList<>();
4001 // System.err.println("Building ws menu again "
4002 // + Thread.currentThread());
4003 // TODO: add support for context dependent disabling of services based
4005 // alignment and current selection
4006 // TODO: add additional serviceHandle parameter to specify abstract
4008 // class independently of AbstractName
4009 // TODO: add in rediscovery GUI function to restart discoverer
4010 // TODO: group services by location as well as function and/or
4012 // object broker mechanism.
4013 final Vector<JMenu> wsmenu = new Vector<>();
4014 final IProgressIndicator af = me;
4017 * do not i18n these strings - they are hard-coded in class
4018 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4019 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4021 final JMenu msawsmenu = new JMenu("Alignment");
4022 final JMenu secstrmenu = new JMenu(
4023 "Secondary Structure Prediction");
4024 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4025 final JMenu analymenu = new JMenu("Analysis");
4026 final JMenu dismenu = new JMenu("Protein Disorder");
4027 // JAL-940 - only show secondary structure prediction services from
4028 // the legacy server
4029 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4031 Discoverer.services != null && (Discoverer.services.size() > 0))
4033 // TODO: refactor to allow list of AbstractName/Handler bindings to
4035 // stored or retrieved from elsewhere
4036 // No MSAWS used any more:
4037 // Vector msaws = null; // (Vector)
4038 // Discoverer.services.get("MsaWS");
4039 Vector secstrpr = (Vector) Discoverer.services
4041 if (secstrpr != null)
4043 // Add any secondary structure prediction services
4044 for (int i = 0, j = secstrpr.size(); i < j; i++)
4046 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4048 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4049 .getServiceClient(sh);
4050 int p = secstrmenu.getItemCount();
4051 impl.attachWSMenuEntry(secstrmenu, me);
4052 int q = secstrmenu.getItemCount();
4053 for (int litm = p; litm < q; litm++)
4055 legacyItems.add(secstrmenu.getItem(litm));
4061 // Add all submenus in the order they should appear on the web
4063 wsmenu.add(msawsmenu);
4064 wsmenu.add(secstrmenu);
4065 wsmenu.add(dismenu);
4066 wsmenu.add(analymenu);
4067 // No search services yet
4068 // wsmenu.add(seqsrchmenu);
4070 javax.swing.SwingUtilities.invokeLater(new Runnable()
4077 webService.removeAll();
4078 // first, add discovered services onto the webservices menu
4079 if (wsmenu.size() > 0)
4081 for (int i = 0, j = wsmenu.size(); i < j; i++)
4083 webService.add(wsmenu.get(i));
4088 webService.add(me.webServiceNoServices);
4090 // TODO: move into separate menu builder class.
4091 boolean new_sspred = false;
4092 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4094 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4095 if (jws2servs != null)
4097 if (jws2servs.hasServices())
4099 jws2servs.attachWSMenuEntry(webService, me);
4100 for (Jws2Instance sv : jws2servs.getServices())
4102 if (sv.description.toLowerCase().contains("jpred"))
4104 for (JMenuItem jmi : legacyItems)
4106 jmi.setVisible(false);
4112 if (jws2servs.isRunning())
4114 JMenuItem tm = new JMenuItem(
4115 "Still discovering JABA Services");
4116 tm.setEnabled(false);
4121 build_urlServiceMenu(me.webService);
4122 build_fetchdbmenu(webService);
4123 for (JMenu item : wsmenu)
4125 if (item.getItemCount() == 0)
4127 item.setEnabled(false);
4131 item.setEnabled(true);
4134 } catch (Exception e)
4137 "Exception during web service menu building process.",
4142 } catch (Exception e)
4145 buildingMenu = false;
4152 * construct any groupURL type service menu entries.
4156 private void build_urlServiceMenu(JMenu webService)
4158 // TODO: remove this code when 2.7 is released
4159 // DEBUG - alignmentView
4161 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4162 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4164 * @Override public void actionPerformed(ActionEvent e) {
4165 * jalview.datamodel.AlignmentView
4166 * .testSelectionViews(af.viewport.getAlignment(),
4167 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4169 * }); webService.add(testAlView);
4171 // TODO: refactor to RestClient discoverer and merge menu entries for
4172 // rest-style services with other types of analysis/calculation service
4173 // SHmmr test client - still being implemented.
4174 // DEBUG - alignmentView
4176 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4179 client.attachWSMenuEntry(
4180 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4186 * Searches the alignment sequences for xRefs and builds the Show
4187 * Cross-References menu (formerly called Show Products), with database
4188 * sources for which cross-references are found (protein sources for a
4189 * nucleotide alignment and vice versa)
4191 * @return true if Show Cross-references menu should be enabled
4193 public boolean canShowProducts()
4195 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4196 AlignmentI dataset = viewport.getAlignment().getDataset();
4198 showProducts.removeAll();
4199 final boolean dna = viewport.getAlignment().isNucleotide();
4201 if (seqs == null || seqs.length == 0)
4203 // nothing to see here.
4207 boolean showp = false;
4210 List<String> ptypes = new CrossRef(seqs, dataset)
4211 .findXrefSourcesForSequences(dna);
4213 for (final String source : ptypes)
4216 final AlignFrame af = this;
4217 JMenuItem xtype = new JMenuItem(source);
4218 xtype.addActionListener(new ActionListener()
4221 public void actionPerformed(ActionEvent e)
4223 showProductsFor(af.viewport.getSequenceSelection(), dna,
4227 showProducts.add(xtype);
4229 showProducts.setVisible(showp);
4230 showProducts.setEnabled(showp);
4231 } catch (Exception e)
4234 "canShowProducts threw an exception - please report to help@jalview.org",
4242 * Finds and displays cross-references for the selected sequences (protein
4243 * products for nucleotide sequences, dna coding sequences for peptides).
4246 * the sequences to show cross-references for
4248 * true if from a nucleotide alignment (so showing proteins)
4250 * the database to show cross-references for
4252 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4253 final String source)
4255 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4260 * Construct and display a new frame containing the translation of this
4261 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4264 public void showTranslation_actionPerformed(ActionEvent e)
4266 AlignmentI al = null;
4269 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4271 al = dna.translateCdna();
4272 } catch (Exception ex)
4274 jalview.bin.Cache.log.error(
4275 "Exception during translation. Please report this !", ex);
4276 final String msg = MessageManager.getString(
4277 "label.error_when_translating_sequences_submit_bug_report");
4278 final String errorTitle = MessageManager
4279 .getString("label.implementation_error")
4280 + MessageManager.getString("label.translation_failed");
4281 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4282 JvOptionPane.ERROR_MESSAGE);
4285 if (al == null || al.getHeight() == 0)
4287 final String msg = MessageManager.getString(
4288 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4289 final String errorTitle = MessageManager
4290 .getString("label.translation_failed");
4291 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4292 JvOptionPane.WARNING_MESSAGE);
4296 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4297 af.setFileFormat(this.currentFileFormat);
4298 final String newTitle = MessageManager
4299 .formatMessage("label.translation_of_params", new Object[]
4300 { this.getTitle() });
4301 af.setTitle(newTitle);
4302 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4304 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4305 viewport.openSplitFrame(af, new Alignment(seqs));
4309 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4316 * Set the file format
4320 public void setFileFormat(FileFormatI format)
4322 this.currentFileFormat = format;
4326 * Try to load a features file onto the alignment.
4329 * contents or path to retrieve file
4331 * access mode of file (see jalview.io.AlignFile)
4332 * @return true if features file was parsed correctly.
4334 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4336 return avc.parseFeaturesFile(file, sourceType,
4337 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4342 public void refreshFeatureUI(boolean enableIfNecessary)
4344 // note - currently this is only still here rather than in the controller
4345 // because of the featureSettings hard reference that is yet to be
4347 if (enableIfNecessary)
4349 viewport.setShowSequenceFeatures(true);
4350 showSeqFeatures.setSelected(true);
4356 public void dragEnter(DropTargetDragEvent evt)
4361 public void dragExit(DropTargetEvent evt)
4366 public void dragOver(DropTargetDragEvent evt)
4371 public void dropActionChanged(DropTargetDragEvent evt)
4376 public void drop(DropTargetDropEvent evt)
4378 // JAL-1552 - acceptDrop required before getTransferable call for
4379 // Java's Transferable for native dnd
4380 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4381 Transferable t = evt.getTransferable();
4382 final AlignFrame thisaf = this;
4383 final List<String> files = new ArrayList<>();
4384 List<DataSourceType> protocols = new ArrayList<>();
4388 Desktop.transferFromDropTarget(files, protocols, evt, t);
4389 } catch (Exception e)
4391 e.printStackTrace();
4395 new Thread(new Runnable()
4402 // check to see if any of these files have names matching sequences
4405 SequenceIdMatcher idm = new SequenceIdMatcher(
4406 viewport.getAlignment().getSequencesArray());
4408 * Object[] { String,SequenceI}
4410 ArrayList<Object[]> filesmatched = new ArrayList<>();
4411 ArrayList<String> filesnotmatched = new ArrayList<>();
4412 for (int i = 0; i < files.size(); i++)
4414 String file = files.get(i).toString();
4416 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4417 if (protocol == DataSourceType.FILE)
4419 File fl = new File(file);
4420 pdbfn = fl.getName();
4422 else if (protocol == DataSourceType.URL)
4424 URL url = new URL(file);
4425 pdbfn = url.getFile();
4427 if (pdbfn.length() > 0)
4429 // attempt to find a match in the alignment
4430 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4431 int l = 0, c = pdbfn.indexOf(".");
4432 while (mtch == null && c != -1)
4437 } while ((c = pdbfn.indexOf(".", l)) > l);
4440 pdbfn = pdbfn.substring(0, l);
4442 mtch = idm.findAllIdMatches(pdbfn);
4446 FileFormatI type = null;
4449 type = new IdentifyFile().identify(file, protocol);
4450 } catch (Exception ex)
4454 if (type != null && type.isStructureFile())
4456 filesmatched.add(new Object[] { file, protocol, mtch });
4460 // File wasn't named like one of the sequences or wasn't a PDB
4462 filesnotmatched.add(file);
4466 if (filesmatched.size() > 0)
4468 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4469 || JvOptionPane.showConfirmDialog(thisaf,
4470 MessageManager.formatMessage(
4471 "label.automatically_associate_structure_files_with_sequences_same_name",
4473 { Integer.valueOf(filesmatched.size())
4475 MessageManager.getString(
4476 "label.automatically_associate_structure_files_by_name"),
4477 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4480 for (Object[] fm : filesmatched)
4482 // try and associate
4483 // TODO: may want to set a standard ID naming formalism for
4484 // associating PDB files which have no IDs.
4485 for (SequenceI toassoc : (SequenceI[]) fm[2])
4487 PDBEntry pe = new AssociatePdbFileWithSeq()
4488 .associatePdbWithSeq((String) fm[0],
4489 (DataSourceType) fm[1], toassoc, false,
4493 System.err.println("Associated file : "
4494 + ((String) fm[0]) + " with "
4495 + toassoc.getDisplayId(true));
4499 // TODO: do we need to update overview ? only if features are
4501 alignPanel.paintAlignment(true, false);
4505 if (filesnotmatched.size() > 0)
4507 if (assocfiles > 0 && (Cache.getDefault(
4508 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4509 || JvOptionPane.showConfirmDialog(thisaf,
4510 "<html>" + MessageManager.formatMessage(
4511 "label.ignore_unmatched_dropped_files_info",
4514 filesnotmatched.size())
4517 MessageManager.getString(
4518 "label.ignore_unmatched_dropped_files"),
4519 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4523 for (String fn : filesnotmatched)
4525 loadJalviewDataFile(fn, null, null, null);
4529 } catch (Exception ex)
4531 ex.printStackTrace();
4539 * Attempt to load a "dropped" file or URL string, by testing in turn for
4541 * <li>an Annotation file</li>
4542 * <li>a JNet file</li>
4543 * <li>a features file</li>
4544 * <li>else try to interpret as an alignment file</li>
4548 * either a filename or a URL string.
4550 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4551 FileFormatI format, SequenceI assocSeq)
4555 if (sourceType == null)
4557 sourceType = FormatAdapter.checkProtocol(file);
4559 // if the file isn't identified, or not positively identified as some
4560 // other filetype (PFAM is default unidentified alignment file type) then
4561 // try to parse as annotation.
4562 boolean isAnnotation = (format == null
4563 || FileFormat.Pfam.equals(format))
4564 ? new AnnotationFile().annotateAlignmentView(viewport,
4570 // first see if its a T-COFFEE score file
4571 TCoffeeScoreFile tcf = null;
4574 tcf = new TCoffeeScoreFile(file, sourceType);
4577 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4581 new TCoffeeColourScheme(viewport.getAlignment()));
4582 isAnnotation = true;
4583 statusBar.setText(MessageManager.getString(
4584 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4588 // some problem - if no warning its probable that the ID matching
4589 // process didn't work
4590 JvOptionPane.showMessageDialog(Desktop.desktop,
4591 tcf.getWarningMessage() == null
4592 ? MessageManager.getString(
4593 "label.check_file_matches_sequence_ids_alignment")
4594 : tcf.getWarningMessage(),
4595 MessageManager.getString(
4596 "label.problem_reading_tcoffee_score_file"),
4597 JvOptionPane.WARNING_MESSAGE);
4604 } catch (Exception x)
4607 "Exception when processing data source as T-COFFEE score file",
4613 // try to see if its a JNet 'concise' style annotation file *before*
4615 // try to parse it as a features file
4618 format = new IdentifyFile().identify(file, sourceType);
4620 if (FileFormat.ScoreMatrix == format)
4622 ScoreMatrixFile sm = new ScoreMatrixFile(
4623 new FileParse(file, sourceType));
4625 // todo: i18n this message
4626 statusBar.setText(MessageManager.formatMessage(
4627 "label.successfully_loaded_matrix",
4628 sm.getMatrixName()));
4630 else if (FileFormat.Jnet.equals(format))
4632 JPredFile predictions = new JPredFile(file, sourceType);
4633 new JnetAnnotationMaker();
4634 JnetAnnotationMaker.add_annotation(predictions,
4635 viewport.getAlignment(), 0, false);
4636 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4637 viewport.getAlignment().setSeqrep(repseq);
4638 HiddenColumns cs = new HiddenColumns();
4639 cs.hideInsertionsFor(repseq);
4640 viewport.getAlignment().setHiddenColumns(cs);
4641 isAnnotation = true;
4643 // else if (IdentifyFile.FeaturesFile.equals(format))
4644 else if (FileFormat.Features.equals(format))
4646 if (parseFeaturesFile(file, sourceType))
4648 alignPanel.paintAlignment(true, true);
4653 new FileLoader().LoadFile(viewport, file, sourceType, format);
4660 alignPanel.adjustAnnotationHeight();
4661 viewport.updateSequenceIdColours();
4662 buildSortByAnnotationScoresMenu();
4663 alignPanel.paintAlignment(true, true);
4665 } catch (Exception ex)
4667 ex.printStackTrace();
4668 } catch (OutOfMemoryError oom)
4673 } catch (Exception x)
4678 + (sourceType != null
4679 ? (sourceType == DataSourceType.PASTE
4681 : "using " + sourceType + " from "
4685 ? "(parsing as '" + format + "' file)"
4687 oom, Desktop.desktop);
4692 * Method invoked by the ChangeListener on the tabbed pane, in other words
4693 * when a different tabbed pane is selected by the user or programmatically.
4696 public void tabSelectionChanged(int index)
4700 alignPanel = alignPanels.get(index);
4701 viewport = alignPanel.av;
4702 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4703 setMenusFromViewport(viewport);
4707 * 'focus' any colour slider that is open to the selected viewport
4709 if (viewport.getConservationSelected())
4711 SliderPanel.setConservationSlider(alignPanel,
4712 viewport.getResidueShading(), alignPanel.getViewName());
4716 SliderPanel.hideConservationSlider();
4718 if (viewport.getAbovePIDThreshold())
4720 SliderPanel.setPIDSliderSource(alignPanel,
4721 viewport.getResidueShading(), alignPanel.getViewName());
4725 SliderPanel.hidePIDSlider();
4729 * If there is a frame linked to this one in a SplitPane, switch it to the
4730 * same view tab index. No infinite recursion of calls should happen, since
4731 * tabSelectionChanged() should not get invoked on setting the selected
4732 * index to an unchanged value. Guard against setting an invalid index
4733 * before the new view peer tab has been created.
4735 final AlignViewportI peer = viewport.getCodingComplement();
4738 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4739 .getAlignPanel().alignFrame;
4740 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4742 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4748 * On right mouse click on view tab, prompt for and set new view name.
4751 public void tabbedPane_mousePressed(MouseEvent e)
4753 if (e.isPopupTrigger())
4755 String msg = MessageManager.getString("label.enter_view_name");
4756 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4757 JvOptionPane.QUESTION_MESSAGE);
4761 viewport.viewName = reply;
4762 // TODO warn if reply is in getExistingViewNames()?
4763 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4768 public AlignViewport getCurrentView()
4774 * Open the dialog for regex description parsing.
4777 protected void extractScores_actionPerformed(ActionEvent e)
4779 ParseProperties pp = new jalview.analysis.ParseProperties(
4780 viewport.getAlignment());
4781 // TODO: verify regex and introduce GUI dialog for version 2.5
4782 // if (pp.getScoresFromDescription("col", "score column ",
4783 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4785 if (pp.getScoresFromDescription("description column",
4786 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4788 buildSortByAnnotationScoresMenu();
4796 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4800 protected void showDbRefs_actionPerformed(ActionEvent e)
4802 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4808 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4812 protected void showNpFeats_actionPerformed(ActionEvent e)
4814 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4818 * find the viewport amongst the tabs in this alignment frame and close that
4823 public boolean closeView(AlignViewportI av)
4827 this.closeMenuItem_actionPerformed(false);
4830 Component[] comp = tabbedPane.getComponents();
4831 for (int i = 0; comp != null && i < comp.length; i++)
4833 if (comp[i] instanceof AlignmentPanel)
4835 if (((AlignmentPanel) comp[i]).av == av)
4838 closeView((AlignmentPanel) comp[i]);
4846 protected void build_fetchdbmenu(JMenu webService)
4848 // Temporary hack - DBRef Fetcher always top level ws entry.
4849 // TODO We probably want to store a sequence database checklist in
4850 // preferences and have checkboxes.. rather than individual sources selected
4852 final JMenu rfetch = new JMenu(
4853 MessageManager.getString("action.fetch_db_references"));
4854 rfetch.setToolTipText(MessageManager.getString(
4855 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4856 webService.add(rfetch);
4858 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4859 MessageManager.getString("option.trim_retrieved_seqs"));
4860 trimrs.setToolTipText(
4861 MessageManager.getString("label.trim_retrieved_sequences"));
4862 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4863 trimrs.addActionListener(new ActionListener()
4866 public void actionPerformed(ActionEvent e)
4868 trimrs.setSelected(trimrs.isSelected());
4869 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4870 Boolean.valueOf(trimrs.isSelected()).toString());
4874 JMenuItem fetchr = new JMenuItem(
4875 MessageManager.getString("label.standard_databases"));
4876 fetchr.setToolTipText(
4877 MessageManager.getString("label.fetch_embl_uniprot"));
4878 fetchr.addActionListener(new ActionListener()
4882 public void actionPerformed(ActionEvent e)
4884 new Thread(new Runnable()
4889 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4890 .getAlignment().isNucleotide();
4891 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4892 alignPanel.av.getSequenceSelection(),
4893 alignPanel.alignFrame, null,
4894 alignPanel.alignFrame.featureSettings, isNucleotide);
4895 dbRefFetcher.addListener(new FetchFinishedListenerI()
4898 public void finished()
4900 AlignFrame.this.setMenusForViewport();
4903 dbRefFetcher.fetchDBRefs(false);
4911 final AlignFrame me = this;
4912 new Thread(new Runnable()
4917 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4918 .getSequenceFetcherSingleton(me);
4919 javax.swing.SwingUtilities.invokeLater(new Runnable()
4924 String[] dbclasses = sf.getOrderedSupportedSources();
4925 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4926 // jalview.util.QuickSort.sort(otherdb, otherdb);
4927 List<DbSourceProxy> otherdb;
4928 JMenu dfetch = new JMenu();
4929 JMenu ifetch = new JMenu();
4930 JMenuItem fetchr = null;
4931 int comp = 0, icomp = 0, mcomp = 15;
4932 String mname = null;
4934 for (String dbclass : dbclasses)
4936 otherdb = sf.getSourceProxy(dbclass);
4937 // add a single entry for this class, or submenu allowing 'fetch
4939 if (otherdb == null || otherdb.size() < 1)
4943 // List<DbSourceProxy> dbs=otherdb;
4944 // otherdb=new ArrayList<DbSourceProxy>();
4945 // for (DbSourceProxy db:dbs)
4947 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4951 mname = "From " + dbclass;
4953 if (otherdb.size() == 1)
4955 final DbSourceProxy[] dassource = otherdb
4956 .toArray(new DbSourceProxy[0]);
4957 DbSourceProxy src = otherdb.get(0);
4958 fetchr = new JMenuItem(src.getDbSource());
4959 fetchr.addActionListener(new ActionListener()
4963 public void actionPerformed(ActionEvent e)
4965 new Thread(new Runnable()
4971 boolean isNucleotide = alignPanel.alignFrame
4972 .getViewport().getAlignment()
4974 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4975 alignPanel.av.getSequenceSelection(),
4976 alignPanel.alignFrame, dassource,
4977 alignPanel.alignFrame.featureSettings,
4980 .addListener(new FetchFinishedListenerI()
4983 public void finished()
4985 AlignFrame.this.setMenusForViewport();
4988 dbRefFetcher.fetchDBRefs(false);
4994 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
4995 MessageManager.formatMessage(
4996 "label.fetch_retrieve_from", new Object[]
4997 { src.getDbName() })));
5003 final DbSourceProxy[] dassource = otherdb
5004 .toArray(new DbSourceProxy[0]);
5006 DbSourceProxy src = otherdb.get(0);
5007 fetchr = new JMenuItem(MessageManager
5008 .formatMessage("label.fetch_all_param", new Object[]
5009 { src.getDbSource() }));
5010 fetchr.addActionListener(new ActionListener()
5013 public void actionPerformed(ActionEvent e)
5015 new Thread(new Runnable()
5021 boolean isNucleotide = alignPanel.alignFrame
5022 .getViewport().getAlignment()
5024 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5025 alignPanel.av.getSequenceSelection(),
5026 alignPanel.alignFrame, dassource,
5027 alignPanel.alignFrame.featureSettings,
5030 .addListener(new FetchFinishedListenerI()
5033 public void finished()
5035 AlignFrame.this.setMenusForViewport();
5038 dbRefFetcher.fetchDBRefs(false);
5044 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5045 MessageManager.formatMessage(
5046 "label.fetch_retrieve_from_all_sources",
5048 { Integer.valueOf(otherdb.size())
5050 src.getDbSource(), src.getDbName() })));
5053 // and then build the rest of the individual menus
5054 ifetch = new JMenu(MessageManager.formatMessage(
5055 "label.source_from_db_source", new Object[]
5056 { src.getDbSource() }));
5058 String imname = null;
5060 for (DbSourceProxy sproxy : otherdb)
5062 String dbname = sproxy.getDbName();
5063 String sname = dbname.length() > 5
5064 ? dbname.substring(0, 5) + "..."
5066 String msname = dbname.length() > 10
5067 ? dbname.substring(0, 10) + "..."
5071 imname = MessageManager
5072 .formatMessage("label.from_msname", new Object[]
5075 fetchr = new JMenuItem(msname);
5076 final DbSourceProxy[] dassrc = { sproxy };
5077 fetchr.addActionListener(new ActionListener()
5081 public void actionPerformed(ActionEvent e)
5083 new Thread(new Runnable()
5089 boolean isNucleotide = alignPanel.alignFrame
5090 .getViewport().getAlignment()
5092 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5093 alignPanel.av.getSequenceSelection(),
5094 alignPanel.alignFrame, dassrc,
5095 alignPanel.alignFrame.featureSettings,
5098 .addListener(new FetchFinishedListenerI()
5101 public void finished()
5103 AlignFrame.this.setMenusForViewport();
5106 dbRefFetcher.fetchDBRefs(false);
5112 fetchr.setToolTipText(
5113 "<html>" + MessageManager.formatMessage(
5114 "label.fetch_retrieve_from", new Object[]
5118 if (++icomp >= mcomp || i == (otherdb.size()))
5120 ifetch.setText(MessageManager.formatMessage(
5121 "label.source_to_target", imname, sname));
5123 ifetch = new JMenu();
5131 if (comp >= mcomp || dbi >= (dbclasses.length))
5133 dfetch.setText(MessageManager.formatMessage(
5134 "label.source_to_target", mname, dbclass));
5136 dfetch = new JMenu();
5149 * Left justify the whole alignment.
5152 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5154 AlignmentI al = viewport.getAlignment();
5156 viewport.firePropertyChange("alignment", null, al);
5160 * Right justify the whole alignment.
5163 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5165 AlignmentI al = viewport.getAlignment();
5167 viewport.firePropertyChange("alignment", null, al);
5171 public void setShowSeqFeatures(boolean b)
5173 showSeqFeatures.setSelected(b);
5174 viewport.setShowSequenceFeatures(b);
5181 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5182 * awt.event.ActionEvent)
5185 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5187 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5188 alignPanel.paintAlignment(false, false);
5195 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5199 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5201 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5202 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5210 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5211 * .event.ActionEvent)
5214 protected void showGroupConservation_actionPerformed(ActionEvent e)
5216 viewport.setShowGroupConservation(showGroupConservation.getState());
5217 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5224 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5225 * .event.ActionEvent)
5228 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5230 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5231 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5238 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5239 * .event.ActionEvent)
5242 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5244 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5245 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5249 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5251 showSequenceLogo.setState(true);
5252 viewport.setShowSequenceLogo(true);
5253 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5254 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5258 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5260 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5267 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5268 * .event.ActionEvent)
5271 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5273 if (avc.makeGroupsFromSelection())
5275 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5276 alignPanel.updateAnnotation();
5277 alignPanel.paintAlignment(true, true);
5281 public void clearAlignmentSeqRep()
5283 // TODO refactor alignmentseqrep to controller
5284 if (viewport.getAlignment().hasSeqrep())
5286 viewport.getAlignment().setSeqrep(null);
5287 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5288 alignPanel.updateAnnotation();
5289 alignPanel.paintAlignment(true, true);
5294 protected void createGroup_actionPerformed(ActionEvent e)
5296 if (avc.createGroup())
5298 alignPanel.alignmentChanged();
5303 protected void unGroup_actionPerformed(ActionEvent e)
5307 alignPanel.alignmentChanged();
5312 * make the given alignmentPanel the currently selected tab
5314 * @param alignmentPanel
5316 public void setDisplayedView(AlignmentPanel alignmentPanel)
5318 if (!viewport.getSequenceSetId()
5319 .equals(alignmentPanel.av.getSequenceSetId()))
5321 throw new Error(MessageManager.getString(
5322 "error.implementation_error_cannot_show_view_alignment_frame"));
5324 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5325 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5327 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5332 * Action on selection of menu options to Show or Hide annotations.
5335 * @param forSequences
5336 * update sequence-related annotations
5337 * @param forAlignment
5338 * update non-sequence-related annotations
5341 protected void setAnnotationsVisibility(boolean visible,
5342 boolean forSequences, boolean forAlignment)
5344 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5345 .getAlignmentAnnotation();
5350 for (AlignmentAnnotation aa : anns)
5353 * don't display non-positional annotations on an alignment
5355 if (aa.annotations == null)
5359 boolean apply = (aa.sequenceRef == null && forAlignment)
5360 || (aa.sequenceRef != null && forSequences);
5363 aa.visible = visible;
5366 alignPanel.validateAnnotationDimensions(true);
5367 alignPanel.alignmentChanged();
5371 * Store selected annotation sort order for the view and repaint.
5374 protected void sortAnnotations_actionPerformed()
5376 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5378 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5379 alignPanel.paintAlignment(false, false);
5384 * @return alignment panels in this alignment frame
5386 public List<? extends AlignmentViewPanel> getAlignPanels()
5388 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5392 * Open a new alignment window, with the cDNA associated with this (protein)
5393 * alignment, aligned as is the protein.
5395 protected void viewAsCdna_actionPerformed()
5397 // TODO no longer a menu action - refactor as required
5398 final AlignmentI alignment = getViewport().getAlignment();
5399 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5400 if (mappings == null)
5404 List<SequenceI> cdnaSeqs = new ArrayList<>();
5405 for (SequenceI aaSeq : alignment.getSequences())
5407 for (AlignedCodonFrame acf : mappings)
5409 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5413 * There is a cDNA mapping for this protein sequence - add to new
5414 * alignment. It will share the same dataset sequence as other mapped
5415 * cDNA (no new mappings need to be created).
5417 final Sequence newSeq = new Sequence(dnaSeq);
5418 newSeq.setDatasetSequence(dnaSeq);
5419 cdnaSeqs.add(newSeq);
5423 if (cdnaSeqs.size() == 0)
5425 // show a warning dialog no mapped cDNA
5428 AlignmentI cdna = new Alignment(
5429 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5430 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5431 AlignFrame.DEFAULT_HEIGHT);
5432 cdna.alignAs(alignment);
5433 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5435 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5436 AlignFrame.DEFAULT_HEIGHT);
5440 * Set visibility of dna/protein complement view (available when shown in a
5446 protected void showComplement_actionPerformed(boolean show)
5448 SplitContainerI sf = getSplitViewContainer();
5451 sf.setComplementVisible(this, show);
5456 * Generate the reverse (optionally complemented) of the selected sequences,
5457 * and add them to the alignment
5460 protected void showReverse_actionPerformed(boolean complement)
5462 AlignmentI al = null;
5465 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5466 al = dna.reverseCdna(complement);
5467 viewport.addAlignment(al, "");
5468 addHistoryItem(new EditCommand(
5469 MessageManager.getString("label.add_sequences"), Action.PASTE,
5470 al.getSequencesArray(), 0, al.getWidth(),
5471 viewport.getAlignment()));
5472 } catch (Exception ex)
5474 System.err.println(ex.getMessage());
5480 * Try to run a script in the Groovy console, having first ensured that this
5481 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5482 * be targeted at this alignment.
5485 protected void runGroovy_actionPerformed()
5487 Jalview.setCurrentAlignFrame(this);
5488 groovy.ui.Console console = Desktop.getGroovyConsole();
5489 if (console != null)
5493 console.runScript();
5494 } catch (Exception ex)
5496 System.err.println((ex.toString()));
5497 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5498 MessageManager.getString("label.couldnt_run_groovy_script"),
5499 MessageManager.getString("label.groovy_support_failed"),
5500 JvOptionPane.ERROR_MESSAGE);
5505 System.err.println("Can't run Groovy script as console not found");
5510 * Hides columns containing (or not containing) a specified feature, provided
5511 * that would not leave all columns hidden
5513 * @param featureType
5514 * @param columnsContaining
5517 public boolean hideFeatureColumns(String featureType,
5518 boolean columnsContaining)
5520 boolean notForHiding = avc.markColumnsContainingFeatures(
5521 columnsContaining, false, false, featureType);
5524 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5525 false, featureType))
5527 getViewport().hideSelectedColumns();
5535 protected void selectHighlightedColumns_actionPerformed(
5536 ActionEvent actionEvent)
5538 // include key modifier check in case user selects from menu
5539 avc.markHighlightedColumns(
5540 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5541 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5542 | ActionEvent.CTRL_MASK)) != 0);
5546 * Rebuilds the Colour menu, including any user-defined colours which have
5547 * been loaded either on startup or during the session
5549 public void buildColourMenu()
5551 colourMenu.removeAll();
5553 colourMenu.add(applyToAllGroups);
5554 colourMenu.add(textColour);
5555 colourMenu.addSeparator();
5557 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5560 colourMenu.addSeparator();
5561 colourMenu.add(conservationMenuItem);
5562 colourMenu.add(modifyConservation);
5563 colourMenu.add(abovePIDThreshold);
5564 colourMenu.add(modifyPID);
5565 colourMenu.add(annotationColour);
5567 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5568 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5572 * Open a dialog (if not already open) that allows the user to select and
5573 * calculate PCA or Tree analysis
5575 protected void openTreePcaDialog()
5577 if (alignPanel.getCalculationDialog() == null)
5579 new CalculationChooser(AlignFrame.this);
5584 class PrintThread extends Thread
5588 public PrintThread(AlignmentPanel ap)
5593 static PageFormat pf;
5598 PrinterJob printJob = PrinterJob.getPrinterJob();
5602 printJob.setPrintable(ap, pf);
5606 printJob.setPrintable(ap);
5609 if (printJob.printDialog())
5614 } catch (Exception PrintException)
5616 PrintException.printStackTrace();