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.HMMFile;
76 import jalview.io.HtmlSvgOutput;
77 import jalview.io.IdentifyFile;
78 import jalview.io.JPredFile;
79 import jalview.io.JalviewFileChooser;
80 import jalview.io.JalviewFileView;
81 import jalview.io.JnetAnnotationMaker;
82 import jalview.io.NewickFile;
83 import jalview.io.ScoreMatrixFile;
84 import jalview.io.TCoffeeScoreFile;
85 import jalview.jbgui.GAlignFrame;
86 import jalview.schemes.ColourSchemeI;
87 import jalview.schemes.ColourSchemes;
88 import jalview.schemes.ResidueColourScheme;
89 import jalview.schemes.TCoffeeColourScheme;
90 import jalview.util.MessageManager;
91 import jalview.viewmodel.AlignmentViewport;
92 import jalview.viewmodel.ViewportRanges;
93 import jalview.ws.DBRefFetcher;
94 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
95 import jalview.ws.jws1.Discoverer;
96 import jalview.ws.jws2.Jws2Discoverer;
97 import jalview.ws.jws2.jabaws2.Jws2Instance;
98 import jalview.ws.seqfetcher.DbSourceProxy;
100 import java.awt.BorderLayout;
101 import java.awt.Component;
102 import java.awt.Rectangle;
103 import java.awt.Toolkit;
104 import java.awt.datatransfer.Clipboard;
105 import java.awt.datatransfer.DataFlavor;
106 import java.awt.datatransfer.StringSelection;
107 import java.awt.datatransfer.Transferable;
108 import java.awt.dnd.DnDConstants;
109 import java.awt.dnd.DropTargetDragEvent;
110 import java.awt.dnd.DropTargetDropEvent;
111 import java.awt.dnd.DropTargetEvent;
112 import java.awt.dnd.DropTargetListener;
113 import java.awt.event.ActionEvent;
114 import java.awt.event.ActionListener;
115 import java.awt.event.FocusAdapter;
116 import java.awt.event.FocusEvent;
117 import java.awt.event.ItemEvent;
118 import java.awt.event.ItemListener;
119 import java.awt.event.KeyAdapter;
120 import java.awt.event.KeyEvent;
121 import java.awt.event.MouseEvent;
122 import java.awt.print.PageFormat;
123 import java.awt.print.PrinterJob;
124 import java.beans.PropertyChangeEvent;
126 import java.io.FileWriter;
127 import java.io.PrintWriter;
129 import java.util.ArrayList;
130 import java.util.Arrays;
131 import java.util.Deque;
132 import java.util.Enumeration;
133 import java.util.Hashtable;
134 import java.util.List;
135 import java.util.Vector;
137 import javax.swing.JCheckBoxMenuItem;
138 import javax.swing.JEditorPane;
139 import javax.swing.JInternalFrame;
140 import javax.swing.JLayeredPane;
141 import javax.swing.JMenu;
142 import javax.swing.JMenuItem;
143 import javax.swing.JScrollPane;
144 import javax.swing.SwingUtilities;
150 * @version $Revision$
152 public class AlignFrame extends GAlignFrame implements DropTargetListener,
153 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
156 public static final int DEFAULT_WIDTH = 700;
158 public static final int DEFAULT_HEIGHT = 500;
161 * The currently displayed panel (selected tabbed view if more than one)
163 public AlignmentPanel alignPanel;
165 AlignViewport viewport;
167 ViewportRanges vpRanges;
169 public AlignViewControllerI avc;
171 List<AlignmentPanel> alignPanels = new ArrayList<>();
174 * Last format used to load or save alignments in this window
176 FileFormatI currentFileFormat = null;
179 * Current filename for this alignment
181 String fileName = null;
184 * Creates a new AlignFrame object with specific width and height.
190 public AlignFrame(AlignmentI al, int width, int height)
192 this(al, null, width, height);
196 * Creates a new AlignFrame object with specific width, height and
202 * @param sequenceSetId
204 public AlignFrame(AlignmentI al, int width, int height,
205 String sequenceSetId)
207 this(al, null, width, height, sequenceSetId);
211 * Creates a new AlignFrame object with specific width, height and
217 * @param sequenceSetId
220 public AlignFrame(AlignmentI al, int width, int height,
221 String sequenceSetId, String viewId)
223 this(al, null, width, height, sequenceSetId, viewId);
227 * new alignment window with hidden columns
231 * @param hiddenColumns
232 * ColumnSelection or null
234 * Width of alignment frame
238 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
239 int width, int height)
241 this(al, hiddenColumns, width, height, null);
245 * Create alignment frame for al with hiddenColumns, a specific width and
246 * height, and specific sequenceId
249 * @param hiddenColumns
252 * @param sequenceSetId
255 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
256 int width, int height, String sequenceSetId)
258 this(al, hiddenColumns, width, height, sequenceSetId, null);
262 * Create alignment frame for al with hiddenColumns, a specific width and
263 * height, and specific sequenceId
266 * @param hiddenColumns
269 * @param sequenceSetId
274 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
275 int width, int height, String sequenceSetId, String viewId)
277 setSize(width, height);
279 if (al.getDataset() == null)
284 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
286 alignPanel = new AlignmentPanel(this, viewport);
288 addAlignmentPanel(alignPanel, true);
292 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
293 HiddenColumns hiddenColumns, int width, int height)
295 setSize(width, height);
297 if (al.getDataset() == null)
302 viewport = new AlignViewport(al, hiddenColumns);
304 if (hiddenSeqs != null && hiddenSeqs.length > 0)
306 viewport.hideSequence(hiddenSeqs);
308 alignPanel = new AlignmentPanel(this, viewport);
309 addAlignmentPanel(alignPanel, true);
314 * Make a new AlignFrame from existing alignmentPanels
321 public AlignFrame(AlignmentPanel ap)
325 addAlignmentPanel(ap, false);
330 * initalise the alignframe from the underlying viewport data and the
335 if (!Jalview.isHeadlessMode())
337 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
340 vpRanges = viewport.getRanges();
341 avc = new jalview.controller.AlignViewController(this, viewport,
343 if (viewport.getAlignmentConservationAnnotation() == null)
345 // BLOSUM62Colour.setEnabled(false);
346 conservationMenuItem.setEnabled(false);
347 modifyConservation.setEnabled(false);
348 // PIDColour.setEnabled(false);
349 // abovePIDThreshold.setEnabled(false);
350 // modifyPID.setEnabled(false);
353 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
356 if (sortby.equals("Id"))
358 sortIDMenuItem_actionPerformed(null);
360 else if (sortby.equals("Pairwise Identity"))
362 sortPairwiseMenuItem_actionPerformed(null);
366 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
368 setMenusFromViewport(viewport);
369 buildSortByAnnotationScoresMenu();
370 calculateTree.addActionListener(new ActionListener()
374 public void actionPerformed(ActionEvent e)
381 if (Desktop.desktop != null)
383 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
384 addServiceListeners();
388 if (viewport.getWrapAlignment())
390 wrapMenuItem_actionPerformed(null);
393 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
395 this.overviewMenuItem_actionPerformed(null);
400 final List<AlignmentPanel> selviews = new ArrayList<>();
401 final List<AlignmentPanel> origview = new ArrayList<>();
402 final String menuLabel = MessageManager
403 .getString("label.copy_format_from");
404 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
405 new ViewSetProvider()
409 public AlignmentPanel[] getAllAlignmentPanels()
412 origview.add(alignPanel);
413 // make an array of all alignment panels except for this one
414 List<AlignmentPanel> aps = new ArrayList<>(
415 Arrays.asList(Desktop.getAlignmentPanels(null)));
416 aps.remove(AlignFrame.this.alignPanel);
417 return aps.toArray(new AlignmentPanel[aps.size()]);
419 }, selviews, new ItemListener()
423 public void itemStateChanged(ItemEvent e)
425 if (origview.size() > 0)
427 final AlignmentPanel ap = origview.get(0);
430 * Copy the ViewStyle of the selected panel to 'this one'.
431 * Don't change value of 'scaleProteinAsCdna' unless copying
434 ViewStyleI vs = selviews.get(0).getAlignViewport()
436 boolean fromSplitFrame = selviews.get(0)
437 .getAlignViewport().getCodingComplement() != null;
440 vs.setScaleProteinAsCdna(ap.getAlignViewport()
441 .getViewStyle().isScaleProteinAsCdna());
443 ap.getAlignViewport().setViewStyle(vs);
446 * Also rescale ViewStyle of SplitFrame complement if there is
447 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
448 * the whole ViewStyle (allow cDNA protein to have different
451 AlignViewportI complement = ap.getAlignViewport()
452 .getCodingComplement();
453 if (complement != null && vs.isScaleProteinAsCdna())
455 AlignFrame af = Desktop.getAlignFrameFor(complement);
456 ((SplitFrame) af.getSplitViewContainer())
458 af.setMenusForViewport();
462 ap.setSelected(true);
463 ap.alignFrame.setMenusForViewport();
468 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
469 .indexOf("devel") > -1
470 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
471 .indexOf("test") > -1)
473 formatMenu.add(vsel);
475 addFocusListener(new FocusAdapter()
478 public void focusGained(FocusEvent e)
480 Jalview.setCurrentAlignFrame(AlignFrame.this);
487 * Change the filename and format for the alignment, and enable the 'reload'
488 * button functionality.
495 public void setFileName(String file, FileFormatI format)
498 setFileFormat(format);
499 reload.setEnabled(true);
503 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
506 void addKeyListener()
508 addKeyListener(new KeyAdapter()
511 public void keyPressed(KeyEvent evt)
513 if (viewport.cursorMode
514 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
515 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
516 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
517 && Character.isDigit(evt.getKeyChar()))
519 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
522 switch (evt.getKeyCode())
525 case 27: // escape key
526 deselectAllSequenceMenuItem_actionPerformed(null);
530 case KeyEvent.VK_DOWN:
531 if (evt.isAltDown() || !viewport.cursorMode)
533 moveSelectedSequences(false);
535 if (viewport.cursorMode)
537 alignPanel.getSeqPanel().moveCursor(0, 1);
542 if (evt.isAltDown() || !viewport.cursorMode)
544 moveSelectedSequences(true);
546 if (viewport.cursorMode)
548 alignPanel.getSeqPanel().moveCursor(0, -1);
553 case KeyEvent.VK_LEFT:
554 if (evt.isAltDown() || !viewport.cursorMode)
556 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
560 alignPanel.getSeqPanel().moveCursor(-1, 0);
565 case KeyEvent.VK_RIGHT:
566 if (evt.isAltDown() || !viewport.cursorMode)
568 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
572 alignPanel.getSeqPanel().moveCursor(1, 0);
576 case KeyEvent.VK_SPACE:
577 if (viewport.cursorMode)
579 alignPanel.getSeqPanel().insertGapAtCursor(
580 evt.isControlDown() || evt.isShiftDown()
585 // case KeyEvent.VK_A:
586 // if (viewport.cursorMode)
588 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
589 // //System.out.println("A");
593 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
594 * System.out.println("closing bracket"); } break;
596 case KeyEvent.VK_DELETE:
597 case KeyEvent.VK_BACK_SPACE:
598 if (!viewport.cursorMode)
600 cut_actionPerformed(null);
604 alignPanel.getSeqPanel().deleteGapAtCursor(
605 evt.isControlDown() || evt.isShiftDown()
612 if (viewport.cursorMode)
614 alignPanel.getSeqPanel().setCursorRow();
618 if (viewport.cursorMode && !evt.isControlDown())
620 alignPanel.getSeqPanel().setCursorColumn();
624 if (viewport.cursorMode)
626 alignPanel.getSeqPanel().setCursorPosition();
630 case KeyEvent.VK_ENTER:
631 case KeyEvent.VK_COMMA:
632 if (viewport.cursorMode)
634 alignPanel.getSeqPanel().setCursorRowAndColumn();
639 if (viewport.cursorMode)
641 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
645 if (viewport.cursorMode)
647 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
652 viewport.cursorMode = !viewport.cursorMode;
653 statusBar.setText(MessageManager.formatMessage(
654 "label.keyboard_editing_mode",
655 new String[] { (viewport.cursorMode ? "on" : "off") }));
656 if (viewport.cursorMode)
658 alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
660 alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
663 alignPanel.getSeqPanel().seqCanvas.repaint();
669 Help.showHelpWindow();
670 } catch (Exception ex)
672 ex.printStackTrace();
677 boolean toggleSeqs = !evt.isControlDown();
678 boolean toggleCols = !evt.isShiftDown();
679 toggleHiddenRegions(toggleSeqs, toggleCols);
684 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
685 boolean modifyExisting = true; // always modify, don't clear
686 // evt.isShiftDown();
687 boolean invertHighlighted = evt.isAltDown();
688 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
692 case KeyEvent.VK_PAGE_UP:
693 if (viewport.getWrapAlignment())
695 vpRanges.scrollUp(true);
702 case KeyEvent.VK_PAGE_DOWN:
703 if (viewport.getWrapAlignment())
705 vpRanges.scrollUp(false);
716 public void keyReleased(KeyEvent evt)
718 switch (evt.getKeyCode())
720 case KeyEvent.VK_LEFT:
721 if (evt.isAltDown() || !viewport.cursorMode)
723 viewport.firePropertyChange("alignment", null, viewport
724 .getAlignment().getSequences());
728 case KeyEvent.VK_RIGHT:
729 if (evt.isAltDown() || !viewport.cursorMode)
731 viewport.firePropertyChange("alignment", null, viewport
732 .getAlignment().getSequences());
740 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
742 ap.alignFrame = this;
743 avc = new jalview.controller.AlignViewController(this, viewport,
748 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
750 int aSize = alignPanels.size();
752 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
754 if (aSize == 1 && ap.av.viewName == null)
756 this.getContentPane().add(ap, BorderLayout.CENTER);
762 setInitialTabVisible();
765 expandViews.setEnabled(true);
766 gatherViews.setEnabled(true);
767 tabbedPane.addTab(ap.av.viewName, ap);
769 ap.setVisible(false);
774 if (ap.av.isPadGaps())
776 ap.av.getAlignment().padGaps();
778 ap.av.updateConservation(ap);
779 ap.av.updateConsensus(ap);
780 ap.av.updateStrucConsensus(ap);
784 public void setInitialTabVisible()
786 expandViews.setEnabled(true);
787 gatherViews.setEnabled(true);
788 tabbedPane.setVisible(true);
789 AlignmentPanel first = alignPanels.get(0);
790 tabbedPane.addTab(first.av.viewName, first);
791 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
794 public AlignViewport getViewport()
799 /* Set up intrinsic listeners for dynamically generated GUI bits. */
800 private void addServiceListeners()
802 final java.beans.PropertyChangeListener thisListener;
803 Desktop.instance.addJalviewPropertyChangeListener("services",
804 thisListener = new java.beans.PropertyChangeListener()
807 public void propertyChange(PropertyChangeEvent evt)
809 // // System.out.println("Discoverer property change.");
810 // if (evt.getPropertyName().equals("services"))
812 SwingUtilities.invokeLater(new Runnable()
819 .println("Rebuild WS Menu for service change");
820 BuildWebServiceMenu();
827 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
830 public void internalFrameClosed(
831 javax.swing.event.InternalFrameEvent evt)
833 // System.out.println("deregistering discoverer listener");
834 Desktop.instance.removeJalviewPropertyChangeListener("services",
836 closeMenuItem_actionPerformed(true);
839 // Finally, build the menu once to get current service state
840 new Thread(new Runnable()
845 BuildWebServiceMenu();
851 * Configure menu items that vary according to whether the alignment is
852 * nucleotide or protein
854 public void setGUINucleotide()
856 AlignmentI al = getViewport().getAlignment();
857 boolean nucleotide = al.isNucleotide();
859 showTranslation.setVisible(nucleotide);
860 showReverse.setVisible(nucleotide);
861 showReverseComplement.setVisible(nucleotide);
862 conservationMenuItem.setEnabled(!nucleotide);
863 modifyConservation.setEnabled(!nucleotide
864 && conservationMenuItem.isSelected());
865 showGroupConservation.setEnabled(!nucleotide);
867 showComplementMenuItem.setText(nucleotide ? MessageManager
868 .getString("label.protein") : MessageManager
869 .getString("label.nucleotide"));
873 * set up menus for the current viewport. This may be called after any
874 * operation that affects the data in the current view (selection changed,
875 * etc) to update the menus to reflect the new state.
878 public void setMenusForViewport()
880 setMenusFromViewport(viewport);
884 * Need to call this method when tabs are selected for multiple views, or when
885 * loading from Jalview2XML.java
890 void setMenusFromViewport(AlignViewport av)
892 padGapsMenuitem.setSelected(av.isPadGaps());
893 colourTextMenuItem.setSelected(av.isShowColourText());
894 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
895 modifyPID.setEnabled(abovePIDThreshold.isSelected());
896 conservationMenuItem.setSelected(av.getConservationSelected());
897 modifyConservation.setEnabled(conservationMenuItem.isSelected());
898 seqLimits.setSelected(av.getShowJVSuffix());
899 idRightAlign.setSelected(av.isRightAlignIds());
900 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
901 renderGapsMenuItem.setSelected(av.isRenderGaps());
902 wrapMenuItem.setSelected(av.getWrapAlignment());
903 scaleAbove.setVisible(av.getWrapAlignment());
904 scaleLeft.setVisible(av.getWrapAlignment());
905 scaleRight.setVisible(av.getWrapAlignment());
906 annotationPanelMenuItem.setState(av.isShowAnnotation());
908 * Show/hide annotations only enabled if annotation panel is shown
910 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
911 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
912 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
913 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
914 viewBoxesMenuItem.setSelected(av.getShowBoxes());
915 viewTextMenuItem.setSelected(av.getShowText());
916 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
917 showGroupConsensus.setSelected(av.isShowGroupConsensus());
918 showGroupConservation.setSelected(av.isShowGroupConservation());
919 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
920 showSequenceLogo.setSelected(av.isShowSequenceLogo());
921 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
923 ColourMenuHelper.setColourSelected(colourMenu,
924 av.getGlobalColourScheme());
926 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
927 hiddenMarkers.setState(av.getShowHiddenMarkers());
928 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
929 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
930 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
931 autoCalculate.setSelected(av.autoCalculateConsensus);
932 sortByTree.setSelected(av.sortByTree);
933 listenToViewSelections.setSelected(av.followSelection);
935 showProducts.setEnabled(canShowProducts());
936 setGroovyEnabled(Desktop.getGroovyConsole() != null);
942 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
946 public void setGroovyEnabled(boolean b)
948 runGroovy.setEnabled(b);
951 private IProgressIndicator progressBar;
956 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
959 public void setProgressBar(String message, long id)
961 progressBar.setProgressBar(message, id);
965 public void registerHandler(final long id,
966 final IProgressIndicatorHandler handler)
968 progressBar.registerHandler(id, handler);
973 * @return true if any progress bars are still active
976 public boolean operationInProgress()
978 return progressBar.operationInProgress();
982 public void setStatus(String text)
984 statusBar.setText(text);
988 * Added so Castor Mapping file can obtain Jalview Version
990 public String getVersion()
992 return jalview.bin.Cache.getProperty("VERSION");
995 public FeatureRenderer getFeatureRenderer()
997 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1001 public void fetchSequence_actionPerformed(ActionEvent e)
1003 new jalview.gui.SequenceFetcher(this);
1007 public void addFromFile_actionPerformed(ActionEvent e)
1009 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1013 public void reload_actionPerformed(ActionEvent e)
1015 if (fileName != null)
1017 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1018 // originating file's format
1019 // TODO: work out how to recover feature settings for correct view(s) when
1020 // file is reloaded.
1021 if (FileFormat.Jalview.equals(currentFileFormat))
1023 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1024 for (int i = 0; i < frames.length; i++)
1026 if (frames[i] instanceof AlignFrame && frames[i] != this
1027 && ((AlignFrame) frames[i]).fileName != null
1028 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1032 frames[i].setSelected(true);
1033 Desktop.instance.closeAssociatedWindows();
1034 } catch (java.beans.PropertyVetoException ex)
1040 Desktop.instance.closeAssociatedWindows();
1042 FileLoader loader = new FileLoader();
1043 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1044 : DataSourceType.FILE;
1045 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1049 Rectangle bounds = this.getBounds();
1051 FileLoader loader = new FileLoader();
1052 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1053 : DataSourceType.FILE;
1054 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1055 protocol, currentFileFormat);
1057 newframe.setBounds(bounds);
1058 if (featureSettings != null && featureSettings.isShowing())
1060 final Rectangle fspos = featureSettings.frame.getBounds();
1061 // TODO: need a 'show feature settings' function that takes bounds -
1062 // need to refactor Desktop.addFrame
1063 newframe.featureSettings_actionPerformed(null);
1064 final FeatureSettings nfs = newframe.featureSettings;
1065 SwingUtilities.invokeLater(new Runnable()
1070 nfs.frame.setBounds(fspos);
1073 this.featureSettings.close();
1074 this.featureSettings = null;
1076 this.closeMenuItem_actionPerformed(true);
1082 public void addFromText_actionPerformed(ActionEvent e)
1084 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1089 public void addFromURL_actionPerformed(ActionEvent e)
1091 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1095 public void save_actionPerformed(ActionEvent e)
1097 if (fileName == null || (currentFileFormat == null)
1098 || fileName.startsWith("http"))
1100 saveAs_actionPerformed(null);
1104 saveAlignment(fileName, currentFileFormat);
1115 public void saveAs_actionPerformed(ActionEvent e)
1117 String format = currentFileFormat == null ? null : currentFileFormat
1119 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1120 Cache.getProperty("LAST_DIRECTORY"), format);
1122 chooser.setFileView(new JalviewFileView());
1123 chooser.setDialogTitle(MessageManager
1124 .getString("label.save_alignment_to_file"));
1125 chooser.setToolTipText(MessageManager.getString("action.save"));
1127 int value = chooser.showSaveDialog(this);
1129 if (value == JalviewFileChooser.APPROVE_OPTION)
1131 currentFileFormat = chooser.getSelectedFormat();
1132 while (currentFileFormat == null)
1135 .showInternalMessageDialog(
1138 .getString("label.select_file_format_before_saving"),
1140 .getString("label.file_format_not_specified"),
1141 JvOptionPane.WARNING_MESSAGE);
1142 currentFileFormat = chooser.getSelectedFormat();
1143 value = chooser.showSaveDialog(this);
1144 if (value != JalviewFileChooser.APPROVE_OPTION)
1150 fileName = chooser.getSelectedFile().getPath();
1152 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1154 Cache.setProperty("LAST_DIRECTORY", fileName);
1155 saveAlignment(fileName, currentFileFormat);
1159 public boolean saveAlignment(String file, FileFormatI format)
1161 boolean success = true;
1163 if (FileFormat.Jalview.equals(format))
1165 String shortName = title;
1167 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1169 shortName = shortName.substring(shortName
1170 .lastIndexOf(java.io.File.separatorChar) + 1);
1173 success = new Jalview2XML().saveAlignment(this, file, shortName);
1175 statusBar.setText(MessageManager.formatMessage(
1176 "label.successfully_saved_to_file_in_format", new Object[] {
1177 fileName, format }));
1182 AlignmentExportData exportData = getAlignmentForExport(format,
1184 if (exportData.getSettings().isCancelled())
1188 FormatAdapter f = new FormatAdapter(alignPanel,
1189 exportData.getSettings());
1190 String output = f.formatSequences(
1192 exportData.getAlignment(), // class cast exceptions will
1193 // occur in the distant future
1194 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1195 f.getCacheSuffixDefault(format), viewport.getAlignment()
1196 .getHiddenColumns());
1206 PrintWriter out = new PrintWriter(new FileWriter(file));
1210 this.setTitle(file);
1211 statusBar.setText(MessageManager.formatMessage(
1212 "label.successfully_saved_to_file_in_format",
1213 new Object[] { fileName, format.getName() }));
1214 } catch (Exception ex)
1217 ex.printStackTrace();
1224 JvOptionPane.showInternalMessageDialog(this, MessageManager
1225 .formatMessage("label.couldnt_save_file",
1226 new Object[] { fileName }), MessageManager
1227 .getString("label.error_saving_file"),
1228 JvOptionPane.WARNING_MESSAGE);
1234 private void warningMessage(String warning, String title)
1236 if (new jalview.util.Platform().isHeadless())
1238 System.err.println("Warning: " + title + "\nWarning: " + warning);
1243 JvOptionPane.showInternalMessageDialog(this, warning, title,
1244 JvOptionPane.WARNING_MESSAGE);
1256 protected void outputText_actionPerformed(ActionEvent e)
1258 FileFormatI fileFormat = FileFormats.getInstance().forName(
1259 e.getActionCommand());
1260 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1262 if (exportData.getSettings().isCancelled())
1266 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1267 cap.setForInput(null);
1270 FileFormatI format = fileFormat;
1271 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1272 .formatSequences(format, exportData.getAlignment(),
1273 exportData.getOmitHidden(),
1275 .getStartEndPostions(), viewport
1276 .getAlignment().getHiddenColumns()));
1277 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1278 "label.alignment_output_command",
1279 new Object[] { e.getActionCommand() }), 600, 500);
1280 } catch (OutOfMemoryError oom)
1282 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1288 public static AlignmentExportData getAlignmentForExport(
1289 FileFormatI format, AlignViewportI viewport,
1290 AlignExportSettingI exportSettings)
1292 AlignmentI alignmentToExport = null;
1293 AlignExportSettingI settings = exportSettings;
1294 String[] omitHidden = null;
1296 HiddenSequences hiddenSeqs = viewport.getAlignment()
1297 .getHiddenSequences();
1299 alignmentToExport = viewport.getAlignment();
1301 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1302 if (settings == null)
1304 settings = new AlignExportSettings(hasHiddenSeqs,
1305 viewport.hasHiddenColumns(), format);
1307 // settings.isExportAnnotations();
1309 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1311 omitHidden = viewport.getViewAsString(false,
1312 settings.isExportHiddenSequences());
1315 int[] alignmentStartEnd = new int[2];
1316 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1318 alignmentToExport = hiddenSeqs.getFullAlignment();
1322 alignmentToExport = viewport.getAlignment();
1324 alignmentStartEnd = alignmentToExport
1325 .getVisibleStartAndEndIndex(viewport.getAlignment()
1327 .getHiddenRegions());
1328 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1329 omitHidden, alignmentStartEnd, settings);
1340 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1342 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1343 htmlSVG.exportHTML(null);
1347 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1349 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1350 bjs.exportHTML(null);
1353 public void createImageMap(File file, String image)
1355 alignPanel.makePNGImageMap(file, image);
1365 public void createPNG(File f)
1367 alignPanel.makePNG(f);
1377 public void createEPS(File f)
1379 alignPanel.makeEPS(f);
1383 public void createSVG(File f)
1385 alignPanel.makeSVG(f);
1389 public void pageSetup_actionPerformed(ActionEvent e)
1391 PrinterJob printJob = PrinterJob.getPrinterJob();
1392 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1402 public void printMenuItem_actionPerformed(ActionEvent e)
1404 // Putting in a thread avoids Swing painting problems
1405 PrintThread thread = new PrintThread(alignPanel);
1410 public void exportFeatures_actionPerformed(ActionEvent e)
1412 new AnnotationExporter().exportFeatures(alignPanel);
1416 public void exportAnnotations_actionPerformed(ActionEvent e)
1418 new AnnotationExporter().exportAnnotations(alignPanel);
1422 public void associatedData_actionPerformed(ActionEvent e)
1424 // Pick the tree file
1425 JalviewFileChooser chooser = new JalviewFileChooser(
1426 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1427 chooser.setFileView(new JalviewFileView());
1428 chooser.setDialogTitle(MessageManager
1429 .getString("label.load_jalview_annotations"));
1430 chooser.setToolTipText(MessageManager
1431 .getString("label.load_jalview_annotations"));
1433 int value = chooser.showOpenDialog(null);
1435 if (value == JalviewFileChooser.APPROVE_OPTION)
1437 String choice = chooser.getSelectedFile().getPath();
1438 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1439 loadJalviewDataFile(choice, null, null, null);
1445 * Close the current view or all views in the alignment frame. If the frame
1446 * only contains one view then the alignment will be removed from memory.
1448 * @param closeAllTabs
1451 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1453 if (alignPanels != null && alignPanels.size() < 2)
1455 closeAllTabs = true;
1460 if (alignPanels != null)
1464 if (this.isClosed())
1466 // really close all the windows - otherwise wait till
1467 // setClosed(true) is called
1468 for (int i = 0; i < alignPanels.size(); i++)
1470 AlignmentPanel ap = alignPanels.get(i);
1477 closeView(alignPanel);
1484 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1485 * be called recursively, with the frame now in 'closed' state
1487 this.setClosed(true);
1489 } catch (Exception ex)
1491 ex.printStackTrace();
1496 * Close the specified panel and close up tabs appropriately.
1498 * @param panelToClose
1500 public void closeView(AlignmentPanel panelToClose)
1502 int index = tabbedPane.getSelectedIndex();
1503 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1504 alignPanels.remove(panelToClose);
1505 panelToClose.closePanel();
1506 panelToClose = null;
1508 tabbedPane.removeTabAt(closedindex);
1509 tabbedPane.validate();
1511 if (index > closedindex || index == tabbedPane.getTabCount())
1513 // modify currently selected tab index if necessary.
1517 this.tabSelectionChanged(index);
1523 void updateEditMenuBar()
1526 if (viewport.getHistoryList().size() > 0)
1528 undoMenuItem.setEnabled(true);
1529 CommandI command = viewport.getHistoryList().peek();
1530 undoMenuItem.setText(MessageManager.formatMessage(
1531 "label.undo_command",
1532 new Object[] { command.getDescription() }));
1536 undoMenuItem.setEnabled(false);
1537 undoMenuItem.setText(MessageManager.getString("action.undo"));
1540 if (viewport.getRedoList().size() > 0)
1542 redoMenuItem.setEnabled(true);
1544 CommandI command = viewport.getRedoList().peek();
1545 redoMenuItem.setText(MessageManager.formatMessage(
1546 "label.redo_command",
1547 new Object[] { command.getDescription() }));
1551 redoMenuItem.setEnabled(false);
1552 redoMenuItem.setText(MessageManager.getString("action.redo"));
1557 public void addHistoryItem(CommandI command)
1559 if (command.getSize() > 0)
1561 viewport.addToHistoryList(command);
1562 viewport.clearRedoList();
1563 updateEditMenuBar();
1564 viewport.updateHiddenColumns();
1565 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1566 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1567 // viewport.getColumnSelection()
1568 // .getHiddenColumns().size() > 0);
1574 * @return alignment objects for all views
1576 AlignmentI[] getViewAlignments()
1578 if (alignPanels != null)
1580 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1582 for (AlignmentPanel ap : alignPanels)
1584 als[i++] = ap.av.getAlignment();
1588 if (viewport != null)
1590 return new AlignmentI[] { viewport.getAlignment() };
1602 protected void undoMenuItem_actionPerformed(ActionEvent e)
1604 if (viewport.getHistoryList().isEmpty())
1608 CommandI command = viewport.getHistoryList().pop();
1609 viewport.addToRedoList(command);
1610 command.undoCommand(getViewAlignments());
1612 AlignmentViewport originalSource = getOriginatingSource(command);
1613 updateEditMenuBar();
1615 if (originalSource != null)
1617 if (originalSource != viewport)
1620 .warn("Implementation worry: mismatch of viewport origin for undo");
1622 originalSource.updateHiddenColumns();
1623 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1625 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1626 // viewport.getColumnSelection()
1627 // .getHiddenColumns().size() > 0);
1628 originalSource.firePropertyChange("alignment", null, originalSource
1629 .getAlignment().getSequences());
1640 protected void redoMenuItem_actionPerformed(ActionEvent e)
1642 if (viewport.getRedoList().size() < 1)
1647 CommandI command = viewport.getRedoList().pop();
1648 viewport.addToHistoryList(command);
1649 command.doCommand(getViewAlignments());
1651 AlignmentViewport originalSource = getOriginatingSource(command);
1652 updateEditMenuBar();
1654 if (originalSource != null)
1657 if (originalSource != viewport)
1660 .warn("Implementation worry: mismatch of viewport origin for redo");
1662 originalSource.updateHiddenColumns();
1663 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1665 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1666 // viewport.getColumnSelection()
1667 // .getHiddenColumns().size() > 0);
1668 originalSource.firePropertyChange("alignment", null, originalSource
1669 .getAlignment().getSequences());
1673 AlignmentViewport getOriginatingSource(CommandI command)
1675 AlignmentViewport originalSource = null;
1676 // For sequence removal and addition, we need to fire
1677 // the property change event FROM the viewport where the
1678 // original alignment was altered
1679 AlignmentI al = null;
1680 if (command instanceof EditCommand)
1682 EditCommand editCommand = (EditCommand) command;
1683 al = editCommand.getAlignment();
1684 List<Component> comps = PaintRefresher.components.get(viewport
1685 .getSequenceSetId());
1687 for (Component comp : comps)
1689 if (comp instanceof AlignmentPanel)
1691 if (al == ((AlignmentPanel) comp).av.getAlignment())
1693 originalSource = ((AlignmentPanel) comp).av;
1700 if (originalSource == null)
1702 // The original view is closed, we must validate
1703 // the current view against the closed view first
1706 PaintRefresher.validateSequences(al, viewport.getAlignment());
1709 originalSource = viewport;
1712 return originalSource;
1721 public void moveSelectedSequences(boolean up)
1723 SequenceGroup sg = viewport.getSelectionGroup();
1729 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1730 viewport.getHiddenRepSequences(), up);
1731 alignPanel.paintAlignment(true);
1734 synchronized void slideSequences(boolean right, int size)
1736 List<SequenceI> sg = new ArrayList<>();
1737 if (viewport.cursorMode)
1739 sg.add(viewport.getAlignment().getSequenceAt(
1740 alignPanel.getSeqPanel().seqCanvas.cursorY));
1742 else if (viewport.getSelectionGroup() != null
1743 && viewport.getSelectionGroup().getSize() != viewport
1744 .getAlignment().getHeight())
1746 sg = viewport.getSelectionGroup().getSequences(
1747 viewport.getHiddenRepSequences());
1755 List<SequenceI> invertGroup = new ArrayList<>();
1757 for (SequenceI seq : viewport.getAlignment().getSequences())
1759 if (!sg.contains(seq))
1761 invertGroup.add(seq);
1765 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1767 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1768 for (int i = 0; i < invertGroup.size(); i++)
1770 seqs2[i] = invertGroup.get(i);
1773 SlideSequencesCommand ssc;
1776 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1777 size, viewport.getGapCharacter());
1781 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1782 size, viewport.getGapCharacter());
1785 int groupAdjustment = 0;
1786 if (ssc.getGapsInsertedBegin() && right)
1788 if (viewport.cursorMode)
1790 alignPanel.getSeqPanel().moveCursor(size, 0);
1794 groupAdjustment = size;
1797 else if (!ssc.getGapsInsertedBegin() && !right)
1799 if (viewport.cursorMode)
1801 alignPanel.getSeqPanel().moveCursor(-size, 0);
1805 groupAdjustment = -size;
1809 if (groupAdjustment != 0)
1811 viewport.getSelectionGroup().setStartRes(
1812 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1813 viewport.getSelectionGroup().setEndRes(
1814 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1818 * just extend the last slide command if compatible; but not if in
1819 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1821 boolean appendHistoryItem = false;
1822 Deque<CommandI> historyList = viewport.getHistoryList();
1823 boolean inSplitFrame = getSplitViewContainer() != null;
1824 if (!inSplitFrame && historyList != null && historyList.size() > 0
1825 && historyList.peek() instanceof SlideSequencesCommand)
1827 appendHistoryItem = ssc
1828 .appendSlideCommand((SlideSequencesCommand) historyList
1832 if (!appendHistoryItem)
1834 addHistoryItem(ssc);
1847 protected void copy_actionPerformed(ActionEvent e)
1850 if (viewport.getSelectionGroup() == null)
1854 // TODO: preserve the ordering of displayed alignment annotation in any
1855 // internal paste (particularly sequence associated annotation)
1856 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1857 String[] omitHidden = null;
1859 if (viewport.hasHiddenColumns())
1861 omitHidden = viewport.getViewAsString(true);
1864 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1865 seqs, omitHidden, null);
1867 StringSelection ss = new StringSelection(output);
1871 jalview.gui.Desktop.internalCopy = true;
1872 // Its really worth setting the clipboard contents
1873 // to empty before setting the large StringSelection!!
1874 Toolkit.getDefaultToolkit().getSystemClipboard()
1875 .setContents(new StringSelection(""), null);
1877 Toolkit.getDefaultToolkit().getSystemClipboard()
1878 .setContents(ss, Desktop.instance);
1879 } catch (OutOfMemoryError er)
1881 new OOMWarning("copying region", er);
1885 ArrayList<int[]> hiddenColumns = null;
1886 if (viewport.hasHiddenColumns())
1888 hiddenColumns = new ArrayList<>();
1889 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1890 .getSelectionGroup().getEndRes();
1891 for (int[] region : viewport.getAlignment().getHiddenColumns()
1892 .getHiddenRegions())
1894 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1896 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1897 region[1] - hiddenOffset });
1902 Desktop.jalviewClipboard = new Object[] { seqs,
1903 viewport.getAlignment().getDataset(), hiddenColumns };
1904 statusBar.setText(MessageManager.formatMessage(
1905 "label.copied_sequences_to_clipboard", new Object[] { Integer
1906 .valueOf(seqs.length).toString() }));
1916 protected void pasteNew_actionPerformed(ActionEvent e)
1928 protected void pasteThis_actionPerformed(ActionEvent e)
1934 * Paste contents of Jalview clipboard
1936 * @param newAlignment
1937 * true to paste to a new alignment, otherwise add to this.
1939 void paste(boolean newAlignment)
1941 boolean externalPaste = true;
1944 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1945 Transferable contents = c.getContents(this);
1947 if (contents == null)
1956 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1957 if (str.length() < 1)
1962 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1964 } catch (OutOfMemoryError er)
1966 new OOMWarning("Out of memory pasting sequences!!", er);
1970 SequenceI[] sequences;
1971 boolean annotationAdded = false;
1972 AlignmentI alignment = null;
1974 if (Desktop.jalviewClipboard != null)
1976 // The clipboard was filled from within Jalview, we must use the
1978 // And dataset from the copied alignment
1979 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1980 // be doubly sure that we create *new* sequence objects.
1981 sequences = new SequenceI[newseq.length];
1982 for (int i = 0; i < newseq.length; i++)
1984 sequences[i] = new Sequence(newseq[i]);
1986 alignment = new Alignment(sequences);
1987 externalPaste = false;
1991 // parse the clipboard as an alignment.
1992 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1994 sequences = alignment.getSequencesArray();
1998 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2004 if (Desktop.jalviewClipboard != null)
2006 // dataset is inherited
2007 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2011 // new dataset is constructed
2012 alignment.setDataset(null);
2014 alwidth = alignment.getWidth() + 1;
2018 AlignmentI pastedal = alignment; // preserve pasted alignment object
2019 // Add pasted sequences and dataset into existing alignment.
2020 alignment = viewport.getAlignment();
2021 alwidth = alignment.getWidth() + 1;
2022 // decide if we need to import sequences from an existing dataset
2023 boolean importDs = Desktop.jalviewClipboard != null
2024 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2025 // importDs==true instructs us to copy over new dataset sequences from
2026 // an existing alignment
2027 Vector newDs = (importDs) ? new Vector() : null; // used to create
2028 // minimum dataset set
2030 for (int i = 0; i < sequences.length; i++)
2034 newDs.addElement(null);
2036 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2038 if (importDs && ds != null)
2040 if (!newDs.contains(ds))
2042 newDs.setElementAt(ds, i);
2043 ds = new Sequence(ds);
2044 // update with new dataset sequence
2045 sequences[i].setDatasetSequence(ds);
2049 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2054 // copy and derive new dataset sequence
2055 sequences[i] = sequences[i].deriveSequence();
2056 alignment.getDataset().addSequence(
2057 sequences[i].getDatasetSequence());
2058 // TODO: avoid creation of duplicate dataset sequences with a
2059 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2061 alignment.addSequence(sequences[i]); // merges dataset
2065 newDs.clear(); // tidy up
2067 if (alignment.getAlignmentAnnotation() != null)
2069 for (AlignmentAnnotation alan : alignment
2070 .getAlignmentAnnotation())
2072 if (alan.graphGroup > fgroup)
2074 fgroup = alan.graphGroup;
2078 if (pastedal.getAlignmentAnnotation() != null)
2080 // Add any annotation attached to alignment.
2081 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2082 for (int i = 0; i < alann.length; i++)
2084 annotationAdded = true;
2085 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2087 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2088 if (newann.graphGroup > -1)
2090 if (newGraphGroups.size() <= newann.graphGroup
2091 || newGraphGroups.get(newann.graphGroup) == null)
2093 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2095 newGraphGroups.add(q, null);
2097 newGraphGroups.set(newann.graphGroup, new Integer(
2100 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2104 newann.padAnnotation(alwidth);
2105 alignment.addAnnotation(newann);
2115 addHistoryItem(new EditCommand(
2116 MessageManager.getString("label.add_sequences"),
2117 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2119 // Add any annotations attached to sequences
2120 for (int i = 0; i < sequences.length; i++)
2122 if (sequences[i].getAnnotation() != null)
2124 AlignmentAnnotation newann;
2125 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2127 annotationAdded = true;
2128 newann = sequences[i].getAnnotation()[a];
2129 newann.adjustForAlignment();
2130 newann.padAnnotation(alwidth);
2131 if (newann.graphGroup > -1)
2133 if (newann.graphGroup > -1)
2135 if (newGraphGroups.size() <= newann.graphGroup
2136 || newGraphGroups.get(newann.graphGroup) == null)
2138 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2140 newGraphGroups.add(q, null);
2142 newGraphGroups.set(newann.graphGroup, new Integer(
2145 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2149 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2154 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2161 // propagate alignment changed.
2162 vpRanges.setEndSeq(alignment.getHeight());
2163 if (annotationAdded)
2165 // Duplicate sequence annotation in all views.
2166 AlignmentI[] alview = this.getViewAlignments();
2167 for (int i = 0; i < sequences.length; i++)
2169 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2174 for (int avnum = 0; avnum < alview.length; avnum++)
2176 if (alview[avnum] != alignment)
2178 // duplicate in a view other than the one with input focus
2179 int avwidth = alview[avnum].getWidth() + 1;
2180 // this relies on sann being preserved after we
2181 // modify the sequence's annotation array for each duplication
2182 for (int a = 0; a < sann.length; a++)
2184 AlignmentAnnotation newann = new AlignmentAnnotation(
2186 sequences[i].addAlignmentAnnotation(newann);
2187 newann.padAnnotation(avwidth);
2188 alview[avnum].addAnnotation(newann); // annotation was
2189 // duplicated earlier
2190 // TODO JAL-1145 graphGroups are not updated for sequence
2191 // annotation added to several views. This may cause
2193 alview[avnum].setAnnotationIndex(newann, a);
2198 buildSortByAnnotationScoresMenu();
2200 viewport.firePropertyChange("alignment", null,
2201 alignment.getSequences());
2202 if (alignPanels != null)
2204 for (AlignmentPanel ap : alignPanels)
2206 ap.validateAnnotationDimensions(false);
2211 alignPanel.validateAnnotationDimensions(false);
2217 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2219 String newtitle = new String("Copied sequences");
2221 if (Desktop.jalviewClipboard != null
2222 && Desktop.jalviewClipboard[2] != null)
2224 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2225 for (int[] region : hc)
2227 af.viewport.hideColumns(region[0], region[1]);
2231 // >>>This is a fix for the moment, until a better solution is
2233 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2235 alignPanel.getSeqPanel().seqCanvas
2236 .getFeatureRenderer());
2238 // TODO: maintain provenance of an alignment, rather than just make the
2239 // title a concatenation of operations.
2242 if (title.startsWith("Copied sequences"))
2248 newtitle = newtitle.concat("- from " + title);
2253 newtitle = new String("Pasted sequences");
2256 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2261 } catch (Exception ex)
2263 ex.printStackTrace();
2264 System.out.println("Exception whilst pasting: " + ex);
2265 // could be anything being pasted in here
2271 protected void expand_newalign(ActionEvent e)
2275 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2276 .getAlignment(), -1);
2277 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2279 String newtitle = new String("Flanking alignment");
2281 if (Desktop.jalviewClipboard != null
2282 && Desktop.jalviewClipboard[2] != null)
2284 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2285 for (int region[] : hc)
2287 af.viewport.hideColumns(region[0], region[1]);
2291 // >>>This is a fix for the moment, until a better solution is
2293 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2295 alignPanel.getSeqPanel().seqCanvas
2296 .getFeatureRenderer());
2298 // TODO: maintain provenance of an alignment, rather than just make the
2299 // title a concatenation of operations.
2301 if (title.startsWith("Copied sequences"))
2307 newtitle = newtitle.concat("- from " + title);
2311 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2313 } catch (Exception ex)
2315 ex.printStackTrace();
2316 System.out.println("Exception whilst pasting: " + ex);
2317 // could be anything being pasted in here
2318 } catch (OutOfMemoryError oom)
2320 new OOMWarning("Viewing flanking region of alignment", oom);
2331 protected void cut_actionPerformed(ActionEvent e)
2333 copy_actionPerformed(null);
2334 delete_actionPerformed(null);
2344 protected void delete_actionPerformed(ActionEvent evt)
2347 SequenceGroup sg = viewport.getSelectionGroup();
2354 * If the cut affects all sequences, warn, remove highlighted columns
2356 if (sg.getSize() == viewport.getAlignment().getHeight())
2358 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2359 .getAlignment().getWidth()) ? true : false;
2360 if (isEntireAlignWidth)
2362 int confirm = JvOptionPane.showConfirmDialog(this,
2363 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2364 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2365 JvOptionPane.OK_CANCEL_OPTION);
2367 if (confirm == JvOptionPane.CANCEL_OPTION
2368 || confirm == JvOptionPane.CLOSED_OPTION)
2373 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2374 sg.getEndRes() + 1);
2376 SequenceI[] cut = sg.getSequences()
2377 .toArray(new SequenceI[sg.getSize()]);
2379 addHistoryItem(new EditCommand(
2380 MessageManager.getString("label.cut_sequences"), Action.CUT,
2381 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2382 viewport.getAlignment()));
2384 viewport.setSelectionGroup(null);
2385 viewport.sendSelection();
2386 viewport.getAlignment().deleteGroup(sg);
2388 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2390 if (viewport.getAlignment().getHeight() < 1)
2394 this.setClosed(true);
2395 } catch (Exception ex)
2408 protected void deleteGroups_actionPerformed(ActionEvent e)
2410 if (avc.deleteGroups())
2412 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2413 alignPanel.updateAnnotation();
2414 alignPanel.paintAlignment(true);
2425 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2427 SequenceGroup sg = new SequenceGroup();
2429 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2431 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2434 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2435 viewport.setSelectionGroup(sg);
2436 viewport.sendSelection();
2437 // JAL-2034 - should delegate to
2438 // alignPanel to decide if overview needs
2440 alignPanel.paintAlignment(false);
2441 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2451 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2453 if (viewport.cursorMode)
2455 alignPanel.getSeqPanel().keyboardNo1 = null;
2456 alignPanel.getSeqPanel().keyboardNo2 = null;
2458 viewport.setSelectionGroup(null);
2459 viewport.getColumnSelection().clear();
2460 viewport.setSelectionGroup(null);
2461 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2462 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2463 // JAL-2034 - should delegate to
2464 // alignPanel to decide if overview needs
2466 alignPanel.paintAlignment(false);
2467 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2468 viewport.sendSelection();
2478 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2480 SequenceGroup sg = viewport.getSelectionGroup();
2484 selectAllSequenceMenuItem_actionPerformed(null);
2489 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2491 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2493 // JAL-2034 - should delegate to
2494 // alignPanel to decide if overview needs
2497 alignPanel.paintAlignment(true);
2498 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2499 viewport.sendSelection();
2503 public void invertColSel_actionPerformed(ActionEvent e)
2505 viewport.invertColumnSelection();
2506 alignPanel.paintAlignment(true);
2507 viewport.sendSelection();
2517 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2519 trimAlignment(true);
2529 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2531 trimAlignment(false);
2534 void trimAlignment(boolean trimLeft)
2536 ColumnSelection colSel = viewport.getColumnSelection();
2539 if (!colSel.isEmpty())
2543 column = colSel.getMin();
2547 column = colSel.getMax();
2551 if (viewport.getSelectionGroup() != null)
2553 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2554 viewport.getHiddenRepSequences());
2558 seqs = viewport.getAlignment().getSequencesArray();
2561 TrimRegionCommand trimRegion;
2564 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2565 column, viewport.getAlignment());
2566 vpRanges.setStartRes(0);
2570 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2571 column, viewport.getAlignment());
2574 statusBar.setText(MessageManager.formatMessage(
2575 "label.removed_columns",
2576 new String[] { Integer.valueOf(trimRegion.getSize())
2579 addHistoryItem(trimRegion);
2581 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2583 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2584 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2586 viewport.getAlignment().deleteGroup(sg);
2590 viewport.firePropertyChange("alignment", null, viewport
2591 .getAlignment().getSequences());
2602 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2604 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2607 if (viewport.getSelectionGroup() != null)
2609 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2610 viewport.getHiddenRepSequences());
2611 start = viewport.getSelectionGroup().getStartRes();
2612 end = viewport.getSelectionGroup().getEndRes();
2616 seqs = viewport.getAlignment().getSequencesArray();
2619 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2620 "Remove Gapped Columns", seqs, start, end,
2621 viewport.getAlignment());
2623 addHistoryItem(removeGapCols);
2625 statusBar.setText(MessageManager.formatMessage(
2626 "label.removed_empty_columns",
2627 new Object[] { Integer.valueOf(removeGapCols.getSize())
2630 // This is to maintain viewport position on first residue
2631 // of first sequence
2632 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2633 int startRes = seq.findPosition(vpRanges.getStartRes());
2634 // ShiftList shifts;
2635 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2636 // edit.alColumnChanges=shifts.getInverse();
2637 // if (viewport.hasHiddenColumns)
2638 // viewport.getColumnSelection().compensateForEdits(shifts);
2639 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2640 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2652 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2654 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2657 if (viewport.getSelectionGroup() != null)
2659 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2660 viewport.getHiddenRepSequences());
2661 start = viewport.getSelectionGroup().getStartRes();
2662 end = viewport.getSelectionGroup().getEndRes();
2666 seqs = viewport.getAlignment().getSequencesArray();
2669 // This is to maintain viewport position on first residue
2670 // of first sequence
2671 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2672 int startRes = seq.findPosition(vpRanges.getStartRes());
2674 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2675 viewport.getAlignment()));
2677 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2679 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2691 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2693 viewport.setPadGaps(padGapsMenuitem.isSelected());
2694 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2705 public void findMenuItem_actionPerformed(ActionEvent e)
2711 * Create a new view of the current alignment.
2714 public void newView_actionPerformed(ActionEvent e)
2716 newView(null, true);
2720 * Creates and shows a new view of the current alignment.
2723 * title of newly created view; if null, one will be generated
2724 * @param copyAnnotation
2725 * if true then duplicate all annnotation, groups and settings
2726 * @return new alignment panel, already displayed.
2728 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2731 * Create a new AlignmentPanel (with its own, new Viewport)
2733 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2735 if (!copyAnnotation)
2738 * remove all groups and annotation except for the automatic stuff
2740 newap.av.getAlignment().deleteAllGroups();
2741 newap.av.getAlignment().deleteAllAnnotations(false);
2744 newap.av.setGatherViewsHere(false);
2746 if (viewport.viewName == null)
2748 viewport.viewName = MessageManager
2749 .getString("label.view_name_original");
2753 * Views share the same edits undo and redo stacks
2755 newap.av.setHistoryList(viewport.getHistoryList());
2756 newap.av.setRedoList(viewport.getRedoList());
2759 * Views share the same mappings; need to deregister any new mappings
2760 * created by copyAlignPanel, and register the new reference to the shared
2763 newap.av.replaceMappings(viewport.getAlignment());
2766 * start up cDNA consensus (if applicable) now mappings are in place
2768 if (newap.av.initComplementConsensus())
2770 newap.refresh(true); // adjust layout of annotations
2773 newap.av.viewName = getNewViewName(viewTitle);
2775 addAlignmentPanel(newap, true);
2776 newap.alignmentChanged();
2778 if (alignPanels.size() == 2)
2780 viewport.setGatherViewsHere(true);
2782 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2787 * Make a new name for the view, ensuring it is unique within the current
2788 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2789 * these now use viewId. Unique view names are still desirable for usability.)
2794 protected String getNewViewName(String viewTitle)
2796 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2797 boolean addFirstIndex = false;
2798 if (viewTitle == null || viewTitle.trim().length() == 0)
2800 viewTitle = MessageManager.getString("action.view");
2801 addFirstIndex = true;
2805 index = 1;// we count from 1 if given a specific name
2807 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2809 List<Component> comps = PaintRefresher.components.get(viewport
2810 .getSequenceSetId());
2812 List<String> existingNames = getExistingViewNames(comps);
2814 while (existingNames.contains(newViewName))
2816 newViewName = viewTitle + " " + (++index);
2822 * Returns a list of distinct view names found in the given list of
2823 * components. View names are held on the viewport of an AlignmentPanel.
2828 protected List<String> getExistingViewNames(List<Component> comps)
2830 List<String> existingNames = new ArrayList<>();
2831 for (Component comp : comps)
2833 if (comp instanceof AlignmentPanel)
2835 AlignmentPanel ap = (AlignmentPanel) comp;
2836 if (!existingNames.contains(ap.av.viewName))
2838 existingNames.add(ap.av.viewName);
2842 return existingNames;
2846 * Explode tabbed views into separate windows.
2849 public void expandViews_actionPerformed(ActionEvent e)
2851 Desktop.explodeViews(this);
2855 * Gather views in separate windows back into a tabbed presentation.
2858 public void gatherViews_actionPerformed(ActionEvent e)
2860 Desktop.instance.gatherViews(this);
2870 public void font_actionPerformed(ActionEvent e)
2872 new FontChooser(alignPanel);
2882 protected void seqLimit_actionPerformed(ActionEvent e)
2884 viewport.setShowJVSuffix(seqLimits.isSelected());
2886 alignPanel.getIdPanel().getIdCanvas()
2887 .setPreferredSize(alignPanel.calculateIdWidth());
2888 alignPanel.paintAlignment(true);
2892 public void idRightAlign_actionPerformed(ActionEvent e)
2894 viewport.setRightAlignIds(idRightAlign.isSelected());
2895 alignPanel.paintAlignment(true);
2899 public void centreColumnLabels_actionPerformed(ActionEvent e)
2901 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2902 alignPanel.paintAlignment(true);
2908 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2911 protected void followHighlight_actionPerformed()
2914 * Set the 'follow' flag on the Viewport (and scroll to position if now
2917 final boolean state = this.followHighlightMenuItem.getState();
2918 viewport.setFollowHighlight(state);
2921 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2932 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2934 viewport.setColourText(colourTextMenuItem.isSelected());
2935 alignPanel.paintAlignment(true);
2945 public void wrapMenuItem_actionPerformed(ActionEvent e)
2947 scaleAbove.setVisible(wrapMenuItem.isSelected());
2948 scaleLeft.setVisible(wrapMenuItem.isSelected());
2949 scaleRight.setVisible(wrapMenuItem.isSelected());
2950 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2951 alignPanel.updateLayout();
2955 public void showAllSeqs_actionPerformed(ActionEvent e)
2957 viewport.showAllHiddenSeqs();
2961 public void showAllColumns_actionPerformed(ActionEvent e)
2963 viewport.showAllHiddenColumns();
2965 viewport.sendSelection();
2969 public void hideSelSequences_actionPerformed(ActionEvent e)
2971 viewport.hideAllSelectedSeqs();
2972 // alignPanel.paintAlignment(true);
2976 * called by key handler and the hide all/show all menu items
2981 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2984 boolean hide = false;
2985 SequenceGroup sg = viewport.getSelectionGroup();
2986 if (!toggleSeqs && !toggleCols)
2988 // Hide everything by the current selection - this is a hack - we do the
2989 // invert and then hide
2990 // first check that there will be visible columns after the invert.
2991 if (viewport.hasSelectedColumns()
2992 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2995 // now invert the sequence set, if required - empty selection implies
2996 // that no hiding is required.
2999 invertSequenceMenuItem_actionPerformed(null);
3000 sg = viewport.getSelectionGroup();
3004 viewport.expandColSelection(sg, true);
3005 // finally invert the column selection and get the new sequence
3007 invertColSel_actionPerformed(null);
3014 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3016 hideSelSequences_actionPerformed(null);
3019 else if (!(toggleCols && viewport.hasSelectedColumns()))
3021 showAllSeqs_actionPerformed(null);
3027 if (viewport.hasSelectedColumns())
3029 hideSelColumns_actionPerformed(null);
3032 viewport.setSelectionGroup(sg);
3037 showAllColumns_actionPerformed(null);
3046 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3047 * event.ActionEvent)
3050 public void hideAllButSelection_actionPerformed(ActionEvent e)
3052 toggleHiddenRegions(false, false);
3053 viewport.sendSelection();
3060 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3064 public void hideAllSelection_actionPerformed(ActionEvent e)
3066 SequenceGroup sg = viewport.getSelectionGroup();
3067 viewport.expandColSelection(sg, false);
3068 viewport.hideAllSelectedSeqs();
3069 viewport.hideSelectedColumns();
3070 alignPanel.paintAlignment(true);
3071 viewport.sendSelection();
3078 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3082 public void showAllhidden_actionPerformed(ActionEvent e)
3084 viewport.showAllHiddenColumns();
3085 viewport.showAllHiddenSeqs();
3086 alignPanel.paintAlignment(true);
3087 viewport.sendSelection();
3091 public void hideSelColumns_actionPerformed(ActionEvent e)
3093 viewport.hideSelectedColumns();
3094 alignPanel.paintAlignment(true);
3095 viewport.sendSelection();
3099 public void hiddenMarkers_actionPerformed(ActionEvent e)
3101 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3112 protected void scaleAbove_actionPerformed(ActionEvent e)
3114 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3115 alignPanel.paintAlignment(true);
3125 protected void scaleLeft_actionPerformed(ActionEvent e)
3127 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3128 alignPanel.paintAlignment(true);
3138 protected void scaleRight_actionPerformed(ActionEvent e)
3140 viewport.setScaleRightWrapped(scaleRight.isSelected());
3141 alignPanel.paintAlignment(true);
3151 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3153 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3154 alignPanel.paintAlignment(true);
3164 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3166 viewport.setShowText(viewTextMenuItem.isSelected());
3167 alignPanel.paintAlignment(true);
3177 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3179 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3180 alignPanel.paintAlignment(true);
3183 public FeatureSettings featureSettings;
3186 public FeatureSettingsControllerI getFeatureSettingsUI()
3188 return featureSettings;
3192 public void featureSettings_actionPerformed(ActionEvent e)
3194 if (featureSettings != null)
3196 featureSettings.close();
3197 featureSettings = null;
3199 if (!showSeqFeatures.isSelected())
3201 // make sure features are actually displayed
3202 showSeqFeatures.setSelected(true);
3203 showSeqFeatures_actionPerformed(null);
3205 featureSettings = new FeatureSettings(this);
3209 * Set or clear 'Show Sequence Features'
3215 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3217 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3218 alignPanel.paintAlignment(true);
3219 if (alignPanel.getOverviewPanel() != null)
3221 alignPanel.getOverviewPanel().updateOverviewImage();
3226 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3227 * the annotations panel as a whole.
3229 * The options to show/hide all annotations should be enabled when the panel
3230 * is shown, and disabled when the panel is hidden.
3235 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3237 final boolean setVisible = annotationPanelMenuItem.isSelected();
3238 viewport.setShowAnnotation(setVisible);
3239 this.showAllSeqAnnotations.setEnabled(setVisible);
3240 this.hideAllSeqAnnotations.setEnabled(setVisible);
3241 this.showAllAlAnnotations.setEnabled(setVisible);
3242 this.hideAllAlAnnotations.setEnabled(setVisible);
3243 alignPanel.updateLayout();
3247 public void alignmentProperties()
3249 JEditorPane editPane = new JEditorPane("text/html", "");
3250 editPane.setEditable(false);
3251 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3253 editPane.setText(MessageManager.formatMessage("label.html_content",
3254 new Object[] { contents.toString() }));
3255 JInternalFrame frame = new JInternalFrame();
3256 frame.getContentPane().add(new JScrollPane(editPane));
3258 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3259 "label.alignment_properties", new Object[] { getTitle() }),
3270 public void overviewMenuItem_actionPerformed(ActionEvent e)
3272 if (alignPanel.overviewPanel != null)
3277 JInternalFrame frame = new JInternalFrame();
3278 OverviewPanel overview = new OverviewPanel(alignPanel);
3279 frame.setContentPane(overview);
3280 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3281 "label.overview_params", new Object[] { this.getTitle() }),
3282 true, frame.getWidth(), frame.getHeight(), true, true);
3284 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3285 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3288 public void internalFrameClosed(
3289 javax.swing.event.InternalFrameEvent evt)
3291 alignPanel.setOverviewPanel(null);
3295 alignPanel.setOverviewPanel(overview);
3299 public void textColour_actionPerformed()
3301 new TextColourChooser().chooseColour(alignPanel, null);
3305 * public void covariationColour_actionPerformed() {
3307 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3311 public void annotationColour_actionPerformed()
3313 new AnnotationColourChooser(viewport, alignPanel);
3317 public void annotationColumn_actionPerformed(ActionEvent e)
3319 new AnnotationColumnChooser(viewport, alignPanel);
3323 * Action on the user checking or unchecking the option to apply the selected
3324 * colour scheme to all groups. If unchecked, groups may have their own
3325 * independent colour schemes.
3330 public void applyToAllGroups_actionPerformed(boolean selected)
3332 viewport.setColourAppliesToAllGroups(selected);
3336 * Action on user selecting a colour from the colour menu
3339 * the name (not the menu item label!) of the colour scheme
3342 public void changeColour_actionPerformed(String name)
3345 * 'User Defined' opens a panel to configure or load a
3346 * user-defined colour scheme
3348 if (ResidueColourScheme.USER_DEFINED.equals(name))
3350 new UserDefinedColours(alignPanel);
3355 * otherwise set the chosen colour scheme (or null for 'None')
3357 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3358 viewport.getAlignment(), viewport.getHiddenRepSequences());
3363 * Actions on setting or changing the alignment colour scheme
3368 public void changeColour(ColourSchemeI cs)
3370 // TODO: pull up to controller method
3371 ColourMenuHelper.setColourSelected(colourMenu, cs);
3373 viewport.setGlobalColourScheme(cs);
3375 alignPanel.paintAlignment(true);
3379 * Show the PID threshold slider panel
3382 protected void modifyPID_actionPerformed()
3384 SliderPanel.setPIDSliderSource(alignPanel,
3385 viewport.getResidueShading(), alignPanel.getViewName());
3386 SliderPanel.showPIDSlider();
3390 * Show the Conservation slider panel
3393 protected void modifyConservation_actionPerformed()
3395 SliderPanel.setConservationSlider(alignPanel,
3396 viewport.getResidueShading(), alignPanel.getViewName());
3397 SliderPanel.showConservationSlider();
3401 * Action on selecting or deselecting (Colour) By Conservation
3404 public void conservationMenuItem_actionPerformed(boolean selected)
3406 modifyConservation.setEnabled(selected);
3407 viewport.setConservationSelected(selected);
3408 viewport.getResidueShading().setConservationApplied(selected);
3410 changeColour(viewport.getGlobalColourScheme());
3413 modifyConservation_actionPerformed();
3417 SliderPanel.hideConservationSlider();
3422 * Action on selecting or deselecting (Colour) Above PID Threshold
3425 public void abovePIDThreshold_actionPerformed(boolean selected)
3427 modifyPID.setEnabled(selected);
3428 viewport.setAbovePIDThreshold(selected);
3431 viewport.getResidueShading().setThreshold(0,
3432 viewport.isIgnoreGapsConsensus());
3435 changeColour(viewport.getGlobalColourScheme());
3438 modifyPID_actionPerformed();
3442 SliderPanel.hidePIDSlider();
3453 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3455 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3456 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3457 .getAlignment().getSequenceAt(0));
3458 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3459 viewport.getAlignment()));
3460 alignPanel.paintAlignment(true);
3470 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3472 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3473 AlignmentSorter.sortByID(viewport.getAlignment());
3474 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3475 viewport.getAlignment()));
3476 alignPanel.paintAlignment(true);
3486 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3488 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3489 AlignmentSorter.sortByLength(viewport.getAlignment());
3490 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3491 viewport.getAlignment()));
3492 alignPanel.paintAlignment(true);
3502 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3504 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3505 AlignmentSorter.sortByGroup(viewport.getAlignment());
3506 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3507 viewport.getAlignment()));
3509 alignPanel.paintAlignment(true);
3519 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3521 new RedundancyPanel(alignPanel, this);
3531 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3533 if ((viewport.getSelectionGroup() == null)
3534 || (viewport.getSelectionGroup().getSize() < 2))
3536 JvOptionPane.showInternalMessageDialog(this, MessageManager
3537 .getString("label.you_must_select_least_two_sequences"),
3538 MessageManager.getString("label.invalid_selection"),
3539 JvOptionPane.WARNING_MESSAGE);
3543 JInternalFrame frame = new JInternalFrame();
3544 frame.setContentPane(new PairwiseAlignPanel(viewport));
3545 Desktop.addInternalFrame(frame,
3546 MessageManager.getString("action.pairwise_alignment"), 600,
3552 public void autoCalculate_actionPerformed(ActionEvent e)
3554 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3555 if (viewport.autoCalculateConsensus)
3557 viewport.firePropertyChange("alignment", null, viewport
3558 .getAlignment().getSequences());
3563 public void sortByTreeOption_actionPerformed(ActionEvent e)
3565 viewport.sortByTree = sortByTree.isSelected();
3569 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3571 viewport.followSelection = listenToViewSelections.isSelected();
3575 * Constructs a tree panel and adds it to the desktop
3578 * tree type (NJ or AV)
3580 * name of score model used to compute the tree
3582 * parameters for the distance or similarity calculation
3584 void newTreePanel(String type, String modelName, SimilarityParamsI options)
3586 String frameTitle = "";
3589 boolean onSelection = false;
3590 if (viewport.getSelectionGroup() != null
3591 && viewport.getSelectionGroup().getSize() > 0)
3593 SequenceGroup sg = viewport.getSelectionGroup();
3595 /* Decide if the selection is a column region */
3596 for (SequenceI _s : sg.getSequences())
3598 if (_s.getLength() < sg.getEndRes())
3604 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3606 .getString("label.sequences_selection_not_aligned"),
3607 JvOptionPane.WARNING_MESSAGE);
3616 if (viewport.getAlignment().getHeight() < 2)
3622 tp = new TreePanel(alignPanel, type, modelName, options);
3623 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3625 frameTitle += " from ";
3627 if (viewport.viewName != null)
3629 frameTitle += viewport.viewName + " of ";
3632 frameTitle += this.title;
3634 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3645 public void addSortByOrderMenuItem(String title,
3646 final AlignmentOrder order)
3648 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3649 "action.by_title_param", new Object[] { title }));
3651 item.addActionListener(new java.awt.event.ActionListener()
3654 public void actionPerformed(ActionEvent e)
3656 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3658 // TODO: JBPNote - have to map order entries to curent SequenceI
3660 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3662 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3665 alignPanel.paintAlignment(true);
3671 * Add a new sort by annotation score menu item
3674 * the menu to add the option to
3676 * the label used to retrieve scores for each sequence on the
3679 public void addSortByAnnotScoreMenuItem(JMenu sort,
3680 final String scoreLabel)
3682 final JMenuItem item = new JMenuItem(scoreLabel);
3684 item.addActionListener(new java.awt.event.ActionListener()
3687 public void actionPerformed(ActionEvent e)
3689 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3690 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3691 viewport.getAlignment());// ,viewport.getSelectionGroup());
3692 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3693 viewport.getAlignment()));
3694 alignPanel.paintAlignment(true);
3700 * last hash for alignment's annotation array - used to minimise cost of
3703 protected int _annotationScoreVectorHash;
3706 * search the alignment and rebuild the sort by annotation score submenu the
3707 * last alignment annotation vector hash is stored to minimize cost of
3708 * rebuilding in subsequence calls.
3712 public void buildSortByAnnotationScoresMenu()
3714 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3719 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3721 sortByAnnotScore.removeAll();
3722 // almost certainly a quicker way to do this - but we keep it simple
3723 Hashtable scoreSorts = new Hashtable();
3724 AlignmentAnnotation aann[];
3725 for (SequenceI sqa : viewport.getAlignment().getSequences())
3727 aann = sqa.getAnnotation();
3728 for (int i = 0; aann != null && i < aann.length; i++)
3730 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3732 scoreSorts.put(aann[i].label, aann[i].label);
3736 Enumeration labels = scoreSorts.keys();
3737 while (labels.hasMoreElements())
3739 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3740 (String) labels.nextElement());
3742 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3745 _annotationScoreVectorHash = viewport.getAlignment()
3746 .getAlignmentAnnotation().hashCode();
3751 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3752 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3753 * call. Listeners are added to remove the menu item when the treePanel is
3754 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3758 public void buildTreeSortMenu()
3760 sortByTreeMenu.removeAll();
3762 List<Component> comps = PaintRefresher.components.get(viewport
3763 .getSequenceSetId());
3764 List<TreePanel> treePanels = new ArrayList<>();
3765 for (Component comp : comps)
3767 if (comp instanceof TreePanel)
3769 treePanels.add((TreePanel) comp);
3773 if (treePanels.size() < 1)
3775 sortByTreeMenu.setVisible(false);
3779 sortByTreeMenu.setVisible(true);
3781 for (final TreePanel tp : treePanels)
3783 final JMenuItem item = new JMenuItem(tp.getTitle());
3784 item.addActionListener(new java.awt.event.ActionListener()
3787 public void actionPerformed(ActionEvent e)
3789 tp.sortByTree_actionPerformed();
3790 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3795 sortByTreeMenu.add(item);
3799 public boolean sortBy(AlignmentOrder alorder, String undoname)
3801 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3802 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3803 if (undoname != null)
3805 addHistoryItem(new OrderCommand(undoname, oldOrder,
3806 viewport.getAlignment()));
3808 alignPanel.paintAlignment(true);
3813 * Work out whether the whole set of sequences or just the selected set will
3814 * be submitted for multiple alignment.
3817 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3819 // Now, check we have enough sequences
3820 AlignmentView msa = null;
3822 if ((viewport.getSelectionGroup() != null)
3823 && (viewport.getSelectionGroup().getSize() > 1))
3825 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3826 // some common interface!
3828 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3829 * SequenceI[sz = seqs.getSize(false)];
3831 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3832 * seqs.getSequenceAt(i); }
3834 msa = viewport.getAlignmentView(true);
3836 else if (viewport.getSelectionGroup() != null
3837 && viewport.getSelectionGroup().getSize() == 1)
3839 int option = JvOptionPane.showConfirmDialog(this,
3840 MessageManager.getString("warn.oneseq_msainput_selection"),
3841 MessageManager.getString("label.invalid_selection"),
3842 JvOptionPane.OK_CANCEL_OPTION);
3843 if (option == JvOptionPane.OK_OPTION)
3845 msa = viewport.getAlignmentView(false);
3850 msa = viewport.getAlignmentView(false);
3856 * Decides what is submitted to a secondary structure prediction service: the
3857 * first sequence in the alignment, or in the current selection, or, if the
3858 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3859 * region or the whole alignment. (where the first sequence in the set is the
3860 * one that the prediction will be for).
3862 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3864 AlignmentView seqs = null;
3866 if ((viewport.getSelectionGroup() != null)
3867 && (viewport.getSelectionGroup().getSize() > 0))
3869 seqs = viewport.getAlignmentView(true);
3873 seqs = viewport.getAlignmentView(false);
3875 // limit sequences - JBPNote in future - could spawn multiple prediction
3877 // TODO: viewport.getAlignment().isAligned is a global state - the local
3878 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3879 if (!viewport.getAlignment().isAligned(false))
3881 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3882 // TODO: if seqs.getSequences().length>1 then should really have warned
3896 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3898 // Pick the tree file
3899 JalviewFileChooser chooser = new JalviewFileChooser(
3900 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3901 chooser.setFileView(new JalviewFileView());
3902 chooser.setDialogTitle(MessageManager
3903 .getString("label.select_newick_like_tree_file"));
3904 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3906 int value = chooser.showOpenDialog(null);
3908 if (value == JalviewFileChooser.APPROVE_OPTION)
3910 String filePath = chooser.getSelectedFile().getPath();
3911 Cache.setProperty("LAST_DIRECTORY", filePath);
3912 NewickFile fin = null;
3915 fin = new NewickFile(filePath, DataSourceType.FILE);
3916 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3917 } catch (Exception ex)
3924 .getString("label.problem_reading_tree_file"),
3925 JvOptionPane.WARNING_MESSAGE);
3926 ex.printStackTrace();
3928 if (fin != null && fin.hasWarningMessage())
3930 JvOptionPane.showMessageDialog(Desktop.desktop, fin
3931 .getWarningMessage(), MessageManager
3932 .getString("label.possible_problem_with_tree_file"),
3933 JvOptionPane.WARNING_MESSAGE);
3938 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3940 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3943 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3944 int h, int x, int y)
3946 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3950 * Add a treeviewer for the tree extracted from a Newick file object to the
3951 * current alignment view
3958 * Associated alignment input data (or null)
3967 * @return TreePanel handle
3969 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3970 AlignmentView input, int w, int h, int x, int y)
3972 TreePanel tp = null;
3978 if (nf.getTree() != null)
3980 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3986 tp.setLocation(x, y);
3989 Desktop.addInternalFrame(tp, treeTitle, w, h);
3991 } catch (Exception ex)
3993 ex.printStackTrace();
3999 private boolean buildingMenu = false;
4002 * Generates menu items and listener event actions for web service clients
4005 public void BuildWebServiceMenu()
4007 while (buildingMenu)
4011 System.err.println("Waiting for building menu to finish.");
4013 } catch (Exception e)
4017 final AlignFrame me = this;
4018 buildingMenu = true;
4019 new Thread(new Runnable()
4024 final List<JMenuItem> legacyItems = new ArrayList<>();
4027 // System.err.println("Building ws menu again "
4028 // + Thread.currentThread());
4029 // TODO: add support for context dependent disabling of services based
4031 // alignment and current selection
4032 // TODO: add additional serviceHandle parameter to specify abstract
4034 // class independently of AbstractName
4035 // TODO: add in rediscovery GUI function to restart discoverer
4036 // TODO: group services by location as well as function and/or
4038 // object broker mechanism.
4039 final Vector<JMenu> wsmenu = new Vector<>();
4040 final IProgressIndicator af = me;
4043 * do not i18n these strings - they are hard-coded in class
4044 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4045 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4047 final JMenu msawsmenu = new JMenu("Alignment");
4048 final JMenu secstrmenu = new JMenu(
4049 "Secondary Structure Prediction");
4050 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4051 final JMenu analymenu = new JMenu("Analysis");
4052 final JMenu dismenu = new JMenu("Protein Disorder");
4053 // JAL-940 - only show secondary structure prediction services from
4054 // the legacy server
4055 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4057 Discoverer.services != null && (Discoverer.services.size() > 0))
4059 // TODO: refactor to allow list of AbstractName/Handler bindings to
4061 // stored or retrieved from elsewhere
4062 // No MSAWS used any more:
4063 // Vector msaws = null; // (Vector)
4064 // Discoverer.services.get("MsaWS");
4065 Vector secstrpr = (Vector) Discoverer.services
4067 if (secstrpr != null)
4069 // Add any secondary structure prediction services
4070 for (int i = 0, j = secstrpr.size(); i < j; i++)
4072 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4074 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4075 .getServiceClient(sh);
4076 int p = secstrmenu.getItemCount();
4077 impl.attachWSMenuEntry(secstrmenu, me);
4078 int q = secstrmenu.getItemCount();
4079 for (int litm = p; litm < q; litm++)
4081 legacyItems.add(secstrmenu.getItem(litm));
4087 // Add all submenus in the order they should appear on the web
4089 wsmenu.add(msawsmenu);
4090 wsmenu.add(secstrmenu);
4091 wsmenu.add(dismenu);
4092 wsmenu.add(analymenu);
4093 // No search services yet
4094 // wsmenu.add(seqsrchmenu);
4096 javax.swing.SwingUtilities.invokeLater(new Runnable()
4103 webService.removeAll();
4104 // first, add discovered services onto the webservices menu
4105 if (wsmenu.size() > 0)
4107 for (int i = 0, j = wsmenu.size(); i < j; i++)
4109 webService.add(wsmenu.get(i));
4114 webService.add(me.webServiceNoServices);
4116 // TODO: move into separate menu builder class.
4117 boolean new_sspred = false;
4118 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4120 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4121 if (jws2servs != null)
4123 if (jws2servs.hasServices())
4125 jws2servs.attachWSMenuEntry(webService, me);
4126 for (Jws2Instance sv : jws2servs.getServices())
4128 if (sv.description.toLowerCase().contains("jpred"))
4130 for (JMenuItem jmi : legacyItems)
4132 jmi.setVisible(false);
4138 if (jws2servs.isRunning())
4140 JMenuItem tm = new JMenuItem(
4141 "Still discovering JABA Services");
4142 tm.setEnabled(false);
4147 build_urlServiceMenu(me.webService);
4148 build_fetchdbmenu(webService);
4149 for (JMenu item : wsmenu)
4151 if (item.getItemCount() == 0)
4153 item.setEnabled(false);
4157 item.setEnabled(true);
4160 } catch (Exception e)
4163 .debug("Exception during web service menu building process.",
4168 } catch (Exception e)
4171 buildingMenu = false;
4178 * construct any groupURL type service menu entries.
4182 private void build_urlServiceMenu(JMenu webService)
4184 // TODO: remove this code when 2.7 is released
4185 // DEBUG - alignmentView
4187 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4188 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4190 * @Override public void actionPerformed(ActionEvent e) {
4191 * jalview.datamodel.AlignmentView
4192 * .testSelectionViews(af.viewport.getAlignment(),
4193 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4195 * }); webService.add(testAlView);
4197 // TODO: refactor to RestClient discoverer and merge menu entries for
4198 // rest-style services with other types of analysis/calculation service
4199 // SHmmr test client - still being implemented.
4200 // DEBUG - alignmentView
4202 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4205 client.attachWSMenuEntry(
4206 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4212 * Searches the alignment sequences for xRefs and builds the Show
4213 * Cross-References menu (formerly called Show Products), with database
4214 * sources for which cross-references are found (protein sources for a
4215 * nucleotide alignment and vice versa)
4217 * @return true if Show Cross-references menu should be enabled
4219 public boolean canShowProducts()
4221 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4222 AlignmentI dataset = viewport.getAlignment().getDataset();
4224 showProducts.removeAll();
4225 final boolean dna = viewport.getAlignment().isNucleotide();
4227 if (seqs == null || seqs.length == 0)
4229 // nothing to see here.
4233 boolean showp = false;
4236 List<String> ptypes = new CrossRef(seqs, dataset)
4237 .findXrefSourcesForSequences(dna);
4239 for (final String source : ptypes)
4242 final AlignFrame af = this;
4243 JMenuItem xtype = new JMenuItem(source);
4244 xtype.addActionListener(new ActionListener()
4247 public void actionPerformed(ActionEvent e)
4249 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4252 showProducts.add(xtype);
4254 showProducts.setVisible(showp);
4255 showProducts.setEnabled(showp);
4256 } catch (Exception e)
4259 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4267 * Finds and displays cross-references for the selected sequences (protein
4268 * products for nucleotide sequences, dna coding sequences for peptides).
4271 * the sequences to show cross-references for
4273 * true if from a nucleotide alignment (so showing proteins)
4275 * the database to show cross-references for
4277 protected void showProductsFor(final SequenceI[] sel,
4278 final boolean _odna, final String source)
4280 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4285 * Construct and display a new frame containing the translation of this
4286 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4289 public void showTranslation_actionPerformed(ActionEvent e)
4291 AlignmentI al = null;
4294 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4296 al = dna.translateCdna();
4297 } catch (Exception ex)
4299 jalview.bin.Cache.log.error(
4300 "Exception during translation. Please report this !", ex);
4301 final String msg = MessageManager
4302 .getString("label.error_when_translating_sequences_submit_bug_report");
4303 final String errorTitle = MessageManager
4304 .getString("label.implementation_error")
4305 + MessageManager.getString("label.translation_failed");
4306 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4307 JvOptionPane.ERROR_MESSAGE);
4310 if (al == null || al.getHeight() == 0)
4312 final String msg = MessageManager
4313 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4314 final String errorTitle = MessageManager
4315 .getString("label.translation_failed");
4316 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4317 JvOptionPane.WARNING_MESSAGE);
4321 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4322 af.setFileFormat(this.currentFileFormat);
4323 final String newTitle = MessageManager.formatMessage(
4324 "label.translation_of_params",
4325 new Object[] { this.getTitle() });
4326 af.setTitle(newTitle);
4327 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4329 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4330 viewport.openSplitFrame(af, new Alignment(seqs));
4334 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4341 * Set the file format
4345 public void setFileFormat(FileFormatI format)
4347 this.currentFileFormat = format;
4351 * Try to load a features file onto the alignment.
4354 * contents or path to retrieve file
4356 * access mode of file (see jalview.io.AlignFile)
4357 * @return true if features file was parsed correctly.
4359 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4361 return avc.parseFeaturesFile(file, sourceType,
4362 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4367 public void refreshFeatureUI(boolean enableIfNecessary)
4369 // note - currently this is only still here rather than in the controller
4370 // because of the featureSettings hard reference that is yet to be
4372 if (enableIfNecessary)
4374 viewport.setShowSequenceFeatures(true);
4375 showSeqFeatures.setSelected(true);
4381 public void dragEnter(DropTargetDragEvent evt)
4386 public void dragExit(DropTargetEvent evt)
4391 public void dragOver(DropTargetDragEvent evt)
4396 public void dropActionChanged(DropTargetDragEvent evt)
4401 public void drop(DropTargetDropEvent evt)
4403 // JAL-1552 - acceptDrop required before getTransferable call for
4404 // Java's Transferable for native dnd
4405 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4406 Transferable t = evt.getTransferable();
4407 List<String> files = new ArrayList<>();
4408 List<DataSourceType> protocols = new ArrayList<>();
4412 Desktop.transferFromDropTarget(files, protocols, evt, t);
4413 } catch (Exception e)
4415 e.printStackTrace();
4421 // check to see if any of these files have names matching sequences in
4423 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4424 .getAlignment().getSequencesArray());
4426 * Object[] { String,SequenceI}
4428 ArrayList<Object[]> filesmatched = new ArrayList<>();
4429 ArrayList<String> filesnotmatched = new ArrayList<>();
4430 for (int i = 0; i < files.size(); i++)
4432 String file = files.get(i).toString();
4434 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4435 if (protocol == DataSourceType.FILE)
4437 File fl = new File(file);
4438 pdbfn = fl.getName();
4440 else if (protocol == DataSourceType.URL)
4442 URL url = new URL(file);
4443 pdbfn = url.getFile();
4445 if (pdbfn.length() > 0)
4447 // attempt to find a match in the alignment
4448 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4449 int l = 0, c = pdbfn.indexOf(".");
4450 while (mtch == null && c != -1)
4455 } while ((c = pdbfn.indexOf(".", l)) > l);
4458 pdbfn = pdbfn.substring(0, l);
4460 mtch = idm.findAllIdMatches(pdbfn);
4464 FileFormatI type = null;
4467 type = new IdentifyFile().identify(file, protocol);
4468 } catch (Exception ex)
4472 if (type != null && type.isStructureFile())
4474 filesmatched.add(new Object[] { file, protocol, mtch });
4478 // File wasn't named like one of the sequences or wasn't a PDB file.
4479 filesnotmatched.add(file);
4483 if (filesmatched.size() > 0)
4485 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4491 "label.automatically_associate_structure_files_with_sequences_same_name",
4492 new Object[] { Integer
4498 .getString("label.automatically_associate_structure_files_by_name"),
4499 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4502 for (Object[] fm : filesmatched)
4504 // try and associate
4505 // TODO: may want to set a standard ID naming formalism for
4506 // associating PDB files which have no IDs.
4507 for (SequenceI toassoc : (SequenceI[]) fm[2])
4509 PDBEntry pe = new AssociatePdbFileWithSeq()
4510 .associatePdbWithSeq((String) fm[0],
4511 (DataSourceType) fm[1], toassoc, false,
4515 System.err.println("Associated file : "
4516 + ((String) fm[0]) + " with "
4517 + toassoc.getDisplayId(true));
4521 alignPanel.paintAlignment(true);
4525 if (filesnotmatched.size() > 0)
4528 && (Cache.getDefault(
4529 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4535 "label.ignore_unmatched_dropped_files_info",
4536 new Object[] { Integer
4543 .getString("label.ignore_unmatched_dropped_files"),
4544 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4548 for (String fn : filesnotmatched)
4550 loadJalviewDataFile(fn, null, null, null);
4554 } catch (Exception ex)
4556 ex.printStackTrace();
4562 * Attempt to load a "dropped" file or URL string, by testing in turn for
4564 * <li>an Annotation file</li>
4565 * <li>a JNet file</li>
4566 * <li>a features file</li>
4567 * <li>else try to interpret as an alignment file</li>
4571 * either a filename or a URL string.
4573 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4574 FileFormatI format, SequenceI assocSeq)
4578 if (sourceType == null)
4580 sourceType = FormatAdapter.checkProtocol(file);
4582 // if the file isn't identified, or not positively identified as some
4583 // other filetype (PFAM is default unidentified alignment file type) then
4584 // try to parse as annotation.
4585 boolean isAnnotation = (format == null || FileFormat.Pfam
4586 .equals(format)) ? new AnnotationFile()
4587 .annotateAlignmentView(viewport, file, sourceType) : false;
4591 // first see if its a T-COFFEE score file
4592 TCoffeeScoreFile tcf = null;
4595 tcf = new TCoffeeScoreFile(file, sourceType);
4598 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4601 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4602 isAnnotation = true;
4604 .setText(MessageManager
4605 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4609 // some problem - if no warning its probable that the ID matching
4610 // process didn't work
4614 tcf.getWarningMessage() == null ? MessageManager
4615 .getString("label.check_file_matches_sequence_ids_alignment")
4616 : tcf.getWarningMessage(),
4618 .getString("label.problem_reading_tcoffee_score_file"),
4619 JvOptionPane.WARNING_MESSAGE);
4626 } catch (Exception x)
4629 .debug("Exception when processing data source as T-COFFEE score file",
4635 // try to see if its a JNet 'concise' style annotation file *before*
4637 // try to parse it as a features file
4640 format = new IdentifyFile().identify(file, sourceType);
4642 if (FileFormat.ScoreMatrix == format)
4644 ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4647 // todo: i18n this message
4649 .setText(MessageManager.formatMessage(
4650 "label.successfully_loaded_matrix",
4651 sm.getMatrixName()));
4653 else if (FileFormat.HMMER3.equals(format))
4655 HMMFile hmm = new HMMFile(new FileParse(file, sourceType));
4657 System.out.println("successful");
4659 else if (FileFormat.Jnet.equals(format))
4661 JPredFile predictions = new JPredFile(file, sourceType);
4662 new JnetAnnotationMaker();
4663 JnetAnnotationMaker.add_annotation(predictions,
4664 viewport.getAlignment(), 0, false);
4665 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4666 viewport.getAlignment().setSeqrep(repseq);
4667 HiddenColumns cs = new HiddenColumns();
4668 cs.hideInsertionsFor(repseq);
4669 viewport.getAlignment().setHiddenColumns(cs);
4670 isAnnotation = true;
4672 // else if (IdentifyFile.FeaturesFile.equals(format))
4673 else if (FileFormat.Features.equals(format))
4675 if (parseFeaturesFile(file, sourceType))
4677 alignPanel.paintAlignment(true);
4682 new FileLoader().LoadFile(viewport, file, sourceType, format);
4689 alignPanel.adjustAnnotationHeight();
4690 viewport.updateSequenceIdColours();
4691 buildSortByAnnotationScoresMenu();
4692 alignPanel.paintAlignment(true);
4694 } catch (Exception ex)
4696 ex.printStackTrace();
4697 } catch (OutOfMemoryError oom)
4702 } catch (Exception x)
4707 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4708 : "using " + sourceType + " from " + file)
4710 + (format != null ? "(parsing as '" + format
4711 + "' file)" : ""), oom, Desktop.desktop);
4716 * Method invoked by the ChangeListener on the tabbed pane, in other words
4717 * when a different tabbed pane is selected by the user or programmatically.
4720 public void tabSelectionChanged(int index)
4724 alignPanel = alignPanels.get(index);
4725 viewport = alignPanel.av;
4726 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4727 setMenusFromViewport(viewport);
4731 * 'focus' any colour slider that is open to the selected viewport
4733 if (viewport.getConservationSelected())
4735 SliderPanel.setConservationSlider(alignPanel,
4736 viewport.getResidueShading(), alignPanel.getViewName());
4740 SliderPanel.hideConservationSlider();
4742 if (viewport.getAbovePIDThreshold())
4744 SliderPanel.setPIDSliderSource(alignPanel,
4745 viewport.getResidueShading(), alignPanel.getViewName());
4749 SliderPanel.hidePIDSlider();
4753 * If there is a frame linked to this one in a SplitPane, switch it to the
4754 * same view tab index. No infinite recursion of calls should happen, since
4755 * tabSelectionChanged() should not get invoked on setting the selected
4756 * index to an unchanged value. Guard against setting an invalid index
4757 * before the new view peer tab has been created.
4759 final AlignViewportI peer = viewport.getCodingComplement();
4762 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4763 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4765 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4771 * On right mouse click on view tab, prompt for and set new view name.
4774 public void tabbedPane_mousePressed(MouseEvent e)
4776 if (e.isPopupTrigger())
4778 String msg = MessageManager.getString("label.enter_view_name");
4779 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4780 JvOptionPane.QUESTION_MESSAGE);
4784 viewport.viewName = reply;
4785 // TODO warn if reply is in getExistingViewNames()?
4786 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4791 public AlignViewport getCurrentView()
4797 * Open the dialog for regex description parsing.
4800 protected void extractScores_actionPerformed(ActionEvent e)
4802 ParseProperties pp = new jalview.analysis.ParseProperties(
4803 viewport.getAlignment());
4804 // TODO: verify regex and introduce GUI dialog for version 2.5
4805 // if (pp.getScoresFromDescription("col", "score column ",
4806 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4808 if (pp.getScoresFromDescription("description column",
4809 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4811 buildSortByAnnotationScoresMenu();
4819 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4823 protected void showDbRefs_actionPerformed(ActionEvent e)
4825 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4831 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4835 protected void showNpFeats_actionPerformed(ActionEvent e)
4837 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4841 * find the viewport amongst the tabs in this alignment frame and close that
4846 public boolean closeView(AlignViewportI av)
4850 this.closeMenuItem_actionPerformed(false);
4853 Component[] comp = tabbedPane.getComponents();
4854 for (int i = 0; comp != null && i < comp.length; i++)
4856 if (comp[i] instanceof AlignmentPanel)
4858 if (((AlignmentPanel) comp[i]).av == av)
4861 closeView((AlignmentPanel) comp[i]);
4869 protected void build_fetchdbmenu(JMenu webService)
4871 // Temporary hack - DBRef Fetcher always top level ws entry.
4872 // TODO We probably want to store a sequence database checklist in
4873 // preferences and have checkboxes.. rather than individual sources selected
4875 final JMenu rfetch = new JMenu(
4876 MessageManager.getString("action.fetch_db_references"));
4877 rfetch.setToolTipText(MessageManager
4878 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4879 webService.add(rfetch);
4881 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4882 MessageManager.getString("option.trim_retrieved_seqs"));
4883 trimrs.setToolTipText(MessageManager
4884 .getString("label.trim_retrieved_sequences"));
4885 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4886 trimrs.addActionListener(new ActionListener()
4889 public void actionPerformed(ActionEvent e)
4891 trimrs.setSelected(trimrs.isSelected());
4892 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4893 Boolean.valueOf(trimrs.isSelected()).toString());
4897 JMenuItem fetchr = new JMenuItem(
4898 MessageManager.getString("label.standard_databases"));
4899 fetchr.setToolTipText(MessageManager
4900 .getString("label.fetch_embl_uniprot"));
4901 fetchr.addActionListener(new ActionListener()
4905 public void actionPerformed(ActionEvent e)
4907 new Thread(new Runnable()
4912 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4913 .getAlignment().isNucleotide();
4914 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
4915 .getSequenceSelection(), alignPanel.alignFrame, null,
4916 alignPanel.alignFrame.featureSettings, isNucleotide);
4917 dbRefFetcher.addListener(new FetchFinishedListenerI()
4920 public void finished()
4922 AlignFrame.this.setMenusForViewport();
4925 dbRefFetcher.fetchDBRefs(false);
4933 final AlignFrame me = this;
4934 new Thread(new Runnable()
4939 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4940 .getSequenceFetcherSingleton(me);
4941 javax.swing.SwingUtilities.invokeLater(new Runnable()
4946 String[] dbclasses = sf.getOrderedSupportedSources();
4947 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4948 // jalview.util.QuickSort.sort(otherdb, otherdb);
4949 List<DbSourceProxy> otherdb;
4950 JMenu dfetch = new JMenu();
4951 JMenu ifetch = new JMenu();
4952 JMenuItem fetchr = null;
4953 int comp = 0, icomp = 0, mcomp = 15;
4954 String mname = null;
4956 for (String dbclass : dbclasses)
4958 otherdb = sf.getSourceProxy(dbclass);
4959 // add a single entry for this class, or submenu allowing 'fetch
4961 if (otherdb == null || otherdb.size() < 1)
4965 // List<DbSourceProxy> dbs=otherdb;
4966 // otherdb=new ArrayList<DbSourceProxy>();
4967 // for (DbSourceProxy db:dbs)
4969 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4973 mname = "From " + dbclass;
4975 if (otherdb.size() == 1)
4977 final DbSourceProxy[] dassource = otherdb
4978 .toArray(new DbSourceProxy[0]);
4979 DbSourceProxy src = otherdb.get(0);
4980 fetchr = new JMenuItem(src.getDbSource());
4981 fetchr.addActionListener(new ActionListener()
4985 public void actionPerformed(ActionEvent e)
4987 new Thread(new Runnable()
4993 boolean isNucleotide = alignPanel.alignFrame
4994 .getViewport().getAlignment()
4996 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4997 alignPanel.av.getSequenceSelection(),
4998 alignPanel.alignFrame, dassource,
4999 alignPanel.alignFrame.featureSettings,
5002 .addListener(new FetchFinishedListenerI()
5005 public void finished()
5007 AlignFrame.this.setMenusForViewport();
5010 dbRefFetcher.fetchDBRefs(false);
5016 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5017 MessageManager.formatMessage(
5018 "label.fetch_retrieve_from",
5019 new Object[] { src.getDbName() })));
5025 final DbSourceProxy[] dassource = otherdb
5026 .toArray(new DbSourceProxy[0]);
5028 DbSourceProxy src = otherdb.get(0);
5029 fetchr = new JMenuItem(MessageManager.formatMessage(
5030 "label.fetch_all_param",
5031 new Object[] { src.getDbSource() }));
5032 fetchr.addActionListener(new ActionListener()
5035 public void actionPerformed(ActionEvent e)
5037 new Thread(new Runnable()
5043 boolean isNucleotide = alignPanel.alignFrame
5044 .getViewport().getAlignment()
5046 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5047 alignPanel.av.getSequenceSelection(),
5048 alignPanel.alignFrame, dassource,
5049 alignPanel.alignFrame.featureSettings,
5052 .addListener(new FetchFinishedListenerI()
5055 public void finished()
5057 AlignFrame.this.setMenusForViewport();
5060 dbRefFetcher.fetchDBRefs(false);
5066 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5067 MessageManager.formatMessage(
5068 "label.fetch_retrieve_from_all_sources",
5070 Integer.valueOf(otherdb.size())
5071 .toString(), src.getDbSource(),
5072 src.getDbName() })));
5075 // and then build the rest of the individual menus
5076 ifetch = new JMenu(MessageManager.formatMessage(
5077 "label.source_from_db_source",
5078 new Object[] { src.getDbSource() }));
5080 String imname = null;
5082 for (DbSourceProxy sproxy : otherdb)
5084 String dbname = sproxy.getDbName();
5085 String sname = dbname.length() > 5 ? dbname.substring(0,
5086 5) + "..." : dbname;
5087 String msname = dbname.length() > 10 ? dbname.substring(
5088 0, 10) + "..." : dbname;
5091 imname = MessageManager.formatMessage(
5092 "label.from_msname", new Object[] { sname });
5094 fetchr = new JMenuItem(msname);
5095 final DbSourceProxy[] dassrc = { sproxy };
5096 fetchr.addActionListener(new ActionListener()
5100 public void actionPerformed(ActionEvent e)
5102 new Thread(new Runnable()
5108 boolean isNucleotide = alignPanel.alignFrame
5109 .getViewport().getAlignment()
5111 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5112 alignPanel.av.getSequenceSelection(),
5113 alignPanel.alignFrame, dassrc,
5114 alignPanel.alignFrame.featureSettings,
5117 .addListener(new FetchFinishedListenerI()
5120 public void finished()
5122 AlignFrame.this.setMenusForViewport();
5125 dbRefFetcher.fetchDBRefs(false);
5131 fetchr.setToolTipText("<html>"
5132 + MessageManager.formatMessage(
5133 "label.fetch_retrieve_from", new Object[]
5137 if (++icomp >= mcomp || i == (otherdb.size()))
5139 ifetch.setText(MessageManager.formatMessage(
5140 "label.source_to_target", imname, sname));
5142 ifetch = new JMenu();
5150 if (comp >= mcomp || dbi >= (dbclasses.length))
5152 dfetch.setText(MessageManager.formatMessage(
5153 "label.source_to_target", mname, dbclass));
5155 dfetch = new JMenu();
5168 * Left justify the whole alignment.
5171 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5173 AlignmentI al = viewport.getAlignment();
5175 viewport.firePropertyChange("alignment", null, al);
5179 * Right justify the whole alignment.
5182 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5184 AlignmentI al = viewport.getAlignment();
5186 viewport.firePropertyChange("alignment", null, al);
5190 public void setShowSeqFeatures(boolean b)
5192 showSeqFeatures.setSelected(b);
5193 viewport.setShowSequenceFeatures(b);
5200 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5201 * awt.event.ActionEvent)
5204 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5206 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5207 alignPanel.paintAlignment(true);
5214 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5218 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5220 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5221 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5229 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5230 * .event.ActionEvent)
5233 protected void showGroupConservation_actionPerformed(ActionEvent e)
5235 viewport.setShowGroupConservation(showGroupConservation.getState());
5236 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5243 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5244 * .event.ActionEvent)
5247 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5249 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5250 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5257 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5258 * .event.ActionEvent)
5261 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5263 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5264 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5268 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5270 showSequenceLogo.setState(true);
5271 viewport.setShowSequenceLogo(true);
5272 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5273 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5277 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5279 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5286 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5287 * .event.ActionEvent)
5290 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5292 if (avc.makeGroupsFromSelection())
5294 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5295 alignPanel.updateAnnotation();
5296 alignPanel.paintAlignment(true);
5300 public void clearAlignmentSeqRep()
5302 // TODO refactor alignmentseqrep to controller
5303 if (viewport.getAlignment().hasSeqrep())
5305 viewport.getAlignment().setSeqrep(null);
5306 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5307 alignPanel.updateAnnotation();
5308 alignPanel.paintAlignment(true);
5313 protected void createGroup_actionPerformed(ActionEvent e)
5315 if (avc.createGroup())
5317 alignPanel.alignmentChanged();
5322 protected void unGroup_actionPerformed(ActionEvent e)
5326 alignPanel.alignmentChanged();
5331 * make the given alignmentPanel the currently selected tab
5333 * @param alignmentPanel
5335 public void setDisplayedView(AlignmentPanel alignmentPanel)
5337 if (!viewport.getSequenceSetId().equals(
5338 alignmentPanel.av.getSequenceSetId()))
5342 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5344 if (tabbedPane != null
5345 && tabbedPane.getTabCount() > 0
5346 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5347 .getSelectedIndex())
5349 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5354 * Action on selection of menu options to Show or Hide annotations.
5357 * @param forSequences
5358 * update sequence-related annotations
5359 * @param forAlignment
5360 * update non-sequence-related annotations
5363 protected void setAnnotationsVisibility(boolean visible,
5364 boolean forSequences, boolean forAlignment)
5366 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5367 .getAlignmentAnnotation();
5372 for (AlignmentAnnotation aa : anns)
5375 * don't display non-positional annotations on an alignment
5377 if (aa.annotations == null)
5381 boolean apply = (aa.sequenceRef == null && forAlignment)
5382 || (aa.sequenceRef != null && forSequences);
5385 aa.visible = visible;
5388 alignPanel.validateAnnotationDimensions(true);
5389 alignPanel.alignmentChanged();
5393 * Store selected annotation sort order for the view and repaint.
5396 protected void sortAnnotations_actionPerformed()
5398 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5400 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5401 alignPanel.paintAlignment(true);
5406 * @return alignment panels in this alignment frame
5408 public List<? extends AlignmentViewPanel> getAlignPanels()
5410 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5414 * Open a new alignment window, with the cDNA associated with this (protein)
5415 * alignment, aligned as is the protein.
5417 protected void viewAsCdna_actionPerformed()
5419 // TODO no longer a menu action - refactor as required
5420 final AlignmentI alignment = getViewport().getAlignment();
5421 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5422 if (mappings == null)
5426 List<SequenceI> cdnaSeqs = new ArrayList<>();
5427 for (SequenceI aaSeq : alignment.getSequences())
5429 for (AlignedCodonFrame acf : mappings)
5431 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5435 * There is a cDNA mapping for this protein sequence - add to new
5436 * alignment. It will share the same dataset sequence as other mapped
5437 * cDNA (no new mappings need to be created).
5439 final Sequence newSeq = new Sequence(dnaSeq);
5440 newSeq.setDatasetSequence(dnaSeq);
5441 cdnaSeqs.add(newSeq);
5445 if (cdnaSeqs.size() == 0)
5447 // show a warning dialog no mapped cDNA
5450 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5452 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5453 AlignFrame.DEFAULT_HEIGHT);
5454 cdna.alignAs(alignment);
5455 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5457 Desktop.addInternalFrame(alignFrame, newtitle,
5458 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5462 * Set visibility of dna/protein complement view (available when shown in a
5468 protected void showComplement_actionPerformed(boolean show)
5470 SplitContainerI sf = getSplitViewContainer();
5473 sf.setComplementVisible(this, show);
5478 * Generate the reverse (optionally complemented) of the selected sequences,
5479 * and add them to the alignment
5482 protected void showReverse_actionPerformed(boolean complement)
5484 AlignmentI al = null;
5487 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5488 al = dna.reverseCdna(complement);
5489 viewport.addAlignment(al, "");
5490 addHistoryItem(new EditCommand(
5491 MessageManager.getString("label.add_sequences"),
5492 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5493 viewport.getAlignment()));
5494 } catch (Exception ex)
5496 System.err.println(ex.getMessage());
5502 * Try to run a script in the Groovy console, having first ensured that this
5503 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5504 * be targeted at this alignment.
5507 protected void runGroovy_actionPerformed()
5509 Jalview.setCurrentAlignFrame(this);
5510 groovy.ui.Console console = Desktop.getGroovyConsole();
5511 if (console != null)
5515 console.runScript();
5516 } catch (Exception ex)
5518 System.err.println((ex.toString()));
5520 .showInternalMessageDialog(Desktop.desktop, MessageManager
5521 .getString("label.couldnt_run_groovy_script"),
5523 .getString("label.groovy_support_failed"),
5524 JvOptionPane.ERROR_MESSAGE);
5529 System.err.println("Can't run Groovy script as console not found");
5534 * Hides columns containing (or not containing) a specified feature, provided
5535 * that would not leave all columns hidden
5537 * @param featureType
5538 * @param columnsContaining
5541 public boolean hideFeatureColumns(String featureType,
5542 boolean columnsContaining)
5544 boolean notForHiding = avc.markColumnsContainingFeatures(
5545 columnsContaining, false, false, featureType);
5548 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5549 false, featureType))
5551 getViewport().hideSelectedColumns();
5559 protected void selectHighlightedColumns_actionPerformed(
5560 ActionEvent actionEvent)
5562 // include key modifier check in case user selects from menu
5563 avc.markHighlightedColumns(
5564 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5566 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5570 * Rebuilds the Colour menu, including any user-defined colours which have
5571 * been loaded either on startup or during the session
5573 public void buildColourMenu()
5575 colourMenu.removeAll();
5577 colourMenu.add(applyToAllGroups);
5578 colourMenu.add(textColour);
5579 colourMenu.addSeparator();
5581 ColourMenuHelper.addMenuItems(colourMenu, this,
5582 viewport.getAlignment(), false);
5584 colourMenu.addSeparator();
5585 colourMenu.add(conservationMenuItem);
5586 colourMenu.add(modifyConservation);
5587 colourMenu.add(abovePIDThreshold);
5588 colourMenu.add(modifyPID);
5589 colourMenu.add(annotationColour);
5591 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5592 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5596 * Open a dialog (if not already open) that allows the user to select and
5597 * calculate PCA or Tree analysis
5599 protected void openTreePcaDialog()
5601 if (alignPanel.getCalculationDialog() == null)
5603 new CalculationChooser(AlignFrame.this);
5608 class PrintThread extends Thread
5612 public PrintThread(AlignmentPanel ap)
5617 static PageFormat pf;
5622 PrinterJob printJob = PrinterJob.getPrinterJob();
5626 printJob.setPrintable(ap, pf);
5630 printJob.setPrintable(ap);
5633 if (printJob.printDialog())
5638 } catch (Exception PrintException)
5640 PrintException.printStackTrace();