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.ScoreModelI;
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.HiddenSequences;
57 import jalview.datamodel.PDBEntry;
58 import jalview.datamodel.SeqCigar;
59 import jalview.datamodel.Sequence;
60 import jalview.datamodel.SequenceGroup;
61 import jalview.datamodel.SequenceI;
62 import jalview.gui.ColourMenuHelper.ColourChangeListener;
63 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
64 import jalview.io.AlignmentProperties;
65 import jalview.io.AnnotationFile;
66 import jalview.io.BioJsHTMLOutput;
67 import jalview.io.DataSourceType;
68 import jalview.io.FileFormat;
69 import jalview.io.FileFormatI;
70 import jalview.io.FileFormats;
71 import jalview.io.FileLoader;
72 import jalview.io.FormatAdapter;
73 import jalview.io.HtmlSvgOutput;
74 import jalview.io.IdentifyFile;
75 import jalview.io.JPredFile;
76 import jalview.io.JalviewFileChooser;
77 import jalview.io.JalviewFileView;
78 import jalview.io.JnetAnnotationMaker;
79 import jalview.io.NewickFile;
80 import jalview.io.TCoffeeScoreFile;
81 import jalview.jbgui.GAlignFrame;
82 import jalview.schemes.ColourSchemeI;
83 import jalview.schemes.ColourSchemes;
84 import jalview.schemes.ResidueColourScheme;
85 import jalview.schemes.ResidueProperties;
86 import jalview.schemes.TCoffeeColourScheme;
87 import jalview.util.MessageManager;
88 import jalview.viewmodel.AlignmentViewport;
89 import jalview.viewmodel.ViewportRanges;
90 import jalview.ws.DBRefFetcher;
91 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
92 import jalview.ws.jws1.Discoverer;
93 import jalview.ws.jws2.Jws2Discoverer;
94 import jalview.ws.jws2.jabaws2.Jws2Instance;
95 import jalview.ws.seqfetcher.DbSourceProxy;
97 import java.awt.BorderLayout;
98 import java.awt.Component;
99 import java.awt.Rectangle;
100 import java.awt.Toolkit;
101 import java.awt.datatransfer.Clipboard;
102 import java.awt.datatransfer.DataFlavor;
103 import java.awt.datatransfer.StringSelection;
104 import java.awt.datatransfer.Transferable;
105 import java.awt.dnd.DnDConstants;
106 import java.awt.dnd.DropTargetDragEvent;
107 import java.awt.dnd.DropTargetDropEvent;
108 import java.awt.dnd.DropTargetEvent;
109 import java.awt.dnd.DropTargetListener;
110 import java.awt.event.ActionEvent;
111 import java.awt.event.ActionListener;
112 import java.awt.event.FocusAdapter;
113 import java.awt.event.FocusEvent;
114 import java.awt.event.ItemEvent;
115 import java.awt.event.ItemListener;
116 import java.awt.event.KeyAdapter;
117 import java.awt.event.KeyEvent;
118 import java.awt.event.MouseEvent;
119 import java.awt.print.PageFormat;
120 import java.awt.print.PrinterJob;
121 import java.beans.PropertyChangeEvent;
123 import java.io.FileWriter;
124 import java.io.PrintWriter;
126 import java.util.ArrayList;
127 import java.util.Arrays;
128 import java.util.Deque;
129 import java.util.Enumeration;
130 import java.util.Hashtable;
131 import java.util.List;
132 import java.util.Vector;
134 import javax.swing.JCheckBoxMenuItem;
135 import javax.swing.JEditorPane;
136 import javax.swing.JInternalFrame;
137 import javax.swing.JLayeredPane;
138 import javax.swing.JMenu;
139 import javax.swing.JMenuItem;
140 import javax.swing.JScrollPane;
141 import javax.swing.SwingUtilities;
147 * @version $Revision$
149 public class AlignFrame extends GAlignFrame implements DropTargetListener,
150 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
153 public static final int DEFAULT_WIDTH = 700;
155 public static final int DEFAULT_HEIGHT = 500;
158 * The currently displayed panel (selected tabbed view if more than one)
160 public AlignmentPanel alignPanel;
162 AlignViewport viewport;
164 ViewportRanges vpRanges;
166 public AlignViewControllerI avc;
168 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
171 * Last format used to load or save alignments in this window
173 FileFormatI currentFileFormat = null;
176 * Current filename for this alignment
178 String fileName = null;
181 * Creates a new AlignFrame object with specific width and height.
187 public AlignFrame(AlignmentI al, int width, int height)
189 this(al, null, width, height);
193 * Creates a new AlignFrame object with specific width, height and
199 * @param sequenceSetId
201 public AlignFrame(AlignmentI al, int width, int height,
202 String sequenceSetId)
204 this(al, null, width, height, sequenceSetId);
208 * Creates a new AlignFrame object with specific width, height and
214 * @param sequenceSetId
217 public AlignFrame(AlignmentI al, int width, int height,
218 String sequenceSetId, String viewId)
220 this(al, null, width, height, sequenceSetId, viewId);
224 * new alignment window with hidden columns
228 * @param hiddenColumns
229 * ColumnSelection or null
231 * Width of alignment frame
235 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
236 int width, int height)
238 this(al, hiddenColumns, width, height, null);
242 * Create alignment frame for al with hiddenColumns, a specific width and
243 * height, and specific sequenceId
246 * @param hiddenColumns
249 * @param sequenceSetId
252 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
253 int width, int height, String sequenceSetId)
255 this(al, hiddenColumns, width, height, sequenceSetId, null);
259 * Create alignment frame for al with hiddenColumns, a specific width and
260 * height, and specific sequenceId
263 * @param hiddenColumns
266 * @param sequenceSetId
271 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
272 int width, int height, String sequenceSetId, String viewId)
274 setSize(width, height);
276 if (al.getDataset() == null)
281 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
283 alignPanel = new AlignmentPanel(this, viewport);
285 addAlignmentPanel(alignPanel, true);
289 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
290 ColumnSelection hiddenColumns, int width, int height)
292 setSize(width, height);
294 if (al.getDataset() == null)
299 viewport = new AlignViewport(al, hiddenColumns);
301 if (hiddenSeqs != null && hiddenSeqs.length > 0)
303 viewport.hideSequence(hiddenSeqs);
305 alignPanel = new AlignmentPanel(this, viewport);
306 addAlignmentPanel(alignPanel, true);
311 * Make a new AlignFrame from existing alignmentPanels
318 public AlignFrame(AlignmentPanel ap)
322 addAlignmentPanel(ap, false);
327 * initalise the alignframe from the underlying viewport data and the
332 if (!Jalview.isHeadlessMode())
334 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
337 vpRanges = viewport.getRanges();
338 avc = new jalview.controller.AlignViewController(this, viewport,
340 if (viewport.getAlignmentConservationAnnotation() == null)
342 // BLOSUM62Colour.setEnabled(false);
343 conservationMenuItem.setEnabled(false);
344 modifyConservation.setEnabled(false);
345 // PIDColour.setEnabled(false);
346 // abovePIDThreshold.setEnabled(false);
347 // modifyPID.setEnabled(false);
350 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
353 if (sortby.equals("Id"))
355 sortIDMenuItem_actionPerformed(null);
357 else if (sortby.equals("Pairwise Identity"))
359 sortPairwiseMenuItem_actionPerformed(null);
363 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
365 setMenusFromViewport(viewport);
366 buildSortByAnnotationScoresMenu();
370 if (Desktop.desktop != null)
372 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
373 addServiceListeners();
377 if (viewport.getWrapAlignment())
379 wrapMenuItem_actionPerformed(null);
382 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
384 this.overviewMenuItem_actionPerformed(null);
389 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
390 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
391 final String menuLabel = MessageManager
392 .getString("label.copy_format_from");
393 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
394 new ViewSetProvider()
398 public AlignmentPanel[] getAllAlignmentPanels()
401 origview.add(alignPanel);
402 // make an array of all alignment panels except for this one
403 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
404 Arrays.asList(Desktop.getAlignmentPanels(null)));
405 aps.remove(AlignFrame.this.alignPanel);
406 return aps.toArray(new AlignmentPanel[aps.size()]);
408 }, selviews, new ItemListener()
412 public void itemStateChanged(ItemEvent e)
414 if (origview.size() > 0)
416 final AlignmentPanel ap = origview.get(0);
419 * Copy the ViewStyle of the selected panel to 'this one'.
420 * Don't change value of 'scaleProteinAsCdna' unless copying
423 ViewStyleI vs = selviews.get(0).getAlignViewport()
425 boolean fromSplitFrame = selviews.get(0)
426 .getAlignViewport().getCodingComplement() != null;
429 vs.setScaleProteinAsCdna(ap.getAlignViewport()
430 .getViewStyle().isScaleProteinAsCdna());
432 ap.getAlignViewport().setViewStyle(vs);
435 * Also rescale ViewStyle of SplitFrame complement if there is
436 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
437 * the whole ViewStyle (allow cDNA protein to have different
440 AlignViewportI complement = ap.getAlignViewport()
441 .getCodingComplement();
442 if (complement != null && vs.isScaleProteinAsCdna())
444 AlignFrame af = Desktop.getAlignFrameFor(complement);
445 ((SplitFrame) af.getSplitViewContainer())
447 af.setMenusForViewport();
451 ap.setSelected(true);
452 ap.alignFrame.setMenusForViewport();
457 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
458 .indexOf("devel") > -1
459 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
460 .indexOf("test") > -1)
462 formatMenu.add(vsel);
464 addFocusListener(new FocusAdapter()
467 public void focusGained(FocusEvent e)
469 Jalview.setCurrentAlignFrame(AlignFrame.this);
476 * Change the filename and format for the alignment, and enable the 'reload'
477 * button functionality.
484 public void setFileName(String file, FileFormatI format)
487 setFileFormat(format);
488 reload.setEnabled(true);
492 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
495 void addKeyListener()
497 addKeyListener(new KeyAdapter()
500 public void keyPressed(KeyEvent evt)
502 if (viewport.cursorMode
503 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
504 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
505 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
506 && Character.isDigit(evt.getKeyChar()))
508 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
511 switch (evt.getKeyCode())
514 case 27: // escape key
515 deselectAllSequenceMenuItem_actionPerformed(null);
519 case KeyEvent.VK_DOWN:
520 if (evt.isAltDown() || !viewport.cursorMode)
522 moveSelectedSequences(false);
524 if (viewport.cursorMode)
526 alignPanel.getSeqPanel().moveCursor(0, 1);
531 if (evt.isAltDown() || !viewport.cursorMode)
533 moveSelectedSequences(true);
535 if (viewport.cursorMode)
537 alignPanel.getSeqPanel().moveCursor(0, -1);
542 case KeyEvent.VK_LEFT:
543 if (evt.isAltDown() || !viewport.cursorMode)
545 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
549 alignPanel.getSeqPanel().moveCursor(-1, 0);
554 case KeyEvent.VK_RIGHT:
555 if (evt.isAltDown() || !viewport.cursorMode)
557 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
561 alignPanel.getSeqPanel().moveCursor(1, 0);
565 case KeyEvent.VK_SPACE:
566 if (viewport.cursorMode)
568 alignPanel.getSeqPanel().insertGapAtCursor(
569 evt.isControlDown() || evt.isShiftDown()
574 // case KeyEvent.VK_A:
575 // if (viewport.cursorMode)
577 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
578 // //System.out.println("A");
582 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
583 * System.out.println("closing bracket"); } break;
585 case KeyEvent.VK_DELETE:
586 case KeyEvent.VK_BACK_SPACE:
587 if (!viewport.cursorMode)
589 cut_actionPerformed(null);
593 alignPanel.getSeqPanel().deleteGapAtCursor(
594 evt.isControlDown() || evt.isShiftDown()
601 if (viewport.cursorMode)
603 alignPanel.getSeqPanel().setCursorRow();
607 if (viewport.cursorMode && !evt.isControlDown())
609 alignPanel.getSeqPanel().setCursorColumn();
613 if (viewport.cursorMode)
615 alignPanel.getSeqPanel().setCursorPosition();
619 case KeyEvent.VK_ENTER:
620 case KeyEvent.VK_COMMA:
621 if (viewport.cursorMode)
623 alignPanel.getSeqPanel().setCursorRowAndColumn();
628 if (viewport.cursorMode)
630 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
634 if (viewport.cursorMode)
636 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
641 viewport.cursorMode = !viewport.cursorMode;
642 statusBar.setText(MessageManager.formatMessage(
643 "label.keyboard_editing_mode",
644 new String[] { (viewport.cursorMode ? "on" : "off") }));
645 if (viewport.cursorMode)
647 alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
649 alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
652 alignPanel.getSeqPanel().seqCanvas.repaint();
658 Help.showHelpWindow();
659 } catch (Exception ex)
661 ex.printStackTrace();
666 boolean toggleSeqs = !evt.isControlDown();
667 boolean toggleCols = !evt.isShiftDown();
668 toggleHiddenRegions(toggleSeqs, toggleCols);
673 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
674 boolean modifyExisting = true; // always modify, don't clear
675 // evt.isShiftDown();
676 boolean invertHighlighted = evt.isAltDown();
677 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
681 case KeyEvent.VK_PAGE_UP:
682 if (viewport.getWrapAlignment())
684 vpRanges.scrollUp(true);
688 vpRanges.setStartSeq(2 * vpRanges.getStartSeq()
689 - vpRanges.getEndSeq());
692 case KeyEvent.VK_PAGE_DOWN:
693 if (viewport.getWrapAlignment())
695 vpRanges.scrollUp(false);
699 vpRanges.setStartSeq(vpRanges.getEndSeq());
706 public void keyReleased(KeyEvent evt)
708 switch (evt.getKeyCode())
710 case KeyEvent.VK_LEFT:
711 if (evt.isAltDown() || !viewport.cursorMode)
713 viewport.firePropertyChange("alignment", null, viewport
714 .getAlignment().getSequences());
718 case KeyEvent.VK_RIGHT:
719 if (evt.isAltDown() || !viewport.cursorMode)
721 viewport.firePropertyChange("alignment", null, viewport
722 .getAlignment().getSequences());
730 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
732 ap.alignFrame = this;
733 avc = new jalview.controller.AlignViewController(this, viewport,
738 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
740 int aSize = alignPanels.size();
742 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
744 if (aSize == 1 && ap.av.viewName == null)
746 this.getContentPane().add(ap, BorderLayout.CENTER);
752 setInitialTabVisible();
755 expandViews.setEnabled(true);
756 gatherViews.setEnabled(true);
757 tabbedPane.addTab(ap.av.viewName, ap);
759 ap.setVisible(false);
764 if (ap.av.isPadGaps())
766 ap.av.getAlignment().padGaps();
768 ap.av.updateConservation(ap);
769 ap.av.updateConsensus(ap);
770 ap.av.updateStrucConsensus(ap);
774 public void setInitialTabVisible()
776 expandViews.setEnabled(true);
777 gatherViews.setEnabled(true);
778 tabbedPane.setVisible(true);
779 AlignmentPanel first = alignPanels.get(0);
780 tabbedPane.addTab(first.av.viewName, first);
781 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
784 public AlignViewport getViewport()
789 /* Set up intrinsic listeners for dynamically generated GUI bits. */
790 private void addServiceListeners()
792 final java.beans.PropertyChangeListener thisListener;
793 Desktop.instance.addJalviewPropertyChangeListener("services",
794 thisListener = new java.beans.PropertyChangeListener()
797 public void propertyChange(PropertyChangeEvent evt)
799 // // System.out.println("Discoverer property change.");
800 // if (evt.getPropertyName().equals("services"))
802 SwingUtilities.invokeLater(new Runnable()
809 .println("Rebuild WS Menu for service change");
810 BuildWebServiceMenu();
817 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
820 public void internalFrameClosed(
821 javax.swing.event.InternalFrameEvent evt)
823 // System.out.println("deregistering discoverer listener");
824 Desktop.instance.removeJalviewPropertyChangeListener("services",
826 closeMenuItem_actionPerformed(true);
829 // Finally, build the menu once to get current service state
830 new Thread(new Runnable()
835 BuildWebServiceMenu();
841 * Configure menu items that vary according to whether the alignment is
842 * nucleotide or protein
844 public void setGUINucleotide()
846 AlignmentI al = getViewport().getAlignment();
847 boolean nucleotide = al.isNucleotide();
849 showTranslation.setVisible(nucleotide);
850 showReverse.setVisible(nucleotide);
851 showReverseComplement.setVisible(nucleotide);
852 conservationMenuItem.setEnabled(!nucleotide);
853 modifyConservation.setEnabled(!nucleotide
854 && conservationMenuItem.isSelected());
855 showGroupConservation.setEnabled(!nucleotide);
857 showComplementMenuItem.setText(nucleotide ? MessageManager
858 .getString("label.protein") : MessageManager
859 .getString("label.nucleotide"));
863 * set up menus for the current viewport. This may be called after any
864 * operation that affects the data in the current view (selection changed,
865 * etc) to update the menus to reflect the new state.
868 public void setMenusForViewport()
870 setMenusFromViewport(viewport);
874 * Need to call this method when tabs are selected for multiple views, or when
875 * loading from Jalview2XML.java
880 void setMenusFromViewport(AlignViewport av)
882 padGapsMenuitem.setSelected(av.isPadGaps());
883 colourTextMenuItem.setSelected(av.isShowColourText());
884 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
885 modifyPID.setEnabled(abovePIDThreshold.isSelected());
886 conservationMenuItem.setSelected(av.getConservationSelected());
887 modifyConservation.setEnabled(conservationMenuItem.isSelected());
888 seqLimits.setSelected(av.getShowJVSuffix());
889 idRightAlign.setSelected(av.isRightAlignIds());
890 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
891 renderGapsMenuItem.setSelected(av.isRenderGaps());
892 wrapMenuItem.setSelected(av.getWrapAlignment());
893 scaleAbove.setVisible(av.getWrapAlignment());
894 scaleLeft.setVisible(av.getWrapAlignment());
895 scaleRight.setVisible(av.getWrapAlignment());
896 annotationPanelMenuItem.setState(av.isShowAnnotation());
898 * Show/hide annotations only enabled if annotation panel is shown
900 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
901 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
902 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
903 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
904 viewBoxesMenuItem.setSelected(av.getShowBoxes());
905 viewTextMenuItem.setSelected(av.getShowText());
906 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
907 showGroupConsensus.setSelected(av.isShowGroupConsensus());
908 showGroupConservation.setSelected(av.isShowGroupConservation());
909 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
910 showSequenceLogo.setSelected(av.isShowSequenceLogo());
911 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
913 ColourMenuHelper.setColourSelected(colourMenu,
914 av.getGlobalColourScheme());
916 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
917 hiddenMarkers.setState(av.getShowHiddenMarkers());
918 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
919 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
920 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
921 autoCalculate.setSelected(av.autoCalculateConsensus);
922 sortByTree.setSelected(av.sortByTree);
923 listenToViewSelections.setSelected(av.followSelection);
925 showProducts.setEnabled(canShowProducts());
926 setGroovyEnabled(Desktop.getGroovyConsole() != null);
932 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
936 public void setGroovyEnabled(boolean b)
938 runGroovy.setEnabled(b);
941 private IProgressIndicator progressBar;
946 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
949 public void setProgressBar(String message, long id)
951 progressBar.setProgressBar(message, id);
955 public void registerHandler(final long id,
956 final IProgressIndicatorHandler handler)
958 progressBar.registerHandler(id, handler);
963 * @return true if any progress bars are still active
966 public boolean operationInProgress()
968 return progressBar.operationInProgress();
972 public void setStatus(String text)
974 statusBar.setText(text);
978 * Added so Castor Mapping file can obtain Jalview Version
980 public String getVersion()
982 return jalview.bin.Cache.getProperty("VERSION");
985 public FeatureRenderer getFeatureRenderer()
987 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
991 public void fetchSequence_actionPerformed(ActionEvent e)
993 new jalview.gui.SequenceFetcher(this);
997 public void addFromFile_actionPerformed(ActionEvent e)
999 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1003 public void reload_actionPerformed(ActionEvent e)
1005 if (fileName != null)
1007 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1008 // originating file's format
1009 // TODO: work out how to recover feature settings for correct view(s) when
1010 // file is reloaded.
1011 if (FileFormat.Jalview.equals(currentFileFormat))
1013 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1014 for (int i = 0; i < frames.length; i++)
1016 if (frames[i] instanceof AlignFrame && frames[i] != this
1017 && ((AlignFrame) frames[i]).fileName != null
1018 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1022 frames[i].setSelected(true);
1023 Desktop.instance.closeAssociatedWindows();
1024 } catch (java.beans.PropertyVetoException ex)
1030 Desktop.instance.closeAssociatedWindows();
1032 FileLoader loader = new FileLoader();
1033 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1034 : DataSourceType.FILE;
1035 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1039 Rectangle bounds = this.getBounds();
1041 FileLoader loader = new FileLoader();
1042 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1043 : DataSourceType.FILE;
1044 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1045 protocol, currentFileFormat);
1047 newframe.setBounds(bounds);
1048 if (featureSettings != null && featureSettings.isShowing())
1050 final Rectangle fspos = featureSettings.frame.getBounds();
1051 // TODO: need a 'show feature settings' function that takes bounds -
1052 // need to refactor Desktop.addFrame
1053 newframe.featureSettings_actionPerformed(null);
1054 final FeatureSettings nfs = newframe.featureSettings;
1055 SwingUtilities.invokeLater(new Runnable()
1060 nfs.frame.setBounds(fspos);
1063 this.featureSettings.close();
1064 this.featureSettings = null;
1066 this.closeMenuItem_actionPerformed(true);
1072 public void addFromText_actionPerformed(ActionEvent e)
1074 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1079 public void addFromURL_actionPerformed(ActionEvent e)
1081 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1085 public void save_actionPerformed(ActionEvent e)
1087 if (fileName == null || (currentFileFormat == null)
1088 || fileName.startsWith("http"))
1090 saveAs_actionPerformed(null);
1094 saveAlignment(fileName, currentFileFormat);
1105 public void saveAs_actionPerformed(ActionEvent e)
1107 String format = currentFileFormat == null ? null : currentFileFormat
1109 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1110 Cache.getProperty("LAST_DIRECTORY"), format);
1112 chooser.setFileView(new JalviewFileView());
1113 chooser.setDialogTitle(MessageManager
1114 .getString("label.save_alignment_to_file"));
1115 chooser.setToolTipText(MessageManager.getString("action.save"));
1117 int value = chooser.showSaveDialog(this);
1119 if (value == JalviewFileChooser.APPROVE_OPTION)
1121 currentFileFormat = chooser.getSelectedFormat();
1122 while (currentFileFormat == null)
1125 .showInternalMessageDialog(
1128 .getString("label.select_file_format_before_saving"),
1130 .getString("label.file_format_not_specified"),
1131 JvOptionPane.WARNING_MESSAGE);
1132 currentFileFormat = chooser.getSelectedFormat();
1133 value = chooser.showSaveDialog(this);
1134 if (value != JalviewFileChooser.APPROVE_OPTION)
1140 fileName = chooser.getSelectedFile().getPath();
1142 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1144 Cache.setProperty("LAST_DIRECTORY", fileName);
1145 saveAlignment(fileName, currentFileFormat);
1149 public boolean saveAlignment(String file, FileFormatI format)
1151 boolean success = true;
1153 if (FileFormat.Jalview.equals(format))
1155 String shortName = title;
1157 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1159 shortName = shortName.substring(shortName
1160 .lastIndexOf(java.io.File.separatorChar) + 1);
1163 success = new Jalview2XML().saveAlignment(this, file, shortName);
1165 statusBar.setText(MessageManager.formatMessage(
1166 "label.successfully_saved_to_file_in_format", new Object[] {
1167 fileName, format }));
1172 AlignmentExportData exportData = getAlignmentForExport(format,
1174 if (exportData.getSettings().isCancelled())
1178 FormatAdapter f = new FormatAdapter(alignPanel,
1179 exportData.getSettings());
1180 String output = f.formatSequences(
1182 exportData.getAlignment(), // class cast exceptions will
1183 // occur in the distant future
1184 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1185 f.getCacheSuffixDefault(format),
1186 viewport.getColumnSelection());
1196 PrintWriter out = new PrintWriter(new FileWriter(file));
1200 this.setTitle(file);
1201 statusBar.setText(MessageManager.formatMessage(
1202 "label.successfully_saved_to_file_in_format",
1203 new Object[] { fileName, format.getName() }));
1204 } catch (Exception ex)
1207 ex.printStackTrace();
1214 JvOptionPane.showInternalMessageDialog(this, MessageManager
1215 .formatMessage("label.couldnt_save_file",
1216 new Object[] { fileName }), MessageManager
1217 .getString("label.error_saving_file"),
1218 JvOptionPane.WARNING_MESSAGE);
1224 private void warningMessage(String warning, String title)
1226 if (new jalview.util.Platform().isHeadless())
1228 System.err.println("Warning: " + title + "\nWarning: " + warning);
1233 JvOptionPane.showInternalMessageDialog(this, warning, title,
1234 JvOptionPane.WARNING_MESSAGE);
1246 protected void outputText_actionPerformed(ActionEvent e)
1248 FileFormatI fileFormat = FileFormats.getInstance().forName(
1249 e.getActionCommand());
1250 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1252 if (exportData.getSettings().isCancelled())
1256 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1257 cap.setForInput(null);
1260 FileFormatI format = fileFormat;
1261 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1262 .formatSequences(format, exportData.getAlignment(),
1263 exportData.getOmitHidden(),
1264 exportData.getStartEndPostions(),
1265 viewport.getColumnSelection()));
1266 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1267 "label.alignment_output_command",
1268 new Object[] { e.getActionCommand() }), 600, 500);
1269 } catch (OutOfMemoryError oom)
1271 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1277 public static AlignmentExportData getAlignmentForExport(
1278 FileFormatI format, AlignViewportI viewport,
1279 AlignExportSettingI exportSettings)
1281 AlignmentI alignmentToExport = null;
1282 AlignExportSettingI settings = exportSettings;
1283 String[] omitHidden = null;
1285 HiddenSequences hiddenSeqs = viewport.getAlignment()
1286 .getHiddenSequences();
1288 alignmentToExport = viewport.getAlignment();
1290 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1291 if (settings == null)
1293 settings = new AlignExportSettings(hasHiddenSeqs,
1294 viewport.hasHiddenColumns(), format);
1296 // settings.isExportAnnotations();
1298 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1300 omitHidden = viewport.getViewAsString(false,
1301 settings.isExportHiddenSequences());
1304 int[] alignmentStartEnd = new int[2];
1305 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1307 alignmentToExport = hiddenSeqs.getFullAlignment();
1311 alignmentToExport = viewport.getAlignment();
1313 alignmentStartEnd = alignmentToExport
1314 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1315 .getHiddenColumns());
1316 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1317 omitHidden, alignmentStartEnd, settings);
1328 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1330 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1331 htmlSVG.exportHTML(null);
1335 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1337 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1338 bjs.exportHTML(null);
1341 public void createImageMap(File file, String image)
1343 alignPanel.makePNGImageMap(file, image);
1353 public void createPNG(File f)
1355 alignPanel.makePNG(f);
1365 public void createEPS(File f)
1367 alignPanel.makeEPS(f);
1371 public void createSVG(File f)
1373 alignPanel.makeSVG(f);
1377 public void pageSetup_actionPerformed(ActionEvent e)
1379 PrinterJob printJob = PrinterJob.getPrinterJob();
1380 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1390 public void printMenuItem_actionPerformed(ActionEvent e)
1392 // Putting in a thread avoids Swing painting problems
1393 PrintThread thread = new PrintThread(alignPanel);
1398 public void exportFeatures_actionPerformed(ActionEvent e)
1400 new AnnotationExporter().exportFeatures(alignPanel);
1404 public void exportAnnotations_actionPerformed(ActionEvent e)
1406 new AnnotationExporter().exportAnnotations(alignPanel);
1410 public void associatedData_actionPerformed(ActionEvent e)
1412 // Pick the tree file
1413 JalviewFileChooser chooser = new JalviewFileChooser(
1414 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1415 chooser.setFileView(new JalviewFileView());
1416 chooser.setDialogTitle(MessageManager
1417 .getString("label.load_jalview_annotations"));
1418 chooser.setToolTipText(MessageManager
1419 .getString("label.load_jalview_annotations"));
1421 int value = chooser.showOpenDialog(null);
1423 if (value == JalviewFileChooser.APPROVE_OPTION)
1425 String choice = chooser.getSelectedFile().getPath();
1426 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1427 loadJalviewDataFile(choice, null, null, null);
1433 * Close the current view or all views in the alignment frame. If the frame
1434 * only contains one view then the alignment will be removed from memory.
1436 * @param closeAllTabs
1439 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1441 if (alignPanels != null && alignPanels.size() < 2)
1443 closeAllTabs = true;
1448 if (alignPanels != null)
1452 if (this.isClosed())
1454 // really close all the windows - otherwise wait till
1455 // setClosed(true) is called
1456 for (int i = 0; i < alignPanels.size(); i++)
1458 AlignmentPanel ap = alignPanels.get(i);
1465 closeView(alignPanel);
1472 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1473 * be called recursively, with the frame now in 'closed' state
1475 this.setClosed(true);
1477 } catch (Exception ex)
1479 ex.printStackTrace();
1484 * Close the specified panel and close up tabs appropriately.
1486 * @param panelToClose
1488 public void closeView(AlignmentPanel panelToClose)
1490 int index = tabbedPane.getSelectedIndex();
1491 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1492 alignPanels.remove(panelToClose);
1493 panelToClose.closePanel();
1494 panelToClose = null;
1496 tabbedPane.removeTabAt(closedindex);
1497 tabbedPane.validate();
1499 if (index > closedindex || index == tabbedPane.getTabCount())
1501 // modify currently selected tab index if necessary.
1505 this.tabSelectionChanged(index);
1511 void updateEditMenuBar()
1514 if (viewport.getHistoryList().size() > 0)
1516 undoMenuItem.setEnabled(true);
1517 CommandI command = viewport.getHistoryList().peek();
1518 undoMenuItem.setText(MessageManager.formatMessage(
1519 "label.undo_command",
1520 new Object[] { command.getDescription() }));
1524 undoMenuItem.setEnabled(false);
1525 undoMenuItem.setText(MessageManager.getString("action.undo"));
1528 if (viewport.getRedoList().size() > 0)
1530 redoMenuItem.setEnabled(true);
1532 CommandI command = viewport.getRedoList().peek();
1533 redoMenuItem.setText(MessageManager.formatMessage(
1534 "label.redo_command",
1535 new Object[] { command.getDescription() }));
1539 redoMenuItem.setEnabled(false);
1540 redoMenuItem.setText(MessageManager.getString("action.redo"));
1545 public void addHistoryItem(CommandI command)
1547 if (command.getSize() > 0)
1549 viewport.addToHistoryList(command);
1550 viewport.clearRedoList();
1551 updateEditMenuBar();
1552 viewport.updateHiddenColumns();
1553 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1554 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1555 // viewport.getColumnSelection()
1556 // .getHiddenColumns().size() > 0);
1562 * @return alignment objects for all views
1564 AlignmentI[] getViewAlignments()
1566 if (alignPanels != null)
1568 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1570 for (AlignmentPanel ap : alignPanels)
1572 als[i++] = ap.av.getAlignment();
1576 if (viewport != null)
1578 return new AlignmentI[] { viewport.getAlignment() };
1590 protected void undoMenuItem_actionPerformed(ActionEvent e)
1592 if (viewport.getHistoryList().isEmpty())
1596 CommandI command = viewport.getHistoryList().pop();
1597 viewport.addToRedoList(command);
1598 command.undoCommand(getViewAlignments());
1600 AlignmentViewport originalSource = getOriginatingSource(command);
1601 updateEditMenuBar();
1603 if (originalSource != null)
1605 if (originalSource != viewport)
1608 .warn("Implementation worry: mismatch of viewport origin for undo");
1610 originalSource.updateHiddenColumns();
1611 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1613 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1614 // viewport.getColumnSelection()
1615 // .getHiddenColumns().size() > 0);
1616 originalSource.firePropertyChange("alignment", null, originalSource
1617 .getAlignment().getSequences());
1628 protected void redoMenuItem_actionPerformed(ActionEvent e)
1630 if (viewport.getRedoList().size() < 1)
1635 CommandI command = viewport.getRedoList().pop();
1636 viewport.addToHistoryList(command);
1637 command.doCommand(getViewAlignments());
1639 AlignmentViewport originalSource = getOriginatingSource(command);
1640 updateEditMenuBar();
1642 if (originalSource != null)
1645 if (originalSource != viewport)
1648 .warn("Implementation worry: mismatch of viewport origin for redo");
1650 originalSource.updateHiddenColumns();
1651 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1653 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1654 // viewport.getColumnSelection()
1655 // .getHiddenColumns().size() > 0);
1656 originalSource.firePropertyChange("alignment", null, originalSource
1657 .getAlignment().getSequences());
1661 AlignmentViewport getOriginatingSource(CommandI command)
1663 AlignmentViewport originalSource = null;
1664 // For sequence removal and addition, we need to fire
1665 // the property change event FROM the viewport where the
1666 // original alignment was altered
1667 AlignmentI al = null;
1668 if (command instanceof EditCommand)
1670 EditCommand editCommand = (EditCommand) command;
1671 al = editCommand.getAlignment();
1672 List<Component> comps = PaintRefresher.components.get(viewport
1673 .getSequenceSetId());
1675 for (Component comp : comps)
1677 if (comp instanceof AlignmentPanel)
1679 if (al == ((AlignmentPanel) comp).av.getAlignment())
1681 originalSource = ((AlignmentPanel) comp).av;
1688 if (originalSource == null)
1690 // The original view is closed, we must validate
1691 // the current view against the closed view first
1694 PaintRefresher.validateSequences(al, viewport.getAlignment());
1697 originalSource = viewport;
1700 return originalSource;
1709 public void moveSelectedSequences(boolean up)
1711 SequenceGroup sg = viewport.getSelectionGroup();
1717 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1718 viewport.getHiddenRepSequences(), up);
1719 alignPanel.paintAlignment(true);
1722 synchronized void slideSequences(boolean right, int size)
1724 List<SequenceI> sg = new ArrayList<SequenceI>();
1725 if (viewport.cursorMode)
1727 sg.add(viewport.getAlignment().getSequenceAt(
1728 alignPanel.getSeqPanel().seqCanvas.cursorY));
1730 else if (viewport.getSelectionGroup() != null
1731 && viewport.getSelectionGroup().getSize() != viewport
1732 .getAlignment().getHeight())
1734 sg = viewport.getSelectionGroup().getSequences(
1735 viewport.getHiddenRepSequences());
1743 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1745 for (SequenceI seq : viewport.getAlignment().getSequences())
1747 if (!sg.contains(seq))
1749 invertGroup.add(seq);
1753 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1755 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1756 for (int i = 0; i < invertGroup.size(); i++)
1758 seqs2[i] = invertGroup.get(i);
1761 SlideSequencesCommand ssc;
1764 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1765 size, viewport.getGapCharacter());
1769 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1770 size, viewport.getGapCharacter());
1773 int groupAdjustment = 0;
1774 if (ssc.getGapsInsertedBegin() && right)
1776 if (viewport.cursorMode)
1778 alignPanel.getSeqPanel().moveCursor(size, 0);
1782 groupAdjustment = size;
1785 else if (!ssc.getGapsInsertedBegin() && !right)
1787 if (viewport.cursorMode)
1789 alignPanel.getSeqPanel().moveCursor(-size, 0);
1793 groupAdjustment = -size;
1797 if (groupAdjustment != 0)
1799 viewport.getSelectionGroup().setStartRes(
1800 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1801 viewport.getSelectionGroup().setEndRes(
1802 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1806 * just extend the last slide command if compatible; but not if in
1807 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1809 boolean appendHistoryItem = false;
1810 Deque<CommandI> historyList = viewport.getHistoryList();
1811 boolean inSplitFrame = getSplitViewContainer() != null;
1812 if (!inSplitFrame && historyList != null && historyList.size() > 0
1813 && historyList.peek() instanceof SlideSequencesCommand)
1815 appendHistoryItem = ssc
1816 .appendSlideCommand((SlideSequencesCommand) historyList
1820 if (!appendHistoryItem)
1822 addHistoryItem(ssc);
1835 protected void copy_actionPerformed(ActionEvent e)
1838 if (viewport.getSelectionGroup() == null)
1842 // TODO: preserve the ordering of displayed alignment annotation in any
1843 // internal paste (particularly sequence associated annotation)
1844 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1845 String[] omitHidden = null;
1847 if (viewport.hasHiddenColumns())
1849 omitHidden = viewport.getViewAsString(true);
1852 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1853 seqs, omitHidden, null);
1855 StringSelection ss = new StringSelection(output);
1859 jalview.gui.Desktop.internalCopy = true;
1860 // Its really worth setting the clipboard contents
1861 // to empty before setting the large StringSelection!!
1862 Toolkit.getDefaultToolkit().getSystemClipboard()
1863 .setContents(new StringSelection(""), null);
1865 Toolkit.getDefaultToolkit().getSystemClipboard()
1866 .setContents(ss, Desktop.instance);
1867 } catch (OutOfMemoryError er)
1869 new OOMWarning("copying region", er);
1873 ArrayList<int[]> hiddenColumns = null;
1874 if (viewport.hasHiddenColumns())
1876 hiddenColumns = new ArrayList<int[]>();
1877 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1878 .getSelectionGroup().getEndRes();
1879 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1881 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1883 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1884 region[1] - hiddenOffset });
1889 Desktop.jalviewClipboard = new Object[] { seqs,
1890 viewport.getAlignment().getDataset(), hiddenColumns };
1891 statusBar.setText(MessageManager.formatMessage(
1892 "label.copied_sequences_to_clipboard", new Object[] { Integer
1893 .valueOf(seqs.length).toString() }));
1903 protected void pasteNew_actionPerformed(ActionEvent e)
1915 protected void pasteThis_actionPerformed(ActionEvent e)
1921 * Paste contents of Jalview clipboard
1923 * @param newAlignment
1924 * true to paste to a new alignment, otherwise add to this.
1926 void paste(boolean newAlignment)
1928 boolean externalPaste = true;
1931 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1932 Transferable contents = c.getContents(this);
1934 if (contents == null)
1943 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1944 if (str.length() < 1)
1949 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1951 } catch (OutOfMemoryError er)
1953 new OOMWarning("Out of memory pasting sequences!!", er);
1957 SequenceI[] sequences;
1958 boolean annotationAdded = false;
1959 AlignmentI alignment = null;
1961 if (Desktop.jalviewClipboard != null)
1963 // The clipboard was filled from within Jalview, we must use the
1965 // And dataset from the copied alignment
1966 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1967 // be doubly sure that we create *new* sequence objects.
1968 sequences = new SequenceI[newseq.length];
1969 for (int i = 0; i < newseq.length; i++)
1971 sequences[i] = new Sequence(newseq[i]);
1973 alignment = new Alignment(sequences);
1974 externalPaste = false;
1978 // parse the clipboard as an alignment.
1979 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1981 sequences = alignment.getSequencesArray();
1985 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1991 if (Desktop.jalviewClipboard != null)
1993 // dataset is inherited
1994 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1998 // new dataset is constructed
1999 alignment.setDataset(null);
2001 alwidth = alignment.getWidth() + 1;
2005 AlignmentI pastedal = alignment; // preserve pasted alignment object
2006 // Add pasted sequences and dataset into existing alignment.
2007 alignment = viewport.getAlignment();
2008 alwidth = alignment.getWidth() + 1;
2009 // decide if we need to import sequences from an existing dataset
2010 boolean importDs = Desktop.jalviewClipboard != null
2011 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2012 // importDs==true instructs us to copy over new dataset sequences from
2013 // an existing alignment
2014 Vector newDs = (importDs) ? new Vector() : null; // used to create
2015 // minimum dataset set
2017 for (int i = 0; i < sequences.length; i++)
2021 newDs.addElement(null);
2023 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2025 if (importDs && ds != null)
2027 if (!newDs.contains(ds))
2029 newDs.setElementAt(ds, i);
2030 ds = new Sequence(ds);
2031 // update with new dataset sequence
2032 sequences[i].setDatasetSequence(ds);
2036 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2041 // copy and derive new dataset sequence
2042 sequences[i] = sequences[i].deriveSequence();
2043 alignment.getDataset().addSequence(
2044 sequences[i].getDatasetSequence());
2045 // TODO: avoid creation of duplicate dataset sequences with a
2046 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2048 alignment.addSequence(sequences[i]); // merges dataset
2052 newDs.clear(); // tidy up
2054 if (alignment.getAlignmentAnnotation() != null)
2056 for (AlignmentAnnotation alan : alignment
2057 .getAlignmentAnnotation())
2059 if (alan.graphGroup > fgroup)
2061 fgroup = alan.graphGroup;
2065 if (pastedal.getAlignmentAnnotation() != null)
2067 // Add any annotation attached to alignment.
2068 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2069 for (int i = 0; i < alann.length; i++)
2071 annotationAdded = true;
2072 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2074 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2075 if (newann.graphGroup > -1)
2077 if (newGraphGroups.size() <= newann.graphGroup
2078 || newGraphGroups.get(newann.graphGroup) == null)
2080 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2082 newGraphGroups.add(q, null);
2084 newGraphGroups.set(newann.graphGroup, new Integer(
2087 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2091 newann.padAnnotation(alwidth);
2092 alignment.addAnnotation(newann);
2102 addHistoryItem(new EditCommand(
2103 MessageManager.getString("label.add_sequences"),
2104 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2106 // Add any annotations attached to sequences
2107 for (int i = 0; i < sequences.length; i++)
2109 if (sequences[i].getAnnotation() != null)
2111 AlignmentAnnotation newann;
2112 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2114 annotationAdded = true;
2115 newann = sequences[i].getAnnotation()[a];
2116 newann.adjustForAlignment();
2117 newann.padAnnotation(alwidth);
2118 if (newann.graphGroup > -1)
2120 if (newann.graphGroup > -1)
2122 if (newGraphGroups.size() <= newann.graphGroup
2123 || newGraphGroups.get(newann.graphGroup) == null)
2125 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2127 newGraphGroups.add(q, null);
2129 newGraphGroups.set(newann.graphGroup, new Integer(
2132 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2136 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2141 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2148 // propagate alignment changed.
2149 vpRanges.setEndSeq(alignment.getHeight());
2150 if (annotationAdded)
2152 // Duplicate sequence annotation in all views.
2153 AlignmentI[] alview = this.getViewAlignments();
2154 for (int i = 0; i < sequences.length; i++)
2156 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2161 for (int avnum = 0; avnum < alview.length; avnum++)
2163 if (alview[avnum] != alignment)
2165 // duplicate in a view other than the one with input focus
2166 int avwidth = alview[avnum].getWidth() + 1;
2167 // this relies on sann being preserved after we
2168 // modify the sequence's annotation array for each duplication
2169 for (int a = 0; a < sann.length; a++)
2171 AlignmentAnnotation newann = new AlignmentAnnotation(
2173 sequences[i].addAlignmentAnnotation(newann);
2174 newann.padAnnotation(avwidth);
2175 alview[avnum].addAnnotation(newann); // annotation was
2176 // duplicated earlier
2177 // TODO JAL-1145 graphGroups are not updated for sequence
2178 // annotation added to several views. This may cause
2180 alview[avnum].setAnnotationIndex(newann, a);
2185 buildSortByAnnotationScoresMenu();
2187 viewport.firePropertyChange("alignment", null,
2188 alignment.getSequences());
2189 if (alignPanels != null)
2191 for (AlignmentPanel ap : alignPanels)
2193 ap.validateAnnotationDimensions(false);
2198 alignPanel.validateAnnotationDimensions(false);
2204 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2206 String newtitle = new String("Copied sequences");
2208 if (Desktop.jalviewClipboard != null
2209 && Desktop.jalviewClipboard[2] != null)
2211 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2212 for (int[] region : hc)
2214 af.viewport.hideColumns(region[0], region[1]);
2218 // >>>This is a fix for the moment, until a better solution is
2220 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2222 alignPanel.getSeqPanel().seqCanvas
2223 .getFeatureRenderer());
2225 // TODO: maintain provenance of an alignment, rather than just make the
2226 // title a concatenation of operations.
2229 if (title.startsWith("Copied sequences"))
2235 newtitle = newtitle.concat("- from " + title);
2240 newtitle = new String("Pasted sequences");
2243 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2248 } catch (Exception ex)
2250 ex.printStackTrace();
2251 System.out.println("Exception whilst pasting: " + ex);
2252 // could be anything being pasted in here
2258 protected void expand_newalign(ActionEvent e)
2262 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2263 .getAlignment(), -1);
2264 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2266 String newtitle = new String("Flanking alignment");
2268 if (Desktop.jalviewClipboard != null
2269 && Desktop.jalviewClipboard[2] != null)
2271 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2272 for (int region[] : hc)
2274 af.viewport.hideColumns(region[0], region[1]);
2278 // >>>This is a fix for the moment, until a better solution is
2280 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2282 alignPanel.getSeqPanel().seqCanvas
2283 .getFeatureRenderer());
2285 // TODO: maintain provenance of an alignment, rather than just make the
2286 // title a concatenation of operations.
2288 if (title.startsWith("Copied sequences"))
2294 newtitle = newtitle.concat("- from " + title);
2298 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2300 } catch (Exception ex)
2302 ex.printStackTrace();
2303 System.out.println("Exception whilst pasting: " + ex);
2304 // could be anything being pasted in here
2305 } catch (OutOfMemoryError oom)
2307 new OOMWarning("Viewing flanking region of alignment", oom);
2318 protected void cut_actionPerformed(ActionEvent e)
2320 copy_actionPerformed(null);
2321 delete_actionPerformed(null);
2331 protected void delete_actionPerformed(ActionEvent evt)
2334 SequenceGroup sg = viewport.getSelectionGroup();
2341 * If the cut affects all sequences, warn, remove highlighted columns
2343 if (sg.getSize() == viewport.getAlignment().getHeight())
2345 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2346 .getAlignment().getWidth()) ? true : false;
2347 if (isEntireAlignWidth)
2349 int confirm = JvOptionPane.showConfirmDialog(this,
2350 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2351 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2352 JvOptionPane.OK_CANCEL_OPTION);
2354 if (confirm == JvOptionPane.CANCEL_OPTION
2355 || confirm == JvOptionPane.CLOSED_OPTION)
2360 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2361 sg.getEndRes() + 1);
2363 SequenceI[] cut = sg.getSequences()
2364 .toArray(new SequenceI[sg.getSize()]);
2366 addHistoryItem(new EditCommand(
2367 MessageManager.getString("label.cut_sequences"), Action.CUT,
2368 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2369 viewport.getAlignment()));
2371 viewport.setSelectionGroup(null);
2372 viewport.sendSelection();
2373 viewport.getAlignment().deleteGroup(sg);
2375 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2377 if (viewport.getAlignment().getHeight() < 1)
2381 this.setClosed(true);
2382 } catch (Exception ex)
2395 protected void deleteGroups_actionPerformed(ActionEvent e)
2397 if (avc.deleteGroups())
2399 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2400 alignPanel.updateAnnotation();
2401 alignPanel.paintAlignment(true);
2412 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2414 SequenceGroup sg = new SequenceGroup();
2416 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2418 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2421 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2422 viewport.setSelectionGroup(sg);
2423 viewport.sendSelection();
2424 // JAL-2034 - should delegate to
2425 // alignPanel to decide if overview needs
2427 alignPanel.paintAlignment(false);
2428 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2438 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2440 if (viewport.cursorMode)
2442 alignPanel.getSeqPanel().keyboardNo1 = null;
2443 alignPanel.getSeqPanel().keyboardNo2 = null;
2445 viewport.setSelectionGroup(null);
2446 viewport.getColumnSelection().clear();
2447 viewport.setSelectionGroup(null);
2448 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2449 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2450 // JAL-2034 - should delegate to
2451 // alignPanel to decide if overview needs
2453 alignPanel.paintAlignment(false);
2454 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2455 viewport.sendSelection();
2465 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2467 SequenceGroup sg = viewport.getSelectionGroup();
2471 selectAllSequenceMenuItem_actionPerformed(null);
2476 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2478 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2480 // JAL-2034 - should delegate to
2481 // alignPanel to decide if overview needs
2484 alignPanel.paintAlignment(true);
2485 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2486 viewport.sendSelection();
2490 public void invertColSel_actionPerformed(ActionEvent e)
2492 viewport.invertColumnSelection();
2493 alignPanel.paintAlignment(true);
2494 viewport.sendSelection();
2504 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2506 trimAlignment(true);
2516 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2518 trimAlignment(false);
2521 void trimAlignment(boolean trimLeft)
2523 ColumnSelection colSel = viewport.getColumnSelection();
2526 if (!colSel.isEmpty())
2530 column = colSel.getMin();
2534 column = colSel.getMax();
2538 if (viewport.getSelectionGroup() != null)
2540 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2541 viewport.getHiddenRepSequences());
2545 seqs = viewport.getAlignment().getSequencesArray();
2548 TrimRegionCommand trimRegion;
2551 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2552 column, viewport.getAlignment());
2553 vpRanges.setStartRes(0);
2557 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2558 column, viewport.getAlignment());
2561 statusBar.setText(MessageManager.formatMessage(
2562 "label.removed_columns",
2563 new String[] { Integer.valueOf(trimRegion.getSize())
2566 addHistoryItem(trimRegion);
2568 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2570 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2571 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2573 viewport.getAlignment().deleteGroup(sg);
2577 viewport.firePropertyChange("alignment", null, viewport
2578 .getAlignment().getSequences());
2589 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2591 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2594 if (viewport.getSelectionGroup() != null)
2596 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2597 viewport.getHiddenRepSequences());
2598 start = viewport.getSelectionGroup().getStartRes();
2599 end = viewport.getSelectionGroup().getEndRes();
2603 seqs = viewport.getAlignment().getSequencesArray();
2606 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2607 "Remove Gapped Columns", seqs, start, end,
2608 viewport.getAlignment());
2610 addHistoryItem(removeGapCols);
2612 statusBar.setText(MessageManager.formatMessage(
2613 "label.removed_empty_columns",
2614 new Object[] { Integer.valueOf(removeGapCols.getSize())
2617 // This is to maintain viewport position on first residue
2618 // of first sequence
2619 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2620 int startRes = seq.findPosition(vpRanges.getStartRes());
2621 // ShiftList shifts;
2622 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2623 // edit.alColumnChanges=shifts.getInverse();
2624 // if (viewport.hasHiddenColumns)
2625 // viewport.getColumnSelection().compensateForEdits(shifts);
2626 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2627 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2639 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2641 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2644 if (viewport.getSelectionGroup() != null)
2646 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2647 viewport.getHiddenRepSequences());
2648 start = viewport.getSelectionGroup().getStartRes();
2649 end = viewport.getSelectionGroup().getEndRes();
2653 seqs = viewport.getAlignment().getSequencesArray();
2656 // This is to maintain viewport position on first residue
2657 // of first sequence
2658 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2659 int startRes = seq.findPosition(vpRanges.getStartRes());
2661 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2662 viewport.getAlignment()));
2664 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2666 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2678 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2680 viewport.setPadGaps(padGapsMenuitem.isSelected());
2681 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2692 public void findMenuItem_actionPerformed(ActionEvent e)
2698 * Create a new view of the current alignment.
2701 public void newView_actionPerformed(ActionEvent e)
2703 newView(null, true);
2707 * Creates and shows a new view of the current alignment.
2710 * title of newly created view; if null, one will be generated
2711 * @param copyAnnotation
2712 * if true then duplicate all annnotation, groups and settings
2713 * @return new alignment panel, already displayed.
2715 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2718 * Create a new AlignmentPanel (with its own, new Viewport)
2720 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2722 if (!copyAnnotation)
2725 * remove all groups and annotation except for the automatic stuff
2727 newap.av.getAlignment().deleteAllGroups();
2728 newap.av.getAlignment().deleteAllAnnotations(false);
2731 newap.av.setGatherViewsHere(false);
2733 if (viewport.viewName == null)
2735 viewport.viewName = MessageManager
2736 .getString("label.view_name_original");
2740 * Views share the same edits undo and redo stacks
2742 newap.av.setHistoryList(viewport.getHistoryList());
2743 newap.av.setRedoList(viewport.getRedoList());
2746 * Views share the same mappings; need to deregister any new mappings
2747 * created by copyAlignPanel, and register the new reference to the shared
2750 newap.av.replaceMappings(viewport.getAlignment());
2753 * start up cDNA consensus (if applicable) now mappings are in place
2755 if (newap.av.initComplementConsensus())
2757 newap.refresh(true); // adjust layout of annotations
2760 newap.av.viewName = getNewViewName(viewTitle);
2762 addAlignmentPanel(newap, true);
2763 newap.alignmentChanged();
2765 if (alignPanels.size() == 2)
2767 viewport.setGatherViewsHere(true);
2769 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2774 * Make a new name for the view, ensuring it is unique within the current
2775 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2776 * these now use viewId. Unique view names are still desirable for usability.)
2781 protected String getNewViewName(String viewTitle)
2783 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2784 boolean addFirstIndex = false;
2785 if (viewTitle == null || viewTitle.trim().length() == 0)
2787 viewTitle = MessageManager.getString("action.view");
2788 addFirstIndex = true;
2792 index = 1;// we count from 1 if given a specific name
2794 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2796 List<Component> comps = PaintRefresher.components.get(viewport
2797 .getSequenceSetId());
2799 List<String> existingNames = getExistingViewNames(comps);
2801 while (existingNames.contains(newViewName))
2803 newViewName = viewTitle + " " + (++index);
2809 * Returns a list of distinct view names found in the given list of
2810 * components. View names are held on the viewport of an AlignmentPanel.
2815 protected List<String> getExistingViewNames(List<Component> comps)
2817 List<String> existingNames = new ArrayList<String>();
2818 for (Component comp : comps)
2820 if (comp instanceof AlignmentPanel)
2822 AlignmentPanel ap = (AlignmentPanel) comp;
2823 if (!existingNames.contains(ap.av.viewName))
2825 existingNames.add(ap.av.viewName);
2829 return existingNames;
2833 * Explode tabbed views into separate windows.
2836 public void expandViews_actionPerformed(ActionEvent e)
2838 Desktop.explodeViews(this);
2842 * Gather views in separate windows back into a tabbed presentation.
2845 public void gatherViews_actionPerformed(ActionEvent e)
2847 Desktop.instance.gatherViews(this);
2857 public void font_actionPerformed(ActionEvent e)
2859 new FontChooser(alignPanel);
2869 protected void seqLimit_actionPerformed(ActionEvent e)
2871 viewport.setShowJVSuffix(seqLimits.isSelected());
2873 alignPanel.getIdPanel().getIdCanvas()
2874 .setPreferredSize(alignPanel.calculateIdWidth());
2875 alignPanel.paintAlignment(true);
2879 public void idRightAlign_actionPerformed(ActionEvent e)
2881 viewport.setRightAlignIds(idRightAlign.isSelected());
2882 alignPanel.paintAlignment(true);
2886 public void centreColumnLabels_actionPerformed(ActionEvent e)
2888 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2889 alignPanel.paintAlignment(true);
2895 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2898 protected void followHighlight_actionPerformed()
2901 * Set the 'follow' flag on the Viewport (and scroll to position if now
2904 final boolean state = this.followHighlightMenuItem.getState();
2905 viewport.setFollowHighlight(state);
2908 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2919 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2921 viewport.setColourText(colourTextMenuItem.isSelected());
2922 alignPanel.paintAlignment(true);
2932 public void wrapMenuItem_actionPerformed(ActionEvent e)
2934 scaleAbove.setVisible(wrapMenuItem.isSelected());
2935 scaleLeft.setVisible(wrapMenuItem.isSelected());
2936 scaleRight.setVisible(wrapMenuItem.isSelected());
2937 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2938 alignPanel.updateLayout();
2942 public void showAllSeqs_actionPerformed(ActionEvent e)
2944 viewport.showAllHiddenSeqs();
2948 public void showAllColumns_actionPerformed(ActionEvent e)
2950 viewport.showAllHiddenColumns();
2952 viewport.sendSelection();
2956 public void hideSelSequences_actionPerformed(ActionEvent e)
2958 viewport.hideAllSelectedSeqs();
2959 // alignPanel.paintAlignment(true);
2963 * called by key handler and the hide all/show all menu items
2968 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2971 boolean hide = false;
2972 SequenceGroup sg = viewport.getSelectionGroup();
2973 if (!toggleSeqs && !toggleCols)
2975 // Hide everything by the current selection - this is a hack - we do the
2976 // invert and then hide
2977 // first check that there will be visible columns after the invert.
2978 if (viewport.hasSelectedColumns()
2979 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2982 // now invert the sequence set, if required - empty selection implies
2983 // that no hiding is required.
2986 invertSequenceMenuItem_actionPerformed(null);
2987 sg = viewport.getSelectionGroup();
2991 viewport.expandColSelection(sg, true);
2992 // finally invert the column selection and get the new sequence
2994 invertColSel_actionPerformed(null);
3001 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3003 hideSelSequences_actionPerformed(null);
3006 else if (!(toggleCols && viewport.hasSelectedColumns()))
3008 showAllSeqs_actionPerformed(null);
3014 if (viewport.hasSelectedColumns())
3016 hideSelColumns_actionPerformed(null);
3019 viewport.setSelectionGroup(sg);
3024 showAllColumns_actionPerformed(null);
3033 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3034 * event.ActionEvent)
3037 public void hideAllButSelection_actionPerformed(ActionEvent e)
3039 toggleHiddenRegions(false, false);
3040 viewport.sendSelection();
3047 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3051 public void hideAllSelection_actionPerformed(ActionEvent e)
3053 SequenceGroup sg = viewport.getSelectionGroup();
3054 viewport.expandColSelection(sg, false);
3055 viewport.hideAllSelectedSeqs();
3056 viewport.hideSelectedColumns();
3057 alignPanel.paintAlignment(true);
3058 viewport.sendSelection();
3065 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3069 public void showAllhidden_actionPerformed(ActionEvent e)
3071 viewport.showAllHiddenColumns();
3072 viewport.showAllHiddenSeqs();
3073 alignPanel.paintAlignment(true);
3074 viewport.sendSelection();
3078 public void hideSelColumns_actionPerformed(ActionEvent e)
3080 viewport.hideSelectedColumns();
3081 alignPanel.paintAlignment(true);
3082 viewport.sendSelection();
3086 public void hiddenMarkers_actionPerformed(ActionEvent e)
3088 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3099 protected void scaleAbove_actionPerformed(ActionEvent e)
3101 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3102 alignPanel.paintAlignment(true);
3112 protected void scaleLeft_actionPerformed(ActionEvent e)
3114 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3115 alignPanel.paintAlignment(true);
3125 protected void scaleRight_actionPerformed(ActionEvent e)
3127 viewport.setScaleRightWrapped(scaleRight.isSelected());
3128 alignPanel.paintAlignment(true);
3138 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3140 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3141 alignPanel.paintAlignment(true);
3151 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3153 viewport.setShowText(viewTextMenuItem.isSelected());
3154 alignPanel.paintAlignment(true);
3164 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3166 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3167 alignPanel.paintAlignment(true);
3170 public FeatureSettings featureSettings;
3173 public FeatureSettingsControllerI getFeatureSettingsUI()
3175 return featureSettings;
3179 public void featureSettings_actionPerformed(ActionEvent e)
3181 if (featureSettings != null)
3183 featureSettings.close();
3184 featureSettings = null;
3186 if (!showSeqFeatures.isSelected())
3188 // make sure features are actually displayed
3189 showSeqFeatures.setSelected(true);
3190 showSeqFeatures_actionPerformed(null);
3192 featureSettings = new FeatureSettings(this);
3196 * Set or clear 'Show Sequence Features'
3202 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3204 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3205 alignPanel.paintAlignment(true);
3206 if (alignPanel.getOverviewPanel() != null)
3208 alignPanel.getOverviewPanel().updateOverviewImage();
3213 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3214 * the annotations panel as a whole.
3216 * The options to show/hide all annotations should be enabled when the panel
3217 * is shown, and disabled when the panel is hidden.
3222 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3224 final boolean setVisible = annotationPanelMenuItem.isSelected();
3225 viewport.setShowAnnotation(setVisible);
3226 this.showAllSeqAnnotations.setEnabled(setVisible);
3227 this.hideAllSeqAnnotations.setEnabled(setVisible);
3228 this.showAllAlAnnotations.setEnabled(setVisible);
3229 this.hideAllAlAnnotations.setEnabled(setVisible);
3230 alignPanel.updateLayout();
3234 public void alignmentProperties()
3236 JEditorPane editPane = new JEditorPane("text/html", "");
3237 editPane.setEditable(false);
3238 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3240 editPane.setText(MessageManager.formatMessage("label.html_content",
3241 new Object[] { contents.toString() }));
3242 JInternalFrame frame = new JInternalFrame();
3243 frame.getContentPane().add(new JScrollPane(editPane));
3245 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3246 "label.alignment_properties", new Object[] { getTitle() }),
3257 public void overviewMenuItem_actionPerformed(ActionEvent e)
3259 if (alignPanel.overviewPanel != null)
3264 JInternalFrame frame = new JInternalFrame();
3265 OverviewPanel overview = new OverviewPanel(alignPanel);
3266 frame.setContentPane(overview);
3267 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3268 "label.overview_params", new Object[] { this.getTitle() }),
3269 frame.getWidth(), frame.getHeight());
3271 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3272 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3275 public void internalFrameClosed(
3276 javax.swing.event.InternalFrameEvent evt)
3278 alignPanel.setOverviewPanel(null);
3282 alignPanel.setOverviewPanel(overview);
3286 public void textColour_actionPerformed()
3288 new TextColourChooser().chooseColour(alignPanel, null);
3292 * public void covariationColour_actionPerformed() {
3294 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3298 public void annotationColour_actionPerformed()
3300 new AnnotationColourChooser(viewport, alignPanel);
3304 public void annotationColumn_actionPerformed(ActionEvent e)
3306 new AnnotationColumnChooser(viewport, alignPanel);
3310 * Action on the user checking or unchecking the option to apply the selected
3311 * colour scheme to all groups. If unchecked, groups may have their own
3312 * independent colour schemes.
3317 public void applyToAllGroups_actionPerformed(boolean selected)
3319 viewport.setColourAppliesToAllGroups(selected);
3323 * Action on user selecting a colour from the colour menu
3326 * the name (not the menu item label!) of the colour scheme
3329 public void changeColour_actionPerformed(String name)
3332 * 'User Defined' opens a panel to configure or load a
3333 * user-defined colour scheme
3335 if (ResidueColourScheme.USER_DEFINED.equals(name))
3337 new UserDefinedColours(alignPanel);
3342 * otherwise set the chosen colour scheme (or null for 'None')
3344 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3345 viewport.getAlignment(), viewport.getHiddenRepSequences());
3350 * Actions on setting or changing the alignment colour scheme
3355 public void changeColour(ColourSchemeI cs)
3357 // TODO: pull up to controller method
3358 ColourMenuHelper.setColourSelected(colourMenu, cs);
3360 viewport.setGlobalColourScheme(cs);
3362 alignPanel.paintAlignment(true);
3366 * Show the PID threshold slider panel
3369 protected void modifyPID_actionPerformed()
3371 SliderPanel.setPIDSliderSource(alignPanel,
3372 viewport.getResidueShading(), alignPanel.getViewName());
3373 SliderPanel.showPIDSlider();
3377 * Show the Conservation slider panel
3380 protected void modifyConservation_actionPerformed()
3382 SliderPanel.setConservationSlider(alignPanel,
3383 viewport.getResidueShading(), alignPanel.getViewName());
3384 SliderPanel.showConservationSlider();
3388 * Action on selecting or deselecting (Colour) By Conservation
3391 public void conservationMenuItem_actionPerformed(boolean selected)
3393 modifyConservation.setEnabled(selected);
3394 viewport.setConservationSelected(selected);
3395 viewport.getResidueShading().setConservationApplied(selected);
3397 changeColour(viewport.getGlobalColourScheme());
3400 modifyConservation_actionPerformed();
3404 SliderPanel.hideConservationSlider();
3409 * Action on selecting or deselecting (Colour) Above PID Threshold
3412 public void abovePIDThreshold_actionPerformed(boolean selected)
3414 modifyPID.setEnabled(selected);
3415 viewport.setAbovePIDThreshold(selected);
3418 viewport.getResidueShading().setThreshold(0,
3419 viewport.isIgnoreGapsConsensus());
3422 changeColour(viewport.getGlobalColourScheme());
3425 modifyPID_actionPerformed();
3429 SliderPanel.hidePIDSlider();
3440 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3442 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3443 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3444 .getAlignment().getSequenceAt(0), null);
3445 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3446 viewport.getAlignment()));
3447 alignPanel.paintAlignment(true);
3457 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3459 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3460 AlignmentSorter.sortByID(viewport.getAlignment());
3461 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3462 viewport.getAlignment()));
3463 alignPanel.paintAlignment(true);
3473 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3475 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3476 AlignmentSorter.sortByLength(viewport.getAlignment());
3477 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3478 viewport.getAlignment()));
3479 alignPanel.paintAlignment(true);
3489 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3491 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3492 AlignmentSorter.sortByGroup(viewport.getAlignment());
3493 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3494 viewport.getAlignment()));
3496 alignPanel.paintAlignment(true);
3506 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3508 new RedundancyPanel(alignPanel, this);
3518 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3520 if ((viewport.getSelectionGroup() == null)
3521 || (viewport.getSelectionGroup().getSize() < 2))
3523 JvOptionPane.showInternalMessageDialog(this, MessageManager
3524 .getString("label.you_must_select_least_two_sequences"),
3525 MessageManager.getString("label.invalid_selection"),
3526 JvOptionPane.WARNING_MESSAGE);
3530 JInternalFrame frame = new JInternalFrame();
3531 frame.setContentPane(new PairwiseAlignPanel(viewport));
3532 Desktop.addInternalFrame(frame,
3533 MessageManager.getString("action.pairwise_alignment"), 600,
3545 public void PCAMenuItem_actionPerformed(ActionEvent e)
3547 if (((viewport.getSelectionGroup() != null)
3548 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3549 .getSelectionGroup().getSize() > 0))
3550 || (viewport.getAlignment().getHeight() < 4))
3553 .showInternalMessageDialog(
3556 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3558 .getString("label.sequence_selection_insufficient"),
3559 JvOptionPane.WARNING_MESSAGE);
3564 new PCAPanel(alignPanel);
3568 public void autoCalculate_actionPerformed(ActionEvent e)
3570 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3571 if (viewport.autoCalculateConsensus)
3573 viewport.firePropertyChange("alignment", null, viewport
3574 .getAlignment().getSequences());
3579 public void sortByTreeOption_actionPerformed(ActionEvent e)
3581 viewport.sortByTree = sortByTree.isSelected();
3585 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3587 viewport.followSelection = listenToViewSelections.isSelected();
3597 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3599 newTreePanel("AV", "PID", "Average distance tree using PID");
3609 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3611 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3621 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3623 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3633 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3635 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3648 void newTreePanel(String type, String pwType, String title)
3652 if (viewport.getSelectionGroup() != null
3653 && viewport.getSelectionGroup().getSize() > 0)
3655 if (viewport.getSelectionGroup().getSize() < 3)
3661 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3663 .getString("label.not_enough_sequences"),
3664 JvOptionPane.WARNING_MESSAGE);
3668 SequenceGroup sg = viewport.getSelectionGroup();
3670 /* Decide if the selection is a column region */
3671 for (SequenceI _s : sg.getSequences())
3673 if (_s.getLength() < sg.getEndRes())
3679 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3681 .getString("label.sequences_selection_not_aligned"),
3682 JvOptionPane.WARNING_MESSAGE);
3688 title = title + " on region";
3689 tp = new TreePanel(alignPanel, type, pwType);
3693 // are the visible sequences aligned?
3694 if (!viewport.getAlignment().isAligned(false))
3700 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3702 .getString("label.sequences_not_aligned"),
3703 JvOptionPane.WARNING_MESSAGE);
3708 if (viewport.getAlignment().getHeight() < 2)
3713 tp = new TreePanel(alignPanel, type, pwType);
3718 if (viewport.viewName != null)
3720 title += viewport.viewName + " of ";
3723 title += this.title;
3725 Desktop.addInternalFrame(tp, title, 600, 500);
3736 public void addSortByOrderMenuItem(String title,
3737 final AlignmentOrder order)
3739 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3740 "action.by_title_param", new Object[] { title }));
3742 item.addActionListener(new java.awt.event.ActionListener()
3745 public void actionPerformed(ActionEvent e)
3747 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3749 // TODO: JBPNote - have to map order entries to curent SequenceI
3751 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3753 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3756 alignPanel.paintAlignment(true);
3762 * Add a new sort by annotation score menu item
3765 * the menu to add the option to
3767 * the label used to retrieve scores for each sequence on the
3770 public void addSortByAnnotScoreMenuItem(JMenu sort,
3771 final String scoreLabel)
3773 final JMenuItem item = new JMenuItem(scoreLabel);
3775 item.addActionListener(new java.awt.event.ActionListener()
3778 public void actionPerformed(ActionEvent e)
3780 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3781 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3782 viewport.getAlignment());// ,viewport.getSelectionGroup());
3783 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3784 viewport.getAlignment()));
3785 alignPanel.paintAlignment(true);
3791 * last hash for alignment's annotation array - used to minimise cost of
3794 protected int _annotationScoreVectorHash;
3797 * search the alignment and rebuild the sort by annotation score submenu the
3798 * last alignment annotation vector hash is stored to minimize cost of
3799 * rebuilding in subsequence calls.
3803 public void buildSortByAnnotationScoresMenu()
3805 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3810 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3812 sortByAnnotScore.removeAll();
3813 // almost certainly a quicker way to do this - but we keep it simple
3814 Hashtable scoreSorts = new Hashtable();
3815 AlignmentAnnotation aann[];
3816 for (SequenceI sqa : viewport.getAlignment().getSequences())
3818 aann = sqa.getAnnotation();
3819 for (int i = 0; aann != null && i < aann.length; i++)
3821 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3823 scoreSorts.put(aann[i].label, aann[i].label);
3827 Enumeration labels = scoreSorts.keys();
3828 while (labels.hasMoreElements())
3830 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3831 (String) labels.nextElement());
3833 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3836 _annotationScoreVectorHash = viewport.getAlignment()
3837 .getAlignmentAnnotation().hashCode();
3842 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3843 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3844 * call. Listeners are added to remove the menu item when the treePanel is
3845 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3849 * Displayed tree window.
3851 * SortBy menu item title.
3854 public void buildTreeMenu()
3856 calculateTree.removeAll();
3857 // build the calculate menu
3859 for (final String type : new String[] { "NJ", "AV" })
3861 String treecalcnm = MessageManager.getString("label.tree_calc_"
3862 + type.toLowerCase());
3863 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
3865 JMenuItem tm = new JMenuItem();
3866 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
3867 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
3868 || sm.isProtein() == !viewport.getAlignment()
3871 String smn = MessageManager.getStringOrReturn(
3872 "label.score_model_", sm.getName());
3873 final String title = MessageManager.formatMessage(
3874 "label.treecalc_title", treecalcnm, smn);
3875 tm.setText(title);//
3876 tm.addActionListener(new java.awt.event.ActionListener()
3879 public void actionPerformed(ActionEvent e)
3881 newTreePanel(type, pwtype, title);
3884 calculateTree.add(tm);
3889 sortByTreeMenu.removeAll();
3891 List<Component> comps = PaintRefresher.components.get(viewport
3892 .getSequenceSetId());
3893 List<TreePanel> treePanels = new ArrayList<TreePanel>();
3894 for (Component comp : comps)
3896 if (comp instanceof TreePanel)
3898 treePanels.add((TreePanel) comp);
3902 if (treePanels.size() < 1)
3904 sortByTreeMenu.setVisible(false);
3908 sortByTreeMenu.setVisible(true);
3910 for (final TreePanel tp : treePanels)
3912 final JMenuItem item = new JMenuItem(tp.getTitle());
3913 item.addActionListener(new java.awt.event.ActionListener()
3916 public void actionPerformed(ActionEvent e)
3918 tp.sortByTree_actionPerformed();
3919 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3924 sortByTreeMenu.add(item);
3928 public boolean sortBy(AlignmentOrder alorder, String undoname)
3930 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3931 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3932 if (undoname != null)
3934 addHistoryItem(new OrderCommand(undoname, oldOrder,
3935 viewport.getAlignment()));
3937 alignPanel.paintAlignment(true);
3942 * Work out whether the whole set of sequences or just the selected set will
3943 * be submitted for multiple alignment.
3946 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3948 // Now, check we have enough sequences
3949 AlignmentView msa = null;
3951 if ((viewport.getSelectionGroup() != null)
3952 && (viewport.getSelectionGroup().getSize() > 1))
3954 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3955 // some common interface!
3957 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3958 * SequenceI[sz = seqs.getSize(false)];
3960 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3961 * seqs.getSequenceAt(i); }
3963 msa = viewport.getAlignmentView(true);
3965 else if (viewport.getSelectionGroup() != null
3966 && viewport.getSelectionGroup().getSize() == 1)
3968 int option = JvOptionPane.showConfirmDialog(this,
3969 MessageManager.getString("warn.oneseq_msainput_selection"),
3970 MessageManager.getString("label.invalid_selection"),
3971 JvOptionPane.OK_CANCEL_OPTION);
3972 if (option == JvOptionPane.OK_OPTION)
3974 msa = viewport.getAlignmentView(false);
3979 msa = viewport.getAlignmentView(false);
3985 * Decides what is submitted to a secondary structure prediction service: the
3986 * first sequence in the alignment, or in the current selection, or, if the
3987 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3988 * region or the whole alignment. (where the first sequence in the set is the
3989 * one that the prediction will be for).
3991 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3993 AlignmentView seqs = null;
3995 if ((viewport.getSelectionGroup() != null)
3996 && (viewport.getSelectionGroup().getSize() > 0))
3998 seqs = viewport.getAlignmentView(true);
4002 seqs = viewport.getAlignmentView(false);
4004 // limit sequences - JBPNote in future - could spawn multiple prediction
4006 // TODO: viewport.getAlignment().isAligned is a global state - the local
4007 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4008 if (!viewport.getAlignment().isAligned(false))
4010 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4011 // TODO: if seqs.getSequences().length>1 then should really have warned
4025 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4027 // Pick the tree file
4028 JalviewFileChooser chooser = new JalviewFileChooser(
4029 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4030 chooser.setFileView(new JalviewFileView());
4031 chooser.setDialogTitle(MessageManager
4032 .getString("label.select_newick_like_tree_file"));
4033 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4035 int value = chooser.showOpenDialog(null);
4037 if (value == JalviewFileChooser.APPROVE_OPTION)
4039 String choice = chooser.getSelectedFile().getPath();
4040 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4041 jalview.io.NewickFile fin = null;
4044 fin = new NewickFile(choice, DataSourceType.FILE);
4045 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4046 } catch (Exception ex)
4053 .getString("label.problem_reading_tree_file"),
4054 JvOptionPane.WARNING_MESSAGE);
4055 ex.printStackTrace();
4057 if (fin != null && fin.hasWarningMessage())
4059 JvOptionPane.showMessageDialog(Desktop.desktop, fin
4060 .getWarningMessage(), MessageManager
4061 .getString("label.possible_problem_with_tree_file"),
4062 JvOptionPane.WARNING_MESSAGE);
4067 public TreePanel ShowNewickTree(NewickFile nf, String title)
4069 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4072 public TreePanel ShowNewickTree(NewickFile nf, String title,
4073 AlignmentView input)
4075 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4078 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4079 int h, int x, int y)
4081 return ShowNewickTree(nf, title, null, w, h, x, y);
4085 * Add a treeviewer for the tree extracted from a newick file object to the
4086 * current alignment view
4093 * Associated alignment input data (or null)
4102 * @return TreePanel handle
4104 public TreePanel ShowNewickTree(NewickFile nf, String title,
4105 AlignmentView input, int w, int h, int x, int y)
4107 TreePanel tp = null;
4113 if (nf.getTree() != null)
4115 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4121 tp.setLocation(x, y);
4124 Desktop.addInternalFrame(tp, title, w, h);
4126 } catch (Exception ex)
4128 ex.printStackTrace();
4134 private boolean buildingMenu = false;
4137 * Generates menu items and listener event actions for web service clients
4140 public void BuildWebServiceMenu()
4142 while (buildingMenu)
4146 System.err.println("Waiting for building menu to finish.");
4148 } catch (Exception e)
4152 final AlignFrame me = this;
4153 buildingMenu = true;
4154 new Thread(new Runnable()
4159 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4162 // System.err.println("Building ws menu again "
4163 // + Thread.currentThread());
4164 // TODO: add support for context dependent disabling of services based
4166 // alignment and current selection
4167 // TODO: add additional serviceHandle parameter to specify abstract
4169 // class independently of AbstractName
4170 // TODO: add in rediscovery GUI function to restart discoverer
4171 // TODO: group services by location as well as function and/or
4173 // object broker mechanism.
4174 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4175 final IProgressIndicator af = me;
4178 * do not i18n these strings - they are hard-coded in class
4179 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4180 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4182 final JMenu msawsmenu = new JMenu("Alignment");
4183 final JMenu secstrmenu = new JMenu(
4184 "Secondary Structure Prediction");
4185 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4186 final JMenu analymenu = new JMenu("Analysis");
4187 final JMenu dismenu = new JMenu("Protein Disorder");
4188 // JAL-940 - only show secondary structure prediction services from
4189 // the legacy server
4190 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4192 Discoverer.services != null && (Discoverer.services.size() > 0))
4194 // TODO: refactor to allow list of AbstractName/Handler bindings to
4196 // stored or retrieved from elsewhere
4197 // No MSAWS used any more:
4198 // Vector msaws = null; // (Vector)
4199 // Discoverer.services.get("MsaWS");
4200 Vector secstrpr = (Vector) Discoverer.services
4202 if (secstrpr != null)
4204 // Add any secondary structure prediction services
4205 for (int i = 0, j = secstrpr.size(); i < j; i++)
4207 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4209 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4210 .getServiceClient(sh);
4211 int p = secstrmenu.getItemCount();
4212 impl.attachWSMenuEntry(secstrmenu, me);
4213 int q = secstrmenu.getItemCount();
4214 for (int litm = p; litm < q; litm++)
4216 legacyItems.add(secstrmenu.getItem(litm));
4222 // Add all submenus in the order they should appear on the web
4224 wsmenu.add(msawsmenu);
4225 wsmenu.add(secstrmenu);
4226 wsmenu.add(dismenu);
4227 wsmenu.add(analymenu);
4228 // No search services yet
4229 // wsmenu.add(seqsrchmenu);
4231 javax.swing.SwingUtilities.invokeLater(new Runnable()
4238 webService.removeAll();
4239 // first, add discovered services onto the webservices menu
4240 if (wsmenu.size() > 0)
4242 for (int i = 0, j = wsmenu.size(); i < j; i++)
4244 webService.add(wsmenu.get(i));
4249 webService.add(me.webServiceNoServices);
4251 // TODO: move into separate menu builder class.
4252 boolean new_sspred = false;
4253 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4255 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4256 if (jws2servs != null)
4258 if (jws2servs.hasServices())
4260 jws2servs.attachWSMenuEntry(webService, me);
4261 for (Jws2Instance sv : jws2servs.getServices())
4263 if (sv.description.toLowerCase().contains("jpred"))
4265 for (JMenuItem jmi : legacyItems)
4267 jmi.setVisible(false);
4273 if (jws2servs.isRunning())
4275 JMenuItem tm = new JMenuItem(
4276 "Still discovering JABA Services");
4277 tm.setEnabled(false);
4282 build_urlServiceMenu(me.webService);
4283 build_fetchdbmenu(webService);
4284 for (JMenu item : wsmenu)
4286 if (item.getItemCount() == 0)
4288 item.setEnabled(false);
4292 item.setEnabled(true);
4295 } catch (Exception e)
4298 .debug("Exception during web service menu building process.",
4303 } catch (Exception e)
4306 buildingMenu = false;
4313 * construct any groupURL type service menu entries.
4317 private void build_urlServiceMenu(JMenu webService)
4319 // TODO: remove this code when 2.7 is released
4320 // DEBUG - alignmentView
4322 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4323 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4325 * @Override public void actionPerformed(ActionEvent e) {
4326 * jalview.datamodel.AlignmentView
4327 * .testSelectionViews(af.viewport.getAlignment(),
4328 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4330 * }); webService.add(testAlView);
4332 // TODO: refactor to RestClient discoverer and merge menu entries for
4333 // rest-style services with other types of analysis/calculation service
4334 // SHmmr test client - still being implemented.
4335 // DEBUG - alignmentView
4337 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4340 client.attachWSMenuEntry(
4341 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4347 * Searches the alignment sequences for xRefs and builds the Show
4348 * Cross-References menu (formerly called Show Products), with database
4349 * sources for which cross-references are found (protein sources for a
4350 * nucleotide alignment and vice versa)
4352 * @return true if Show Cross-references menu should be enabled
4354 public boolean canShowProducts()
4356 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4357 AlignmentI dataset = viewport.getAlignment().getDataset();
4359 showProducts.removeAll();
4360 final boolean dna = viewport.getAlignment().isNucleotide();
4362 if (seqs == null || seqs.length == 0)
4364 // nothing to see here.
4368 boolean showp = false;
4371 List<String> ptypes = new CrossRef(seqs, dataset)
4372 .findXrefSourcesForSequences(dna);
4374 for (final String source : ptypes)
4377 final AlignFrame af = this;
4378 JMenuItem xtype = new JMenuItem(source);
4379 xtype.addActionListener(new ActionListener()
4382 public void actionPerformed(ActionEvent e)
4384 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4387 showProducts.add(xtype);
4389 showProducts.setVisible(showp);
4390 showProducts.setEnabled(showp);
4391 } catch (Exception e)
4394 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4402 * Finds and displays cross-references for the selected sequences (protein
4403 * products for nucleotide sequences, dna coding sequences for peptides).
4406 * the sequences to show cross-references for
4408 * true if from a nucleotide alignment (so showing proteins)
4410 * the database to show cross-references for
4412 protected void showProductsFor(final SequenceI[] sel,
4413 final boolean _odna, final String source)
4415 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4420 * Construct and display a new frame containing the translation of this
4421 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4424 public void showTranslation_actionPerformed(ActionEvent e)
4426 AlignmentI al = null;
4429 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4431 al = dna.translateCdna();
4432 } catch (Exception ex)
4434 jalview.bin.Cache.log.error(
4435 "Exception during translation. Please report this !", ex);
4436 final String msg = MessageManager
4437 .getString("label.error_when_translating_sequences_submit_bug_report");
4438 final String errorTitle = MessageManager
4439 .getString("label.implementation_error")
4440 + MessageManager.getString("label.translation_failed");
4441 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4442 JvOptionPane.ERROR_MESSAGE);
4445 if (al == null || al.getHeight() == 0)
4447 final String msg = MessageManager
4448 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4449 final String errorTitle = MessageManager
4450 .getString("label.translation_failed");
4451 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4452 JvOptionPane.WARNING_MESSAGE);
4456 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4457 af.setFileFormat(this.currentFileFormat);
4458 final String newTitle = MessageManager.formatMessage(
4459 "label.translation_of_params",
4460 new Object[] { this.getTitle() });
4461 af.setTitle(newTitle);
4462 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4464 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4465 viewport.openSplitFrame(af, new Alignment(seqs));
4469 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4476 * Set the file format
4480 public void setFileFormat(FileFormatI format)
4482 this.currentFileFormat = format;
4486 * Try to load a features file onto the alignment.
4489 * contents or path to retrieve file
4491 * access mode of file (see jalview.io.AlignFile)
4492 * @return true if features file was parsed correctly.
4494 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4496 return avc.parseFeaturesFile(file, sourceType,
4497 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4502 public void refreshFeatureUI(boolean enableIfNecessary)
4504 // note - currently this is only still here rather than in the controller
4505 // because of the featureSettings hard reference that is yet to be
4507 if (enableIfNecessary)
4509 viewport.setShowSequenceFeatures(true);
4510 showSeqFeatures.setSelected(true);
4516 public void dragEnter(DropTargetDragEvent evt)
4521 public void dragExit(DropTargetEvent evt)
4526 public void dragOver(DropTargetDragEvent evt)
4531 public void dropActionChanged(DropTargetDragEvent evt)
4536 public void drop(DropTargetDropEvent evt)
4538 // JAL-1552 - acceptDrop required before getTransferable call for
4539 // Java's Transferable for native dnd
4540 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4541 Transferable t = evt.getTransferable();
4542 List<String> files = new ArrayList<String>();
4543 List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4547 Desktop.transferFromDropTarget(files, protocols, evt, t);
4548 } catch (Exception e)
4550 e.printStackTrace();
4556 // check to see if any of these files have names matching sequences in
4558 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4559 .getAlignment().getSequencesArray());
4561 * Object[] { String,SequenceI}
4563 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4564 ArrayList<String> filesnotmatched = new ArrayList<String>();
4565 for (int i = 0; i < files.size(); i++)
4567 String file = files.get(i).toString();
4569 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4570 if (protocol == DataSourceType.FILE)
4572 File fl = new File(file);
4573 pdbfn = fl.getName();
4575 else if (protocol == DataSourceType.URL)
4577 URL url = new URL(file);
4578 pdbfn = url.getFile();
4580 if (pdbfn.length() > 0)
4582 // attempt to find a match in the alignment
4583 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4584 int l = 0, c = pdbfn.indexOf(".");
4585 while (mtch == null && c != -1)
4590 } while ((c = pdbfn.indexOf(".", l)) > l);
4593 pdbfn = pdbfn.substring(0, l);
4595 mtch = idm.findAllIdMatches(pdbfn);
4599 FileFormatI type = null;
4602 type = new IdentifyFile().identify(file, protocol);
4603 } catch (Exception ex)
4607 if (type != null && type.isStructureFile())
4609 filesmatched.add(new Object[] { file, protocol, mtch });
4613 // File wasn't named like one of the sequences or wasn't a PDB file.
4614 filesnotmatched.add(file);
4618 if (filesmatched.size() > 0)
4620 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4626 "label.automatically_associate_structure_files_with_sequences_same_name",
4627 new Object[] { Integer
4633 .getString("label.automatically_associate_structure_files_by_name"),
4634 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4637 for (Object[] fm : filesmatched)
4639 // try and associate
4640 // TODO: may want to set a standard ID naming formalism for
4641 // associating PDB files which have no IDs.
4642 for (SequenceI toassoc : (SequenceI[]) fm[2])
4644 PDBEntry pe = new AssociatePdbFileWithSeq()
4645 .associatePdbWithSeq((String) fm[0],
4646 (DataSourceType) fm[1], toassoc, false,
4650 System.err.println("Associated file : "
4651 + ((String) fm[0]) + " with "
4652 + toassoc.getDisplayId(true));
4656 alignPanel.paintAlignment(true);
4660 if (filesnotmatched.size() > 0)
4663 && (Cache.getDefault(
4664 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4670 "label.ignore_unmatched_dropped_files_info",
4671 new Object[] { Integer
4678 .getString("label.ignore_unmatched_dropped_files"),
4679 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4683 for (String fn : filesnotmatched)
4685 loadJalviewDataFile(fn, null, null, null);
4689 } catch (Exception ex)
4691 ex.printStackTrace();
4697 * Attempt to load a "dropped" file or URL string: First by testing whether
4698 * it's an Annotation file, then a JNet file, and finally a features file. If
4699 * all are false then the user may have dropped an alignment file onto this
4703 * either a filename or a URL string.
4705 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4706 FileFormatI format, SequenceI assocSeq)
4710 if (sourceType == null)
4712 sourceType = FormatAdapter.checkProtocol(file);
4714 // if the file isn't identified, or not positively identified as some
4715 // other filetype (PFAM is default unidentified alignment file type) then
4716 // try to parse as annotation.
4717 boolean isAnnotation = (format == null || FileFormat.Pfam
4718 .equals(format)) ? new AnnotationFile()
4719 .annotateAlignmentView(viewport, file, sourceType) : false;
4723 // first see if its a T-COFFEE score file
4724 TCoffeeScoreFile tcf = null;
4727 tcf = new TCoffeeScoreFile(file, sourceType);
4730 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4733 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4734 isAnnotation = true;
4736 .setText(MessageManager
4737 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4741 // some problem - if no warning its probable that the ID matching
4742 // process didn't work
4746 tcf.getWarningMessage() == null ? MessageManager
4747 .getString("label.check_file_matches_sequence_ids_alignment")
4748 : tcf.getWarningMessage(),
4750 .getString("label.problem_reading_tcoffee_score_file"),
4751 JvOptionPane.WARNING_MESSAGE);
4758 } catch (Exception x)
4761 .debug("Exception when processing data source as T-COFFEE score file",
4767 // try to see if its a JNet 'concise' style annotation file *before*
4769 // try to parse it as a features file
4772 format = new IdentifyFile().identify(file, sourceType);
4774 if (FileFormat.Jnet.equals(format))
4776 JPredFile predictions = new JPredFile(file, sourceType);
4777 new JnetAnnotationMaker();
4778 JnetAnnotationMaker.add_annotation(predictions,
4779 viewport.getAlignment(), 0, false);
4780 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4781 viewport.getAlignment().setSeqrep(repseq);
4782 ColumnSelection cs = new ColumnSelection();
4783 cs.hideInsertionsFor(repseq);
4784 viewport.setColumnSelection(cs);
4785 isAnnotation = true;
4787 // else if (IdentifyFile.FeaturesFile.equals(format))
4788 else if (FileFormat.Features.equals(format))
4790 if (parseFeaturesFile(file, sourceType))
4792 alignPanel.paintAlignment(true);
4797 new FileLoader().LoadFile(viewport, file, sourceType, format);
4804 alignPanel.adjustAnnotationHeight();
4805 viewport.updateSequenceIdColours();
4806 buildSortByAnnotationScoresMenu();
4807 alignPanel.paintAlignment(true);
4809 } catch (Exception ex)
4811 ex.printStackTrace();
4812 } catch (OutOfMemoryError oom)
4817 } catch (Exception x)
4822 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4823 : "using " + sourceType + " from " + file)
4825 + (format != null ? "(parsing as '" + format
4826 + "' file)" : ""), oom, Desktop.desktop);
4831 * Method invoked by the ChangeListener on the tabbed pane, in other words
4832 * when a different tabbed pane is selected by the user or programmatically.
4835 public void tabSelectionChanged(int index)
4839 alignPanel = alignPanels.get(index);
4840 viewport = alignPanel.av;
4841 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4842 setMenusFromViewport(viewport);
4846 * 'focus' any colour slider that is open to the selected viewport
4848 if (viewport.getConservationSelected())
4850 SliderPanel.setConservationSlider(alignPanel,
4851 viewport.getResidueShading(), alignPanel.getViewName());
4855 SliderPanel.hideConservationSlider();
4857 if (viewport.getAbovePIDThreshold())
4859 SliderPanel.setPIDSliderSource(alignPanel,
4860 viewport.getResidueShading(), alignPanel.getViewName());
4864 SliderPanel.hidePIDSlider();
4868 * If there is a frame linked to this one in a SplitPane, switch it to the
4869 * same view tab index. No infinite recursion of calls should happen, since
4870 * tabSelectionChanged() should not get invoked on setting the selected
4871 * index to an unchanged value. Guard against setting an invalid index
4872 * before the new view peer tab has been created.
4874 final AlignViewportI peer = viewport.getCodingComplement();
4877 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4878 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4880 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4886 * On right mouse click on view tab, prompt for and set new view name.
4889 public void tabbedPane_mousePressed(MouseEvent e)
4891 if (e.isPopupTrigger())
4893 String msg = MessageManager.getString("label.enter_view_name");
4894 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4895 JvOptionPane.QUESTION_MESSAGE);
4899 viewport.viewName = reply;
4900 // TODO warn if reply is in getExistingViewNames()?
4901 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4906 public AlignViewport getCurrentView()
4912 * Open the dialog for regex description parsing.
4915 protected void extractScores_actionPerformed(ActionEvent e)
4917 ParseProperties pp = new jalview.analysis.ParseProperties(
4918 viewport.getAlignment());
4919 // TODO: verify regex and introduce GUI dialog for version 2.5
4920 // if (pp.getScoresFromDescription("col", "score column ",
4921 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4923 if (pp.getScoresFromDescription("description column",
4924 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4926 buildSortByAnnotationScoresMenu();
4934 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4938 protected void showDbRefs_actionPerformed(ActionEvent e)
4940 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4946 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4950 protected void showNpFeats_actionPerformed(ActionEvent e)
4952 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4956 * find the viewport amongst the tabs in this alignment frame and close that
4961 public boolean closeView(AlignViewportI av)
4965 this.closeMenuItem_actionPerformed(false);
4968 Component[] comp = tabbedPane.getComponents();
4969 for (int i = 0; comp != null && i < comp.length; i++)
4971 if (comp[i] instanceof AlignmentPanel)
4973 if (((AlignmentPanel) comp[i]).av == av)
4976 closeView((AlignmentPanel) comp[i]);
4984 protected void build_fetchdbmenu(JMenu webService)
4986 // Temporary hack - DBRef Fetcher always top level ws entry.
4987 // TODO We probably want to store a sequence database checklist in
4988 // preferences and have checkboxes.. rather than individual sources selected
4990 final JMenu rfetch = new JMenu(
4991 MessageManager.getString("action.fetch_db_references"));
4992 rfetch.setToolTipText(MessageManager
4993 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4994 webService.add(rfetch);
4996 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4997 MessageManager.getString("option.trim_retrieved_seqs"));
4998 trimrs.setToolTipText(MessageManager
4999 .getString("label.trim_retrieved_sequences"));
5000 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5001 trimrs.addActionListener(new ActionListener()
5004 public void actionPerformed(ActionEvent e)
5006 trimrs.setSelected(trimrs.isSelected());
5007 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5008 Boolean.valueOf(trimrs.isSelected()).toString());
5012 JMenuItem fetchr = new JMenuItem(
5013 MessageManager.getString("label.standard_databases"));
5014 fetchr.setToolTipText(MessageManager
5015 .getString("label.fetch_embl_uniprot"));
5016 fetchr.addActionListener(new ActionListener()
5020 public void actionPerformed(ActionEvent e)
5022 new Thread(new Runnable()
5027 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5028 .getAlignment().isNucleotide();
5029 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5030 .getSequenceSelection(), alignPanel.alignFrame, null,
5031 alignPanel.alignFrame.featureSettings, isNucleotide);
5032 dbRefFetcher.addListener(new FetchFinishedListenerI()
5035 public void finished()
5037 AlignFrame.this.setMenusForViewport();
5040 dbRefFetcher.fetchDBRefs(false);
5048 final AlignFrame me = this;
5049 new Thread(new Runnable()
5054 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5055 .getSequenceFetcherSingleton(me);
5056 javax.swing.SwingUtilities.invokeLater(new Runnable()
5061 String[] dbclasses = sf.getOrderedSupportedSources();
5062 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5063 // jalview.util.QuickSort.sort(otherdb, otherdb);
5064 List<DbSourceProxy> otherdb;
5065 JMenu dfetch = new JMenu();
5066 JMenu ifetch = new JMenu();
5067 JMenuItem fetchr = null;
5068 int comp = 0, icomp = 0, mcomp = 15;
5069 String mname = null;
5071 for (String dbclass : dbclasses)
5073 otherdb = sf.getSourceProxy(dbclass);
5074 // add a single entry for this class, or submenu allowing 'fetch
5076 if (otherdb == null || otherdb.size() < 1)
5080 // List<DbSourceProxy> dbs=otherdb;
5081 // otherdb=new ArrayList<DbSourceProxy>();
5082 // for (DbSourceProxy db:dbs)
5084 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5088 mname = "From " + dbclass;
5090 if (otherdb.size() == 1)
5092 final DbSourceProxy[] dassource = otherdb
5093 .toArray(new DbSourceProxy[0]);
5094 DbSourceProxy src = otherdb.get(0);
5095 fetchr = new JMenuItem(src.getDbSource());
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, dassource,
5114 alignPanel.alignFrame.featureSettings,
5117 .addListener(new FetchFinishedListenerI()
5120 public void finished()
5122 AlignFrame.this.setMenusForViewport();
5125 dbRefFetcher.fetchDBRefs(false);
5131 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5132 MessageManager.formatMessage(
5133 "label.fetch_retrieve_from",
5134 new Object[] { src.getDbName() })));
5140 final DbSourceProxy[] dassource = otherdb
5141 .toArray(new DbSourceProxy[0]);
5143 DbSourceProxy src = otherdb.get(0);
5144 fetchr = new JMenuItem(MessageManager.formatMessage(
5145 "label.fetch_all_param",
5146 new Object[] { src.getDbSource() }));
5147 fetchr.addActionListener(new ActionListener()
5150 public void actionPerformed(ActionEvent e)
5152 new Thread(new Runnable()
5158 boolean isNucleotide = alignPanel.alignFrame
5159 .getViewport().getAlignment()
5161 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5162 alignPanel.av.getSequenceSelection(),
5163 alignPanel.alignFrame, dassource,
5164 alignPanel.alignFrame.featureSettings,
5167 .addListener(new FetchFinishedListenerI()
5170 public void finished()
5172 AlignFrame.this.setMenusForViewport();
5175 dbRefFetcher.fetchDBRefs(false);
5181 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5182 MessageManager.formatMessage(
5183 "label.fetch_retrieve_from_all_sources",
5185 Integer.valueOf(otherdb.size())
5186 .toString(), src.getDbSource(),
5187 src.getDbName() })));
5190 // and then build the rest of the individual menus
5191 ifetch = new JMenu(MessageManager.formatMessage(
5192 "label.source_from_db_source",
5193 new Object[] { src.getDbSource() }));
5195 String imname = null;
5197 for (DbSourceProxy sproxy : otherdb)
5199 String dbname = sproxy.getDbName();
5200 String sname = dbname.length() > 5 ? dbname.substring(0,
5201 5) + "..." : dbname;
5202 String msname = dbname.length() > 10 ? dbname.substring(
5203 0, 10) + "..." : dbname;
5206 imname = MessageManager.formatMessage(
5207 "label.from_msname", new Object[] { sname });
5209 fetchr = new JMenuItem(msname);
5210 final DbSourceProxy[] dassrc = { sproxy };
5211 fetchr.addActionListener(new ActionListener()
5215 public void actionPerformed(ActionEvent e)
5217 new Thread(new Runnable()
5223 boolean isNucleotide = alignPanel.alignFrame
5224 .getViewport().getAlignment()
5226 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5227 alignPanel.av.getSequenceSelection(),
5228 alignPanel.alignFrame, dassrc,
5229 alignPanel.alignFrame.featureSettings,
5232 .addListener(new FetchFinishedListenerI()
5235 public void finished()
5237 AlignFrame.this.setMenusForViewport();
5240 dbRefFetcher.fetchDBRefs(false);
5246 fetchr.setToolTipText("<html>"
5247 + MessageManager.formatMessage(
5248 "label.fetch_retrieve_from", new Object[]
5252 if (++icomp >= mcomp || i == (otherdb.size()))
5254 ifetch.setText(MessageManager.formatMessage(
5255 "label.source_to_target", imname, sname));
5257 ifetch = new JMenu();
5265 if (comp >= mcomp || dbi >= (dbclasses.length))
5267 dfetch.setText(MessageManager.formatMessage(
5268 "label.source_to_target", mname, dbclass));
5270 dfetch = new JMenu();
5283 * Left justify the whole alignment.
5286 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5288 AlignmentI al = viewport.getAlignment();
5290 viewport.firePropertyChange("alignment", null, al);
5294 * Right justify the whole alignment.
5297 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5299 AlignmentI al = viewport.getAlignment();
5301 viewport.firePropertyChange("alignment", null, al);
5305 public void setShowSeqFeatures(boolean b)
5307 showSeqFeatures.setSelected(b);
5308 viewport.setShowSequenceFeatures(b);
5315 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5316 * awt.event.ActionEvent)
5319 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5321 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5322 alignPanel.paintAlignment(true);
5329 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5333 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5335 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5336 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5344 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5345 * .event.ActionEvent)
5348 protected void showGroupConservation_actionPerformed(ActionEvent e)
5350 viewport.setShowGroupConservation(showGroupConservation.getState());
5351 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5358 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5359 * .event.ActionEvent)
5362 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5364 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5365 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5372 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5373 * .event.ActionEvent)
5376 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5378 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5379 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5383 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5385 showSequenceLogo.setState(true);
5386 viewport.setShowSequenceLogo(true);
5387 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5388 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5392 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5394 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5401 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5402 * .event.ActionEvent)
5405 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5407 if (avc.makeGroupsFromSelection())
5409 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5410 alignPanel.updateAnnotation();
5411 alignPanel.paintAlignment(true);
5415 public void clearAlignmentSeqRep()
5417 // TODO refactor alignmentseqrep to controller
5418 if (viewport.getAlignment().hasSeqrep())
5420 viewport.getAlignment().setSeqrep(null);
5421 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5422 alignPanel.updateAnnotation();
5423 alignPanel.paintAlignment(true);
5428 protected void createGroup_actionPerformed(ActionEvent e)
5430 if (avc.createGroup())
5432 alignPanel.alignmentChanged();
5437 protected void unGroup_actionPerformed(ActionEvent e)
5441 alignPanel.alignmentChanged();
5446 * make the given alignmentPanel the currently selected tab
5448 * @param alignmentPanel
5450 public void setDisplayedView(AlignmentPanel alignmentPanel)
5452 if (!viewport.getSequenceSetId().equals(
5453 alignmentPanel.av.getSequenceSetId()))
5457 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5459 if (tabbedPane != null
5460 && tabbedPane.getTabCount() > 0
5461 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5462 .getSelectedIndex())
5464 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5469 * Action on selection of menu options to Show or Hide annotations.
5472 * @param forSequences
5473 * update sequence-related annotations
5474 * @param forAlignment
5475 * update non-sequence-related annotations
5478 protected void setAnnotationsVisibility(boolean visible,
5479 boolean forSequences, boolean forAlignment)
5481 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5482 .getAlignmentAnnotation();
5487 for (AlignmentAnnotation aa : anns)
5490 * don't display non-positional annotations on an alignment
5492 if (aa.annotations == null)
5496 boolean apply = (aa.sequenceRef == null && forAlignment)
5497 || (aa.sequenceRef != null && forSequences);
5500 aa.visible = visible;
5503 alignPanel.validateAnnotationDimensions(true);
5504 alignPanel.alignmentChanged();
5508 * Store selected annotation sort order for the view and repaint.
5511 protected void sortAnnotations_actionPerformed()
5513 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5515 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5516 alignPanel.paintAlignment(true);
5521 * @return alignment panels in this alignment frame
5523 public List<? extends AlignmentViewPanel> getAlignPanels()
5525 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5529 * Open a new alignment window, with the cDNA associated with this (protein)
5530 * alignment, aligned as is the protein.
5532 protected void viewAsCdna_actionPerformed()
5534 // TODO no longer a menu action - refactor as required
5535 final AlignmentI alignment = getViewport().getAlignment();
5536 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5537 if (mappings == null)
5541 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5542 for (SequenceI aaSeq : alignment.getSequences())
5544 for (AlignedCodonFrame acf : mappings)
5546 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5550 * There is a cDNA mapping for this protein sequence - add to new
5551 * alignment. It will share the same dataset sequence as other mapped
5552 * cDNA (no new mappings need to be created).
5554 final Sequence newSeq = new Sequence(dnaSeq);
5555 newSeq.setDatasetSequence(dnaSeq);
5556 cdnaSeqs.add(newSeq);
5560 if (cdnaSeqs.size() == 0)
5562 // show a warning dialog no mapped cDNA
5565 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5567 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5568 AlignFrame.DEFAULT_HEIGHT);
5569 cdna.alignAs(alignment);
5570 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5572 Desktop.addInternalFrame(alignFrame, newtitle,
5573 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5577 * Set visibility of dna/protein complement view (available when shown in a
5583 protected void showComplement_actionPerformed(boolean show)
5585 SplitContainerI sf = getSplitViewContainer();
5588 sf.setComplementVisible(this, show);
5593 * Generate the reverse (optionally complemented) of the selected sequences,
5594 * and add them to the alignment
5597 protected void showReverse_actionPerformed(boolean complement)
5599 AlignmentI al = null;
5602 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5603 al = dna.reverseCdna(complement);
5604 viewport.addAlignment(al, "");
5605 addHistoryItem(new EditCommand(
5606 MessageManager.getString("label.add_sequences"),
5607 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5608 viewport.getAlignment()));
5609 } catch (Exception ex)
5611 System.err.println(ex.getMessage());
5617 * Try to run a script in the Groovy console, having first ensured that this
5618 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5619 * be targeted at this alignment.
5622 protected void runGroovy_actionPerformed()
5624 Jalview.setCurrentAlignFrame(this);
5625 groovy.ui.Console console = Desktop.getGroovyConsole();
5626 if (console != null)
5630 console.runScript();
5631 } catch (Exception ex)
5633 System.err.println((ex.toString()));
5635 .showInternalMessageDialog(Desktop.desktop, MessageManager
5636 .getString("label.couldnt_run_groovy_script"),
5638 .getString("label.groovy_support_failed"),
5639 JvOptionPane.ERROR_MESSAGE);
5644 System.err.println("Can't run Groovy script as console not found");
5649 * Hides columns containing (or not containing) a specified feature, provided
5650 * that would not leave all columns hidden
5652 * @param featureType
5653 * @param columnsContaining
5656 public boolean hideFeatureColumns(String featureType,
5657 boolean columnsContaining)
5659 boolean notForHiding = avc.markColumnsContainingFeatures(
5660 columnsContaining, false, false, featureType);
5663 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5664 false, featureType))
5666 getViewport().hideSelectedColumns();
5674 protected void selectHighlightedColumns_actionPerformed(
5675 ActionEvent actionEvent)
5677 // include key modifier check in case user selects from menu
5678 avc.markHighlightedColumns(
5679 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5681 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5685 * Rebuilds the Colour menu, including any user-defined colours which have
5686 * been loaded either on startup or during the session
5688 public void buildColourMenu()
5690 colourMenu.removeAll();
5692 colourMenu.add(applyToAllGroups);
5693 colourMenu.add(textColour);
5694 colourMenu.addSeparator();
5696 ColourMenuHelper.addMenuItems(colourMenu, this,
5697 viewport.getAlignment(), false);
5699 colourMenu.addSeparator();
5700 colourMenu.add(conservationMenuItem);
5701 colourMenu.add(modifyConservation);
5702 colourMenu.add(abovePIDThreshold);
5703 colourMenu.add(modifyPID);
5704 colourMenu.add(annotationColour);
5706 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5707 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5711 class PrintThread extends Thread
5715 public PrintThread(AlignmentPanel ap)
5720 static PageFormat pf;
5725 PrinterJob printJob = PrinterJob.getPrinterJob();
5729 printJob.setPrintable(ap, pf);
5733 printJob.setPrintable(ap);
5736 if (printJob.printDialog())
5741 } catch (Exception PrintException)
5743 PrintException.printStackTrace();