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.FeatureSettingsModelI;
36 import jalview.api.SplitContainerI;
37 import jalview.api.ViewStyleI;
38 import jalview.api.analysis.ScoreModelI;
39 import jalview.bin.Cache;
40 import jalview.bin.Jalview;
41 import jalview.commands.CommandI;
42 import jalview.commands.EditCommand;
43 import jalview.commands.EditCommand.Action;
44 import jalview.commands.OrderCommand;
45 import jalview.commands.RemoveGapColCommand;
46 import jalview.commands.RemoveGapsCommand;
47 import jalview.commands.SlideSequencesCommand;
48 import jalview.commands.TrimRegionCommand;
49 import jalview.datamodel.AlignedCodonFrame;
50 import jalview.datamodel.Alignment;
51 import jalview.datamodel.AlignmentAnnotation;
52 import jalview.datamodel.AlignmentExportData;
53 import jalview.datamodel.AlignmentI;
54 import jalview.datamodel.AlignmentOrder;
55 import jalview.datamodel.AlignmentView;
56 import jalview.datamodel.ColumnSelection;
57 import jalview.datamodel.DBRefSource;
58 import jalview.datamodel.HiddenSequences;
59 import jalview.datamodel.PDBEntry;
60 import jalview.datamodel.SeqCigar;
61 import jalview.datamodel.Sequence;
62 import jalview.datamodel.SequenceGroup;
63 import jalview.datamodel.SequenceI;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.FileLoader;
69 import jalview.io.FormatAdapter;
70 import jalview.io.HtmlSvgOutput;
71 import jalview.io.IdentifyFile;
72 import jalview.io.JalviewFileChooser;
73 import jalview.io.JalviewFileView;
74 import jalview.io.JnetAnnotationMaker;
75 import jalview.io.NewickFile;
76 import jalview.io.TCoffeeScoreFile;
77 import jalview.io.gff.SequenceOntologyI;
78 import jalview.jbgui.GAlignFrame;
79 import jalview.schemes.Blosum62ColourScheme;
80 import jalview.schemes.BuriedColourScheme;
81 import jalview.schemes.ClustalxColourScheme;
82 import jalview.schemes.ColourSchemeI;
83 import jalview.schemes.ColourSchemeProperty;
84 import jalview.schemes.HelixColourScheme;
85 import jalview.schemes.HydrophobicColourScheme;
86 import jalview.schemes.NucleotideColourScheme;
87 import jalview.schemes.PIDColourScheme;
88 import jalview.schemes.PurinePyrimidineColourScheme;
89 import jalview.schemes.RNAHelicesColourChooser;
90 import jalview.schemes.ResidueProperties;
91 import jalview.schemes.StrandColourScheme;
92 import jalview.schemes.TCoffeeColourScheme;
93 import jalview.schemes.TaylorColourScheme;
94 import jalview.schemes.TurnColourScheme;
95 import jalview.schemes.UserColourScheme;
96 import jalview.schemes.ZappoColourScheme;
97 import jalview.structure.StructureSelectionManager;
98 import jalview.util.MessageManager;
99 import jalview.viewmodel.AlignmentViewport;
100 import jalview.ws.DBRefFetcher;
101 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
102 import jalview.ws.SequenceFetcher;
103 import jalview.ws.jws1.Discoverer;
104 import jalview.ws.jws2.Jws2Discoverer;
105 import jalview.ws.jws2.jabaws2.Jws2Instance;
106 import jalview.ws.seqfetcher.DbSourceProxy;
108 import java.awt.BorderLayout;
109 import java.awt.Component;
110 import java.awt.Rectangle;
111 import java.awt.Toolkit;
112 import java.awt.datatransfer.Clipboard;
113 import java.awt.datatransfer.DataFlavor;
114 import java.awt.datatransfer.StringSelection;
115 import java.awt.datatransfer.Transferable;
116 import java.awt.dnd.DnDConstants;
117 import java.awt.dnd.DropTargetDragEvent;
118 import java.awt.dnd.DropTargetDropEvent;
119 import java.awt.dnd.DropTargetEvent;
120 import java.awt.dnd.DropTargetListener;
121 import java.awt.event.ActionEvent;
122 import java.awt.event.ActionListener;
123 import java.awt.event.FocusAdapter;
124 import java.awt.event.FocusEvent;
125 import java.awt.event.ItemEvent;
126 import java.awt.event.ItemListener;
127 import java.awt.event.KeyAdapter;
128 import java.awt.event.KeyEvent;
129 import java.awt.event.MouseAdapter;
130 import java.awt.event.MouseEvent;
131 import java.awt.print.PageFormat;
132 import java.awt.print.PrinterJob;
133 import java.beans.PropertyChangeEvent;
136 import java.util.ArrayList;
137 import java.util.Arrays;
138 import java.util.Deque;
139 import java.util.Enumeration;
140 import java.util.Hashtable;
141 import java.util.List;
142 import java.util.Vector;
144 import javax.swing.JCheckBoxMenuItem;
145 import javax.swing.JEditorPane;
146 import javax.swing.JInternalFrame;
147 import javax.swing.JLayeredPane;
148 import javax.swing.JMenu;
149 import javax.swing.JMenuItem;
150 import javax.swing.JOptionPane;
151 import javax.swing.JRadioButtonMenuItem;
152 import javax.swing.JScrollPane;
153 import javax.swing.SwingUtilities;
159 * @version $Revision$
161 public class AlignFrame extends GAlignFrame implements DropTargetListener,
162 IProgressIndicator, AlignViewControllerGuiI
165 public static final int DEFAULT_WIDTH = 700;
167 public static final int DEFAULT_HEIGHT = 500;
170 * The currently displayed panel (selected tabbed view if more than one)
172 public AlignmentPanel alignPanel;
174 AlignViewport viewport;
176 public AlignViewControllerI avc;
178 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
181 * Last format used to load or save alignments in this window
183 String currentFileFormat = null;
186 * Current filename for this alignment
188 String fileName = null;
191 * Creates a new AlignFrame object with specific width and height.
197 public AlignFrame(AlignmentI al, int width, int height)
199 this(al, null, width, height);
203 * Creates a new AlignFrame object with specific width, height and
209 * @param sequenceSetId
211 public AlignFrame(AlignmentI al, int width, int height,
212 String sequenceSetId)
214 this(al, null, width, height, sequenceSetId);
218 * Creates a new AlignFrame object with specific width, height and
224 * @param sequenceSetId
227 public AlignFrame(AlignmentI al, int width, int height,
228 String sequenceSetId, String viewId)
230 this(al, null, width, height, sequenceSetId, viewId);
234 * new alignment window with hidden columns
238 * @param hiddenColumns
239 * ColumnSelection or null
241 * Width of alignment frame
245 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
246 int width, int height)
248 this(al, hiddenColumns, width, height, null);
252 * Create alignment frame for al with hiddenColumns, a specific width and
253 * height, and specific sequenceId
256 * @param hiddenColumns
259 * @param sequenceSetId
262 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
263 int width, int height, String sequenceSetId)
265 this(al, hiddenColumns, width, height, sequenceSetId, null);
269 * Create alignment frame for al with hiddenColumns, a specific width and
270 * height, and specific sequenceId
273 * @param hiddenColumns
276 * @param sequenceSetId
281 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
282 int width, int height, String sequenceSetId, String viewId)
284 setSize(width, height);
286 if (al.getDataset() == null)
291 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
293 alignPanel = new AlignmentPanel(this, viewport);
295 addAlignmentPanel(alignPanel, true);
299 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
300 ColumnSelection hiddenColumns, int width, int height)
302 setSize(width, height);
304 if (al.getDataset() == null)
309 viewport = new AlignViewport(al, hiddenColumns);
311 if (hiddenSeqs != null && hiddenSeqs.length > 0)
313 viewport.hideSequence(hiddenSeqs);
315 alignPanel = new AlignmentPanel(this, viewport);
316 addAlignmentPanel(alignPanel, true);
321 * Make a new AlignFrame from existing alignmentPanels
328 public AlignFrame(AlignmentPanel ap)
332 addAlignmentPanel(ap, false);
337 * initalise the alignframe from the underlying viewport data and the
342 if (!Jalview.isHeadlessMode())
344 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
347 avc = new jalview.controller.AlignViewController(this, viewport,
349 if (viewport.getAlignmentConservationAnnotation() == null)
351 BLOSUM62Colour.setEnabled(false);
352 conservationMenuItem.setEnabled(false);
353 modifyConservation.setEnabled(false);
354 // PIDColour.setEnabled(false);
355 // abovePIDThreshold.setEnabled(false);
356 // modifyPID.setEnabled(false);
359 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
362 if (sortby.equals("Id"))
364 sortIDMenuItem_actionPerformed(null);
366 else if (sortby.equals("Pairwise Identity"))
368 sortPairwiseMenuItem_actionPerformed(null);
371 if (Desktop.desktop != null)
373 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
374 addServiceListeners();
375 setGUINucleotide(viewport.getAlignment().isNucleotide());
379 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
381 setMenusFromViewport(viewport);
382 buildSortByAnnotationScoresMenu();
385 if (viewport.getWrapAlignment())
387 wrapMenuItem_actionPerformed(null);
390 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
392 this.overviewMenuItem_actionPerformed(null);
397 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
398 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
399 final String menuLabel = MessageManager
400 .getString("label.copy_format_from");
401 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
402 new ViewSetProvider()
406 public AlignmentPanel[] getAllAlignmentPanels()
409 origview.add(alignPanel);
410 // make an array of all alignment panels except for this one
411 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
412 Arrays.asList(Desktop.getAlignmentPanels(null)));
413 aps.remove(AlignFrame.this.alignPanel);
414 return aps.toArray(new AlignmentPanel[aps.size()]);
416 }, selviews, new ItemListener()
420 public void itemStateChanged(ItemEvent e)
422 if (origview.size() > 0)
424 final AlignmentPanel ap = origview.get(0);
427 * Copy the ViewStyle of the selected panel to 'this one'.
428 * Don't change value of 'scaleProteinAsCdna' unless copying
431 ViewStyleI vs = selviews.get(0).getAlignViewport()
433 boolean fromSplitFrame = selviews.get(0)
434 .getAlignViewport().getCodingComplement() != null;
437 vs.setScaleProteinAsCdna(ap.getAlignViewport()
438 .getViewStyle().isScaleProteinAsCdna());
440 ap.getAlignViewport().setViewStyle(vs);
443 * Also rescale ViewStyle of SplitFrame complement if there is
444 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
445 * the whole ViewStyle (allow cDNA protein to have different
448 AlignViewportI complement = ap.getAlignViewport()
449 .getCodingComplement();
450 if (complement != null && vs.isScaleProteinAsCdna())
452 AlignFrame af = Desktop.getAlignFrameFor(complement);
453 ((SplitFrame) af.getSplitViewContainer())
455 af.setMenusForViewport();
459 ap.setSelected(true);
460 ap.alignFrame.setMenusForViewport();
465 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
466 .indexOf("devel") > -1
467 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
468 .indexOf("test") > -1)
470 formatMenu.add(vsel);
472 addFocusListener(new FocusAdapter()
475 public void focusGained(FocusEvent e)
477 Desktop.setCurrentAlignFrame(AlignFrame.this);
484 * Change the filename and format for the alignment, and enable the 'reload'
485 * button functionality.
492 public void setFileName(String file, String format)
495 setFileFormat(format);
496 reload.setEnabled(true);
500 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
503 void addKeyListener()
505 addKeyListener(new KeyAdapter()
508 public void keyPressed(KeyEvent evt)
510 if (viewport.cursorMode
511 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
512 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
513 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
514 && Character.isDigit(evt.getKeyChar()))
516 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
519 switch (evt.getKeyCode())
522 case 27: // escape key
523 deselectAllSequenceMenuItem_actionPerformed(null);
527 case KeyEvent.VK_DOWN:
528 if (evt.isAltDown() || !viewport.cursorMode)
530 moveSelectedSequences(false);
532 if (viewport.cursorMode)
534 alignPanel.getSeqPanel().moveCursor(0, 1);
539 if (evt.isAltDown() || !viewport.cursorMode)
541 moveSelectedSequences(true);
543 if (viewport.cursorMode)
545 alignPanel.getSeqPanel().moveCursor(0, -1);
550 case KeyEvent.VK_LEFT:
551 if (evt.isAltDown() || !viewport.cursorMode)
553 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
557 alignPanel.getSeqPanel().moveCursor(-1, 0);
562 case KeyEvent.VK_RIGHT:
563 if (evt.isAltDown() || !viewport.cursorMode)
565 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
569 alignPanel.getSeqPanel().moveCursor(1, 0);
573 case KeyEvent.VK_SPACE:
574 if (viewport.cursorMode)
576 alignPanel.getSeqPanel().insertGapAtCursor(
577 evt.isControlDown() || evt.isShiftDown()
582 // case KeyEvent.VK_A:
583 // if (viewport.cursorMode)
585 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
586 // //System.out.println("A");
590 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
591 * System.out.println("closing bracket"); } break;
593 case KeyEvent.VK_DELETE:
594 case KeyEvent.VK_BACK_SPACE:
595 if (!viewport.cursorMode)
597 cut_actionPerformed(null);
601 alignPanel.getSeqPanel().deleteGapAtCursor(
602 evt.isControlDown() || evt.isShiftDown()
609 if (viewport.cursorMode)
611 alignPanel.getSeqPanel().setCursorRow();
615 if (viewport.cursorMode && !evt.isControlDown())
617 alignPanel.getSeqPanel().setCursorColumn();
621 if (viewport.cursorMode)
623 alignPanel.getSeqPanel().setCursorPosition();
627 case KeyEvent.VK_ENTER:
628 case KeyEvent.VK_COMMA:
629 if (viewport.cursorMode)
631 alignPanel.getSeqPanel().setCursorRowAndColumn();
636 if (viewport.cursorMode)
638 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
642 if (viewport.cursorMode)
644 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
649 viewport.cursorMode = !viewport.cursorMode;
650 statusBar.setText(MessageManager.formatMessage(
651 "label.keyboard_editing_mode",
652 new String[] { (viewport.cursorMode ? "on" : "off") }));
653 if (viewport.cursorMode)
655 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
656 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
658 alignPanel.getSeqPanel().seqCanvas.repaint();
664 Help.showHelpWindow();
665 } catch (Exception ex)
667 ex.printStackTrace();
672 boolean toggleSeqs = !evt.isControlDown();
673 boolean toggleCols = !evt.isShiftDown();
674 toggleHiddenRegions(toggleSeqs, toggleCols);
677 case KeyEvent.VK_PAGE_UP:
678 if (viewport.getWrapAlignment())
680 alignPanel.scrollUp(true);
684 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
685 - viewport.endSeq + viewport.startSeq);
688 case KeyEvent.VK_PAGE_DOWN:
689 if (viewport.getWrapAlignment())
691 alignPanel.scrollUp(false);
695 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
696 + viewport.endSeq - viewport.startSeq);
703 public void keyReleased(KeyEvent evt)
705 switch (evt.getKeyCode())
707 case KeyEvent.VK_LEFT:
708 if (evt.isAltDown() || !viewport.cursorMode)
710 viewport.firePropertyChange("alignment", null, viewport
711 .getAlignment().getSequences());
715 case KeyEvent.VK_RIGHT:
716 if (evt.isAltDown() || !viewport.cursorMode)
718 viewport.firePropertyChange("alignment", null, viewport
719 .getAlignment().getSequences());
727 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
729 ap.alignFrame = this;
730 avc = new jalview.controller.AlignViewController(this, viewport,
735 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
737 int aSize = alignPanels.size();
739 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
741 if (aSize == 1 && ap.av.viewName == null)
743 this.getContentPane().add(ap, BorderLayout.CENTER);
749 setInitialTabVisible();
752 expandViews.setEnabled(true);
753 gatherViews.setEnabled(true);
754 tabbedPane.addTab(ap.av.viewName, ap);
756 ap.setVisible(false);
761 if (ap.av.isPadGaps())
763 ap.av.getAlignment().padGaps();
765 ap.av.updateConservation(ap);
766 ap.av.updateConsensus(ap);
767 ap.av.updateStrucConsensus(ap);
771 public void setInitialTabVisible()
773 expandViews.setEnabled(true);
774 gatherViews.setEnabled(true);
775 tabbedPane.setVisible(true);
776 AlignmentPanel first = alignPanels.get(0);
777 tabbedPane.addTab(first.av.viewName, first);
778 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
781 public AlignViewport getViewport()
786 /* Set up intrinsic listeners for dynamically generated GUI bits. */
787 private void addServiceListeners()
789 final java.beans.PropertyChangeListener thisListener;
790 Desktop.instance.addJalviewPropertyChangeListener("services",
791 thisListener = new java.beans.PropertyChangeListener()
794 public void propertyChange(PropertyChangeEvent evt)
796 // // System.out.println("Discoverer property change.");
797 // if (evt.getPropertyName().equals("services"))
799 SwingUtilities.invokeLater(new Runnable()
806 .println("Rebuild WS Menu for service change");
807 BuildWebServiceMenu();
814 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
817 public void internalFrameClosed(
818 javax.swing.event.InternalFrameEvent evt)
820 // System.out.println("deregistering discoverer listener");
821 Desktop.instance.removeJalviewPropertyChangeListener("services",
823 closeMenuItem_actionPerformed(true);
826 // Finally, build the menu once to get current service state
827 new Thread(new Runnable()
832 BuildWebServiceMenu();
838 * Configure menu items that vary according to whether the alignment is
839 * nucleotide or protein
843 public void setGUINucleotide(boolean nucleotide)
845 showTranslation.setVisible(nucleotide);
846 showReverse.setVisible(nucleotide);
847 showReverseComplement.setVisible(nucleotide);
848 conservationMenuItem.setEnabled(!nucleotide);
849 modifyConservation.setEnabled(!nucleotide);
850 showGroupConservation.setEnabled(!nucleotide);
851 rnahelicesColour.setEnabled(nucleotide);
852 purinePyrimidineColour.setEnabled(nucleotide);
853 showComplementMenuItem.setText(MessageManager
854 .getString(nucleotide ? "label.protein" : "label.nucleotide"));
855 setColourSelected(jalview.bin.Cache.getDefault(
856 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
857 : Preferences.DEFAULT_COLOUR_PROT, "None"));
861 * set up menus for the current viewport. This may be called after any
862 * operation that affects the data in the current view (selection changed,
863 * etc) to update the menus to reflect the new state.
866 public void setMenusForViewport()
868 setMenusFromViewport(viewport);
872 * Need to call this method when tabs are selected for multiple views, or when
873 * loading from Jalview2XML.java
878 void setMenusFromViewport(AlignViewport av)
880 padGapsMenuitem.setSelected(av.isPadGaps());
881 colourTextMenuItem.setSelected(av.isShowColourText());
882 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
883 conservationMenuItem.setSelected(av.getConservationSelected());
884 seqLimits.setSelected(av.getShowJVSuffix());
885 idRightAlign.setSelected(av.isRightAlignIds());
886 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
887 renderGapsMenuItem.setSelected(av.isRenderGaps());
888 wrapMenuItem.setSelected(av.getWrapAlignment());
889 scaleAbove.setVisible(av.getWrapAlignment());
890 scaleLeft.setVisible(av.getWrapAlignment());
891 scaleRight.setVisible(av.getWrapAlignment());
892 annotationPanelMenuItem.setState(av.isShowAnnotation());
894 * Show/hide annotations only enabled if annotation panel is shown
896 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
897 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
898 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
899 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
900 viewBoxesMenuItem.setSelected(av.getShowBoxes());
901 viewTextMenuItem.setSelected(av.getShowText());
902 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
903 showGroupConsensus.setSelected(av.isShowGroupConsensus());
904 showGroupConservation.setSelected(av.isShowGroupConservation());
905 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
906 showSequenceLogo.setSelected(av.isShowSequenceLogo());
907 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
909 setColourSelected(ColourSchemeProperty.getColourName(av
910 .getGlobalColourScheme()));
912 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
913 hiddenMarkers.setState(av.getShowHiddenMarkers());
914 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
915 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
916 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
917 autoCalculate.setSelected(av.autoCalculateConsensus);
918 sortByTree.setSelected(av.sortByTree);
919 listenToViewSelections.setSelected(av.followSelection);
920 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
922 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
924 showProducts.setEnabled(canShowProducts());
925 setGroovyEnabled(Desktop.getGroovyConsole() != null);
931 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
935 public void setGroovyEnabled(boolean b)
937 runGroovy.setEnabled(b);
940 private IProgressIndicator progressBar;
945 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
948 public void setProgressBar(String message, long id)
950 progressBar.setProgressBar(message, id);
954 public void registerHandler(final long id,
955 final IProgressIndicatorHandler handler)
957 progressBar.registerHandler(id, handler);
962 * @return true if any progress bars are still active
965 public boolean operationInProgress()
967 return progressBar.operationInProgress();
971 public void setStatus(String text)
973 statusBar.setText(text);
977 * Added so Castor Mapping file can obtain Jalview Version
979 public String getVersion()
981 return jalview.bin.Cache.getProperty("VERSION");
984 public FeatureRenderer getFeatureRenderer()
986 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
990 public void fetchSequence_actionPerformed(ActionEvent e)
992 new jalview.gui.SequenceFetcher(this);
996 public void addFromFile_actionPerformed(ActionEvent e)
998 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1002 public void reload_actionPerformed(ActionEvent e)
1004 if (fileName != null)
1006 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1007 // originating file's format
1008 // TODO: work out how to recover feature settings for correct view(s) when
1009 // file is reloaded.
1010 if (currentFileFormat.equals("Jalview"))
1012 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1013 for (int i = 0; i < frames.length; i++)
1015 if (frames[i] instanceof AlignFrame && frames[i] != this
1016 && ((AlignFrame) frames[i]).fileName != null
1017 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1021 frames[i].setSelected(true);
1022 Desktop.instance.closeAssociatedWindows();
1023 } catch (java.beans.PropertyVetoException ex)
1029 Desktop.instance.closeAssociatedWindows();
1031 FileLoader loader = new FileLoader();
1032 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1033 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1037 Rectangle bounds = this.getBounds();
1039 FileLoader loader = new FileLoader();
1040 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1041 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1042 protocol, currentFileFormat);
1044 newframe.setBounds(bounds);
1045 if (featureSettings != null && featureSettings.isShowing())
1047 final Rectangle fspos = featureSettings.frame.getBounds();
1048 // TODO: need a 'show feature settings' function that takes bounds -
1049 // need to refactor Desktop.addFrame
1050 newframe.featureSettings_actionPerformed(null);
1051 final FeatureSettings nfs = newframe.featureSettings;
1052 SwingUtilities.invokeLater(new Runnable()
1057 nfs.frame.setBounds(fspos);
1060 this.featureSettings.close();
1061 this.featureSettings = null;
1063 this.closeMenuItem_actionPerformed(true);
1069 public void addFromText_actionPerformed(ActionEvent e)
1071 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1076 public void addFromURL_actionPerformed(ActionEvent e)
1078 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1082 public void save_actionPerformed(ActionEvent e)
1084 if (fileName == null
1085 || (currentFileFormat == null || !jalview.io.FormatAdapter
1086 .isValidIOFormat(currentFileFormat, true))
1087 || fileName.startsWith("http"))
1089 saveAs_actionPerformed(null);
1093 saveAlignment(fileName, currentFileFormat);
1104 public void saveAs_actionPerformed(ActionEvent e)
1106 JalviewFileChooser chooser = new JalviewFileChooser(
1107 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1108 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1109 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1110 currentFileFormat, false);
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 JOptionPane.WARNING_MESSAGE);
1132 currentFileFormat = chooser.getSelectedFormat();
1133 value = chooser.showSaveDialog(this);
1134 if (value != JalviewFileChooser.APPROVE_OPTION)
1140 fileName = chooser.getSelectedFile().getPath();
1142 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1145 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1146 if (currentFileFormat.indexOf(" ") > -1)
1148 currentFileFormat = currentFileFormat.substring(0,
1149 currentFileFormat.indexOf(" "));
1151 saveAlignment(fileName, currentFileFormat);
1155 public boolean saveAlignment(String file, String format)
1157 boolean success = true;
1159 if (format.equalsIgnoreCase("Jalview"))
1161 String shortName = title;
1163 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1165 shortName = shortName.substring(shortName
1166 .lastIndexOf(java.io.File.separatorChar) + 1);
1169 success = new Jalview2XML().saveAlignment(this, file, shortName);
1171 statusBar.setText(MessageManager.formatMessage(
1172 "label.successfully_saved_to_file_in_format", new Object[] {
1173 fileName, format }));
1178 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1180 warningMessage("Cannot save file " + fileName + " using format "
1181 + format, "Alignment output format not supported");
1182 if (!Jalview.isHeadlessMode())
1184 saveAs_actionPerformed(null);
1189 AlignmentExportData exportData = getAlignmentForExport(format,
1191 if (exportData.getSettings().isCancelled())
1195 FormatAdapter f = new FormatAdapter(alignPanel,
1196 exportData.getSettings());
1197 String output = f.formatSequences(
1199 exportData.getAlignment(), // class cast exceptions will
1200 // occur in the distant future
1201 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1202 f.getCacheSuffixDefault(format),
1203 viewport.getColumnSelection());
1213 java.io.PrintWriter out = new java.io.PrintWriter(
1214 new java.io.FileWriter(file));
1218 this.setTitle(file);
1219 statusBar.setText(MessageManager.formatMessage(
1220 "label.successfully_saved_to_file_in_format",
1221 new Object[] { fileName, format }));
1222 } catch (Exception ex)
1225 ex.printStackTrace();
1232 JOptionPane.showInternalMessageDialog(this, MessageManager
1233 .formatMessage("label.couldnt_save_file",
1234 new Object[] { fileName }), MessageManager
1235 .getString("label.error_saving_file"),
1236 JOptionPane.WARNING_MESSAGE);
1242 private void warningMessage(String warning, String title)
1244 if (new jalview.util.Platform().isHeadless())
1246 System.err.println("Warning: " + title + "\nWarning: " + warning);
1251 JOptionPane.showInternalMessageDialog(this, warning, title,
1252 JOptionPane.WARNING_MESSAGE);
1264 protected void outputText_actionPerformed(ActionEvent e)
1267 AlignmentExportData exportData = getAlignmentForExport(
1268 e.getActionCommand(), viewport, null);
1269 if (exportData.getSettings().isCancelled())
1273 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1274 cap.setForInput(null);
1277 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1278 .formatSequences(e.getActionCommand(),
1279 exportData.getAlignment(),
1280 exportData.getOmitHidden(),
1281 exportData.getStartEndPostions(),
1282 viewport.getColumnSelection()));
1283 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1284 "label.alignment_output_command",
1285 new Object[] { e.getActionCommand() }), 600, 500);
1286 } catch (OutOfMemoryError oom)
1288 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1294 public static AlignmentExportData getAlignmentForExport(
1295 String exportFormat, AlignViewportI viewport,
1296 AlignExportSettingI exportSettings)
1298 AlignmentI alignmentToExport = null;
1299 AlignExportSettingI settings = exportSettings;
1300 String[] omitHidden = null;
1302 HiddenSequences hiddenSeqs = viewport.getAlignment()
1303 .getHiddenSequences();
1305 alignmentToExport = viewport.getAlignment();
1307 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1308 if (settings == null)
1310 settings = new AlignExportSettings(hasHiddenSeqs,
1311 viewport.hasHiddenColumns(), exportFormat);
1313 // settings.isExportAnnotations();
1315 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1317 omitHidden = viewport.getViewAsString(false);
1320 int[] alignmentStartEnd = new int[2];
1321 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1323 alignmentToExport = hiddenSeqs.getFullAlignment();
1327 alignmentToExport = viewport.getAlignment();
1328 alignmentStartEnd = viewport.getAlignment()
1329 .getVisibleStartAndEndIndex(
1331 .getColumnSelection().getHiddenColumns());
1333 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1334 omitHidden, alignmentStartEnd, settings);
1346 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1348 new HtmlSvgOutput(null, alignPanel);
1352 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1354 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1355 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1358 public void createImageMap(File file, String image)
1360 alignPanel.makePNGImageMap(file, image);
1370 public void createPNG(File f)
1372 alignPanel.makePNG(f);
1382 public void createEPS(File f)
1384 alignPanel.makeEPS(f);
1388 public void createSVG(File f)
1390 alignPanel.makeSVG(f);
1394 public void pageSetup_actionPerformed(ActionEvent e)
1396 PrinterJob printJob = PrinterJob.getPrinterJob();
1397 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1407 public void printMenuItem_actionPerformed(ActionEvent e)
1409 // Putting in a thread avoids Swing painting problems
1410 PrintThread thread = new PrintThread(alignPanel);
1415 public void exportFeatures_actionPerformed(ActionEvent e)
1417 new AnnotationExporter().exportFeatures(alignPanel);
1421 public void exportAnnotations_actionPerformed(ActionEvent e)
1423 new AnnotationExporter().exportAnnotations(alignPanel);
1427 public void associatedData_actionPerformed(ActionEvent e)
1429 // Pick the tree file
1430 JalviewFileChooser chooser = new JalviewFileChooser(
1431 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1432 chooser.setFileView(new JalviewFileView());
1433 chooser.setDialogTitle(MessageManager
1434 .getString("label.load_jalview_annotations"));
1435 chooser.setToolTipText(MessageManager
1436 .getString("label.load_jalview_annotations"));
1438 int value = chooser.showOpenDialog(null);
1440 if (value == JalviewFileChooser.APPROVE_OPTION)
1442 String choice = chooser.getSelectedFile().getPath();
1443 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1444 loadJalviewDataFile(choice, null, null, null);
1450 * Close the current view or all views in the alignment frame. If the frame
1451 * only contains one view then the alignment will be removed from memory.
1453 * @param closeAllTabs
1456 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1458 if (alignPanels != null && alignPanels.size() < 2)
1460 closeAllTabs = true;
1465 if (alignPanels != null)
1469 if (this.isClosed())
1471 // really close all the windows - otherwise wait till
1472 // setClosed(true) is called
1473 for (int i = 0; i < alignPanels.size(); i++)
1475 AlignmentPanel ap = alignPanels.get(i);
1482 closeView(alignPanel);
1489 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1490 * be called recursively, with the frame now in 'closed' state
1492 this.setClosed(true);
1494 } catch (Exception ex)
1496 ex.printStackTrace();
1501 * Close the specified panel and close up tabs appropriately.
1503 * @param panelToClose
1505 public void closeView(AlignmentPanel panelToClose)
1507 int index = tabbedPane.getSelectedIndex();
1508 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1509 alignPanels.remove(panelToClose);
1510 panelToClose.closePanel();
1511 panelToClose = null;
1513 tabbedPane.removeTabAt(closedindex);
1514 tabbedPane.validate();
1516 if (index > closedindex || index == tabbedPane.getTabCount())
1518 // modify currently selected tab index if necessary.
1522 this.tabSelectionChanged(index);
1528 void updateEditMenuBar()
1531 if (viewport.getHistoryList().size() > 0)
1533 undoMenuItem.setEnabled(true);
1534 CommandI command = viewport.getHistoryList().peek();
1535 undoMenuItem.setText(MessageManager.formatMessage(
1536 "label.undo_command",
1537 new Object[] { command.getDescription() }));
1541 undoMenuItem.setEnabled(false);
1542 undoMenuItem.setText(MessageManager.getString("action.undo"));
1545 if (viewport.getRedoList().size() > 0)
1547 redoMenuItem.setEnabled(true);
1549 CommandI command = viewport.getRedoList().peek();
1550 redoMenuItem.setText(MessageManager.formatMessage(
1551 "label.redo_command",
1552 new Object[] { command.getDescription() }));
1556 redoMenuItem.setEnabled(false);
1557 redoMenuItem.setText(MessageManager.getString("action.redo"));
1562 public void addHistoryItem(CommandI command)
1564 if (command.getSize() > 0)
1566 viewport.addToHistoryList(command);
1567 viewport.clearRedoList();
1568 updateEditMenuBar();
1569 viewport.updateHiddenColumns();
1570 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1571 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1572 // viewport.getColumnSelection()
1573 // .getHiddenColumns().size() > 0);
1579 * @return alignment objects for all views
1581 AlignmentI[] getViewAlignments()
1583 if (alignPanels != null)
1585 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1587 for (AlignmentPanel ap : alignPanels)
1589 als[i++] = ap.av.getAlignment();
1593 if (viewport != null)
1595 return new AlignmentI[] { viewport.getAlignment() };
1607 protected void undoMenuItem_actionPerformed(ActionEvent e)
1609 if (viewport.getHistoryList().isEmpty())
1613 CommandI command = viewport.getHistoryList().pop();
1614 viewport.addToRedoList(command);
1615 command.undoCommand(getViewAlignments());
1617 AlignmentViewport originalSource = getOriginatingSource(command);
1618 updateEditMenuBar();
1620 if (originalSource != null)
1622 if (originalSource != viewport)
1625 .warn("Implementation worry: mismatch of viewport origin for undo");
1627 originalSource.updateHiddenColumns();
1628 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1630 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1631 // viewport.getColumnSelection()
1632 // .getHiddenColumns().size() > 0);
1633 originalSource.firePropertyChange("alignment", null, originalSource
1634 .getAlignment().getSequences());
1645 protected void redoMenuItem_actionPerformed(ActionEvent e)
1647 if (viewport.getRedoList().size() < 1)
1652 CommandI command = viewport.getRedoList().pop();
1653 viewport.addToHistoryList(command);
1654 command.doCommand(getViewAlignments());
1656 AlignmentViewport originalSource = getOriginatingSource(command);
1657 updateEditMenuBar();
1659 if (originalSource != null)
1662 if (originalSource != viewport)
1665 .warn("Implementation worry: mismatch of viewport origin for redo");
1667 originalSource.updateHiddenColumns();
1668 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1670 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1671 // viewport.getColumnSelection()
1672 // .getHiddenColumns().size() > 0);
1673 originalSource.firePropertyChange("alignment", null, originalSource
1674 .getAlignment().getSequences());
1678 AlignmentViewport getOriginatingSource(CommandI command)
1680 AlignmentViewport originalSource = null;
1681 // For sequence removal and addition, we need to fire
1682 // the property change event FROM the viewport where the
1683 // original alignment was altered
1684 AlignmentI al = null;
1685 if (command instanceof EditCommand)
1687 EditCommand editCommand = (EditCommand) command;
1688 al = editCommand.getAlignment();
1689 List<Component> comps = PaintRefresher.components.get(viewport
1690 .getSequenceSetId());
1692 for (Component comp : comps)
1694 if (comp instanceof AlignmentPanel)
1696 if (al == ((AlignmentPanel) comp).av.getAlignment())
1698 originalSource = ((AlignmentPanel) comp).av;
1705 if (originalSource == null)
1707 // The original view is closed, we must validate
1708 // the current view against the closed view first
1711 PaintRefresher.validateSequences(al, viewport.getAlignment());
1714 originalSource = viewport;
1717 return originalSource;
1726 public void moveSelectedSequences(boolean up)
1728 SequenceGroup sg = viewport.getSelectionGroup();
1734 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1735 viewport.getHiddenRepSequences(), up);
1736 alignPanel.paintAlignment(true);
1739 synchronized void slideSequences(boolean right, int size)
1741 List<SequenceI> sg = new ArrayList<SequenceI>();
1742 if (viewport.cursorMode)
1744 sg.add(viewport.getAlignment().getSequenceAt(
1745 alignPanel.getSeqPanel().seqCanvas.cursorY));
1747 else if (viewport.getSelectionGroup() != null
1748 && viewport.getSelectionGroup().getSize() != viewport
1749 .getAlignment().getHeight())
1751 sg = viewport.getSelectionGroup().getSequences(
1752 viewport.getHiddenRepSequences());
1760 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1762 for (SequenceI seq : viewport.getAlignment().getSequences())
1764 if (!sg.contains(seq))
1766 invertGroup.add(seq);
1770 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1772 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1773 for (int i = 0; i < invertGroup.size(); i++)
1775 seqs2[i] = invertGroup.get(i);
1778 SlideSequencesCommand ssc;
1781 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1782 size, viewport.getGapCharacter());
1786 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1787 size, viewport.getGapCharacter());
1790 int groupAdjustment = 0;
1791 if (ssc.getGapsInsertedBegin() && right)
1793 if (viewport.cursorMode)
1795 alignPanel.getSeqPanel().moveCursor(size, 0);
1799 groupAdjustment = size;
1802 else if (!ssc.getGapsInsertedBegin() && !right)
1804 if (viewport.cursorMode)
1806 alignPanel.getSeqPanel().moveCursor(-size, 0);
1810 groupAdjustment = -size;
1814 if (groupAdjustment != 0)
1816 viewport.getSelectionGroup().setStartRes(
1817 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1818 viewport.getSelectionGroup().setEndRes(
1819 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1823 * just extend the last slide command if compatible; but not if in
1824 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1826 boolean appendHistoryItem = false;
1827 Deque<CommandI> historyList = viewport.getHistoryList();
1828 boolean inSplitFrame = getSplitViewContainer() != null;
1829 if (!inSplitFrame && historyList != null && historyList.size() > 0
1830 && historyList.peek() instanceof SlideSequencesCommand)
1832 appendHistoryItem = ssc
1833 .appendSlideCommand((SlideSequencesCommand) historyList
1837 if (!appendHistoryItem)
1839 addHistoryItem(ssc);
1852 protected void copy_actionPerformed(ActionEvent e)
1855 if (viewport.getSelectionGroup() == null)
1859 // TODO: preserve the ordering of displayed alignment annotation in any
1860 // internal paste (particularly sequence associated annotation)
1861 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1862 String[] omitHidden = null;
1864 if (viewport.hasHiddenColumns())
1866 omitHidden = viewport.getViewAsString(true);
1869 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1872 StringSelection ss = new StringSelection(output);
1876 jalview.gui.Desktop.internalCopy = true;
1877 // Its really worth setting the clipboard contents
1878 // to empty before setting the large StringSelection!!
1879 Toolkit.getDefaultToolkit().getSystemClipboard()
1880 .setContents(new StringSelection(""), null);
1882 Toolkit.getDefaultToolkit().getSystemClipboard()
1883 .setContents(ss, Desktop.instance);
1884 } catch (OutOfMemoryError er)
1886 new OOMWarning("copying region", er);
1890 ArrayList<int[]> hiddenColumns = null;
1891 if (viewport.hasHiddenColumns())
1893 hiddenColumns = new ArrayList<int[]>();
1894 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1895 .getSelectionGroup().getEndRes();
1896 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1898 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1900 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1901 region[1] - hiddenOffset });
1906 Desktop.jalviewClipboard = new Object[] { seqs,
1907 viewport.getAlignment().getDataset(), hiddenColumns };
1908 statusBar.setText(MessageManager.formatMessage(
1909 "label.copied_sequences_to_clipboard", new Object[] { Integer
1910 .valueOf(seqs.length).toString() }));
1920 protected void pasteNew_actionPerformed(ActionEvent e)
1932 protected void pasteThis_actionPerformed(ActionEvent e)
1938 * Paste contents of Jalview clipboard
1940 * @param newAlignment
1941 * true to paste to a new alignment, otherwise add to this.
1943 void paste(boolean newAlignment)
1945 boolean externalPaste = true;
1948 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1949 Transferable contents = c.getContents(this);
1951 if (contents == null)
1959 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1960 if (str.length() < 1)
1965 format = new IdentifyFile().identify(str, "Paste");
1967 } catch (OutOfMemoryError er)
1969 new OOMWarning("Out of memory pasting sequences!!", er);
1973 SequenceI[] sequences;
1974 boolean annotationAdded = false;
1975 AlignmentI alignment = null;
1977 if (Desktop.jalviewClipboard != null)
1979 // The clipboard was filled from within Jalview, we must use the
1981 // And dataset from the copied alignment
1982 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1983 // be doubly sure that we create *new* sequence objects.
1984 sequences = new SequenceI[newseq.length];
1985 for (int i = 0; i < newseq.length; i++)
1987 sequences[i] = new Sequence(newseq[i]);
1989 alignment = new Alignment(sequences);
1990 externalPaste = false;
1994 // parse the clipboard as an alignment.
1995 alignment = new FormatAdapter().readFile(str, "Paste", format);
1996 sequences = alignment.getSequencesArray();
2000 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2006 if (Desktop.jalviewClipboard != null)
2008 // dataset is inherited
2009 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2013 // new dataset is constructed
2014 alignment.setDataset(null);
2016 alwidth = alignment.getWidth() + 1;
2020 AlignmentI pastedal = alignment; // preserve pasted alignment object
2021 // Add pasted sequences and dataset into existing alignment.
2022 alignment = viewport.getAlignment();
2023 alwidth = alignment.getWidth() + 1;
2024 // decide if we need to import sequences from an existing dataset
2025 boolean importDs = Desktop.jalviewClipboard != null
2026 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2027 // importDs==true instructs us to copy over new dataset sequences from
2028 // an existing alignment
2029 Vector newDs = (importDs) ? new Vector() : null; // used to create
2030 // minimum dataset set
2032 for (int i = 0; i < sequences.length; i++)
2036 newDs.addElement(null);
2038 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2040 if (importDs && ds != null)
2042 if (!newDs.contains(ds))
2044 newDs.setElementAt(ds, i);
2045 ds = new Sequence(ds);
2046 // update with new dataset sequence
2047 sequences[i].setDatasetSequence(ds);
2051 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2056 // copy and derive new dataset sequence
2057 sequences[i] = sequences[i].deriveSequence();
2058 alignment.getDataset().addSequence(
2059 sequences[i].getDatasetSequence());
2060 // TODO: avoid creation of duplicate dataset sequences with a
2061 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2063 alignment.addSequence(sequences[i]); // merges dataset
2067 newDs.clear(); // tidy up
2069 if (alignment.getAlignmentAnnotation() != null)
2071 for (AlignmentAnnotation alan : alignment
2072 .getAlignmentAnnotation())
2074 if (alan.graphGroup > fgroup)
2076 fgroup = alan.graphGroup;
2080 if (pastedal.getAlignmentAnnotation() != null)
2082 // Add any annotation attached to alignment.
2083 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2084 for (int i = 0; i < alann.length; i++)
2086 annotationAdded = true;
2087 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2089 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2090 if (newann.graphGroup > -1)
2092 if (newGraphGroups.size() <= newann.graphGroup
2093 || newGraphGroups.get(newann.graphGroup) == null)
2095 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2097 newGraphGroups.add(q, null);
2099 newGraphGroups.set(newann.graphGroup, new Integer(
2102 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2106 newann.padAnnotation(alwidth);
2107 alignment.addAnnotation(newann);
2117 addHistoryItem(new EditCommand(
2118 MessageManager.getString("label.add_sequences"),
2119 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2121 // Add any annotations attached to sequences
2122 for (int i = 0; i < sequences.length; i++)
2124 if (sequences[i].getAnnotation() != null)
2126 AlignmentAnnotation newann;
2127 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2129 annotationAdded = true;
2130 newann = sequences[i].getAnnotation()[a];
2131 newann.adjustForAlignment();
2132 newann.padAnnotation(alwidth);
2133 if (newann.graphGroup > -1)
2135 if (newann.graphGroup > -1)
2137 if (newGraphGroups.size() <= newann.graphGroup
2138 || newGraphGroups.get(newann.graphGroup) == null)
2140 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2142 newGraphGroups.add(q, null);
2144 newGraphGroups.set(newann.graphGroup, new Integer(
2147 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2151 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2156 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2163 // propagate alignment changed.
2164 viewport.setEndSeq(alignment.getHeight());
2165 if (annotationAdded)
2167 // Duplicate sequence annotation in all views.
2168 AlignmentI[] alview = this.getViewAlignments();
2169 for (int i = 0; i < sequences.length; i++)
2171 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2176 for (int avnum = 0; avnum < alview.length; avnum++)
2178 if (alview[avnum] != alignment)
2180 // duplicate in a view other than the one with input focus
2181 int avwidth = alview[avnum].getWidth() + 1;
2182 // this relies on sann being preserved after we
2183 // modify the sequence's annotation array for each duplication
2184 for (int a = 0; a < sann.length; a++)
2186 AlignmentAnnotation newann = new AlignmentAnnotation(
2188 sequences[i].addAlignmentAnnotation(newann);
2189 newann.padAnnotation(avwidth);
2190 alview[avnum].addAnnotation(newann); // annotation was
2191 // duplicated earlier
2192 // TODO JAL-1145 graphGroups are not updated for sequence
2193 // annotation added to several views. This may cause
2195 alview[avnum].setAnnotationIndex(newann, a);
2200 buildSortByAnnotationScoresMenu();
2202 viewport.firePropertyChange("alignment", null,
2203 alignment.getSequences());
2204 if (alignPanels != null)
2206 for (AlignmentPanel ap : alignPanels)
2208 ap.validateAnnotationDimensions(false);
2213 alignPanel.validateAnnotationDimensions(false);
2219 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2221 String newtitle = new String("Copied sequences");
2223 if (Desktop.jalviewClipboard != null
2224 && Desktop.jalviewClipboard[2] != null)
2226 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2227 for (int[] region : hc)
2229 af.viewport.hideColumns(region[0], region[1]);
2233 // >>>This is a fix for the moment, until a better solution is
2235 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2237 alignPanel.getSeqPanel().seqCanvas
2238 .getFeatureRenderer());
2240 // TODO: maintain provenance of an alignment, rather than just make the
2241 // title a concatenation of operations.
2244 if (title.startsWith("Copied sequences"))
2250 newtitle = newtitle.concat("- from " + title);
2255 newtitle = new String("Pasted sequences");
2258 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2263 } catch (Exception ex)
2265 ex.printStackTrace();
2266 System.out.println("Exception whilst pasting: " + ex);
2267 // could be anything being pasted in here
2273 protected void expand_newalign(ActionEvent e)
2277 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2278 .getAlignment(), -1);
2279 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2281 String newtitle = new String("Flanking alignment");
2283 if (Desktop.jalviewClipboard != null
2284 && Desktop.jalviewClipboard[2] != null)
2286 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2287 for (int region[] : hc)
2289 af.viewport.hideColumns(region[0], region[1]);
2293 // >>>This is a fix for the moment, until a better solution is
2295 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2297 alignPanel.getSeqPanel().seqCanvas
2298 .getFeatureRenderer());
2300 // TODO: maintain provenance of an alignment, rather than just make the
2301 // title a concatenation of operations.
2303 if (title.startsWith("Copied sequences"))
2309 newtitle = newtitle.concat("- from " + title);
2313 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2315 } catch (Exception ex)
2317 ex.printStackTrace();
2318 System.out.println("Exception whilst pasting: " + ex);
2319 // could be anything being pasted in here
2320 } catch (OutOfMemoryError oom)
2322 new OOMWarning("Viewing flanking region of alignment", oom);
2333 protected void cut_actionPerformed(ActionEvent e)
2335 copy_actionPerformed(null);
2336 delete_actionPerformed(null);
2346 protected void delete_actionPerformed(ActionEvent evt)
2349 SequenceGroup sg = viewport.getSelectionGroup();
2356 * If the cut affects all sequences, warn, remove highlighted columns
2358 if (sg.getSize() == viewport.getAlignment().getHeight())
2360 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2361 .getAlignment().getWidth()) ? true : false;
2362 if (isEntireAlignWidth)
2364 int confirm = JOptionPane.showConfirmDialog(this,
2365 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2366 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2367 JOptionPane.OK_CANCEL_OPTION);
2369 if (confirm == JOptionPane.CANCEL_OPTION
2370 || confirm == JOptionPane.CLOSED_OPTION)
2375 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2376 sg.getEndRes() + 1);
2378 SequenceI[] cut = sg.getSequences()
2379 .toArray(new SequenceI[sg.getSize()]);
2381 addHistoryItem(new EditCommand(
2382 MessageManager.getString("label.cut_sequences"), Action.CUT,
2383 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2384 viewport.getAlignment()));
2386 viewport.setSelectionGroup(null);
2387 viewport.sendSelection();
2388 viewport.getAlignment().deleteGroup(sg);
2390 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2392 if (viewport.getAlignment().getHeight() < 1)
2396 this.setClosed(true);
2397 } catch (Exception ex)
2410 protected void deleteGroups_actionPerformed(ActionEvent e)
2412 if (avc.deleteGroups())
2414 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2415 alignPanel.updateAnnotation();
2416 alignPanel.paintAlignment(true);
2427 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2429 SequenceGroup sg = new SequenceGroup();
2431 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2433 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2436 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2437 viewport.setSelectionGroup(sg);
2438 viewport.sendSelection();
2439 alignPanel.paintAlignment(true);
2440 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2450 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2452 if (viewport.cursorMode)
2454 alignPanel.getSeqPanel().keyboardNo1 = null;
2455 alignPanel.getSeqPanel().keyboardNo2 = null;
2457 viewport.setSelectionGroup(null);
2458 viewport.getColumnSelection().clear();
2459 viewport.setSelectionGroup(null);
2460 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2461 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2462 alignPanel.paintAlignment(true);
2463 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2464 viewport.sendSelection();
2474 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2476 SequenceGroup sg = viewport.getSelectionGroup();
2480 selectAllSequenceMenuItem_actionPerformed(null);
2485 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2487 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2490 alignPanel.paintAlignment(true);
2491 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2492 viewport.sendSelection();
2496 public void invertColSel_actionPerformed(ActionEvent e)
2498 viewport.invertColumnSelection();
2499 alignPanel.paintAlignment(true);
2500 viewport.sendSelection();
2510 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2512 trimAlignment(true);
2522 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2524 trimAlignment(false);
2527 void trimAlignment(boolean trimLeft)
2529 ColumnSelection colSel = viewport.getColumnSelection();
2532 if (!colSel.isEmpty())
2536 column = colSel.getMin();
2540 column = colSel.getMax();
2544 if (viewport.getSelectionGroup() != null)
2546 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2547 viewport.getHiddenRepSequences());
2551 seqs = viewport.getAlignment().getSequencesArray();
2554 TrimRegionCommand trimRegion;
2557 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2558 column, viewport.getAlignment());
2559 viewport.setStartRes(0);
2563 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2564 column, viewport.getAlignment());
2567 statusBar.setText(MessageManager.formatMessage(
2568 "label.removed_columns",
2569 new String[] { Integer.valueOf(trimRegion.getSize())
2572 addHistoryItem(trimRegion);
2574 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2576 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2577 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2579 viewport.getAlignment().deleteGroup(sg);
2583 viewport.firePropertyChange("alignment", null, viewport
2584 .getAlignment().getSequences());
2595 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2597 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2600 if (viewport.getSelectionGroup() != null)
2602 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2603 viewport.getHiddenRepSequences());
2604 start = viewport.getSelectionGroup().getStartRes();
2605 end = viewport.getSelectionGroup().getEndRes();
2609 seqs = viewport.getAlignment().getSequencesArray();
2612 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2613 "Remove Gapped Columns", seqs, start, end,
2614 viewport.getAlignment());
2616 addHistoryItem(removeGapCols);
2618 statusBar.setText(MessageManager.formatMessage(
2619 "label.removed_empty_columns",
2620 new Object[] { Integer.valueOf(removeGapCols.getSize())
2623 // This is to maintain viewport position on first residue
2624 // of first sequence
2625 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2626 int startRes = seq.findPosition(viewport.startRes);
2627 // ShiftList shifts;
2628 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2629 // edit.alColumnChanges=shifts.getInverse();
2630 // if (viewport.hasHiddenColumns)
2631 // viewport.getColumnSelection().compensateForEdits(shifts);
2632 viewport.setStartRes(seq.findIndex(startRes) - 1);
2633 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2645 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2647 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2650 if (viewport.getSelectionGroup() != null)
2652 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2653 viewport.getHiddenRepSequences());
2654 start = viewport.getSelectionGroup().getStartRes();
2655 end = viewport.getSelectionGroup().getEndRes();
2659 seqs = viewport.getAlignment().getSequencesArray();
2662 // This is to maintain viewport position on first residue
2663 // of first sequence
2664 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2665 int startRes = seq.findPosition(viewport.startRes);
2667 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2668 viewport.getAlignment()));
2670 viewport.setStartRes(seq.findIndex(startRes) - 1);
2672 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2684 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2686 viewport.setPadGaps(padGapsMenuitem.isSelected());
2687 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2698 public void findMenuItem_actionPerformed(ActionEvent e)
2704 * Create a new view of the current alignment.
2707 public void newView_actionPerformed(ActionEvent e)
2709 newView(null, true);
2713 * Creates and shows a new view of the current alignment.
2716 * title of newly created view; if null, one will be generated
2717 * @param copyAnnotation
2718 * if true then duplicate all annnotation, groups and settings
2719 * @return new alignment panel, already displayed.
2721 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2724 * Create a new AlignmentPanel (with its own, new Viewport)
2726 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2728 if (!copyAnnotation)
2731 * remove all groups and annotation except for the automatic stuff
2733 newap.av.getAlignment().deleteAllGroups();
2734 newap.av.getAlignment().deleteAllAnnotations(false);
2737 newap.av.setGatherViewsHere(false);
2739 if (viewport.viewName == null)
2741 viewport.viewName = MessageManager
2742 .getString("label.view_name_original");
2746 * Views share the same edits undo and redo stacks
2748 newap.av.setHistoryList(viewport.getHistoryList());
2749 newap.av.setRedoList(viewport.getRedoList());
2752 * Views share the same mappings; need to deregister any new mappings
2753 * created by copyAlignPanel, and register the new reference to the shared
2756 newap.av.replaceMappings(viewport.getAlignment());
2758 newap.av.viewName = getNewViewName(viewTitle);
2760 addAlignmentPanel(newap, true);
2761 newap.alignmentChanged();
2763 if (alignPanels.size() == 2)
2765 viewport.setGatherViewsHere(true);
2767 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2772 * Make a new name for the view, ensuring it is unique within the current
2773 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2774 * these now use viewId. Unique view names are still desirable for usability.)
2779 protected String getNewViewName(String viewTitle)
2781 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2782 boolean addFirstIndex = false;
2783 if (viewTitle == null || viewTitle.trim().length() == 0)
2785 viewTitle = MessageManager.getString("action.view");
2786 addFirstIndex = true;
2790 index = 1;// we count from 1 if given a specific name
2792 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2794 List<Component> comps = PaintRefresher.components.get(viewport
2795 .getSequenceSetId());
2797 List<String> existingNames = getExistingViewNames(comps);
2799 while (existingNames.contains(newViewName))
2801 newViewName = viewTitle + " " + (++index);
2807 * Returns a list of distinct view names found in the given list of
2808 * components. View names are held on the viewport of an AlignmentPanel.
2813 protected List<String> getExistingViewNames(List<Component> comps)
2815 List<String> existingNames = new ArrayList<String>();
2816 for (Component comp : comps)
2818 if (comp instanceof AlignmentPanel)
2820 AlignmentPanel ap = (AlignmentPanel) comp;
2821 if (!existingNames.contains(ap.av.viewName))
2823 existingNames.add(ap.av.viewName);
2827 return existingNames;
2831 * Explode tabbed views into separate windows.
2834 public void expandViews_actionPerformed(ActionEvent e)
2836 Desktop.instance.explodeViews(this);
2840 * Gather views in separate windows back into a tabbed presentation.
2843 public void gatherViews_actionPerformed(ActionEvent e)
2845 Desktop.instance.gatherViews(this);
2855 public void font_actionPerformed(ActionEvent e)
2857 new FontChooser(alignPanel);
2867 protected void seqLimit_actionPerformed(ActionEvent e)
2869 viewport.setShowJVSuffix(seqLimits.isSelected());
2871 alignPanel.getIdPanel().getIdCanvas()
2872 .setPreferredSize(alignPanel.calculateIdWidth());
2873 alignPanel.paintAlignment(true);
2877 public void idRightAlign_actionPerformed(ActionEvent e)
2879 viewport.setRightAlignIds(idRightAlign.isSelected());
2880 alignPanel.paintAlignment(true);
2884 public void centreColumnLabels_actionPerformed(ActionEvent e)
2886 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2887 alignPanel.paintAlignment(true);
2893 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2896 protected void followHighlight_actionPerformed()
2899 * Set the 'follow' flag on the Viewport (and scroll to position if now
2902 final boolean state = this.followHighlightMenuItem.getState();
2903 viewport.setFollowHighlight(state);
2906 alignPanel.scrollToPosition(
2907 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2918 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2920 viewport.setColourText(colourTextMenuItem.isSelected());
2921 alignPanel.paintAlignment(true);
2931 public void wrapMenuItem_actionPerformed(ActionEvent e)
2933 scaleAbove.setVisible(wrapMenuItem.isSelected());
2934 scaleLeft.setVisible(wrapMenuItem.isSelected());
2935 scaleRight.setVisible(wrapMenuItem.isSelected());
2936 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2937 alignPanel.updateLayout();
2941 public void showAllSeqs_actionPerformed(ActionEvent e)
2943 viewport.showAllHiddenSeqs();
2947 public void showAllColumns_actionPerformed(ActionEvent e)
2949 viewport.showAllHiddenColumns();
2951 viewport.sendSelection();
2955 public void hideSelSequences_actionPerformed(ActionEvent e)
2957 viewport.hideAllSelectedSeqs();
2958 // alignPanel.paintAlignment(true);
2962 * called by key handler and the hide all/show all menu items
2967 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2970 boolean hide = false;
2971 SequenceGroup sg = viewport.getSelectionGroup();
2972 if (!toggleSeqs && !toggleCols)
2974 // Hide everything by the current selection - this is a hack - we do the
2975 // invert and then hide
2976 // first check that there will be visible columns after the invert.
2977 if ((viewport.getColumnSelection() != null
2978 && viewport.getColumnSelection().getSelected() != null && viewport
2979 .getColumnSelection().getSelected().size() > 0)
2980 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2983 // now invert the sequence set, if required - empty selection implies
2984 // that no hiding is required.
2987 invertSequenceMenuItem_actionPerformed(null);
2988 sg = viewport.getSelectionGroup();
2992 viewport.expandColSelection(sg, true);
2993 // finally invert the column selection and get the new sequence
2995 invertColSel_actionPerformed(null);
3002 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3004 hideSelSequences_actionPerformed(null);
3007 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3010 showAllSeqs_actionPerformed(null);
3016 if (viewport.getColumnSelection().getSelected().size() > 0)
3018 hideSelColumns_actionPerformed(null);
3021 viewport.setSelectionGroup(sg);
3026 showAllColumns_actionPerformed(null);
3035 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3036 * event.ActionEvent)
3039 public void hideAllButSelection_actionPerformed(ActionEvent e)
3041 toggleHiddenRegions(false, false);
3042 viewport.sendSelection();
3049 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3053 public void hideAllSelection_actionPerformed(ActionEvent e)
3055 SequenceGroup sg = viewport.getSelectionGroup();
3056 viewport.expandColSelection(sg, false);
3057 viewport.hideAllSelectedSeqs();
3058 viewport.hideSelectedColumns();
3059 alignPanel.paintAlignment(true);
3060 viewport.sendSelection();
3067 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3071 public void showAllhidden_actionPerformed(ActionEvent e)
3073 viewport.showAllHiddenColumns();
3074 viewport.showAllHiddenSeqs();
3075 alignPanel.paintAlignment(true);
3076 viewport.sendSelection();
3080 public void hideSelColumns_actionPerformed(ActionEvent e)
3082 viewport.hideSelectedColumns();
3083 alignPanel.paintAlignment(true);
3084 viewport.sendSelection();
3088 public void hiddenMarkers_actionPerformed(ActionEvent e)
3090 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3101 protected void scaleAbove_actionPerformed(ActionEvent e)
3103 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3104 alignPanel.paintAlignment(true);
3114 protected void scaleLeft_actionPerformed(ActionEvent e)
3116 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3117 alignPanel.paintAlignment(true);
3127 protected void scaleRight_actionPerformed(ActionEvent e)
3129 viewport.setScaleRightWrapped(scaleRight.isSelected());
3130 alignPanel.paintAlignment(true);
3140 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3142 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3143 alignPanel.paintAlignment(true);
3153 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3155 viewport.setShowText(viewTextMenuItem.isSelected());
3156 alignPanel.paintAlignment(true);
3166 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3168 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3169 alignPanel.paintAlignment(true);
3172 public FeatureSettings featureSettings;
3175 public FeatureSettingsControllerI getFeatureSettingsUI()
3177 return featureSettings;
3181 public void featureSettings_actionPerformed(ActionEvent e)
3183 if (featureSettings != null)
3185 featureSettings.close();
3186 featureSettings = null;
3188 if (!showSeqFeatures.isSelected())
3190 // make sure features are actually displayed
3191 showSeqFeatures.setSelected(true);
3192 showSeqFeatures_actionPerformed(null);
3194 featureSettings = new FeatureSettings(this);
3198 * Set or clear 'Show Sequence Features'
3204 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3206 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3207 alignPanel.paintAlignment(true);
3208 if (alignPanel.getOverviewPanel() != null)
3210 alignPanel.getOverviewPanel().updateOverviewImage();
3215 * Set or clear 'Show Sequence Features'
3221 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3223 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3225 if (viewport.isShowSequenceFeaturesHeight())
3227 // ensure we're actually displaying features
3228 viewport.setShowSequenceFeatures(true);
3229 showSeqFeatures.setSelected(true);
3231 alignPanel.paintAlignment(true);
3232 if (alignPanel.getOverviewPanel() != null)
3234 alignPanel.getOverviewPanel().updateOverviewImage();
3239 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3240 * the annotations panel as a whole.
3242 * The options to show/hide all annotations should be enabled when the panel
3243 * is shown, and disabled when the panel is hidden.
3248 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3250 final boolean setVisible = annotationPanelMenuItem.isSelected();
3251 viewport.setShowAnnotation(setVisible);
3252 this.showAllSeqAnnotations.setEnabled(setVisible);
3253 this.hideAllSeqAnnotations.setEnabled(setVisible);
3254 this.showAllAlAnnotations.setEnabled(setVisible);
3255 this.hideAllAlAnnotations.setEnabled(setVisible);
3256 alignPanel.updateLayout();
3260 public void alignmentProperties()
3262 JEditorPane editPane = new JEditorPane("text/html", "");
3263 editPane.setEditable(false);
3264 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3266 editPane.setText(MessageManager.formatMessage("label.html_content",
3267 new Object[] { contents.toString() }));
3268 JInternalFrame frame = new JInternalFrame();
3269 frame.getContentPane().add(new JScrollPane(editPane));
3271 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3272 "label.alignment_properties", new Object[] { getTitle() }),
3283 public void overviewMenuItem_actionPerformed(ActionEvent e)
3285 if (alignPanel.overviewPanel != null)
3290 JInternalFrame frame = new JInternalFrame();
3291 OverviewPanel overview = new OverviewPanel(alignPanel);
3292 frame.setContentPane(overview);
3293 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3294 "label.overview_params", new Object[] { this.getTitle() }),
3295 frame.getWidth(), frame.getHeight());
3297 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3298 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3301 public void internalFrameClosed(
3302 javax.swing.event.InternalFrameEvent evt)
3304 alignPanel.setOverviewPanel(null);
3308 alignPanel.setOverviewPanel(overview);
3312 public void textColour_actionPerformed(ActionEvent e)
3314 new TextColourChooser().chooseColour(alignPanel, null);
3324 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3336 public void clustalColour_actionPerformed(ActionEvent e)
3338 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3339 viewport.getHiddenRepSequences()));
3349 public void zappoColour_actionPerformed(ActionEvent e)
3351 changeColour(new ZappoColourScheme());
3361 public void taylorColour_actionPerformed(ActionEvent e)
3363 changeColour(new TaylorColourScheme());
3373 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3375 changeColour(new HydrophobicColourScheme());
3385 public void helixColour_actionPerformed(ActionEvent e)
3387 changeColour(new HelixColourScheme());
3397 public void strandColour_actionPerformed(ActionEvent e)
3399 changeColour(new StrandColourScheme());
3409 public void turnColour_actionPerformed(ActionEvent e)
3411 changeColour(new TurnColourScheme());
3421 public void buriedColour_actionPerformed(ActionEvent e)
3423 changeColour(new BuriedColourScheme());
3433 public void nucleotideColour_actionPerformed(ActionEvent e)
3435 changeColour(new NucleotideColourScheme());
3439 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3441 changeColour(new PurinePyrimidineColourScheme());
3445 * public void covariationColour_actionPerformed(ActionEvent e) {
3447 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3451 public void annotationColour_actionPerformed(ActionEvent e)
3453 new AnnotationColourChooser(viewport, alignPanel);
3457 public void annotationColumn_actionPerformed(ActionEvent e)
3459 new AnnotationColumnChooser(viewport, alignPanel);
3463 public void rnahelicesColour_actionPerformed(ActionEvent e)
3465 new RNAHelicesColourChooser(viewport, alignPanel);
3475 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3477 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3487 public void changeColour(ColourSchemeI cs)
3489 // TODO: pull up to controller method
3493 // Make sure viewport is up to date w.r.t. any sliders
3494 if (viewport.getAbovePIDThreshold())
3496 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3498 viewport.setThreshold(threshold);
3501 if (viewport.getConservationSelected())
3503 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3506 if (cs instanceof TCoffeeColourScheme)
3508 tcoffeeColour.setEnabled(true);
3509 tcoffeeColour.setSelected(true);
3513 viewport.setGlobalColourScheme(cs);
3515 alignPanel.paintAlignment(true);
3525 protected void modifyPID_actionPerformed(ActionEvent e)
3527 if (viewport.getAbovePIDThreshold()
3528 && viewport.getGlobalColourScheme() != null)
3530 SliderPanel.setPIDSliderSource(alignPanel,
3531 viewport.getGlobalColourScheme(), "Background");
3532 SliderPanel.showPIDSlider();
3543 protected void modifyConservation_actionPerformed(ActionEvent e)
3545 if (viewport.getConservationSelected()
3546 && viewport.getGlobalColourScheme() != null)
3548 SliderPanel.setConservationSlider(alignPanel,
3549 viewport.getGlobalColourScheme(), "Background");
3550 SliderPanel.showConservationSlider();
3561 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3563 viewport.setConservationSelected(conservationMenuItem.isSelected());
3565 viewport.setAbovePIDThreshold(false);
3566 abovePIDThreshold.setSelected(false);
3568 changeColour(viewport.getGlobalColourScheme());
3570 modifyConservation_actionPerformed(null);
3580 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3582 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3584 conservationMenuItem.setSelected(false);
3585 viewport.setConservationSelected(false);
3587 changeColour(viewport.getGlobalColourScheme());
3589 modifyPID_actionPerformed(null);
3599 public void userDefinedColour_actionPerformed(ActionEvent e)
3601 if (e.getActionCommand().equals(
3602 MessageManager.getString("action.user_defined")))
3604 new UserDefinedColours(alignPanel, null);
3608 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3609 .getUserColourSchemes().get(e.getActionCommand());
3615 public void updateUserColourMenu()
3618 Component[] menuItems = colourMenu.getMenuComponents();
3619 int iSize = menuItems.length;
3620 for (int i = 0; i < iSize; i++)
3622 if (menuItems[i].getName() != null
3623 && menuItems[i].getName().equals("USER_DEFINED"))
3625 colourMenu.remove(menuItems[i]);
3629 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3631 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3632 .getUserColourSchemes().keys();
3634 while (userColours.hasMoreElements())
3636 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3637 userColours.nextElement().toString());
3638 radioItem.setName("USER_DEFINED");
3639 radioItem.addMouseListener(new MouseAdapter()
3642 public void mousePressed(MouseEvent evt)
3644 if (evt.isPopupTrigger())
3646 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3648 int option = JOptionPane.showInternalConfirmDialog(
3649 jalview.gui.Desktop.desktop,
3651 .getString("label.remove_from_default_list"),
3653 .getString("label.remove_user_defined_colour"),
3654 JOptionPane.YES_NO_OPTION);
3655 if (option == JOptionPane.YES_OPTION)
3657 jalview.gui.UserDefinedColours
3658 .removeColourFromDefaults(radioItem.getText());
3659 colourMenu.remove(radioItem);
3663 radioItem.addActionListener(new ActionListener()
3666 public void actionPerformed(ActionEvent evt)
3668 userDefinedColour_actionPerformed(evt);
3675 radioItem.addActionListener(new ActionListener()
3678 public void actionPerformed(ActionEvent evt)
3680 userDefinedColour_actionPerformed(evt);
3684 colourMenu.insert(radioItem, 15);
3685 colours.add(radioItem);
3697 public void PIDColour_actionPerformed(ActionEvent e)
3699 changeColour(new PIDColourScheme());
3709 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3711 changeColour(new Blosum62ColourScheme());
3721 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3723 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3724 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3725 .getAlignment().getSequenceAt(0), null);
3726 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3727 viewport.getAlignment()));
3728 alignPanel.paintAlignment(true);
3738 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3740 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3741 AlignmentSorter.sortByID(viewport.getAlignment());
3742 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3743 viewport.getAlignment()));
3744 alignPanel.paintAlignment(true);
3754 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3756 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3757 AlignmentSorter.sortByLength(viewport.getAlignment());
3758 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3759 viewport.getAlignment()));
3760 alignPanel.paintAlignment(true);
3770 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3772 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3773 AlignmentSorter.sortByGroup(viewport.getAlignment());
3774 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3775 viewport.getAlignment()));
3777 alignPanel.paintAlignment(true);
3787 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3789 new RedundancyPanel(alignPanel, this);
3799 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3801 if ((viewport.getSelectionGroup() == null)
3802 || (viewport.getSelectionGroup().getSize() < 2))
3804 JOptionPane.showInternalMessageDialog(this, MessageManager
3805 .getString("label.you_must_select_least_two_sequences"),
3806 MessageManager.getString("label.invalid_selection"),
3807 JOptionPane.WARNING_MESSAGE);
3811 JInternalFrame frame = new JInternalFrame();
3812 frame.setContentPane(new PairwiseAlignPanel(viewport));
3813 Desktop.addInternalFrame(frame,
3814 MessageManager.getString("action.pairwise_alignment"), 600,
3826 public void PCAMenuItem_actionPerformed(ActionEvent e)
3828 if (((viewport.getSelectionGroup() != null)
3829 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3830 .getSelectionGroup().getSize() > 0))
3831 || (viewport.getAlignment().getHeight() < 4))
3834 .showInternalMessageDialog(
3837 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3839 .getString("label.sequence_selection_insufficient"),
3840 JOptionPane.WARNING_MESSAGE);
3845 new PCAPanel(alignPanel);
3849 public void autoCalculate_actionPerformed(ActionEvent e)
3851 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3852 if (viewport.autoCalculateConsensus)
3854 viewport.firePropertyChange("alignment", null, viewport
3855 .getAlignment().getSequences());
3860 public void sortByTreeOption_actionPerformed(ActionEvent e)
3862 viewport.sortByTree = sortByTree.isSelected();
3866 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3868 viewport.followSelection = listenToViewSelections.isSelected();
3878 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3880 newTreePanel("AV", "PID", "Average distance tree using PID");
3890 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3892 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3902 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3904 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3914 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3916 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3929 void newTreePanel(String type, String pwType, String title)
3933 if (viewport.getSelectionGroup() != null
3934 && viewport.getSelectionGroup().getSize() > 0)
3936 if (viewport.getSelectionGroup().getSize() < 3)
3942 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3944 .getString("label.not_enough_sequences"),
3945 JOptionPane.WARNING_MESSAGE);
3949 SequenceGroup sg = viewport.getSelectionGroup();
3951 /* Decide if the selection is a column region */
3952 for (SequenceI _s : sg.getSequences())
3954 if (_s.getLength() < sg.getEndRes())
3960 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3962 .getString("label.sequences_selection_not_aligned"),
3963 JOptionPane.WARNING_MESSAGE);
3969 title = title + " on region";
3970 tp = new TreePanel(alignPanel, type, pwType);
3974 // are the visible sequences aligned?
3975 if (!viewport.getAlignment().isAligned(false))
3981 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3983 .getString("label.sequences_not_aligned"),
3984 JOptionPane.WARNING_MESSAGE);
3989 if (viewport.getAlignment().getHeight() < 2)
3994 tp = new TreePanel(alignPanel, type, pwType);
3999 if (viewport.viewName != null)
4001 title += viewport.viewName + " of ";
4004 title += this.title;
4006 Desktop.addInternalFrame(tp, title, 600, 500);
4017 public void addSortByOrderMenuItem(String title,
4018 final AlignmentOrder order)
4020 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4021 "action.by_title_param", new Object[] { title }));
4023 item.addActionListener(new java.awt.event.ActionListener()
4026 public void actionPerformed(ActionEvent e)
4028 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4030 // TODO: JBPNote - have to map order entries to curent SequenceI
4032 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4034 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4037 alignPanel.paintAlignment(true);
4043 * Add a new sort by annotation score menu item
4046 * the menu to add the option to
4048 * the label used to retrieve scores for each sequence on the
4051 public void addSortByAnnotScoreMenuItem(JMenu sort,
4052 final String scoreLabel)
4054 final JMenuItem item = new JMenuItem(scoreLabel);
4056 item.addActionListener(new java.awt.event.ActionListener()
4059 public void actionPerformed(ActionEvent e)
4061 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4062 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4063 viewport.getAlignment());// ,viewport.getSelectionGroup());
4064 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4065 viewport.getAlignment()));
4066 alignPanel.paintAlignment(true);
4072 * last hash for alignment's annotation array - used to minimise cost of
4075 protected int _annotationScoreVectorHash;
4078 * search the alignment and rebuild the sort by annotation score submenu the
4079 * last alignment annotation vector hash is stored to minimize cost of
4080 * rebuilding in subsequence calls.
4084 public void buildSortByAnnotationScoresMenu()
4086 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4091 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4093 sortByAnnotScore.removeAll();
4094 // almost certainly a quicker way to do this - but we keep it simple
4095 Hashtable scoreSorts = new Hashtable();
4096 AlignmentAnnotation aann[];
4097 for (SequenceI sqa : viewport.getAlignment().getSequences())
4099 aann = sqa.getAnnotation();
4100 for (int i = 0; aann != null && i < aann.length; i++)
4102 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4104 scoreSorts.put(aann[i].label, aann[i].label);
4108 Enumeration labels = scoreSorts.keys();
4109 while (labels.hasMoreElements())
4111 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4112 (String) labels.nextElement());
4114 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4117 _annotationScoreVectorHash = viewport.getAlignment()
4118 .getAlignmentAnnotation().hashCode();
4123 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4124 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4125 * call. Listeners are added to remove the menu item when the treePanel is
4126 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4130 * Displayed tree window.
4132 * SortBy menu item title.
4135 public void buildTreeMenu()
4137 calculateTree.removeAll();
4138 // build the calculate menu
4140 for (final String type : new String[] { "NJ", "AV" })
4142 String treecalcnm = MessageManager.getString("label.tree_calc_"
4143 + type.toLowerCase());
4144 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4146 JMenuItem tm = new JMenuItem();
4147 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4148 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4149 || sm.isProtein() == !viewport.getAlignment()
4152 String smn = MessageManager.getStringOrReturn(
4153 "label.score_model_", sm.getName());
4154 final String title = MessageManager.formatMessage(
4155 "label.treecalc_title", treecalcnm, smn);
4156 tm.setText(title);//
4157 tm.addActionListener(new java.awt.event.ActionListener()
4160 public void actionPerformed(ActionEvent e)
4162 newTreePanel(type, pwtype, title);
4165 calculateTree.add(tm);
4170 sortByTreeMenu.removeAll();
4172 List<Component> comps = PaintRefresher.components.get(viewport
4173 .getSequenceSetId());
4174 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4175 for (Component comp : comps)
4177 if (comp instanceof TreePanel)
4179 treePanels.add((TreePanel) comp);
4183 if (treePanels.size() < 1)
4185 sortByTreeMenu.setVisible(false);
4189 sortByTreeMenu.setVisible(true);
4191 for (final TreePanel tp : treePanels)
4193 final JMenuItem item = new JMenuItem(tp.getTitle());
4194 item.addActionListener(new java.awt.event.ActionListener()
4197 public void actionPerformed(ActionEvent e)
4199 tp.sortByTree_actionPerformed();
4200 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4205 sortByTreeMenu.add(item);
4209 public boolean sortBy(AlignmentOrder alorder, String undoname)
4211 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4212 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4213 if (undoname != null)
4215 addHistoryItem(new OrderCommand(undoname, oldOrder,
4216 viewport.getAlignment()));
4218 alignPanel.paintAlignment(true);
4223 * Work out whether the whole set of sequences or just the selected set will
4224 * be submitted for multiple alignment.
4227 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4229 // Now, check we have enough sequences
4230 AlignmentView msa = null;
4232 if ((viewport.getSelectionGroup() != null)
4233 && (viewport.getSelectionGroup().getSize() > 1))
4235 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4236 // some common interface!
4238 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4239 * SequenceI[sz = seqs.getSize(false)];
4241 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4242 * seqs.getSequenceAt(i); }
4244 msa = viewport.getAlignmentView(true);
4246 else if (viewport.getSelectionGroup() != null
4247 && viewport.getSelectionGroup().getSize() == 1)
4249 int option = JOptionPane.showConfirmDialog(this,
4250 MessageManager.getString("warn.oneseq_msainput_selection"),
4251 MessageManager.getString("label.invalid_selection"),
4252 JOptionPane.OK_CANCEL_OPTION);
4253 if (option == JOptionPane.OK_OPTION)
4255 msa = viewport.getAlignmentView(false);
4260 msa = viewport.getAlignmentView(false);
4266 * Decides what is submitted to a secondary structure prediction service: the
4267 * first sequence in the alignment, or in the current selection, or, if the
4268 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4269 * region or the whole alignment. (where the first sequence in the set is the
4270 * one that the prediction will be for).
4272 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4274 AlignmentView seqs = null;
4276 if ((viewport.getSelectionGroup() != null)
4277 && (viewport.getSelectionGroup().getSize() > 0))
4279 seqs = viewport.getAlignmentView(true);
4283 seqs = viewport.getAlignmentView(false);
4285 // limit sequences - JBPNote in future - could spawn multiple prediction
4287 // TODO: viewport.getAlignment().isAligned is a global state - the local
4288 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4289 if (!viewport.getAlignment().isAligned(false))
4291 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4292 // TODO: if seqs.getSequences().length>1 then should really have warned
4306 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4308 // Pick the tree file
4309 JalviewFileChooser chooser = new JalviewFileChooser(
4310 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4311 chooser.setFileView(new JalviewFileView());
4312 chooser.setDialogTitle(MessageManager
4313 .getString("label.select_newick_like_tree_file"));
4314 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4316 int value = chooser.showOpenDialog(null);
4318 if (value == JalviewFileChooser.APPROVE_OPTION)
4320 String choice = chooser.getSelectedFile().getPath();
4321 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4322 jalview.io.NewickFile fin = null;
4325 fin = new jalview.io.NewickFile(choice, "File");
4326 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4327 } catch (Exception ex)
4334 .getString("label.problem_reading_tree_file"),
4335 JOptionPane.WARNING_MESSAGE);
4336 ex.printStackTrace();
4338 if (fin != null && fin.hasWarningMessage())
4340 JOptionPane.showMessageDialog(Desktop.desktop, fin
4341 .getWarningMessage(), MessageManager
4342 .getString("label.possible_problem_with_tree_file"),
4343 JOptionPane.WARNING_MESSAGE);
4349 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4351 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4354 public TreePanel ShowNewickTree(NewickFile nf, String title)
4356 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4359 public TreePanel ShowNewickTree(NewickFile nf, String title,
4360 AlignmentView input)
4362 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4365 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4366 int h, int x, int y)
4368 return ShowNewickTree(nf, title, null, w, h, x, y);
4372 * Add a treeviewer for the tree extracted from a newick file object to the
4373 * current alignment view
4380 * Associated alignment input data (or null)
4389 * @return TreePanel handle
4391 public TreePanel ShowNewickTree(NewickFile nf, String title,
4392 AlignmentView input, int w, int h, int x, int y)
4394 TreePanel tp = null;
4400 if (nf.getTree() != null)
4402 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4408 tp.setLocation(x, y);
4411 Desktop.addInternalFrame(tp, title, w, h);
4413 } catch (Exception ex)
4415 ex.printStackTrace();
4421 private boolean buildingMenu = false;
4424 * Generates menu items and listener event actions for web service clients
4427 public void BuildWebServiceMenu()
4429 while (buildingMenu)
4433 System.err.println("Waiting for building menu to finish.");
4435 } catch (Exception e)
4439 final AlignFrame me = this;
4440 buildingMenu = true;
4441 new Thread(new Runnable()
4446 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4449 // System.err.println("Building ws menu again "
4450 // + Thread.currentThread());
4451 // TODO: add support for context dependent disabling of services based
4453 // alignment and current selection
4454 // TODO: add additional serviceHandle parameter to specify abstract
4456 // class independently of AbstractName
4457 // TODO: add in rediscovery GUI function to restart discoverer
4458 // TODO: group services by location as well as function and/or
4460 // object broker mechanism.
4461 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4462 final IProgressIndicator af = me;
4463 final JMenu msawsmenu = new JMenu("Alignment");
4464 final JMenu secstrmenu = new JMenu(
4465 "Secondary Structure Prediction");
4466 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4467 final JMenu analymenu = new JMenu("Analysis");
4468 final JMenu dismenu = new JMenu("Protein Disorder");
4469 // final JMenu msawsmenu = new
4470 // JMenu(MessageManager.getString("label.alignment"));
4471 // final JMenu secstrmenu = new
4472 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4473 // final JMenu seqsrchmenu = new
4474 // JMenu(MessageManager.getString("label.sequence_database_search"));
4475 // final JMenu analymenu = new
4476 // JMenu(MessageManager.getString("label.analysis"));
4477 // final JMenu dismenu = new
4478 // JMenu(MessageManager.getString("label.protein_disorder"));
4479 // JAL-940 - only show secondary structure prediction services from
4480 // the legacy server
4481 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4483 Discoverer.services != null && (Discoverer.services.size() > 0))
4485 // TODO: refactor to allow list of AbstractName/Handler bindings to
4487 // stored or retrieved from elsewhere
4488 // No MSAWS used any more:
4489 // Vector msaws = null; // (Vector)
4490 // Discoverer.services.get("MsaWS");
4491 Vector secstrpr = (Vector) Discoverer.services
4493 if (secstrpr != null)
4495 // Add any secondary structure prediction services
4496 for (int i = 0, j = secstrpr.size(); i < j; i++)
4498 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4500 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4501 .getServiceClient(sh);
4502 int p = secstrmenu.getItemCount();
4503 impl.attachWSMenuEntry(secstrmenu, me);
4504 int q = secstrmenu.getItemCount();
4505 for (int litm = p; litm < q; litm++)
4507 legacyItems.add(secstrmenu.getItem(litm));
4513 // Add all submenus in the order they should appear on the web
4515 wsmenu.add(msawsmenu);
4516 wsmenu.add(secstrmenu);
4517 wsmenu.add(dismenu);
4518 wsmenu.add(analymenu);
4519 // No search services yet
4520 // wsmenu.add(seqsrchmenu);
4522 javax.swing.SwingUtilities.invokeLater(new Runnable()
4529 webService.removeAll();
4530 // first, add discovered services onto the webservices menu
4531 if (wsmenu.size() > 0)
4533 for (int i = 0, j = wsmenu.size(); i < j; i++)
4535 webService.add(wsmenu.get(i));
4540 webService.add(me.webServiceNoServices);
4542 // TODO: move into separate menu builder class.
4543 boolean new_sspred = false;
4544 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4546 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4547 if (jws2servs != null)
4549 if (jws2servs.hasServices())
4551 jws2servs.attachWSMenuEntry(webService, me);
4552 for (Jws2Instance sv : jws2servs.getServices())
4554 if (sv.description.toLowerCase().contains("jpred"))
4556 for (JMenuItem jmi : legacyItems)
4558 jmi.setVisible(false);
4564 if (jws2servs.isRunning())
4566 JMenuItem tm = new JMenuItem(
4567 "Still discovering JABA Services");
4568 tm.setEnabled(false);
4573 build_urlServiceMenu(me.webService);
4574 build_fetchdbmenu(webService);
4575 for (JMenu item : wsmenu)
4577 if (item.getItemCount() == 0)
4579 item.setEnabled(false);
4583 item.setEnabled(true);
4586 } catch (Exception e)
4589 .debug("Exception during web service menu building process.",
4594 } catch (Exception e)
4597 buildingMenu = false;
4604 * construct any groupURL type service menu entries.
4608 private void build_urlServiceMenu(JMenu webService)
4610 // TODO: remove this code when 2.7 is released
4611 // DEBUG - alignmentView
4613 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4614 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4616 * @Override public void actionPerformed(ActionEvent e) {
4617 * jalview.datamodel.AlignmentView
4618 * .testSelectionViews(af.viewport.getAlignment(),
4619 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4621 * }); webService.add(testAlView);
4623 // TODO: refactor to RestClient discoverer and merge menu entries for
4624 // rest-style services with other types of analysis/calculation service
4625 // SHmmr test client - still being implemented.
4626 // DEBUG - alignmentView
4628 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4631 client.attachWSMenuEntry(
4632 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4638 * Searches selected sequences for xRef products and builds the Show
4639 * Cross-References menu (formerly called Show Products)
4641 * @return true if Show Cross-references menu should be enabled.
4643 public boolean canShowProducts()
4645 SequenceI[] selection = viewport.getSequenceSelection();
4646 AlignmentI dataset = viewport.getAlignment().getDataset();
4647 boolean showp = false;
4650 showProducts.removeAll();
4651 final boolean dna = viewport.getAlignment().isNucleotide();
4652 String[] ptypes = (selection == null || selection.length == 0) ? null
4653 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4655 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4658 final AlignFrame af = this;
4659 final String source = ptypes[t];
4660 JMenuItem xtype = new JMenuItem(ptypes[t]);
4661 xtype.addActionListener(new ActionListener()
4665 public void actionPerformed(ActionEvent e)
4667 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4671 showProducts.add(xtype);
4673 showProducts.setVisible(showp);
4674 showProducts.setEnabled(showp);
4675 } catch (Exception e)
4677 jalview.bin.Cache.log
4678 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4685 protected void showProductsFor(final SequenceI[] sel, final boolean dna,
4686 final String source)
4688 Runnable foo = new Runnable()
4694 final long sttime = System.currentTimeMillis();
4695 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4696 "status.searching_for_sequences_from",
4697 new Object[] { source }), sttime);
4700 AlignmentI alignment = AlignFrame.this.getViewport()
4702 AlignmentI xrefs = CrossRef.findXrefSequences(sel, dna, source,
4707 * get display scheme (if any) to apply to features
4709 FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
4710 .getFeatureColourScheme(source);
4712 AlignmentI al = makeCrossReferencesAlignment(
4713 alignment.getDataset(), xrefs);
4715 AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
4717 if (Cache.getDefault("HIDE_INTRONS", true))
4719 newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
4721 String newtitle = String.format("%s %s %s",
4722 MessageManager.getString(dna ? "label.proteins"
4723 : "label.nucleotides"), MessageManager
4724 .getString("label.for"), getTitle());
4725 newFrame.setTitle(newtitle);
4727 if (!Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4730 * split frame display is turned off in preferences file
4732 Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4734 return; // via finally clause
4738 * Make a copy of this alignment (sharing the same dataset
4739 * sequences). If we are DNA, drop introns and update mappings
4741 AlignmentI copyAlignment = null;
4742 final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4743 .getSequenceSelection();
4744 List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4745 boolean copyAlignmentIsAligned = false;
4748 copyAlignment = AlignmentUtils.makeCdsAlignment(
4749 sequenceSelection, cf, alignment);
4750 if (copyAlignment.getHeight() == 0)
4752 System.err.println("Failed to make CDS alignment");
4754 al.getCodonFrames().clear();
4755 al.getCodonFrames().addAll(copyAlignment.getCodonFrames());
4758 * pending getting Embl transcripts to 'align',
4759 * we are only doing this for Ensembl
4761 // TODO proper criteria for 'can align as cdna'
4762 if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
4763 || AlignmentUtils.looksLikeEnsembl(alignment))
4765 copyAlignment.alignAs(alignment);
4766 copyAlignmentIsAligned = true;
4771 copyAlignment = AlignmentUtils.makeCopyAlignment(
4772 sequenceSelection, xrefs.getSequencesArray());
4773 copyAlignment.getCodonFrames().addAll(cf);
4775 copyAlignment.setGapCharacter(AlignFrame.this.viewport
4776 .getGapCharacter());
4778 StructureSelectionManager ssm = StructureSelectionManager
4779 .getStructureSelectionManager(Desktop.instance);
4780 ssm.registerMappings(cf);
4782 if (copyAlignment.getHeight() <= 0)
4784 System.err.println("No Sequences generated for xRef type "
4789 * align protein to dna
4791 if (dna && copyAlignmentIsAligned)
4793 al.alignAs(copyAlignment);
4798 * align cdna to protein - currently only if
4799 * fetching and aligning Ensembl transcripts!
4801 if (DBRefSource.ENSEMBL.equalsIgnoreCase(source))
4803 copyAlignment.alignAs(al);
4807 AlignFrame copyThis = new AlignFrame(copyAlignment,
4808 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4809 copyThis.setTitle(AlignFrame.this.getTitle());
4811 boolean showSequenceFeatures = viewport
4812 .isShowSequenceFeatures();
4813 newFrame.setShowSeqFeatures(showSequenceFeatures);
4814 copyThis.setShowSeqFeatures(showSequenceFeatures);
4815 FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4816 .getFeatureRenderer();
4819 * copy feature rendering settings to split frame
4821 newFrame.alignPanel.getSeqPanel().seqCanvas
4822 .getFeatureRenderer()
4823 .transferSettings(myFeatureStyling);
4824 copyThis.alignPanel.getSeqPanel().seqCanvas
4825 .getFeatureRenderer()
4826 .transferSettings(myFeatureStyling);
4829 * apply 'database source' feature configuration
4832 // TODO is this the feature colouring for the original
4833 // alignment or the fetched xrefs? either could be Ensembl
4834 newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
4835 copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
4837 SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4838 dna ? newFrame : copyThis);
4839 newFrame.setVisible(true);
4840 copyThis.setVisible(true);
4841 String linkedTitle = MessageManager
4842 .getString("label.linked_view_title");
4843 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4846 } catch (Exception e)
4849 "Exception when finding crossreferences", e);
4850 } catch (OutOfMemoryError e)
4852 new OOMWarning("whilst fetching crossreferences", e);
4853 } catch (Throwable e)
4855 Cache.log.error("Error when finding crossreferences",
4859 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4860 "status.finished_searching_for_sequences_from",
4861 new Object[] { source }), sttime);
4866 * Makes an alignment containing the given sequences. If this is of the
4867 * same type as the given dataset (nucleotide/protein), then the new
4868 * alignment shares the same dataset, and its dataset sequences are added
4869 * to it. Otherwise a new dataset sequence is created for the
4876 protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
4879 boolean sameType = dataset.isNucleotide() == seqs.isNucleotide();
4881 SequenceI[] sprods = new SequenceI[seqs.getHeight()];
4882 for (int s = 0; s < sprods.length; s++)
4884 sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
4887 if (dataset.getSequences() == null
4888 || !dataset.getSequences().contains(
4889 sprods[s].getDatasetSequence()))
4891 dataset.addSequence(sprods[s].getDatasetSequence());
4894 sprods[s].updatePDBIds();
4896 Alignment al = new Alignment(sprods);
4899 al.setDataset((Alignment) dataset);
4903 al.createDatasetAlignment();
4909 Thread frunner = new Thread(foo);
4914 * Construct and display a new frame containing the translation of this
4915 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4918 public void showTranslation_actionPerformed(ActionEvent e)
4920 AlignmentI al = null;
4923 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4925 al = dna.translateCdna();
4926 } catch (Exception ex)
4928 jalview.bin.Cache.log.error(
4929 "Exception during translation. Please report this !", ex);
4930 final String msg = MessageManager
4931 .getString("label.error_when_translating_sequences_submit_bug_report");
4932 final String errorTitle = MessageManager
4933 .getString("label.implementation_error")
4934 + MessageManager.getString("translation_failed");
4935 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4936 JOptionPane.ERROR_MESSAGE);
4939 if (al == null || al.getHeight() == 0)
4941 final String msg = MessageManager
4942 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4943 final String errorTitle = MessageManager
4944 .getString("label.translation_failed");
4945 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4946 JOptionPane.WARNING_MESSAGE);
4950 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4951 af.setFileFormat(this.currentFileFormat);
4952 final String newTitle = MessageManager.formatMessage(
4953 "label.translation_of_params",
4954 new Object[] { this.getTitle() });
4955 af.setTitle(newTitle);
4956 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4958 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4959 viewport.openSplitFrame(af, new Alignment(seqs));
4963 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4970 * Set the file format
4974 public void setFileFormat(String fileFormat)
4976 this.currentFileFormat = fileFormat;
4980 * Try to load a features file onto the alignment.
4983 * contents or path to retrieve file
4985 * access mode of file (see jalview.io.AlignFile)
4986 * @return true if features file was parsed correctly.
4988 public boolean parseFeaturesFile(String file, String type)
4990 return avc.parseFeaturesFile(file, type,
4991 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4996 public void refreshFeatureUI(boolean enableIfNecessary)
4998 // note - currently this is only still here rather than in the controller
4999 // because of the featureSettings hard reference that is yet to be
5001 if (enableIfNecessary)
5003 viewport.setShowSequenceFeatures(true);
5004 showSeqFeatures.setSelected(true);
5010 public void dragEnter(DropTargetDragEvent evt)
5015 public void dragExit(DropTargetEvent evt)
5020 public void dragOver(DropTargetDragEvent evt)
5025 public void dropActionChanged(DropTargetDragEvent evt)
5030 public void drop(DropTargetDropEvent evt)
5032 Transferable t = evt.getTransferable();
5033 java.util.List files = null;
5037 DataFlavor uriListFlavor = new DataFlavor(
5038 "text/uri-list;class=java.lang.String");
5039 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5041 // Works on Windows and MacOSX
5042 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5043 files = (java.util.List) t
5044 .getTransferData(DataFlavor.javaFileListFlavor);
5046 else if (t.isDataFlavorSupported(uriListFlavor))
5048 // This is used by Unix drag system
5049 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5050 String data = (String) t.getTransferData(uriListFlavor);
5051 files = new java.util.ArrayList(1);
5052 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5053 data, "\r\n"); st.hasMoreTokens();)
5055 String s = st.nextToken();
5056 if (s.startsWith("#"))
5058 // the line is a comment (as per the RFC 2483)
5062 java.net.URI uri = new java.net.URI(s);
5063 // check to see if we can handle this kind of URI
5064 if (uri.getScheme().toLowerCase().startsWith("http"))
5066 files.add(uri.toString());
5070 // otherwise preserve old behaviour: catch all for file objects
5071 java.io.File file = new java.io.File(uri);
5072 files.add(file.toString());
5076 } catch (Exception e)
5078 e.printStackTrace();
5084 // check to see if any of these files have names matching sequences in
5086 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5087 .getAlignment().getSequencesArray());
5089 * Object[] { String,SequenceI}
5091 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5092 ArrayList<String> filesnotmatched = new ArrayList<String>();
5093 for (int i = 0; i < files.size(); i++)
5095 String file = files.get(i).toString();
5097 String protocol = FormatAdapter.checkProtocol(file);
5098 if (protocol == jalview.io.FormatAdapter.FILE)
5100 File fl = new File(file);
5101 pdbfn = fl.getName();
5103 else if (protocol == jalview.io.FormatAdapter.URL)
5105 URL url = new URL(file);
5106 pdbfn = url.getFile();
5108 if (pdbfn.length() > 0)
5110 // attempt to find a match in the alignment
5111 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5112 int l = 0, c = pdbfn.indexOf(".");
5113 while (mtch == null && c != -1)
5118 } while ((c = pdbfn.indexOf(".", l)) > l);
5121 pdbfn = pdbfn.substring(0, l);
5123 mtch = idm.findAllIdMatches(pdbfn);
5130 type = new IdentifyFile().identify(file, protocol);
5131 } catch (Exception ex)
5137 if (type.equalsIgnoreCase("PDB"))
5139 filesmatched.add(new Object[] { file, protocol, mtch });
5144 // File wasn't named like one of the sequences or wasn't a PDB file.
5145 filesnotmatched.add(file);
5149 if (filesmatched.size() > 0)
5151 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5157 "label.automatically_associate_pdb_files_with_sequences_same_name",
5158 new Object[] { Integer
5164 .getString("label.automatically_associate_pdb_files_by_name"),
5165 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5168 for (Object[] fm : filesmatched)
5170 // try and associate
5171 // TODO: may want to set a standard ID naming formalism for
5172 // associating PDB files which have no IDs.
5173 for (SequenceI toassoc : (SequenceI[]) fm[2])
5175 PDBEntry pe = new AssociatePdbFileWithSeq()
5176 .associatePdbWithSeq((String) fm[0],
5177 (String) fm[1], toassoc, false,
5181 System.err.println("Associated file : "
5182 + ((String) fm[0]) + " with "
5183 + toassoc.getDisplayId(true));
5187 alignPanel.paintAlignment(true);
5191 if (filesnotmatched.size() > 0)
5194 && (Cache.getDefault(
5195 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5201 "label.ignore_unmatched_dropped_files_info",
5202 new Object[] { Integer
5209 .getString("label.ignore_unmatched_dropped_files"),
5210 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5214 for (String fn : filesnotmatched)
5216 loadJalviewDataFile(fn, null, null, null);
5220 } catch (Exception ex)
5222 ex.printStackTrace();
5228 * Attempt to load a "dropped" file or URL string: First by testing whether
5229 * it's an Annotation file, then a JNet file, and finally a features file. If
5230 * all are false then the user may have dropped an alignment file onto this
5234 * either a filename or a URL string.
5236 public void loadJalviewDataFile(String file, String protocol,
5237 String format, SequenceI assocSeq)
5241 if (protocol == null)
5243 protocol = FormatAdapter.checkProtocol(file);
5245 // if the file isn't identified, or not positively identified as some
5246 // other filetype (PFAM is default unidentified alignment file type) then
5247 // try to parse as annotation.
5248 boolean isAnnotation = (format == null || format
5249 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5250 .annotateAlignmentView(viewport, file, protocol) : false;
5254 // first see if its a T-COFFEE score file
5255 TCoffeeScoreFile tcf = null;
5258 tcf = new TCoffeeScoreFile(file, protocol);
5261 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5263 tcoffeeColour.setEnabled(true);
5264 tcoffeeColour.setSelected(true);
5265 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5266 isAnnotation = true;
5268 .setText(MessageManager
5269 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5273 // some problem - if no warning its probable that the ID matching
5274 // process didn't work
5278 tcf.getWarningMessage() == null ? MessageManager
5279 .getString("label.check_file_matches_sequence_ids_alignment")
5280 : tcf.getWarningMessage(),
5282 .getString("label.problem_reading_tcoffee_score_file"),
5283 JOptionPane.WARNING_MESSAGE);
5290 } catch (Exception x)
5293 .debug("Exception when processing data source as T-COFFEE score file",
5299 // try to see if its a JNet 'concise' style annotation file *before*
5301 // try to parse it as a features file
5304 format = new IdentifyFile().identify(file, protocol);
5306 if (format.equalsIgnoreCase("JnetFile"))
5308 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5310 new JnetAnnotationMaker();
5311 JnetAnnotationMaker.add_annotation(predictions,
5312 viewport.getAlignment(), 0, false);
5313 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5314 viewport.getAlignment().setSeqrep(repseq);
5315 ColumnSelection cs = new ColumnSelection();
5316 cs.hideInsertionsFor(repseq);
5317 viewport.setColumnSelection(cs);
5318 isAnnotation = true;
5320 else if (IdentifyFile.FeaturesFile.equals(format))
5322 if (parseFeaturesFile(file, protocol))
5324 alignPanel.paintAlignment(true);
5329 new FileLoader().LoadFile(viewport, file, protocol, format);
5336 alignPanel.adjustAnnotationHeight();
5337 viewport.updateSequenceIdColours();
5338 buildSortByAnnotationScoresMenu();
5339 alignPanel.paintAlignment(true);
5341 } catch (Exception ex)
5343 ex.printStackTrace();
5344 } catch (OutOfMemoryError oom)
5349 } catch (Exception x)
5354 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5355 : "using " + protocol + " from " + file)
5357 + (format != null ? "(parsing as '" + format
5358 + "' file)" : ""), oom, Desktop.desktop);
5363 * Method invoked by the ChangeListener on the tabbed pane, in other words
5364 * when a different tabbed pane is selected by the user or programmatically.
5367 public void tabSelectionChanged(int index)
5371 alignPanel = alignPanels.get(index);
5372 viewport = alignPanel.av;
5373 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5374 setMenusFromViewport(viewport);
5378 * If there is a frame linked to this one in a SplitPane, switch it to the
5379 * same view tab index. No infinite recursion of calls should happen, since
5380 * tabSelectionChanged() should not get invoked on setting the selected
5381 * index to an unchanged value. Guard against setting an invalid index
5382 * before the new view peer tab has been created.
5384 final AlignViewportI peer = viewport.getCodingComplement();
5387 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5388 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5390 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5396 * On right mouse click on view tab, prompt for and set new view name.
5399 public void tabbedPane_mousePressed(MouseEvent e)
5401 if (e.isPopupTrigger())
5403 String msg = MessageManager.getString("label.enter_view_name");
5404 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5405 JOptionPane.QUESTION_MESSAGE);
5409 viewport.viewName = reply;
5410 // TODO warn if reply is in getExistingViewNames()?
5411 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5416 public AlignViewport getCurrentView()
5422 * Open the dialog for regex description parsing.
5425 protected void extractScores_actionPerformed(ActionEvent e)
5427 ParseProperties pp = new jalview.analysis.ParseProperties(
5428 viewport.getAlignment());
5429 // TODO: verify regex and introduce GUI dialog for version 2.5
5430 // if (pp.getScoresFromDescription("col", "score column ",
5431 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5433 if (pp.getScoresFromDescription("description column",
5434 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5436 buildSortByAnnotationScoresMenu();
5444 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5448 protected void showDbRefs_actionPerformed(ActionEvent e)
5450 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5456 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5460 protected void showNpFeats_actionPerformed(ActionEvent e)
5462 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5466 * find the viewport amongst the tabs in this alignment frame and close that
5471 public boolean closeView(AlignViewportI av)
5475 this.closeMenuItem_actionPerformed(false);
5478 Component[] comp = tabbedPane.getComponents();
5479 for (int i = 0; comp != null && i < comp.length; i++)
5481 if (comp[i] instanceof AlignmentPanel)
5483 if (((AlignmentPanel) comp[i]).av == av)
5486 closeView((AlignmentPanel) comp[i]);
5494 protected void build_fetchdbmenu(JMenu webService)
5496 // Temporary hack - DBRef Fetcher always top level ws entry.
5497 // TODO We probably want to store a sequence database checklist in
5498 // preferences and have checkboxes.. rather than individual sources selected
5500 final JMenu rfetch = new JMenu(
5501 MessageManager.getString("action.fetch_db_references"));
5502 rfetch.setToolTipText(MessageManager
5503 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5504 webService.add(rfetch);
5506 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5507 MessageManager.getString("option.trim_retrieved_seqs"));
5508 trimrs.setToolTipText(MessageManager
5509 .getString("label.trim_retrieved_sequences"));
5510 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5511 trimrs.addActionListener(new ActionListener()
5514 public void actionPerformed(ActionEvent e)
5516 trimrs.setSelected(trimrs.isSelected());
5517 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5518 Boolean.valueOf(trimrs.isSelected()).toString());
5522 JMenuItem fetchr = new JMenuItem(
5523 MessageManager.getString("label.standard_databases"));
5524 fetchr.setToolTipText(MessageManager
5525 .getString("label.fetch_embl_uniprot"));
5526 fetchr.addActionListener(new ActionListener()
5530 public void actionPerformed(ActionEvent e)
5532 new Thread(new Runnable()
5537 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5538 .getAlignment().isNucleotide();
5539 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5540 .getSequenceSelection(), alignPanel.alignFrame, null,
5541 alignPanel.alignFrame.featureSettings, isNucleotide);
5542 dbRefFetcher.addListener(new FetchFinishedListenerI()
5545 public void finished()
5547 AlignFrame.this.setMenusForViewport();
5551 .fetchDBRefs(false);
5559 final AlignFrame me = this;
5560 new Thread(new Runnable()
5565 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5566 .getSequenceFetcherSingleton(me);
5567 javax.swing.SwingUtilities.invokeLater(new Runnable()
5572 String[] dbclasses = sf.getOrderedSupportedSources();
5573 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5574 // jalview.util.QuickSort.sort(otherdb, otherdb);
5575 List<DbSourceProxy> otherdb;
5576 JMenu dfetch = new JMenu();
5577 JMenu ifetch = new JMenu();
5578 JMenuItem fetchr = null;
5579 int comp = 0, icomp = 0, mcomp = 15;
5580 String mname = null;
5582 for (String dbclass : dbclasses)
5584 otherdb = sf.getSourceProxy(dbclass);
5585 // add a single entry for this class, or submenu allowing 'fetch
5587 if (otherdb == null || otherdb.size() < 1)
5591 // List<DbSourceProxy> dbs=otherdb;
5592 // otherdb=new ArrayList<DbSourceProxy>();
5593 // for (DbSourceProxy db:dbs)
5595 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5599 mname = "From " + dbclass;
5601 if (otherdb.size() == 1)
5603 final DbSourceProxy[] dassource = otherdb
5604 .toArray(new DbSourceProxy[0]);
5605 DbSourceProxy src = otherdb.get(0);
5606 fetchr = new JMenuItem(src.getDbSource());
5607 fetchr.addActionListener(new ActionListener()
5611 public void actionPerformed(ActionEvent e)
5613 new Thread(new Runnable()
5619 boolean isNucleotide = alignPanel.alignFrame
5620 .getViewport().getAlignment()
5622 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5623 alignPanel.av.getSequenceSelection(),
5624 alignPanel.alignFrame, dassource,
5625 alignPanel.alignFrame.featureSettings,
5628 .addListener(new FetchFinishedListenerI()
5631 public void finished()
5633 AlignFrame.this.setMenusForViewport();
5636 dbRefFetcher.fetchDBRefs(false);
5642 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5643 MessageManager.formatMessage(
5644 "label.fetch_retrieve_from",
5645 new Object[] { src.getDbName() })));
5651 final DbSourceProxy[] dassource = otherdb
5652 .toArray(new DbSourceProxy[0]);
5654 DbSourceProxy src = otherdb.get(0);
5655 fetchr = new JMenuItem(MessageManager.formatMessage(
5656 "label.fetch_all_param",
5657 new Object[] { src.getDbSource() }));
5658 fetchr.addActionListener(new ActionListener()
5661 public void actionPerformed(ActionEvent e)
5663 new Thread(new Runnable()
5669 boolean isNucleotide = alignPanel.alignFrame
5670 .getViewport().getAlignment()
5672 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5673 alignPanel.av.getSequenceSelection(),
5674 alignPanel.alignFrame, dassource,
5675 alignPanel.alignFrame.featureSettings,
5678 .addListener(new FetchFinishedListenerI()
5681 public void finished()
5683 AlignFrame.this.setMenusForViewport();
5686 dbRefFetcher.fetchDBRefs(false);
5692 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5693 MessageManager.formatMessage(
5694 "label.fetch_retrieve_from_all_sources",
5696 Integer.valueOf(otherdb.size())
5697 .toString(), src.getDbSource(),
5698 src.getDbName() })));
5701 // and then build the rest of the individual menus
5702 ifetch = new JMenu(MessageManager.formatMessage(
5703 "label.source_from_db_source",
5704 new Object[] { src.getDbSource() }));
5706 String imname = null;
5708 for (DbSourceProxy sproxy : otherdb)
5710 String dbname = sproxy.getDbName();
5711 String sname = dbname.length() > 5 ? dbname.substring(0,
5712 5) + "..." : dbname;
5713 String msname = dbname.length() > 10 ? dbname.substring(
5714 0, 10) + "..." : dbname;
5717 imname = MessageManager.formatMessage(
5718 "label.from_msname", new Object[] { sname });
5720 fetchr = new JMenuItem(msname);
5721 final DbSourceProxy[] dassrc = { sproxy };
5722 fetchr.addActionListener(new ActionListener()
5726 public void actionPerformed(ActionEvent e)
5728 new Thread(new Runnable()
5734 boolean isNucleotide = alignPanel.alignFrame
5735 .getViewport().getAlignment()
5737 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5738 alignPanel.av.getSequenceSelection(),
5739 alignPanel.alignFrame, dassrc,
5740 alignPanel.alignFrame.featureSettings,
5743 .addListener(new FetchFinishedListenerI()
5746 public void finished()
5748 AlignFrame.this.setMenusForViewport();
5751 dbRefFetcher.fetchDBRefs(false);
5757 fetchr.setToolTipText("<html>"
5758 + MessageManager.formatMessage(
5759 "label.fetch_retrieve_from", new Object[]
5763 if (++icomp >= mcomp || i == (otherdb.size()))
5765 ifetch.setText(MessageManager.formatMessage(
5766 "label.source_to_target", imname, sname));
5768 ifetch = new JMenu();
5776 if (comp >= mcomp || dbi >= (dbclasses.length))
5778 dfetch.setText(MessageManager.formatMessage(
5779 "label.source_to_target", mname, dbclass));
5781 dfetch = new JMenu();
5794 * Left justify the whole alignment.
5797 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5799 AlignmentI al = viewport.getAlignment();
5801 viewport.firePropertyChange("alignment", null, al);
5805 * Right justify the whole alignment.
5808 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5810 AlignmentI al = viewport.getAlignment();
5812 viewport.firePropertyChange("alignment", null, al);
5816 public void setShowSeqFeatures(boolean b)
5818 showSeqFeatures.setSelected(b);
5819 viewport.setShowSequenceFeatures(b);
5826 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5827 * awt.event.ActionEvent)
5830 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5832 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5833 alignPanel.paintAlignment(true);
5840 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5844 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5846 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5847 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5855 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5856 * .event.ActionEvent)
5859 protected void showGroupConservation_actionPerformed(ActionEvent e)
5861 viewport.setShowGroupConservation(showGroupConservation.getState());
5862 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5869 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5870 * .event.ActionEvent)
5873 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5875 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5876 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5883 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5884 * .event.ActionEvent)
5887 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5889 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5890 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5894 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5896 showSequenceLogo.setState(true);
5897 viewport.setShowSequenceLogo(true);
5898 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5899 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5903 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5905 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5912 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5913 * .event.ActionEvent)
5916 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5918 if (avc.makeGroupsFromSelection())
5920 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5921 alignPanel.updateAnnotation();
5922 alignPanel.paintAlignment(true);
5926 public void clearAlignmentSeqRep()
5928 // TODO refactor alignmentseqrep to controller
5929 if (viewport.getAlignment().hasSeqrep())
5931 viewport.getAlignment().setSeqrep(null);
5932 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5933 alignPanel.updateAnnotation();
5934 alignPanel.paintAlignment(true);
5939 protected void createGroup_actionPerformed(ActionEvent e)
5941 if (avc.createGroup())
5943 alignPanel.alignmentChanged();
5948 protected void unGroup_actionPerformed(ActionEvent e)
5952 alignPanel.alignmentChanged();
5957 * make the given alignmentPanel the currently selected tab
5959 * @param alignmentPanel
5961 public void setDisplayedView(AlignmentPanel alignmentPanel)
5963 if (!viewport.getSequenceSetId().equals(
5964 alignmentPanel.av.getSequenceSetId()))
5968 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5970 if (tabbedPane != null
5971 && tabbedPane.getTabCount() > 0
5972 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5973 .getSelectedIndex())
5975 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5980 * Action on selection of menu options to Show or Hide annotations.
5983 * @param forSequences
5984 * update sequence-related annotations
5985 * @param forAlignment
5986 * update non-sequence-related annotations
5989 protected void setAnnotationsVisibility(boolean visible,
5990 boolean forSequences, boolean forAlignment)
5992 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5993 .getAlignmentAnnotation())
5996 * don't display non-positional annotations on an alignment
5998 if (aa.annotations == null)
6002 boolean apply = (aa.sequenceRef == null && forAlignment)
6003 || (aa.sequenceRef != null && forSequences);
6006 aa.visible = visible;
6009 alignPanel.validateAnnotationDimensions(true);
6010 alignPanel.alignmentChanged();
6014 * Store selected annotation sort order for the view and repaint.
6017 protected void sortAnnotations_actionPerformed()
6019 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
6021 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
6022 alignPanel.paintAlignment(true);
6027 * @return alignment panels in this alignment frame
6029 public List<? extends AlignmentViewPanel> getAlignPanels()
6031 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
6035 * Open a new alignment window, with the cDNA associated with this (protein)
6036 * alignment, aligned as is the protein.
6038 protected void viewAsCdna_actionPerformed()
6040 // TODO no longer a menu action - refactor as required
6041 final AlignmentI alignment = getViewport().getAlignment();
6042 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6043 if (mappings == null)
6047 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6048 for (SequenceI aaSeq : alignment.getSequences())
6050 for (AlignedCodonFrame acf : mappings)
6052 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6056 * There is a cDNA mapping for this protein sequence - add to new
6057 * alignment. It will share the same dataset sequence as other mapped
6058 * cDNA (no new mappings need to be created).
6060 final Sequence newSeq = new Sequence(dnaSeq);
6061 newSeq.setDatasetSequence(dnaSeq);
6062 cdnaSeqs.add(newSeq);
6066 if (cdnaSeqs.size() == 0)
6068 // show a warning dialog no mapped cDNA
6071 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6073 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6074 AlignFrame.DEFAULT_HEIGHT);
6075 cdna.alignAs(alignment);
6076 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6078 Desktop.addInternalFrame(alignFrame, newtitle,
6079 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6083 * Set visibility of dna/protein complement view (available when shown in a
6089 protected void showComplement_actionPerformed(boolean show)
6091 SplitContainerI sf = getSplitViewContainer();
6094 sf.setComplementVisible(this, show);
6099 * Generate the reverse (optionally complemented) of the selected sequences,
6100 * and add them to the alignment
6103 protected void showReverse_actionPerformed(boolean complement)
6105 AlignmentI al = null;
6108 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6110 al = dna.reverseCdna(complement);
6111 viewport.addAlignment(al, "");
6112 } catch (Exception ex)
6114 System.err.println(ex.getMessage());
6120 * Try to run a script in the Groovy console, having first ensured that this
6121 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
6122 * be targeted at this alignment.
6125 protected void runGroovy_actionPerformed()
6127 Desktop.setCurrentAlignFrame(this);
6128 groovy.ui.Console console = Desktop.getGroovyConsole();
6129 if (console != null)
6133 console.runScript();
6134 } catch (Exception ex)
6136 System.err.println((ex.toString()));
6138 .showInternalMessageDialog(Desktop.desktop, MessageManager
6139 .getString("label.couldnt_run_groovy_script"),
6141 .getString("label.groovy_support_failed"),
6142 JOptionPane.ERROR_MESSAGE);
6147 System.err.println("Can't run Groovy script as console not found");
6152 * Hides columns containing (or not containing) a specified feature, provided
6153 * that would not leave all columns hidden
6155 * @param featureType
6156 * @param columnsContaining
6159 public boolean hideFeatureColumns(String featureType,
6160 boolean columnsContaining)
6162 boolean notForHiding = avc.markColumnsContainingFeatures(
6163 columnsContaining, false, false, featureType);
6166 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
6167 false, featureType))
6169 getViewport().hideSelectedColumns();
6177 class PrintThread extends Thread
6181 public PrintThread(AlignmentPanel ap)
6186 static PageFormat pf;
6191 PrinterJob printJob = PrinterJob.getPrinterJob();
6195 printJob.setPrintable(ap, pf);
6199 printJob.setPrintable(ap);
6202 if (printJob.printDialog())
6207 } catch (Exception PrintException)
6209 PrintException.printStackTrace();