2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
3 * Copyright (C) 2015 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.ScoreModelI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenSequences;
57 import jalview.datamodel.PDBEntry;
58 import jalview.datamodel.SeqCigar;
59 import jalview.datamodel.Sequence;
60 import jalview.datamodel.SequenceGroup;
61 import jalview.datamodel.SequenceI;
62 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
63 import jalview.io.AlignmentProperties;
64 import jalview.io.AnnotationFile;
65 import jalview.io.BioJsHTMLOutput;
66 import jalview.io.FileLoader;
67 import jalview.io.FormatAdapter;
68 import jalview.io.HtmlSvgOutput;
69 import jalview.io.IdentifyFile;
70 import jalview.io.JalviewFileChooser;
71 import jalview.io.JalviewFileView;
72 import jalview.io.JnetAnnotationMaker;
73 import jalview.io.NewickFile;
74 import jalview.io.TCoffeeScoreFile;
75 import jalview.jbgui.GAlignFrame;
76 import jalview.schemes.Blosum62ColourScheme;
77 import jalview.schemes.BuriedColourScheme;
78 import jalview.schemes.ClustalxColourScheme;
79 import jalview.schemes.ColourSchemeI;
80 import jalview.schemes.ColourSchemeProperty;
81 import jalview.schemes.HelixColourScheme;
82 import jalview.schemes.HydrophobicColourScheme;
83 import jalview.schemes.NucleotideColourScheme;
84 import jalview.schemes.PIDColourScheme;
85 import jalview.schemes.PurinePyrimidineColourScheme;
86 import jalview.schemes.RNAHelicesColourChooser;
87 import jalview.schemes.ResidueProperties;
88 import jalview.schemes.StrandColourScheme;
89 import jalview.schemes.TCoffeeColourScheme;
90 import jalview.schemes.TaylorColourScheme;
91 import jalview.schemes.TurnColourScheme;
92 import jalview.schemes.UserColourScheme;
93 import jalview.schemes.ZappoColourScheme;
94 import jalview.structure.StructureSelectionManager;
95 import jalview.util.MessageManager;
96 import jalview.viewmodel.AlignmentViewport;
97 import jalview.ws.jws1.Discoverer;
98 import jalview.ws.jws2.Jws2Discoverer;
99 import jalview.ws.jws2.jabaws2.Jws2Instance;
100 import jalview.ws.seqfetcher.DbSourceProxy;
102 import java.awt.BorderLayout;
103 import java.awt.Component;
104 import java.awt.Rectangle;
105 import java.awt.Toolkit;
106 import java.awt.datatransfer.Clipboard;
107 import java.awt.datatransfer.DataFlavor;
108 import java.awt.datatransfer.StringSelection;
109 import java.awt.datatransfer.Transferable;
110 import java.awt.dnd.DnDConstants;
111 import java.awt.dnd.DropTargetDragEvent;
112 import java.awt.dnd.DropTargetDropEvent;
113 import java.awt.dnd.DropTargetEvent;
114 import java.awt.dnd.DropTargetListener;
115 import java.awt.event.ActionEvent;
116 import java.awt.event.ActionListener;
117 import java.awt.event.ItemEvent;
118 import java.awt.event.ItemListener;
119 import java.awt.event.KeyAdapter;
120 import java.awt.event.KeyEvent;
121 import java.awt.event.MouseAdapter;
122 import java.awt.event.MouseEvent;
123 import java.awt.print.PageFormat;
124 import java.awt.print.PrinterJob;
125 import java.beans.PropertyChangeEvent;
128 import java.util.ArrayList;
129 import java.util.Arrays;
130 import java.util.Deque;
131 import java.util.Enumeration;
132 import java.util.Hashtable;
133 import java.util.List;
134 import java.util.Set;
135 import java.util.Vector;
137 import javax.swing.JCheckBoxMenuItem;
138 import javax.swing.JEditorPane;
139 import javax.swing.JInternalFrame;
140 import javax.swing.JLayeredPane;
141 import javax.swing.JMenu;
142 import javax.swing.JMenuItem;
143 import javax.swing.JOptionPane;
144 import javax.swing.JRadioButtonMenuItem;
145 import javax.swing.JScrollPane;
146 import javax.swing.SwingUtilities;
152 * @version $Revision$
154 public class AlignFrame extends GAlignFrame implements DropTargetListener,
155 IProgressIndicator, AlignViewControllerGuiI
158 public static final int DEFAULT_WIDTH = 700;
160 public static final int DEFAULT_HEIGHT = 500;
163 * The currently displayed panel (selected tabbed view if more than one)
165 public AlignmentPanel alignPanel;
167 AlignViewport viewport;
169 public AlignViewControllerI avc;
171 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
174 * Last format used to load or save alignments in this window
176 String currentFileFormat = null;
179 * Current filename for this alignment
181 String fileName = null;
184 * Creates a new AlignFrame object with specific width and height.
190 public AlignFrame(AlignmentI al, int width, int height)
192 this(al, null, width, height);
196 * Creates a new AlignFrame object with specific width, height and
202 * @param sequenceSetId
204 public AlignFrame(AlignmentI al, int width, int height,
205 String sequenceSetId)
207 this(al, null, width, height, sequenceSetId);
211 * Creates a new AlignFrame object with specific width, height and
217 * @param sequenceSetId
220 public AlignFrame(AlignmentI al, int width, int height,
221 String sequenceSetId, String viewId)
223 this(al, null, width, height, sequenceSetId, viewId);
227 * new alignment window with hidden columns
231 * @param hiddenColumns
232 * ColumnSelection or null
234 * Width of alignment frame
238 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
239 int width, int height)
241 this(al, hiddenColumns, width, height, null);
245 * Create alignment frame for al with hiddenColumns, a specific width and
246 * height, and specific sequenceId
249 * @param hiddenColumns
252 * @param sequenceSetId
255 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
256 int width, int height, String sequenceSetId)
258 this(al, hiddenColumns, width, height, sequenceSetId, null);
262 * Create alignment frame for al with hiddenColumns, a specific width and
263 * height, and specific sequenceId
266 * @param hiddenColumns
269 * @param sequenceSetId
274 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
275 int width, int height, String sequenceSetId, String viewId)
277 setSize(width, height);
279 if (al.getDataset() == null)
284 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
286 alignPanel = new AlignmentPanel(this, viewport);
288 addAlignmentPanel(alignPanel, true);
292 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
293 ColumnSelection hiddenColumns, int width, int height)
295 setSize(width, height);
297 if (al.getDataset() == null)
302 viewport = new AlignViewport(al, hiddenColumns);
304 if (hiddenSeqs != null && hiddenSeqs.length > 0)
306 viewport.hideSequence(hiddenSeqs);
308 alignPanel = new AlignmentPanel(this, viewport);
309 addAlignmentPanel(alignPanel, true);
314 * Make a new AlignFrame from existing alignmentPanels
321 public AlignFrame(AlignmentPanel ap)
325 addAlignmentPanel(ap, false);
330 * initalise the alignframe from the underlying viewport data and the
335 if (!Jalview.isHeadlessMode())
337 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
340 avc = new jalview.controller.AlignViewController(this, viewport,
342 if (viewport.getAlignmentConservationAnnotation() == null)
344 BLOSUM62Colour.setEnabled(false);
345 conservationMenuItem.setEnabled(false);
346 modifyConservation.setEnabled(false);
347 // PIDColour.setEnabled(false);
348 // abovePIDThreshold.setEnabled(false);
349 // modifyPID.setEnabled(false);
352 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
355 if (sortby.equals("Id"))
357 sortIDMenuItem_actionPerformed(null);
359 else if (sortby.equals("Pairwise Identity"))
361 sortPairwiseMenuItem_actionPerformed(null);
364 if (Desktop.desktop != null)
366 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
367 addServiceListeners();
368 setGUINucleotide(viewport.getAlignment().isNucleotide());
372 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
374 setMenusFromViewport(viewport);
375 buildSortByAnnotationScoresMenu();
378 if (viewport.getWrapAlignment())
380 wrapMenuItem_actionPerformed(null);
383 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
385 this.overviewMenuItem_actionPerformed(null);
390 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
391 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
392 final String menuLabel = MessageManager
393 .getString("label.copy_format_from");
394 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
395 new ViewSetProvider()
399 public AlignmentPanel[] getAllAlignmentPanels()
402 origview.add(alignPanel);
403 // make an array of all alignment panels except for this one
404 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
405 Arrays.asList(Desktop.getAlignmentPanels(null)));
406 aps.remove(AlignFrame.this.alignPanel);
407 return aps.toArray(new AlignmentPanel[aps.size()]);
409 }, selviews, new ItemListener()
413 public void itemStateChanged(ItemEvent e)
415 if (origview.size() > 0)
417 final AlignmentPanel ap = origview.get(0);
420 * Copy the ViewStyle of the selected panel to 'this one'.
421 * Don't change value of 'scaleProteinAsCdna' unless copying
424 ViewStyleI vs = selviews.get(0).getAlignViewport()
426 boolean fromSplitFrame = selviews.get(0)
427 .getAlignViewport().getCodingComplement() != null;
430 vs.setScaleProteinAsCdna(ap.getAlignViewport()
431 .getViewStyle().isScaleProteinAsCdna());
433 ap.getAlignViewport().setViewStyle(vs);
436 * Also rescale ViewStyle of SplitFrame complement if there is
437 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
438 * the whole ViewStyle (allow cDNA protein to have different
441 AlignViewportI complement = ap.getAlignViewport()
442 .getCodingComplement();
443 if (complement != null && vs.isScaleProteinAsCdna())
445 AlignFrame af = Desktop.getAlignFrameFor(complement);
446 ((SplitFrame) af.getSplitViewContainer())
448 af.setMenusForViewport();
452 ap.setSelected(true);
453 ap.alignFrame.setMenusForViewport();
458 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
459 .indexOf("devel") > -1
460 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
461 .indexOf("test") > -1)
463 formatMenu.add(vsel);
469 * Change the filename and format for the alignment, and enable the 'reload'
470 * button functionality.
477 public void setFileName(String file, String format)
480 setFileFormat(format);
481 reload.setEnabled(true);
485 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
488 void addKeyListener()
490 addKeyListener(new KeyAdapter()
493 public void keyPressed(KeyEvent evt)
495 if (viewport.cursorMode
496 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
497 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
498 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
499 && Character.isDigit(evt.getKeyChar()))
501 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
504 switch (evt.getKeyCode())
507 case 27: // escape key
508 deselectAllSequenceMenuItem_actionPerformed(null);
512 case KeyEvent.VK_DOWN:
513 if (evt.isAltDown() || !viewport.cursorMode)
515 moveSelectedSequences(false);
517 if (viewport.cursorMode)
519 alignPanel.getSeqPanel().moveCursor(0, 1);
524 if (evt.isAltDown() || !viewport.cursorMode)
526 moveSelectedSequences(true);
528 if (viewport.cursorMode)
530 alignPanel.getSeqPanel().moveCursor(0, -1);
535 case KeyEvent.VK_LEFT:
536 if (evt.isAltDown() || !viewport.cursorMode)
538 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
542 alignPanel.getSeqPanel().moveCursor(-1, 0);
547 case KeyEvent.VK_RIGHT:
548 if (evt.isAltDown() || !viewport.cursorMode)
550 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
554 alignPanel.getSeqPanel().moveCursor(1, 0);
558 case KeyEvent.VK_SPACE:
559 if (viewport.cursorMode)
561 alignPanel.getSeqPanel().insertGapAtCursor(
562 evt.isControlDown() || evt.isShiftDown()
567 // case KeyEvent.VK_A:
568 // if (viewport.cursorMode)
570 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
571 // //System.out.println("A");
575 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
576 * System.out.println("closing bracket"); } break;
578 case KeyEvent.VK_DELETE:
579 case KeyEvent.VK_BACK_SPACE:
580 if (!viewport.cursorMode)
582 cut_actionPerformed(null);
586 alignPanel.getSeqPanel().deleteGapAtCursor(
587 evt.isControlDown() || evt.isShiftDown()
594 if (viewport.cursorMode)
596 alignPanel.getSeqPanel().setCursorRow();
600 if (viewport.cursorMode && !evt.isControlDown())
602 alignPanel.getSeqPanel().setCursorColumn();
606 if (viewport.cursorMode)
608 alignPanel.getSeqPanel().setCursorPosition();
612 case KeyEvent.VK_ENTER:
613 case KeyEvent.VK_COMMA:
614 if (viewport.cursorMode)
616 alignPanel.getSeqPanel().setCursorRowAndColumn();
621 if (viewport.cursorMode)
623 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
627 if (viewport.cursorMode)
629 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
634 viewport.cursorMode = !viewport.cursorMode;
635 statusBar.setText(MessageManager.formatMessage(
636 "label.keyboard_editing_mode",
637 new String[] { (viewport.cursorMode ? "on" : "off") }));
638 if (viewport.cursorMode)
640 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
641 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
643 alignPanel.getSeqPanel().seqCanvas.repaint();
649 Help.showHelpWindow();
650 } catch (Exception ex)
652 ex.printStackTrace();
657 boolean toggleSeqs = !evt.isControlDown();
658 boolean toggleCols = !evt.isShiftDown();
659 toggleHiddenRegions(toggleSeqs, toggleCols);
662 case KeyEvent.VK_PAGE_UP:
663 if (viewport.getWrapAlignment())
665 alignPanel.scrollUp(true);
669 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
670 - viewport.endSeq + viewport.startSeq);
673 case KeyEvent.VK_PAGE_DOWN:
674 if (viewport.getWrapAlignment())
676 alignPanel.scrollUp(false);
680 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
681 + viewport.endSeq - viewport.startSeq);
688 public void keyReleased(KeyEvent evt)
690 switch (evt.getKeyCode())
692 case KeyEvent.VK_LEFT:
693 if (evt.isAltDown() || !viewport.cursorMode)
695 viewport.firePropertyChange("alignment", null, viewport
696 .getAlignment().getSequences());
700 case KeyEvent.VK_RIGHT:
701 if (evt.isAltDown() || !viewport.cursorMode)
703 viewport.firePropertyChange("alignment", null, viewport
704 .getAlignment().getSequences());
712 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
714 ap.alignFrame = this;
715 avc = new jalview.controller.AlignViewController(this, viewport,
720 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
722 int aSize = alignPanels.size();
724 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
726 if (aSize == 1 && ap.av.viewName == null)
728 this.getContentPane().add(ap, BorderLayout.CENTER);
734 setInitialTabVisible();
737 expandViews.setEnabled(true);
738 gatherViews.setEnabled(true);
739 tabbedPane.addTab(ap.av.viewName, ap);
741 ap.setVisible(false);
746 if (ap.av.isPadGaps())
748 ap.av.getAlignment().padGaps();
750 ap.av.updateConservation(ap);
751 ap.av.updateConsensus(ap);
752 ap.av.updateStrucConsensus(ap);
756 public void setInitialTabVisible()
758 expandViews.setEnabled(true);
759 gatherViews.setEnabled(true);
760 tabbedPane.setVisible(true);
761 AlignmentPanel first = alignPanels.get(0);
762 tabbedPane.addTab(first.av.viewName, first);
763 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
766 public AlignViewport getViewport()
771 /* Set up intrinsic listeners for dynamically generated GUI bits. */
772 private void addServiceListeners()
774 final java.beans.PropertyChangeListener thisListener;
775 Desktop.instance.addJalviewPropertyChangeListener("services",
776 thisListener = new java.beans.PropertyChangeListener()
779 public void propertyChange(PropertyChangeEvent evt)
781 // // System.out.println("Discoverer property change.");
782 // if (evt.getPropertyName().equals("services"))
784 SwingUtilities.invokeLater(new Runnable()
791 .println("Rebuild WS Menu for service change");
792 BuildWebServiceMenu();
799 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
802 public void internalFrameClosed(
803 javax.swing.event.InternalFrameEvent evt)
805 // System.out.println("deregistering discoverer listener");
806 Desktop.instance.removeJalviewPropertyChangeListener("services",
808 closeMenuItem_actionPerformed(true);
811 // Finally, build the menu once to get current service state
812 new Thread(new Runnable()
817 BuildWebServiceMenu();
823 * Configure menu items that vary according to whether the alignment is
824 * nucleotide or protein
828 public void setGUINucleotide(boolean nucleotide)
830 showTranslation.setVisible(nucleotide);
831 conservationMenuItem.setEnabled(!nucleotide);
832 modifyConservation.setEnabled(!nucleotide);
833 showGroupConservation.setEnabled(!nucleotide);
834 rnahelicesColour.setEnabled(nucleotide);
835 purinePyrimidineColour.setEnabled(nucleotide);
836 showComplementMenuItem.setText(MessageManager
837 .getString(nucleotide ? "label.protein" : "label.nucleotide"));
838 setColourSelected(jalview.bin.Cache.getDefault(
839 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
840 : Preferences.DEFAULT_COLOUR_PROT, "None"));
844 * set up menus for the current viewport. This may be called after any
845 * operation that affects the data in the current view (selection changed,
846 * etc) to update the menus to reflect the new state.
849 public void setMenusForViewport()
851 setMenusFromViewport(viewport);
855 * Need to call this method when tabs are selected for multiple views, or when
856 * loading from Jalview2XML.java
861 void setMenusFromViewport(AlignViewport av)
863 padGapsMenuitem.setSelected(av.isPadGaps());
864 colourTextMenuItem.setSelected(av.isShowColourText());
865 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
866 conservationMenuItem.setSelected(av.getConservationSelected());
867 seqLimits.setSelected(av.getShowJVSuffix());
868 idRightAlign.setSelected(av.isRightAlignIds());
869 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
870 renderGapsMenuItem.setSelected(av.isRenderGaps());
871 wrapMenuItem.setSelected(av.getWrapAlignment());
872 scaleAbove.setVisible(av.getWrapAlignment());
873 scaleLeft.setVisible(av.getWrapAlignment());
874 scaleRight.setVisible(av.getWrapAlignment());
875 annotationPanelMenuItem.setState(av.isShowAnnotation());
877 * Show/hide annotations only enabled if annotation panel is shown
879 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
880 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
881 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
882 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
883 viewBoxesMenuItem.setSelected(av.getShowBoxes());
884 viewTextMenuItem.setSelected(av.getShowText());
885 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
886 showGroupConsensus.setSelected(av.isShowGroupConsensus());
887 showGroupConservation.setSelected(av.isShowGroupConservation());
888 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
889 showSequenceLogo.setSelected(av.isShowSequenceLogo());
890 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
892 setColourSelected(ColourSchemeProperty.getColourName(av
893 .getGlobalColourScheme()));
895 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
896 hiddenMarkers.setState(av.getShowHiddenMarkers());
897 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
898 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
899 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
900 autoCalculate.setSelected(av.autoCalculateConsensus);
901 sortByTree.setSelected(av.sortByTree);
902 listenToViewSelections.setSelected(av.followSelection);
903 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
905 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
906 setShowProductsEnabled();
910 private IProgressIndicator progressBar;
915 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
918 public void setProgressBar(String message, long id)
920 progressBar.setProgressBar(message, id);
924 public void registerHandler(final long id,
925 final IProgressIndicatorHandler handler)
927 progressBar.registerHandler(id, handler);
932 * @return true if any progress bars are still active
935 public boolean operationInProgress()
937 return progressBar.operationInProgress();
941 public void setStatus(String text)
943 statusBar.setText(text);
947 * Added so Castor Mapping file can obtain Jalview Version
949 public String getVersion()
951 return jalview.bin.Cache.getProperty("VERSION");
954 public FeatureRenderer getFeatureRenderer()
956 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
960 public void fetchSequence_actionPerformed(ActionEvent e)
962 new SequenceFetcher(this);
966 public void addFromFile_actionPerformed(ActionEvent e)
968 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
972 public void reload_actionPerformed(ActionEvent e)
974 if (fileName != null)
976 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
977 // originating file's format
978 // TODO: work out how to recover feature settings for correct view(s) when
980 if (currentFileFormat.equals("Jalview"))
982 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
983 for (int i = 0; i < frames.length; i++)
985 if (frames[i] instanceof AlignFrame && frames[i] != this
986 && ((AlignFrame) frames[i]).fileName != null
987 && ((AlignFrame) frames[i]).fileName.equals(fileName))
991 frames[i].setSelected(true);
992 Desktop.instance.closeAssociatedWindows();
993 } catch (java.beans.PropertyVetoException ex)
999 Desktop.instance.closeAssociatedWindows();
1001 FileLoader loader = new FileLoader();
1002 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1003 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1007 Rectangle bounds = this.getBounds();
1009 FileLoader loader = new FileLoader();
1010 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1011 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1012 protocol, currentFileFormat);
1014 newframe.setBounds(bounds);
1015 if (featureSettings != null && featureSettings.isShowing())
1017 final Rectangle fspos = featureSettings.frame.getBounds();
1018 // TODO: need a 'show feature settings' function that takes bounds -
1019 // need to refactor Desktop.addFrame
1020 newframe.featureSettings_actionPerformed(null);
1021 final FeatureSettings nfs = newframe.featureSettings;
1022 SwingUtilities.invokeLater(new Runnable()
1027 nfs.frame.setBounds(fspos);
1030 this.featureSettings.close();
1031 this.featureSettings = null;
1033 this.closeMenuItem_actionPerformed(true);
1039 public void addFromText_actionPerformed(ActionEvent e)
1041 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1046 public void addFromURL_actionPerformed(ActionEvent e)
1048 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1052 public void save_actionPerformed(ActionEvent e)
1054 if (fileName == null
1055 || (currentFileFormat == null || !jalview.io.FormatAdapter
1056 .isValidIOFormat(currentFileFormat, true))
1057 || fileName.startsWith("http"))
1059 saveAs_actionPerformed(null);
1063 saveAlignment(fileName, currentFileFormat);
1074 public void saveAs_actionPerformed(ActionEvent e)
1076 JalviewFileChooser chooser = new JalviewFileChooser(
1077 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1078 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1079 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1080 currentFileFormat, false);
1082 chooser.setFileView(new JalviewFileView());
1083 chooser.setDialogTitle(MessageManager
1084 .getString("label.save_alignment_to_file"));
1085 chooser.setToolTipText(MessageManager.getString("action.save"));
1087 int value = chooser.showSaveDialog(this);
1089 if (value == JalviewFileChooser.APPROVE_OPTION)
1091 currentFileFormat = chooser.getSelectedFormat();
1092 while (currentFileFormat == null)
1095 .showInternalMessageDialog(
1098 .getString("label.select_file_format_before_saving"),
1100 .getString("label.file_format_not_specified"),
1101 JOptionPane.WARNING_MESSAGE);
1102 currentFileFormat = chooser.getSelectedFormat();
1103 value = chooser.showSaveDialog(this);
1104 if (value != JalviewFileChooser.APPROVE_OPTION)
1110 fileName = chooser.getSelectedFile().getPath();
1112 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1115 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1116 if (currentFileFormat.indexOf(" ") > -1)
1118 currentFileFormat = currentFileFormat.substring(0,
1119 currentFileFormat.indexOf(" "));
1121 saveAlignment(fileName, currentFileFormat);
1125 public boolean saveAlignment(String file, String format)
1127 boolean success = true;
1129 if (format.equalsIgnoreCase("Jalview"))
1131 String shortName = title;
1133 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1135 shortName = shortName.substring(shortName
1136 .lastIndexOf(java.io.File.separatorChar) + 1);
1139 success = new Jalview2XML().saveAlignment(this, file, shortName);
1141 statusBar.setText(MessageManager.formatMessage(
1142 "label.successfully_saved_to_file_in_format", new Object[] {
1143 fileName, format }));
1148 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1150 warningMessage("Cannot save file " + fileName + " using format "
1151 + format, "Alignment output format not supported");
1152 if (!Jalview.isHeadlessMode())
1154 saveAs_actionPerformed(null);
1159 AlignmentExportData exportData = getAlignmentForExport(format,
1161 if (exportData.getSettings().isCancelled())
1165 FormatAdapter f = new FormatAdapter(alignPanel,
1166 exportData.getSettings());
1167 String output = f.formatSequences(
1169 exportData.getAlignment(), // class cast exceptions will
1170 // occur in the distant future
1171 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1172 f.getCacheSuffixDefault(format),
1173 viewport.getColumnSelection());
1183 java.io.PrintWriter out = new java.io.PrintWriter(
1184 new java.io.FileWriter(file));
1188 this.setTitle(file);
1189 statusBar.setText(MessageManager.formatMessage(
1190 "label.successfully_saved_to_file_in_format",
1191 new Object[] { fileName, format }));
1192 } catch (Exception ex)
1195 ex.printStackTrace();
1202 JOptionPane.showInternalMessageDialog(this, MessageManager
1203 .formatMessage("label.couldnt_save_file",
1204 new Object[] { fileName }), MessageManager
1205 .getString("label.error_saving_file"),
1206 JOptionPane.WARNING_MESSAGE);
1212 private void warningMessage(String warning, String title)
1214 if (new jalview.util.Platform().isHeadless())
1216 System.err.println("Warning: " + title + "\nWarning: " + warning);
1221 JOptionPane.showInternalMessageDialog(this, warning, title,
1222 JOptionPane.WARNING_MESSAGE);
1234 protected void outputText_actionPerformed(ActionEvent e)
1237 AlignmentExportData exportData = getAlignmentForExport(
1238 e.getActionCommand(), viewport, null);
1239 if (exportData.getSettings().isCancelled())
1243 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1244 cap.setForInput(null);
1247 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1248 .formatSequences(e.getActionCommand(),
1249 exportData.getAlignment(),
1250 exportData.getOmitHidden(),
1251 exportData.getStartEndPostions(),
1252 viewport.getColumnSelection()));
1253 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1254 "label.alignment_output_command",
1255 new Object[] { e.getActionCommand() }), 600, 500);
1256 } catch (OutOfMemoryError oom)
1258 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1264 public static AlignmentExportData getAlignmentForExport(
1265 String exportFormat, AlignViewportI viewport,
1266 AlignExportSettingI exportSettings)
1268 AlignmentI alignmentToExport = null;
1269 AlignExportSettingI settings = exportSettings;
1270 String[] omitHidden = null;
1271 int[] alignmentStartEnd = new int[2];
1273 HiddenSequences hiddenSeqs = viewport.getAlignment()
1274 .getHiddenSequences();
1276 alignmentToExport = viewport.getAlignment();
1277 alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
1279 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1280 if (settings == null)
1282 settings = new AlignExportSettings(hasHiddenSeqs,
1283 viewport.hasHiddenColumns(), exportFormat);
1285 // settings.isExportAnnotations();
1287 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1289 omitHidden = viewport.getViewAsString(false);
1292 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1294 alignmentToExport = hiddenSeqs.getFullAlignment();
1298 alignmentToExport = viewport.getAlignment();
1299 alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
1300 .getColumnSelection().getHiddenColumns());
1302 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1303 omitHidden, alignmentStartEnd, settings);
1307 public static int[] getStartEnd(int[] aligmentStartEnd,
1308 List<int[]> hiddenCols)
1310 int startPos = aligmentStartEnd[0];
1311 int endPos = aligmentStartEnd[1];
1313 int[] lowestRange = new int[] { -1, -1 };
1314 int[] higestRange = new int[] { -1, -1 };
1316 for (int[] hiddenCol : hiddenCols)
1318 lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1319 higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1322 if (lowestRange[0] == -1 && lowestRange[1] == -1)
1324 startPos = aligmentStartEnd[0];
1328 startPos = lowestRange[1] + 1;
1331 if (higestRange[0] == -1 && higestRange[1] == -1)
1333 endPos = aligmentStartEnd[1];
1337 endPos = higestRange[0] - 1;
1340 // System.out.println("Export range : " + startPos + " - " + endPos);
1341 return new int[] { startPos, endPos };
1344 public static void main(String[] args)
1346 ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1347 hiddenCols.add(new int[] { 0, 0 });
1348 hiddenCols.add(new int[] { 6, 9 });
1349 hiddenCols.add(new int[] { 11, 12 });
1350 hiddenCols.add(new int[] { 33, 33 });
1351 hiddenCols.add(new int[] { 50, 50 });
1353 int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
1354 // System.out.println("Export range : " + x[0] + " - " + x[1]);
1364 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1366 new HtmlSvgOutput(null, alignPanel);
1370 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1372 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1373 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1376 public void createImageMap(File file, String image)
1378 alignPanel.makePNGImageMap(file, image);
1388 public void createPNG(File f)
1390 alignPanel.makePNG(f);
1400 public void createEPS(File f)
1402 alignPanel.makeEPS(f);
1406 public void createSVG(File f)
1408 alignPanel.makeSVG(f);
1412 public void pageSetup_actionPerformed(ActionEvent e)
1414 PrinterJob printJob = PrinterJob.getPrinterJob();
1415 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1425 public void printMenuItem_actionPerformed(ActionEvent e)
1427 // Putting in a thread avoids Swing painting problems
1428 PrintThread thread = new PrintThread(alignPanel);
1433 public void exportFeatures_actionPerformed(ActionEvent e)
1435 new AnnotationExporter().exportFeatures(alignPanel);
1439 public void exportAnnotations_actionPerformed(ActionEvent e)
1441 new AnnotationExporter().exportAnnotations(alignPanel);
1445 public void associatedData_actionPerformed(ActionEvent e)
1447 // Pick the tree file
1448 JalviewFileChooser chooser = new JalviewFileChooser(
1449 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1450 chooser.setFileView(new JalviewFileView());
1451 chooser.setDialogTitle(MessageManager
1452 .getString("label.load_jalview_annotations"));
1453 chooser.setToolTipText(MessageManager
1454 .getString("label.load_jalview_annotations"));
1456 int value = chooser.showOpenDialog(null);
1458 if (value == JalviewFileChooser.APPROVE_OPTION)
1460 String choice = chooser.getSelectedFile().getPath();
1461 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1462 loadJalviewDataFile(choice, null, null, null);
1468 * Close the current view or all views in the alignment frame. If the frame
1469 * only contains one view then the alignment will be removed from memory.
1471 * @param closeAllTabs
1474 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1476 if (alignPanels != null && alignPanels.size() < 2)
1478 closeAllTabs = true;
1483 if (alignPanels != null)
1487 if (this.isClosed())
1489 // really close all the windows - otherwise wait till
1490 // setClosed(true) is called
1491 for (int i = 0; i < alignPanels.size(); i++)
1493 AlignmentPanel ap = alignPanels.get(i);
1500 closeView(alignPanel);
1507 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1508 * be called recursively, with the frame now in 'closed' state
1510 this.setClosed(true);
1512 } catch (Exception ex)
1514 ex.printStackTrace();
1519 * Close the specified panel and close up tabs appropriately.
1521 * @param panelToClose
1523 public void closeView(AlignmentPanel panelToClose)
1525 int index = tabbedPane.getSelectedIndex();
1526 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1527 alignPanels.remove(panelToClose);
1528 panelToClose.closePanel();
1529 panelToClose = null;
1531 tabbedPane.removeTabAt(closedindex);
1532 tabbedPane.validate();
1534 if (index > closedindex || index == tabbedPane.getTabCount())
1536 // modify currently selected tab index if necessary.
1540 this.tabSelectionChanged(index);
1546 void updateEditMenuBar()
1549 if (viewport.getHistoryList().size() > 0)
1551 undoMenuItem.setEnabled(true);
1552 CommandI command = viewport.getHistoryList().peek();
1553 undoMenuItem.setText(MessageManager.formatMessage(
1554 "label.undo_command",
1555 new Object[] { command.getDescription() }));
1559 undoMenuItem.setEnabled(false);
1560 undoMenuItem.setText(MessageManager.getString("action.undo"));
1563 if (viewport.getRedoList().size() > 0)
1565 redoMenuItem.setEnabled(true);
1567 CommandI command = viewport.getRedoList().peek();
1568 redoMenuItem.setText(MessageManager.formatMessage(
1569 "label.redo_command",
1570 new Object[] { command.getDescription() }));
1574 redoMenuItem.setEnabled(false);
1575 redoMenuItem.setText(MessageManager.getString("action.redo"));
1580 public void addHistoryItem(CommandI command)
1582 if (command.getSize() > 0)
1584 viewport.addToHistoryList(command);
1585 viewport.clearRedoList();
1586 updateEditMenuBar();
1587 viewport.updateHiddenColumns();
1588 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1589 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1590 // viewport.getColumnSelection()
1591 // .getHiddenColumns().size() > 0);
1597 * @return alignment objects for all views
1599 AlignmentI[] getViewAlignments()
1601 if (alignPanels != null)
1603 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1605 for (AlignmentPanel ap : alignPanels)
1607 als[i++] = ap.av.getAlignment();
1611 if (viewport != null)
1613 return new AlignmentI[] { viewport.getAlignment() };
1625 protected void undoMenuItem_actionPerformed(ActionEvent e)
1627 if (viewport.getHistoryList().isEmpty())
1631 CommandI command = viewport.getHistoryList().pop();
1632 viewport.addToRedoList(command);
1633 command.undoCommand(getViewAlignments());
1635 AlignmentViewport originalSource = getOriginatingSource(command);
1636 updateEditMenuBar();
1638 if (originalSource != null)
1640 if (originalSource != viewport)
1643 .warn("Implementation worry: mismatch of viewport origin for undo");
1645 originalSource.updateHiddenColumns();
1646 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1648 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1649 // viewport.getColumnSelection()
1650 // .getHiddenColumns().size() > 0);
1651 originalSource.firePropertyChange("alignment", null, originalSource
1652 .getAlignment().getSequences());
1663 protected void redoMenuItem_actionPerformed(ActionEvent e)
1665 if (viewport.getRedoList().size() < 1)
1670 CommandI command = viewport.getRedoList().pop();
1671 viewport.addToHistoryList(command);
1672 command.doCommand(getViewAlignments());
1674 AlignmentViewport originalSource = getOriginatingSource(command);
1675 updateEditMenuBar();
1677 if (originalSource != null)
1680 if (originalSource != viewport)
1683 .warn("Implementation worry: mismatch of viewport origin for redo");
1685 originalSource.updateHiddenColumns();
1686 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1688 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1689 // viewport.getColumnSelection()
1690 // .getHiddenColumns().size() > 0);
1691 originalSource.firePropertyChange("alignment", null, originalSource
1692 .getAlignment().getSequences());
1696 AlignmentViewport getOriginatingSource(CommandI command)
1698 AlignmentViewport originalSource = null;
1699 // For sequence removal and addition, we need to fire
1700 // the property change event FROM the viewport where the
1701 // original alignment was altered
1702 AlignmentI al = null;
1703 if (command instanceof EditCommand)
1705 EditCommand editCommand = (EditCommand) command;
1706 al = editCommand.getAlignment();
1707 List<Component> comps = PaintRefresher.components.get(viewport
1708 .getSequenceSetId());
1710 for (Component comp : comps)
1712 if (comp instanceof AlignmentPanel)
1714 if (al == ((AlignmentPanel) comp).av.getAlignment())
1716 originalSource = ((AlignmentPanel) comp).av;
1723 if (originalSource == null)
1725 // The original view is closed, we must validate
1726 // the current view against the closed view first
1729 PaintRefresher.validateSequences(al, viewport.getAlignment());
1732 originalSource = viewport;
1735 return originalSource;
1744 public void moveSelectedSequences(boolean up)
1746 SequenceGroup sg = viewport.getSelectionGroup();
1752 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1753 viewport.getHiddenRepSequences(), up);
1754 alignPanel.paintAlignment(true);
1757 synchronized void slideSequences(boolean right, int size)
1759 List<SequenceI> sg = new ArrayList<SequenceI>();
1760 if (viewport.cursorMode)
1762 sg.add(viewport.getAlignment().getSequenceAt(
1763 alignPanel.getSeqPanel().seqCanvas.cursorY));
1765 else if (viewport.getSelectionGroup() != null
1766 && viewport.getSelectionGroup().getSize() != viewport
1767 .getAlignment().getHeight())
1769 sg = viewport.getSelectionGroup().getSequences(
1770 viewport.getHiddenRepSequences());
1778 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1780 for (SequenceI seq : viewport.getAlignment().getSequences())
1782 if (!sg.contains(seq))
1784 invertGroup.add(seq);
1788 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1790 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1791 for (int i = 0; i < invertGroup.size(); i++)
1793 seqs2[i] = invertGroup.get(i);
1796 SlideSequencesCommand ssc;
1799 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1800 size, viewport.getGapCharacter());
1804 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1805 size, viewport.getGapCharacter());
1808 int groupAdjustment = 0;
1809 if (ssc.getGapsInsertedBegin() && right)
1811 if (viewport.cursorMode)
1813 alignPanel.getSeqPanel().moveCursor(size, 0);
1817 groupAdjustment = size;
1820 else if (!ssc.getGapsInsertedBegin() && !right)
1822 if (viewport.cursorMode)
1824 alignPanel.getSeqPanel().moveCursor(-size, 0);
1828 groupAdjustment = -size;
1832 if (groupAdjustment != 0)
1834 viewport.getSelectionGroup().setStartRes(
1835 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1836 viewport.getSelectionGroup().setEndRes(
1837 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1841 * just extend the last slide command if compatible; but not if in
1842 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1844 boolean appendHistoryItem = false;
1845 Deque<CommandI> historyList = viewport.getHistoryList();
1846 boolean inSplitFrame = getSplitViewContainer() != null;
1847 if (!inSplitFrame && historyList != null && historyList.size() > 0
1848 && historyList.peek() instanceof SlideSequencesCommand)
1850 appendHistoryItem = ssc
1851 .appendSlideCommand((SlideSequencesCommand) historyList
1855 if (!appendHistoryItem)
1857 addHistoryItem(ssc);
1870 protected void copy_actionPerformed(ActionEvent e)
1873 if (viewport.getSelectionGroup() == null)
1877 // TODO: preserve the ordering of displayed alignment annotation in any
1878 // internal paste (particularly sequence associated annotation)
1879 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1880 String[] omitHidden = null;
1882 if (viewport.hasHiddenColumns())
1884 omitHidden = viewport.getViewAsString(true);
1887 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1890 StringSelection ss = new StringSelection(output);
1894 jalview.gui.Desktop.internalCopy = true;
1895 // Its really worth setting the clipboard contents
1896 // to empty before setting the large StringSelection!!
1897 Toolkit.getDefaultToolkit().getSystemClipboard()
1898 .setContents(new StringSelection(""), null);
1900 Toolkit.getDefaultToolkit().getSystemClipboard()
1901 .setContents(ss, Desktop.instance);
1902 } catch (OutOfMemoryError er)
1904 new OOMWarning("copying region", er);
1908 ArrayList<int[]> hiddenColumns = null;
1909 if (viewport.hasHiddenColumns())
1911 hiddenColumns = new ArrayList<int[]>();
1912 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1913 .getSelectionGroup().getEndRes();
1914 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1916 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1918 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1919 region[1] - hiddenOffset });
1924 Desktop.jalviewClipboard = new Object[] { seqs,
1925 viewport.getAlignment().getDataset(), hiddenColumns };
1926 statusBar.setText(MessageManager.formatMessage(
1927 "label.copied_sequences_to_clipboard", new Object[] { Integer
1928 .valueOf(seqs.length).toString() }));
1938 protected void pasteNew_actionPerformed(ActionEvent e)
1950 protected void pasteThis_actionPerformed(ActionEvent e)
1956 * Paste contents of Jalview clipboard
1958 * @param newAlignment
1959 * true to paste to a new alignment, otherwise add to this.
1961 void paste(boolean newAlignment)
1963 boolean externalPaste = true;
1966 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1967 Transferable contents = c.getContents(this);
1969 if (contents == null)
1977 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1978 if (str.length() < 1)
1983 format = new IdentifyFile().Identify(str, "Paste");
1985 } catch (OutOfMemoryError er)
1987 new OOMWarning("Out of memory pasting sequences!!", er);
1991 SequenceI[] sequences;
1992 boolean annotationAdded = false;
1993 AlignmentI alignment = null;
1995 if (Desktop.jalviewClipboard != null)
1997 // The clipboard was filled from within Jalview, we must use the
1999 // And dataset from the copied alignment
2000 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2001 // be doubly sure that we create *new* sequence objects.
2002 sequences = new SequenceI[newseq.length];
2003 for (int i = 0; i < newseq.length; i++)
2005 sequences[i] = new Sequence(newseq[i]);
2007 alignment = new Alignment(sequences);
2008 externalPaste = false;
2012 // parse the clipboard as an alignment.
2013 alignment = new FormatAdapter().readFile(str, "Paste", format);
2014 sequences = alignment.getSequencesArray();
2018 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2024 if (Desktop.jalviewClipboard != null)
2026 // dataset is inherited
2027 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2031 // new dataset is constructed
2032 alignment.setDataset(null);
2034 alwidth = alignment.getWidth() + 1;
2038 AlignmentI pastedal = alignment; // preserve pasted alignment object
2039 // Add pasted sequences and dataset into existing alignment.
2040 alignment = viewport.getAlignment();
2041 alwidth = alignment.getWidth() + 1;
2042 // decide if we need to import sequences from an existing dataset
2043 boolean importDs = Desktop.jalviewClipboard != null
2044 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2045 // importDs==true instructs us to copy over new dataset sequences from
2046 // an existing alignment
2047 Vector newDs = (importDs) ? new Vector() : null; // used to create
2048 // minimum dataset set
2050 for (int i = 0; i < sequences.length; i++)
2054 newDs.addElement(null);
2056 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2058 if (importDs && ds != null)
2060 if (!newDs.contains(ds))
2062 newDs.setElementAt(ds, i);
2063 ds = new Sequence(ds);
2064 // update with new dataset sequence
2065 sequences[i].setDatasetSequence(ds);
2069 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2074 // copy and derive new dataset sequence
2075 sequences[i] = sequences[i].deriveSequence();
2076 alignment.getDataset().addSequence(
2077 sequences[i].getDatasetSequence());
2078 // TODO: avoid creation of duplicate dataset sequences with a
2079 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2081 alignment.addSequence(sequences[i]); // merges dataset
2085 newDs.clear(); // tidy up
2087 if (alignment.getAlignmentAnnotation() != null)
2089 for (AlignmentAnnotation alan : alignment
2090 .getAlignmentAnnotation())
2092 if (alan.graphGroup > fgroup)
2094 fgroup = alan.graphGroup;
2098 if (pastedal.getAlignmentAnnotation() != null)
2100 // Add any annotation attached to alignment.
2101 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2102 for (int i = 0; i < alann.length; i++)
2104 annotationAdded = true;
2105 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2107 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2108 if (newann.graphGroup > -1)
2110 if (newGraphGroups.size() <= newann.graphGroup
2111 || newGraphGroups.get(newann.graphGroup) == null)
2113 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2115 newGraphGroups.add(q, null);
2117 newGraphGroups.set(newann.graphGroup, new Integer(
2120 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2124 newann.padAnnotation(alwidth);
2125 alignment.addAnnotation(newann);
2135 addHistoryItem(new EditCommand(
2136 MessageManager.getString("label.add_sequences"),
2137 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2139 // Add any annotations attached to sequences
2140 for (int i = 0; i < sequences.length; i++)
2142 if (sequences[i].getAnnotation() != null)
2144 AlignmentAnnotation newann;
2145 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2147 annotationAdded = true;
2148 newann = sequences[i].getAnnotation()[a];
2149 newann.adjustForAlignment();
2150 newann.padAnnotation(alwidth);
2151 if (newann.graphGroup > -1)
2153 if (newann.graphGroup > -1)
2155 if (newGraphGroups.size() <= newann.graphGroup
2156 || newGraphGroups.get(newann.graphGroup) == null)
2158 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2160 newGraphGroups.add(q, null);
2162 newGraphGroups.set(newann.graphGroup, new Integer(
2165 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2169 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2174 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2181 // propagate alignment changed.
2182 viewport.setEndSeq(alignment.getHeight());
2183 if (annotationAdded)
2185 // Duplicate sequence annotation in all views.
2186 AlignmentI[] alview = this.getViewAlignments();
2187 for (int i = 0; i < sequences.length; i++)
2189 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2194 for (int avnum = 0; avnum < alview.length; avnum++)
2196 if (alview[avnum] != alignment)
2198 // duplicate in a view other than the one with input focus
2199 int avwidth = alview[avnum].getWidth() + 1;
2200 // this relies on sann being preserved after we
2201 // modify the sequence's annotation array for each duplication
2202 for (int a = 0; a < sann.length; a++)
2204 AlignmentAnnotation newann = new AlignmentAnnotation(
2206 sequences[i].addAlignmentAnnotation(newann);
2207 newann.padAnnotation(avwidth);
2208 alview[avnum].addAnnotation(newann); // annotation was
2209 // duplicated earlier
2210 // TODO JAL-1145 graphGroups are not updated for sequence
2211 // annotation added to several views. This may cause
2213 alview[avnum].setAnnotationIndex(newann, a);
2218 buildSortByAnnotationScoresMenu();
2220 viewport.firePropertyChange("alignment", null,
2221 alignment.getSequences());
2222 if (alignPanels != null)
2224 for (AlignmentPanel ap : alignPanels)
2226 ap.validateAnnotationDimensions(false);
2231 alignPanel.validateAnnotationDimensions(false);
2237 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2239 String newtitle = new String("Copied sequences");
2241 if (Desktop.jalviewClipboard != null
2242 && Desktop.jalviewClipboard[2] != null)
2244 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2245 for (int[] region : hc)
2247 af.viewport.hideColumns(region[0], region[1]);
2251 // >>>This is a fix for the moment, until a better solution is
2253 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2255 alignPanel.getSeqPanel().seqCanvas
2256 .getFeatureRenderer());
2258 // TODO: maintain provenance of an alignment, rather than just make the
2259 // title a concatenation of operations.
2262 if (title.startsWith("Copied sequences"))
2268 newtitle = newtitle.concat("- from " + title);
2273 newtitle = new String("Pasted sequences");
2276 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2281 } catch (Exception ex)
2283 ex.printStackTrace();
2284 System.out.println("Exception whilst pasting: " + ex);
2285 // could be anything being pasted in here
2291 protected void expand_newalign(ActionEvent e)
2295 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2296 .getAlignment(), -1);
2297 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2299 String newtitle = new String("Flanking alignment");
2301 if (Desktop.jalviewClipboard != null
2302 && Desktop.jalviewClipboard[2] != null)
2304 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2305 for (int region[] : hc)
2307 af.viewport.hideColumns(region[0], region[1]);
2311 // >>>This is a fix for the moment, until a better solution is
2313 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2315 alignPanel.getSeqPanel().seqCanvas
2316 .getFeatureRenderer());
2318 // TODO: maintain provenance of an alignment, rather than just make the
2319 // title a concatenation of operations.
2321 if (title.startsWith("Copied sequences"))
2327 newtitle = newtitle.concat("- from " + title);
2331 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2333 } catch (Exception ex)
2335 ex.printStackTrace();
2336 System.out.println("Exception whilst pasting: " + ex);
2337 // could be anything being pasted in here
2338 } catch (OutOfMemoryError oom)
2340 new OOMWarning("Viewing flanking region of alignment", oom);
2351 protected void cut_actionPerformed(ActionEvent e)
2353 copy_actionPerformed(null);
2354 delete_actionPerformed(null);
2364 protected void delete_actionPerformed(ActionEvent evt)
2367 SequenceGroup sg = viewport.getSelectionGroup();
2374 * If the cut affects all sequences, warn, remove highlighted columns
2376 if (sg.getSize() == viewport.getAlignment().getHeight())
2378 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2379 .getAlignment().getWidth()) ? true : false;
2380 if (isEntireAlignWidth)
2382 int confirm = JOptionPane.showConfirmDialog(this,
2383 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2384 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2385 JOptionPane.OK_CANCEL_OPTION);
2387 if (confirm == JOptionPane.CANCEL_OPTION
2388 || confirm == JOptionPane.CLOSED_OPTION)
2393 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2394 sg.getEndRes() + 1);
2396 SequenceI[] cut = sg.getSequences()
2397 .toArray(new SequenceI[sg.getSize()]);
2399 addHistoryItem(new EditCommand(
2400 MessageManager.getString("label.cut_sequences"), Action.CUT,
2401 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2402 viewport.getAlignment()));
2404 viewport.setSelectionGroup(null);
2405 viewport.sendSelection();
2406 viewport.getAlignment().deleteGroup(sg);
2408 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2410 if (viewport.getAlignment().getHeight() < 1)
2414 this.setClosed(true);
2415 } catch (Exception ex)
2428 protected void deleteGroups_actionPerformed(ActionEvent e)
2430 if (avc.deleteGroups())
2432 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2433 alignPanel.updateAnnotation();
2434 alignPanel.paintAlignment(true);
2445 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2447 SequenceGroup sg = new SequenceGroup();
2449 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2451 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2454 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2455 viewport.setSelectionGroup(sg);
2456 viewport.sendSelection();
2457 alignPanel.paintAlignment(true);
2458 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2468 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2470 if (viewport.cursorMode)
2472 alignPanel.getSeqPanel().keyboardNo1 = null;
2473 alignPanel.getSeqPanel().keyboardNo2 = null;
2475 viewport.setSelectionGroup(null);
2476 viewport.getColumnSelection().clear();
2477 viewport.setSelectionGroup(null);
2478 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2479 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2480 alignPanel.paintAlignment(true);
2481 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2482 viewport.sendSelection();
2492 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2494 SequenceGroup sg = viewport.getSelectionGroup();
2498 selectAllSequenceMenuItem_actionPerformed(null);
2503 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2505 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2508 alignPanel.paintAlignment(true);
2509 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2510 viewport.sendSelection();
2514 public void invertColSel_actionPerformed(ActionEvent e)
2516 viewport.invertColumnSelection();
2517 alignPanel.paintAlignment(true);
2518 viewport.sendSelection();
2528 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2530 trimAlignment(true);
2540 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2542 trimAlignment(false);
2545 void trimAlignment(boolean trimLeft)
2547 ColumnSelection colSel = viewport.getColumnSelection();
2550 if (colSel.size() > 0)
2554 column = colSel.getMin();
2558 column = colSel.getMax();
2562 if (viewport.getSelectionGroup() != null)
2564 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2565 viewport.getHiddenRepSequences());
2569 seqs = viewport.getAlignment().getSequencesArray();
2572 TrimRegionCommand trimRegion;
2575 trimRegion = new TrimRegionCommand("Remove Left",
2576 TrimRegionCommand.TRIM_LEFT, seqs, column,
2577 viewport.getAlignment(), viewport.getColumnSelection(),
2578 viewport.getSelectionGroup());
2579 viewport.setStartRes(0);
2583 trimRegion = new TrimRegionCommand("Remove Right",
2584 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2585 viewport.getAlignment(), viewport.getColumnSelection(),
2586 viewport.getSelectionGroup());
2589 statusBar.setText(MessageManager.formatMessage(
2590 "label.removed_columns",
2591 new String[] { Integer.valueOf(trimRegion.getSize())
2594 addHistoryItem(trimRegion);
2596 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2598 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2599 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2601 viewport.getAlignment().deleteGroup(sg);
2605 viewport.firePropertyChange("alignment", null, viewport
2606 .getAlignment().getSequences());
2617 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2619 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2622 if (viewport.getSelectionGroup() != null)
2624 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2625 viewport.getHiddenRepSequences());
2626 start = viewport.getSelectionGroup().getStartRes();
2627 end = viewport.getSelectionGroup().getEndRes();
2631 seqs = viewport.getAlignment().getSequencesArray();
2634 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2635 "Remove Gapped Columns", seqs, start, end,
2636 viewport.getAlignment());
2638 addHistoryItem(removeGapCols);
2640 statusBar.setText(MessageManager.formatMessage(
2641 "label.removed_empty_columns",
2642 new Object[] { Integer.valueOf(removeGapCols.getSize())
2645 // This is to maintain viewport position on first residue
2646 // of first sequence
2647 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2648 int startRes = seq.findPosition(viewport.startRes);
2649 // ShiftList shifts;
2650 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2651 // edit.alColumnChanges=shifts.getInverse();
2652 // if (viewport.hasHiddenColumns)
2653 // viewport.getColumnSelection().compensateForEdits(shifts);
2654 viewport.setStartRes(seq.findIndex(startRes) - 1);
2655 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2667 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2669 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2672 if (viewport.getSelectionGroup() != null)
2674 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2675 viewport.getHiddenRepSequences());
2676 start = viewport.getSelectionGroup().getStartRes();
2677 end = viewport.getSelectionGroup().getEndRes();
2681 seqs = viewport.getAlignment().getSequencesArray();
2684 // This is to maintain viewport position on first residue
2685 // of first sequence
2686 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2687 int startRes = seq.findPosition(viewport.startRes);
2689 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2690 viewport.getAlignment()));
2692 viewport.setStartRes(seq.findIndex(startRes) - 1);
2694 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2706 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2708 viewport.setPadGaps(padGapsMenuitem.isSelected());
2709 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2720 public void findMenuItem_actionPerformed(ActionEvent e)
2726 * Create a new view of the current alignment.
2729 public void newView_actionPerformed(ActionEvent e)
2731 newView(null, true);
2735 * Creates and shows a new view of the current alignment.
2738 * title of newly created view; if null, one will be generated
2739 * @param copyAnnotation
2740 * if true then duplicate all annnotation, groups and settings
2741 * @return new alignment panel, already displayed.
2743 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2746 * Create a new AlignmentPanel (with its own, new Viewport)
2748 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2750 if (!copyAnnotation)
2753 * remove all groups and annotation except for the automatic stuff
2755 newap.av.getAlignment().deleteAllGroups();
2756 newap.av.getAlignment().deleteAllAnnotations(false);
2759 newap.av.setGatherViewsHere(false);
2761 if (viewport.viewName == null)
2763 viewport.viewName = MessageManager
2764 .getString("label.view_name_original");
2768 * Views share the same edits undo and redo stacks
2770 newap.av.setHistoryList(viewport.getHistoryList());
2771 newap.av.setRedoList(viewport.getRedoList());
2774 * Views share the same mappings; need to deregister any new mappings
2775 * created by copyAlignPanel, and register the new reference to the shared
2778 newap.av.replaceMappings(viewport.getAlignment());
2780 newap.av.viewName = getNewViewName(viewTitle);
2782 addAlignmentPanel(newap, true);
2783 newap.alignmentChanged();
2785 if (alignPanels.size() == 2)
2787 viewport.setGatherViewsHere(true);
2789 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2794 * Make a new name for the view, ensuring it is unique within the current
2795 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2796 * these now use viewId. Unique view names are still desirable for usability.)
2801 protected String getNewViewName(String viewTitle)
2803 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2804 boolean addFirstIndex = false;
2805 if (viewTitle == null || viewTitle.trim().length() == 0)
2807 viewTitle = MessageManager.getString("action.view");
2808 addFirstIndex = true;
2812 index = 1;// we count from 1 if given a specific name
2814 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2816 List<Component> comps = PaintRefresher.components.get(viewport
2817 .getSequenceSetId());
2819 List<String> existingNames = getExistingViewNames(comps);
2821 while (existingNames.contains(newViewName))
2823 newViewName = viewTitle + " " + (++index);
2829 * Returns a list of distinct view names found in the given list of
2830 * components. View names are held on the viewport of an AlignmentPanel.
2835 protected List<String> getExistingViewNames(List<Component> comps)
2837 List<String> existingNames = new ArrayList<String>();
2838 for (Component comp : comps)
2840 if (comp instanceof AlignmentPanel)
2842 AlignmentPanel ap = (AlignmentPanel) comp;
2843 if (!existingNames.contains(ap.av.viewName))
2845 existingNames.add(ap.av.viewName);
2849 return existingNames;
2853 * Explode tabbed views into separate windows.
2856 public void expandViews_actionPerformed(ActionEvent e)
2858 Desktop.instance.explodeViews(this);
2862 * Gather views in separate windows back into a tabbed presentation.
2865 public void gatherViews_actionPerformed(ActionEvent e)
2867 Desktop.instance.gatherViews(this);
2877 public void font_actionPerformed(ActionEvent e)
2879 new FontChooser(alignPanel);
2889 protected void seqLimit_actionPerformed(ActionEvent e)
2891 viewport.setShowJVSuffix(seqLimits.isSelected());
2893 alignPanel.getIdPanel().getIdCanvas()
2894 .setPreferredSize(alignPanel.calculateIdWidth());
2895 alignPanel.paintAlignment(true);
2899 public void idRightAlign_actionPerformed(ActionEvent e)
2901 viewport.setRightAlignIds(idRightAlign.isSelected());
2902 alignPanel.paintAlignment(true);
2906 public void centreColumnLabels_actionPerformed(ActionEvent e)
2908 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2909 alignPanel.paintAlignment(true);
2915 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2918 protected void followHighlight_actionPerformed()
2921 * Set the 'follow' flag on the Viewport (and scroll to position if now
2924 final boolean state = this.followHighlightMenuItem.getState();
2925 viewport.setFollowHighlight(state);
2928 alignPanel.scrollToPosition(
2929 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2940 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2942 viewport.setColourText(colourTextMenuItem.isSelected());
2943 alignPanel.paintAlignment(true);
2953 public void wrapMenuItem_actionPerformed(ActionEvent e)
2955 scaleAbove.setVisible(wrapMenuItem.isSelected());
2956 scaleLeft.setVisible(wrapMenuItem.isSelected());
2957 scaleRight.setVisible(wrapMenuItem.isSelected());
2958 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2959 alignPanel.updateLayout();
2963 public void showAllSeqs_actionPerformed(ActionEvent e)
2965 viewport.showAllHiddenSeqs();
2969 public void showAllColumns_actionPerformed(ActionEvent e)
2971 viewport.showAllHiddenColumns();
2976 public void hideSelSequences_actionPerformed(ActionEvent e)
2978 viewport.hideAllSelectedSeqs();
2979 // alignPanel.paintAlignment(true);
2983 * called by key handler and the hide all/show all menu items
2988 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2991 boolean hide = false;
2992 SequenceGroup sg = viewport.getSelectionGroup();
2993 if (!toggleSeqs && !toggleCols)
2995 // Hide everything by the current selection - this is a hack - we do the
2996 // invert and then hide
2997 // first check that there will be visible columns after the invert.
2998 if ((viewport.getColumnSelection() != null
2999 && viewport.getColumnSelection().getSelected() != null && viewport
3000 .getColumnSelection().getSelected().size() > 0)
3001 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3004 // now invert the sequence set, if required - empty selection implies
3005 // that no hiding is required.
3008 invertSequenceMenuItem_actionPerformed(null);
3009 sg = viewport.getSelectionGroup();
3013 viewport.expandColSelection(sg, true);
3014 // finally invert the column selection and get the new sequence
3016 invertColSel_actionPerformed(null);
3023 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3025 hideSelSequences_actionPerformed(null);
3028 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3031 showAllSeqs_actionPerformed(null);
3037 if (viewport.getColumnSelection().getSelected().size() > 0)
3039 hideSelColumns_actionPerformed(null);
3042 viewport.setSelectionGroup(sg);
3047 showAllColumns_actionPerformed(null);
3056 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3057 * event.ActionEvent)
3060 public void hideAllButSelection_actionPerformed(ActionEvent e)
3062 toggleHiddenRegions(false, false);
3069 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3073 public void hideAllSelection_actionPerformed(ActionEvent e)
3075 SequenceGroup sg = viewport.getSelectionGroup();
3076 viewport.expandColSelection(sg, false);
3077 viewport.hideAllSelectedSeqs();
3078 viewport.hideSelectedColumns();
3079 alignPanel.paintAlignment(true);
3086 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3090 public void showAllhidden_actionPerformed(ActionEvent e)
3092 viewport.showAllHiddenColumns();
3093 viewport.showAllHiddenSeqs();
3094 alignPanel.paintAlignment(true);
3098 public void hideSelColumns_actionPerformed(ActionEvent e)
3100 viewport.hideSelectedColumns();
3101 alignPanel.paintAlignment(true);
3105 public void hiddenMarkers_actionPerformed(ActionEvent e)
3107 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3118 protected void scaleAbove_actionPerformed(ActionEvent e)
3120 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3121 alignPanel.paintAlignment(true);
3131 protected void scaleLeft_actionPerformed(ActionEvent e)
3133 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3134 alignPanel.paintAlignment(true);
3144 protected void scaleRight_actionPerformed(ActionEvent e)
3146 viewport.setScaleRightWrapped(scaleRight.isSelected());
3147 alignPanel.paintAlignment(true);
3157 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3159 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3160 alignPanel.paintAlignment(true);
3170 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3172 viewport.setShowText(viewTextMenuItem.isSelected());
3173 alignPanel.paintAlignment(true);
3183 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3185 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3186 alignPanel.paintAlignment(true);
3189 public FeatureSettings featureSettings;
3192 public FeatureSettingsControllerI getFeatureSettingsUI()
3194 return featureSettings;
3198 public void featureSettings_actionPerformed(ActionEvent e)
3200 if (featureSettings != null)
3202 featureSettings.close();
3203 featureSettings = null;
3205 if (!showSeqFeatures.isSelected())
3207 // make sure features are actually displayed
3208 showSeqFeatures.setSelected(true);
3209 showSeqFeatures_actionPerformed(null);
3211 featureSettings = new FeatureSettings(this);
3215 * Set or clear 'Show Sequence Features'
3221 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3223 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3224 alignPanel.paintAlignment(true);
3225 if (alignPanel.getOverviewPanel() != null)
3227 alignPanel.getOverviewPanel().updateOverviewImage();
3232 * Set or clear 'Show Sequence Features'
3238 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3240 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3242 if (viewport.isShowSequenceFeaturesHeight())
3244 // ensure we're actually displaying features
3245 viewport.setShowSequenceFeatures(true);
3246 showSeqFeatures.setSelected(true);
3248 alignPanel.paintAlignment(true);
3249 if (alignPanel.getOverviewPanel() != null)
3251 alignPanel.getOverviewPanel().updateOverviewImage();
3256 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3257 * the annotations panel as a whole.
3259 * The options to show/hide all annotations should be enabled when the panel
3260 * is shown, and disabled when the panel is hidden.
3265 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3267 final boolean setVisible = annotationPanelMenuItem.isSelected();
3268 viewport.setShowAnnotation(setVisible);
3269 this.showAllSeqAnnotations.setEnabled(setVisible);
3270 this.hideAllSeqAnnotations.setEnabled(setVisible);
3271 this.showAllAlAnnotations.setEnabled(setVisible);
3272 this.hideAllAlAnnotations.setEnabled(setVisible);
3273 alignPanel.updateLayout();
3277 public void alignmentProperties()
3279 JEditorPane editPane = new JEditorPane("text/html", "");
3280 editPane.setEditable(false);
3281 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3283 editPane.setText(MessageManager.formatMessage("label.html_content",
3284 new Object[] { contents.toString() }));
3285 JInternalFrame frame = new JInternalFrame();
3286 frame.getContentPane().add(new JScrollPane(editPane));
3288 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3289 "label.alignment_properties", new Object[] { getTitle() }),
3300 public void overviewMenuItem_actionPerformed(ActionEvent e)
3302 if (alignPanel.overviewPanel != null)
3307 JInternalFrame frame = new JInternalFrame();
3308 OverviewPanel overview = new OverviewPanel(alignPanel);
3309 frame.setContentPane(overview);
3310 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3311 "label.overview_params", new Object[] { this.getTitle() }),
3312 frame.getWidth(), frame.getHeight());
3314 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3315 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3318 public void internalFrameClosed(
3319 javax.swing.event.InternalFrameEvent evt)
3321 alignPanel.setOverviewPanel(null);
3325 alignPanel.setOverviewPanel(overview);
3329 public void textColour_actionPerformed(ActionEvent e)
3331 new TextColourChooser().chooseColour(alignPanel, null);
3341 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3353 public void clustalColour_actionPerformed(ActionEvent e)
3355 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3356 viewport.getHiddenRepSequences()));
3366 public void zappoColour_actionPerformed(ActionEvent e)
3368 changeColour(new ZappoColourScheme());
3378 public void taylorColour_actionPerformed(ActionEvent e)
3380 changeColour(new TaylorColourScheme());
3390 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3392 changeColour(new HydrophobicColourScheme());
3402 public void helixColour_actionPerformed(ActionEvent e)
3404 changeColour(new HelixColourScheme());
3414 public void strandColour_actionPerformed(ActionEvent e)
3416 changeColour(new StrandColourScheme());
3426 public void turnColour_actionPerformed(ActionEvent e)
3428 changeColour(new TurnColourScheme());
3438 public void buriedColour_actionPerformed(ActionEvent e)
3440 changeColour(new BuriedColourScheme());
3450 public void nucleotideColour_actionPerformed(ActionEvent e)
3452 changeColour(new NucleotideColourScheme());
3456 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3458 changeColour(new PurinePyrimidineColourScheme());
3462 * public void covariationColour_actionPerformed(ActionEvent e) {
3464 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3468 public void annotationColour_actionPerformed(ActionEvent e)
3470 new AnnotationColourChooser(viewport, alignPanel);
3474 public void annotationColumn_actionPerformed(ActionEvent e)
3476 new AnnotationColumnChooser(viewport, alignPanel);
3480 public void rnahelicesColour_actionPerformed(ActionEvent e)
3482 new RNAHelicesColourChooser(viewport, alignPanel);
3492 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3494 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3504 public void changeColour(ColourSchemeI cs)
3506 // TODO: pull up to controller method
3510 // Make sure viewport is up to date w.r.t. any sliders
3511 if (viewport.getAbovePIDThreshold())
3513 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3515 viewport.setThreshold(threshold);
3518 if (viewport.getConservationSelected())
3520 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3523 if (cs instanceof TCoffeeColourScheme)
3525 tcoffeeColour.setEnabled(true);
3526 tcoffeeColour.setSelected(true);
3530 viewport.setGlobalColourScheme(cs);
3532 alignPanel.paintAlignment(true);
3542 protected void modifyPID_actionPerformed(ActionEvent e)
3544 if (viewport.getAbovePIDThreshold()
3545 && viewport.getGlobalColourScheme() != null)
3547 SliderPanel.setPIDSliderSource(alignPanel,
3548 viewport.getGlobalColourScheme(), "Background");
3549 SliderPanel.showPIDSlider();
3560 protected void modifyConservation_actionPerformed(ActionEvent e)
3562 if (viewport.getConservationSelected()
3563 && viewport.getGlobalColourScheme() != null)
3565 SliderPanel.setConservationSlider(alignPanel,
3566 viewport.getGlobalColourScheme(), "Background");
3567 SliderPanel.showConservationSlider();
3578 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3580 viewport.setConservationSelected(conservationMenuItem.isSelected());
3582 viewport.setAbovePIDThreshold(false);
3583 abovePIDThreshold.setSelected(false);
3585 changeColour(viewport.getGlobalColourScheme());
3587 modifyConservation_actionPerformed(null);
3597 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3599 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3601 conservationMenuItem.setSelected(false);
3602 viewport.setConservationSelected(false);
3604 changeColour(viewport.getGlobalColourScheme());
3606 modifyPID_actionPerformed(null);
3616 public void userDefinedColour_actionPerformed(ActionEvent e)
3618 if (e.getActionCommand().equals(
3619 MessageManager.getString("action.user_defined")))
3621 new UserDefinedColours(alignPanel, null);
3625 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3626 .getUserColourSchemes().get(e.getActionCommand());
3632 public void updateUserColourMenu()
3635 Component[] menuItems = colourMenu.getMenuComponents();
3636 int iSize = menuItems.length;
3637 for (int i = 0; i < iSize; i++)
3639 if (menuItems[i].getName() != null
3640 && menuItems[i].getName().equals("USER_DEFINED"))
3642 colourMenu.remove(menuItems[i]);
3646 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3648 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3649 .getUserColourSchemes().keys();
3651 while (userColours.hasMoreElements())
3653 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3654 userColours.nextElement().toString());
3655 radioItem.setName("USER_DEFINED");
3656 radioItem.addMouseListener(new MouseAdapter()
3659 public void mousePressed(MouseEvent evt)
3661 if (evt.isControlDown()
3662 || SwingUtilities.isRightMouseButton(evt))
3664 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3666 int option = JOptionPane.showInternalConfirmDialog(
3667 jalview.gui.Desktop.desktop,
3669 .getString("label.remove_from_default_list"),
3671 .getString("label.remove_user_defined_colour"),
3672 JOptionPane.YES_NO_OPTION);
3673 if (option == JOptionPane.YES_OPTION)
3675 jalview.gui.UserDefinedColours
3676 .removeColourFromDefaults(radioItem.getText());
3677 colourMenu.remove(radioItem);
3681 radioItem.addActionListener(new ActionListener()
3684 public void actionPerformed(ActionEvent evt)
3686 userDefinedColour_actionPerformed(evt);
3693 radioItem.addActionListener(new ActionListener()
3696 public void actionPerformed(ActionEvent evt)
3698 userDefinedColour_actionPerformed(evt);
3702 colourMenu.insert(radioItem, 15);
3703 colours.add(radioItem);
3715 public void PIDColour_actionPerformed(ActionEvent e)
3717 changeColour(new PIDColourScheme());
3727 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3729 changeColour(new Blosum62ColourScheme());
3739 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3741 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3742 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3743 .getAlignment().getSequenceAt(0), null);
3744 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3745 viewport.getAlignment()));
3746 alignPanel.paintAlignment(true);
3756 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3758 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3759 AlignmentSorter.sortByID(viewport.getAlignment());
3760 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3761 viewport.getAlignment()));
3762 alignPanel.paintAlignment(true);
3772 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3774 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3775 AlignmentSorter.sortByLength(viewport.getAlignment());
3776 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3777 viewport.getAlignment()));
3778 alignPanel.paintAlignment(true);
3788 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3790 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3791 AlignmentSorter.sortByGroup(viewport.getAlignment());
3792 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3793 viewport.getAlignment()));
3795 alignPanel.paintAlignment(true);
3805 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3807 new RedundancyPanel(alignPanel, this);
3817 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3819 if ((viewport.getSelectionGroup() == null)
3820 || (viewport.getSelectionGroup().getSize() < 2))
3822 JOptionPane.showInternalMessageDialog(this, MessageManager
3823 .getString("label.you_must_select_least_two_sequences"),
3824 MessageManager.getString("label.invalid_selection"),
3825 JOptionPane.WARNING_MESSAGE);
3829 JInternalFrame frame = new JInternalFrame();
3830 frame.setContentPane(new PairwiseAlignPanel(viewport));
3831 Desktop.addInternalFrame(frame,
3832 MessageManager.getString("action.pairwise_alignment"), 600,
3844 public void PCAMenuItem_actionPerformed(ActionEvent e)
3846 if (((viewport.getSelectionGroup() != null)
3847 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3848 .getSelectionGroup().getSize() > 0))
3849 || (viewport.getAlignment().getHeight() < 4))
3852 .showInternalMessageDialog(
3855 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3857 .getString("label.sequence_selection_insufficient"),
3858 JOptionPane.WARNING_MESSAGE);
3863 new PCAPanel(alignPanel);
3867 public void autoCalculate_actionPerformed(ActionEvent e)
3869 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3870 if (viewport.autoCalculateConsensus)
3872 viewport.firePropertyChange("alignment", null, viewport
3873 .getAlignment().getSequences());
3878 public void sortByTreeOption_actionPerformed(ActionEvent e)
3880 viewport.sortByTree = sortByTree.isSelected();
3884 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3886 viewport.followSelection = listenToViewSelections.isSelected();
3896 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3898 newTreePanel("AV", "PID", "Average distance tree using PID");
3908 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3910 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3920 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3922 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3932 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3934 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3947 void newTreePanel(String type, String pwType, String title)
3951 if (viewport.getSelectionGroup() != null
3952 && viewport.getSelectionGroup().getSize() > 0)
3954 if (viewport.getSelectionGroup().getSize() < 3)
3960 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3962 .getString("label.not_enough_sequences"),
3963 JOptionPane.WARNING_MESSAGE);
3967 SequenceGroup sg = viewport.getSelectionGroup();
3969 /* Decide if the selection is a column region */
3970 for (SequenceI _s : sg.getSequences())
3972 if (_s.getLength() < sg.getEndRes())
3978 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3980 .getString("label.sequences_selection_not_aligned"),
3981 JOptionPane.WARNING_MESSAGE);
3987 title = title + " on region";
3988 tp = new TreePanel(alignPanel, type, pwType);
3992 // are the visible sequences aligned?
3993 if (!viewport.getAlignment().isAligned(false))
3999 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4001 .getString("label.sequences_not_aligned"),
4002 JOptionPane.WARNING_MESSAGE);
4007 if (viewport.getAlignment().getHeight() < 2)
4012 tp = new TreePanel(alignPanel, type, pwType);
4017 if (viewport.viewName != null)
4019 title += viewport.viewName + " of ";
4022 title += this.title;
4024 Desktop.addInternalFrame(tp, title, 600, 500);
4035 public void addSortByOrderMenuItem(String title,
4036 final AlignmentOrder order)
4038 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4039 "action.by_title_param", new Object[] { title }));
4041 item.addActionListener(new java.awt.event.ActionListener()
4044 public void actionPerformed(ActionEvent e)
4046 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4048 // TODO: JBPNote - have to map order entries to curent SequenceI
4050 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4052 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4055 alignPanel.paintAlignment(true);
4061 * Add a new sort by annotation score menu item
4064 * the menu to add the option to
4066 * the label used to retrieve scores for each sequence on the
4069 public void addSortByAnnotScoreMenuItem(JMenu sort,
4070 final String scoreLabel)
4072 final JMenuItem item = new JMenuItem(scoreLabel);
4074 item.addActionListener(new java.awt.event.ActionListener()
4077 public void actionPerformed(ActionEvent e)
4079 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4080 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4081 viewport.getAlignment());// ,viewport.getSelectionGroup());
4082 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4083 viewport.getAlignment()));
4084 alignPanel.paintAlignment(true);
4090 * last hash for alignment's annotation array - used to minimise cost of
4093 protected int _annotationScoreVectorHash;
4096 * search the alignment and rebuild the sort by annotation score submenu the
4097 * last alignment annotation vector hash is stored to minimize cost of
4098 * rebuilding in subsequence calls.
4102 public void buildSortByAnnotationScoresMenu()
4104 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4109 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4111 sortByAnnotScore.removeAll();
4112 // almost certainly a quicker way to do this - but we keep it simple
4113 Hashtable scoreSorts = new Hashtable();
4114 AlignmentAnnotation aann[];
4115 for (SequenceI sqa : viewport.getAlignment().getSequences())
4117 aann = sqa.getAnnotation();
4118 for (int i = 0; aann != null && i < aann.length; i++)
4120 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4122 scoreSorts.put(aann[i].label, aann[i].label);
4126 Enumeration labels = scoreSorts.keys();
4127 while (labels.hasMoreElements())
4129 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4130 (String) labels.nextElement());
4132 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4135 _annotationScoreVectorHash = viewport.getAlignment()
4136 .getAlignmentAnnotation().hashCode();
4141 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4142 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4143 * call. Listeners are added to remove the menu item when the treePanel is
4144 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4148 * Displayed tree window.
4150 * SortBy menu item title.
4153 public void buildTreeMenu()
4155 calculateTree.removeAll();
4156 // build the calculate menu
4158 for (final String type : new String[] { "NJ", "AV" })
4160 String treecalcnm = MessageManager.getString("label.tree_calc_"
4161 + type.toLowerCase());
4162 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4164 JMenuItem tm = new JMenuItem();
4165 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4166 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4168 String smn = MessageManager.getStringOrReturn(
4169 "label.score_model_", sm.getName());
4170 final String title = MessageManager.formatMessage(
4171 "label.treecalc_title", treecalcnm, smn);
4172 tm.setText(title);//
4173 tm.addActionListener(new java.awt.event.ActionListener()
4176 public void actionPerformed(ActionEvent e)
4178 newTreePanel(type, pwtype, title);
4181 calculateTree.add(tm);
4186 sortByTreeMenu.removeAll();
4188 List<Component> comps = PaintRefresher.components.get(viewport
4189 .getSequenceSetId());
4190 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4191 for (Component comp : comps)
4193 if (comp instanceof TreePanel)
4195 treePanels.add((TreePanel) comp);
4199 if (treePanels.size() < 1)
4201 sortByTreeMenu.setVisible(false);
4205 sortByTreeMenu.setVisible(true);
4207 for (final TreePanel tp : treePanels)
4209 final JMenuItem item = new JMenuItem(tp.getTitle());
4210 item.addActionListener(new java.awt.event.ActionListener()
4213 public void actionPerformed(ActionEvent e)
4215 tp.sortByTree_actionPerformed();
4216 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4221 sortByTreeMenu.add(item);
4225 public boolean sortBy(AlignmentOrder alorder, String undoname)
4227 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4228 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4229 if (undoname != null)
4231 addHistoryItem(new OrderCommand(undoname, oldOrder,
4232 viewport.getAlignment()));
4234 alignPanel.paintAlignment(true);
4239 * Work out whether the whole set of sequences or just the selected set will
4240 * be submitted for multiple alignment.
4243 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4245 // Now, check we have enough sequences
4246 AlignmentView msa = null;
4248 if ((viewport.getSelectionGroup() != null)
4249 && (viewport.getSelectionGroup().getSize() > 1))
4251 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4252 // some common interface!
4254 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4255 * SequenceI[sz = seqs.getSize(false)];
4257 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4258 * seqs.getSequenceAt(i); }
4260 msa = viewport.getAlignmentView(true);
4262 else if (viewport.getSelectionGroup() != null
4263 && viewport.getSelectionGroup().getSize() == 1)
4265 int option = JOptionPane.showConfirmDialog(this,
4266 MessageManager.getString("warn.oneseq_msainput_selection"),
4267 MessageManager.getString("label.invalid_selection"),
4268 JOptionPane.OK_CANCEL_OPTION);
4269 if (option == JOptionPane.OK_OPTION)
4271 msa = viewport.getAlignmentView(false);
4276 msa = viewport.getAlignmentView(false);
4282 * Decides what is submitted to a secondary structure prediction service: the
4283 * first sequence in the alignment, or in the current selection, or, if the
4284 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4285 * region or the whole alignment. (where the first sequence in the set is the
4286 * one that the prediction will be for).
4288 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4290 AlignmentView seqs = null;
4292 if ((viewport.getSelectionGroup() != null)
4293 && (viewport.getSelectionGroup().getSize() > 0))
4295 seqs = viewport.getAlignmentView(true);
4299 seqs = viewport.getAlignmentView(false);
4301 // limit sequences - JBPNote in future - could spawn multiple prediction
4303 // TODO: viewport.getAlignment().isAligned is a global state - the local
4304 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4305 if (!viewport.getAlignment().isAligned(false))
4307 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4308 // TODO: if seqs.getSequences().length>1 then should really have warned
4322 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4324 // Pick the tree file
4325 JalviewFileChooser chooser = new JalviewFileChooser(
4326 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4327 chooser.setFileView(new JalviewFileView());
4328 chooser.setDialogTitle(MessageManager
4329 .getString("label.select_newick_like_tree_file"));
4330 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4332 int value = chooser.showOpenDialog(null);
4334 if (value == JalviewFileChooser.APPROVE_OPTION)
4336 String choice = chooser.getSelectedFile().getPath();
4337 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4338 jalview.io.NewickFile fin = null;
4341 fin = new jalview.io.NewickFile(choice, "File");
4342 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4343 } catch (Exception ex)
4350 .getString("label.problem_reading_tree_file"),
4351 JOptionPane.WARNING_MESSAGE);
4352 ex.printStackTrace();
4354 if (fin != null && fin.hasWarningMessage())
4356 JOptionPane.showMessageDialog(Desktop.desktop, fin
4357 .getWarningMessage(), MessageManager
4358 .getString("label.possible_problem_with_tree_file"),
4359 JOptionPane.WARNING_MESSAGE);
4365 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4367 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4370 public TreePanel ShowNewickTree(NewickFile nf, String title)
4372 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4375 public TreePanel ShowNewickTree(NewickFile nf, String title,
4376 AlignmentView input)
4378 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4381 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4382 int h, int x, int y)
4384 return ShowNewickTree(nf, title, null, w, h, x, y);
4388 * Add a treeviewer for the tree extracted from a newick file object to the
4389 * current alignment view
4396 * Associated alignment input data (or null)
4405 * @return TreePanel handle
4407 public TreePanel ShowNewickTree(NewickFile nf, String title,
4408 AlignmentView input, int w, int h, int x, int y)
4410 TreePanel tp = null;
4416 if (nf.getTree() != null)
4418 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4424 tp.setLocation(x, y);
4427 Desktop.addInternalFrame(tp, title, w, h);
4429 } catch (Exception ex)
4431 ex.printStackTrace();
4437 private boolean buildingMenu = false;
4440 * Generates menu items and listener event actions for web service clients
4443 public void BuildWebServiceMenu()
4445 while (buildingMenu)
4449 System.err.println("Waiting for building menu to finish.");
4451 } catch (Exception e)
4455 final AlignFrame me = this;
4456 buildingMenu = true;
4457 new Thread(new Runnable()
4462 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4465 // System.err.println("Building ws menu again "
4466 // + Thread.currentThread());
4467 // TODO: add support for context dependent disabling of services based
4469 // alignment and current selection
4470 // TODO: add additional serviceHandle parameter to specify abstract
4472 // class independently of AbstractName
4473 // TODO: add in rediscovery GUI function to restart discoverer
4474 // TODO: group services by location as well as function and/or
4476 // object broker mechanism.
4477 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4478 final IProgressIndicator af = me;
4479 final JMenu msawsmenu = new JMenu("Alignment");
4480 final JMenu secstrmenu = new JMenu(
4481 "Secondary Structure Prediction");
4482 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4483 final JMenu analymenu = new JMenu("Analysis");
4484 final JMenu dismenu = new JMenu("Protein Disorder");
4485 // final JMenu msawsmenu = new
4486 // JMenu(MessageManager.getString("label.alignment"));
4487 // final JMenu secstrmenu = new
4488 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4489 // final JMenu seqsrchmenu = new
4490 // JMenu(MessageManager.getString("label.sequence_database_search"));
4491 // final JMenu analymenu = new
4492 // JMenu(MessageManager.getString("label.analysis"));
4493 // final JMenu dismenu = new
4494 // JMenu(MessageManager.getString("label.protein_disorder"));
4495 // JAL-940 - only show secondary structure prediction services from
4496 // the legacy server
4497 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4499 Discoverer.services != null && (Discoverer.services.size() > 0))
4501 // TODO: refactor to allow list of AbstractName/Handler bindings to
4503 // stored or retrieved from elsewhere
4504 // No MSAWS used any more:
4505 // Vector msaws = null; // (Vector)
4506 // Discoverer.services.get("MsaWS");
4507 Vector secstrpr = (Vector) Discoverer.services
4509 if (secstrpr != null)
4511 // Add any secondary structure prediction services
4512 for (int i = 0, j = secstrpr.size(); i < j; i++)
4514 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4516 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4517 .getServiceClient(sh);
4518 int p = secstrmenu.getItemCount();
4519 impl.attachWSMenuEntry(secstrmenu, me);
4520 int q = secstrmenu.getItemCount();
4521 for (int litm = p; litm < q; litm++)
4523 legacyItems.add(secstrmenu.getItem(litm));
4529 // Add all submenus in the order they should appear on the web
4531 wsmenu.add(msawsmenu);
4532 wsmenu.add(secstrmenu);
4533 wsmenu.add(dismenu);
4534 wsmenu.add(analymenu);
4535 // No search services yet
4536 // wsmenu.add(seqsrchmenu);
4538 javax.swing.SwingUtilities.invokeLater(new Runnable()
4545 webService.removeAll();
4546 // first, add discovered services onto the webservices menu
4547 if (wsmenu.size() > 0)
4549 for (int i = 0, j = wsmenu.size(); i < j; i++)
4551 webService.add(wsmenu.get(i));
4556 webService.add(me.webServiceNoServices);
4558 // TODO: move into separate menu builder class.
4559 boolean new_sspred = false;
4560 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4562 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4563 if (jws2servs != null)
4565 if (jws2servs.hasServices())
4567 jws2servs.attachWSMenuEntry(webService, me);
4568 for (Jws2Instance sv : jws2servs.getServices())
4570 if (sv.description.toLowerCase().contains("jpred"))
4572 for (JMenuItem jmi : legacyItems)
4574 jmi.setVisible(false);
4580 if (jws2servs.isRunning())
4582 JMenuItem tm = new JMenuItem(
4583 "Still discovering JABA Services");
4584 tm.setEnabled(false);
4589 build_urlServiceMenu(me.webService);
4590 build_fetchdbmenu(webService);
4591 for (JMenu item : wsmenu)
4593 if (item.getItemCount() == 0)
4595 item.setEnabled(false);
4599 item.setEnabled(true);
4602 } catch (Exception e)
4605 .debug("Exception during web service menu building process.",
4610 } catch (Exception e)
4613 buildingMenu = false;
4620 * construct any groupURL type service menu entries.
4624 private void build_urlServiceMenu(JMenu webService)
4626 // TODO: remove this code when 2.7 is released
4627 // DEBUG - alignmentView
4629 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4630 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4632 * @Override public void actionPerformed(ActionEvent e) {
4633 * jalview.datamodel.AlignmentView
4634 * .testSelectionViews(af.viewport.getAlignment(),
4635 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4637 * }); webService.add(testAlView);
4639 // TODO: refactor to RestClient discoverer and merge menu entries for
4640 // rest-style services with other types of analysis/calculation service
4641 // SHmmr test client - still being implemented.
4642 // DEBUG - alignmentView
4644 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4647 client.attachWSMenuEntry(
4648 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4654 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4655 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4656 * getProperty("LAST_DIRECTORY"));
4658 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4659 * to Vamsas file"); chooser.setToolTipText("Export");
4661 * int value = chooser.showSaveDialog(this);
4663 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4664 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4665 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4666 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4669 * prototype of an automatically enabled/disabled analysis function
4672 protected void setShowProductsEnabled()
4674 SequenceI[] selection = viewport.getSequenceSelection();
4675 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4676 viewport.getAlignment().getDataset()))
4678 showProducts.setEnabled(true);
4683 showProducts.setEnabled(false);
4688 * search selection for sequence xRef products and build the show products
4693 * @return true if showProducts menu should be enabled.
4695 public boolean canShowProducts(SequenceI[] selection,
4696 boolean isRegionSelection, Alignment dataset)
4698 boolean showp = false;
4701 showProducts.removeAll();
4702 final boolean dna = viewport.getAlignment().isNucleotide();
4703 final Alignment ds = dataset;
4704 String[] ptypes = (selection == null || selection.length == 0) ? null
4705 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4707 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4708 // selection, dataset, true);
4709 final SequenceI[] sel = selection;
4710 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4713 final boolean isRegSel = isRegionSelection;
4714 final AlignFrame af = this;
4715 final String source = ptypes[t];
4716 JMenuItem xtype = new JMenuItem(ptypes[t]);
4717 xtype.addActionListener(new ActionListener()
4721 public void actionPerformed(ActionEvent e)
4723 // TODO: new thread for this call with vis-delay
4724 af.showProductsFor(af.viewport.getSequenceSelection(),
4725 isRegSel, dna, source);
4729 showProducts.add(xtype);
4731 showProducts.setVisible(showp);
4732 showProducts.setEnabled(showp);
4733 } catch (Exception e)
4735 jalview.bin.Cache.log
4736 .warn("canTranslate threw an exception - please report to help@jalview.org",
4743 protected void showProductsFor(final SequenceI[] sel,
4744 final boolean isRegSel, final boolean dna, final String source)
4746 Runnable foo = new Runnable()
4752 final long sttime = System.currentTimeMillis();
4753 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4754 "status.searching_for_sequences_from",
4755 new Object[] { source }), sttime);
4758 // update our local dataset reference
4759 AlignmentI alignment = AlignFrame.this.getViewport()
4761 Alignment ds = alignment.getDataset();
4762 Alignment prods = CrossRef
4763 .findXrefSequences(sel, dna, source, ds);
4766 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4767 for (int s = 0; s < sprods.length; s++)
4769 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4770 if (ds.getSequences() == null
4771 || !ds.getSequences().contains(
4772 sprods[s].getDatasetSequence()))
4774 ds.addSequence(sprods[s].getDatasetSequence());
4776 sprods[s].updatePDBIds();
4778 Alignment al = new Alignment(sprods);
4782 * Copy dna-to-protein mappings to new alignment
4784 // TODO 1: no mappings are set up for EMBL product
4785 // TODO 2: if they were, should add them to protein alignment, not
4787 Set<AlignedCodonFrame> cf = prods.getCodonFrames();
4788 for (AlignedCodonFrame acf : cf)
4790 al.addCodonFrame(acf);
4792 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4794 String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
4795 + " for " + ((isRegSel) ? "selected region of " : "")
4797 naf.setTitle(newtitle);
4799 // temporary flag until SplitFrame is released
4800 boolean asSplitFrame = Cache.getDefault(
4801 Preferences.ENABLE_SPLIT_FRAME, true);
4805 * Make a copy of this alignment (sharing the same dataset
4806 * sequences). If we are DNA, drop introns and update mappings
4808 AlignmentI copyAlignment = null;
4809 final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4810 .getSequenceSelection();
4813 copyAlignment = AlignmentUtils.makeExonAlignment(
4814 sequenceSelection, cf, alignment);
4815 al.getCodonFrames().clear();
4816 al.getCodonFrames().addAll(cf);
4817 final StructureSelectionManager ssm = StructureSelectionManager
4818 .getStructureSelectionManager(Desktop.instance);
4819 ssm.registerMappings(cf);
4823 copyAlignment = new Alignment(new Alignment(
4824 sequenceSelection));
4826 AlignFrame copyThis = new AlignFrame(copyAlignment,
4827 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4828 copyThis.setTitle(AlignFrame.this.getTitle());
4829 // SplitFrame with dna above, protein below
4830 SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
4831 dna ? naf : copyThis);
4832 naf.setVisible(true);
4833 copyThis.setVisible(true);
4834 String linkedTitle = MessageManager
4835 .getString("label.linked_view_title");
4836 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4840 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4846 System.err.println("No Sequences generated for xRef type "
4849 } catch (Exception e)
4851 jalview.bin.Cache.log.error(
4852 "Exception when finding crossreferences", e);
4853 } catch (OutOfMemoryError e)
4855 new OOMWarning("whilst fetching crossreferences", e);
4858 jalview.bin.Cache.log.error("Error when finding crossreferences",
4861 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4862 "status.finished_searching_for_sequences_from",
4863 new Object[] { source }), sttime);
4867 Thread frunner = new Thread(foo);
4871 public boolean canShowTranslationProducts(SequenceI[] selection,
4872 AlignmentI alignment)
4877 return (jalview.analysis.Dna.canTranslate(selection,
4878 viewport.getViewAsVisibleContigs(true)));
4879 } catch (Exception e)
4881 jalview.bin.Cache.log
4882 .warn("canTranslate threw an exception - please report to help@jalview.org",
4889 * Construct and display a new frame containing the translation of this
4890 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4893 public void showTranslation_actionPerformed(ActionEvent e)
4895 AlignmentI al = null;
4898 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4900 al = dna.translateCdna();
4901 } catch (Exception ex)
4903 jalview.bin.Cache.log.error(
4904 "Exception during translation. Please report this !", ex);
4905 final String msg = MessageManager
4906 .getString("label.error_when_translating_sequences_submit_bug_report");
4907 final String errorTitle = MessageManager
4908 .getString("label.implementation_error")
4909 + MessageManager.getString("translation_failed");
4910 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4911 JOptionPane.ERROR_MESSAGE);
4914 if (al == null || al.getHeight() == 0)
4916 final String msg = MessageManager
4917 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4918 final String errorTitle = MessageManager
4919 .getString("label.translation_failed");
4920 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4921 JOptionPane.WARNING_MESSAGE);
4925 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4926 af.setFileFormat(this.currentFileFormat);
4927 final String newTitle = MessageManager.formatMessage(
4928 "label.translation_of_params",
4929 new Object[] { this.getTitle() });
4930 af.setTitle(newTitle);
4931 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4933 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4934 viewport.openSplitFrame(af, new Alignment(seqs));
4938 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4945 * Set the file format
4949 public void setFileFormat(String fileFormat)
4951 this.currentFileFormat = fileFormat;
4955 * Try to load a features file onto the alignment.
4958 * contents or path to retrieve file
4960 * access mode of file (see jalview.io.AlignFile)
4961 * @return true if features file was parsed correctly.
4963 public boolean parseFeaturesFile(String file, String type)
4965 return avc.parseFeaturesFile(file, type,
4966 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4971 public void refreshFeatureUI(boolean enableIfNecessary)
4973 // note - currently this is only still here rather than in the controller
4974 // because of the featureSettings hard reference that is yet to be
4976 if (enableIfNecessary)
4978 viewport.setShowSequenceFeatures(true);
4979 showSeqFeatures.setSelected(true);
4985 public void dragEnter(DropTargetDragEvent evt)
4990 public void dragExit(DropTargetEvent evt)
4995 public void dragOver(DropTargetDragEvent evt)
5000 public void dropActionChanged(DropTargetDragEvent evt)
5005 public void drop(DropTargetDropEvent evt)
5007 Transferable t = evt.getTransferable();
5008 java.util.List files = null;
5012 DataFlavor uriListFlavor = new DataFlavor(
5013 "text/uri-list;class=java.lang.String");
5014 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5016 // Works on Windows and MacOSX
5017 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5018 files = (java.util.List) t
5019 .getTransferData(DataFlavor.javaFileListFlavor);
5021 else if (t.isDataFlavorSupported(uriListFlavor))
5023 // This is used by Unix drag system
5024 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5025 String data = (String) t.getTransferData(uriListFlavor);
5026 files = new java.util.ArrayList(1);
5027 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5028 data, "\r\n"); st.hasMoreTokens();)
5030 String s = st.nextToken();
5031 if (s.startsWith("#"))
5033 // the line is a comment (as per the RFC 2483)
5037 java.net.URI uri = new java.net.URI(s);
5038 // check to see if we can handle this kind of URI
5039 if (uri.getScheme().toLowerCase().startsWith("http"))
5041 files.add(uri.toString());
5045 // otherwise preserve old behaviour: catch all for file objects
5046 java.io.File file = new java.io.File(uri);
5047 files.add(file.toString());
5051 } catch (Exception e)
5053 e.printStackTrace();
5059 // check to see if any of these files have names matching sequences in
5061 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5062 .getAlignment().getSequencesArray());
5064 * Object[] { String,SequenceI}
5066 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5067 ArrayList<String> filesnotmatched = new ArrayList<String>();
5068 for (int i = 0; i < files.size(); i++)
5070 String file = files.get(i).toString();
5072 String protocol = FormatAdapter.checkProtocol(file);
5073 if (protocol == jalview.io.FormatAdapter.FILE)
5075 File fl = new File(file);
5076 pdbfn = fl.getName();
5078 else if (protocol == jalview.io.FormatAdapter.URL)
5080 URL url = new URL(file);
5081 pdbfn = url.getFile();
5083 if (pdbfn.length() > 0)
5085 // attempt to find a match in the alignment
5086 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5087 int l = 0, c = pdbfn.indexOf(".");
5088 while (mtch == null && c != -1)
5093 } while ((c = pdbfn.indexOf(".", l)) > l);
5096 pdbfn = pdbfn.substring(0, l);
5098 mtch = idm.findAllIdMatches(pdbfn);
5105 type = new IdentifyFile().Identify(file, protocol);
5106 } catch (Exception ex)
5112 if (type.equalsIgnoreCase("PDB"))
5114 filesmatched.add(new Object[] { file, protocol, mtch });
5119 // File wasn't named like one of the sequences or wasn't a PDB file.
5120 filesnotmatched.add(file);
5124 if (filesmatched.size() > 0)
5126 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5132 "label.automatically_associate_pdb_files_with_sequences_same_name",
5133 new Object[] { Integer
5139 .getString("label.automatically_associate_pdb_files_by_name"),
5140 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5143 for (Object[] fm : filesmatched)
5145 // try and associate
5146 // TODO: may want to set a standard ID naming formalism for
5147 // associating PDB files which have no IDs.
5148 for (SequenceI toassoc : (SequenceI[]) fm[2])
5150 PDBEntry pe = new AssociatePdbFileWithSeq()
5151 .associatePdbWithSeq((String) fm[0],
5152 (String) fm[1], toassoc, false,
5156 System.err.println("Associated file : "
5157 + ((String) fm[0]) + " with "
5158 + toassoc.getDisplayId(true));
5162 alignPanel.paintAlignment(true);
5166 if (filesnotmatched.size() > 0)
5169 && (Cache.getDefault(
5170 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5176 "label.ignore_unmatched_dropped_files_info",
5177 new Object[] { Integer
5184 .getString("label.ignore_unmatched_dropped_files"),
5185 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5189 for (String fn : filesnotmatched)
5191 loadJalviewDataFile(fn, null, null, null);
5195 } catch (Exception ex)
5197 ex.printStackTrace();
5203 * Attempt to load a "dropped" file or URL string: First by testing whether
5204 * it's and Annotation file, then a JNet file, and finally a features file. If
5205 * all are false then the user may have dropped an alignment file onto this
5209 * either a filename or a URL string.
5211 public void loadJalviewDataFile(String file, String protocol,
5212 String format, SequenceI assocSeq)
5216 if (protocol == null)
5218 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5220 // if the file isn't identified, or not positively identified as some
5221 // other filetype (PFAM is default unidentified alignment file type) then
5222 // try to parse as annotation.
5223 boolean isAnnotation = (format == null || format
5224 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5225 .annotateAlignmentView(viewport, file, protocol) : false;
5229 // first see if its a T-COFFEE score file
5230 TCoffeeScoreFile tcf = null;
5233 tcf = new TCoffeeScoreFile(file, protocol);
5236 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5238 tcoffeeColour.setEnabled(true);
5239 tcoffeeColour.setSelected(true);
5240 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5241 isAnnotation = true;
5243 .setText(MessageManager
5244 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5248 // some problem - if no warning its probable that the ID matching
5249 // process didn't work
5253 tcf.getWarningMessage() == null ? MessageManager
5254 .getString("label.check_file_matches_sequence_ids_alignment")
5255 : tcf.getWarningMessage(),
5257 .getString("label.problem_reading_tcoffee_score_file"),
5258 JOptionPane.WARNING_MESSAGE);
5265 } catch (Exception x)
5268 .debug("Exception when processing data source as T-COFFEE score file",
5274 // try to see if its a JNet 'concise' style annotation file *before*
5276 // try to parse it as a features file
5279 format = new IdentifyFile().Identify(file, protocol);
5281 if (format.equalsIgnoreCase("JnetFile"))
5283 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5285 new JnetAnnotationMaker();
5286 JnetAnnotationMaker.add_annotation(predictions,
5287 viewport.getAlignment(), 0, false);
5288 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5289 viewport.getAlignment().setSeqrep(repseq);
5290 ColumnSelection cs = new ColumnSelection();
5291 cs.hideInsertionsFor(repseq);
5292 viewport.setColumnSelection(cs);
5293 isAnnotation = true;
5298 * if (format.equalsIgnoreCase("PDB")) {
5300 * String pdbfn = ""; // try to match up filename with sequence id
5301 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5302 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5303 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5304 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5305 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5306 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5307 * // attempt to find a match in the alignment SequenceI mtch =
5308 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5309 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5310 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5311 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5312 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5313 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5314 * { System.err.println("Associated file : " + file + " with " +
5315 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5316 * TODO: maybe need to load as normal otherwise return; } }
5318 // try to parse it as a features file
5319 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5320 // if it wasn't a features file then we just treat it as a general
5321 // alignment file to load into the current view.
5324 new FileLoader().LoadFile(viewport, file, protocol, format);
5328 alignPanel.paintAlignment(true);
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)
5355 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5356 : "using " + protocol + " from " + file)
5358 + (format != null ? "(parsing as '" + format
5359 + "' file)" : ""), oom, Desktop.desktop);
5364 * Method invoked by the ChangeListener on the tabbed pane, in other words
5365 * when a different tabbed pane is selected by the user or programmatically.
5368 public void tabSelectionChanged(int index)
5372 alignPanel = alignPanels.get(index);
5373 viewport = alignPanel.av;
5374 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5375 setMenusFromViewport(viewport);
5379 * If there is a frame linked to this one in a SplitPane, switch it to the
5380 * same view tab index. No infinite recursion of calls should happen, since
5381 * tabSelectionChanged() should not get invoked on setting the selected
5382 * index to an unchanged value. Guard against setting an invalid index
5383 * before the new view peer tab has been created.
5385 final AlignViewportI peer = viewport.getCodingComplement();
5388 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5389 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5391 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5397 * On right mouse click on view tab, prompt for and set new view name.
5400 public void tabbedPane_mousePressed(MouseEvent e)
5402 if (SwingUtilities.isRightMouseButton(e))
5404 String msg = MessageManager.getString("label.enter_view_name");
5405 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5406 JOptionPane.QUESTION_MESSAGE);
5410 viewport.viewName = reply;
5411 // TODO warn if reply is in getExistingViewNames()?
5412 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5417 public AlignViewport getCurrentView()
5423 * Open the dialog for regex description parsing.
5426 protected void extractScores_actionPerformed(ActionEvent e)
5428 ParseProperties pp = new jalview.analysis.ParseProperties(
5429 viewport.getAlignment());
5430 // TODO: verify regex and introduce GUI dialog for version 2.5
5431 // if (pp.getScoresFromDescription("col", "score column ",
5432 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5434 if (pp.getScoresFromDescription("description column",
5435 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5437 buildSortByAnnotationScoresMenu();
5445 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5449 protected void showDbRefs_actionPerformed(ActionEvent e)
5451 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5457 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5461 protected void showNpFeats_actionPerformed(ActionEvent e)
5463 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5467 * find the viewport amongst the tabs in this alignment frame and close that
5472 public boolean closeView(AlignViewportI av)
5476 this.closeMenuItem_actionPerformed(false);
5479 Component[] comp = tabbedPane.getComponents();
5480 for (int i = 0; comp != null && i < comp.length; i++)
5482 if (comp[i] instanceof AlignmentPanel)
5484 if (((AlignmentPanel) comp[i]).av == av)
5487 closeView((AlignmentPanel) comp[i]);
5495 protected void build_fetchdbmenu(JMenu webService)
5497 // Temporary hack - DBRef Fetcher always top level ws entry.
5498 // TODO We probably want to store a sequence database checklist in
5499 // preferences and have checkboxes.. rather than individual sources selected
5501 final JMenu rfetch = new JMenu(
5502 MessageManager.getString("action.fetch_db_references"));
5503 rfetch.setToolTipText(MessageManager
5504 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5505 webService.add(rfetch);
5507 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5508 MessageManager.getString("option.trim_retrieved_seqs"));
5509 trimrs.setToolTipText(MessageManager
5510 .getString("label.trim_retrieved_sequences"));
5511 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5512 trimrs.addActionListener(new ActionListener()
5515 public void actionPerformed(ActionEvent e)
5517 trimrs.setSelected(trimrs.isSelected());
5518 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5519 Boolean.valueOf(trimrs.isSelected()).toString());
5523 JMenuItem fetchr = new JMenuItem(
5524 MessageManager.getString("label.standard_databases"));
5525 fetchr.setToolTipText(MessageManager
5526 .getString("label.fetch_embl_uniprot"));
5527 fetchr.addActionListener(new ActionListener()
5531 public void actionPerformed(ActionEvent e)
5533 new Thread(new Runnable()
5539 new jalview.ws.DBRefFetcher(alignPanel.av
5540 .getSequenceSelection(), alignPanel.alignFrame)
5541 .fetchDBRefs(false);
5549 final AlignFrame me = this;
5550 new Thread(new Runnable()
5555 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5556 .getSequenceFetcherSingleton(me);
5557 javax.swing.SwingUtilities.invokeLater(new Runnable()
5562 String[] dbclasses = sf.getOrderedSupportedSources();
5563 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5564 // jalview.util.QuickSort.sort(otherdb, otherdb);
5565 List<DbSourceProxy> otherdb;
5566 JMenu dfetch = new JMenu();
5567 JMenu ifetch = new JMenu();
5568 JMenuItem fetchr = null;
5569 int comp = 0, icomp = 0, mcomp = 15;
5570 String mname = null;
5572 for (String dbclass : dbclasses)
5574 otherdb = sf.getSourceProxy(dbclass);
5575 // add a single entry for this class, or submenu allowing 'fetch
5577 if (otherdb == null || otherdb.size() < 1)
5581 // List<DbSourceProxy> dbs=otherdb;
5582 // otherdb=new ArrayList<DbSourceProxy>();
5583 // for (DbSourceProxy db:dbs)
5585 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5589 mname = "From " + dbclass;
5591 if (otherdb.size() == 1)
5593 final DbSourceProxy[] dassource = otherdb
5594 .toArray(new DbSourceProxy[0]);
5595 DbSourceProxy src = otherdb.get(0);
5596 fetchr = new JMenuItem(src.getDbSource());
5597 fetchr.addActionListener(new ActionListener()
5601 public void actionPerformed(ActionEvent e)
5603 new Thread(new Runnable()
5609 new jalview.ws.DBRefFetcher(alignPanel.av
5610 .getSequenceSelection(),
5611 alignPanel.alignFrame, dassource)
5612 .fetchDBRefs(false);
5618 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5619 MessageManager.formatMessage(
5620 "label.fetch_retrieve_from",
5621 new Object[] { src.getDbName() })));
5627 final DbSourceProxy[] dassource = otherdb
5628 .toArray(new DbSourceProxy[0]);
5630 DbSourceProxy src = otherdb.get(0);
5631 fetchr = new JMenuItem(MessageManager.formatMessage(
5632 "label.fetch_all_param",
5633 new Object[] { src.getDbSource() }));
5634 fetchr.addActionListener(new ActionListener()
5637 public void actionPerformed(ActionEvent e)
5639 new Thread(new Runnable()
5645 new jalview.ws.DBRefFetcher(alignPanel.av
5646 .getSequenceSelection(),
5647 alignPanel.alignFrame, dassource)
5648 .fetchDBRefs(false);
5654 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5655 MessageManager.formatMessage(
5656 "label.fetch_retrieve_from_all_sources",
5658 Integer.valueOf(otherdb.size())
5659 .toString(), src.getDbSource(),
5660 src.getDbName() })));
5663 // and then build the rest of the individual menus
5664 ifetch = new JMenu(MessageManager.formatMessage(
5665 "label.source_from_db_source",
5666 new Object[] { src.getDbSource() }));
5668 String imname = null;
5670 for (DbSourceProxy sproxy : otherdb)
5672 String dbname = sproxy.getDbName();
5673 String sname = dbname.length() > 5 ? dbname.substring(0,
5674 5) + "..." : dbname;
5675 String msname = dbname.length() > 10 ? dbname.substring(
5676 0, 10) + "..." : dbname;
5679 imname = MessageManager.formatMessage(
5680 "label.from_msname", new Object[] { sname });
5682 fetchr = new JMenuItem(msname);
5683 final DbSourceProxy[] dassrc = { sproxy };
5684 fetchr.addActionListener(new ActionListener()
5688 public void actionPerformed(ActionEvent e)
5690 new Thread(new Runnable()
5696 new jalview.ws.DBRefFetcher(alignPanel.av
5697 .getSequenceSelection(),
5698 alignPanel.alignFrame, dassrc)
5699 .fetchDBRefs(false);
5705 fetchr.setToolTipText("<html>"
5706 + MessageManager.formatMessage(
5707 "label.fetch_retrieve_from", new Object[]
5711 if (++icomp >= mcomp || i == (otherdb.size()))
5713 ifetch.setText(MessageManager.formatMessage(
5714 "label.source_to_target", imname, sname));
5716 ifetch = new JMenu();
5724 if (comp >= mcomp || dbi >= (dbclasses.length))
5726 dfetch.setText(MessageManager.formatMessage(
5727 "label.source_to_target", mname, dbclass));
5729 dfetch = new JMenu();
5742 * Left justify the whole alignment.
5745 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5747 AlignmentI al = viewport.getAlignment();
5749 viewport.firePropertyChange("alignment", null, al);
5753 * Right justify the whole alignment.
5756 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5758 AlignmentI al = viewport.getAlignment();
5760 viewport.firePropertyChange("alignment", null, al);
5764 public void setShowSeqFeatures(boolean b)
5766 showSeqFeatures.setSelected(b);
5767 viewport.setShowSequenceFeatures(b);
5774 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5775 * awt.event.ActionEvent)
5778 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5780 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5781 alignPanel.paintAlignment(true);
5788 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5792 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5794 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5795 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5803 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5804 * .event.ActionEvent)
5807 protected void showGroupConservation_actionPerformed(ActionEvent e)
5809 viewport.setShowGroupConservation(showGroupConservation.getState());
5810 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5817 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5818 * .event.ActionEvent)
5821 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5823 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5824 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5831 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5832 * .event.ActionEvent)
5835 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5837 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5838 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5842 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5844 showSequenceLogo.setState(true);
5845 viewport.setShowSequenceLogo(true);
5846 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5847 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5851 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5853 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5860 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5861 * .event.ActionEvent)
5864 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5866 if (avc.makeGroupsFromSelection())
5868 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5869 alignPanel.updateAnnotation();
5870 alignPanel.paintAlignment(true);
5874 public void clearAlignmentSeqRep()
5876 // TODO refactor alignmentseqrep to controller
5877 if (viewport.getAlignment().hasSeqrep())
5879 viewport.getAlignment().setSeqrep(null);
5880 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5881 alignPanel.updateAnnotation();
5882 alignPanel.paintAlignment(true);
5887 protected void createGroup_actionPerformed(ActionEvent e)
5889 if (avc.createGroup())
5891 alignPanel.alignmentChanged();
5896 protected void unGroup_actionPerformed(ActionEvent e)
5900 alignPanel.alignmentChanged();
5905 * make the given alignmentPanel the currently selected tab
5907 * @param alignmentPanel
5909 public void setDisplayedView(AlignmentPanel alignmentPanel)
5911 if (!viewport.getSequenceSetId().equals(
5912 alignmentPanel.av.getSequenceSetId()))
5916 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5918 if (tabbedPane != null
5919 && tabbedPane.getTabCount() > 0
5920 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5921 .getSelectedIndex())
5923 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5928 * Action on selection of menu options to Show or Hide annotations.
5931 * @param forSequences
5932 * update sequence-related annotations
5933 * @param forAlignment
5934 * update non-sequence-related annotations
5937 protected void setAnnotationsVisibility(boolean visible,
5938 boolean forSequences, boolean forAlignment)
5940 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5941 .getAlignmentAnnotation())
5944 * don't display non-positional annotations on an alignment
5946 if (aa.annotations == null)
5950 boolean apply = (aa.sequenceRef == null && forAlignment)
5951 || (aa.sequenceRef != null && forSequences);
5954 aa.visible = visible;
5957 alignPanel.validateAnnotationDimensions(true);
5958 alignPanel.alignmentChanged();
5962 * Store selected annotation sort order for the view and repaint.
5965 protected void sortAnnotations_actionPerformed()
5967 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5969 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5970 alignPanel.paintAlignment(true);
5975 * @return alignment panels in this alignment frame
5977 public List<? extends AlignmentViewPanel> getAlignPanels()
5979 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5983 * Open a new alignment window, with the cDNA associated with this (protein)
5984 * alignment, aligned as is the protein.
5986 protected void viewAsCdna_actionPerformed()
5988 // TODO no longer a menu action - refactor as required
5989 final AlignmentI alignment = getViewport().getAlignment();
5990 Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5991 if (mappings == null)
5995 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5996 for (SequenceI aaSeq : alignment.getSequences())
5998 for (AlignedCodonFrame acf : mappings)
6000 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6004 * There is a cDNA mapping for this protein sequence - add to new
6005 * alignment. It will share the same dataset sequence as other mapped
6006 * cDNA (no new mappings need to be created).
6008 final Sequence newSeq = new Sequence(dnaSeq);
6009 newSeq.setDatasetSequence(dnaSeq);
6010 cdnaSeqs.add(newSeq);
6014 if (cdnaSeqs.size() == 0)
6016 // show a warning dialog no mapped cDNA
6019 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6021 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6022 AlignFrame.DEFAULT_HEIGHT);
6023 cdna.alignAs(alignment);
6024 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6026 Desktop.addInternalFrame(alignFrame, newtitle,
6027 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6031 * Set visibility of dna/protein complement view (available when shown in a
6037 protected void showComplement_actionPerformed(boolean show)
6039 SplitContainerI sf = getSplitViewContainer();
6042 sf.setComplementVisible(this, show);
6047 class PrintThread extends Thread
6051 public PrintThread(AlignmentPanel ap)
6056 static PageFormat pf;
6061 PrinterJob printJob = PrinterJob.getPrinterJob();
6065 printJob.setPrintable(ap, pf);
6069 printJob.setPrintable(ap);
6072 if (printJob.printDialog())
6077 } catch (Exception PrintException)
6079 PrintException.printStackTrace();