2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AAFrequency;
24 import jalview.analysis.AlignmentSorter;
25 import jalview.analysis.AlignmentUtils;
26 import jalview.analysis.Conservation;
27 import jalview.analysis.CrossRef;
28 import jalview.analysis.Dna;
29 import jalview.analysis.ParseProperties;
30 import jalview.analysis.SequenceIdMatcher;
31 import jalview.api.AlignExportSettingI;
32 import jalview.api.AlignViewControllerGuiI;
33 import jalview.api.AlignViewControllerI;
34 import jalview.api.AlignViewportI;
35 import jalview.api.AlignmentViewPanel;
36 import jalview.api.FeatureSettingsControllerI;
37 import jalview.api.SplitContainerI;
38 import jalview.api.ViewStyleI;
39 import jalview.api.analysis.ScoreModelI;
40 import jalview.bin.Cache;
41 import jalview.bin.Jalview;
42 import jalview.commands.CommandI;
43 import jalview.commands.EditCommand;
44 import jalview.commands.EditCommand.Action;
45 import jalview.commands.OrderCommand;
46 import jalview.commands.RemoveGapColCommand;
47 import jalview.commands.RemoveGapsCommand;
48 import jalview.commands.SlideSequencesCommand;
49 import jalview.commands.TrimRegionCommand;
50 import jalview.datamodel.AlignedCodonFrame;
51 import jalview.datamodel.Alignment;
52 import jalview.datamodel.AlignmentAnnotation;
53 import jalview.datamodel.AlignmentExportData;
54 import jalview.datamodel.AlignmentI;
55 import jalview.datamodel.AlignmentOrder;
56 import jalview.datamodel.AlignmentView;
57 import jalview.datamodel.ColumnSelection;
58 import jalview.datamodel.HiddenSequences;
59 import jalview.datamodel.PDBEntry;
60 import jalview.datamodel.SeqCigar;
61 import jalview.datamodel.Sequence;
62 import jalview.datamodel.SequenceGroup;
63 import jalview.datamodel.SequenceI;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.FileLoader;
69 import jalview.io.FormatAdapter;
70 import jalview.io.HtmlSvgOutput;
71 import jalview.io.IdentifyFile;
72 import jalview.io.JalviewFileChooser;
73 import jalview.io.JalviewFileView;
74 import jalview.io.JnetAnnotationMaker;
75 import jalview.io.NewickFile;
76 import jalview.io.TCoffeeScoreFile;
77 import jalview.jbgui.GAlignFrame;
78 import jalview.schemes.Blosum62ColourScheme;
79 import jalview.schemes.BuriedColourScheme;
80 import jalview.schemes.ClustalxColourScheme;
81 import jalview.schemes.ColourSchemeI;
82 import jalview.schemes.ColourSchemeProperty;
83 import jalview.schemes.HelixColourScheme;
84 import jalview.schemes.HydrophobicColourScheme;
85 import jalview.schemes.NucleotideColourScheme;
86 import jalview.schemes.PIDColourScheme;
87 import jalview.schemes.PurinePyrimidineColourScheme;
88 import jalview.schemes.RNAHelicesColourChooser;
89 import jalview.schemes.ResidueProperties;
90 import jalview.schemes.StrandColourScheme;
91 import jalview.schemes.TCoffeeColourScheme;
92 import jalview.schemes.TaylorColourScheme;
93 import jalview.schemes.TurnColourScheme;
94 import jalview.schemes.UserColourScheme;
95 import jalview.schemes.ZappoColourScheme;
96 import jalview.structure.StructureSelectionManager;
97 import jalview.util.MessageManager;
98 import jalview.viewmodel.AlignmentViewport;
99 import jalview.ws.jws1.Discoverer;
100 import jalview.ws.jws2.Jws2Discoverer;
101 import jalview.ws.jws2.jabaws2.Jws2Instance;
102 import jalview.ws.seqfetcher.DbSourceProxy;
104 import java.awt.BorderLayout;
105 import java.awt.Component;
106 import java.awt.Rectangle;
107 import java.awt.Toolkit;
108 import java.awt.datatransfer.Clipboard;
109 import java.awt.datatransfer.DataFlavor;
110 import java.awt.datatransfer.StringSelection;
111 import java.awt.datatransfer.Transferable;
112 import java.awt.dnd.DnDConstants;
113 import java.awt.dnd.DropTargetDragEvent;
114 import java.awt.dnd.DropTargetDropEvent;
115 import java.awt.dnd.DropTargetEvent;
116 import java.awt.dnd.DropTargetListener;
117 import java.awt.event.ActionEvent;
118 import java.awt.event.ActionListener;
119 import java.awt.event.ItemEvent;
120 import java.awt.event.ItemListener;
121 import java.awt.event.KeyAdapter;
122 import java.awt.event.KeyEvent;
123 import java.awt.event.MouseAdapter;
124 import java.awt.event.MouseEvent;
125 import java.awt.print.PageFormat;
126 import java.awt.print.PrinterJob;
127 import java.beans.PropertyChangeEvent;
130 import java.util.ArrayList;
131 import java.util.Arrays;
132 import java.util.Deque;
133 import java.util.Enumeration;
134 import java.util.Hashtable;
135 import java.util.List;
136 import java.util.Set;
137 import java.util.Vector;
139 import javax.swing.JCheckBoxMenuItem;
140 import javax.swing.JEditorPane;
141 import javax.swing.JInternalFrame;
142 import javax.swing.JLayeredPane;
143 import javax.swing.JMenu;
144 import javax.swing.JMenuItem;
145 import javax.swing.JOptionPane;
146 import javax.swing.JRadioButtonMenuItem;
147 import javax.swing.JScrollPane;
148 import javax.swing.SwingUtilities;
154 * @version $Revision$
156 public class AlignFrame extends GAlignFrame implements DropTargetListener,
157 IProgressIndicator, AlignViewControllerGuiI
160 public static final int DEFAULT_WIDTH = 700;
162 public static final int DEFAULT_HEIGHT = 500;
165 * The currently displayed panel (selected tabbed view if more than one)
167 public AlignmentPanel alignPanel;
169 AlignViewport viewport;
171 public AlignViewControllerI avc;
173 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
176 * Last format used to load or save alignments in this window
178 String currentFileFormat = null;
181 * Current filename for this alignment
183 String fileName = null;
186 * Creates a new AlignFrame object with specific width and height.
192 public AlignFrame(AlignmentI al, int width, int height)
194 this(al, null, width, height);
198 * Creates a new AlignFrame object with specific width, height and
204 * @param sequenceSetId
206 public AlignFrame(AlignmentI al, int width, int height,
207 String sequenceSetId)
209 this(al, null, width, height, sequenceSetId);
213 * Creates a new AlignFrame object with specific width, height and
219 * @param sequenceSetId
222 public AlignFrame(AlignmentI al, int width, int height,
223 String sequenceSetId, String viewId)
225 this(al, null, width, height, sequenceSetId, viewId);
229 * new alignment window with hidden columns
233 * @param hiddenColumns
234 * ColumnSelection or null
236 * Width of alignment frame
240 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
241 int width, int height)
243 this(al, hiddenColumns, width, height, null);
248 * Create alignment frame for al with hiddenColumns, a specific width and
249 * height, and specific sequenceId
252 * @param hiddenColumns
255 * @param sequenceSetId
258 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
259 int width, int height, String sequenceSetId)
261 this(al, hiddenColumns, width, height, sequenceSetId, null);
265 * Create alignment frame for al with hiddenColumns, a specific width and
266 * height, and specific sequenceId
269 * @param hiddenColumns
272 * @param sequenceSetId
277 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
278 int width, int height, String sequenceSetId, String viewId)
280 setSize(width, height);
282 if (al.getDataset() == null)
287 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
289 alignPanel = new AlignmentPanel(this, viewport);
292 addAlignmentPanel(alignPanel, true);
296 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
297 ColumnSelection hiddenColumns, int width, int height)
299 setSize(width, height);
301 if (al.getDataset() == null)
306 viewport = new AlignViewport(al, hiddenColumns);
308 if (hiddenSeqs != null && hiddenSeqs.length > 0)
310 viewport.hideSequence(hiddenSeqs);
312 alignPanel = new AlignmentPanel(this, viewport);
313 addAlignmentPanel(alignPanel, true);
319 * Make a new AlignFrame from existing alignmentPanels
326 public AlignFrame(AlignmentPanel ap)
330 addAlignmentPanel(ap, false);
335 * initalise the alignframe from the underlying viewport data and the
340 if (!Jalview.isHeadlessMode())
342 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
345 avc = new jalview.controller.AlignViewController(this, viewport,
347 if (viewport.getAlignmentConservationAnnotation() == null)
349 BLOSUM62Colour.setEnabled(false);
350 conservationMenuItem.setEnabled(false);
351 modifyConservation.setEnabled(false);
352 // PIDColour.setEnabled(false);
353 // abovePIDThreshold.setEnabled(false);
354 // modifyPID.setEnabled(false);
357 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
360 if (sortby.equals("Id"))
362 sortIDMenuItem_actionPerformed(null);
364 else if (sortby.equals("Pairwise Identity"))
366 sortPairwiseMenuItem_actionPerformed(null);
369 if (Desktop.desktop != null)
371 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
372 addServiceListeners();
373 setGUINucleotide(viewport.getAlignment().isNucleotide());
376 setMenusFromViewport(viewport);
377 buildSortByAnnotationScoresMenu();
380 if (viewport.getWrapAlignment())
382 wrapMenuItem_actionPerformed(null);
385 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
387 this.overviewMenuItem_actionPerformed(null);
392 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
393 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
394 final String menuLabel = MessageManager
395 .getString("label.copy_format_from");
396 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
397 new ViewSetProvider()
401 public AlignmentPanel[] getAllAlignmentPanels()
404 origview.add(alignPanel);
405 // make an array of all alignment panels except for this one
406 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
407 Arrays.asList(Desktop.getAlignmentPanels(null)));
408 aps.remove(AlignFrame.this.alignPanel);
409 return aps.toArray(new AlignmentPanel[aps.size()]);
411 }, selviews, new ItemListener()
415 public void itemStateChanged(ItemEvent e)
417 if (origview.size() > 0)
419 final AlignmentPanel ap = origview.get(0);
422 * Copy the ViewStyle of the selected panel to 'this one'.
423 * Don't change value of 'scaleProteinAsCdna' unless copying
426 ViewStyleI vs = selviews.get(0).getAlignViewport()
428 boolean fromSplitFrame = selviews.get(0)
429 .getAlignViewport().getCodingComplement() != null;
432 vs.setScaleProteinAsCdna(ap.getAlignViewport()
433 .getViewStyle().isScaleProteinAsCdna());
435 ap.getAlignViewport().setViewStyle(vs);
438 * Also rescale ViewStyle of SplitFrame complement if there is
439 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
440 * the whole ViewStyle (allow cDNA protein to have different
443 AlignViewportI complement = ap.getAlignViewport()
444 .getCodingComplement();
445 if (complement != null && vs.isScaleProteinAsCdna())
447 AlignFrame af = Desktop.getAlignFrameFor(complement);
448 ((SplitFrame) af.getSplitViewContainer())
450 af.setMenusForViewport();
454 ap.setSelected(true);
455 ap.alignFrame.setMenusForViewport();
460 formatMenu.add(vsel);
465 * Change the filename and format for the alignment, and enable the 'reload'
466 * button functionality.
473 public void setFileName(String file, String format)
476 setFileFormat(format);
477 reload.setEnabled(true);
481 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
484 void addKeyListener()
486 addKeyListener(new KeyAdapter()
489 public void keyPressed(KeyEvent evt)
491 if (viewport.cursorMode
492 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
493 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
494 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
495 && Character.isDigit(evt.getKeyChar()))
497 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
500 switch (evt.getKeyCode())
503 case 27: // escape key
504 deselectAllSequenceMenuItem_actionPerformed(null);
508 case KeyEvent.VK_DOWN:
509 if (evt.isAltDown() || !viewport.cursorMode)
511 moveSelectedSequences(false);
513 if (viewport.cursorMode)
515 alignPanel.getSeqPanel().moveCursor(0, 1);
520 if (evt.isAltDown() || !viewport.cursorMode)
522 moveSelectedSequences(true);
524 if (viewport.cursorMode)
526 alignPanel.getSeqPanel().moveCursor(0, -1);
531 case KeyEvent.VK_LEFT:
532 if (evt.isAltDown() || !viewport.cursorMode)
534 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
538 alignPanel.getSeqPanel().moveCursor(-1, 0);
543 case KeyEvent.VK_RIGHT:
544 if (evt.isAltDown() || !viewport.cursorMode)
546 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
550 alignPanel.getSeqPanel().moveCursor(1, 0);
554 case KeyEvent.VK_SPACE:
555 if (viewport.cursorMode)
557 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
558 || evt.isShiftDown() || evt.isAltDown());
562 // case KeyEvent.VK_A:
563 // if (viewport.cursorMode)
565 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
566 // //System.out.println("A");
570 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
571 * System.out.println("closing bracket"); } break;
573 case KeyEvent.VK_DELETE:
574 case KeyEvent.VK_BACK_SPACE:
575 if (!viewport.cursorMode)
577 cut_actionPerformed(null);
581 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
582 || evt.isShiftDown() || evt.isAltDown());
588 if (viewport.cursorMode)
590 alignPanel.getSeqPanel().setCursorRow();
594 if (viewport.cursorMode && !evt.isControlDown())
596 alignPanel.getSeqPanel().setCursorColumn();
600 if (viewport.cursorMode)
602 alignPanel.getSeqPanel().setCursorPosition();
606 case KeyEvent.VK_ENTER:
607 case KeyEvent.VK_COMMA:
608 if (viewport.cursorMode)
610 alignPanel.getSeqPanel().setCursorRowAndColumn();
615 if (viewport.cursorMode)
617 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
621 if (viewport.cursorMode)
623 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
628 viewport.cursorMode = !viewport.cursorMode;
629 statusBar.setText(MessageManager.formatMessage(
630 "label.keyboard_editing_mode", new String[]
631 { (viewport.cursorMode ? "on" : "off") }));
632 if (viewport.cursorMode)
634 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
635 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
637 alignPanel.getSeqPanel().seqCanvas.repaint();
643 Help.showHelpWindow();
644 } catch (Exception ex)
646 ex.printStackTrace();
651 boolean toggleSeqs = !evt.isControlDown();
652 boolean toggleCols = !evt.isShiftDown();
653 toggleHiddenRegions(toggleSeqs, toggleCols);
656 case KeyEvent.VK_PAGE_UP:
657 if (viewport.getWrapAlignment())
659 alignPanel.scrollUp(true);
663 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
664 - viewport.endSeq + viewport.startSeq);
667 case KeyEvent.VK_PAGE_DOWN:
668 if (viewport.getWrapAlignment())
670 alignPanel.scrollUp(false);
674 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
675 + viewport.endSeq - viewport.startSeq);
682 public void keyReleased(KeyEvent evt)
684 switch (evt.getKeyCode())
686 case KeyEvent.VK_LEFT:
687 if (evt.isAltDown() || !viewport.cursorMode)
689 viewport.firePropertyChange("alignment", null, viewport
690 .getAlignment().getSequences());
694 case KeyEvent.VK_RIGHT:
695 if (evt.isAltDown() || !viewport.cursorMode)
697 viewport.firePropertyChange("alignment", null, viewport
698 .getAlignment().getSequences());
706 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
708 ap.alignFrame = this;
709 avc = new jalview.controller.AlignViewController(this, viewport,
714 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
716 int aSize = alignPanels.size();
718 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
720 if (aSize == 1 && ap.av.viewName == null)
722 this.getContentPane().add(ap, BorderLayout.CENTER);
728 setInitialTabVisible();
731 expandViews.setEnabled(true);
732 gatherViews.setEnabled(true);
733 tabbedPane.addTab(ap.av.viewName, ap);
735 ap.setVisible(false);
740 if (ap.av.isPadGaps())
742 ap.av.getAlignment().padGaps();
744 ap.av.updateConservation(ap);
745 ap.av.updateConsensus(ap);
746 ap.av.updateStrucConsensus(ap);
750 public void setInitialTabVisible()
752 expandViews.setEnabled(true);
753 gatherViews.setEnabled(true);
754 tabbedPane.setVisible(true);
755 AlignmentPanel first = alignPanels.get(0);
756 tabbedPane.addTab(first.av.viewName, first);
757 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
760 public AlignViewport getViewport()
765 /* Set up intrinsic listeners for dynamically generated GUI bits. */
766 private void addServiceListeners()
768 final java.beans.PropertyChangeListener thisListener;
769 Desktop.instance.addJalviewPropertyChangeListener("services",
770 thisListener = new java.beans.PropertyChangeListener()
773 public void propertyChange(PropertyChangeEvent evt)
775 // // System.out.println("Discoverer property change.");
776 // if (evt.getPropertyName().equals("services"))
778 SwingUtilities.invokeLater(new Runnable()
785 .println("Rebuild WS Menu for service change");
786 BuildWebServiceMenu();
793 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
796 public void internalFrameClosed(
797 javax.swing.event.InternalFrameEvent evt)
799 // System.out.println("deregistering discoverer listener");
800 Desktop.instance.removeJalviewPropertyChangeListener("services",
802 closeMenuItem_actionPerformed(true);
805 // Finally, build the menu once to get current service state
806 new Thread(new Runnable()
811 BuildWebServiceMenu();
817 * Configure menu items that vary according to whether the alignment is
818 * nucleotide or protein
822 public void setGUINucleotide(boolean nucleotide)
824 showTranslation.setVisible(nucleotide);
825 conservationMenuItem.setEnabled(!nucleotide);
826 modifyConservation.setEnabled(!nucleotide);
827 showGroupConservation.setEnabled(!nucleotide);
828 rnahelicesColour.setEnabled(nucleotide);
829 purinePyrimidineColour.setEnabled(nucleotide);
830 showComplementMenuItem.setText(MessageManager
831 .getString(nucleotide ? "label.protein" : "label.nucleotide"));
832 setColourSelected(jalview.bin.Cache.getDefault(
833 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
834 : Preferences.DEFAULT_COLOUR_PROT, "None"));
838 * set up menus for the current viewport. This may be called after any
839 * operation that affects the data in the current view (selection changed,
840 * etc) to update the menus to reflect the new state.
842 public void setMenusForViewport()
844 setMenusFromViewport(viewport);
848 * Need to call this method when tabs are selected for multiple views, or when
849 * loading from Jalview2XML.java
854 void setMenusFromViewport(AlignViewport av)
856 padGapsMenuitem.setSelected(av.isPadGaps());
857 colourTextMenuItem.setSelected(av.isShowColourText());
858 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
859 conservationMenuItem.setSelected(av.getConservationSelected());
860 seqLimits.setSelected(av.getShowJVSuffix());
861 idRightAlign.setSelected(av.isRightAlignIds());
862 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
863 renderGapsMenuItem.setSelected(av.isRenderGaps());
864 wrapMenuItem.setSelected(av.getWrapAlignment());
865 scaleAbove.setVisible(av.getWrapAlignment());
866 scaleLeft.setVisible(av.getWrapAlignment());
867 scaleRight.setVisible(av.getWrapAlignment());
868 annotationPanelMenuItem.setState(av.isShowAnnotation());
870 * Show/hide annotations only enabled if annotation panel is shown
872 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
873 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
874 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
875 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
876 viewBoxesMenuItem.setSelected(av.getShowBoxes());
877 viewTextMenuItem.setSelected(av.getShowText());
878 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
879 showGroupConsensus.setSelected(av.isShowGroupConsensus());
880 showGroupConservation.setSelected(av.isShowGroupConservation());
881 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
882 showSequenceLogo.setSelected(av.isShowSequenceLogo());
883 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
885 setColourSelected(ColourSchemeProperty.getColourName(av
886 .getGlobalColourScheme()));
888 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
889 hiddenMarkers.setState(av.getShowHiddenMarkers());
890 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
891 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
892 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
893 autoCalculate.setSelected(av.autoCalculateConsensus);
894 sortByTree.setSelected(av.sortByTree);
895 listenToViewSelections.setSelected(av.followSelection);
896 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
898 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
899 setShowProductsEnabled();
903 private IProgressIndicator progressBar;
908 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
911 public void setProgressBar(String message, long id)
913 progressBar.setProgressBar(message, id);
917 public void registerHandler(final long id,
918 final IProgressIndicatorHandler handler)
920 progressBar.registerHandler(id, handler);
925 * @return true if any progress bars are still active
928 public boolean operationInProgress()
930 return progressBar.operationInProgress();
934 public void setStatus(String text)
936 statusBar.setText(text);
940 * Added so Castor Mapping file can obtain Jalview Version
942 public String getVersion()
944 return jalview.bin.Cache.getProperty("VERSION");
947 public FeatureRenderer getFeatureRenderer()
949 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
953 public void fetchSequence_actionPerformed(ActionEvent e)
955 new SequenceFetcher(this);
959 public void addFromFile_actionPerformed(ActionEvent e)
961 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
965 public void reload_actionPerformed(ActionEvent e)
967 if (fileName != null)
969 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
970 // originating file's format
971 // TODO: work out how to recover feature settings for correct view(s) when
973 if (currentFileFormat.equals("Jalview"))
975 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
976 for (int i = 0; i < frames.length; i++)
978 if (frames[i] instanceof AlignFrame && frames[i] != this
979 && ((AlignFrame) frames[i]).fileName != null
980 && ((AlignFrame) frames[i]).fileName.equals(fileName))
984 frames[i].setSelected(true);
985 Desktop.instance.closeAssociatedWindows();
986 } catch (java.beans.PropertyVetoException ex)
992 Desktop.instance.closeAssociatedWindows();
994 FileLoader loader = new FileLoader();
995 String protocol = fileName.startsWith("http:") ? "URL" : "File";
996 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1000 Rectangle bounds = this.getBounds();
1002 FileLoader loader = new FileLoader();
1003 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1004 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1005 protocol, currentFileFormat);
1007 newframe.setBounds(bounds);
1008 if (featureSettings != null && featureSettings.isShowing())
1010 final Rectangle fspos = featureSettings.frame.getBounds();
1011 // TODO: need a 'show feature settings' function that takes bounds -
1012 // need to refactor Desktop.addFrame
1013 newframe.featureSettings_actionPerformed(null);
1014 final FeatureSettings nfs = newframe.featureSettings;
1015 SwingUtilities.invokeLater(new Runnable()
1020 nfs.frame.setBounds(fspos);
1023 this.featureSettings.close();
1024 this.featureSettings = null;
1026 this.closeMenuItem_actionPerformed(true);
1032 public void addFromText_actionPerformed(ActionEvent e)
1034 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1039 public void addFromURL_actionPerformed(ActionEvent e)
1041 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1045 public void save_actionPerformed(ActionEvent e)
1047 if (fileName == null
1048 || (currentFileFormat == null || !jalview.io.FormatAdapter
1049 .isValidIOFormat(currentFileFormat, true))
1050 || fileName.startsWith("http"))
1052 saveAs_actionPerformed(null);
1056 saveAlignment(fileName, currentFileFormat);
1067 public void saveAs_actionPerformed(ActionEvent e)
1069 JalviewFileChooser chooser = new JalviewFileChooser(
1070 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1071 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1072 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1073 currentFileFormat, false);
1075 chooser.setFileView(new JalviewFileView());
1076 chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
1077 chooser.setToolTipText(MessageManager.getString("action.save"));
1079 int value = chooser.showSaveDialog(this);
1081 if (value == JalviewFileChooser.APPROVE_OPTION)
1083 currentFileFormat = chooser.getSelectedFormat();
1084 while (currentFileFormat == null)
1087 .showInternalMessageDialog(
1090 .getString("label.select_file_format_before_saving"),
1092 .getString("label.file_format_not_specified"),
1093 JOptionPane.WARNING_MESSAGE);
1094 currentFileFormat = chooser.getSelectedFormat();
1095 value = chooser.showSaveDialog(this);
1096 if (value != JalviewFileChooser.APPROVE_OPTION)
1102 fileName = chooser.getSelectedFile().getPath();
1104 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1107 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1108 if (currentFileFormat.indexOf(" ") > -1)
1110 currentFileFormat = currentFileFormat.substring(0,
1111 currentFileFormat.indexOf(" "));
1113 saveAlignment(fileName, currentFileFormat);
1117 public boolean saveAlignment(String file, String format)
1119 boolean success = true;
1121 if (format.equalsIgnoreCase("Jalview"))
1123 String shortName = title;
1125 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1127 shortName = shortName.substring(shortName
1128 .lastIndexOf(java.io.File.separatorChar) + 1);
1131 success = new Jalview2XML().saveAlignment(this, file, shortName);
1133 statusBar.setText(MessageManager.formatMessage(
1134 "label.successfully_saved_to_file_in_format", new Object[]
1135 { fileName, format }));
1140 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1142 warningMessage("Cannot save file " + fileName + " using format "
1143 + format, "Alignment output format not supported");
1144 if (!Jalview.isHeadlessMode())
1146 saveAs_actionPerformed(null);
1151 AlignmentExportData exportData = getAlignmentForExport(format,
1153 if (exportData.getSettings().isCancelled())
1157 FormatAdapter f = new FormatAdapter(alignPanel,
1158 exportData.getSettings());
1159 String output = f.formatSequences(format,
1160 exportData.getAlignment(), // class cast exceptions will
1161 // occur in the distant future
1162 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1163 f.getCacheSuffixDefault(format),
1164 viewport.getColumnSelection());
1174 java.io.PrintWriter out = new java.io.PrintWriter(
1175 new java.io.FileWriter(file));
1179 this.setTitle(file);
1180 statusBar.setText(MessageManager.formatMessage(
1181 "label.successfully_saved_to_file_in_format",
1183 { fileName, format }));
1184 } catch (Exception ex)
1187 ex.printStackTrace();
1194 JOptionPane.showInternalMessageDialog(this, MessageManager
1195 .formatMessage("label.couldnt_save_file", new Object[]
1196 { fileName }), MessageManager
1197 .getString("label.error_saving_file"),
1198 JOptionPane.WARNING_MESSAGE);
1205 private void warningMessage(String warning, String title)
1207 if (new jalview.util.Platform().isHeadless())
1209 System.err.println("Warning: " + title + "\nWarning: " + warning);
1214 JOptionPane.showInternalMessageDialog(this, warning, title,
1215 JOptionPane.WARNING_MESSAGE);
1227 protected void outputText_actionPerformed(ActionEvent e)
1230 AlignmentExportData exportData = getAlignmentForExport(
1231 e.getActionCommand(), viewport, null);
1232 if (exportData.getSettings().isCancelled())
1236 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1237 cap.setForInput(null);
1240 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1242 e.getActionCommand(),
1243 exportData.getAlignment(),
1244 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1245 viewport.getColumnSelection()));
1246 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1247 "label.alignment_output_command", new Object[]
1248 { e.getActionCommand() }), 600, 500);
1249 } catch (OutOfMemoryError oom)
1251 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1257 public static AlignmentExportData getAlignmentForExport(String exportFormat,
1258 AlignViewportI viewport,
1259 AlignExportSettingI exportSettings)
1261 AlignmentI alignmentToExport = null;
1262 AlignExportSettingI settings = exportSettings;
1263 String[] omitHidden = null;
1264 int[] alignmentStartEnd = new int[2];
1266 HiddenSequences hiddenSeqs = viewport.getAlignment()
1267 .getHiddenSequences();
1270 alignmentToExport = viewport.getAlignment();
1271 alignmentStartEnd = new int[]
1272 { 0, alignmentToExport.getWidth() - 1 };
1274 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1275 if (settings == null)
1277 settings = new AlignExportSettings(hasHiddenSeqs,
1278 viewport.hasHiddenColumns(), exportFormat);
1280 // settings.isExportAnnotations();
1282 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1284 omitHidden = viewport.getViewAsString(false);
1287 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1289 alignmentToExport = hiddenSeqs.getFullAlignment();
1293 alignmentToExport = viewport.getAlignment();
1294 alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
1295 .getColumnSelection().getHiddenColumns());
1297 AlignmentExportData ed = new AlignmentExportData(alignmentToExport, omitHidden, alignmentStartEnd,
1302 public static int[] getStartEnd(int[] aligmentStartEnd,
1303 List<int[]> hiddenCols)
1305 int startPos = aligmentStartEnd[0];
1306 int endPos = aligmentStartEnd[1];
1308 int[] lowestRange = new int[2];
1309 int[] higestRange = new int[2];
1311 for (int[] hiddenCol : hiddenCols)
1313 // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]);
1314 lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1315 higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1317 // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]);
1318 // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]);
1320 if (lowestRange[0] == 0 && lowestRange[1] == 0)
1322 startPos = aligmentStartEnd[0];
1326 startPos = lowestRange[1] + 1;
1329 if (higestRange[0] == 0 && higestRange[1] == 0)
1331 endPos = aligmentStartEnd[1];
1335 endPos = higestRange[0];
1338 // System.out.println("Export range : " + minPos + " - " + maxPos);
1340 { startPos, endPos };
1343 public static void main(String[] args)
1345 ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1346 hiddenCols.add(new int[]
1348 hiddenCols.add(new int[]
1350 hiddenCols.add(new int[]
1352 hiddenCols.add(new int[]
1354 hiddenCols.add(new int[]
1357 int[] x = getStartEnd(new int[]
1358 { 0, 50 }, hiddenCols);
1359 // System.out.println("Export range : " + x[0] + " - " + x[1]);
1369 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1371 new HtmlSvgOutput(null, alignPanel);
1375 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1377 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1378 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1380 public void createImageMap(File file, String image)
1382 alignPanel.makePNGImageMap(file, image);
1392 public void createPNG(File f)
1394 alignPanel.makePNG(f);
1404 public void createEPS(File f)
1406 alignPanel.makeEPS(f);
1409 public void createSVG(File f)
1411 alignPanel.makeSVG(f);
1414 public void pageSetup_actionPerformed(ActionEvent e)
1416 PrinterJob printJob = PrinterJob.getPrinterJob();
1417 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1427 public void printMenuItem_actionPerformed(ActionEvent e)
1429 // Putting in a thread avoids Swing painting problems
1430 PrintThread thread = new PrintThread(alignPanel);
1435 public void exportFeatures_actionPerformed(ActionEvent e)
1437 new AnnotationExporter().exportFeatures(alignPanel);
1441 public void exportAnnotations_actionPerformed(ActionEvent e)
1443 new AnnotationExporter().exportAnnotations(alignPanel);
1447 public void associatedData_actionPerformed(ActionEvent e)
1449 // Pick the tree file
1450 JalviewFileChooser chooser = new JalviewFileChooser(
1451 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1452 chooser.setFileView(new JalviewFileView());
1453 chooser.setDialogTitle(MessageManager
1454 .getString("label.load_jalview_annotations"));
1455 chooser.setToolTipText(MessageManager
1456 .getString("label.load_jalview_annotations"));
1458 int value = chooser.showOpenDialog(null);
1460 if (value == JalviewFileChooser.APPROVE_OPTION)
1462 String choice = chooser.getSelectedFile().getPath();
1463 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1464 loadJalviewDataFile(choice, null, null, null);
1470 * Close the current view or all views in the alignment frame. If the frame
1471 * only contains one view then the alignment will be removed from memory.
1473 * @param closeAllTabs
1476 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1478 if (alignPanels != null && alignPanels.size() < 2)
1480 closeAllTabs = true;
1485 if (alignPanels != null)
1489 if (this.isClosed())
1491 // really close all the windows - otherwise wait till
1492 // setClosed(true) is called
1493 for (int i = 0; i < alignPanels.size(); i++)
1495 AlignmentPanel ap = alignPanels.get(i);
1502 closeView(alignPanel);
1509 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1510 * be called recursively, with the frame now in 'closed' state
1512 this.setClosed(true);
1514 } catch (Exception ex)
1516 ex.printStackTrace();
1521 * Close the specified panel and close up tabs appropriately.
1523 * @param panelToClose
1525 public void closeView(AlignmentPanel panelToClose)
1527 int index = tabbedPane.getSelectedIndex();
1528 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1529 alignPanels.remove(panelToClose);
1530 panelToClose.closePanel();
1531 panelToClose = null;
1533 tabbedPane.removeTabAt(closedindex);
1534 tabbedPane.validate();
1536 if (index > closedindex || index == tabbedPane.getTabCount())
1538 // modify currently selected tab index if necessary.
1542 this.tabSelectionChanged(index);
1548 void updateEditMenuBar()
1551 if (viewport.getHistoryList().size() > 0)
1553 undoMenuItem.setEnabled(true);
1554 CommandI command = viewport.getHistoryList().peek();
1555 undoMenuItem.setText(MessageManager.formatMessage(
1556 "label.undo_command", new Object[]
1557 { command.getDescription() }));
1561 undoMenuItem.setEnabled(false);
1562 undoMenuItem.setText(MessageManager.getString("action.undo"));
1565 if (viewport.getRedoList().size() > 0)
1567 redoMenuItem.setEnabled(true);
1569 CommandI command = viewport.getRedoList().peek();
1570 redoMenuItem.setText(MessageManager.formatMessage(
1571 "label.redo_command", new Object[]
1572 { command.getDescription() }));
1576 redoMenuItem.setEnabled(false);
1577 redoMenuItem.setText(MessageManager.getString("action.redo"));
1581 public void addHistoryItem(CommandI command)
1583 if (command.getSize() > 0)
1585 viewport.addToHistoryList(command);
1586 viewport.clearRedoList();
1587 updateEditMenuBar();
1588 viewport.updateHiddenColumns();
1589 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1590 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1591 // viewport.getColumnSelection()
1592 // .getHiddenColumns().size() > 0);
1598 * @return alignment objects for all views
1600 AlignmentI[] getViewAlignments()
1602 if (alignPanels != null)
1604 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1606 for (AlignmentPanel ap : alignPanels)
1608 als[i++] = ap.av.getAlignment();
1612 if (viewport != null)
1614 return new AlignmentI[]
1615 { viewport.getAlignment() };
1627 protected void undoMenuItem_actionPerformed(ActionEvent e)
1629 if (viewport.getHistoryList().isEmpty())
1633 CommandI command = viewport.getHistoryList().pop();
1634 viewport.addToRedoList(command);
1635 command.undoCommand(getViewAlignments());
1637 AlignmentViewport originalSource = getOriginatingSource(command);
1638 updateEditMenuBar();
1640 if (originalSource != null)
1642 if (originalSource != viewport)
1645 .warn("Implementation worry: mismatch of viewport origin for undo");
1647 originalSource.updateHiddenColumns();
1648 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1650 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1651 // viewport.getColumnSelection()
1652 // .getHiddenColumns().size() > 0);
1653 originalSource.firePropertyChange("alignment", null, originalSource
1654 .getAlignment().getSequences());
1665 protected void redoMenuItem_actionPerformed(ActionEvent e)
1667 if (viewport.getRedoList().size() < 1)
1672 CommandI command = viewport.getRedoList().pop();
1673 viewport.addToHistoryList(command);
1674 command.doCommand(getViewAlignments());
1676 AlignmentViewport originalSource = getOriginatingSource(command);
1677 updateEditMenuBar();
1679 if (originalSource != null)
1682 if (originalSource != viewport)
1685 .warn("Implementation worry: mismatch of viewport origin for redo");
1687 originalSource.updateHiddenColumns();
1688 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1690 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1691 // viewport.getColumnSelection()
1692 // .getHiddenColumns().size() > 0);
1693 originalSource.firePropertyChange("alignment", null, originalSource
1694 .getAlignment().getSequences());
1698 AlignmentViewport getOriginatingSource(CommandI command)
1700 AlignmentViewport originalSource = null;
1701 // For sequence removal and addition, we need to fire
1702 // the property change event FROM the viewport where the
1703 // original alignment was altered
1704 AlignmentI al = null;
1705 if (command instanceof EditCommand)
1707 EditCommand editCommand = (EditCommand) command;
1708 al = editCommand.getAlignment();
1709 List<Component> comps = PaintRefresher.components.get(viewport
1710 .getSequenceSetId());
1712 for (Component comp : comps)
1714 if (comp instanceof AlignmentPanel)
1716 if (al == ((AlignmentPanel) comp).av.getAlignment())
1718 originalSource = ((AlignmentPanel) comp).av;
1725 if (originalSource == null)
1727 // The original view is closed, we must validate
1728 // the current view against the closed view first
1731 PaintRefresher.validateSequences(al, viewport.getAlignment());
1734 originalSource = viewport;
1737 return originalSource;
1746 public void moveSelectedSequences(boolean up)
1748 SequenceGroup sg = viewport.getSelectionGroup();
1754 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1755 viewport.getHiddenRepSequences(), up);
1756 alignPanel.paintAlignment(true);
1759 synchronized void slideSequences(boolean right, int size)
1761 List<SequenceI> sg = new ArrayList<SequenceI>();
1762 if (viewport.cursorMode)
1764 sg.add(viewport.getAlignment().getSequenceAt(
1765 alignPanel.getSeqPanel().seqCanvas.cursorY));
1767 else if (viewport.getSelectionGroup() != null
1768 && viewport.getSelectionGroup().getSize() != viewport
1769 .getAlignment().getHeight())
1771 sg = viewport.getSelectionGroup().getSequences(
1772 viewport.getHiddenRepSequences());
1780 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1782 for (SequenceI seq : viewport.getAlignment().getSequences())
1784 if (!sg.contains(seq))
1786 invertGroup.add(seq);
1790 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1792 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1793 for (int i = 0; i < invertGroup.size(); i++)
1795 seqs2[i] = invertGroup.get(i);
1798 SlideSequencesCommand ssc;
1801 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1802 size, viewport.getGapCharacter());
1806 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1807 size, viewport.getGapCharacter());
1810 int groupAdjustment = 0;
1811 if (ssc.getGapsInsertedBegin() && right)
1813 if (viewport.cursorMode)
1815 alignPanel.getSeqPanel().moveCursor(size, 0);
1819 groupAdjustment = size;
1822 else if (!ssc.getGapsInsertedBegin() && !right)
1824 if (viewport.cursorMode)
1826 alignPanel.getSeqPanel().moveCursor(-size, 0);
1830 groupAdjustment = -size;
1834 if (groupAdjustment != 0)
1836 viewport.getSelectionGroup().setStartRes(
1837 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1838 viewport.getSelectionGroup().setEndRes(
1839 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1843 * just extend the last slide command if compatible; but not if in
1844 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1846 boolean appendHistoryItem = false;
1847 Deque<CommandI> historyList = viewport.getHistoryList();
1848 boolean inSplitFrame = getSplitViewContainer() != null;
1849 if (!inSplitFrame && historyList != null
1850 && historyList.size() > 0
1851 && historyList.peek() instanceof SlideSequencesCommand)
1853 appendHistoryItem = ssc
1854 .appendSlideCommand((SlideSequencesCommand) historyList
1858 if (!appendHistoryItem)
1860 addHistoryItem(ssc);
1873 protected void copy_actionPerformed(ActionEvent e)
1876 if (viewport.getSelectionGroup() == null)
1880 // TODO: preserve the ordering of displayed alignment annotation in any
1881 // internal paste (particularly sequence associated annotation)
1882 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1883 String[] omitHidden = null;
1885 if (viewport.hasHiddenColumns())
1887 omitHidden = viewport.getViewAsString(true);
1890 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1893 StringSelection ss = new StringSelection(output);
1897 jalview.gui.Desktop.internalCopy = true;
1898 // Its really worth setting the clipboard contents
1899 // to empty before setting the large StringSelection!!
1900 Toolkit.getDefaultToolkit().getSystemClipboard()
1901 .setContents(new StringSelection(""), null);
1903 Toolkit.getDefaultToolkit().getSystemClipboard()
1904 .setContents(ss, Desktop.instance);
1905 } catch (OutOfMemoryError er)
1907 new OOMWarning("copying region", er);
1911 ArrayList<int[]> hiddenColumns = null;
1912 if (viewport.hasHiddenColumns())
1914 hiddenColumns = new ArrayList<int[]>();
1915 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1916 .getSelectionGroup().getEndRes();
1917 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1919 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1921 hiddenColumns.add(new int[]
1922 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1927 Desktop.jalviewClipboard = new Object[]
1928 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1929 statusBar.setText(MessageManager.formatMessage(
1930 "label.copied_sequences_to_clipboard", new Object[]
1931 { Integer.valueOf(seqs.length).toString() }));
1941 protected void pasteNew_actionPerformed(ActionEvent e)
1953 protected void pasteThis_actionPerformed(ActionEvent e)
1959 * Paste contents of Jalview clipboard
1961 * @param newAlignment
1962 * true to paste to a new alignment, otherwise add to this.
1964 void paste(boolean newAlignment)
1966 boolean externalPaste = true;
1969 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1970 Transferable contents = c.getContents(this);
1972 if (contents == null)
1980 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1981 if (str.length() < 1)
1986 format = new IdentifyFile().Identify(str, "Paste");
1988 } catch (OutOfMemoryError er)
1990 new OOMWarning("Out of memory pasting sequences!!", er);
1994 SequenceI[] sequences;
1995 boolean annotationAdded = false;
1996 AlignmentI alignment = null;
1998 if (Desktop.jalviewClipboard != null)
2000 // The clipboard was filled from within Jalview, we must use the
2002 // And dataset from the copied alignment
2003 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2004 // be doubly sure that we create *new* sequence objects.
2005 sequences = new SequenceI[newseq.length];
2006 for (int i = 0; i < newseq.length; i++)
2008 sequences[i] = new Sequence(newseq[i]);
2010 alignment = new Alignment(sequences);
2011 externalPaste = false;
2015 // parse the clipboard as an alignment.
2016 alignment = new FormatAdapter().readFile(str, "Paste", format);
2017 sequences = alignment.getSequencesArray();
2021 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2027 if (Desktop.jalviewClipboard != null)
2029 // dataset is inherited
2030 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2034 // new dataset is constructed
2035 alignment.setDataset(null);
2037 alwidth = alignment.getWidth() + 1;
2041 AlignmentI pastedal = alignment; // preserve pasted alignment object
2042 // Add pasted sequences and dataset into existing alignment.
2043 alignment = viewport.getAlignment();
2044 alwidth = alignment.getWidth() + 1;
2045 // decide if we need to import sequences from an existing dataset
2046 boolean importDs = Desktop.jalviewClipboard != null
2047 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2048 // importDs==true instructs us to copy over new dataset sequences from
2049 // an existing alignment
2050 Vector newDs = (importDs) ? new Vector() : null; // used to create
2051 // minimum dataset set
2053 for (int i = 0; i < sequences.length; i++)
2057 newDs.addElement(null);
2059 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2061 if (importDs && ds != null)
2063 if (!newDs.contains(ds))
2065 newDs.setElementAt(ds, i);
2066 ds = new Sequence(ds);
2067 // update with new dataset sequence
2068 sequences[i].setDatasetSequence(ds);
2072 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2077 // copy and derive new dataset sequence
2078 sequences[i] = sequences[i].deriveSequence();
2079 alignment.getDataset().addSequence(
2080 sequences[i].getDatasetSequence());
2081 // TODO: avoid creation of duplicate dataset sequences with a
2082 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2084 alignment.addSequence(sequences[i]); // merges dataset
2088 newDs.clear(); // tidy up
2090 if (alignment.getAlignmentAnnotation() != null)
2092 for (AlignmentAnnotation alan : alignment
2093 .getAlignmentAnnotation())
2095 if (alan.graphGroup > fgroup)
2097 fgroup = alan.graphGroup;
2101 if (pastedal.getAlignmentAnnotation() != null)
2103 // Add any annotation attached to alignment.
2104 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2105 for (int i = 0; i < alann.length; i++)
2107 annotationAdded = true;
2108 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2110 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2111 if (newann.graphGroup > -1)
2113 if (newGraphGroups.size() <= newann.graphGroup
2114 || newGraphGroups.get(newann.graphGroup) == null)
2116 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2118 newGraphGroups.add(q, null);
2120 newGraphGroups.set(newann.graphGroup, new Integer(
2123 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2127 newann.padAnnotation(alwidth);
2128 alignment.addAnnotation(newann);
2138 addHistoryItem(new EditCommand(
2139 MessageManager.getString("label.add_sequences"),
2141 sequences, 0, alignment.getWidth(), alignment));
2143 // Add any annotations attached to sequences
2144 for (int i = 0; i < sequences.length; i++)
2146 if (sequences[i].getAnnotation() != null)
2148 AlignmentAnnotation newann;
2149 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2151 annotationAdded = true;
2152 newann = sequences[i].getAnnotation()[a];
2153 newann.adjustForAlignment();
2154 newann.padAnnotation(alwidth);
2155 if (newann.graphGroup > -1)
2157 if (newann.graphGroup > -1)
2159 if (newGraphGroups.size() <= newann.graphGroup
2160 || newGraphGroups.get(newann.graphGroup) == null)
2162 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2164 newGraphGroups.add(q, null);
2166 newGraphGroups.set(newann.graphGroup, new Integer(
2169 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2173 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2178 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2185 // propagate alignment changed.
2186 viewport.setEndSeq(alignment.getHeight());
2187 if (annotationAdded)
2189 // Duplicate sequence annotation in all views.
2190 AlignmentI[] alview = this.getViewAlignments();
2191 for (int i = 0; i < sequences.length; i++)
2193 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2198 for (int avnum = 0; avnum < alview.length; avnum++)
2200 if (alview[avnum] != alignment)
2202 // duplicate in a view other than the one with input focus
2203 int avwidth = alview[avnum].getWidth() + 1;
2204 // this relies on sann being preserved after we
2205 // modify the sequence's annotation array for each duplication
2206 for (int a = 0; a < sann.length; a++)
2208 AlignmentAnnotation newann = new AlignmentAnnotation(
2210 sequences[i].addAlignmentAnnotation(newann);
2211 newann.padAnnotation(avwidth);
2212 alview[avnum].addAnnotation(newann); // annotation was
2213 // duplicated earlier
2214 // TODO JAL-1145 graphGroups are not updated for sequence
2215 // annotation added to several views. This may cause
2217 alview[avnum].setAnnotationIndex(newann, a);
2222 buildSortByAnnotationScoresMenu();
2224 viewport.firePropertyChange("alignment", null,
2225 alignment.getSequences());
2226 if (alignPanels != null)
2228 for (AlignmentPanel ap : alignPanels)
2230 ap.validateAnnotationDimensions(false);
2235 alignPanel.validateAnnotationDimensions(false);
2241 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2243 String newtitle = new String("Copied sequences");
2245 if (Desktop.jalviewClipboard != null
2246 && Desktop.jalviewClipboard[2] != null)
2248 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2249 for (int[] region : hc)
2251 af.viewport.hideColumns(region[0], region[1]);
2255 // >>>This is a fix for the moment, until a better solution is
2257 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2259 alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
2261 // TODO: maintain provenance of an alignment, rather than just make the
2262 // title a concatenation of operations.
2265 if (title.startsWith("Copied sequences"))
2271 newtitle = newtitle.concat("- from " + title);
2276 newtitle = new String("Pasted sequences");
2279 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2284 } catch (Exception ex)
2286 ex.printStackTrace();
2287 System.out.println("Exception whilst pasting: " + ex);
2288 // could be anything being pasted in here
2294 protected void expand_newalign(ActionEvent e)
2298 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2299 .getAlignment(), -1);
2300 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2302 String newtitle = new String("Flanking alignment");
2304 if (Desktop.jalviewClipboard != null
2305 && Desktop.jalviewClipboard[2] != null)
2307 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2308 for (int region[] : hc)
2310 af.viewport.hideColumns(region[0], region[1]);
2314 // >>>This is a fix for the moment, until a better solution is
2316 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2318 alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
2320 // TODO: maintain provenance of an alignment, rather than just make the
2321 // title a concatenation of operations.
2323 if (title.startsWith("Copied sequences"))
2329 newtitle = newtitle.concat("- from " + title);
2333 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2335 } catch (Exception ex)
2337 ex.printStackTrace();
2338 System.out.println("Exception whilst pasting: " + ex);
2339 // could be anything being pasted in here
2340 } catch (OutOfMemoryError oom)
2342 new OOMWarning("Viewing flanking region of alignment", oom);
2353 protected void cut_actionPerformed(ActionEvent e)
2355 copy_actionPerformed(null);
2356 delete_actionPerformed(null);
2366 protected void delete_actionPerformed(ActionEvent evt)
2369 SequenceGroup sg = viewport.getSelectionGroup();
2376 * If the cut affects all sequences, warn, remove highlighted columns
2378 if (sg.getSize() == viewport.getAlignment().getHeight())
2380 int confirm = JOptionPane.showConfirmDialog(this,
2381 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2382 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2383 JOptionPane.OK_CANCEL_OPTION);
2385 if (confirm == JOptionPane.CANCEL_OPTION
2386 || confirm == JOptionPane.CLOSED_OPTION)
2390 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2391 sg.getEndRes() + 1);
2394 SequenceI[] cut = sg.getSequences()
2395 .toArray(new SequenceI[sg.getSize()]);
2397 addHistoryItem(new EditCommand(
2398 MessageManager.getString("label.cut_sequences"), Action.CUT,
2399 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2400 viewport.getAlignment()));
2402 viewport.setSelectionGroup(null);
2403 viewport.sendSelection();
2404 viewport.getAlignment().deleteGroup(sg);
2406 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2408 if (viewport.getAlignment().getHeight() < 1)
2412 this.setClosed(true);
2413 } catch (Exception ex)
2426 protected void deleteGroups_actionPerformed(ActionEvent e)
2428 if (avc.deleteGroups())
2430 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2431 alignPanel.updateAnnotation();
2432 alignPanel.paintAlignment(true);
2443 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2445 SequenceGroup sg = new SequenceGroup();
2447 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2449 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2452 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2453 viewport.setSelectionGroup(sg);
2454 viewport.sendSelection();
2455 alignPanel.paintAlignment(true);
2456 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2466 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2468 if (viewport.cursorMode)
2470 alignPanel.getSeqPanel().keyboardNo1 = null;
2471 alignPanel.getSeqPanel().keyboardNo2 = null;
2473 viewport.setSelectionGroup(null);
2474 viewport.getColumnSelection().clear();
2475 viewport.setSelectionGroup(null);
2476 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2477 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2478 alignPanel.paintAlignment(true);
2479 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2480 viewport.sendSelection();
2490 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2492 SequenceGroup sg = viewport.getSelectionGroup();
2496 selectAllSequenceMenuItem_actionPerformed(null);
2501 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2503 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2506 alignPanel.paintAlignment(true);
2507 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2508 viewport.sendSelection();
2512 public void invertColSel_actionPerformed(ActionEvent e)
2514 viewport.invertColumnSelection();
2515 alignPanel.paintAlignment(true);
2516 viewport.sendSelection();
2526 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2528 trimAlignment(true);
2538 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2540 trimAlignment(false);
2543 void trimAlignment(boolean trimLeft)
2545 ColumnSelection colSel = viewport.getColumnSelection();
2548 if (colSel.size() > 0)
2552 column = colSel.getMin();
2556 column = colSel.getMax();
2560 if (viewport.getSelectionGroup() != null)
2562 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2563 viewport.getHiddenRepSequences());
2567 seqs = viewport.getAlignment().getSequencesArray();
2570 TrimRegionCommand trimRegion;
2573 trimRegion = new TrimRegionCommand("Remove Left",
2574 TrimRegionCommand.TRIM_LEFT, seqs, column,
2575 viewport.getAlignment(), viewport.getColumnSelection(),
2576 viewport.getSelectionGroup());
2577 viewport.setStartRes(0);
2581 trimRegion = new TrimRegionCommand("Remove Right",
2582 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2583 viewport.getAlignment(), viewport.getColumnSelection(),
2584 viewport.getSelectionGroup());
2587 statusBar.setText(MessageManager.formatMessage(
2588 "label.removed_columns", new String[]
2589 { Integer.valueOf(trimRegion.getSize()).toString() }));
2591 addHistoryItem(trimRegion);
2593 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2595 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2596 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2598 viewport.getAlignment().deleteGroup(sg);
2602 viewport.firePropertyChange("alignment", null, viewport
2603 .getAlignment().getSequences());
2614 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2616 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2619 if (viewport.getSelectionGroup() != null)
2621 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2622 viewport.getHiddenRepSequences());
2623 start = viewport.getSelectionGroup().getStartRes();
2624 end = viewport.getSelectionGroup().getEndRes();
2628 seqs = viewport.getAlignment().getSequencesArray();
2631 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2632 "Remove Gapped Columns", seqs, start, end,
2633 viewport.getAlignment());
2635 addHistoryItem(removeGapCols);
2637 statusBar.setText(MessageManager.formatMessage(
2638 "label.removed_empty_columns", new Object[]
2639 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2641 // This is to maintain viewport position on first residue
2642 // of first sequence
2643 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2644 int startRes = seq.findPosition(viewport.startRes);
2645 // ShiftList shifts;
2646 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2647 // edit.alColumnChanges=shifts.getInverse();
2648 // if (viewport.hasHiddenColumns)
2649 // viewport.getColumnSelection().compensateForEdits(shifts);
2650 viewport.setStartRes(seq.findIndex(startRes) - 1);
2651 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2663 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2665 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2668 if (viewport.getSelectionGroup() != null)
2670 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2671 viewport.getHiddenRepSequences());
2672 start = viewport.getSelectionGroup().getStartRes();
2673 end = viewport.getSelectionGroup().getEndRes();
2677 seqs = viewport.getAlignment().getSequencesArray();
2680 // This is to maintain viewport position on first residue
2681 // of first sequence
2682 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2683 int startRes = seq.findPosition(viewport.startRes);
2685 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2686 viewport.getAlignment()));
2688 viewport.setStartRes(seq.findIndex(startRes) - 1);
2690 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2702 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2704 viewport.setPadGaps(padGapsMenuitem.isSelected());
2705 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2716 public void findMenuItem_actionPerformed(ActionEvent e)
2722 * Create a new view of the current alignment.
2725 public void newView_actionPerformed(ActionEvent e)
2727 newView(null, true);
2731 * Creates and shows a new view of the current alignment.
2734 * title of newly created view; if null, one will be generated
2735 * @param copyAnnotation
2736 * if true then duplicate all annnotation, groups and settings
2737 * @return new alignment panel, already displayed.
2739 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2742 * Create a new AlignmentPanel (with its own, new Viewport)
2744 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2746 if (!copyAnnotation)
2749 * remove all groups and annotation except for the automatic stuff
2751 newap.av.getAlignment().deleteAllGroups();
2752 newap.av.getAlignment().deleteAllAnnotations(false);
2755 newap.av.setGatherViewsHere(false);
2757 if (viewport.viewName == null)
2759 viewport.viewName = MessageManager
2760 .getString("label.view_name_original");
2764 * Views share the same edits undo and redo stacks
2766 newap.av.setHistoryList(viewport.getHistoryList());
2767 newap.av.setRedoList(viewport.getRedoList());
2770 * Views share the same mappings; need to deregister any new mappings
2771 * created by copyAlignPanel, and register the new reference to the shared
2774 newap.av.replaceMappings(viewport.getAlignment());
2776 newap.av.viewName = getNewViewName(viewTitle);
2778 addAlignmentPanel(newap, true);
2779 newap.alignmentChanged();
2781 if (alignPanels.size() == 2)
2783 viewport.setGatherViewsHere(true);
2785 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2790 * Make a new name for the view, ensuring it is unique within the current
2791 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2792 * these now use viewId. Unique view names are still desirable for usability.)
2797 protected String getNewViewName(String viewTitle)
2799 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2800 boolean addFirstIndex = false;
2801 if (viewTitle == null || viewTitle.trim().length() == 0)
2803 viewTitle = MessageManager.getString("action.view");
2804 addFirstIndex = true;
2808 index = 1;// we count from 1 if given a specific name
2810 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2812 List<Component> comps = PaintRefresher.components.get(viewport
2813 .getSequenceSetId());
2815 List<String> existingNames = getExistingViewNames(comps);
2817 while (existingNames.contains(newViewName))
2819 newViewName = viewTitle + " " + (++index);
2825 * Returns a list of distinct view names found in the given list of
2826 * components. View names are held on the viewport of an AlignmentPanel.
2831 protected List<String> getExistingViewNames(List<Component> comps)
2833 List<String> existingNames = new ArrayList<String>();
2834 for (Component comp : comps)
2836 if (comp instanceof AlignmentPanel)
2838 AlignmentPanel ap = (AlignmentPanel) comp;
2839 if (!existingNames.contains(ap.av.viewName))
2841 existingNames.add(ap.av.viewName);
2845 return existingNames;
2849 * Explode tabbed views into separate windows.
2852 public void expandViews_actionPerformed(ActionEvent e)
2854 Desktop.instance.explodeViews(this);
2858 * Gather views in separate windows back into a tabbed presentation.
2861 public void gatherViews_actionPerformed(ActionEvent e)
2863 Desktop.instance.gatherViews(this);
2873 public void font_actionPerformed(ActionEvent e)
2875 new FontChooser(alignPanel);
2885 protected void seqLimit_actionPerformed(ActionEvent e)
2887 viewport.setShowJVSuffix(seqLimits.isSelected());
2889 alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
2890 .calculateIdWidth());
2891 alignPanel.paintAlignment(true);
2895 public void idRightAlign_actionPerformed(ActionEvent e)
2897 viewport.setRightAlignIds(idRightAlign.isSelected());
2898 alignPanel.paintAlignment(true);
2902 public void centreColumnLabels_actionPerformed(ActionEvent e)
2904 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2905 alignPanel.paintAlignment(true);
2911 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2914 protected void followHighlight_actionPerformed()
2917 * Set the 'follow' flag on the Viewport (and scroll to position if now
2920 final boolean state = this.followHighlightMenuItem.getState();
2921 viewport.setFollowHighlight(state);
2924 alignPanel.scrollToPosition(
2925 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2936 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2938 viewport.setColourText(colourTextMenuItem.isSelected());
2939 alignPanel.paintAlignment(true);
2949 public void wrapMenuItem_actionPerformed(ActionEvent e)
2951 scaleAbove.setVisible(wrapMenuItem.isSelected());
2952 scaleLeft.setVisible(wrapMenuItem.isSelected());
2953 scaleRight.setVisible(wrapMenuItem.isSelected());
2954 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2955 alignPanel.updateLayout();
2959 public void showAllSeqs_actionPerformed(ActionEvent e)
2961 viewport.showAllHiddenSeqs();
2965 public void showAllColumns_actionPerformed(ActionEvent e)
2967 viewport.showAllHiddenColumns();
2972 public void hideSelSequences_actionPerformed(ActionEvent e)
2974 viewport.hideAllSelectedSeqs();
2975 // alignPanel.paintAlignment(true);
2979 * called by key handler and the hide all/show all menu items
2984 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2987 boolean hide = false;
2988 SequenceGroup sg = viewport.getSelectionGroup();
2989 if (!toggleSeqs && !toggleCols)
2991 // Hide everything by the current selection - this is a hack - we do the
2992 // invert and then hide
2993 // first check that there will be visible columns after the invert.
2994 if ((viewport.getColumnSelection() != null
2995 && viewport.getColumnSelection().getSelected() != null && viewport
2996 .getColumnSelection().getSelected().size() > 0)
2997 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3000 // now invert the sequence set, if required - empty selection implies
3001 // that no hiding is required.
3004 invertSequenceMenuItem_actionPerformed(null);
3005 sg = viewport.getSelectionGroup();
3009 viewport.expandColSelection(sg, true);
3010 // finally invert the column selection and get the new sequence
3012 invertColSel_actionPerformed(null);
3019 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3021 hideSelSequences_actionPerformed(null);
3024 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3027 showAllSeqs_actionPerformed(null);
3033 if (viewport.getColumnSelection().getSelected().size() > 0)
3035 hideSelColumns_actionPerformed(null);
3038 viewport.setSelectionGroup(sg);
3043 showAllColumns_actionPerformed(null);
3052 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3053 * event.ActionEvent)
3056 public void hideAllButSelection_actionPerformed(ActionEvent e)
3058 toggleHiddenRegions(false, false);
3065 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3069 public void hideAllSelection_actionPerformed(ActionEvent e)
3071 SequenceGroup sg = viewport.getSelectionGroup();
3072 viewport.expandColSelection(sg, false);
3073 viewport.hideAllSelectedSeqs();
3074 viewport.hideSelectedColumns();
3075 alignPanel.paintAlignment(true);
3082 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3086 public void showAllhidden_actionPerformed(ActionEvent e)
3088 viewport.showAllHiddenColumns();
3089 viewport.showAllHiddenSeqs();
3090 alignPanel.paintAlignment(true);
3094 public void hideSelColumns_actionPerformed(ActionEvent e)
3096 viewport.hideSelectedColumns();
3097 alignPanel.paintAlignment(true);
3101 public void hiddenMarkers_actionPerformed(ActionEvent e)
3103 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3114 protected void scaleAbove_actionPerformed(ActionEvent e)
3116 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3117 alignPanel.paintAlignment(true);
3127 protected void scaleLeft_actionPerformed(ActionEvent e)
3129 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3130 alignPanel.paintAlignment(true);
3140 protected void scaleRight_actionPerformed(ActionEvent e)
3142 viewport.setScaleRightWrapped(scaleRight.isSelected());
3143 alignPanel.paintAlignment(true);
3153 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3155 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3156 alignPanel.paintAlignment(true);
3166 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3168 viewport.setShowText(viewTextMenuItem.isSelected());
3169 alignPanel.paintAlignment(true);
3179 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3181 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3182 alignPanel.paintAlignment(true);
3185 public FeatureSettings featureSettings;
3188 public FeatureSettingsControllerI getFeatureSettingsUI()
3190 return featureSettings;
3194 public void featureSettings_actionPerformed(ActionEvent e)
3196 if (featureSettings != null)
3198 featureSettings.close();
3199 featureSettings = null;
3201 if (!showSeqFeatures.isSelected())
3203 // make sure features are actually displayed
3204 showSeqFeatures.setSelected(true);
3205 showSeqFeatures_actionPerformed(null);
3207 featureSettings = new FeatureSettings(this);
3211 * Set or clear 'Show Sequence Features'
3217 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3219 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3220 alignPanel.paintAlignment(true);
3221 if (alignPanel.getOverviewPanel() != null)
3223 alignPanel.getOverviewPanel().updateOverviewImage();
3228 * Set or clear 'Show Sequence Features'
3234 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3236 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3238 if (viewport.isShowSequenceFeaturesHeight())
3240 // ensure we're actually displaying features
3241 viewport.setShowSequenceFeatures(true);
3242 showSeqFeatures.setSelected(true);
3244 alignPanel.paintAlignment(true);
3245 if (alignPanel.getOverviewPanel() != null)
3247 alignPanel.getOverviewPanel().updateOverviewImage();
3252 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3253 * the annotations panel as a whole.
3255 * The options to show/hide all annotations should be enabled when the panel
3256 * is shown, and disabled when the panel is hidden.
3261 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3263 final boolean setVisible = annotationPanelMenuItem.isSelected();
3264 viewport.setShowAnnotation(setVisible);
3265 this.showAllSeqAnnotations.setEnabled(setVisible);
3266 this.hideAllSeqAnnotations.setEnabled(setVisible);
3267 this.showAllAlAnnotations.setEnabled(setVisible);
3268 this.hideAllAlAnnotations.setEnabled(setVisible);
3269 alignPanel.updateLayout();
3273 public void alignmentProperties()
3275 JEditorPane editPane = new JEditorPane("text/html", "");
3276 editPane.setEditable(false);
3277 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3279 editPane.setText(MessageManager.formatMessage("label.html_content",
3281 { contents.toString() }));
3282 JInternalFrame frame = new JInternalFrame();
3283 frame.getContentPane().add(new JScrollPane(editPane));
3285 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3286 "label.alignment_properties", new Object[]
3287 { getTitle() }), 500, 400);
3297 public void overviewMenuItem_actionPerformed(ActionEvent e)
3299 if (alignPanel.overviewPanel != null)
3304 JInternalFrame frame = new JInternalFrame();
3305 OverviewPanel overview = new OverviewPanel(alignPanel);
3306 frame.setContentPane(overview);
3307 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3308 "label.overview_params", new Object[]
3309 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3311 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3312 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3315 public void internalFrameClosed(
3316 javax.swing.event.InternalFrameEvent evt)
3318 alignPanel.setOverviewPanel(null);
3322 alignPanel.setOverviewPanel(overview);
3326 public void textColour_actionPerformed(ActionEvent e)
3328 new TextColourChooser().chooseColour(alignPanel, null);
3338 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3350 public void clustalColour_actionPerformed(ActionEvent e)
3352 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3353 viewport.getHiddenRepSequences()));
3363 public void zappoColour_actionPerformed(ActionEvent e)
3365 changeColour(new ZappoColourScheme());
3375 public void taylorColour_actionPerformed(ActionEvent e)
3377 changeColour(new TaylorColourScheme());
3387 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3389 changeColour(new HydrophobicColourScheme());
3399 public void helixColour_actionPerformed(ActionEvent e)
3401 changeColour(new HelixColourScheme());
3411 public void strandColour_actionPerformed(ActionEvent e)
3413 changeColour(new StrandColourScheme());
3423 public void turnColour_actionPerformed(ActionEvent e)
3425 changeColour(new TurnColourScheme());
3435 public void buriedColour_actionPerformed(ActionEvent e)
3437 changeColour(new BuriedColourScheme());
3447 public void nucleotideColour_actionPerformed(ActionEvent e)
3449 changeColour(new NucleotideColourScheme());
3453 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3455 changeColour(new PurinePyrimidineColourScheme());
3459 * public void covariationColour_actionPerformed(ActionEvent e) {
3461 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3465 public void annotationColour_actionPerformed(ActionEvent e)
3467 new AnnotationColourChooser(viewport, alignPanel);
3471 public void annotationColumn_actionPerformed(ActionEvent e)
3473 new AnnotationColumnChooser(viewport, alignPanel);
3477 public void rnahelicesColour_actionPerformed(ActionEvent e)
3479 new RNAHelicesColourChooser(viewport, alignPanel);
3489 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3491 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3500 public void changeColour(ColourSchemeI cs)
3502 // TODO: compare with applet and pull up to model method
3507 if (viewport.getAbovePIDThreshold())
3509 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3511 cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
3515 cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
3518 if (viewport.getConservationSelected())
3521 Alignment al = (Alignment) viewport.getAlignment();
3522 Conservation c = new Conservation("All",
3523 ResidueProperties.propHash, 3, al.getSequences(), 0,
3527 c.verdict(false, viewport.getConsPercGaps());
3529 cs.setConservation(c);
3531 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3536 cs.setConservation(null);
3539 cs.setConsensus(viewport.getSequenceConsensusHash());
3542 viewport.setGlobalColourScheme(cs);
3544 if (viewport.getColourAppliesToAllGroups())
3547 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3555 if (cs instanceof ClustalxColourScheme)
3557 sg.cs = new ClustalxColourScheme(sg,
3558 viewport.getHiddenRepSequences());
3560 else if (cs instanceof UserColourScheme)
3562 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3568 sg.cs = cs.getClass().newInstance();
3569 } catch (Exception ex)
3574 if (viewport.getAbovePIDThreshold()
3575 || cs instanceof PIDColourScheme
3576 || cs instanceof Blosum62ColourScheme)
3578 sg.cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
3580 sg.cs.setConsensus(AAFrequency.calculate(
3581 sg.getSequences(viewport.getHiddenRepSequences()),
3582 sg.getStartRes(), sg.getEndRes() + 1));
3586 sg.cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
3589 if (viewport.getConservationSelected())
3591 Conservation c = new Conservation("Group",
3592 ResidueProperties.propHash, 3, sg.getSequences(viewport
3593 .getHiddenRepSequences()), sg.getStartRes(),
3594 sg.getEndRes() + 1);
3596 c.verdict(false, viewport.getConsPercGaps());
3597 sg.cs.setConservation(c);
3601 sg.cs.setConservation(null);
3606 if (alignPanel.getOverviewPanel() != null)
3608 alignPanel.getOverviewPanel().updateOverviewImage();
3611 alignPanel.paintAlignment(true);
3621 protected void modifyPID_actionPerformed(ActionEvent e)
3623 if (viewport.getAbovePIDThreshold()
3624 && viewport.getGlobalColourScheme() != null)
3626 SliderPanel.setPIDSliderSource(alignPanel,
3627 viewport.getGlobalColourScheme(), "Background");
3628 SliderPanel.showPIDSlider();
3639 protected void modifyConservation_actionPerformed(ActionEvent e)
3641 if (viewport.getConservationSelected()
3642 && viewport.getGlobalColourScheme() != null)
3644 SliderPanel.setConservationSlider(alignPanel,
3645 viewport.getGlobalColourScheme(), "Background");
3646 SliderPanel.showConservationSlider();
3657 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3659 viewport.setConservationSelected(conservationMenuItem.isSelected());
3661 viewport.setAbovePIDThreshold(false);
3662 abovePIDThreshold.setSelected(false);
3664 changeColour(viewport.getGlobalColourScheme());
3666 modifyConservation_actionPerformed(null);
3676 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3678 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3680 conservationMenuItem.setSelected(false);
3681 viewport.setConservationSelected(false);
3683 changeColour(viewport.getGlobalColourScheme());
3685 modifyPID_actionPerformed(null);
3695 public void userDefinedColour_actionPerformed(ActionEvent e)
3697 if (e.getActionCommand().equals(
3698 MessageManager.getString("action.user_defined")))
3700 new UserDefinedColours(alignPanel, null);
3704 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3705 .getUserColourSchemes().get(e.getActionCommand());
3711 public void updateUserColourMenu()
3714 Component[] menuItems = colourMenu.getMenuComponents();
3715 int iSize = menuItems.length;
3716 for (int i = 0; i < iSize; i++)
3718 if (menuItems[i].getName() != null
3719 && menuItems[i].getName().equals("USER_DEFINED"))
3721 colourMenu.remove(menuItems[i]);
3725 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3727 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3728 .getUserColourSchemes().keys();
3730 while (userColours.hasMoreElements())
3732 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3733 userColours.nextElement().toString());
3734 radioItem.setName("USER_DEFINED");
3735 radioItem.addMouseListener(new MouseAdapter()
3738 public void mousePressed(MouseEvent evt)
3740 if (evt.isControlDown()
3741 || SwingUtilities.isRightMouseButton(evt))
3743 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3745 int option = JOptionPane.showInternalConfirmDialog(
3746 jalview.gui.Desktop.desktop,
3748 .getString("label.remove_from_default_list"),
3750 .getString("label.remove_user_defined_colour"),
3751 JOptionPane.YES_NO_OPTION);
3752 if (option == JOptionPane.YES_OPTION)
3754 jalview.gui.UserDefinedColours
3755 .removeColourFromDefaults(radioItem.getText());
3756 colourMenu.remove(radioItem);
3760 radioItem.addActionListener(new ActionListener()
3763 public void actionPerformed(ActionEvent evt)
3765 userDefinedColour_actionPerformed(evt);
3772 radioItem.addActionListener(new ActionListener()
3775 public void actionPerformed(ActionEvent evt)
3777 userDefinedColour_actionPerformed(evt);
3781 colourMenu.insert(radioItem, 15);
3782 colours.add(radioItem);
3794 public void PIDColour_actionPerformed(ActionEvent e)
3796 changeColour(new PIDColourScheme());
3806 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3808 changeColour(new Blosum62ColourScheme());
3818 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3820 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3821 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3822 .getAlignment().getSequenceAt(0), null);
3823 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3824 viewport.getAlignment()));
3825 alignPanel.paintAlignment(true);
3835 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3837 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3838 AlignmentSorter.sortByID(viewport.getAlignment());
3839 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3840 viewport.getAlignment()));
3841 alignPanel.paintAlignment(true);
3851 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3853 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3854 AlignmentSorter.sortByLength(viewport.getAlignment());
3855 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3856 viewport.getAlignment()));
3857 alignPanel.paintAlignment(true);
3867 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3869 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3870 AlignmentSorter.sortByGroup(viewport.getAlignment());
3871 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3872 viewport.getAlignment()));
3874 alignPanel.paintAlignment(true);
3884 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3886 new RedundancyPanel(alignPanel, this);
3896 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3898 if ((viewport.getSelectionGroup() == null)
3899 || (viewport.getSelectionGroup().getSize() < 2))
3901 JOptionPane.showInternalMessageDialog(this, MessageManager
3902 .getString("label.you_must_select_least_two_sequences"),
3903 MessageManager.getString("label.invalid_selection"),
3904 JOptionPane.WARNING_MESSAGE);
3908 JInternalFrame frame = new JInternalFrame();
3909 frame.setContentPane(new PairwiseAlignPanel(viewport));
3910 Desktop.addInternalFrame(frame,
3911 MessageManager.getString("action.pairwise_alignment"), 600,
3923 public void PCAMenuItem_actionPerformed(ActionEvent e)
3925 if (((viewport.getSelectionGroup() != null)
3926 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3927 .getSelectionGroup().getSize() > 0))
3928 || (viewport.getAlignment().getHeight() < 4))
3931 .showInternalMessageDialog(
3934 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3936 .getString("label.sequence_selection_insufficient"),
3937 JOptionPane.WARNING_MESSAGE);
3942 new PCAPanel(alignPanel);
3946 public void autoCalculate_actionPerformed(ActionEvent e)
3948 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3949 if (viewport.autoCalculateConsensus)
3951 viewport.firePropertyChange("alignment", null, viewport
3952 .getAlignment().getSequences());
3957 public void sortByTreeOption_actionPerformed(ActionEvent e)
3959 viewport.sortByTree = sortByTree.isSelected();
3963 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3965 viewport.followSelection = listenToViewSelections.isSelected();
3975 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3977 newTreePanel("AV", "PID", "Average distance tree using PID");
3987 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3989 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3999 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
4001 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
4011 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
4013 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
4026 void newTreePanel(String type, String pwType, String title)
4030 if (viewport.getSelectionGroup() != null
4031 && viewport.getSelectionGroup().getSize() > 0)
4033 if (viewport.getSelectionGroup().getSize() < 3)
4039 .getString("label.you_need_more_two_sequences_selected_build_tree"),
4041 .getString("label.not_enough_sequences"),
4042 JOptionPane.WARNING_MESSAGE);
4046 SequenceGroup sg = viewport.getSelectionGroup();
4048 /* Decide if the selection is a column region */
4049 for (SequenceI _s : sg.getSequences())
4051 if (_s.getLength() < sg.getEndRes())
4057 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
4059 .getString("label.sequences_selection_not_aligned"),
4060 JOptionPane.WARNING_MESSAGE);
4066 title = title + " on region";
4067 tp = new TreePanel(alignPanel, type, pwType);
4071 // are the visible sequences aligned?
4072 if (!viewport.getAlignment().isAligned(false))
4078 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4080 .getString("label.sequences_not_aligned"),
4081 JOptionPane.WARNING_MESSAGE);
4086 if (viewport.getAlignment().getHeight() < 2)
4091 tp = new TreePanel(alignPanel, type, pwType);
4096 if (viewport.viewName != null)
4098 title += viewport.viewName + " of ";
4101 title += this.title;
4103 Desktop.addInternalFrame(tp, title, 600, 500);
4114 public void addSortByOrderMenuItem(String title,
4115 final AlignmentOrder order)
4117 final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new Object[]{title}));
4119 item.addActionListener(new java.awt.event.ActionListener()
4122 public void actionPerformed(ActionEvent e)
4124 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4126 // TODO: JBPNote - have to map order entries to curent SequenceI
4128 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4130 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4133 alignPanel.paintAlignment(true);
4139 * Add a new sort by annotation score menu item
4142 * the menu to add the option to
4144 * the label used to retrieve scores for each sequence on the
4147 public void addSortByAnnotScoreMenuItem(JMenu sort,
4148 final String scoreLabel)
4150 final JMenuItem item = new JMenuItem(scoreLabel);
4152 item.addActionListener(new java.awt.event.ActionListener()
4155 public void actionPerformed(ActionEvent e)
4157 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4158 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4159 viewport.getAlignment());// ,viewport.getSelectionGroup());
4160 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4161 viewport.getAlignment()));
4162 alignPanel.paintAlignment(true);
4168 * last hash for alignment's annotation array - used to minimise cost of
4171 protected int _annotationScoreVectorHash;
4174 * search the alignment and rebuild the sort by annotation score submenu the
4175 * last alignment annotation vector hash is stored to minimize cost of
4176 * rebuilding in subsequence calls.
4180 public void buildSortByAnnotationScoresMenu()
4182 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4187 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4189 sortByAnnotScore.removeAll();
4190 // almost certainly a quicker way to do this - but we keep it simple
4191 Hashtable scoreSorts = new Hashtable();
4192 AlignmentAnnotation aann[];
4193 for (SequenceI sqa : viewport.getAlignment().getSequences())
4195 aann = sqa.getAnnotation();
4196 for (int i = 0; aann != null && i < aann.length; i++)
4198 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4200 scoreSorts.put(aann[i].label, aann[i].label);
4204 Enumeration labels = scoreSorts.keys();
4205 while (labels.hasMoreElements())
4207 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4208 (String) labels.nextElement());
4210 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4213 _annotationScoreVectorHash = viewport.getAlignment()
4214 .getAlignmentAnnotation().hashCode();
4219 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4220 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4221 * call. Listeners are added to remove the menu item when the treePanel is
4222 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4226 * Displayed tree window.
4228 * SortBy menu item title.
4231 public void buildTreeMenu()
4233 calculateTree.removeAll();
4234 // build the calculate menu
4236 for (final String type : new String[]
4239 String treecalcnm = MessageManager.getString("label.tree_calc_"
4240 + type.toLowerCase());
4241 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4243 JMenuItem tm = new JMenuItem();
4244 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4245 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4247 String smn = MessageManager.getStringOrReturn(
4248 "label.score_model_", sm.getName());
4249 final String title = MessageManager.formatMessage(
4250 "label.treecalc_title", treecalcnm, smn);
4251 tm.setText(title);//
4252 tm.addActionListener(new java.awt.event.ActionListener()
4255 public void actionPerformed(ActionEvent e)
4257 newTreePanel(type, pwtype, title);
4260 calculateTree.add(tm);
4265 sortByTreeMenu.removeAll();
4267 List<Component> comps = PaintRefresher.components.get(viewport
4268 .getSequenceSetId());
4269 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4270 for (Component comp : comps)
4272 if (comp instanceof TreePanel)
4274 treePanels.add((TreePanel) comp);
4278 if (treePanels.size() < 1)
4280 sortByTreeMenu.setVisible(false);
4284 sortByTreeMenu.setVisible(true);
4286 for (final TreePanel tp : treePanels)
4288 final JMenuItem item = new JMenuItem(tp.getTitle());
4289 item.addActionListener(new java.awt.event.ActionListener()
4292 public void actionPerformed(ActionEvent e)
4294 tp.sortByTree_actionPerformed();
4295 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4300 sortByTreeMenu.add(item);
4304 public boolean sortBy(AlignmentOrder alorder, String undoname)
4306 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4307 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4308 if (undoname != null)
4310 addHistoryItem(new OrderCommand(undoname, oldOrder,
4311 viewport.getAlignment()));
4313 alignPanel.paintAlignment(true);
4318 * Work out whether the whole set of sequences or just the selected set will
4319 * be submitted for multiple alignment.
4322 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4324 // Now, check we have enough sequences
4325 AlignmentView msa = null;
4327 if ((viewport.getSelectionGroup() != null)
4328 && (viewport.getSelectionGroup().getSize() > 1))
4330 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4331 // some common interface!
4333 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4334 * SequenceI[sz = seqs.getSize(false)];
4336 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4337 * seqs.getSequenceAt(i); }
4339 msa = viewport.getAlignmentView(true);
4341 else if (viewport.getSelectionGroup() != null
4342 && viewport.getSelectionGroup().getSize() == 1)
4344 int option = JOptionPane.showConfirmDialog(this,
4345 MessageManager.getString("warn.oneseq_msainput_selection"),
4346 MessageManager.getString("label.invalid_selection"),
4347 JOptionPane.OK_CANCEL_OPTION);
4348 if (option == JOptionPane.OK_OPTION)
4350 msa = viewport.getAlignmentView(false);
4355 msa = viewport.getAlignmentView(false);
4361 * Decides what is submitted to a secondary structure prediction service: the
4362 * first sequence in the alignment, or in the current selection, or, if the
4363 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4364 * region or the whole alignment. (where the first sequence in the set is the
4365 * one that the prediction will be for).
4367 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4369 AlignmentView seqs = null;
4371 if ((viewport.getSelectionGroup() != null)
4372 && (viewport.getSelectionGroup().getSize() > 0))
4374 seqs = viewport.getAlignmentView(true);
4378 seqs = viewport.getAlignmentView(false);
4380 // limit sequences - JBPNote in future - could spawn multiple prediction
4382 // TODO: viewport.getAlignment().isAligned is a global state - the local
4383 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4384 if (!viewport.getAlignment().isAligned(false))
4386 seqs.setSequences(new SeqCigar[]
4387 { seqs.getSequences()[0] });
4388 // TODO: if seqs.getSequences().length>1 then should really have warned
4402 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4404 // Pick the tree file
4405 JalviewFileChooser chooser = new JalviewFileChooser(
4406 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4407 chooser.setFileView(new JalviewFileView());
4408 chooser.setDialogTitle(MessageManager
4409 .getString("label.select_newick_like_tree_file"));
4410 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4412 int value = chooser.showOpenDialog(null);
4414 if (value == JalviewFileChooser.APPROVE_OPTION)
4416 String choice = chooser.getSelectedFile().getPath();
4417 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4418 jalview.io.NewickFile fin = null;
4421 fin = new jalview.io.NewickFile(choice, "File");
4422 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4423 } catch (Exception ex)
4430 .getString("label.problem_reading_tree_file"),
4431 JOptionPane.WARNING_MESSAGE);
4432 ex.printStackTrace();
4434 if (fin != null && fin.hasWarningMessage())
4436 JOptionPane.showMessageDialog(Desktop.desktop, fin
4437 .getWarningMessage(), MessageManager
4438 .getString("label.possible_problem_with_tree_file"),
4439 JOptionPane.WARNING_MESSAGE);
4445 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4447 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4450 public TreePanel ShowNewickTree(NewickFile nf, String title)
4452 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4455 public TreePanel ShowNewickTree(NewickFile nf, String title,
4456 AlignmentView input)
4458 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4461 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4462 int h, int x, int y)
4464 return ShowNewickTree(nf, title, null, w, h, x, y);
4468 * Add a treeviewer for the tree extracted from a newick file object to the
4469 * current alignment view
4476 * Associated alignment input data (or null)
4485 * @return TreePanel handle
4487 public TreePanel ShowNewickTree(NewickFile nf, String title,
4488 AlignmentView input, int w, int h, int x, int y)
4490 TreePanel tp = null;
4496 if (nf.getTree() != null)
4498 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4504 tp.setLocation(x, y);
4507 Desktop.addInternalFrame(tp, title, w, h);
4509 } catch (Exception ex)
4511 ex.printStackTrace();
4517 private boolean buildingMenu = false;
4520 * Generates menu items and listener event actions for web service clients
4523 public void BuildWebServiceMenu()
4525 while (buildingMenu)
4529 System.err.println("Waiting for building menu to finish.");
4531 } catch (Exception e)
4535 final AlignFrame me = this;
4536 buildingMenu = true;
4537 new Thread(new Runnable()
4542 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4545 // System.err.println("Building ws menu again "
4546 // + Thread.currentThread());
4547 // TODO: add support for context dependent disabling of services based
4549 // alignment and current selection
4550 // TODO: add additional serviceHandle parameter to specify abstract
4552 // class independently of AbstractName
4553 // TODO: add in rediscovery GUI function to restart discoverer
4554 // TODO: group services by location as well as function and/or
4556 // object broker mechanism.
4557 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4558 final IProgressIndicator af = me;
4559 final JMenu msawsmenu = new JMenu("Alignment");
4560 final JMenu secstrmenu = new JMenu(
4561 "Secondary Structure Prediction");
4562 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4563 final JMenu analymenu = new JMenu("Analysis");
4564 final JMenu dismenu = new JMenu("Protein Disorder");
4565 // final JMenu msawsmenu = new
4566 // JMenu(MessageManager.getString("label.alignment"));
4567 // final JMenu secstrmenu = new
4568 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4569 // final JMenu seqsrchmenu = new
4570 // JMenu(MessageManager.getString("label.sequence_database_search"));
4571 // final JMenu analymenu = new
4572 // JMenu(MessageManager.getString("label.analysis"));
4573 // final JMenu dismenu = new
4574 // JMenu(MessageManager.getString("label.protein_disorder"));
4575 // JAL-940 - only show secondary structure prediction services from
4576 // the legacy server
4577 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4579 Discoverer.services != null && (Discoverer.services.size() > 0))
4581 // TODO: refactor to allow list of AbstractName/Handler bindings to
4583 // stored or retrieved from elsewhere
4584 // No MSAWS used any more:
4585 // Vector msaws = null; // (Vector)
4586 // Discoverer.services.get("MsaWS");
4587 Vector secstrpr = (Vector) Discoverer.services
4589 if (secstrpr != null)
4591 // Add any secondary structure prediction services
4592 for (int i = 0, j = secstrpr.size(); i < j; i++)
4594 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4596 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4597 .getServiceClient(sh);
4598 int p = secstrmenu.getItemCount();
4599 impl.attachWSMenuEntry(secstrmenu, me);
4600 int q = secstrmenu.getItemCount();
4601 for (int litm = p; litm < q; litm++)
4603 legacyItems.add(secstrmenu.getItem(litm));
4609 // Add all submenus in the order they should appear on the web
4611 wsmenu.add(msawsmenu);
4612 wsmenu.add(secstrmenu);
4613 wsmenu.add(dismenu);
4614 wsmenu.add(analymenu);
4615 // No search services yet
4616 // wsmenu.add(seqsrchmenu);
4618 javax.swing.SwingUtilities.invokeLater(new Runnable()
4625 webService.removeAll();
4626 // first, add discovered services onto the webservices menu
4627 if (wsmenu.size() > 0)
4629 for (int i = 0, j = wsmenu.size(); i < j; i++)
4631 webService.add(wsmenu.get(i));
4636 webService.add(me.webServiceNoServices);
4638 // TODO: move into separate menu builder class.
4639 boolean new_sspred = false;
4640 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4642 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4643 if (jws2servs != null)
4645 if (jws2servs.hasServices())
4647 jws2servs.attachWSMenuEntry(webService, me);
4648 for (Jws2Instance sv : jws2servs.getServices())
4650 if (sv.description.toLowerCase().contains("jpred"))
4652 for (JMenuItem jmi : legacyItems)
4654 jmi.setVisible(false);
4660 if (jws2servs.isRunning())
4662 JMenuItem tm = new JMenuItem(
4663 "Still discovering JABA Services");
4664 tm.setEnabled(false);
4669 build_urlServiceMenu(me.webService);
4670 build_fetchdbmenu(webService);
4671 for (JMenu item : wsmenu)
4673 if (item.getItemCount() == 0)
4675 item.setEnabled(false);
4679 item.setEnabled(true);
4682 } catch (Exception e)
4685 .debug("Exception during web service menu building process.",
4690 } catch (Exception e)
4693 buildingMenu = false;
4700 * construct any groupURL type service menu entries.
4704 private void build_urlServiceMenu(JMenu webService)
4706 // TODO: remove this code when 2.7 is released
4707 // DEBUG - alignmentView
4709 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4710 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4712 * @Override public void actionPerformed(ActionEvent e) {
4713 * jalview.datamodel.AlignmentView
4714 * .testSelectionViews(af.viewport.getAlignment(),
4715 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4717 * }); webService.add(testAlView);
4719 // TODO: refactor to RestClient discoverer and merge menu entries for
4720 // rest-style services with other types of analysis/calculation service
4721 // SHmmr test client - still being implemented.
4722 // DEBUG - alignmentView
4724 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4727 client.attachWSMenuEntry(
4728 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4734 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4735 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4736 * getProperty("LAST_DIRECTORY"));
4738 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4739 * to Vamsas file"); chooser.setToolTipText("Export");
4741 * int value = chooser.showSaveDialog(this);
4743 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4744 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4745 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4746 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4749 * prototype of an automatically enabled/disabled analysis function
4752 protected void setShowProductsEnabled()
4754 SequenceI[] selection = viewport.getSequenceSelection();
4755 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4756 viewport.getAlignment().getDataset()))
4758 showProducts.setEnabled(true);
4763 showProducts.setEnabled(false);
4768 * search selection for sequence xRef products and build the show products
4773 * @return true if showProducts menu should be enabled.
4775 public boolean canShowProducts(SequenceI[] selection,
4776 boolean isRegionSelection, Alignment dataset)
4778 boolean showp = false;
4781 showProducts.removeAll();
4782 final boolean dna = viewport.getAlignment().isNucleotide();
4783 final Alignment ds = dataset;
4784 String[] ptypes = (selection == null || selection.length == 0) ? null
4785 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4787 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4788 // selection, dataset, true);
4789 final SequenceI[] sel = selection;
4790 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4793 final boolean isRegSel = isRegionSelection;
4794 final AlignFrame af = this;
4795 final String source = ptypes[t];
4796 JMenuItem xtype = new JMenuItem(ptypes[t]);
4797 xtype.addActionListener(new ActionListener()
4801 public void actionPerformed(ActionEvent e)
4803 // TODO: new thread for this call with vis-delay
4804 af.showProductsFor(af.viewport.getSequenceSelection(),
4805 isRegSel, dna, source);
4809 showProducts.add(xtype);
4811 showProducts.setVisible(showp);
4812 showProducts.setEnabled(showp);
4813 } catch (Exception e)
4815 jalview.bin.Cache.log
4816 .warn("canTranslate threw an exception - please report to help@jalview.org",
4823 protected void showProductsFor(final SequenceI[] sel,
4824 final boolean isRegSel, final boolean dna, final String source)
4826 Runnable foo = new Runnable()
4832 final long sttime = System.currentTimeMillis();
4833 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4834 "status.searching_for_sequences_from", new Object[]
4835 { source }), sttime);
4838 // update our local dataset reference
4839 Alignment ds = AlignFrame.this.getViewport().getAlignment()
4841 Alignment prods = CrossRef
4842 .findXrefSequences(sel, dna, source, ds);
4845 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4846 for (int s = 0; s < sprods.length; s++)
4848 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4849 if (ds.getSequences() == null
4850 || !ds.getSequences().contains(
4851 sprods[s].getDatasetSequence()))
4853 ds.addSequence(sprods[s].getDatasetSequence());
4855 sprods[s].updatePDBIds();
4857 Alignment al = new Alignment(sprods);
4861 * Copy dna-to-protein mappings to new alignment
4863 // TODO 1: no mappings are set up for EMBL product
4864 // TODO 2: if they were, should add them to protein alignment, not
4866 Set<AlignedCodonFrame> cf = prods.getCodonFrames();
4867 for (AlignedCodonFrame acf : cf)
4869 al.addCodonFrame(acf);
4871 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4873 String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
4874 + " for " + ((isRegSel) ? "selected region of " : "")
4876 naf.setTitle(newtitle);
4878 // temporary flag until SplitFrame is released
4879 boolean asSplitFrame = Cache.getDefault(
4880 Preferences.ENABLE_SPLIT_FRAME, true);
4884 * Make a copy of this alignment (sharing the same dataset
4885 * sequences). If we are DNA, drop introns and update mappings
4887 AlignmentI copyAlignment = null;
4888 final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4889 .getSequenceSelection();
4892 copyAlignment = AlignmentUtils.makeExonAlignment(
4893 sequenceSelection, cf);
4894 al.getCodonFrames().clear();
4895 al.getCodonFrames().addAll(cf);
4896 final StructureSelectionManager ssm = StructureSelectionManager
4897 .getStructureSelectionManager(Desktop.instance);
4898 ssm.registerMappings(cf);
4902 copyAlignment = new Alignment(new Alignment(
4903 sequenceSelection));
4905 AlignFrame copyThis = new AlignFrame(copyAlignment,
4906 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4907 copyThis.setTitle(AlignFrame.this.getTitle());
4908 // SplitFrame with dna above, protein below
4909 SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
4910 dna ? naf : copyThis);
4911 naf.setVisible(true);
4912 copyThis.setVisible(true);
4913 String linkedTitle = MessageManager
4914 .getString("label.linked_view_title");
4915 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4919 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4925 System.err.println("No Sequences generated for xRef type "
4928 } catch (Exception e)
4930 jalview.bin.Cache.log.error(
4931 "Exception when finding crossreferences", e);
4932 } catch (OutOfMemoryError e)
4934 new OOMWarning("whilst fetching crossreferences", e);
4937 jalview.bin.Cache.log.error("Error when finding crossreferences",
4940 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4941 "status.finished_searching_for_sequences_from",
4948 Thread frunner = new Thread(foo);
4952 public boolean canShowTranslationProducts(SequenceI[] selection,
4953 AlignmentI alignment)
4958 return (jalview.analysis.Dna.canTranslate(selection,
4959 viewport.getViewAsVisibleContigs(true)));
4960 } catch (Exception e)
4962 jalview.bin.Cache.log
4963 .warn("canTranslate threw an exception - please report to help@jalview.org",
4970 * Construct and display a new frame containing the translation of this
4971 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4974 public void showTranslation_actionPerformed(ActionEvent e)
4976 AlignmentI al = null;
4979 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4981 al = dna.translateCdna();
4982 } catch (Exception ex)
4984 jalview.bin.Cache.log.error(
4985 "Exception during translation. Please report this !", ex);
4986 final String msg = MessageManager
4987 .getString("label.error_when_translating_sequences_submit_bug_report");
4988 final String errorTitle = MessageManager
4989 .getString("label.implementation_error")
4990 + MessageManager.getString("translation_failed");
4991 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4992 JOptionPane.ERROR_MESSAGE);
4995 if (al == null || al.getHeight() == 0)
4997 final String msg = MessageManager
4998 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4999 final String errorTitle = MessageManager
5000 .getString("label.translation_failed");
5001 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
5002 JOptionPane.WARNING_MESSAGE);
5006 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
5007 af.setFileFormat(this.currentFileFormat);
5008 final String newTitle = MessageManager.formatMessage(
5009 "label.translation_of_params", new Object[]
5010 { this.getTitle() });
5011 af.setTitle(newTitle);
5012 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
5014 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
5015 viewport.openSplitFrame(af, new Alignment(seqs));
5019 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
5026 * Set the file format
5030 public void setFileFormat(String fileFormat)
5032 this.currentFileFormat = fileFormat;
5036 * Try to load a features file onto the alignment.
5039 * contents or path to retrieve file
5041 * access mode of file (see jalview.io.AlignFile)
5042 * @return true if features file was parsed correctly.
5044 public boolean parseFeaturesFile(String file, String type)
5046 return avc.parseFeaturesFile(file, type,
5047 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
5052 public void refreshFeatureUI(boolean enableIfNecessary)
5054 // note - currently this is only still here rather than in the controller
5055 // because of the featureSettings hard reference that is yet to be
5057 if (enableIfNecessary)
5059 viewport.setShowSequenceFeatures(true);
5060 showSeqFeatures.setSelected(true);
5066 public void dragEnter(DropTargetDragEvent evt)
5071 public void dragExit(DropTargetEvent evt)
5076 public void dragOver(DropTargetDragEvent evt)
5081 public void dropActionChanged(DropTargetDragEvent evt)
5086 public void drop(DropTargetDropEvent evt)
5088 Transferable t = evt.getTransferable();
5089 java.util.List files = null;
5093 DataFlavor uriListFlavor = new DataFlavor(
5094 "text/uri-list;class=java.lang.String");
5095 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5097 // Works on Windows and MacOSX
5098 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5099 files = (java.util.List) t
5100 .getTransferData(DataFlavor.javaFileListFlavor);
5102 else if (t.isDataFlavorSupported(uriListFlavor))
5104 // This is used by Unix drag system
5105 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5106 String data = (String) t.getTransferData(uriListFlavor);
5107 files = new java.util.ArrayList(1);
5108 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5109 data, "\r\n"); st.hasMoreTokens();)
5111 String s = st.nextToken();
5112 if (s.startsWith("#"))
5114 // the line is a comment (as per the RFC 2483)
5118 java.net.URI uri = new java.net.URI(s);
5119 // check to see if we can handle this kind of URI
5120 if (uri.getScheme().toLowerCase().startsWith("http"))
5122 files.add(uri.toString());
5126 // otherwise preserve old behaviour: catch all for file objects
5127 java.io.File file = new java.io.File(uri);
5128 files.add(file.toString());
5132 } catch (Exception e)
5134 e.printStackTrace();
5140 // check to see if any of these files have names matching sequences in
5142 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5143 .getAlignment().getSequencesArray());
5145 * Object[] { String,SequenceI}
5147 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5148 ArrayList<String> filesnotmatched = new ArrayList<String>();
5149 for (int i = 0; i < files.size(); i++)
5151 String file = files.get(i).toString();
5153 String protocol = FormatAdapter.checkProtocol(file);
5154 if (protocol == jalview.io.FormatAdapter.FILE)
5156 File fl = new File(file);
5157 pdbfn = fl.getName();
5159 else if (protocol == jalview.io.FormatAdapter.URL)
5161 URL url = new URL(file);
5162 pdbfn = url.getFile();
5164 if (pdbfn.length() > 0)
5166 // attempt to find a match in the alignment
5167 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5168 int l = 0, c = pdbfn.indexOf(".");
5169 while (mtch == null && c != -1)
5174 } while ((c = pdbfn.indexOf(".", l)) > l);
5177 pdbfn = pdbfn.substring(0, l);
5179 mtch = idm.findAllIdMatches(pdbfn);
5186 type = new IdentifyFile().Identify(file, protocol);
5187 } catch (Exception ex)
5193 if (type.equalsIgnoreCase("PDB"))
5195 filesmatched.add(new Object[]
5196 { file, protocol, mtch });
5201 // File wasn't named like one of the sequences or wasn't a PDB file.
5202 filesnotmatched.add(file);
5206 if (filesmatched.size() > 0)
5208 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5214 "label.automatically_associate_pdb_files_with_sequences_same_name",
5221 .getString("label.automatically_associate_pdb_files_by_name"),
5222 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5225 for (Object[] fm : filesmatched)
5227 // try and associate
5228 // TODO: may want to set a standard ID naming formalism for
5229 // associating PDB files which have no IDs.
5230 for (SequenceI toassoc : (SequenceI[]) fm[2])
5232 PDBEntry pe = new AssociatePdbFileWithSeq()
5233 .associatePdbWithSeq((String) fm[0],
5234 (String) fm[1], toassoc, false,
5238 System.err.println("Associated file : "
5239 + ((String) fm[0]) + " with "
5240 + toassoc.getDisplayId(true));
5244 alignPanel.paintAlignment(true);
5248 if (filesnotmatched.size() > 0)
5251 && (Cache.getDefault(
5252 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5255 "<html>"+MessageManager
5257 "label.ignore_unmatched_dropped_files_info",
5262 .toString() })+"</html>",
5264 .getString("label.ignore_unmatched_dropped_files"),
5265 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5269 for (String fn : filesnotmatched)
5271 loadJalviewDataFile(fn, null, null, null);
5275 } catch (Exception ex)
5277 ex.printStackTrace();
5283 * Attempt to load a "dropped" file or URL string: First by testing whether
5284 * it's and Annotation file, then a JNet file, and finally a features file. If
5285 * all are false then the user may have dropped an alignment file onto this
5289 * either a filename or a URL string.
5291 public void loadJalviewDataFile(String file, String protocol,
5292 String format, SequenceI assocSeq)
5296 if (protocol == null)
5298 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5300 // if the file isn't identified, or not positively identified as some
5301 // other filetype (PFAM is default unidentified alignment file type) then
5302 // try to parse as annotation.
5303 boolean isAnnotation = (format == null || format
5304 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5305 .annotateAlignmentView(viewport, file, protocol)
5310 // first see if its a T-COFFEE score file
5311 TCoffeeScoreFile tcf = null;
5314 tcf = new TCoffeeScoreFile(file, protocol);
5317 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5319 tcoffeeColour.setEnabled(true);
5320 tcoffeeColour.setSelected(true);
5321 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5322 isAnnotation = true;
5324 .setText(MessageManager
5325 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5329 // some problem - if no warning its probable that the ID matching
5330 // process didn't work
5334 tcf.getWarningMessage() == null ? MessageManager
5335 .getString("label.check_file_matches_sequence_ids_alignment")
5336 : tcf.getWarningMessage(),
5338 .getString("label.problem_reading_tcoffee_score_file"),
5339 JOptionPane.WARNING_MESSAGE);
5346 } catch (Exception x)
5349 .debug("Exception when processing data source as T-COFFEE score file",
5355 // try to see if its a JNet 'concise' style annotation file *before*
5357 // try to parse it as a features file
5360 format = new IdentifyFile().Identify(file, protocol);
5362 if (format.equalsIgnoreCase("JnetFile"))
5364 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5366 new JnetAnnotationMaker();
5367 JnetAnnotationMaker.add_annotation(predictions,
5368 viewport.getAlignment(), 0, false);
5369 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5370 viewport.getAlignment().setSeqrep(repseq);
5371 ColumnSelection cs = new ColumnSelection();
5372 cs.hideInsertionsFor(repseq);
5373 viewport.setColumnSelection(cs);
5374 isAnnotation = true;
5379 * if (format.equalsIgnoreCase("PDB")) {
5381 * String pdbfn = ""; // try to match up filename with sequence id
5382 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5383 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5384 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5385 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5386 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5387 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5388 * // attempt to find a match in the alignment SequenceI mtch =
5389 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5390 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5391 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5392 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5393 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5394 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5395 * { System.err.println("Associated file : " + file + " with " +
5396 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5397 * TODO: maybe need to load as normal otherwise return; } }
5399 // try to parse it as a features file
5400 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5401 // if it wasn't a features file then we just treat it as a general
5402 // alignment file to load into the current view.
5405 new FileLoader().LoadFile(viewport, file, protocol, format);
5409 alignPanel.paintAlignment(true);
5417 alignPanel.adjustAnnotationHeight();
5418 viewport.updateSequenceIdColours();
5419 buildSortByAnnotationScoresMenu();
5420 alignPanel.paintAlignment(true);
5422 } catch (Exception ex)
5424 ex.printStackTrace();
5425 } catch (OutOfMemoryError oom)
5430 } catch (Exception x)
5436 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5437 : "using " + protocol + " from " + file)
5439 + (format != null ? "(parsing as '" + format
5440 + "' file)" : ""), oom, Desktop.desktop);
5445 * Method invoked by the ChangeListener on the tabbed pane, in other words
5446 * when a different tabbed pane is selected by the user or programmatically.
5449 public void tabSelectionChanged(int index)
5453 alignPanel = alignPanels.get(index);
5454 viewport = alignPanel.av;
5455 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5456 setMenusFromViewport(viewport);
5460 * If there is a frame linked to this one in a SplitPane, switch it to the
5461 * same view tab index. No infinite recursion of calls should happen, since
5462 * tabSelectionChanged() should not get invoked on setting the selected
5463 * index to an unchanged value. Guard against setting an invalid index
5464 * before the new view peer tab has been created.
5466 final AlignViewportI peer = viewport.getCodingComplement();
5469 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5470 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5472 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5478 * On right mouse click on view tab, prompt for and set new view name.
5481 public void tabbedPane_mousePressed(MouseEvent e)
5483 if (SwingUtilities.isRightMouseButton(e))
5485 String msg = MessageManager.getString("label.enter_view_name");
5486 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5487 JOptionPane.QUESTION_MESSAGE);
5491 viewport.viewName = reply;
5492 // TODO warn if reply is in getExistingViewNames()?
5493 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5498 public AlignViewport getCurrentView()
5504 * Open the dialog for regex description parsing.
5507 protected void extractScores_actionPerformed(ActionEvent e)
5509 ParseProperties pp = new jalview.analysis.ParseProperties(
5510 viewport.getAlignment());
5511 // TODO: verify regex and introduce GUI dialog for version 2.5
5512 // if (pp.getScoresFromDescription("col", "score column ",
5513 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5515 if (pp.getScoresFromDescription("description column",
5516 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5518 buildSortByAnnotationScoresMenu();
5526 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5530 protected void showDbRefs_actionPerformed(ActionEvent e)
5532 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5538 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5542 protected void showNpFeats_actionPerformed(ActionEvent e)
5544 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5548 * find the viewport amongst the tabs in this alignment frame and close that
5553 public boolean closeView(AlignViewportI av)
5557 this.closeMenuItem_actionPerformed(false);
5560 Component[] comp = tabbedPane.getComponents();
5561 for (int i = 0; comp != null && i < comp.length; i++)
5563 if (comp[i] instanceof AlignmentPanel)
5565 if (((AlignmentPanel) comp[i]).av == av)
5568 closeView((AlignmentPanel) comp[i]);
5576 protected void build_fetchdbmenu(JMenu webService)
5578 // Temporary hack - DBRef Fetcher always top level ws entry.
5579 // TODO We probably want to store a sequence database checklist in
5580 // preferences and have checkboxes.. rather than individual sources selected
5582 final JMenu rfetch = new JMenu(
5583 MessageManager.getString("action.fetch_db_references"));
5584 rfetch.setToolTipText(MessageManager
5585 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5586 webService.add(rfetch);
5588 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5589 MessageManager.getString("option.trim_retrieved_seqs"));
5590 trimrs.setToolTipText(MessageManager
5591 .getString("label.trim_retrieved_sequences"));
5592 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5593 trimrs.addActionListener(new ActionListener()
5596 public void actionPerformed(ActionEvent e)
5598 trimrs.setSelected(trimrs.isSelected());
5599 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5600 Boolean.valueOf(trimrs.isSelected()).toString());
5604 JMenuItem fetchr = new JMenuItem(
5605 MessageManager.getString("label.standard_databases"));
5606 fetchr.setToolTipText(MessageManager
5607 .getString("label.fetch_embl_uniprot"));
5608 fetchr.addActionListener(new ActionListener()
5612 public void actionPerformed(ActionEvent e)
5614 new Thread(new Runnable()
5620 new jalview.ws.DBRefFetcher(alignPanel.av
5621 .getSequenceSelection(), alignPanel.alignFrame)
5622 .fetchDBRefs(false);
5630 final AlignFrame me = this;
5631 new Thread(new Runnable()
5636 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5637 .getSequenceFetcherSingleton(me);
5638 javax.swing.SwingUtilities.invokeLater(new Runnable()
5643 String[] dbclasses = sf.getOrderedSupportedSources();
5644 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5645 // jalview.util.QuickSort.sort(otherdb, otherdb);
5646 List<DbSourceProxy> otherdb;
5647 JMenu dfetch = new JMenu();
5648 JMenu ifetch = new JMenu();
5649 JMenuItem fetchr = null;
5650 int comp = 0, icomp = 0, mcomp = 15;
5651 String mname = null;
5653 for (String dbclass : dbclasses)
5655 otherdb = sf.getSourceProxy(dbclass);
5656 // add a single entry for this class, or submenu allowing 'fetch
5658 if (otherdb == null || otherdb.size() < 1)
5662 // List<DbSourceProxy> dbs=otherdb;
5663 // otherdb=new ArrayList<DbSourceProxy>();
5664 // for (DbSourceProxy db:dbs)
5666 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5670 mname = "From " + dbclass;
5672 if (otherdb.size() == 1)
5674 final DbSourceProxy[] dassource = otherdb
5675 .toArray(new DbSourceProxy[0]);
5676 DbSourceProxy src = otherdb.get(0);
5677 fetchr = new JMenuItem(src.getDbSource());
5678 fetchr.addActionListener(new ActionListener()
5682 public void actionPerformed(ActionEvent e)
5684 new Thread(new Runnable()
5690 new jalview.ws.DBRefFetcher(alignPanel.av
5691 .getSequenceSelection(),
5692 alignPanel.alignFrame, dassource)
5693 .fetchDBRefs(false);
5699 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{src.getDbName()})));
5705 final DbSourceProxy[] dassource = otherdb
5706 .toArray(new DbSourceProxy[0]);
5708 DbSourceProxy src = otherdb.get(0);
5709 fetchr = new JMenuItem(MessageManager.formatMessage(
5710 "label.fetch_all_param", new Object[]
5711 { src.getDbSource() }));
5712 fetchr.addActionListener(new ActionListener()
5715 public void actionPerformed(ActionEvent e)
5717 new Thread(new Runnable()
5723 new jalview.ws.DBRefFetcher(alignPanel.av
5724 .getSequenceSelection(),
5725 alignPanel.alignFrame, dassource)
5726 .fetchDBRefs(false);
5732 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new Object[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5735 // and then build the rest of the individual menus
5736 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new Object[]{src.getDbSource()}));
5738 String imname = null;
5740 for (DbSourceProxy sproxy : otherdb)
5742 String dbname = sproxy.getDbName();
5743 String sname = dbname.length() > 5 ? dbname.substring(0,
5744 5) + "..." : dbname;
5745 String msname = dbname.length() > 10 ? dbname.substring(
5746 0, 10) + "..." : dbname;
5749 imname = MessageManager.formatMessage("label.from_msname", new Object[]{sname});
5751 fetchr = new JMenuItem(msname);
5752 final DbSourceProxy[] dassrc =
5754 fetchr.addActionListener(new ActionListener()
5758 public void actionPerformed(ActionEvent e)
5760 new Thread(new Runnable()
5766 new jalview.ws.DBRefFetcher(alignPanel.av
5767 .getSequenceSelection(),
5768 alignPanel.alignFrame, dassrc)
5769 .fetchDBRefs(false);
5775 fetchr.setToolTipText("<html>"
5776 + MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{dbname}));
5779 if (++icomp >= mcomp || i == (otherdb.size()))
5781 ifetch.setText(MessageManager.formatMessage(
5782 "label.source_to_target", imname, sname));
5784 ifetch = new JMenu();
5792 if (comp >= mcomp || dbi >= (dbclasses.length))
5794 dfetch.setText(MessageManager.formatMessage(
5795 "label.source_to_target", mname, dbclass));
5797 dfetch = new JMenu();
5810 * Left justify the whole alignment.
5813 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5815 AlignmentI al = viewport.getAlignment();
5817 viewport.firePropertyChange("alignment", null, al);
5821 * Right justify the whole alignment.
5824 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5826 AlignmentI al = viewport.getAlignment();
5828 viewport.firePropertyChange("alignment", null, al);
5831 public void setShowSeqFeatures(boolean b)
5833 showSeqFeatures.setSelected(b);
5834 viewport.setShowSequenceFeatures(b);
5841 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5842 * awt.event.ActionEvent)
5845 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5847 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5848 alignPanel.paintAlignment(true);
5855 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5859 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5861 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5862 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5870 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5871 * .event.ActionEvent)
5874 protected void showGroupConservation_actionPerformed(ActionEvent e)
5876 viewport.setShowGroupConservation(showGroupConservation.getState());
5877 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5884 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5885 * .event.ActionEvent)
5888 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5890 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5891 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5898 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5899 * .event.ActionEvent)
5902 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5904 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5905 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5909 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5911 showSequenceLogo.setState(true);
5912 viewport.setShowSequenceLogo(true);
5913 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5914 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5918 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5920 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5927 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5928 * .event.ActionEvent)
5931 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5933 if (avc.makeGroupsFromSelection())
5935 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5936 alignPanel.updateAnnotation();
5937 alignPanel.paintAlignment(true);
5940 public void clearAlignmentSeqRep()
5942 // TODO refactor alignmentseqrep to controller
5943 if (viewport.getAlignment().hasSeqrep()) {
5944 viewport.getAlignment().setSeqrep(null);
5945 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5946 alignPanel.updateAnnotation();
5947 alignPanel.paintAlignment(true);
5952 protected void createGroup_actionPerformed(ActionEvent e)
5954 if (avc.createGroup())
5956 alignPanel.alignmentChanged();
5961 protected void unGroup_actionPerformed(ActionEvent e)
5965 alignPanel.alignmentChanged();
5970 * make the given alignmentPanel the currently selected tab
5972 * @param alignmentPanel
5974 public void setDisplayedView(AlignmentPanel alignmentPanel)
5976 if (!viewport.getSequenceSetId().equals(
5977 alignmentPanel.av.getSequenceSetId()))
5979 throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5981 if (tabbedPane != null
5982 && tabbedPane.getTabCount() > 0
5983 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5984 .getSelectedIndex())
5986 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5991 * Action on selection of menu options to Show or Hide annotations.
5994 * @param forSequences
5995 * update sequence-related annotations
5996 * @param forAlignment
5997 * update non-sequence-related annotations
6000 protected void setAnnotationsVisibility(boolean visible,
6001 boolean forSequences, boolean forAlignment)
6003 for (AlignmentAnnotation aa : alignPanel.getAlignment()
6004 .getAlignmentAnnotation())
6007 * don't display non-positional annotations on an alignment
6009 if (aa.annotations == null)
6013 boolean apply = (aa.sequenceRef == null && forAlignment)
6014 || (aa.sequenceRef != null && forSequences);
6017 aa.visible = visible;
6020 alignPanel.validateAnnotationDimensions(true);
6021 alignPanel.alignmentChanged();
6025 * Store selected annotation sort order for the view and repaint.
6028 protected void sortAnnotations_actionPerformed()
6030 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
6032 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
6033 alignPanel.paintAlignment(true);
6038 * @return alignment panels in this alignment frame
6040 public List<? extends AlignmentViewPanel> getAlignPanels()
6042 return alignPanels == null ? Arrays.asList(alignPanel)
6047 * Open a new alignment window, with the cDNA associated with this (protein)
6048 * alignment, aligned as is the protein.
6050 protected void viewAsCdna_actionPerformed()
6052 // TODO no longer a menu action - refactor as required
6053 final AlignmentI alignment = getViewport().getAlignment();
6054 Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6055 if (mappings == null)
6059 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6060 for (SequenceI aaSeq : alignment.getSequences()) {
6061 for (AlignedCodonFrame acf : mappings) {
6062 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6066 * There is a cDNA mapping for this protein sequence - add to new
6067 * alignment. It will share the same dataset sequence as other mapped
6068 * cDNA (no new mappings need to be created).
6070 final Sequence newSeq = new Sequence(dnaSeq);
6071 newSeq.setDatasetSequence(dnaSeq);
6072 cdnaSeqs.add(newSeq);
6076 if (cdnaSeqs.size() == 0)
6078 // show a warning dialog no mapped cDNA
6081 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6083 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6084 AlignFrame.DEFAULT_HEIGHT);
6085 cdna.alignAs(alignment);
6086 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6088 Desktop.addInternalFrame(alignFrame, newtitle,
6089 AlignFrame.DEFAULT_WIDTH,
6090 AlignFrame.DEFAULT_HEIGHT);
6094 * Set visibility of dna/protein complement view (available when shown in a
6100 protected void showComplement_actionPerformed(boolean show)
6102 SplitContainerI sf = getSplitViewContainer();
6104 sf.setComplementVisible(this, show);
6109 class PrintThread extends Thread
6113 public PrintThread(AlignmentPanel ap)
6118 static PageFormat pf;
6123 PrinterJob printJob = PrinterJob.getPrinterJob();
6127 printJob.setPrintable(ap, pf);
6131 printJob.setPrintable(ap);
6134 if (printJob.printDialog())
6139 } catch (Exception PrintException)
6141 PrintException.printStackTrace();