2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.FeatureSettingsModelI;
36 import jalview.api.SplitContainerI;
37 import jalview.api.ViewStyleI;
38 import jalview.api.analysis.ScoreModelI;
39 import jalview.bin.Cache;
40 import jalview.bin.Jalview;
41 import jalview.commands.CommandI;
42 import jalview.commands.EditCommand;
43 import jalview.commands.EditCommand.Action;
44 import jalview.commands.OrderCommand;
45 import jalview.commands.RemoveGapColCommand;
46 import jalview.commands.RemoveGapsCommand;
47 import jalview.commands.SlideSequencesCommand;
48 import jalview.commands.TrimRegionCommand;
49 import jalview.datamodel.AlignedCodonFrame;
50 import jalview.datamodel.Alignment;
51 import jalview.datamodel.AlignmentAnnotation;
52 import jalview.datamodel.AlignmentExportData;
53 import jalview.datamodel.AlignmentI;
54 import jalview.datamodel.AlignmentOrder;
55 import jalview.datamodel.AlignmentView;
56 import jalview.datamodel.ColumnSelection;
57 import jalview.datamodel.DBRefSource;
58 import jalview.datamodel.HiddenSequences;
59 import jalview.datamodel.PDBEntry;
60 import jalview.datamodel.SeqCigar;
61 import jalview.datamodel.Sequence;
62 import jalview.datamodel.SequenceGroup;
63 import jalview.datamodel.SequenceI;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.FileLoader;
69 import jalview.io.FormatAdapter;
70 import jalview.io.HtmlSvgOutput;
71 import jalview.io.IdentifyFile;
72 import jalview.io.JalviewFileChooser;
73 import jalview.io.JalviewFileView;
74 import jalview.io.JnetAnnotationMaker;
75 import jalview.io.NewickFile;
76 import jalview.io.TCoffeeScoreFile;
77 import jalview.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.DBRefFetcher;
100 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
101 import jalview.ws.SequenceFetcher;
102 import jalview.ws.jws1.Discoverer;
103 import jalview.ws.jws2.Jws2Discoverer;
104 import jalview.ws.jws2.jabaws2.Jws2Instance;
105 import jalview.ws.seqfetcher.DbSourceProxy;
107 import java.awt.BorderLayout;
108 import java.awt.Component;
109 import java.awt.Rectangle;
110 import java.awt.Toolkit;
111 import java.awt.datatransfer.Clipboard;
112 import java.awt.datatransfer.DataFlavor;
113 import java.awt.datatransfer.StringSelection;
114 import java.awt.datatransfer.Transferable;
115 import java.awt.dnd.DnDConstants;
116 import java.awt.dnd.DropTargetDragEvent;
117 import java.awt.dnd.DropTargetDropEvent;
118 import java.awt.dnd.DropTargetEvent;
119 import java.awt.dnd.DropTargetListener;
120 import java.awt.event.ActionEvent;
121 import java.awt.event.ActionListener;
122 import java.awt.event.ItemEvent;
123 import java.awt.event.ItemListener;
124 import java.awt.event.KeyAdapter;
125 import java.awt.event.KeyEvent;
126 import java.awt.event.MouseAdapter;
127 import java.awt.event.MouseEvent;
128 import java.awt.print.PageFormat;
129 import java.awt.print.PrinterJob;
130 import java.beans.PropertyChangeEvent;
133 import java.util.ArrayList;
134 import java.util.Arrays;
135 import java.util.Deque;
136 import java.util.Enumeration;
137 import java.util.Hashtable;
138 import java.util.List;
139 import java.util.Vector;
141 import javax.swing.JCheckBoxMenuItem;
142 import javax.swing.JEditorPane;
143 import javax.swing.JInternalFrame;
144 import javax.swing.JLayeredPane;
145 import javax.swing.JMenu;
146 import javax.swing.JMenuItem;
147 import javax.swing.JOptionPane;
148 import javax.swing.JRadioButtonMenuItem;
149 import javax.swing.JScrollPane;
150 import javax.swing.SwingUtilities;
156 * @version $Revision$
158 public class AlignFrame extends GAlignFrame implements DropTargetListener,
159 IProgressIndicator, AlignViewControllerGuiI
162 public static final int DEFAULT_WIDTH = 700;
164 public static final int DEFAULT_HEIGHT = 500;
167 * The currently displayed panel (selected tabbed view if more than one)
169 public AlignmentPanel alignPanel;
171 AlignViewport viewport;
173 public AlignViewControllerI avc;
175 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
178 * Last format used to load or save alignments in this window
180 String currentFileFormat = null;
183 * Current filename for this alignment
185 String fileName = null;
188 * Creates a new AlignFrame object with specific width and height.
194 public AlignFrame(AlignmentI al, int width, int height)
196 this(al, null, width, height);
200 * Creates a new AlignFrame object with specific width, height and
206 * @param sequenceSetId
208 public AlignFrame(AlignmentI al, int width, int height,
209 String sequenceSetId)
211 this(al, null, width, height, sequenceSetId);
215 * Creates a new AlignFrame object with specific width, height and
221 * @param sequenceSetId
224 public AlignFrame(AlignmentI al, int width, int height,
225 String sequenceSetId, String viewId)
227 this(al, null, width, height, sequenceSetId, viewId);
231 * new alignment window with hidden columns
235 * @param hiddenColumns
236 * ColumnSelection or null
238 * Width of alignment frame
242 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
243 int width, int height)
245 this(al, hiddenColumns, width, height, null);
249 * Create alignment frame for al with hiddenColumns, a specific width and
250 * height, and specific sequenceId
253 * @param hiddenColumns
256 * @param sequenceSetId
259 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
260 int width, int height, String sequenceSetId)
262 this(al, hiddenColumns, width, height, sequenceSetId, null);
266 * Create alignment frame for al with hiddenColumns, a specific width and
267 * height, and specific sequenceId
270 * @param hiddenColumns
273 * @param sequenceSetId
278 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
279 int width, int height, String sequenceSetId, String viewId)
281 setSize(width, height);
283 if (al.getDataset() == null)
288 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
290 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);
318 * Make a new AlignFrame from existing alignmentPanels
325 public AlignFrame(AlignmentPanel ap)
329 addAlignmentPanel(ap, false);
334 * initalise the alignframe from the underlying viewport data and the
339 if (!Jalview.isHeadlessMode())
341 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
344 avc = new jalview.controller.AlignViewController(this, viewport,
346 if (viewport.getAlignmentConservationAnnotation() == null)
348 BLOSUM62Colour.setEnabled(false);
349 conservationMenuItem.setEnabled(false);
350 modifyConservation.setEnabled(false);
351 // PIDColour.setEnabled(false);
352 // abovePIDThreshold.setEnabled(false);
353 // modifyPID.setEnabled(false);
356 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
359 if (sortby.equals("Id"))
361 sortIDMenuItem_actionPerformed(null);
363 else if (sortby.equals("Pairwise Identity"))
365 sortPairwiseMenuItem_actionPerformed(null);
368 if (Desktop.desktop != null)
370 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
371 addServiceListeners();
372 setGUINucleotide(viewport.getAlignment().isNucleotide());
376 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
378 setMenusFromViewport(viewport);
379 buildSortByAnnotationScoresMenu();
382 if (viewport.getWrapAlignment())
384 wrapMenuItem_actionPerformed(null);
387 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
389 this.overviewMenuItem_actionPerformed(null);
394 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
395 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
396 final String menuLabel = MessageManager
397 .getString("label.copy_format_from");
398 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
399 new ViewSetProvider()
403 public AlignmentPanel[] getAllAlignmentPanels()
406 origview.add(alignPanel);
407 // make an array of all alignment panels except for this one
408 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
409 Arrays.asList(Desktop.getAlignmentPanels(null)));
410 aps.remove(AlignFrame.this.alignPanel);
411 return aps.toArray(new AlignmentPanel[aps.size()]);
413 }, selviews, new ItemListener()
417 public void itemStateChanged(ItemEvent e)
419 if (origview.size() > 0)
421 final AlignmentPanel ap = origview.get(0);
424 * Copy the ViewStyle of the selected panel to 'this one'.
425 * Don't change value of 'scaleProteinAsCdna' unless copying
428 ViewStyleI vs = selviews.get(0).getAlignViewport()
430 boolean fromSplitFrame = selviews.get(0)
431 .getAlignViewport().getCodingComplement() != null;
434 vs.setScaleProteinAsCdna(ap.getAlignViewport()
435 .getViewStyle().isScaleProteinAsCdna());
437 ap.getAlignViewport().setViewStyle(vs);
440 * Also rescale ViewStyle of SplitFrame complement if there is
441 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
442 * the whole ViewStyle (allow cDNA protein to have different
445 AlignViewportI complement = ap.getAlignViewport()
446 .getCodingComplement();
447 if (complement != null && vs.isScaleProteinAsCdna())
449 AlignFrame af = Desktop.getAlignFrameFor(complement);
450 ((SplitFrame) af.getSplitViewContainer())
452 af.setMenusForViewport();
456 ap.setSelected(true);
457 ap.alignFrame.setMenusForViewport();
462 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
463 .indexOf("devel") > -1
464 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
465 .indexOf("test") > -1)
467 formatMenu.add(vsel);
473 * Change the filename and format for the alignment, and enable the 'reload'
474 * button functionality.
481 public void setFileName(String file, String format)
484 setFileFormat(format);
485 reload.setEnabled(true);
489 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
492 void addKeyListener()
494 addKeyListener(new KeyAdapter()
497 public void keyPressed(KeyEvent evt)
499 if (viewport.cursorMode
500 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
501 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
502 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
503 && Character.isDigit(evt.getKeyChar()))
505 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
508 switch (evt.getKeyCode())
511 case 27: // escape key
512 deselectAllSequenceMenuItem_actionPerformed(null);
516 case KeyEvent.VK_DOWN:
517 if (evt.isAltDown() || !viewport.cursorMode)
519 moveSelectedSequences(false);
521 if (viewport.cursorMode)
523 alignPanel.getSeqPanel().moveCursor(0, 1);
528 if (evt.isAltDown() || !viewport.cursorMode)
530 moveSelectedSequences(true);
532 if (viewport.cursorMode)
534 alignPanel.getSeqPanel().moveCursor(0, -1);
539 case KeyEvent.VK_LEFT:
540 if (evt.isAltDown() || !viewport.cursorMode)
542 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
546 alignPanel.getSeqPanel().moveCursor(-1, 0);
551 case KeyEvent.VK_RIGHT:
552 if (evt.isAltDown() || !viewport.cursorMode)
554 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
558 alignPanel.getSeqPanel().moveCursor(1, 0);
562 case KeyEvent.VK_SPACE:
563 if (viewport.cursorMode)
565 alignPanel.getSeqPanel().insertGapAtCursor(
566 evt.isControlDown() || evt.isShiftDown()
571 // case KeyEvent.VK_A:
572 // if (viewport.cursorMode)
574 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
575 // //System.out.println("A");
579 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
580 * System.out.println("closing bracket"); } break;
582 case KeyEvent.VK_DELETE:
583 case KeyEvent.VK_BACK_SPACE:
584 if (!viewport.cursorMode)
586 cut_actionPerformed(null);
590 alignPanel.getSeqPanel().deleteGapAtCursor(
591 evt.isControlDown() || evt.isShiftDown()
598 if (viewport.cursorMode)
600 alignPanel.getSeqPanel().setCursorRow();
604 if (viewport.cursorMode && !evt.isControlDown())
606 alignPanel.getSeqPanel().setCursorColumn();
610 if (viewport.cursorMode)
612 alignPanel.getSeqPanel().setCursorPosition();
616 case KeyEvent.VK_ENTER:
617 case KeyEvent.VK_COMMA:
618 if (viewport.cursorMode)
620 alignPanel.getSeqPanel().setCursorRowAndColumn();
625 if (viewport.cursorMode)
627 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
631 if (viewport.cursorMode)
633 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
638 viewport.cursorMode = !viewport.cursorMode;
639 statusBar.setText(MessageManager.formatMessage(
640 "label.keyboard_editing_mode",
641 new String[] { (viewport.cursorMode ? "on" : "off") }));
642 if (viewport.cursorMode)
644 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
645 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
647 alignPanel.getSeqPanel().seqCanvas.repaint();
653 Help.showHelpWindow();
654 } catch (Exception ex)
656 ex.printStackTrace();
661 boolean toggleSeqs = !evt.isControlDown();
662 boolean toggleCols = !evt.isShiftDown();
663 toggleHiddenRegions(toggleSeqs, toggleCols);
666 case KeyEvent.VK_PAGE_UP:
667 if (viewport.getWrapAlignment())
669 alignPanel.scrollUp(true);
673 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
674 - viewport.endSeq + viewport.startSeq);
677 case KeyEvent.VK_PAGE_DOWN:
678 if (viewport.getWrapAlignment())
680 alignPanel.scrollUp(false);
684 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
685 + viewport.endSeq - viewport.startSeq);
692 public void keyReleased(KeyEvent evt)
694 switch (evt.getKeyCode())
696 case KeyEvent.VK_LEFT:
697 if (evt.isAltDown() || !viewport.cursorMode)
699 viewport.firePropertyChange("alignment", null, viewport
700 .getAlignment().getSequences());
704 case KeyEvent.VK_RIGHT:
705 if (evt.isAltDown() || !viewport.cursorMode)
707 viewport.firePropertyChange("alignment", null, viewport
708 .getAlignment().getSequences());
716 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
718 ap.alignFrame = this;
719 avc = new jalview.controller.AlignViewController(this, viewport,
724 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
726 int aSize = alignPanels.size();
728 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
730 if (aSize == 1 && ap.av.viewName == null)
732 this.getContentPane().add(ap, BorderLayout.CENTER);
738 setInitialTabVisible();
741 expandViews.setEnabled(true);
742 gatherViews.setEnabled(true);
743 tabbedPane.addTab(ap.av.viewName, ap);
745 ap.setVisible(false);
750 if (ap.av.isPadGaps())
752 ap.av.getAlignment().padGaps();
754 ap.av.updateConservation(ap);
755 ap.av.updateConsensus(ap);
756 ap.av.updateStrucConsensus(ap);
760 public void setInitialTabVisible()
762 expandViews.setEnabled(true);
763 gatherViews.setEnabled(true);
764 tabbedPane.setVisible(true);
765 AlignmentPanel first = alignPanels.get(0);
766 tabbedPane.addTab(first.av.viewName, first);
767 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
770 public AlignViewport getViewport()
775 /* Set up intrinsic listeners for dynamically generated GUI bits. */
776 private void addServiceListeners()
778 final java.beans.PropertyChangeListener thisListener;
779 Desktop.instance.addJalviewPropertyChangeListener("services",
780 thisListener = new java.beans.PropertyChangeListener()
783 public void propertyChange(PropertyChangeEvent evt)
785 // // System.out.println("Discoverer property change.");
786 // if (evt.getPropertyName().equals("services"))
788 SwingUtilities.invokeLater(new Runnable()
795 .println("Rebuild WS Menu for service change");
796 BuildWebServiceMenu();
803 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
806 public void internalFrameClosed(
807 javax.swing.event.InternalFrameEvent evt)
809 // System.out.println("deregistering discoverer listener");
810 Desktop.instance.removeJalviewPropertyChangeListener("services",
812 closeMenuItem_actionPerformed(true);
815 // Finally, build the menu once to get current service state
816 new Thread(new Runnable()
821 BuildWebServiceMenu();
827 * Configure menu items that vary according to whether the alignment is
828 * nucleotide or protein
832 public void setGUINucleotide(boolean nucleotide)
834 showTranslation.setVisible(nucleotide);
835 showReverse.setVisible(nucleotide);
836 showReverseComplement.setVisible(nucleotide);
837 conservationMenuItem.setEnabled(!nucleotide);
838 modifyConservation.setEnabled(!nucleotide);
839 showGroupConservation.setEnabled(!nucleotide);
840 rnahelicesColour.setEnabled(nucleotide);
841 purinePyrimidineColour.setEnabled(nucleotide);
842 showComplementMenuItem.setText(MessageManager
843 .getString(nucleotide ? "label.protein" : "label.nucleotide"));
844 setColourSelected(jalview.bin.Cache.getDefault(
845 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
846 : Preferences.DEFAULT_COLOUR_PROT, "None"));
850 * set up menus for the current viewport. This may be called after any
851 * operation that affects the data in the current view (selection changed,
852 * etc) to update the menus to reflect the new state.
855 public void setMenusForViewport()
857 setMenusFromViewport(viewport);
861 * Need to call this method when tabs are selected for multiple views, or when
862 * loading from Jalview2XML.java
867 void setMenusFromViewport(AlignViewport av)
869 padGapsMenuitem.setSelected(av.isPadGaps());
870 colourTextMenuItem.setSelected(av.isShowColourText());
871 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
872 conservationMenuItem.setSelected(av.getConservationSelected());
873 seqLimits.setSelected(av.getShowJVSuffix());
874 idRightAlign.setSelected(av.isRightAlignIds());
875 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
876 renderGapsMenuItem.setSelected(av.isRenderGaps());
877 wrapMenuItem.setSelected(av.getWrapAlignment());
878 scaleAbove.setVisible(av.getWrapAlignment());
879 scaleLeft.setVisible(av.getWrapAlignment());
880 scaleRight.setVisible(av.getWrapAlignment());
881 annotationPanelMenuItem.setState(av.isShowAnnotation());
883 * Show/hide annotations only enabled if annotation panel is shown
885 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
886 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
887 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
888 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
889 viewBoxesMenuItem.setSelected(av.getShowBoxes());
890 viewTextMenuItem.setSelected(av.getShowText());
891 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
892 showGroupConsensus.setSelected(av.isShowGroupConsensus());
893 showGroupConservation.setSelected(av.isShowGroupConservation());
894 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
895 showSequenceLogo.setSelected(av.isShowSequenceLogo());
896 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
898 setColourSelected(ColourSchemeProperty.getColourName(av
899 .getGlobalColourScheme()));
901 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
902 hiddenMarkers.setState(av.getShowHiddenMarkers());
903 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
904 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
905 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
906 autoCalculate.setSelected(av.autoCalculateConsensus);
907 sortByTree.setSelected(av.sortByTree);
908 listenToViewSelections.setSelected(av.followSelection);
909 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
911 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
913 showProducts.setEnabled(canShowProducts());
918 private IProgressIndicator progressBar;
923 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
926 public void setProgressBar(String message, long id)
928 progressBar.setProgressBar(message, id);
932 public void registerHandler(final long id,
933 final IProgressIndicatorHandler handler)
935 progressBar.registerHandler(id, handler);
940 * @return true if any progress bars are still active
943 public boolean operationInProgress()
945 return progressBar.operationInProgress();
949 public void setStatus(String text)
951 statusBar.setText(text);
955 * Added so Castor Mapping file can obtain Jalview Version
957 public String getVersion()
959 return jalview.bin.Cache.getProperty("VERSION");
962 public FeatureRenderer getFeatureRenderer()
964 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
968 public void fetchSequence_actionPerformed(ActionEvent e)
970 new jalview.gui.SequenceFetcher(this);
974 public void addFromFile_actionPerformed(ActionEvent e)
976 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
980 public void reload_actionPerformed(ActionEvent e)
982 if (fileName != null)
984 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
985 // originating file's format
986 // TODO: work out how to recover feature settings for correct view(s) when
988 if (currentFileFormat.equals("Jalview"))
990 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
991 for (int i = 0; i < frames.length; i++)
993 if (frames[i] instanceof AlignFrame && frames[i] != this
994 && ((AlignFrame) frames[i]).fileName != null
995 && ((AlignFrame) frames[i]).fileName.equals(fileName))
999 frames[i].setSelected(true);
1000 Desktop.instance.closeAssociatedWindows();
1001 } catch (java.beans.PropertyVetoException ex)
1007 Desktop.instance.closeAssociatedWindows();
1009 FileLoader loader = new FileLoader();
1010 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1011 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1015 Rectangle bounds = this.getBounds();
1017 FileLoader loader = new FileLoader();
1018 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1019 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1020 protocol, currentFileFormat);
1022 newframe.setBounds(bounds);
1023 if (featureSettings != null && featureSettings.isShowing())
1025 final Rectangle fspos = featureSettings.frame.getBounds();
1026 // TODO: need a 'show feature settings' function that takes bounds -
1027 // need to refactor Desktop.addFrame
1028 newframe.featureSettings_actionPerformed(null);
1029 final FeatureSettings nfs = newframe.featureSettings;
1030 SwingUtilities.invokeLater(new Runnable()
1035 nfs.frame.setBounds(fspos);
1038 this.featureSettings.close();
1039 this.featureSettings = null;
1041 this.closeMenuItem_actionPerformed(true);
1047 public void addFromText_actionPerformed(ActionEvent e)
1049 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1054 public void addFromURL_actionPerformed(ActionEvent e)
1056 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1060 public void save_actionPerformed(ActionEvent e)
1062 if (fileName == null
1063 || (currentFileFormat == null || !jalview.io.FormatAdapter
1064 .isValidIOFormat(currentFileFormat, true))
1065 || fileName.startsWith("http"))
1067 saveAs_actionPerformed(null);
1071 saveAlignment(fileName, currentFileFormat);
1082 public void saveAs_actionPerformed(ActionEvent e)
1084 JalviewFileChooser chooser = new JalviewFileChooser(
1085 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1086 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1087 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1088 currentFileFormat, false);
1090 chooser.setFileView(new JalviewFileView());
1091 chooser.setDialogTitle(MessageManager
1092 .getString("label.save_alignment_to_file"));
1093 chooser.setToolTipText(MessageManager.getString("action.save"));
1095 int value = chooser.showSaveDialog(this);
1097 if (value == JalviewFileChooser.APPROVE_OPTION)
1099 currentFileFormat = chooser.getSelectedFormat();
1100 while (currentFileFormat == null)
1103 .showInternalMessageDialog(
1106 .getString("label.select_file_format_before_saving"),
1108 .getString("label.file_format_not_specified"),
1109 JOptionPane.WARNING_MESSAGE);
1110 currentFileFormat = chooser.getSelectedFormat();
1111 value = chooser.showSaveDialog(this);
1112 if (value != JalviewFileChooser.APPROVE_OPTION)
1118 fileName = chooser.getSelectedFile().getPath();
1120 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1123 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1124 if (currentFileFormat.indexOf(" ") > -1)
1126 currentFileFormat = currentFileFormat.substring(0,
1127 currentFileFormat.indexOf(" "));
1129 saveAlignment(fileName, currentFileFormat);
1133 public boolean saveAlignment(String file, String format)
1135 boolean success = true;
1137 if (format.equalsIgnoreCase("Jalview"))
1139 String shortName = title;
1141 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1143 shortName = shortName.substring(shortName
1144 .lastIndexOf(java.io.File.separatorChar) + 1);
1147 success = new Jalview2XML().saveAlignment(this, file, shortName);
1149 statusBar.setText(MessageManager.formatMessage(
1150 "label.successfully_saved_to_file_in_format", new Object[] {
1151 fileName, format }));
1156 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1158 warningMessage("Cannot save file " + fileName + " using format "
1159 + format, "Alignment output format not supported");
1160 if (!Jalview.isHeadlessMode())
1162 saveAs_actionPerformed(null);
1167 AlignmentExportData exportData = getAlignmentForExport(format,
1169 if (exportData.getSettings().isCancelled())
1173 FormatAdapter f = new FormatAdapter(alignPanel,
1174 exportData.getSettings());
1175 String output = f.formatSequences(
1177 exportData.getAlignment(), // class cast exceptions will
1178 // occur in the distant future
1179 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1180 f.getCacheSuffixDefault(format),
1181 viewport.getColumnSelection());
1191 java.io.PrintWriter out = new java.io.PrintWriter(
1192 new java.io.FileWriter(file));
1196 this.setTitle(file);
1197 statusBar.setText(MessageManager.formatMessage(
1198 "label.successfully_saved_to_file_in_format",
1199 new Object[] { fileName, format }));
1200 } catch (Exception ex)
1203 ex.printStackTrace();
1210 JOptionPane.showInternalMessageDialog(this, MessageManager
1211 .formatMessage("label.couldnt_save_file",
1212 new Object[] { fileName }), MessageManager
1213 .getString("label.error_saving_file"),
1214 JOptionPane.WARNING_MESSAGE);
1220 private void warningMessage(String warning, String title)
1222 if (new jalview.util.Platform().isHeadless())
1224 System.err.println("Warning: " + title + "\nWarning: " + warning);
1229 JOptionPane.showInternalMessageDialog(this, warning, title,
1230 JOptionPane.WARNING_MESSAGE);
1242 protected void outputText_actionPerformed(ActionEvent e)
1245 AlignmentExportData exportData = getAlignmentForExport(
1246 e.getActionCommand(), viewport, null);
1247 if (exportData.getSettings().isCancelled())
1251 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1252 cap.setForInput(null);
1255 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1256 .formatSequences(e.getActionCommand(),
1257 exportData.getAlignment(),
1258 exportData.getOmitHidden(),
1259 exportData.getStartEndPostions(),
1260 viewport.getColumnSelection()));
1261 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1262 "label.alignment_output_command",
1263 new Object[] { e.getActionCommand() }), 600, 500);
1264 } catch (OutOfMemoryError oom)
1266 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1272 public static AlignmentExportData getAlignmentForExport(
1273 String exportFormat, AlignViewportI viewport,
1274 AlignExportSettingI exportSettings)
1276 AlignmentI alignmentToExport = null;
1277 AlignExportSettingI settings = exportSettings;
1278 String[] omitHidden = null;
1279 int[] alignmentStartEnd = new int[2];
1281 HiddenSequences hiddenSeqs = viewport.getAlignment()
1282 .getHiddenSequences();
1284 alignmentToExport = viewport.getAlignment();
1285 alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
1287 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1288 if (settings == null)
1290 settings = new AlignExportSettings(hasHiddenSeqs,
1291 viewport.hasHiddenColumns(), exportFormat);
1293 // settings.isExportAnnotations();
1295 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1297 omitHidden = viewport.getViewAsString(false);
1300 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1302 alignmentToExport = hiddenSeqs.getFullAlignment();
1306 alignmentToExport = viewport.getAlignment();
1307 alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
1308 .getColumnSelection().getHiddenColumns());
1310 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1311 omitHidden, alignmentStartEnd, settings);
1315 public static int[] getStartEnd(int[] aligmentStartEnd,
1316 List<int[]> hiddenCols)
1318 int startPos = aligmentStartEnd[0];
1319 int endPos = aligmentStartEnd[1];
1321 int[] lowestRange = new int[] { -1, -1 };
1322 int[] higestRange = new int[] { -1, -1 };
1324 for (int[] hiddenCol : hiddenCols)
1326 lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1327 higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1330 if (lowestRange[0] == -1 && lowestRange[1] == -1)
1332 startPos = aligmentStartEnd[0];
1336 startPos = lowestRange[1] + 1;
1339 if (higestRange[0] == -1 && higestRange[1] == -1)
1341 endPos = aligmentStartEnd[1];
1345 endPos = higestRange[0] - 1;
1348 // System.out.println("Export range : " + startPos + " - " + endPos);
1349 return new int[] { startPos, endPos };
1352 public static void main(String[] args)
1354 ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1355 hiddenCols.add(new int[] { 0, 0 });
1356 hiddenCols.add(new int[] { 6, 9 });
1357 hiddenCols.add(new int[] { 11, 12 });
1358 hiddenCols.add(new int[] { 33, 33 });
1359 hiddenCols.add(new int[] { 50, 50 });
1361 int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
1362 // System.out.println("Export range : " + x[0] + " - " + x[1]);
1372 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1374 new HtmlSvgOutput(null, alignPanel);
1378 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1380 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1381 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1384 public void createImageMap(File file, String image)
1386 alignPanel.makePNGImageMap(file, image);
1396 public void createPNG(File f)
1398 alignPanel.makePNG(f);
1408 public void createEPS(File f)
1410 alignPanel.makeEPS(f);
1414 public void createSVG(File f)
1416 alignPanel.makeSVG(f);
1420 public void pageSetup_actionPerformed(ActionEvent e)
1422 PrinterJob printJob = PrinterJob.getPrinterJob();
1423 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1433 public void printMenuItem_actionPerformed(ActionEvent e)
1435 // Putting in a thread avoids Swing painting problems
1436 PrintThread thread = new PrintThread(alignPanel);
1441 public void exportFeatures_actionPerformed(ActionEvent e)
1443 new AnnotationExporter().exportFeatures(alignPanel);
1447 public void exportAnnotations_actionPerformed(ActionEvent e)
1449 new AnnotationExporter().exportAnnotations(alignPanel);
1453 public void associatedData_actionPerformed(ActionEvent e)
1455 // Pick the tree file
1456 JalviewFileChooser chooser = new JalviewFileChooser(
1457 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1458 chooser.setFileView(new JalviewFileView());
1459 chooser.setDialogTitle(MessageManager
1460 .getString("label.load_jalview_annotations"));
1461 chooser.setToolTipText(MessageManager
1462 .getString("label.load_jalview_annotations"));
1464 int value = chooser.showOpenDialog(null);
1466 if (value == JalviewFileChooser.APPROVE_OPTION)
1468 String choice = chooser.getSelectedFile().getPath();
1469 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1470 loadJalviewDataFile(choice, null, null, null);
1476 * Close the current view or all views in the alignment frame. If the frame
1477 * only contains one view then the alignment will be removed from memory.
1479 * @param closeAllTabs
1482 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1484 if (alignPanels != null && alignPanels.size() < 2)
1486 closeAllTabs = true;
1491 if (alignPanels != null)
1495 if (this.isClosed())
1497 // really close all the windows - otherwise wait till
1498 // setClosed(true) is called
1499 for (int i = 0; i < alignPanels.size(); i++)
1501 AlignmentPanel ap = alignPanels.get(i);
1508 closeView(alignPanel);
1515 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1516 * be called recursively, with the frame now in 'closed' state
1518 this.setClosed(true);
1520 } catch (Exception ex)
1522 ex.printStackTrace();
1527 * Close the specified panel and close up tabs appropriately.
1529 * @param panelToClose
1531 public void closeView(AlignmentPanel panelToClose)
1533 int index = tabbedPane.getSelectedIndex();
1534 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1535 alignPanels.remove(panelToClose);
1536 panelToClose.closePanel();
1537 panelToClose = null;
1539 tabbedPane.removeTabAt(closedindex);
1540 tabbedPane.validate();
1542 if (index > closedindex || index == tabbedPane.getTabCount())
1544 // modify currently selected tab index if necessary.
1548 this.tabSelectionChanged(index);
1554 void updateEditMenuBar()
1557 if (viewport.getHistoryList().size() > 0)
1559 undoMenuItem.setEnabled(true);
1560 CommandI command = viewport.getHistoryList().peek();
1561 undoMenuItem.setText(MessageManager.formatMessage(
1562 "label.undo_command",
1563 new Object[] { command.getDescription() }));
1567 undoMenuItem.setEnabled(false);
1568 undoMenuItem.setText(MessageManager.getString("action.undo"));
1571 if (viewport.getRedoList().size() > 0)
1573 redoMenuItem.setEnabled(true);
1575 CommandI command = viewport.getRedoList().peek();
1576 redoMenuItem.setText(MessageManager.formatMessage(
1577 "label.redo_command",
1578 new Object[] { command.getDescription() }));
1582 redoMenuItem.setEnabled(false);
1583 redoMenuItem.setText(MessageManager.getString("action.redo"));
1588 public void addHistoryItem(CommandI command)
1590 if (command.getSize() > 0)
1592 viewport.addToHistoryList(command);
1593 viewport.clearRedoList();
1594 updateEditMenuBar();
1595 viewport.updateHiddenColumns();
1596 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1597 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1598 // viewport.getColumnSelection()
1599 // .getHiddenColumns().size() > 0);
1605 * @return alignment objects for all views
1607 AlignmentI[] getViewAlignments()
1609 if (alignPanels != null)
1611 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1613 for (AlignmentPanel ap : alignPanels)
1615 als[i++] = ap.av.getAlignment();
1619 if (viewport != null)
1621 return new AlignmentI[] { viewport.getAlignment() };
1633 protected void undoMenuItem_actionPerformed(ActionEvent e)
1635 if (viewport.getHistoryList().isEmpty())
1639 CommandI command = viewport.getHistoryList().pop();
1640 viewport.addToRedoList(command);
1641 command.undoCommand(getViewAlignments());
1643 AlignmentViewport originalSource = getOriginatingSource(command);
1644 updateEditMenuBar();
1646 if (originalSource != null)
1648 if (originalSource != viewport)
1651 .warn("Implementation worry: mismatch of viewport origin for undo");
1653 originalSource.updateHiddenColumns();
1654 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1656 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1657 // viewport.getColumnSelection()
1658 // .getHiddenColumns().size() > 0);
1659 originalSource.firePropertyChange("alignment", null, originalSource
1660 .getAlignment().getSequences());
1671 protected void redoMenuItem_actionPerformed(ActionEvent e)
1673 if (viewport.getRedoList().size() < 1)
1678 CommandI command = viewport.getRedoList().pop();
1679 viewport.addToHistoryList(command);
1680 command.doCommand(getViewAlignments());
1682 AlignmentViewport originalSource = getOriginatingSource(command);
1683 updateEditMenuBar();
1685 if (originalSource != null)
1688 if (originalSource != viewport)
1691 .warn("Implementation worry: mismatch of viewport origin for redo");
1693 originalSource.updateHiddenColumns();
1694 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1696 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1697 // viewport.getColumnSelection()
1698 // .getHiddenColumns().size() > 0);
1699 originalSource.firePropertyChange("alignment", null, originalSource
1700 .getAlignment().getSequences());
1704 AlignmentViewport getOriginatingSource(CommandI command)
1706 AlignmentViewport originalSource = null;
1707 // For sequence removal and addition, we need to fire
1708 // the property change event FROM the viewport where the
1709 // original alignment was altered
1710 AlignmentI al = null;
1711 if (command instanceof EditCommand)
1713 EditCommand editCommand = (EditCommand) command;
1714 al = editCommand.getAlignment();
1715 List<Component> comps = PaintRefresher.components.get(viewport
1716 .getSequenceSetId());
1718 for (Component comp : comps)
1720 if (comp instanceof AlignmentPanel)
1722 if (al == ((AlignmentPanel) comp).av.getAlignment())
1724 originalSource = ((AlignmentPanel) comp).av;
1731 if (originalSource == null)
1733 // The original view is closed, we must validate
1734 // the current view against the closed view first
1737 PaintRefresher.validateSequences(al, viewport.getAlignment());
1740 originalSource = viewport;
1743 return originalSource;
1752 public void moveSelectedSequences(boolean up)
1754 SequenceGroup sg = viewport.getSelectionGroup();
1760 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1761 viewport.getHiddenRepSequences(), up);
1762 alignPanel.paintAlignment(true);
1765 synchronized void slideSequences(boolean right, int size)
1767 List<SequenceI> sg = new ArrayList<SequenceI>();
1768 if (viewport.cursorMode)
1770 sg.add(viewport.getAlignment().getSequenceAt(
1771 alignPanel.getSeqPanel().seqCanvas.cursorY));
1773 else if (viewport.getSelectionGroup() != null
1774 && viewport.getSelectionGroup().getSize() != viewport
1775 .getAlignment().getHeight())
1777 sg = viewport.getSelectionGroup().getSequences(
1778 viewport.getHiddenRepSequences());
1786 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1788 for (SequenceI seq : viewport.getAlignment().getSequences())
1790 if (!sg.contains(seq))
1792 invertGroup.add(seq);
1796 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1798 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1799 for (int i = 0; i < invertGroup.size(); i++)
1801 seqs2[i] = invertGroup.get(i);
1804 SlideSequencesCommand ssc;
1807 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1808 size, viewport.getGapCharacter());
1812 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1813 size, viewport.getGapCharacter());
1816 int groupAdjustment = 0;
1817 if (ssc.getGapsInsertedBegin() && right)
1819 if (viewport.cursorMode)
1821 alignPanel.getSeqPanel().moveCursor(size, 0);
1825 groupAdjustment = size;
1828 else if (!ssc.getGapsInsertedBegin() && !right)
1830 if (viewport.cursorMode)
1832 alignPanel.getSeqPanel().moveCursor(-size, 0);
1836 groupAdjustment = -size;
1840 if (groupAdjustment != 0)
1842 viewport.getSelectionGroup().setStartRes(
1843 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1844 viewport.getSelectionGroup().setEndRes(
1845 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1849 * just extend the last slide command if compatible; but not if in
1850 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1852 boolean appendHistoryItem = false;
1853 Deque<CommandI> historyList = viewport.getHistoryList();
1854 boolean inSplitFrame = getSplitViewContainer() != null;
1855 if (!inSplitFrame && historyList != null && historyList.size() > 0
1856 && historyList.peek() instanceof SlideSequencesCommand)
1858 appendHistoryItem = ssc
1859 .appendSlideCommand((SlideSequencesCommand) historyList
1863 if (!appendHistoryItem)
1865 addHistoryItem(ssc);
1878 protected void copy_actionPerformed(ActionEvent e)
1881 if (viewport.getSelectionGroup() == null)
1885 // TODO: preserve the ordering of displayed alignment annotation in any
1886 // internal paste (particularly sequence associated annotation)
1887 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1888 String[] omitHidden = null;
1890 if (viewport.hasHiddenColumns())
1892 omitHidden = viewport.getViewAsString(true);
1895 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1898 StringSelection ss = new StringSelection(output);
1902 jalview.gui.Desktop.internalCopy = true;
1903 // Its really worth setting the clipboard contents
1904 // to empty before setting the large StringSelection!!
1905 Toolkit.getDefaultToolkit().getSystemClipboard()
1906 .setContents(new StringSelection(""), null);
1908 Toolkit.getDefaultToolkit().getSystemClipboard()
1909 .setContents(ss, Desktop.instance);
1910 } catch (OutOfMemoryError er)
1912 new OOMWarning("copying region", er);
1916 ArrayList<int[]> hiddenColumns = null;
1917 if (viewport.hasHiddenColumns())
1919 hiddenColumns = new ArrayList<int[]>();
1920 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1921 .getSelectionGroup().getEndRes();
1922 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1924 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1926 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1927 region[1] - hiddenOffset });
1932 Desktop.jalviewClipboard = new Object[] { seqs,
1933 viewport.getAlignment().getDataset(), hiddenColumns };
1934 statusBar.setText(MessageManager.formatMessage(
1935 "label.copied_sequences_to_clipboard", new Object[] { Integer
1936 .valueOf(seqs.length).toString() }));
1946 protected void pasteNew_actionPerformed(ActionEvent e)
1958 protected void pasteThis_actionPerformed(ActionEvent e)
1964 * Paste contents of Jalview clipboard
1966 * @param newAlignment
1967 * true to paste to a new alignment, otherwise add to this.
1969 void paste(boolean newAlignment)
1971 boolean externalPaste = true;
1974 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1975 Transferable contents = c.getContents(this);
1977 if (contents == null)
1985 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1986 if (str.length() < 1)
1991 format = new IdentifyFile().identify(str, "Paste");
1993 } catch (OutOfMemoryError er)
1995 new OOMWarning("Out of memory pasting sequences!!", er);
1999 SequenceI[] sequences;
2000 boolean annotationAdded = false;
2001 AlignmentI alignment = null;
2003 if (Desktop.jalviewClipboard != null)
2005 // The clipboard was filled from within Jalview, we must use the
2007 // And dataset from the copied alignment
2008 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2009 // be doubly sure that we create *new* sequence objects.
2010 sequences = new SequenceI[newseq.length];
2011 for (int i = 0; i < newseq.length; i++)
2013 sequences[i] = new Sequence(newseq[i]);
2015 alignment = new Alignment(sequences);
2016 externalPaste = false;
2020 // parse the clipboard as an alignment.
2021 alignment = new FormatAdapter().readFile(str, "Paste", format);
2022 sequences = alignment.getSequencesArray();
2026 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2032 if (Desktop.jalviewClipboard != null)
2034 // dataset is inherited
2035 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2039 // new dataset is constructed
2040 alignment.setDataset(null);
2042 alwidth = alignment.getWidth() + 1;
2046 AlignmentI pastedal = alignment; // preserve pasted alignment object
2047 // Add pasted sequences and dataset into existing alignment.
2048 alignment = viewport.getAlignment();
2049 alwidth = alignment.getWidth() + 1;
2050 // decide if we need to import sequences from an existing dataset
2051 boolean importDs = Desktop.jalviewClipboard != null
2052 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2053 // importDs==true instructs us to copy over new dataset sequences from
2054 // an existing alignment
2055 Vector newDs = (importDs) ? new Vector() : null; // used to create
2056 // minimum dataset set
2058 for (int i = 0; i < sequences.length; i++)
2062 newDs.addElement(null);
2064 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2066 if (importDs && ds != null)
2068 if (!newDs.contains(ds))
2070 newDs.setElementAt(ds, i);
2071 ds = new Sequence(ds);
2072 // update with new dataset sequence
2073 sequences[i].setDatasetSequence(ds);
2077 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2082 // copy and derive new dataset sequence
2083 sequences[i] = sequences[i].deriveSequence();
2084 alignment.getDataset().addSequence(
2085 sequences[i].getDatasetSequence());
2086 // TODO: avoid creation of duplicate dataset sequences with a
2087 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2089 alignment.addSequence(sequences[i]); // merges dataset
2093 newDs.clear(); // tidy up
2095 if (alignment.getAlignmentAnnotation() != null)
2097 for (AlignmentAnnotation alan : alignment
2098 .getAlignmentAnnotation())
2100 if (alan.graphGroup > fgroup)
2102 fgroup = alan.graphGroup;
2106 if (pastedal.getAlignmentAnnotation() != null)
2108 // Add any annotation attached to alignment.
2109 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2110 for (int i = 0; i < alann.length; i++)
2112 annotationAdded = true;
2113 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2115 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2116 if (newann.graphGroup > -1)
2118 if (newGraphGroups.size() <= newann.graphGroup
2119 || newGraphGroups.get(newann.graphGroup) == null)
2121 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2123 newGraphGroups.add(q, null);
2125 newGraphGroups.set(newann.graphGroup, new Integer(
2128 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2132 newann.padAnnotation(alwidth);
2133 alignment.addAnnotation(newann);
2143 addHistoryItem(new EditCommand(
2144 MessageManager.getString("label.add_sequences"),
2145 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2147 // Add any annotations attached to sequences
2148 for (int i = 0; i < sequences.length; i++)
2150 if (sequences[i].getAnnotation() != null)
2152 AlignmentAnnotation newann;
2153 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2155 annotationAdded = true;
2156 newann = sequences[i].getAnnotation()[a];
2157 newann.adjustForAlignment();
2158 newann.padAnnotation(alwidth);
2159 if (newann.graphGroup > -1)
2161 if (newann.graphGroup > -1)
2163 if (newGraphGroups.size() <= newann.graphGroup
2164 || newGraphGroups.get(newann.graphGroup) == null)
2166 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2168 newGraphGroups.add(q, null);
2170 newGraphGroups.set(newann.graphGroup, new Integer(
2173 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2177 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2182 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2189 // propagate alignment changed.
2190 viewport.setEndSeq(alignment.getHeight());
2191 if (annotationAdded)
2193 // Duplicate sequence annotation in all views.
2194 AlignmentI[] alview = this.getViewAlignments();
2195 for (int i = 0; i < sequences.length; i++)
2197 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2202 for (int avnum = 0; avnum < alview.length; avnum++)
2204 if (alview[avnum] != alignment)
2206 // duplicate in a view other than the one with input focus
2207 int avwidth = alview[avnum].getWidth() + 1;
2208 // this relies on sann being preserved after we
2209 // modify the sequence's annotation array for each duplication
2210 for (int a = 0; a < sann.length; a++)
2212 AlignmentAnnotation newann = new AlignmentAnnotation(
2214 sequences[i].addAlignmentAnnotation(newann);
2215 newann.padAnnotation(avwidth);
2216 alview[avnum].addAnnotation(newann); // annotation was
2217 // duplicated earlier
2218 // TODO JAL-1145 graphGroups are not updated for sequence
2219 // annotation added to several views. This may cause
2221 alview[avnum].setAnnotationIndex(newann, a);
2226 buildSortByAnnotationScoresMenu();
2228 viewport.firePropertyChange("alignment", null,
2229 alignment.getSequences());
2230 if (alignPanels != null)
2232 for (AlignmentPanel ap : alignPanels)
2234 ap.validateAnnotationDimensions(false);
2239 alignPanel.validateAnnotationDimensions(false);
2245 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2247 String newtitle = new String("Copied sequences");
2249 if (Desktop.jalviewClipboard != null
2250 && Desktop.jalviewClipboard[2] != null)
2252 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2253 for (int[] region : hc)
2255 af.viewport.hideColumns(region[0], region[1]);
2259 // >>>This is a fix for the moment, until a better solution is
2261 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2263 alignPanel.getSeqPanel().seqCanvas
2264 .getFeatureRenderer());
2266 // TODO: maintain provenance of an alignment, rather than just make the
2267 // title a concatenation of operations.
2270 if (title.startsWith("Copied sequences"))
2276 newtitle = newtitle.concat("- from " + title);
2281 newtitle = new String("Pasted sequences");
2284 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2289 } catch (Exception ex)
2291 ex.printStackTrace();
2292 System.out.println("Exception whilst pasting: " + ex);
2293 // could be anything being pasted in here
2299 protected void expand_newalign(ActionEvent e)
2303 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2304 .getAlignment(), -1);
2305 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2307 String newtitle = new String("Flanking alignment");
2309 if (Desktop.jalviewClipboard != null
2310 && Desktop.jalviewClipboard[2] != null)
2312 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2313 for (int region[] : hc)
2315 af.viewport.hideColumns(region[0], region[1]);
2319 // >>>This is a fix for the moment, until a better solution is
2321 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2323 alignPanel.getSeqPanel().seqCanvas
2324 .getFeatureRenderer());
2326 // TODO: maintain provenance of an alignment, rather than just make the
2327 // title a concatenation of operations.
2329 if (title.startsWith("Copied sequences"))
2335 newtitle = newtitle.concat("- from " + title);
2339 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2341 } catch (Exception ex)
2343 ex.printStackTrace();
2344 System.out.println("Exception whilst pasting: " + ex);
2345 // could be anything being pasted in here
2346 } catch (OutOfMemoryError oom)
2348 new OOMWarning("Viewing flanking region of alignment", oom);
2359 protected void cut_actionPerformed(ActionEvent e)
2361 copy_actionPerformed(null);
2362 delete_actionPerformed(null);
2372 protected void delete_actionPerformed(ActionEvent evt)
2375 SequenceGroup sg = viewport.getSelectionGroup();
2382 * If the cut affects all sequences, warn, remove highlighted columns
2384 if (sg.getSize() == viewport.getAlignment().getHeight())
2386 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2387 .getAlignment().getWidth()) ? true : false;
2388 if (isEntireAlignWidth)
2390 int confirm = JOptionPane.showConfirmDialog(this,
2391 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2392 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2393 JOptionPane.OK_CANCEL_OPTION);
2395 if (confirm == JOptionPane.CANCEL_OPTION
2396 || confirm == JOptionPane.CLOSED_OPTION)
2401 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2402 sg.getEndRes() + 1);
2404 SequenceI[] cut = sg.getSequences()
2405 .toArray(new SequenceI[sg.getSize()]);
2407 addHistoryItem(new EditCommand(
2408 MessageManager.getString("label.cut_sequences"), Action.CUT,
2409 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2410 viewport.getAlignment()));
2412 viewport.setSelectionGroup(null);
2413 viewport.sendSelection();
2414 viewport.getAlignment().deleteGroup(sg);
2416 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2418 if (viewport.getAlignment().getHeight() < 1)
2422 this.setClosed(true);
2423 } catch (Exception ex)
2436 protected void deleteGroups_actionPerformed(ActionEvent e)
2438 if (avc.deleteGroups())
2440 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2441 alignPanel.updateAnnotation();
2442 alignPanel.paintAlignment(true);
2453 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2455 SequenceGroup sg = new SequenceGroup();
2457 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2459 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2462 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2463 viewport.setSelectionGroup(sg);
2464 viewport.sendSelection();
2465 // JAL-2034 - should delegate to
2466 // alignPanel to decide if overview needs
2468 alignPanel.paintAlignment(false);
2469 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2479 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2481 if (viewport.cursorMode)
2483 alignPanel.getSeqPanel().keyboardNo1 = null;
2484 alignPanel.getSeqPanel().keyboardNo2 = null;
2486 viewport.setSelectionGroup(null);
2487 viewport.getColumnSelection().clear();
2488 viewport.setSelectionGroup(null);
2489 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2490 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2491 // JAL-2034 - should delegate to
2492 // alignPanel to decide if overview needs
2494 alignPanel.paintAlignment(false);
2495 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2496 viewport.sendSelection();
2506 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2508 SequenceGroup sg = viewport.getSelectionGroup();
2512 selectAllSequenceMenuItem_actionPerformed(null);
2517 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2519 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2521 // JAL-2034 - should delegate to
2522 // alignPanel to decide if overview needs
2525 alignPanel.paintAlignment(true);
2526 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2527 viewport.sendSelection();
2531 public void invertColSel_actionPerformed(ActionEvent e)
2533 viewport.invertColumnSelection();
2534 alignPanel.paintAlignment(true);
2535 viewport.sendSelection();
2545 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2547 trimAlignment(true);
2557 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2559 trimAlignment(false);
2562 void trimAlignment(boolean trimLeft)
2564 ColumnSelection colSel = viewport.getColumnSelection();
2567 if (!colSel.isEmpty())
2571 column = colSel.getMin();
2575 column = colSel.getMax();
2579 if (viewport.getSelectionGroup() != null)
2581 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2582 viewport.getHiddenRepSequences());
2586 seqs = viewport.getAlignment().getSequencesArray();
2589 TrimRegionCommand trimRegion;
2592 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2593 column, viewport.getAlignment());
2594 viewport.setStartRes(0);
2598 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2599 column, viewport.getAlignment());
2602 statusBar.setText(MessageManager.formatMessage(
2603 "label.removed_columns",
2604 new String[] { Integer.valueOf(trimRegion.getSize())
2607 addHistoryItem(trimRegion);
2609 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2611 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2612 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2614 viewport.getAlignment().deleteGroup(sg);
2618 viewport.firePropertyChange("alignment", null, viewport
2619 .getAlignment().getSequences());
2630 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2632 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2635 if (viewport.getSelectionGroup() != null)
2637 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2638 viewport.getHiddenRepSequences());
2639 start = viewport.getSelectionGroup().getStartRes();
2640 end = viewport.getSelectionGroup().getEndRes();
2644 seqs = viewport.getAlignment().getSequencesArray();
2647 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2648 "Remove Gapped Columns", seqs, start, end,
2649 viewport.getAlignment());
2651 addHistoryItem(removeGapCols);
2653 statusBar.setText(MessageManager.formatMessage(
2654 "label.removed_empty_columns",
2655 new Object[] { Integer.valueOf(removeGapCols.getSize())
2658 // This is to maintain viewport position on first residue
2659 // of first sequence
2660 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2661 int startRes = seq.findPosition(viewport.startRes);
2662 // ShiftList shifts;
2663 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2664 // edit.alColumnChanges=shifts.getInverse();
2665 // if (viewport.hasHiddenColumns)
2666 // viewport.getColumnSelection().compensateForEdits(shifts);
2667 viewport.setStartRes(seq.findIndex(startRes) - 1);
2668 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2680 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2682 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2685 if (viewport.getSelectionGroup() != null)
2687 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2688 viewport.getHiddenRepSequences());
2689 start = viewport.getSelectionGroup().getStartRes();
2690 end = viewport.getSelectionGroup().getEndRes();
2694 seqs = viewport.getAlignment().getSequencesArray();
2697 // This is to maintain viewport position on first residue
2698 // of first sequence
2699 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2700 int startRes = seq.findPosition(viewport.startRes);
2702 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2703 viewport.getAlignment()));
2705 viewport.setStartRes(seq.findIndex(startRes) - 1);
2707 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2719 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2721 viewport.setPadGaps(padGapsMenuitem.isSelected());
2722 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2733 public void findMenuItem_actionPerformed(ActionEvent e)
2739 * Create a new view of the current alignment.
2742 public void newView_actionPerformed(ActionEvent e)
2744 newView(null, true);
2748 * Creates and shows a new view of the current alignment.
2751 * title of newly created view; if null, one will be generated
2752 * @param copyAnnotation
2753 * if true then duplicate all annnotation, groups and settings
2754 * @return new alignment panel, already displayed.
2756 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2759 * Create a new AlignmentPanel (with its own, new Viewport)
2761 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2763 if (!copyAnnotation)
2766 * remove all groups and annotation except for the automatic stuff
2768 newap.av.getAlignment().deleteAllGroups();
2769 newap.av.getAlignment().deleteAllAnnotations(false);
2772 newap.av.setGatherViewsHere(false);
2774 if (viewport.viewName == null)
2776 viewport.viewName = MessageManager
2777 .getString("label.view_name_original");
2781 * Views share the same edits undo and redo stacks
2783 newap.av.setHistoryList(viewport.getHistoryList());
2784 newap.av.setRedoList(viewport.getRedoList());
2787 * Views share the same mappings; need to deregister any new mappings
2788 * created by copyAlignPanel, and register the new reference to the shared
2791 newap.av.replaceMappings(viewport.getAlignment());
2793 newap.av.viewName = getNewViewName(viewTitle);
2795 addAlignmentPanel(newap, true);
2796 newap.alignmentChanged();
2798 if (alignPanels.size() == 2)
2800 viewport.setGatherViewsHere(true);
2802 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2807 * Make a new name for the view, ensuring it is unique within the current
2808 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2809 * these now use viewId. Unique view names are still desirable for usability.)
2814 protected String getNewViewName(String viewTitle)
2816 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2817 boolean addFirstIndex = false;
2818 if (viewTitle == null || viewTitle.trim().length() == 0)
2820 viewTitle = MessageManager.getString("action.view");
2821 addFirstIndex = true;
2825 index = 1;// we count from 1 if given a specific name
2827 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2829 List<Component> comps = PaintRefresher.components.get(viewport
2830 .getSequenceSetId());
2832 List<String> existingNames = getExistingViewNames(comps);
2834 while (existingNames.contains(newViewName))
2836 newViewName = viewTitle + " " + (++index);
2842 * Returns a list of distinct view names found in the given list of
2843 * components. View names are held on the viewport of an AlignmentPanel.
2848 protected List<String> getExistingViewNames(List<Component> comps)
2850 List<String> existingNames = new ArrayList<String>();
2851 for (Component comp : comps)
2853 if (comp instanceof AlignmentPanel)
2855 AlignmentPanel ap = (AlignmentPanel) comp;
2856 if (!existingNames.contains(ap.av.viewName))
2858 existingNames.add(ap.av.viewName);
2862 return existingNames;
2866 * Explode tabbed views into separate windows.
2869 public void expandViews_actionPerformed(ActionEvent e)
2871 Desktop.instance.explodeViews(this);
2875 * Gather views in separate windows back into a tabbed presentation.
2878 public void gatherViews_actionPerformed(ActionEvent e)
2880 Desktop.instance.gatherViews(this);
2890 public void font_actionPerformed(ActionEvent e)
2892 new FontChooser(alignPanel);
2902 protected void seqLimit_actionPerformed(ActionEvent e)
2904 viewport.setShowJVSuffix(seqLimits.isSelected());
2906 alignPanel.getIdPanel().getIdCanvas()
2907 .setPreferredSize(alignPanel.calculateIdWidth());
2908 alignPanel.paintAlignment(true);
2912 public void idRightAlign_actionPerformed(ActionEvent e)
2914 viewport.setRightAlignIds(idRightAlign.isSelected());
2915 alignPanel.paintAlignment(true);
2919 public void centreColumnLabels_actionPerformed(ActionEvent e)
2921 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2922 alignPanel.paintAlignment(true);
2928 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2931 protected void followHighlight_actionPerformed()
2934 * Set the 'follow' flag on the Viewport (and scroll to position if now
2937 final boolean state = this.followHighlightMenuItem.getState();
2938 viewport.setFollowHighlight(state);
2941 alignPanel.scrollToPosition(
2942 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2953 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2955 viewport.setColourText(colourTextMenuItem.isSelected());
2956 alignPanel.paintAlignment(true);
2966 public void wrapMenuItem_actionPerformed(ActionEvent e)
2968 scaleAbove.setVisible(wrapMenuItem.isSelected());
2969 scaleLeft.setVisible(wrapMenuItem.isSelected());
2970 scaleRight.setVisible(wrapMenuItem.isSelected());
2971 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2972 alignPanel.updateLayout();
2976 public void showAllSeqs_actionPerformed(ActionEvent e)
2978 viewport.showAllHiddenSeqs();
2982 public void showAllColumns_actionPerformed(ActionEvent e)
2984 viewport.showAllHiddenColumns();
2986 viewport.sendSelection();
2990 public void hideSelSequences_actionPerformed(ActionEvent e)
2992 viewport.hideAllSelectedSeqs();
2993 // alignPanel.paintAlignment(true);
2997 * called by key handler and the hide all/show all menu items
3002 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3005 boolean hide = false;
3006 SequenceGroup sg = viewport.getSelectionGroup();
3007 if (!toggleSeqs && !toggleCols)
3009 // Hide everything by the current selection - this is a hack - we do the
3010 // invert and then hide
3011 // first check that there will be visible columns after the invert.
3012 if ((viewport.getColumnSelection() != null
3013 && viewport.getColumnSelection().getSelected() != null && viewport
3014 .getColumnSelection().getSelected().size() > 0)
3015 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3018 // now invert the sequence set, if required - empty selection implies
3019 // that no hiding is required.
3022 invertSequenceMenuItem_actionPerformed(null);
3023 sg = viewport.getSelectionGroup();
3027 viewport.expandColSelection(sg, true);
3028 // finally invert the column selection and get the new sequence
3030 invertColSel_actionPerformed(null);
3037 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3039 hideSelSequences_actionPerformed(null);
3042 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3045 showAllSeqs_actionPerformed(null);
3051 if (viewport.getColumnSelection().getSelected().size() > 0)
3053 hideSelColumns_actionPerformed(null);
3056 viewport.setSelectionGroup(sg);
3061 showAllColumns_actionPerformed(null);
3070 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3071 * event.ActionEvent)
3074 public void hideAllButSelection_actionPerformed(ActionEvent e)
3076 toggleHiddenRegions(false, false);
3077 viewport.sendSelection();
3084 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3088 public void hideAllSelection_actionPerformed(ActionEvent e)
3090 SequenceGroup sg = viewport.getSelectionGroup();
3091 viewport.expandColSelection(sg, false);
3092 viewport.hideAllSelectedSeqs();
3093 viewport.hideSelectedColumns();
3094 alignPanel.paintAlignment(true);
3095 viewport.sendSelection();
3102 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3106 public void showAllhidden_actionPerformed(ActionEvent e)
3108 viewport.showAllHiddenColumns();
3109 viewport.showAllHiddenSeqs();
3110 alignPanel.paintAlignment(true);
3111 viewport.sendSelection();
3115 public void hideSelColumns_actionPerformed(ActionEvent e)
3117 viewport.hideSelectedColumns();
3118 alignPanel.paintAlignment(true);
3119 viewport.sendSelection();
3123 public void hiddenMarkers_actionPerformed(ActionEvent e)
3125 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3136 protected void scaleAbove_actionPerformed(ActionEvent e)
3138 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3139 alignPanel.paintAlignment(true);
3149 protected void scaleLeft_actionPerformed(ActionEvent e)
3151 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3152 alignPanel.paintAlignment(true);
3162 protected void scaleRight_actionPerformed(ActionEvent e)
3164 viewport.setScaleRightWrapped(scaleRight.isSelected());
3165 alignPanel.paintAlignment(true);
3175 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3177 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3178 alignPanel.paintAlignment(true);
3188 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3190 viewport.setShowText(viewTextMenuItem.isSelected());
3191 alignPanel.paintAlignment(true);
3201 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3203 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3204 alignPanel.paintAlignment(true);
3207 public FeatureSettings featureSettings;
3210 public FeatureSettingsControllerI getFeatureSettingsUI()
3212 return featureSettings;
3216 public void featureSettings_actionPerformed(ActionEvent e)
3218 if (featureSettings != null)
3220 featureSettings.close();
3221 featureSettings = null;
3223 if (!showSeqFeatures.isSelected())
3225 // make sure features are actually displayed
3226 showSeqFeatures.setSelected(true);
3227 showSeqFeatures_actionPerformed(null);
3229 featureSettings = new FeatureSettings(this);
3233 * Set or clear 'Show Sequence Features'
3239 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3241 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3242 alignPanel.paintAlignment(true);
3243 if (alignPanel.getOverviewPanel() != null)
3245 alignPanel.getOverviewPanel().updateOverviewImage();
3250 * Set or clear 'Show Sequence Features'
3256 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3258 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3260 if (viewport.isShowSequenceFeaturesHeight())
3262 // ensure we're actually displaying features
3263 viewport.setShowSequenceFeatures(true);
3264 showSeqFeatures.setSelected(true);
3266 alignPanel.paintAlignment(true);
3267 if (alignPanel.getOverviewPanel() != null)
3269 alignPanel.getOverviewPanel().updateOverviewImage();
3274 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3275 * the annotations panel as a whole.
3277 * The options to show/hide all annotations should be enabled when the panel
3278 * is shown, and disabled when the panel is hidden.
3283 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3285 final boolean setVisible = annotationPanelMenuItem.isSelected();
3286 viewport.setShowAnnotation(setVisible);
3287 this.showAllSeqAnnotations.setEnabled(setVisible);
3288 this.hideAllSeqAnnotations.setEnabled(setVisible);
3289 this.showAllAlAnnotations.setEnabled(setVisible);
3290 this.hideAllAlAnnotations.setEnabled(setVisible);
3291 alignPanel.updateLayout();
3295 public void alignmentProperties()
3297 JEditorPane editPane = new JEditorPane("text/html", "");
3298 editPane.setEditable(false);
3299 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3301 editPane.setText(MessageManager.formatMessage("label.html_content",
3302 new Object[] { contents.toString() }));
3303 JInternalFrame frame = new JInternalFrame();
3304 frame.getContentPane().add(new JScrollPane(editPane));
3306 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3307 "label.alignment_properties", new Object[] { getTitle() }),
3318 public void overviewMenuItem_actionPerformed(ActionEvent e)
3320 if (alignPanel.overviewPanel != null)
3325 JInternalFrame frame = new JInternalFrame();
3326 OverviewPanel overview = new OverviewPanel(alignPanel);
3327 frame.setContentPane(overview);
3328 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3329 "label.overview_params", new Object[] { this.getTitle() }),
3330 frame.getWidth(), frame.getHeight());
3332 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3333 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3336 public void internalFrameClosed(
3337 javax.swing.event.InternalFrameEvent evt)
3339 alignPanel.setOverviewPanel(null);
3343 alignPanel.setOverviewPanel(overview);
3347 public void textColour_actionPerformed(ActionEvent e)
3349 new TextColourChooser().chooseColour(alignPanel, null);
3359 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3371 public void clustalColour_actionPerformed(ActionEvent e)
3373 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3374 viewport.getHiddenRepSequences()));
3384 public void zappoColour_actionPerformed(ActionEvent e)
3386 changeColour(new ZappoColourScheme());
3396 public void taylorColour_actionPerformed(ActionEvent e)
3398 changeColour(new TaylorColourScheme());
3408 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3410 changeColour(new HydrophobicColourScheme());
3420 public void helixColour_actionPerformed(ActionEvent e)
3422 changeColour(new HelixColourScheme());
3432 public void strandColour_actionPerformed(ActionEvent e)
3434 changeColour(new StrandColourScheme());
3444 public void turnColour_actionPerformed(ActionEvent e)
3446 changeColour(new TurnColourScheme());
3456 public void buriedColour_actionPerformed(ActionEvent e)
3458 changeColour(new BuriedColourScheme());
3468 public void nucleotideColour_actionPerformed(ActionEvent e)
3470 changeColour(new NucleotideColourScheme());
3474 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3476 changeColour(new PurinePyrimidineColourScheme());
3480 * public void covariationColour_actionPerformed(ActionEvent e) {
3482 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3486 public void annotationColour_actionPerformed(ActionEvent e)
3488 new AnnotationColourChooser(viewport, alignPanel);
3492 public void annotationColumn_actionPerformed(ActionEvent e)
3494 new AnnotationColumnChooser(viewport, alignPanel);
3498 public void rnahelicesColour_actionPerformed(ActionEvent e)
3500 new RNAHelicesColourChooser(viewport, alignPanel);
3510 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3512 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3522 public void changeColour(ColourSchemeI cs)
3524 // TODO: pull up to controller method
3528 // Make sure viewport is up to date w.r.t. any sliders
3529 if (viewport.getAbovePIDThreshold())
3531 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3533 viewport.setThreshold(threshold);
3536 if (viewport.getConservationSelected())
3538 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3541 if (cs instanceof TCoffeeColourScheme)
3543 tcoffeeColour.setEnabled(true);
3544 tcoffeeColour.setSelected(true);
3548 viewport.setGlobalColourScheme(cs);
3550 alignPanel.paintAlignment(true);
3560 protected void modifyPID_actionPerformed(ActionEvent e)
3562 if (viewport.getAbovePIDThreshold()
3563 && viewport.getGlobalColourScheme() != null)
3565 SliderPanel.setPIDSliderSource(alignPanel,
3566 viewport.getGlobalColourScheme(), "Background");
3567 SliderPanel.showPIDSlider();
3578 protected void modifyConservation_actionPerformed(ActionEvent e)
3580 if (viewport.getConservationSelected()
3581 && viewport.getGlobalColourScheme() != null)
3583 SliderPanel.setConservationSlider(alignPanel,
3584 viewport.getGlobalColourScheme(), "Background");
3585 SliderPanel.showConservationSlider();
3596 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3598 viewport.setConservationSelected(conservationMenuItem.isSelected());
3600 viewport.setAbovePIDThreshold(false);
3601 abovePIDThreshold.setSelected(false);
3603 changeColour(viewport.getGlobalColourScheme());
3605 modifyConservation_actionPerformed(null);
3615 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3617 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3619 conservationMenuItem.setSelected(false);
3620 viewport.setConservationSelected(false);
3622 changeColour(viewport.getGlobalColourScheme());
3624 modifyPID_actionPerformed(null);
3634 public void userDefinedColour_actionPerformed(ActionEvent e)
3636 if (e.getActionCommand().equals(
3637 MessageManager.getString("action.user_defined")))
3639 new UserDefinedColours(alignPanel, null);
3643 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3644 .getUserColourSchemes().get(e.getActionCommand());
3650 public void updateUserColourMenu()
3653 Component[] menuItems = colourMenu.getMenuComponents();
3654 int iSize = menuItems.length;
3655 for (int i = 0; i < iSize; i++)
3657 if (menuItems[i].getName() != null
3658 && menuItems[i].getName().equals("USER_DEFINED"))
3660 colourMenu.remove(menuItems[i]);
3664 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3666 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3667 .getUserColourSchemes().keys();
3669 while (userColours.hasMoreElements())
3671 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3672 userColours.nextElement().toString());
3673 radioItem.setName("USER_DEFINED");
3674 radioItem.addMouseListener(new MouseAdapter()
3677 public void mousePressed(MouseEvent evt)
3679 if (evt.isControlDown()
3680 || SwingUtilities.isRightMouseButton(evt))
3682 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3684 int option = JOptionPane.showInternalConfirmDialog(
3685 jalview.gui.Desktop.desktop,
3687 .getString("label.remove_from_default_list"),
3689 .getString("label.remove_user_defined_colour"),
3690 JOptionPane.YES_NO_OPTION);
3691 if (option == JOptionPane.YES_OPTION)
3693 jalview.gui.UserDefinedColours
3694 .removeColourFromDefaults(radioItem.getText());
3695 colourMenu.remove(radioItem);
3699 radioItem.addActionListener(new ActionListener()
3702 public void actionPerformed(ActionEvent evt)
3704 userDefinedColour_actionPerformed(evt);
3711 radioItem.addActionListener(new ActionListener()
3714 public void actionPerformed(ActionEvent evt)
3716 userDefinedColour_actionPerformed(evt);
3720 colourMenu.insert(radioItem, 15);
3721 colours.add(radioItem);
3733 public void PIDColour_actionPerformed(ActionEvent e)
3735 changeColour(new PIDColourScheme());
3745 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3747 changeColour(new Blosum62ColourScheme());
3757 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3759 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3760 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3761 .getAlignment().getSequenceAt(0), null);
3762 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3763 viewport.getAlignment()));
3764 alignPanel.paintAlignment(true);
3774 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3776 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3777 AlignmentSorter.sortByID(viewport.getAlignment());
3778 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3779 viewport.getAlignment()));
3780 alignPanel.paintAlignment(true);
3790 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3792 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3793 AlignmentSorter.sortByLength(viewport.getAlignment());
3794 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3795 viewport.getAlignment()));
3796 alignPanel.paintAlignment(true);
3806 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3808 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3809 AlignmentSorter.sortByGroup(viewport.getAlignment());
3810 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3811 viewport.getAlignment()));
3813 alignPanel.paintAlignment(true);
3823 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3825 new RedundancyPanel(alignPanel, this);
3835 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3837 if ((viewport.getSelectionGroup() == null)
3838 || (viewport.getSelectionGroup().getSize() < 2))
3840 JOptionPane.showInternalMessageDialog(this, MessageManager
3841 .getString("label.you_must_select_least_two_sequences"),
3842 MessageManager.getString("label.invalid_selection"),
3843 JOptionPane.WARNING_MESSAGE);
3847 JInternalFrame frame = new JInternalFrame();
3848 frame.setContentPane(new PairwiseAlignPanel(viewport));
3849 Desktop.addInternalFrame(frame,
3850 MessageManager.getString("action.pairwise_alignment"), 600,
3862 public void PCAMenuItem_actionPerformed(ActionEvent e)
3864 if (((viewport.getSelectionGroup() != null)
3865 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3866 .getSelectionGroup().getSize() > 0))
3867 || (viewport.getAlignment().getHeight() < 4))
3870 .showInternalMessageDialog(
3873 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3875 .getString("label.sequence_selection_insufficient"),
3876 JOptionPane.WARNING_MESSAGE);
3881 new PCAPanel(alignPanel);
3885 public void autoCalculate_actionPerformed(ActionEvent e)
3887 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3888 if (viewport.autoCalculateConsensus)
3890 viewport.firePropertyChange("alignment", null, viewport
3891 .getAlignment().getSequences());
3896 public void sortByTreeOption_actionPerformed(ActionEvent e)
3898 viewport.sortByTree = sortByTree.isSelected();
3902 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3904 viewport.followSelection = listenToViewSelections.isSelected();
3914 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3916 newTreePanel("AV", "PID", "Average distance tree using PID");
3926 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3928 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3938 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3940 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3950 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3952 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3965 void newTreePanel(String type, String pwType, String title)
3969 if (viewport.getSelectionGroup() != null
3970 && viewport.getSelectionGroup().getSize() > 0)
3972 if (viewport.getSelectionGroup().getSize() < 3)
3978 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3980 .getString("label.not_enough_sequences"),
3981 JOptionPane.WARNING_MESSAGE);
3985 SequenceGroup sg = viewport.getSelectionGroup();
3987 /* Decide if the selection is a column region */
3988 for (SequenceI _s : sg.getSequences())
3990 if (_s.getLength() < sg.getEndRes())
3996 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3998 .getString("label.sequences_selection_not_aligned"),
3999 JOptionPane.WARNING_MESSAGE);
4005 title = title + " on region";
4006 tp = new TreePanel(alignPanel, type, pwType);
4010 // are the visible sequences aligned?
4011 if (!viewport.getAlignment().isAligned(false))
4017 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4019 .getString("label.sequences_not_aligned"),
4020 JOptionPane.WARNING_MESSAGE);
4025 if (viewport.getAlignment().getHeight() < 2)
4030 tp = new TreePanel(alignPanel, type, pwType);
4035 if (viewport.viewName != null)
4037 title += viewport.viewName + " of ";
4040 title += this.title;
4042 Desktop.addInternalFrame(tp, title, 600, 500);
4053 public void addSortByOrderMenuItem(String title,
4054 final AlignmentOrder order)
4056 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4057 "action.by_title_param", new Object[] { title }));
4059 item.addActionListener(new java.awt.event.ActionListener()
4062 public void actionPerformed(ActionEvent e)
4064 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4066 // TODO: JBPNote - have to map order entries to curent SequenceI
4068 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4070 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4073 alignPanel.paintAlignment(true);
4079 * Add a new sort by annotation score menu item
4082 * the menu to add the option to
4084 * the label used to retrieve scores for each sequence on the
4087 public void addSortByAnnotScoreMenuItem(JMenu sort,
4088 final String scoreLabel)
4090 final JMenuItem item = new JMenuItem(scoreLabel);
4092 item.addActionListener(new java.awt.event.ActionListener()
4095 public void actionPerformed(ActionEvent e)
4097 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4098 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4099 viewport.getAlignment());// ,viewport.getSelectionGroup());
4100 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4101 viewport.getAlignment()));
4102 alignPanel.paintAlignment(true);
4108 * last hash for alignment's annotation array - used to minimise cost of
4111 protected int _annotationScoreVectorHash;
4114 * search the alignment and rebuild the sort by annotation score submenu the
4115 * last alignment annotation vector hash is stored to minimize cost of
4116 * rebuilding in subsequence calls.
4120 public void buildSortByAnnotationScoresMenu()
4122 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4127 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4129 sortByAnnotScore.removeAll();
4130 // almost certainly a quicker way to do this - but we keep it simple
4131 Hashtable scoreSorts = new Hashtable();
4132 AlignmentAnnotation aann[];
4133 for (SequenceI sqa : viewport.getAlignment().getSequences())
4135 aann = sqa.getAnnotation();
4136 for (int i = 0; aann != null && i < aann.length; i++)
4138 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4140 scoreSorts.put(aann[i].label, aann[i].label);
4144 Enumeration labels = scoreSorts.keys();
4145 while (labels.hasMoreElements())
4147 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4148 (String) labels.nextElement());
4150 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4153 _annotationScoreVectorHash = viewport.getAlignment()
4154 .getAlignmentAnnotation().hashCode();
4159 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4160 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4161 * call. Listeners are added to remove the menu item when the treePanel is
4162 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4166 * Displayed tree window.
4168 * SortBy menu item title.
4171 public void buildTreeMenu()
4173 calculateTree.removeAll();
4174 // build the calculate menu
4176 for (final String type : new String[] { "NJ", "AV" })
4178 String treecalcnm = MessageManager.getString("label.tree_calc_"
4179 + type.toLowerCase());
4180 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4182 JMenuItem tm = new JMenuItem();
4183 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4184 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4186 String smn = MessageManager.getStringOrReturn(
4187 "label.score_model_", sm.getName());
4188 final String title = MessageManager.formatMessage(
4189 "label.treecalc_title", treecalcnm, smn);
4190 tm.setText(title);//
4191 tm.addActionListener(new java.awt.event.ActionListener()
4194 public void actionPerformed(ActionEvent e)
4196 newTreePanel(type, pwtype, title);
4199 calculateTree.add(tm);
4204 sortByTreeMenu.removeAll();
4206 List<Component> comps = PaintRefresher.components.get(viewport
4207 .getSequenceSetId());
4208 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4209 for (Component comp : comps)
4211 if (comp instanceof TreePanel)
4213 treePanels.add((TreePanel) comp);
4217 if (treePanels.size() < 1)
4219 sortByTreeMenu.setVisible(false);
4223 sortByTreeMenu.setVisible(true);
4225 for (final TreePanel tp : treePanels)
4227 final JMenuItem item = new JMenuItem(tp.getTitle());
4228 item.addActionListener(new java.awt.event.ActionListener()
4231 public void actionPerformed(ActionEvent e)
4233 tp.sortByTree_actionPerformed();
4234 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4239 sortByTreeMenu.add(item);
4243 public boolean sortBy(AlignmentOrder alorder, String undoname)
4245 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4246 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4247 if (undoname != null)
4249 addHistoryItem(new OrderCommand(undoname, oldOrder,
4250 viewport.getAlignment()));
4252 alignPanel.paintAlignment(true);
4257 * Work out whether the whole set of sequences or just the selected set will
4258 * be submitted for multiple alignment.
4261 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4263 // Now, check we have enough sequences
4264 AlignmentView msa = null;
4266 if ((viewport.getSelectionGroup() != null)
4267 && (viewport.getSelectionGroup().getSize() > 1))
4269 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4270 // some common interface!
4272 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4273 * SequenceI[sz = seqs.getSize(false)];
4275 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4276 * seqs.getSequenceAt(i); }
4278 msa = viewport.getAlignmentView(true);
4280 else if (viewport.getSelectionGroup() != null
4281 && viewport.getSelectionGroup().getSize() == 1)
4283 int option = JOptionPane.showConfirmDialog(this,
4284 MessageManager.getString("warn.oneseq_msainput_selection"),
4285 MessageManager.getString("label.invalid_selection"),
4286 JOptionPane.OK_CANCEL_OPTION);
4287 if (option == JOptionPane.OK_OPTION)
4289 msa = viewport.getAlignmentView(false);
4294 msa = viewport.getAlignmentView(false);
4300 * Decides what is submitted to a secondary structure prediction service: the
4301 * first sequence in the alignment, or in the current selection, or, if the
4302 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4303 * region or the whole alignment. (where the first sequence in the set is the
4304 * one that the prediction will be for).
4306 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4308 AlignmentView seqs = null;
4310 if ((viewport.getSelectionGroup() != null)
4311 && (viewport.getSelectionGroup().getSize() > 0))
4313 seqs = viewport.getAlignmentView(true);
4317 seqs = viewport.getAlignmentView(false);
4319 // limit sequences - JBPNote in future - could spawn multiple prediction
4321 // TODO: viewport.getAlignment().isAligned is a global state - the local
4322 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4323 if (!viewport.getAlignment().isAligned(false))
4325 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4326 // TODO: if seqs.getSequences().length>1 then should really have warned
4340 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4342 // Pick the tree file
4343 JalviewFileChooser chooser = new JalviewFileChooser(
4344 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4345 chooser.setFileView(new JalviewFileView());
4346 chooser.setDialogTitle(MessageManager
4347 .getString("label.select_newick_like_tree_file"));
4348 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4350 int value = chooser.showOpenDialog(null);
4352 if (value == JalviewFileChooser.APPROVE_OPTION)
4354 String choice = chooser.getSelectedFile().getPath();
4355 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4356 jalview.io.NewickFile fin = null;
4359 fin = new jalview.io.NewickFile(choice, "File");
4360 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4361 } catch (Exception ex)
4368 .getString("label.problem_reading_tree_file"),
4369 JOptionPane.WARNING_MESSAGE);
4370 ex.printStackTrace();
4372 if (fin != null && fin.hasWarningMessage())
4374 JOptionPane.showMessageDialog(Desktop.desktop, fin
4375 .getWarningMessage(), MessageManager
4376 .getString("label.possible_problem_with_tree_file"),
4377 JOptionPane.WARNING_MESSAGE);
4383 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4385 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4388 public TreePanel ShowNewickTree(NewickFile nf, String title)
4390 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4393 public TreePanel ShowNewickTree(NewickFile nf, String title,
4394 AlignmentView input)
4396 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4399 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4400 int h, int x, int y)
4402 return ShowNewickTree(nf, title, null, w, h, x, y);
4406 * Add a treeviewer for the tree extracted from a newick file object to the
4407 * current alignment view
4414 * Associated alignment input data (or null)
4423 * @return TreePanel handle
4425 public TreePanel ShowNewickTree(NewickFile nf, String title,
4426 AlignmentView input, int w, int h, int x, int y)
4428 TreePanel tp = null;
4434 if (nf.getTree() != null)
4436 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4442 tp.setLocation(x, y);
4445 Desktop.addInternalFrame(tp, title, w, h);
4447 } catch (Exception ex)
4449 ex.printStackTrace();
4455 private boolean buildingMenu = false;
4458 * Generates menu items and listener event actions for web service clients
4461 public void BuildWebServiceMenu()
4463 while (buildingMenu)
4467 System.err.println("Waiting for building menu to finish.");
4469 } catch (Exception e)
4473 final AlignFrame me = this;
4474 buildingMenu = true;
4475 new Thread(new Runnable()
4480 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4483 // System.err.println("Building ws menu again "
4484 // + Thread.currentThread());
4485 // TODO: add support for context dependent disabling of services based
4487 // alignment and current selection
4488 // TODO: add additional serviceHandle parameter to specify abstract
4490 // class independently of AbstractName
4491 // TODO: add in rediscovery GUI function to restart discoverer
4492 // TODO: group services by location as well as function and/or
4494 // object broker mechanism.
4495 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4496 final IProgressIndicator af = me;
4497 final JMenu msawsmenu = new JMenu("Alignment");
4498 final JMenu secstrmenu = new JMenu(
4499 "Secondary Structure Prediction");
4500 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4501 final JMenu analymenu = new JMenu("Analysis");
4502 final JMenu dismenu = new JMenu("Protein Disorder");
4503 // final JMenu msawsmenu = new
4504 // JMenu(MessageManager.getString("label.alignment"));
4505 // final JMenu secstrmenu = new
4506 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4507 // final JMenu seqsrchmenu = new
4508 // JMenu(MessageManager.getString("label.sequence_database_search"));
4509 // final JMenu analymenu = new
4510 // JMenu(MessageManager.getString("label.analysis"));
4511 // final JMenu dismenu = new
4512 // JMenu(MessageManager.getString("label.protein_disorder"));
4513 // JAL-940 - only show secondary structure prediction services from
4514 // the legacy server
4515 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4517 Discoverer.services != null && (Discoverer.services.size() > 0))
4519 // TODO: refactor to allow list of AbstractName/Handler bindings to
4521 // stored or retrieved from elsewhere
4522 // No MSAWS used any more:
4523 // Vector msaws = null; // (Vector)
4524 // Discoverer.services.get("MsaWS");
4525 Vector secstrpr = (Vector) Discoverer.services
4527 if (secstrpr != null)
4529 // Add any secondary structure prediction services
4530 for (int i = 0, j = secstrpr.size(); i < j; i++)
4532 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4534 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4535 .getServiceClient(sh);
4536 int p = secstrmenu.getItemCount();
4537 impl.attachWSMenuEntry(secstrmenu, me);
4538 int q = secstrmenu.getItemCount();
4539 for (int litm = p; litm < q; litm++)
4541 legacyItems.add(secstrmenu.getItem(litm));
4547 // Add all submenus in the order they should appear on the web
4549 wsmenu.add(msawsmenu);
4550 wsmenu.add(secstrmenu);
4551 wsmenu.add(dismenu);
4552 wsmenu.add(analymenu);
4553 // No search services yet
4554 // wsmenu.add(seqsrchmenu);
4556 javax.swing.SwingUtilities.invokeLater(new Runnable()
4563 webService.removeAll();
4564 // first, add discovered services onto the webservices menu
4565 if (wsmenu.size() > 0)
4567 for (int i = 0, j = wsmenu.size(); i < j; i++)
4569 webService.add(wsmenu.get(i));
4574 webService.add(me.webServiceNoServices);
4576 // TODO: move into separate menu builder class.
4577 boolean new_sspred = false;
4578 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4580 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4581 if (jws2servs != null)
4583 if (jws2servs.hasServices())
4585 jws2servs.attachWSMenuEntry(webService, me);
4586 for (Jws2Instance sv : jws2servs.getServices())
4588 if (sv.description.toLowerCase().contains("jpred"))
4590 for (JMenuItem jmi : legacyItems)
4592 jmi.setVisible(false);
4598 if (jws2servs.isRunning())
4600 JMenuItem tm = new JMenuItem(
4601 "Still discovering JABA Services");
4602 tm.setEnabled(false);
4607 build_urlServiceMenu(me.webService);
4608 build_fetchdbmenu(webService);
4609 for (JMenu item : wsmenu)
4611 if (item.getItemCount() == 0)
4613 item.setEnabled(false);
4617 item.setEnabled(true);
4620 } catch (Exception e)
4623 .debug("Exception during web service menu building process.",
4628 } catch (Exception e)
4631 buildingMenu = false;
4638 * construct any groupURL type service menu entries.
4642 private void build_urlServiceMenu(JMenu webService)
4644 // TODO: remove this code when 2.7 is released
4645 // DEBUG - alignmentView
4647 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4648 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4650 * @Override public void actionPerformed(ActionEvent e) {
4651 * jalview.datamodel.AlignmentView
4652 * .testSelectionViews(af.viewport.getAlignment(),
4653 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4655 * }); webService.add(testAlView);
4657 // TODO: refactor to RestClient discoverer and merge menu entries for
4658 // rest-style services with other types of analysis/calculation service
4659 // SHmmr test client - still being implemented.
4660 // DEBUG - alignmentView
4662 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4665 client.attachWSMenuEntry(
4666 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4672 * Searches selected sequences for xRef products and builds the Show
4673 * Cross-References menu (formerly called Show Products)
4675 * @return true if Show Cross-references menu should be enabled.
4677 public boolean canShowProducts()
4679 SequenceI[] selection = viewport.getSequenceSelection();
4680 AlignmentI dataset = viewport.getAlignment().getDataset();
4681 boolean showp = false;
4684 showProducts.removeAll();
4685 final boolean dna = viewport.getAlignment().isNucleotide();
4686 String[] ptypes = (selection == null || selection.length == 0) ? null
4687 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4689 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4692 final AlignFrame af = this;
4693 final String source = ptypes[t];
4694 JMenuItem xtype = new JMenuItem(ptypes[t]);
4695 xtype.addActionListener(new ActionListener()
4699 public void actionPerformed(ActionEvent e)
4701 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4705 showProducts.add(xtype);
4707 showProducts.setVisible(showp);
4708 showProducts.setEnabled(showp);
4709 } catch (Exception e)
4711 jalview.bin.Cache.log
4712 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4719 protected void showProductsFor(final SequenceI[] sel, final boolean dna,
4720 final String source)
4722 Runnable foo = new Runnable()
4728 final long sttime = System.currentTimeMillis();
4729 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4730 "status.searching_for_sequences_from",
4731 new Object[] { source }), sttime);
4734 AlignmentI alignment = AlignFrame.this.getViewport()
4736 AlignmentI xrefs = CrossRef.findXrefSequences(sel, dna, source,
4741 * get display scheme (if any) to apply to features
4743 FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
4744 .getFeatureColourScheme(source);
4746 AlignmentI al = makeCrossReferencesAlignment(
4747 alignment.getDataset(), xrefs);
4749 AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
4751 String newtitle = String.format("%s %s %s",
4752 MessageManager.getString(dna ? "label.proteins"
4753 : "label.nucleotides"), MessageManager
4754 .getString("label.for"), getTitle());
4755 newFrame.setTitle(newtitle);
4757 if (!Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4760 * split frame display is turned off in preferences file
4762 Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4764 return; // via finally clause
4768 * Make a copy of this alignment (sharing the same dataset
4769 * sequences). If we are DNA, drop introns and update mappings
4771 AlignmentI copyAlignment = null;
4772 final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4773 .getSequenceSelection();
4774 List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4775 boolean copyAlignmentIsAligned = false;
4778 copyAlignment = AlignmentUtils.makeCdsAlignment(
4779 sequenceSelection, cf, alignment);
4780 if (copyAlignment.getHeight() == 0)
4782 System.err.println("Failed to make CDS alignment");
4784 al.getCodonFrames().clear();
4785 al.getCodonFrames().addAll(copyAlignment.getCodonFrames());
4788 * pending getting Embl transcripts to 'align',
4789 * we are only doing this for Ensembl
4791 // TODO proper criteria for 'can align as cdna'
4792 if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
4793 || AlignmentUtils.looksLikeEnsembl(alignment))
4795 copyAlignment.alignAs(alignment);
4796 copyAlignmentIsAligned = true;
4801 copyAlignment = AlignmentUtils.makeCopyAlignment(
4802 sequenceSelection, xrefs.getSequencesArray());
4803 copyAlignment.getCodonFrames().addAll(cf);
4805 copyAlignment.setGapCharacter(AlignFrame.this.viewport
4806 .getGapCharacter());
4808 StructureSelectionManager ssm = StructureSelectionManager
4809 .getStructureSelectionManager(Desktop.instance);
4810 ssm.registerMappings(cf);
4812 if (copyAlignment.getHeight() <= 0)
4814 System.err.println("No Sequences generated for xRef type "
4819 * align protein to dna
4821 if (dna && copyAlignmentIsAligned)
4823 al.alignAs(copyAlignment);
4828 * align cdna to protein - currently only if
4829 * fetching and aligning Ensembl transcripts!
4831 if (DBRefSource.ENSEMBL.equalsIgnoreCase(source))
4833 copyAlignment.alignAs(al);
4837 AlignFrame copyThis = new AlignFrame(copyAlignment,
4838 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4839 copyThis.setTitle(AlignFrame.this.getTitle());
4841 boolean showSequenceFeatures = viewport
4842 .isShowSequenceFeatures();
4843 newFrame.setShowSeqFeatures(showSequenceFeatures);
4844 copyThis.setShowSeqFeatures(showSequenceFeatures);
4845 FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4846 .getFeatureRenderer();
4849 * copy feature rendering settings to split frame
4851 newFrame.alignPanel.getSeqPanel().seqCanvas
4852 .getFeatureRenderer()
4853 .transferSettings(myFeatureStyling);
4854 copyThis.alignPanel.getSeqPanel().seqCanvas
4855 .getFeatureRenderer()
4856 .transferSettings(myFeatureStyling);
4859 * apply 'database source' feature configuration
4862 // TODO is this the feature colouring for the original
4863 // alignment or the fetched xrefs? either could be Ensembl
4864 newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
4865 copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
4867 SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4868 dna ? newFrame : copyThis);
4869 newFrame.setVisible(true);
4870 copyThis.setVisible(true);
4871 String linkedTitle = MessageManager
4872 .getString("label.linked_view_title");
4873 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4876 } catch (Exception e)
4879 "Exception when finding crossreferences", e);
4880 } catch (OutOfMemoryError e)
4882 new OOMWarning("whilst fetching crossreferences", e);
4883 } catch (Throwable e)
4885 Cache.log.error("Error when finding crossreferences",
4889 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4890 "status.finished_searching_for_sequences_from",
4891 new Object[] { source }), sttime);
4896 * Makes an alignment containing the given sequences. If this is of the
4897 * same type as the given dataset (nucleotide/protein), then the new
4898 * alignment shares the same dataset, and its dataset sequences are added
4899 * to it. Otherwise a new dataset sequence is created for the
4906 protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
4909 boolean sameType = dataset.isNucleotide() == seqs.isNucleotide();
4911 SequenceI[] sprods = new SequenceI[seqs.getHeight()];
4912 for (int s = 0; s < sprods.length; s++)
4914 sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
4917 if (dataset.getSequences() == null
4918 || !dataset.getSequences().contains(
4919 sprods[s].getDatasetSequence()))
4921 dataset.addSequence(sprods[s].getDatasetSequence());
4924 sprods[s].updatePDBIds();
4926 Alignment al = new Alignment(sprods);
4929 al.setDataset((Alignment) dataset);
4933 al.createDatasetAlignment();
4939 Thread frunner = new Thread(foo);
4944 * Construct and display a new frame containing the translation of this
4945 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4948 public void showTranslation_actionPerformed(ActionEvent e)
4950 AlignmentI al = null;
4953 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4955 al = dna.translateCdna();
4956 } catch (Exception ex)
4958 jalview.bin.Cache.log.error(
4959 "Exception during translation. Please report this !", ex);
4960 final String msg = MessageManager
4961 .getString("label.error_when_translating_sequences_submit_bug_report");
4962 final String errorTitle = MessageManager
4963 .getString("label.implementation_error")
4964 + MessageManager.getString("translation_failed");
4965 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4966 JOptionPane.ERROR_MESSAGE);
4969 if (al == null || al.getHeight() == 0)
4971 final String msg = MessageManager
4972 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4973 final String errorTitle = MessageManager
4974 .getString("label.translation_failed");
4975 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4976 JOptionPane.WARNING_MESSAGE);
4980 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4981 af.setFileFormat(this.currentFileFormat);
4982 final String newTitle = MessageManager.formatMessage(
4983 "label.translation_of_params",
4984 new Object[] { this.getTitle() });
4985 af.setTitle(newTitle);
4986 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4988 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4989 viewport.openSplitFrame(af, new Alignment(seqs));
4993 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
5000 * Set the file format
5004 public void setFileFormat(String fileFormat)
5006 this.currentFileFormat = fileFormat;
5010 * Try to load a features file onto the alignment.
5013 * contents or path to retrieve file
5015 * access mode of file (see jalview.io.AlignFile)
5016 * @return true if features file was parsed correctly.
5018 public boolean parseFeaturesFile(String file, String type)
5020 return avc.parseFeaturesFile(file, type,
5021 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
5026 public void refreshFeatureUI(boolean enableIfNecessary)
5028 // note - currently this is only still here rather than in the controller
5029 // because of the featureSettings hard reference that is yet to be
5031 if (enableIfNecessary)
5033 viewport.setShowSequenceFeatures(true);
5034 showSeqFeatures.setSelected(true);
5040 public void dragEnter(DropTargetDragEvent evt)
5045 public void dragExit(DropTargetEvent evt)
5050 public void dragOver(DropTargetDragEvent evt)
5055 public void dropActionChanged(DropTargetDragEvent evt)
5060 public void drop(DropTargetDropEvent evt)
5062 Transferable t = evt.getTransferable();
5063 java.util.List files = null;
5067 DataFlavor uriListFlavor = new DataFlavor(
5068 "text/uri-list;class=java.lang.String");
5069 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5071 // Works on Windows and MacOSX
5072 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5073 files = (java.util.List) t
5074 .getTransferData(DataFlavor.javaFileListFlavor);
5076 else if (t.isDataFlavorSupported(uriListFlavor))
5078 // This is used by Unix drag system
5079 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5080 String data = (String) t.getTransferData(uriListFlavor);
5081 files = new java.util.ArrayList(1);
5082 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5083 data, "\r\n"); st.hasMoreTokens();)
5085 String s = st.nextToken();
5086 if (s.startsWith("#"))
5088 // the line is a comment (as per the RFC 2483)
5092 java.net.URI uri = new java.net.URI(s);
5093 // check to see if we can handle this kind of URI
5094 if (uri.getScheme().toLowerCase().startsWith("http"))
5096 files.add(uri.toString());
5100 // otherwise preserve old behaviour: catch all for file objects
5101 java.io.File file = new java.io.File(uri);
5102 files.add(file.toString());
5106 } catch (Exception e)
5108 e.printStackTrace();
5114 // check to see if any of these files have names matching sequences in
5116 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5117 .getAlignment().getSequencesArray());
5119 * Object[] { String,SequenceI}
5121 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5122 ArrayList<String> filesnotmatched = new ArrayList<String>();
5123 for (int i = 0; i < files.size(); i++)
5125 String file = files.get(i).toString();
5127 String protocol = FormatAdapter.checkProtocol(file);
5128 if (protocol == jalview.io.FormatAdapter.FILE)
5130 File fl = new File(file);
5131 pdbfn = fl.getName();
5133 else if (protocol == jalview.io.FormatAdapter.URL)
5135 URL url = new URL(file);
5136 pdbfn = url.getFile();
5138 if (pdbfn.length() > 0)
5140 // attempt to find a match in the alignment
5141 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5142 int l = 0, c = pdbfn.indexOf(".");
5143 while (mtch == null && c != -1)
5148 } while ((c = pdbfn.indexOf(".", l)) > l);
5151 pdbfn = pdbfn.substring(0, l);
5153 mtch = idm.findAllIdMatches(pdbfn);
5160 type = new IdentifyFile().identify(file, protocol);
5161 } catch (Exception ex)
5167 if (type.equalsIgnoreCase("PDB"))
5169 filesmatched.add(new Object[] { file, protocol, mtch });
5174 // File wasn't named like one of the sequences or wasn't a PDB file.
5175 filesnotmatched.add(file);
5179 if (filesmatched.size() > 0)
5181 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5187 "label.automatically_associate_pdb_files_with_sequences_same_name",
5188 new Object[] { Integer
5194 .getString("label.automatically_associate_pdb_files_by_name"),
5195 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5198 for (Object[] fm : filesmatched)
5200 // try and associate
5201 // TODO: may want to set a standard ID naming formalism for
5202 // associating PDB files which have no IDs.
5203 for (SequenceI toassoc : (SequenceI[]) fm[2])
5205 PDBEntry pe = new AssociatePdbFileWithSeq()
5206 .associatePdbWithSeq((String) fm[0],
5207 (String) fm[1], toassoc, false,
5211 System.err.println("Associated file : "
5212 + ((String) fm[0]) + " with "
5213 + toassoc.getDisplayId(true));
5217 alignPanel.paintAlignment(true);
5221 if (filesnotmatched.size() > 0)
5224 && (Cache.getDefault(
5225 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5231 "label.ignore_unmatched_dropped_files_info",
5232 new Object[] { Integer
5239 .getString("label.ignore_unmatched_dropped_files"),
5240 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5244 for (String fn : filesnotmatched)
5246 loadJalviewDataFile(fn, null, null, null);
5250 } catch (Exception ex)
5252 ex.printStackTrace();
5258 * Attempt to load a "dropped" file or URL string: First by testing whether
5259 * it's an Annotation file, then a JNet file, and finally a features file. If
5260 * all are false then the user may have dropped an alignment file onto this
5264 * either a filename or a URL string.
5266 public void loadJalviewDataFile(String file, String protocol,
5267 String format, SequenceI assocSeq)
5271 if (protocol == null)
5273 protocol = FormatAdapter.checkProtocol(file);
5275 // if the file isn't identified, or not positively identified as some
5276 // other filetype (PFAM is default unidentified alignment file type) then
5277 // try to parse as annotation.
5278 boolean isAnnotation = (format == null || format
5279 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5280 .annotateAlignmentView(viewport, file, protocol) : false;
5284 // first see if its a T-COFFEE score file
5285 TCoffeeScoreFile tcf = null;
5288 tcf = new TCoffeeScoreFile(file, protocol);
5291 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5293 tcoffeeColour.setEnabled(true);
5294 tcoffeeColour.setSelected(true);
5295 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5296 isAnnotation = true;
5298 .setText(MessageManager
5299 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5303 // some problem - if no warning its probable that the ID matching
5304 // process didn't work
5308 tcf.getWarningMessage() == null ? MessageManager
5309 .getString("label.check_file_matches_sequence_ids_alignment")
5310 : tcf.getWarningMessage(),
5312 .getString("label.problem_reading_tcoffee_score_file"),
5313 JOptionPane.WARNING_MESSAGE);
5320 } catch (Exception x)
5323 .debug("Exception when processing data source as T-COFFEE score file",
5329 // try to see if its a JNet 'concise' style annotation file *before*
5331 // try to parse it as a features file
5334 format = new IdentifyFile().identify(file, protocol);
5336 if (format.equalsIgnoreCase("JnetFile"))
5338 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5340 new JnetAnnotationMaker();
5341 JnetAnnotationMaker.add_annotation(predictions,
5342 viewport.getAlignment(), 0, false);
5343 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5344 viewport.getAlignment().setSeqrep(repseq);
5345 ColumnSelection cs = new ColumnSelection();
5346 cs.hideInsertionsFor(repseq);
5347 viewport.setColumnSelection(cs);
5348 isAnnotation = true;
5350 else if (IdentifyFile.FeaturesFile.equals(format))
5352 if (parseFeaturesFile(file, protocol))
5354 alignPanel.paintAlignment(true);
5359 new FileLoader().LoadFile(viewport, file, protocol, format);
5366 alignPanel.adjustAnnotationHeight();
5367 viewport.updateSequenceIdColours();
5368 buildSortByAnnotationScoresMenu();
5369 alignPanel.paintAlignment(true);
5371 } catch (Exception ex)
5373 ex.printStackTrace();
5374 } catch (OutOfMemoryError oom)
5379 } catch (Exception x)
5384 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5385 : "using " + protocol + " from " + file)
5387 + (format != null ? "(parsing as '" + format
5388 + "' file)" : ""), oom, Desktop.desktop);
5393 * Method invoked by the ChangeListener on the tabbed pane, in other words
5394 * when a different tabbed pane is selected by the user or programmatically.
5397 public void tabSelectionChanged(int index)
5401 alignPanel = alignPanels.get(index);
5402 viewport = alignPanel.av;
5403 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5404 setMenusFromViewport(viewport);
5408 * If there is a frame linked to this one in a SplitPane, switch it to the
5409 * same view tab index. No infinite recursion of calls should happen, since
5410 * tabSelectionChanged() should not get invoked on setting the selected
5411 * index to an unchanged value. Guard against setting an invalid index
5412 * before the new view peer tab has been created.
5414 final AlignViewportI peer = viewport.getCodingComplement();
5417 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5418 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5420 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5426 * On right mouse click on view tab, prompt for and set new view name.
5429 public void tabbedPane_mousePressed(MouseEvent e)
5431 if (SwingUtilities.isRightMouseButton(e))
5433 String msg = MessageManager.getString("label.enter_view_name");
5434 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5435 JOptionPane.QUESTION_MESSAGE);
5439 viewport.viewName = reply;
5440 // TODO warn if reply is in getExistingViewNames()?
5441 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5446 public AlignViewport getCurrentView()
5452 * Open the dialog for regex description parsing.
5455 protected void extractScores_actionPerformed(ActionEvent e)
5457 ParseProperties pp = new jalview.analysis.ParseProperties(
5458 viewport.getAlignment());
5459 // TODO: verify regex and introduce GUI dialog for version 2.5
5460 // if (pp.getScoresFromDescription("col", "score column ",
5461 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5463 if (pp.getScoresFromDescription("description column",
5464 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5466 buildSortByAnnotationScoresMenu();
5474 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5478 protected void showDbRefs_actionPerformed(ActionEvent e)
5480 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5486 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5490 protected void showNpFeats_actionPerformed(ActionEvent e)
5492 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5496 * find the viewport amongst the tabs in this alignment frame and close that
5501 public boolean closeView(AlignViewportI av)
5505 this.closeMenuItem_actionPerformed(false);
5508 Component[] comp = tabbedPane.getComponents();
5509 for (int i = 0; comp != null && i < comp.length; i++)
5511 if (comp[i] instanceof AlignmentPanel)
5513 if (((AlignmentPanel) comp[i]).av == av)
5516 closeView((AlignmentPanel) comp[i]);
5524 protected void build_fetchdbmenu(JMenu webService)
5526 // Temporary hack - DBRef Fetcher always top level ws entry.
5527 // TODO We probably want to store a sequence database checklist in
5528 // preferences and have checkboxes.. rather than individual sources selected
5530 final JMenu rfetch = new JMenu(
5531 MessageManager.getString("action.fetch_db_references"));
5532 rfetch.setToolTipText(MessageManager
5533 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5534 webService.add(rfetch);
5536 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5537 MessageManager.getString("option.trim_retrieved_seqs"));
5538 trimrs.setToolTipText(MessageManager
5539 .getString("label.trim_retrieved_sequences"));
5540 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5541 trimrs.addActionListener(new ActionListener()
5544 public void actionPerformed(ActionEvent e)
5546 trimrs.setSelected(trimrs.isSelected());
5547 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5548 Boolean.valueOf(trimrs.isSelected()).toString());
5552 JMenuItem fetchr = new JMenuItem(
5553 MessageManager.getString("label.standard_databases"));
5554 fetchr.setToolTipText(MessageManager
5555 .getString("label.fetch_embl_uniprot"));
5556 fetchr.addActionListener(new ActionListener()
5560 public void actionPerformed(ActionEvent e)
5562 new Thread(new Runnable()
5567 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5568 .getAlignment().isNucleotide();
5569 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5570 .getSequenceSelection(), alignPanel.alignFrame, null,
5571 alignPanel.alignFrame.featureSettings, isNucleotide);
5572 dbRefFetcher.addListener(new FetchFinishedListenerI()
5575 public void finished()
5577 AlignFrame.this.setMenusForViewport();
5581 .fetchDBRefs(false);
5589 final AlignFrame me = this;
5590 new Thread(new Runnable()
5595 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5596 .getSequenceFetcherSingleton(me);
5597 javax.swing.SwingUtilities.invokeLater(new Runnable()
5602 String[] dbclasses = sf.getOrderedSupportedSources();
5603 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5604 // jalview.util.QuickSort.sort(otherdb, otherdb);
5605 List<DbSourceProxy> otherdb;
5606 JMenu dfetch = new JMenu();
5607 JMenu ifetch = new JMenu();
5608 JMenuItem fetchr = null;
5609 int comp = 0, icomp = 0, mcomp = 15;
5610 String mname = null;
5612 for (String dbclass : dbclasses)
5614 otherdb = sf.getSourceProxy(dbclass);
5615 // add a single entry for this class, or submenu allowing 'fetch
5617 if (otherdb == null || otherdb.size() < 1)
5621 // List<DbSourceProxy> dbs=otherdb;
5622 // otherdb=new ArrayList<DbSourceProxy>();
5623 // for (DbSourceProxy db:dbs)
5625 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5629 mname = "From " + dbclass;
5631 if (otherdb.size() == 1)
5633 final DbSourceProxy[] dassource = otherdb
5634 .toArray(new DbSourceProxy[0]);
5635 DbSourceProxy src = otherdb.get(0);
5636 fetchr = new JMenuItem(src.getDbSource());
5637 fetchr.addActionListener(new ActionListener()
5641 public void actionPerformed(ActionEvent e)
5643 new Thread(new Runnable()
5649 boolean isNucleotide = alignPanel.alignFrame
5650 .getViewport().getAlignment()
5652 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5653 alignPanel.av.getSequenceSelection(),
5654 alignPanel.alignFrame, dassource,
5655 alignPanel.alignFrame.featureSettings,
5658 .addListener(new FetchFinishedListenerI()
5661 public void finished()
5663 AlignFrame.this.setMenusForViewport();
5666 dbRefFetcher.fetchDBRefs(false);
5672 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5673 MessageManager.formatMessage(
5674 "label.fetch_retrieve_from",
5675 new Object[] { src.getDbName() })));
5681 final DbSourceProxy[] dassource = otherdb
5682 .toArray(new DbSourceProxy[0]);
5684 DbSourceProxy src = otherdb.get(0);
5685 fetchr = new JMenuItem(MessageManager.formatMessage(
5686 "label.fetch_all_param",
5687 new Object[] { src.getDbSource() }));
5688 fetchr.addActionListener(new ActionListener()
5691 public void actionPerformed(ActionEvent e)
5693 new Thread(new Runnable()
5699 boolean isNucleotide = alignPanel.alignFrame
5700 .getViewport().getAlignment()
5702 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5703 alignPanel.av.getSequenceSelection(),
5704 alignPanel.alignFrame, dassource,
5705 alignPanel.alignFrame.featureSettings,
5708 .addListener(new FetchFinishedListenerI()
5711 public void finished()
5713 AlignFrame.this.setMenusForViewport();
5716 dbRefFetcher.fetchDBRefs(false);
5722 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5723 MessageManager.formatMessage(
5724 "label.fetch_retrieve_from_all_sources",
5726 Integer.valueOf(otherdb.size())
5727 .toString(), src.getDbSource(),
5728 src.getDbName() })));
5731 // and then build the rest of the individual menus
5732 ifetch = new JMenu(MessageManager.formatMessage(
5733 "label.source_from_db_source",
5734 new Object[] { src.getDbSource() }));
5736 String imname = null;
5738 for (DbSourceProxy sproxy : otherdb)
5740 String dbname = sproxy.getDbName();
5741 String sname = dbname.length() > 5 ? dbname.substring(0,
5742 5) + "..." : dbname;
5743 String msname = dbname.length() > 10 ? dbname.substring(
5744 0, 10) + "..." : dbname;
5747 imname = MessageManager.formatMessage(
5748 "label.from_msname", new Object[] { sname });
5750 fetchr = new JMenuItem(msname);
5751 final DbSourceProxy[] dassrc = { sproxy };
5752 fetchr.addActionListener(new ActionListener()
5756 public void actionPerformed(ActionEvent e)
5758 new Thread(new Runnable()
5764 boolean isNucleotide = alignPanel.alignFrame
5765 .getViewport().getAlignment()
5767 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5768 alignPanel.av.getSequenceSelection(),
5769 alignPanel.alignFrame, dassrc,
5770 alignPanel.alignFrame.featureSettings,
5773 .addListener(new FetchFinishedListenerI()
5776 public void finished()
5778 AlignFrame.this.setMenusForViewport();
5781 dbRefFetcher.fetchDBRefs(false);
5787 fetchr.setToolTipText("<html>"
5788 + MessageManager.formatMessage(
5789 "label.fetch_retrieve_from", new Object[]
5793 if (++icomp >= mcomp || i == (otherdb.size()))
5795 ifetch.setText(MessageManager.formatMessage(
5796 "label.source_to_target", imname, sname));
5798 ifetch = new JMenu();
5806 if (comp >= mcomp || dbi >= (dbclasses.length))
5808 dfetch.setText(MessageManager.formatMessage(
5809 "label.source_to_target", mname, dbclass));
5811 dfetch = new JMenu();
5824 * Left justify the whole alignment.
5827 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5829 AlignmentI al = viewport.getAlignment();
5831 viewport.firePropertyChange("alignment", null, al);
5835 * Right justify the whole alignment.
5838 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5840 AlignmentI al = viewport.getAlignment();
5842 viewport.firePropertyChange("alignment", null, al);
5846 public void setShowSeqFeatures(boolean b)
5848 showSeqFeatures.setSelected(b);
5849 viewport.setShowSequenceFeatures(b);
5856 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5857 * awt.event.ActionEvent)
5860 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5862 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5863 alignPanel.paintAlignment(true);
5870 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5874 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5876 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5877 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5885 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5886 * .event.ActionEvent)
5889 protected void showGroupConservation_actionPerformed(ActionEvent e)
5891 viewport.setShowGroupConservation(showGroupConservation.getState());
5892 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5899 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5900 * .event.ActionEvent)
5903 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5905 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5906 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5913 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5914 * .event.ActionEvent)
5917 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5919 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5920 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5924 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5926 showSequenceLogo.setState(true);
5927 viewport.setShowSequenceLogo(true);
5928 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5929 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5933 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5935 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5942 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5943 * .event.ActionEvent)
5946 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5948 if (avc.makeGroupsFromSelection())
5950 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5951 alignPanel.updateAnnotation();
5952 alignPanel.paintAlignment(true);
5956 public void clearAlignmentSeqRep()
5958 // TODO refactor alignmentseqrep to controller
5959 if (viewport.getAlignment().hasSeqrep())
5961 viewport.getAlignment().setSeqrep(null);
5962 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5963 alignPanel.updateAnnotation();
5964 alignPanel.paintAlignment(true);
5969 protected void createGroup_actionPerformed(ActionEvent e)
5971 if (avc.createGroup())
5973 alignPanel.alignmentChanged();
5978 protected void unGroup_actionPerformed(ActionEvent e)
5982 alignPanel.alignmentChanged();
5987 * make the given alignmentPanel the currently selected tab
5989 * @param alignmentPanel
5991 public void setDisplayedView(AlignmentPanel alignmentPanel)
5993 if (!viewport.getSequenceSetId().equals(
5994 alignmentPanel.av.getSequenceSetId()))
5998 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
6000 if (tabbedPane != null
6001 && tabbedPane.getTabCount() > 0
6002 && alignPanels.indexOf(alignmentPanel) != tabbedPane
6003 .getSelectedIndex())
6005 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
6010 * Action on selection of menu options to Show or Hide annotations.
6013 * @param forSequences
6014 * update sequence-related annotations
6015 * @param forAlignment
6016 * update non-sequence-related annotations
6019 protected void setAnnotationsVisibility(boolean visible,
6020 boolean forSequences, boolean forAlignment)
6022 for (AlignmentAnnotation aa : alignPanel.getAlignment()
6023 .getAlignmentAnnotation())
6026 * don't display non-positional annotations on an alignment
6028 if (aa.annotations == null)
6032 boolean apply = (aa.sequenceRef == null && forAlignment)
6033 || (aa.sequenceRef != null && forSequences);
6036 aa.visible = visible;
6039 alignPanel.validateAnnotationDimensions(true);
6040 alignPanel.alignmentChanged();
6044 * Store selected annotation sort order for the view and repaint.
6047 protected void sortAnnotations_actionPerformed()
6049 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
6051 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
6052 alignPanel.paintAlignment(true);
6057 * @return alignment panels in this alignment frame
6059 public List<? extends AlignmentViewPanel> getAlignPanels()
6061 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
6065 * Open a new alignment window, with the cDNA associated with this (protein)
6066 * alignment, aligned as is the protein.
6068 protected void viewAsCdna_actionPerformed()
6070 // TODO no longer a menu action - refactor as required
6071 final AlignmentI alignment = getViewport().getAlignment();
6072 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6073 if (mappings == null)
6077 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6078 for (SequenceI aaSeq : alignment.getSequences())
6080 for (AlignedCodonFrame acf : mappings)
6082 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6086 * There is a cDNA mapping for this protein sequence - add to new
6087 * alignment. It will share the same dataset sequence as other mapped
6088 * cDNA (no new mappings need to be created).
6090 final Sequence newSeq = new Sequence(dnaSeq);
6091 newSeq.setDatasetSequence(dnaSeq);
6092 cdnaSeqs.add(newSeq);
6096 if (cdnaSeqs.size() == 0)
6098 // show a warning dialog no mapped cDNA
6101 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6103 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6104 AlignFrame.DEFAULT_HEIGHT);
6105 cdna.alignAs(alignment);
6106 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6108 Desktop.addInternalFrame(alignFrame, newtitle,
6109 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6113 * Set visibility of dna/protein complement view (available when shown in a
6119 protected void showComplement_actionPerformed(boolean show)
6121 SplitContainerI sf = getSplitViewContainer();
6124 sf.setComplementVisible(this, show);
6129 * Generate the reverse (optionally complemented) of the selected sequences,
6130 * and add them to the alignment
6133 protected void showReverse_actionPerformed(boolean complement)
6135 AlignmentI al = null;
6138 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6140 al = dna.reverseCdna(complement);
6141 viewport.addAlignment(al, "");
6142 } catch (Exception ex)
6144 System.err.println(ex.getMessage());
6150 class PrintThread extends Thread
6154 public PrintThread(AlignmentPanel ap)
6159 static PageFormat pf;
6164 PrinterJob printJob = PrinterJob.getPrinterJob();
6168 printJob.setPrintable(ap, pf);
6172 printJob.setPrintable(ap);
6175 if (printJob.printDialog())
6180 } catch (Exception PrintException)
6182 PrintException.printStackTrace();