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 alignPanel.paintAlignment(true);
2466 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2476 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2478 if (viewport.cursorMode)
2480 alignPanel.getSeqPanel().keyboardNo1 = null;
2481 alignPanel.getSeqPanel().keyboardNo2 = null;
2483 viewport.setSelectionGroup(null);
2484 viewport.getColumnSelection().clear();
2485 viewport.setSelectionGroup(null);
2486 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2487 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2488 alignPanel.paintAlignment(true);
2489 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2490 viewport.sendSelection();
2500 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2502 SequenceGroup sg = viewport.getSelectionGroup();
2506 selectAllSequenceMenuItem_actionPerformed(null);
2511 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2513 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2516 alignPanel.paintAlignment(true);
2517 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2518 viewport.sendSelection();
2522 public void invertColSel_actionPerformed(ActionEvent e)
2524 viewport.invertColumnSelection();
2525 alignPanel.paintAlignment(true);
2526 viewport.sendSelection();
2536 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2538 trimAlignment(true);
2548 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2550 trimAlignment(false);
2553 void trimAlignment(boolean trimLeft)
2555 ColumnSelection colSel = viewport.getColumnSelection();
2558 if (!colSel.isEmpty())
2562 column = colSel.getMin();
2566 column = colSel.getMax();
2570 if (viewport.getSelectionGroup() != null)
2572 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2573 viewport.getHiddenRepSequences());
2577 seqs = viewport.getAlignment().getSequencesArray();
2580 TrimRegionCommand trimRegion;
2583 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2584 column, viewport.getAlignment());
2585 viewport.setStartRes(0);
2589 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2590 column, viewport.getAlignment());
2593 statusBar.setText(MessageManager.formatMessage(
2594 "label.removed_columns",
2595 new String[] { Integer.valueOf(trimRegion.getSize())
2598 addHistoryItem(trimRegion);
2600 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2602 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2603 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2605 viewport.getAlignment().deleteGroup(sg);
2609 viewport.firePropertyChange("alignment", null, viewport
2610 .getAlignment().getSequences());
2621 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2623 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2626 if (viewport.getSelectionGroup() != null)
2628 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2629 viewport.getHiddenRepSequences());
2630 start = viewport.getSelectionGroup().getStartRes();
2631 end = viewport.getSelectionGroup().getEndRes();
2635 seqs = viewport.getAlignment().getSequencesArray();
2638 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2639 "Remove Gapped Columns", seqs, start, end,
2640 viewport.getAlignment());
2642 addHistoryItem(removeGapCols);
2644 statusBar.setText(MessageManager.formatMessage(
2645 "label.removed_empty_columns",
2646 new Object[] { Integer.valueOf(removeGapCols.getSize())
2649 // This is to maintain viewport position on first residue
2650 // of first sequence
2651 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2652 int startRes = seq.findPosition(viewport.startRes);
2653 // ShiftList shifts;
2654 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2655 // edit.alColumnChanges=shifts.getInverse();
2656 // if (viewport.hasHiddenColumns)
2657 // viewport.getColumnSelection().compensateForEdits(shifts);
2658 viewport.setStartRes(seq.findIndex(startRes) - 1);
2659 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2671 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2673 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2676 if (viewport.getSelectionGroup() != null)
2678 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2679 viewport.getHiddenRepSequences());
2680 start = viewport.getSelectionGroup().getStartRes();
2681 end = viewport.getSelectionGroup().getEndRes();
2685 seqs = viewport.getAlignment().getSequencesArray();
2688 // This is to maintain viewport position on first residue
2689 // of first sequence
2690 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2691 int startRes = seq.findPosition(viewport.startRes);
2693 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2694 viewport.getAlignment()));
2696 viewport.setStartRes(seq.findIndex(startRes) - 1);
2698 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2710 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2712 viewport.setPadGaps(padGapsMenuitem.isSelected());
2713 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2724 public void findMenuItem_actionPerformed(ActionEvent e)
2730 * Create a new view of the current alignment.
2733 public void newView_actionPerformed(ActionEvent e)
2735 newView(null, true);
2739 * Creates and shows a new view of the current alignment.
2742 * title of newly created view; if null, one will be generated
2743 * @param copyAnnotation
2744 * if true then duplicate all annnotation, groups and settings
2745 * @return new alignment panel, already displayed.
2747 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2750 * Create a new AlignmentPanel (with its own, new Viewport)
2752 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2754 if (!copyAnnotation)
2757 * remove all groups and annotation except for the automatic stuff
2759 newap.av.getAlignment().deleteAllGroups();
2760 newap.av.getAlignment().deleteAllAnnotations(false);
2763 newap.av.setGatherViewsHere(false);
2765 if (viewport.viewName == null)
2767 viewport.viewName = MessageManager
2768 .getString("label.view_name_original");
2772 * Views share the same edits undo and redo stacks
2774 newap.av.setHistoryList(viewport.getHistoryList());
2775 newap.av.setRedoList(viewport.getRedoList());
2778 * Views share the same mappings; need to deregister any new mappings
2779 * created by copyAlignPanel, and register the new reference to the shared
2782 newap.av.replaceMappings(viewport.getAlignment());
2784 newap.av.viewName = getNewViewName(viewTitle);
2786 addAlignmentPanel(newap, true);
2787 newap.alignmentChanged();
2789 if (alignPanels.size() == 2)
2791 viewport.setGatherViewsHere(true);
2793 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2798 * Make a new name for the view, ensuring it is unique within the current
2799 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2800 * these now use viewId. Unique view names are still desirable for usability.)
2805 protected String getNewViewName(String viewTitle)
2807 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2808 boolean addFirstIndex = false;
2809 if (viewTitle == null || viewTitle.trim().length() == 0)
2811 viewTitle = MessageManager.getString("action.view");
2812 addFirstIndex = true;
2816 index = 1;// we count from 1 if given a specific name
2818 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2820 List<Component> comps = PaintRefresher.components.get(viewport
2821 .getSequenceSetId());
2823 List<String> existingNames = getExistingViewNames(comps);
2825 while (existingNames.contains(newViewName))
2827 newViewName = viewTitle + " " + (++index);
2833 * Returns a list of distinct view names found in the given list of
2834 * components. View names are held on the viewport of an AlignmentPanel.
2839 protected List<String> getExistingViewNames(List<Component> comps)
2841 List<String> existingNames = new ArrayList<String>();
2842 for (Component comp : comps)
2844 if (comp instanceof AlignmentPanel)
2846 AlignmentPanel ap = (AlignmentPanel) comp;
2847 if (!existingNames.contains(ap.av.viewName))
2849 existingNames.add(ap.av.viewName);
2853 return existingNames;
2857 * Explode tabbed views into separate windows.
2860 public void expandViews_actionPerformed(ActionEvent e)
2862 Desktop.instance.explodeViews(this);
2866 * Gather views in separate windows back into a tabbed presentation.
2869 public void gatherViews_actionPerformed(ActionEvent e)
2871 Desktop.instance.gatherViews(this);
2881 public void font_actionPerformed(ActionEvent e)
2883 new FontChooser(alignPanel);
2893 protected void seqLimit_actionPerformed(ActionEvent e)
2895 viewport.setShowJVSuffix(seqLimits.isSelected());
2897 alignPanel.getIdPanel().getIdCanvas()
2898 .setPreferredSize(alignPanel.calculateIdWidth());
2899 alignPanel.paintAlignment(true);
2903 public void idRightAlign_actionPerformed(ActionEvent e)
2905 viewport.setRightAlignIds(idRightAlign.isSelected());
2906 alignPanel.paintAlignment(true);
2910 public void centreColumnLabels_actionPerformed(ActionEvent e)
2912 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2913 alignPanel.paintAlignment(true);
2919 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2922 protected void followHighlight_actionPerformed()
2925 * Set the 'follow' flag on the Viewport (and scroll to position if now
2928 final boolean state = this.followHighlightMenuItem.getState();
2929 viewport.setFollowHighlight(state);
2932 alignPanel.scrollToPosition(
2933 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2944 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2946 viewport.setColourText(colourTextMenuItem.isSelected());
2947 alignPanel.paintAlignment(true);
2957 public void wrapMenuItem_actionPerformed(ActionEvent e)
2959 scaleAbove.setVisible(wrapMenuItem.isSelected());
2960 scaleLeft.setVisible(wrapMenuItem.isSelected());
2961 scaleRight.setVisible(wrapMenuItem.isSelected());
2962 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2963 alignPanel.updateLayout();
2967 public void showAllSeqs_actionPerformed(ActionEvent e)
2969 viewport.showAllHiddenSeqs();
2973 public void showAllColumns_actionPerformed(ActionEvent e)
2975 viewport.showAllHiddenColumns();
2977 viewport.sendSelection();
2981 public void hideSelSequences_actionPerformed(ActionEvent e)
2983 viewport.hideAllSelectedSeqs();
2984 // alignPanel.paintAlignment(true);
2988 * called by key handler and the hide all/show all menu items
2993 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2996 boolean hide = false;
2997 SequenceGroup sg = viewport.getSelectionGroup();
2998 if (!toggleSeqs && !toggleCols)
3000 // Hide everything by the current selection - this is a hack - we do the
3001 // invert and then hide
3002 // first check that there will be visible columns after the invert.
3003 if ((viewport.getColumnSelection() != null
3004 && viewport.getColumnSelection().getSelected() != null && viewport
3005 .getColumnSelection().getSelected().size() > 0)
3006 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3009 // now invert the sequence set, if required - empty selection implies
3010 // that no hiding is required.
3013 invertSequenceMenuItem_actionPerformed(null);
3014 sg = viewport.getSelectionGroup();
3018 viewport.expandColSelection(sg, true);
3019 // finally invert the column selection and get the new sequence
3021 invertColSel_actionPerformed(null);
3028 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3030 hideSelSequences_actionPerformed(null);
3033 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3036 showAllSeqs_actionPerformed(null);
3042 if (viewport.getColumnSelection().getSelected().size() > 0)
3044 hideSelColumns_actionPerformed(null);
3047 viewport.setSelectionGroup(sg);
3052 showAllColumns_actionPerformed(null);
3061 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3062 * event.ActionEvent)
3065 public void hideAllButSelection_actionPerformed(ActionEvent e)
3067 toggleHiddenRegions(false, false);
3068 viewport.sendSelection();
3075 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3079 public void hideAllSelection_actionPerformed(ActionEvent e)
3081 SequenceGroup sg = viewport.getSelectionGroup();
3082 viewport.expandColSelection(sg, false);
3083 viewport.hideAllSelectedSeqs();
3084 viewport.hideSelectedColumns();
3085 alignPanel.paintAlignment(true);
3086 viewport.sendSelection();
3093 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3097 public void showAllhidden_actionPerformed(ActionEvent e)
3099 viewport.showAllHiddenColumns();
3100 viewport.showAllHiddenSeqs();
3101 alignPanel.paintAlignment(true);
3102 viewport.sendSelection();
3106 public void hideSelColumns_actionPerformed(ActionEvent e)
3108 viewport.hideSelectedColumns();
3109 alignPanel.paintAlignment(true);
3110 viewport.sendSelection();
3114 public void hiddenMarkers_actionPerformed(ActionEvent e)
3116 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3127 protected void scaleAbove_actionPerformed(ActionEvent e)
3129 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3130 alignPanel.paintAlignment(true);
3140 protected void scaleLeft_actionPerformed(ActionEvent e)
3142 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3143 alignPanel.paintAlignment(true);
3153 protected void scaleRight_actionPerformed(ActionEvent e)
3155 viewport.setScaleRightWrapped(scaleRight.isSelected());
3156 alignPanel.paintAlignment(true);
3166 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3168 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3169 alignPanel.paintAlignment(true);
3179 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3181 viewport.setShowText(viewTextMenuItem.isSelected());
3182 alignPanel.paintAlignment(true);
3192 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3194 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3195 alignPanel.paintAlignment(true);
3198 public FeatureSettings featureSettings;
3201 public FeatureSettingsControllerI getFeatureSettingsUI()
3203 return featureSettings;
3207 public void featureSettings_actionPerformed(ActionEvent e)
3209 if (featureSettings != null)
3211 featureSettings.close();
3212 featureSettings = null;
3214 if (!showSeqFeatures.isSelected())
3216 // make sure features are actually displayed
3217 showSeqFeatures.setSelected(true);
3218 showSeqFeatures_actionPerformed(null);
3220 featureSettings = new FeatureSettings(this);
3224 * Set or clear 'Show Sequence Features'
3230 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3232 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3233 alignPanel.paintAlignment(true);
3234 if (alignPanel.getOverviewPanel() != null)
3236 alignPanel.getOverviewPanel().updateOverviewImage();
3241 * Set or clear 'Show Sequence Features'
3247 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3249 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3251 if (viewport.isShowSequenceFeaturesHeight())
3253 // ensure we're actually displaying features
3254 viewport.setShowSequenceFeatures(true);
3255 showSeqFeatures.setSelected(true);
3257 alignPanel.paintAlignment(true);
3258 if (alignPanel.getOverviewPanel() != null)
3260 alignPanel.getOverviewPanel().updateOverviewImage();
3265 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3266 * the annotations panel as a whole.
3268 * The options to show/hide all annotations should be enabled when the panel
3269 * is shown, and disabled when the panel is hidden.
3274 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3276 final boolean setVisible = annotationPanelMenuItem.isSelected();
3277 viewport.setShowAnnotation(setVisible);
3278 this.showAllSeqAnnotations.setEnabled(setVisible);
3279 this.hideAllSeqAnnotations.setEnabled(setVisible);
3280 this.showAllAlAnnotations.setEnabled(setVisible);
3281 this.hideAllAlAnnotations.setEnabled(setVisible);
3282 alignPanel.updateLayout();
3286 public void alignmentProperties()
3288 JEditorPane editPane = new JEditorPane("text/html", "");
3289 editPane.setEditable(false);
3290 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3292 editPane.setText(MessageManager.formatMessage("label.html_content",
3293 new Object[] { contents.toString() }));
3294 JInternalFrame frame = new JInternalFrame();
3295 frame.getContentPane().add(new JScrollPane(editPane));
3297 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3298 "label.alignment_properties", new Object[] { getTitle() }),
3309 public void overviewMenuItem_actionPerformed(ActionEvent e)
3311 if (alignPanel.overviewPanel != null)
3316 JInternalFrame frame = new JInternalFrame();
3317 OverviewPanel overview = new OverviewPanel(alignPanel);
3318 frame.setContentPane(overview);
3319 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3320 "label.overview_params", new Object[] { this.getTitle() }),
3321 frame.getWidth(), frame.getHeight());
3323 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3324 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3327 public void internalFrameClosed(
3328 javax.swing.event.InternalFrameEvent evt)
3330 alignPanel.setOverviewPanel(null);
3334 alignPanel.setOverviewPanel(overview);
3338 public void textColour_actionPerformed(ActionEvent e)
3340 new TextColourChooser().chooseColour(alignPanel, null);
3350 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3362 public void clustalColour_actionPerformed(ActionEvent e)
3364 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3365 viewport.getHiddenRepSequences()));
3375 public void zappoColour_actionPerformed(ActionEvent e)
3377 changeColour(new ZappoColourScheme());
3387 public void taylorColour_actionPerformed(ActionEvent e)
3389 changeColour(new TaylorColourScheme());
3399 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3401 changeColour(new HydrophobicColourScheme());
3411 public void helixColour_actionPerformed(ActionEvent e)
3413 changeColour(new HelixColourScheme());
3423 public void strandColour_actionPerformed(ActionEvent e)
3425 changeColour(new StrandColourScheme());
3435 public void turnColour_actionPerformed(ActionEvent e)
3437 changeColour(new TurnColourScheme());
3447 public void buriedColour_actionPerformed(ActionEvent e)
3449 changeColour(new BuriedColourScheme());
3459 public void nucleotideColour_actionPerformed(ActionEvent e)
3461 changeColour(new NucleotideColourScheme());
3465 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3467 changeColour(new PurinePyrimidineColourScheme());
3471 * public void covariationColour_actionPerformed(ActionEvent e) {
3473 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3477 public void annotationColour_actionPerformed(ActionEvent e)
3479 new AnnotationColourChooser(viewport, alignPanel);
3483 public void annotationColumn_actionPerformed(ActionEvent e)
3485 new AnnotationColumnChooser(viewport, alignPanel);
3489 public void rnahelicesColour_actionPerformed(ActionEvent e)
3491 new RNAHelicesColourChooser(viewport, alignPanel);
3501 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3503 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3513 public void changeColour(ColourSchemeI cs)
3515 // TODO: pull up to controller method
3519 // Make sure viewport is up to date w.r.t. any sliders
3520 if (viewport.getAbovePIDThreshold())
3522 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3524 viewport.setThreshold(threshold);
3527 if (viewport.getConservationSelected())
3529 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3532 if (cs instanceof TCoffeeColourScheme)
3534 tcoffeeColour.setEnabled(true);
3535 tcoffeeColour.setSelected(true);
3539 viewport.setGlobalColourScheme(cs);
3541 alignPanel.paintAlignment(true);
3551 protected void modifyPID_actionPerformed(ActionEvent e)
3553 if (viewport.getAbovePIDThreshold()
3554 && viewport.getGlobalColourScheme() != null)
3556 SliderPanel.setPIDSliderSource(alignPanel,
3557 viewport.getGlobalColourScheme(), "Background");
3558 SliderPanel.showPIDSlider();
3569 protected void modifyConservation_actionPerformed(ActionEvent e)
3571 if (viewport.getConservationSelected()
3572 && viewport.getGlobalColourScheme() != null)
3574 SliderPanel.setConservationSlider(alignPanel,
3575 viewport.getGlobalColourScheme(), "Background");
3576 SliderPanel.showConservationSlider();
3587 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3589 viewport.setConservationSelected(conservationMenuItem.isSelected());
3591 viewport.setAbovePIDThreshold(false);
3592 abovePIDThreshold.setSelected(false);
3594 changeColour(viewport.getGlobalColourScheme());
3596 modifyConservation_actionPerformed(null);
3606 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3608 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3610 conservationMenuItem.setSelected(false);
3611 viewport.setConservationSelected(false);
3613 changeColour(viewport.getGlobalColourScheme());
3615 modifyPID_actionPerformed(null);
3625 public void userDefinedColour_actionPerformed(ActionEvent e)
3627 if (e.getActionCommand().equals(
3628 MessageManager.getString("action.user_defined")))
3630 new UserDefinedColours(alignPanel, null);
3634 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3635 .getUserColourSchemes().get(e.getActionCommand());
3641 public void updateUserColourMenu()
3644 Component[] menuItems = colourMenu.getMenuComponents();
3645 int iSize = menuItems.length;
3646 for (int i = 0; i < iSize; i++)
3648 if (menuItems[i].getName() != null
3649 && menuItems[i].getName().equals("USER_DEFINED"))
3651 colourMenu.remove(menuItems[i]);
3655 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3657 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3658 .getUserColourSchemes().keys();
3660 while (userColours.hasMoreElements())
3662 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3663 userColours.nextElement().toString());
3664 radioItem.setName("USER_DEFINED");
3665 radioItem.addMouseListener(new MouseAdapter()
3668 public void mousePressed(MouseEvent evt)
3670 if (evt.isControlDown()
3671 || SwingUtilities.isRightMouseButton(evt))
3673 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3675 int option = JOptionPane.showInternalConfirmDialog(
3676 jalview.gui.Desktop.desktop,
3678 .getString("label.remove_from_default_list"),
3680 .getString("label.remove_user_defined_colour"),
3681 JOptionPane.YES_NO_OPTION);
3682 if (option == JOptionPane.YES_OPTION)
3684 jalview.gui.UserDefinedColours
3685 .removeColourFromDefaults(radioItem.getText());
3686 colourMenu.remove(radioItem);
3690 radioItem.addActionListener(new ActionListener()
3693 public void actionPerformed(ActionEvent evt)
3695 userDefinedColour_actionPerformed(evt);
3702 radioItem.addActionListener(new ActionListener()
3705 public void actionPerformed(ActionEvent evt)
3707 userDefinedColour_actionPerformed(evt);
3711 colourMenu.insert(radioItem, 15);
3712 colours.add(radioItem);
3724 public void PIDColour_actionPerformed(ActionEvent e)
3726 changeColour(new PIDColourScheme());
3736 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3738 changeColour(new Blosum62ColourScheme());
3748 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3750 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3751 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3752 .getAlignment().getSequenceAt(0), null);
3753 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3754 viewport.getAlignment()));
3755 alignPanel.paintAlignment(true);
3765 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3767 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3768 AlignmentSorter.sortByID(viewport.getAlignment());
3769 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3770 viewport.getAlignment()));
3771 alignPanel.paintAlignment(true);
3781 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3783 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3784 AlignmentSorter.sortByLength(viewport.getAlignment());
3785 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3786 viewport.getAlignment()));
3787 alignPanel.paintAlignment(true);
3797 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3799 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3800 AlignmentSorter.sortByGroup(viewport.getAlignment());
3801 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3802 viewport.getAlignment()));
3804 alignPanel.paintAlignment(true);
3814 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3816 new RedundancyPanel(alignPanel, this);
3826 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3828 if ((viewport.getSelectionGroup() == null)
3829 || (viewport.getSelectionGroup().getSize() < 2))
3831 JOptionPane.showInternalMessageDialog(this, MessageManager
3832 .getString("label.you_must_select_least_two_sequences"),
3833 MessageManager.getString("label.invalid_selection"),
3834 JOptionPane.WARNING_MESSAGE);
3838 JInternalFrame frame = new JInternalFrame();
3839 frame.setContentPane(new PairwiseAlignPanel(viewport));
3840 Desktop.addInternalFrame(frame,
3841 MessageManager.getString("action.pairwise_alignment"), 600,
3853 public void PCAMenuItem_actionPerformed(ActionEvent e)
3855 if (((viewport.getSelectionGroup() != null)
3856 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3857 .getSelectionGroup().getSize() > 0))
3858 || (viewport.getAlignment().getHeight() < 4))
3861 .showInternalMessageDialog(
3864 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3866 .getString("label.sequence_selection_insufficient"),
3867 JOptionPane.WARNING_MESSAGE);
3872 new PCAPanel(alignPanel);
3876 public void autoCalculate_actionPerformed(ActionEvent e)
3878 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3879 if (viewport.autoCalculateConsensus)
3881 viewport.firePropertyChange("alignment", null, viewport
3882 .getAlignment().getSequences());
3887 public void sortByTreeOption_actionPerformed(ActionEvent e)
3889 viewport.sortByTree = sortByTree.isSelected();
3893 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3895 viewport.followSelection = listenToViewSelections.isSelected();
3905 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3907 newTreePanel("AV", "PID", "Average distance tree using PID");
3917 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3919 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3929 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3931 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3941 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3943 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3956 void newTreePanel(String type, String pwType, String title)
3960 if (viewport.getSelectionGroup() != null
3961 && viewport.getSelectionGroup().getSize() > 0)
3963 if (viewport.getSelectionGroup().getSize() < 3)
3969 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3971 .getString("label.not_enough_sequences"),
3972 JOptionPane.WARNING_MESSAGE);
3976 SequenceGroup sg = viewport.getSelectionGroup();
3978 /* Decide if the selection is a column region */
3979 for (SequenceI _s : sg.getSequences())
3981 if (_s.getLength() < sg.getEndRes())
3987 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3989 .getString("label.sequences_selection_not_aligned"),
3990 JOptionPane.WARNING_MESSAGE);
3996 title = title + " on region";
3997 tp = new TreePanel(alignPanel, type, pwType);
4001 // are the visible sequences aligned?
4002 if (!viewport.getAlignment().isAligned(false))
4008 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4010 .getString("label.sequences_not_aligned"),
4011 JOptionPane.WARNING_MESSAGE);
4016 if (viewport.getAlignment().getHeight() < 2)
4021 tp = new TreePanel(alignPanel, type, pwType);
4026 if (viewport.viewName != null)
4028 title += viewport.viewName + " of ";
4031 title += this.title;
4033 Desktop.addInternalFrame(tp, title, 600, 500);
4044 public void addSortByOrderMenuItem(String title,
4045 final AlignmentOrder order)
4047 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4048 "action.by_title_param", new Object[] { title }));
4050 item.addActionListener(new java.awt.event.ActionListener()
4053 public void actionPerformed(ActionEvent e)
4055 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4057 // TODO: JBPNote - have to map order entries to curent SequenceI
4059 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4061 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4064 alignPanel.paintAlignment(true);
4070 * Add a new sort by annotation score menu item
4073 * the menu to add the option to
4075 * the label used to retrieve scores for each sequence on the
4078 public void addSortByAnnotScoreMenuItem(JMenu sort,
4079 final String scoreLabel)
4081 final JMenuItem item = new JMenuItem(scoreLabel);
4083 item.addActionListener(new java.awt.event.ActionListener()
4086 public void actionPerformed(ActionEvent e)
4088 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4089 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4090 viewport.getAlignment());// ,viewport.getSelectionGroup());
4091 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4092 viewport.getAlignment()));
4093 alignPanel.paintAlignment(true);
4099 * last hash for alignment's annotation array - used to minimise cost of
4102 protected int _annotationScoreVectorHash;
4105 * search the alignment and rebuild the sort by annotation score submenu the
4106 * last alignment annotation vector hash is stored to minimize cost of
4107 * rebuilding in subsequence calls.
4111 public void buildSortByAnnotationScoresMenu()
4113 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4118 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4120 sortByAnnotScore.removeAll();
4121 // almost certainly a quicker way to do this - but we keep it simple
4122 Hashtable scoreSorts = new Hashtable();
4123 AlignmentAnnotation aann[];
4124 for (SequenceI sqa : viewport.getAlignment().getSequences())
4126 aann = sqa.getAnnotation();
4127 for (int i = 0; aann != null && i < aann.length; i++)
4129 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4131 scoreSorts.put(aann[i].label, aann[i].label);
4135 Enumeration labels = scoreSorts.keys();
4136 while (labels.hasMoreElements())
4138 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4139 (String) labels.nextElement());
4141 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4144 _annotationScoreVectorHash = viewport.getAlignment()
4145 .getAlignmentAnnotation().hashCode();
4150 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4151 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4152 * call. Listeners are added to remove the menu item when the treePanel is
4153 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4157 * Displayed tree window.
4159 * SortBy menu item title.
4162 public void buildTreeMenu()
4164 calculateTree.removeAll();
4165 // build the calculate menu
4167 for (final String type : new String[] { "NJ", "AV" })
4169 String treecalcnm = MessageManager.getString("label.tree_calc_"
4170 + type.toLowerCase());
4171 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4173 JMenuItem tm = new JMenuItem();
4174 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4175 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4177 String smn = MessageManager.getStringOrReturn(
4178 "label.score_model_", sm.getName());
4179 final String title = MessageManager.formatMessage(
4180 "label.treecalc_title", treecalcnm, smn);
4181 tm.setText(title);//
4182 tm.addActionListener(new java.awt.event.ActionListener()
4185 public void actionPerformed(ActionEvent e)
4187 newTreePanel(type, pwtype, title);
4190 calculateTree.add(tm);
4195 sortByTreeMenu.removeAll();
4197 List<Component> comps = PaintRefresher.components.get(viewport
4198 .getSequenceSetId());
4199 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4200 for (Component comp : comps)
4202 if (comp instanceof TreePanel)
4204 treePanels.add((TreePanel) comp);
4208 if (treePanels.size() < 1)
4210 sortByTreeMenu.setVisible(false);
4214 sortByTreeMenu.setVisible(true);
4216 for (final TreePanel tp : treePanels)
4218 final JMenuItem item = new JMenuItem(tp.getTitle());
4219 item.addActionListener(new java.awt.event.ActionListener()
4222 public void actionPerformed(ActionEvent e)
4224 tp.sortByTree_actionPerformed();
4225 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4230 sortByTreeMenu.add(item);
4234 public boolean sortBy(AlignmentOrder alorder, String undoname)
4236 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4237 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4238 if (undoname != null)
4240 addHistoryItem(new OrderCommand(undoname, oldOrder,
4241 viewport.getAlignment()));
4243 alignPanel.paintAlignment(true);
4248 * Work out whether the whole set of sequences or just the selected set will
4249 * be submitted for multiple alignment.
4252 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4254 // Now, check we have enough sequences
4255 AlignmentView msa = null;
4257 if ((viewport.getSelectionGroup() != null)
4258 && (viewport.getSelectionGroup().getSize() > 1))
4260 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4261 // some common interface!
4263 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4264 * SequenceI[sz = seqs.getSize(false)];
4266 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4267 * seqs.getSequenceAt(i); }
4269 msa = viewport.getAlignmentView(true);
4271 else if (viewport.getSelectionGroup() != null
4272 && viewport.getSelectionGroup().getSize() == 1)
4274 int option = JOptionPane.showConfirmDialog(this,
4275 MessageManager.getString("warn.oneseq_msainput_selection"),
4276 MessageManager.getString("label.invalid_selection"),
4277 JOptionPane.OK_CANCEL_OPTION);
4278 if (option == JOptionPane.OK_OPTION)
4280 msa = viewport.getAlignmentView(false);
4285 msa = viewport.getAlignmentView(false);
4291 * Decides what is submitted to a secondary structure prediction service: the
4292 * first sequence in the alignment, or in the current selection, or, if the
4293 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4294 * region or the whole alignment. (where the first sequence in the set is the
4295 * one that the prediction will be for).
4297 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4299 AlignmentView seqs = null;
4301 if ((viewport.getSelectionGroup() != null)
4302 && (viewport.getSelectionGroup().getSize() > 0))
4304 seqs = viewport.getAlignmentView(true);
4308 seqs = viewport.getAlignmentView(false);
4310 // limit sequences - JBPNote in future - could spawn multiple prediction
4312 // TODO: viewport.getAlignment().isAligned is a global state - the local
4313 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4314 if (!viewport.getAlignment().isAligned(false))
4316 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4317 // TODO: if seqs.getSequences().length>1 then should really have warned
4331 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4333 // Pick the tree file
4334 JalviewFileChooser chooser = new JalviewFileChooser(
4335 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4336 chooser.setFileView(new JalviewFileView());
4337 chooser.setDialogTitle(MessageManager
4338 .getString("label.select_newick_like_tree_file"));
4339 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4341 int value = chooser.showOpenDialog(null);
4343 if (value == JalviewFileChooser.APPROVE_OPTION)
4345 String choice = chooser.getSelectedFile().getPath();
4346 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4347 jalview.io.NewickFile fin = null;
4350 fin = new jalview.io.NewickFile(choice, "File");
4351 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4352 } catch (Exception ex)
4359 .getString("label.problem_reading_tree_file"),
4360 JOptionPane.WARNING_MESSAGE);
4361 ex.printStackTrace();
4363 if (fin != null && fin.hasWarningMessage())
4365 JOptionPane.showMessageDialog(Desktop.desktop, fin
4366 .getWarningMessage(), MessageManager
4367 .getString("label.possible_problem_with_tree_file"),
4368 JOptionPane.WARNING_MESSAGE);
4374 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4376 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4379 public TreePanel ShowNewickTree(NewickFile nf, String title)
4381 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4384 public TreePanel ShowNewickTree(NewickFile nf, String title,
4385 AlignmentView input)
4387 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4390 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4391 int h, int x, int y)
4393 return ShowNewickTree(nf, title, null, w, h, x, y);
4397 * Add a treeviewer for the tree extracted from a newick file object to the
4398 * current alignment view
4405 * Associated alignment input data (or null)
4414 * @return TreePanel handle
4416 public TreePanel ShowNewickTree(NewickFile nf, String title,
4417 AlignmentView input, int w, int h, int x, int y)
4419 TreePanel tp = null;
4425 if (nf.getTree() != null)
4427 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4433 tp.setLocation(x, y);
4436 Desktop.addInternalFrame(tp, title, w, h);
4438 } catch (Exception ex)
4440 ex.printStackTrace();
4446 private boolean buildingMenu = false;
4449 * Generates menu items and listener event actions for web service clients
4452 public void BuildWebServiceMenu()
4454 while (buildingMenu)
4458 System.err.println("Waiting for building menu to finish.");
4460 } catch (Exception e)
4464 final AlignFrame me = this;
4465 buildingMenu = true;
4466 new Thread(new Runnable()
4471 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4474 // System.err.println("Building ws menu again "
4475 // + Thread.currentThread());
4476 // TODO: add support for context dependent disabling of services based
4478 // alignment and current selection
4479 // TODO: add additional serviceHandle parameter to specify abstract
4481 // class independently of AbstractName
4482 // TODO: add in rediscovery GUI function to restart discoverer
4483 // TODO: group services by location as well as function and/or
4485 // object broker mechanism.
4486 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4487 final IProgressIndicator af = me;
4488 final JMenu msawsmenu = new JMenu("Alignment");
4489 final JMenu secstrmenu = new JMenu(
4490 "Secondary Structure Prediction");
4491 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4492 final JMenu analymenu = new JMenu("Analysis");
4493 final JMenu dismenu = new JMenu("Protein Disorder");
4494 // final JMenu msawsmenu = new
4495 // JMenu(MessageManager.getString("label.alignment"));
4496 // final JMenu secstrmenu = new
4497 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4498 // final JMenu seqsrchmenu = new
4499 // JMenu(MessageManager.getString("label.sequence_database_search"));
4500 // final JMenu analymenu = new
4501 // JMenu(MessageManager.getString("label.analysis"));
4502 // final JMenu dismenu = new
4503 // JMenu(MessageManager.getString("label.protein_disorder"));
4504 // JAL-940 - only show secondary structure prediction services from
4505 // the legacy server
4506 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4508 Discoverer.services != null && (Discoverer.services.size() > 0))
4510 // TODO: refactor to allow list of AbstractName/Handler bindings to
4512 // stored or retrieved from elsewhere
4513 // No MSAWS used any more:
4514 // Vector msaws = null; // (Vector)
4515 // Discoverer.services.get("MsaWS");
4516 Vector secstrpr = (Vector) Discoverer.services
4518 if (secstrpr != null)
4520 // Add any secondary structure prediction services
4521 for (int i = 0, j = secstrpr.size(); i < j; i++)
4523 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4525 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4526 .getServiceClient(sh);
4527 int p = secstrmenu.getItemCount();
4528 impl.attachWSMenuEntry(secstrmenu, me);
4529 int q = secstrmenu.getItemCount();
4530 for (int litm = p; litm < q; litm++)
4532 legacyItems.add(secstrmenu.getItem(litm));
4538 // Add all submenus in the order they should appear on the web
4540 wsmenu.add(msawsmenu);
4541 wsmenu.add(secstrmenu);
4542 wsmenu.add(dismenu);
4543 wsmenu.add(analymenu);
4544 // No search services yet
4545 // wsmenu.add(seqsrchmenu);
4547 javax.swing.SwingUtilities.invokeLater(new Runnable()
4554 webService.removeAll();
4555 // first, add discovered services onto the webservices menu
4556 if (wsmenu.size() > 0)
4558 for (int i = 0, j = wsmenu.size(); i < j; i++)
4560 webService.add(wsmenu.get(i));
4565 webService.add(me.webServiceNoServices);
4567 // TODO: move into separate menu builder class.
4568 boolean new_sspred = false;
4569 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4571 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4572 if (jws2servs != null)
4574 if (jws2servs.hasServices())
4576 jws2servs.attachWSMenuEntry(webService, me);
4577 for (Jws2Instance sv : jws2servs.getServices())
4579 if (sv.description.toLowerCase().contains("jpred"))
4581 for (JMenuItem jmi : legacyItems)
4583 jmi.setVisible(false);
4589 if (jws2servs.isRunning())
4591 JMenuItem tm = new JMenuItem(
4592 "Still discovering JABA Services");
4593 tm.setEnabled(false);
4598 build_urlServiceMenu(me.webService);
4599 build_fetchdbmenu(webService);
4600 for (JMenu item : wsmenu)
4602 if (item.getItemCount() == 0)
4604 item.setEnabled(false);
4608 item.setEnabled(true);
4611 } catch (Exception e)
4614 .debug("Exception during web service menu building process.",
4619 } catch (Exception e)
4622 buildingMenu = false;
4629 * construct any groupURL type service menu entries.
4633 private void build_urlServiceMenu(JMenu webService)
4635 // TODO: remove this code when 2.7 is released
4636 // DEBUG - alignmentView
4638 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4639 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4641 * @Override public void actionPerformed(ActionEvent e) {
4642 * jalview.datamodel.AlignmentView
4643 * .testSelectionViews(af.viewport.getAlignment(),
4644 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4646 * }); webService.add(testAlView);
4648 // TODO: refactor to RestClient discoverer and merge menu entries for
4649 // rest-style services with other types of analysis/calculation service
4650 // SHmmr test client - still being implemented.
4651 // DEBUG - alignmentView
4653 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4656 client.attachWSMenuEntry(
4657 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4663 * Searches selected sequences for xRef products and builds the Show
4664 * Cross-References menu (formerly called Show Products)
4666 * @return true if Show Cross-references menu should be enabled.
4668 public boolean canShowProducts()
4670 SequenceI[] selection = viewport.getSequenceSelection();
4671 AlignmentI dataset = viewport.getAlignment().getDataset();
4672 boolean showp = false;
4675 showProducts.removeAll();
4676 final boolean dna = viewport.getAlignment().isNucleotide();
4677 String[] ptypes = (selection == null || selection.length == 0) ? null
4678 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4680 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4683 final AlignFrame af = this;
4684 final String source = ptypes[t];
4685 JMenuItem xtype = new JMenuItem(ptypes[t]);
4686 xtype.addActionListener(new ActionListener()
4690 public void actionPerformed(ActionEvent e)
4692 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4696 showProducts.add(xtype);
4698 showProducts.setVisible(showp);
4699 showProducts.setEnabled(showp);
4700 } catch (Exception e)
4702 jalview.bin.Cache.log
4703 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4710 protected void showProductsFor(final SequenceI[] sel, final boolean dna,
4711 final String source)
4713 Runnable foo = new Runnable()
4719 final long sttime = System.currentTimeMillis();
4720 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4721 "status.searching_for_sequences_from",
4722 new Object[] { source }), sttime);
4725 AlignmentI alignment = AlignFrame.this.getViewport()
4727 AlignmentI xrefs = CrossRef.findXrefSequences(sel, dna, source,
4732 * get display scheme (if any) to apply to features
4734 FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
4735 .getFeatureColourScheme(source);
4737 AlignmentI al = makeCrossReferencesAlignment(
4738 alignment.getDataset(), xrefs);
4740 AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
4742 String newtitle = String.format("%s %s %s",
4743 MessageManager.getString(dna ? "label.proteins"
4744 : "label.nucleotides"), MessageManager
4745 .getString("label.for"), getTitle());
4746 newFrame.setTitle(newtitle);
4748 if (!Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4751 * split frame display is turned off in preferences file
4753 Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4755 return; // via finally clause
4759 * Make a copy of this alignment (sharing the same dataset
4760 * sequences). If we are DNA, drop introns and update mappings
4762 AlignmentI copyAlignment = null;
4763 final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4764 .getSequenceSelection();
4765 List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4766 boolean copyAlignmentIsAligned = false;
4769 copyAlignment = AlignmentUtils.makeCdsAlignment(
4770 sequenceSelection, cf, alignment);
4771 if (copyAlignment.getHeight() == 0)
4773 System.err.println("Failed to make CDS alignment");
4775 al.getCodonFrames().clear();
4776 al.getCodonFrames().addAll(copyAlignment.getCodonFrames());
4779 * pending getting Embl transcripts to 'align',
4780 * we are only doing this for Ensembl
4782 // TODO proper criteria for 'can align as cdna'
4783 if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
4784 || AlignmentUtils.looksLikeEnsembl(alignment))
4786 copyAlignment.alignAs(alignment);
4787 copyAlignmentIsAligned = true;
4792 copyAlignment = AlignmentUtils.makeCopyAlignment(
4793 sequenceSelection, xrefs.getSequencesArray());
4794 copyAlignment.getCodonFrames().addAll(cf);
4796 copyAlignment.setGapCharacter(AlignFrame.this.viewport
4797 .getGapCharacter());
4799 StructureSelectionManager ssm = StructureSelectionManager
4800 .getStructureSelectionManager(Desktop.instance);
4801 ssm.registerMappings(cf);
4803 if (copyAlignment.getHeight() <= 0)
4805 System.err.println("No Sequences generated for xRef type "
4810 * align protein to dna
4812 if (dna && copyAlignmentIsAligned)
4814 al.alignAs(copyAlignment);
4819 * align cdna to protein - currently only if
4820 * fetching and aligning Ensembl transcripts!
4822 if (DBRefSource.ENSEMBL.equalsIgnoreCase(source))
4824 copyAlignment.alignAs(al);
4828 AlignFrame copyThis = new AlignFrame(copyAlignment,
4829 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4830 copyThis.setTitle(AlignFrame.this.getTitle());
4832 boolean showSequenceFeatures = viewport
4833 .isShowSequenceFeatures();
4834 newFrame.setShowSeqFeatures(showSequenceFeatures);
4835 copyThis.setShowSeqFeatures(showSequenceFeatures);
4836 FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4837 .getFeatureRenderer();
4840 * copy feature rendering settings to split frame
4842 newFrame.alignPanel.getSeqPanel().seqCanvas
4843 .getFeatureRenderer()
4844 .transferSettings(myFeatureStyling);
4845 copyThis.alignPanel.getSeqPanel().seqCanvas
4846 .getFeatureRenderer()
4847 .transferSettings(myFeatureStyling);
4850 * apply 'database source' feature configuration
4853 // TODO is this the feature colouring for the original
4854 // alignment or the fetched xrefs? either could be Ensembl
4855 newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
4856 copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
4858 SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4859 dna ? newFrame : copyThis);
4860 newFrame.setVisible(true);
4861 copyThis.setVisible(true);
4862 String linkedTitle = MessageManager
4863 .getString("label.linked_view_title");
4864 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4867 } catch (Exception e)
4870 "Exception when finding crossreferences", e);
4871 } catch (OutOfMemoryError e)
4873 new OOMWarning("whilst fetching crossreferences", e);
4874 } catch (Throwable e)
4876 Cache.log.error("Error when finding crossreferences",
4880 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4881 "status.finished_searching_for_sequences_from",
4882 new Object[] { source }), sttime);
4887 * Makes an alignment containing the given sequences. If this is of the
4888 * same type as the given dataset (nucleotide/protein), then the new
4889 * alignment shares the same dataset, and its dataset sequences are added
4890 * to it. Otherwise a new dataset sequence is created for the
4897 protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
4900 boolean sameType = dataset.isNucleotide() == seqs.isNucleotide();
4902 SequenceI[] sprods = new SequenceI[seqs.getHeight()];
4903 for (int s = 0; s < sprods.length; s++)
4905 sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
4908 if (dataset.getSequences() == null
4909 || !dataset.getSequences().contains(
4910 sprods[s].getDatasetSequence()))
4912 dataset.addSequence(sprods[s].getDatasetSequence());
4915 sprods[s].updatePDBIds();
4917 Alignment al = new Alignment(sprods);
4920 al.setDataset((Alignment) dataset);
4924 al.createDatasetAlignment();
4930 Thread frunner = new Thread(foo);
4935 * Construct and display a new frame containing the translation of this
4936 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4939 public void showTranslation_actionPerformed(ActionEvent e)
4941 AlignmentI al = null;
4944 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4946 al = dna.translateCdna();
4947 } catch (Exception ex)
4949 jalview.bin.Cache.log.error(
4950 "Exception during translation. Please report this !", ex);
4951 final String msg = MessageManager
4952 .getString("label.error_when_translating_sequences_submit_bug_report");
4953 final String errorTitle = MessageManager
4954 .getString("label.implementation_error")
4955 + MessageManager.getString("translation_failed");
4956 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4957 JOptionPane.ERROR_MESSAGE);
4960 if (al == null || al.getHeight() == 0)
4962 final String msg = MessageManager
4963 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4964 final String errorTitle = MessageManager
4965 .getString("label.translation_failed");
4966 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4967 JOptionPane.WARNING_MESSAGE);
4971 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4972 af.setFileFormat(this.currentFileFormat);
4973 final String newTitle = MessageManager.formatMessage(
4974 "label.translation_of_params",
4975 new Object[] { this.getTitle() });
4976 af.setTitle(newTitle);
4977 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4979 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4980 viewport.openSplitFrame(af, new Alignment(seqs));
4984 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4991 * Set the file format
4995 public void setFileFormat(String fileFormat)
4997 this.currentFileFormat = fileFormat;
5001 * Try to load a features file onto the alignment.
5004 * contents or path to retrieve file
5006 * access mode of file (see jalview.io.AlignFile)
5007 * @return true if features file was parsed correctly.
5009 public boolean parseFeaturesFile(String file, String type)
5011 return avc.parseFeaturesFile(file, type,
5012 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
5017 public void refreshFeatureUI(boolean enableIfNecessary)
5019 // note - currently this is only still here rather than in the controller
5020 // because of the featureSettings hard reference that is yet to be
5022 if (enableIfNecessary)
5024 viewport.setShowSequenceFeatures(true);
5025 showSeqFeatures.setSelected(true);
5031 public void dragEnter(DropTargetDragEvent evt)
5036 public void dragExit(DropTargetEvent evt)
5041 public void dragOver(DropTargetDragEvent evt)
5046 public void dropActionChanged(DropTargetDragEvent evt)
5051 public void drop(DropTargetDropEvent evt)
5053 Transferable t = evt.getTransferable();
5054 java.util.List files = null;
5058 DataFlavor uriListFlavor = new DataFlavor(
5059 "text/uri-list;class=java.lang.String");
5060 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5062 // Works on Windows and MacOSX
5063 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5064 files = (java.util.List) t
5065 .getTransferData(DataFlavor.javaFileListFlavor);
5067 else if (t.isDataFlavorSupported(uriListFlavor))
5069 // This is used by Unix drag system
5070 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5071 String data = (String) t.getTransferData(uriListFlavor);
5072 files = new java.util.ArrayList(1);
5073 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5074 data, "\r\n"); st.hasMoreTokens();)
5076 String s = st.nextToken();
5077 if (s.startsWith("#"))
5079 // the line is a comment (as per the RFC 2483)
5083 java.net.URI uri = new java.net.URI(s);
5084 // check to see if we can handle this kind of URI
5085 if (uri.getScheme().toLowerCase().startsWith("http"))
5087 files.add(uri.toString());
5091 // otherwise preserve old behaviour: catch all for file objects
5092 java.io.File file = new java.io.File(uri);
5093 files.add(file.toString());
5097 } catch (Exception e)
5099 e.printStackTrace();
5105 // check to see if any of these files have names matching sequences in
5107 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5108 .getAlignment().getSequencesArray());
5110 * Object[] { String,SequenceI}
5112 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5113 ArrayList<String> filesnotmatched = new ArrayList<String>();
5114 for (int i = 0; i < files.size(); i++)
5116 String file = files.get(i).toString();
5118 String protocol = FormatAdapter.checkProtocol(file);
5119 if (protocol == jalview.io.FormatAdapter.FILE)
5121 File fl = new File(file);
5122 pdbfn = fl.getName();
5124 else if (protocol == jalview.io.FormatAdapter.URL)
5126 URL url = new URL(file);
5127 pdbfn = url.getFile();
5129 if (pdbfn.length() > 0)
5131 // attempt to find a match in the alignment
5132 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5133 int l = 0, c = pdbfn.indexOf(".");
5134 while (mtch == null && c != -1)
5139 } while ((c = pdbfn.indexOf(".", l)) > l);
5142 pdbfn = pdbfn.substring(0, l);
5144 mtch = idm.findAllIdMatches(pdbfn);
5151 type = new IdentifyFile().identify(file, protocol);
5152 } catch (Exception ex)
5158 if (type.equalsIgnoreCase("PDB"))
5160 filesmatched.add(new Object[] { file, protocol, mtch });
5165 // File wasn't named like one of the sequences or wasn't a PDB file.
5166 filesnotmatched.add(file);
5170 if (filesmatched.size() > 0)
5172 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5178 "label.automatically_associate_pdb_files_with_sequences_same_name",
5179 new Object[] { Integer
5185 .getString("label.automatically_associate_pdb_files_by_name"),
5186 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5189 for (Object[] fm : filesmatched)
5191 // try and associate
5192 // TODO: may want to set a standard ID naming formalism for
5193 // associating PDB files which have no IDs.
5194 for (SequenceI toassoc : (SequenceI[]) fm[2])
5196 PDBEntry pe = new AssociatePdbFileWithSeq()
5197 .associatePdbWithSeq((String) fm[0],
5198 (String) fm[1], toassoc, false,
5202 System.err.println("Associated file : "
5203 + ((String) fm[0]) + " with "
5204 + toassoc.getDisplayId(true));
5208 alignPanel.paintAlignment(true);
5212 if (filesnotmatched.size() > 0)
5215 && (Cache.getDefault(
5216 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5222 "label.ignore_unmatched_dropped_files_info",
5223 new Object[] { Integer
5230 .getString("label.ignore_unmatched_dropped_files"),
5231 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5235 for (String fn : filesnotmatched)
5237 loadJalviewDataFile(fn, null, null, null);
5241 } catch (Exception ex)
5243 ex.printStackTrace();
5249 * Attempt to load a "dropped" file or URL string: First by testing whether
5250 * it's an Annotation file, then a JNet file, and finally a features file. If
5251 * all are false then the user may have dropped an alignment file onto this
5255 * either a filename or a URL string.
5257 public void loadJalviewDataFile(String file, String protocol,
5258 String format, SequenceI assocSeq)
5262 if (protocol == null)
5264 protocol = FormatAdapter.checkProtocol(file);
5266 // if the file isn't identified, or not positively identified as some
5267 // other filetype (PFAM is default unidentified alignment file type) then
5268 // try to parse as annotation.
5269 boolean isAnnotation = (format == null || format
5270 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5271 .annotateAlignmentView(viewport, file, protocol) : false;
5275 // first see if its a T-COFFEE score file
5276 TCoffeeScoreFile tcf = null;
5279 tcf = new TCoffeeScoreFile(file, protocol);
5282 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5284 tcoffeeColour.setEnabled(true);
5285 tcoffeeColour.setSelected(true);
5286 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5287 isAnnotation = true;
5289 .setText(MessageManager
5290 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5294 // some problem - if no warning its probable that the ID matching
5295 // process didn't work
5299 tcf.getWarningMessage() == null ? MessageManager
5300 .getString("label.check_file_matches_sequence_ids_alignment")
5301 : tcf.getWarningMessage(),
5303 .getString("label.problem_reading_tcoffee_score_file"),
5304 JOptionPane.WARNING_MESSAGE);
5311 } catch (Exception x)
5314 .debug("Exception when processing data source as T-COFFEE score file",
5320 // try to see if its a JNet 'concise' style annotation file *before*
5322 // try to parse it as a features file
5325 format = new IdentifyFile().identify(file, protocol);
5327 if (format.equalsIgnoreCase("JnetFile"))
5329 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5331 new JnetAnnotationMaker();
5332 JnetAnnotationMaker.add_annotation(predictions,
5333 viewport.getAlignment(), 0, false);
5334 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5335 viewport.getAlignment().setSeqrep(repseq);
5336 ColumnSelection cs = new ColumnSelection();
5337 cs.hideInsertionsFor(repseq);
5338 viewport.setColumnSelection(cs);
5339 isAnnotation = true;
5341 else if (IdentifyFile.FeaturesFile.equals(format))
5343 if (parseFeaturesFile(file, protocol))
5345 alignPanel.paintAlignment(true);
5350 new FileLoader().LoadFile(viewport, file, protocol, format);
5357 alignPanel.adjustAnnotationHeight();
5358 viewport.updateSequenceIdColours();
5359 buildSortByAnnotationScoresMenu();
5360 alignPanel.paintAlignment(true);
5362 } catch (Exception ex)
5364 ex.printStackTrace();
5365 } catch (OutOfMemoryError oom)
5370 } catch (Exception x)
5375 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5376 : "using " + protocol + " from " + file)
5378 + (format != null ? "(parsing as '" + format
5379 + "' file)" : ""), oom, Desktop.desktop);
5384 * Method invoked by the ChangeListener on the tabbed pane, in other words
5385 * when a different tabbed pane is selected by the user or programmatically.
5388 public void tabSelectionChanged(int index)
5392 alignPanel = alignPanels.get(index);
5393 viewport = alignPanel.av;
5394 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5395 setMenusFromViewport(viewport);
5399 * If there is a frame linked to this one in a SplitPane, switch it to the
5400 * same view tab index. No infinite recursion of calls should happen, since
5401 * tabSelectionChanged() should not get invoked on setting the selected
5402 * index to an unchanged value. Guard against setting an invalid index
5403 * before the new view peer tab has been created.
5405 final AlignViewportI peer = viewport.getCodingComplement();
5408 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5409 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5411 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5417 * On right mouse click on view tab, prompt for and set new view name.
5420 public void tabbedPane_mousePressed(MouseEvent e)
5422 if (SwingUtilities.isRightMouseButton(e))
5424 String msg = MessageManager.getString("label.enter_view_name");
5425 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5426 JOptionPane.QUESTION_MESSAGE);
5430 viewport.viewName = reply;
5431 // TODO warn if reply is in getExistingViewNames()?
5432 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5437 public AlignViewport getCurrentView()
5443 * Open the dialog for regex description parsing.
5446 protected void extractScores_actionPerformed(ActionEvent e)
5448 ParseProperties pp = new jalview.analysis.ParseProperties(
5449 viewport.getAlignment());
5450 // TODO: verify regex and introduce GUI dialog for version 2.5
5451 // if (pp.getScoresFromDescription("col", "score column ",
5452 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5454 if (pp.getScoresFromDescription("description column",
5455 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5457 buildSortByAnnotationScoresMenu();
5465 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5469 protected void showDbRefs_actionPerformed(ActionEvent e)
5471 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5477 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5481 protected void showNpFeats_actionPerformed(ActionEvent e)
5483 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5487 * find the viewport amongst the tabs in this alignment frame and close that
5492 public boolean closeView(AlignViewportI av)
5496 this.closeMenuItem_actionPerformed(false);
5499 Component[] comp = tabbedPane.getComponents();
5500 for (int i = 0; comp != null && i < comp.length; i++)
5502 if (comp[i] instanceof AlignmentPanel)
5504 if (((AlignmentPanel) comp[i]).av == av)
5507 closeView((AlignmentPanel) comp[i]);
5515 protected void build_fetchdbmenu(JMenu webService)
5517 // Temporary hack - DBRef Fetcher always top level ws entry.
5518 // TODO We probably want to store a sequence database checklist in
5519 // preferences and have checkboxes.. rather than individual sources selected
5521 final JMenu rfetch = new JMenu(
5522 MessageManager.getString("action.fetch_db_references"));
5523 rfetch.setToolTipText(MessageManager
5524 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5525 webService.add(rfetch);
5527 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5528 MessageManager.getString("option.trim_retrieved_seqs"));
5529 trimrs.setToolTipText(MessageManager
5530 .getString("label.trim_retrieved_sequences"));
5531 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5532 trimrs.addActionListener(new ActionListener()
5535 public void actionPerformed(ActionEvent e)
5537 trimrs.setSelected(trimrs.isSelected());
5538 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5539 Boolean.valueOf(trimrs.isSelected()).toString());
5543 JMenuItem fetchr = new JMenuItem(
5544 MessageManager.getString("label.standard_databases"));
5545 fetchr.setToolTipText(MessageManager
5546 .getString("label.fetch_embl_uniprot"));
5547 fetchr.addActionListener(new ActionListener()
5551 public void actionPerformed(ActionEvent e)
5553 new Thread(new Runnable()
5558 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5559 .getAlignment().isNucleotide();
5560 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5561 .getSequenceSelection(), alignPanel.alignFrame, null,
5562 alignPanel.alignFrame.featureSettings, isNucleotide);
5563 dbRefFetcher.addListener(new FetchFinishedListenerI()
5566 public void finished()
5568 AlignFrame.this.setMenusForViewport();
5572 .fetchDBRefs(false);
5580 final AlignFrame me = this;
5581 new Thread(new Runnable()
5586 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5587 .getSequenceFetcherSingleton(me);
5588 javax.swing.SwingUtilities.invokeLater(new Runnable()
5593 String[] dbclasses = sf.getOrderedSupportedSources();
5594 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5595 // jalview.util.QuickSort.sort(otherdb, otherdb);
5596 List<DbSourceProxy> otherdb;
5597 JMenu dfetch = new JMenu();
5598 JMenu ifetch = new JMenu();
5599 JMenuItem fetchr = null;
5600 int comp = 0, icomp = 0, mcomp = 15;
5601 String mname = null;
5603 for (String dbclass : dbclasses)
5605 otherdb = sf.getSourceProxy(dbclass);
5606 // add a single entry for this class, or submenu allowing 'fetch
5608 if (otherdb == null || otherdb.size() < 1)
5612 // List<DbSourceProxy> dbs=otherdb;
5613 // otherdb=new ArrayList<DbSourceProxy>();
5614 // for (DbSourceProxy db:dbs)
5616 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5620 mname = "From " + dbclass;
5622 if (otherdb.size() == 1)
5624 final DbSourceProxy[] dassource = otherdb
5625 .toArray(new DbSourceProxy[0]);
5626 DbSourceProxy src = otherdb.get(0);
5627 fetchr = new JMenuItem(src.getDbSource());
5628 fetchr.addActionListener(new ActionListener()
5632 public void actionPerformed(ActionEvent e)
5634 new Thread(new Runnable()
5640 boolean isNucleotide = alignPanel.alignFrame
5641 .getViewport().getAlignment()
5643 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5644 alignPanel.av.getSequenceSelection(),
5645 alignPanel.alignFrame, dassource,
5646 alignPanel.alignFrame.featureSettings,
5649 .addListener(new FetchFinishedListenerI()
5652 public void finished()
5654 AlignFrame.this.setMenusForViewport();
5657 dbRefFetcher.fetchDBRefs(false);
5663 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5664 MessageManager.formatMessage(
5665 "label.fetch_retrieve_from",
5666 new Object[] { src.getDbName() })));
5672 final DbSourceProxy[] dassource = otherdb
5673 .toArray(new DbSourceProxy[0]);
5675 DbSourceProxy src = otherdb.get(0);
5676 fetchr = new JMenuItem(MessageManager.formatMessage(
5677 "label.fetch_all_param",
5678 new Object[] { src.getDbSource() }));
5679 fetchr.addActionListener(new ActionListener()
5682 public void actionPerformed(ActionEvent e)
5684 new Thread(new Runnable()
5690 boolean isNucleotide = alignPanel.alignFrame
5691 .getViewport().getAlignment()
5693 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5694 alignPanel.av.getSequenceSelection(),
5695 alignPanel.alignFrame, dassource,
5696 alignPanel.alignFrame.featureSettings,
5699 .addListener(new FetchFinishedListenerI()
5702 public void finished()
5704 AlignFrame.this.setMenusForViewport();
5707 dbRefFetcher.fetchDBRefs(false);
5713 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5714 MessageManager.formatMessage(
5715 "label.fetch_retrieve_from_all_sources",
5717 Integer.valueOf(otherdb.size())
5718 .toString(), src.getDbSource(),
5719 src.getDbName() })));
5722 // and then build the rest of the individual menus
5723 ifetch = new JMenu(MessageManager.formatMessage(
5724 "label.source_from_db_source",
5725 new Object[] { src.getDbSource() }));
5727 String imname = null;
5729 for (DbSourceProxy sproxy : otherdb)
5731 String dbname = sproxy.getDbName();
5732 String sname = dbname.length() > 5 ? dbname.substring(0,
5733 5) + "..." : dbname;
5734 String msname = dbname.length() > 10 ? dbname.substring(
5735 0, 10) + "..." : dbname;
5738 imname = MessageManager.formatMessage(
5739 "label.from_msname", new Object[] { sname });
5741 fetchr = new JMenuItem(msname);
5742 final DbSourceProxy[] dassrc = { sproxy };
5743 fetchr.addActionListener(new ActionListener()
5747 public void actionPerformed(ActionEvent e)
5749 new Thread(new Runnable()
5755 boolean isNucleotide = alignPanel.alignFrame
5756 .getViewport().getAlignment()
5758 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5759 alignPanel.av.getSequenceSelection(),
5760 alignPanel.alignFrame, dassrc,
5761 alignPanel.alignFrame.featureSettings,
5764 .addListener(new FetchFinishedListenerI()
5767 public void finished()
5769 AlignFrame.this.setMenusForViewport();
5772 dbRefFetcher.fetchDBRefs(false);
5778 fetchr.setToolTipText("<html>"
5779 + MessageManager.formatMessage(
5780 "label.fetch_retrieve_from", new Object[]
5784 if (++icomp >= mcomp || i == (otherdb.size()))
5786 ifetch.setText(MessageManager.formatMessage(
5787 "label.source_to_target", imname, sname));
5789 ifetch = new JMenu();
5797 if (comp >= mcomp || dbi >= (dbclasses.length))
5799 dfetch.setText(MessageManager.formatMessage(
5800 "label.source_to_target", mname, dbclass));
5802 dfetch = new JMenu();
5815 * Left justify the whole alignment.
5818 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5820 AlignmentI al = viewport.getAlignment();
5822 viewport.firePropertyChange("alignment", null, al);
5826 * Right justify the whole alignment.
5829 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5831 AlignmentI al = viewport.getAlignment();
5833 viewport.firePropertyChange("alignment", null, al);
5837 public void setShowSeqFeatures(boolean b)
5839 showSeqFeatures.setSelected(b);
5840 viewport.setShowSequenceFeatures(b);
5847 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5848 * awt.event.ActionEvent)
5851 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5853 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5854 alignPanel.paintAlignment(true);
5861 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5865 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5867 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5868 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5876 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5877 * .event.ActionEvent)
5880 protected void showGroupConservation_actionPerformed(ActionEvent e)
5882 viewport.setShowGroupConservation(showGroupConservation.getState());
5883 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5890 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5891 * .event.ActionEvent)
5894 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5896 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5897 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5904 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5905 * .event.ActionEvent)
5908 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5910 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5911 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5915 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5917 showSequenceLogo.setState(true);
5918 viewport.setShowSequenceLogo(true);
5919 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5920 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5924 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5926 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5933 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5934 * .event.ActionEvent)
5937 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5939 if (avc.makeGroupsFromSelection())
5941 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5942 alignPanel.updateAnnotation();
5943 alignPanel.paintAlignment(true);
5947 public void clearAlignmentSeqRep()
5949 // TODO refactor alignmentseqrep to controller
5950 if (viewport.getAlignment().hasSeqrep())
5952 viewport.getAlignment().setSeqrep(null);
5953 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5954 alignPanel.updateAnnotation();
5955 alignPanel.paintAlignment(true);
5960 protected void createGroup_actionPerformed(ActionEvent e)
5962 if (avc.createGroup())
5964 alignPanel.alignmentChanged();
5969 protected void unGroup_actionPerformed(ActionEvent e)
5973 alignPanel.alignmentChanged();
5978 * make the given alignmentPanel the currently selected tab
5980 * @param alignmentPanel
5982 public void setDisplayedView(AlignmentPanel alignmentPanel)
5984 if (!viewport.getSequenceSetId().equals(
5985 alignmentPanel.av.getSequenceSetId()))
5989 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5991 if (tabbedPane != null
5992 && tabbedPane.getTabCount() > 0
5993 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5994 .getSelectedIndex())
5996 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
6001 * Action on selection of menu options to Show or Hide annotations.
6004 * @param forSequences
6005 * update sequence-related annotations
6006 * @param forAlignment
6007 * update non-sequence-related annotations
6010 protected void setAnnotationsVisibility(boolean visible,
6011 boolean forSequences, boolean forAlignment)
6013 for (AlignmentAnnotation aa : alignPanel.getAlignment()
6014 .getAlignmentAnnotation())
6017 * don't display non-positional annotations on an alignment
6019 if (aa.annotations == null)
6023 boolean apply = (aa.sequenceRef == null && forAlignment)
6024 || (aa.sequenceRef != null && forSequences);
6027 aa.visible = visible;
6030 alignPanel.validateAnnotationDimensions(true);
6031 alignPanel.alignmentChanged();
6035 * Store selected annotation sort order for the view and repaint.
6038 protected void sortAnnotations_actionPerformed()
6040 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
6042 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
6043 alignPanel.paintAlignment(true);
6048 * @return alignment panels in this alignment frame
6050 public List<? extends AlignmentViewPanel> getAlignPanels()
6052 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
6056 * Open a new alignment window, with the cDNA associated with this (protein)
6057 * alignment, aligned as is the protein.
6059 protected void viewAsCdna_actionPerformed()
6061 // TODO no longer a menu action - refactor as required
6062 final AlignmentI alignment = getViewport().getAlignment();
6063 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6064 if (mappings == null)
6068 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6069 for (SequenceI aaSeq : alignment.getSequences())
6071 for (AlignedCodonFrame acf : mappings)
6073 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6077 * There is a cDNA mapping for this protein sequence - add to new
6078 * alignment. It will share the same dataset sequence as other mapped
6079 * cDNA (no new mappings need to be created).
6081 final Sequence newSeq = new Sequence(dnaSeq);
6082 newSeq.setDatasetSequence(dnaSeq);
6083 cdnaSeqs.add(newSeq);
6087 if (cdnaSeqs.size() == 0)
6089 // show a warning dialog no mapped cDNA
6092 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6094 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6095 AlignFrame.DEFAULT_HEIGHT);
6096 cdna.alignAs(alignment);
6097 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6099 Desktop.addInternalFrame(alignFrame, newtitle,
6100 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6104 * Set visibility of dna/protein complement view (available when shown in a
6110 protected void showComplement_actionPerformed(boolean show)
6112 SplitContainerI sf = getSplitViewContainer();
6115 sf.setComplementVisible(this, show);
6120 * Generate the reverse (optionally complemented) of the selected sequences,
6121 * and add them to the alignment
6124 protected void showReverse_actionPerformed(boolean complement)
6126 AlignmentI al = null;
6129 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6131 al = dna.reverseCdna(complement);
6132 viewport.addAlignment(al, "");
6133 } catch (Exception ex)
6135 System.err.println(ex.getMessage());
6141 class PrintThread extends Thread
6145 public PrintThread(AlignmentPanel ap)
6150 static PageFormat pf;
6155 PrinterJob printJob = PrinterJob.getPrinterJob();
6159 printJob.setPrintable(ap, pf);
6163 printJob.setPrintable(ap);
6166 if (printJob.printDialog())
6171 } catch (Exception PrintException)
6173 PrintException.printStackTrace();