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.FeatureSettingsI;
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.HiddenSequences;
58 import jalview.datamodel.PDBEntry;
59 import jalview.datamodel.SeqCigar;
60 import jalview.datamodel.Sequence;
61 import jalview.datamodel.SequenceGroup;
62 import jalview.datamodel.SequenceI;
63 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
64 import jalview.io.AlignmentProperties;
65 import jalview.io.AnnotationFile;
66 import jalview.io.BioJsHTMLOutput;
67 import jalview.io.FileLoader;
68 import jalview.io.FormatAdapter;
69 import jalview.io.HtmlSvgOutput;
70 import jalview.io.IdentifyFile;
71 import jalview.io.JalviewFileChooser;
72 import jalview.io.JalviewFileView;
73 import jalview.io.JnetAnnotationMaker;
74 import jalview.io.NewickFile;
75 import jalview.io.TCoffeeScoreFile;
76 import jalview.jbgui.GAlignFrame;
77 import jalview.schemes.Blosum62ColourScheme;
78 import jalview.schemes.BuriedColourScheme;
79 import jalview.schemes.ClustalxColourScheme;
80 import jalview.schemes.ColourSchemeI;
81 import jalview.schemes.ColourSchemeProperty;
82 import jalview.schemes.HelixColourScheme;
83 import jalview.schemes.HydrophobicColourScheme;
84 import jalview.schemes.NucleotideColourScheme;
85 import jalview.schemes.PIDColourScheme;
86 import jalview.schemes.PurinePyrimidineColourScheme;
87 import jalview.schemes.RNAHelicesColourChooser;
88 import jalview.schemes.ResidueProperties;
89 import jalview.schemes.StrandColourScheme;
90 import jalview.schemes.TCoffeeColourScheme;
91 import jalview.schemes.TaylorColourScheme;
92 import jalview.schemes.TurnColourScheme;
93 import jalview.schemes.UserColourScheme;
94 import jalview.schemes.ZappoColourScheme;
95 import jalview.structure.StructureSelectionManager;
96 import jalview.util.MessageManager;
97 import jalview.viewmodel.AlignmentViewport;
98 import jalview.ws.SequenceFetcher;
99 import jalview.ws.jws1.Discoverer;
100 import jalview.ws.jws2.Jws2Discoverer;
101 import jalview.ws.jws2.jabaws2.Jws2Instance;
102 import jalview.ws.seqfetcher.ASequenceFetcher;
103 import jalview.ws.seqfetcher.DbSourceProxy;
105 import java.awt.BorderLayout;
106 import java.awt.Component;
107 import java.awt.Rectangle;
108 import java.awt.Toolkit;
109 import java.awt.datatransfer.Clipboard;
110 import java.awt.datatransfer.DataFlavor;
111 import java.awt.datatransfer.StringSelection;
112 import java.awt.datatransfer.Transferable;
113 import java.awt.dnd.DnDConstants;
114 import java.awt.dnd.DropTargetDragEvent;
115 import java.awt.dnd.DropTargetDropEvent;
116 import java.awt.dnd.DropTargetEvent;
117 import java.awt.dnd.DropTargetListener;
118 import java.awt.event.ActionEvent;
119 import java.awt.event.ActionListener;
120 import java.awt.event.ItemEvent;
121 import java.awt.event.ItemListener;
122 import java.awt.event.KeyAdapter;
123 import java.awt.event.KeyEvent;
124 import java.awt.event.MouseAdapter;
125 import java.awt.event.MouseEvent;
126 import java.awt.print.PageFormat;
127 import java.awt.print.PrinterJob;
128 import java.beans.PropertyChangeEvent;
131 import java.util.ArrayList;
132 import java.util.Arrays;
133 import java.util.Deque;
134 import java.util.Enumeration;
135 import java.util.Hashtable;
136 import java.util.List;
137 import java.util.Vector;
139 import javax.swing.JCheckBoxMenuItem;
140 import javax.swing.JEditorPane;
141 import javax.swing.JInternalFrame;
142 import javax.swing.JLayeredPane;
143 import javax.swing.JMenu;
144 import javax.swing.JMenuItem;
145 import javax.swing.JOptionPane;
146 import javax.swing.JRadioButtonMenuItem;
147 import javax.swing.JScrollPane;
148 import javax.swing.SwingUtilities;
154 * @version $Revision$
156 public class AlignFrame extends GAlignFrame implements DropTargetListener,
157 IProgressIndicator, AlignViewControllerGuiI
160 public static final int DEFAULT_WIDTH = 700;
162 public static final int DEFAULT_HEIGHT = 500;
165 * The currently displayed panel (selected tabbed view if more than one)
167 public AlignmentPanel alignPanel;
169 AlignViewport viewport;
171 public AlignViewControllerI avc;
173 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
176 * Last format used to load or save alignments in this window
178 String currentFileFormat = null;
181 * Current filename for this alignment
183 String fileName = null;
186 * Creates a new AlignFrame object with specific width and height.
192 public AlignFrame(AlignmentI al, int width, int height)
194 this(al, null, width, height);
198 * Creates a new AlignFrame object with specific width, height and
204 * @param sequenceSetId
206 public AlignFrame(AlignmentI al, int width, int height,
207 String sequenceSetId)
209 this(al, null, width, height, sequenceSetId);
213 * Creates a new AlignFrame object with specific width, height and
219 * @param sequenceSetId
222 public AlignFrame(AlignmentI al, int width, int height,
223 String sequenceSetId, String viewId)
225 this(al, null, width, height, sequenceSetId, viewId);
229 * new alignment window with hidden columns
233 * @param hiddenColumns
234 * ColumnSelection or null
236 * Width of alignment frame
240 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
241 int width, int height)
243 this(al, hiddenColumns, width, height, null);
247 * Create alignment frame for al with hiddenColumns, a specific width and
248 * height, and specific sequenceId
251 * @param hiddenColumns
254 * @param sequenceSetId
257 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
258 int width, int height, String sequenceSetId)
260 this(al, hiddenColumns, width, height, sequenceSetId, null);
264 * Create alignment frame for al with hiddenColumns, a specific width and
265 * height, and specific sequenceId
268 * @param hiddenColumns
271 * @param sequenceSetId
276 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
277 int width, int height, String sequenceSetId, String viewId)
279 setSize(width, height);
281 if (al.getDataset() == null)
286 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
288 alignPanel = new AlignmentPanel(this, viewport);
290 addAlignmentPanel(alignPanel, true);
294 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
295 ColumnSelection hiddenColumns, int width, int height)
297 setSize(width, height);
299 if (al.getDataset() == null)
304 viewport = new AlignViewport(al, hiddenColumns);
306 if (hiddenSeqs != null && hiddenSeqs.length > 0)
308 viewport.hideSequence(hiddenSeqs);
310 alignPanel = new AlignmentPanel(this, viewport);
311 addAlignmentPanel(alignPanel, true);
316 * Make a new AlignFrame from existing alignmentPanels
323 public AlignFrame(AlignmentPanel ap)
327 addAlignmentPanel(ap, false);
332 * initalise the alignframe from the underlying viewport data and the
337 if (!Jalview.isHeadlessMode())
339 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
342 avc = new jalview.controller.AlignViewController(this, viewport,
344 if (viewport.getAlignmentConservationAnnotation() == null)
346 BLOSUM62Colour.setEnabled(false);
347 conservationMenuItem.setEnabled(false);
348 modifyConservation.setEnabled(false);
349 // PIDColour.setEnabled(false);
350 // abovePIDThreshold.setEnabled(false);
351 // modifyPID.setEnabled(false);
354 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
357 if (sortby.equals("Id"))
359 sortIDMenuItem_actionPerformed(null);
361 else if (sortby.equals("Pairwise Identity"))
363 sortPairwiseMenuItem_actionPerformed(null);
366 if (Desktop.desktop != null)
368 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
369 addServiceListeners();
370 setGUINucleotide(viewport.getAlignment().isNucleotide());
374 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
376 setMenusFromViewport(viewport);
377 buildSortByAnnotationScoresMenu();
380 if (viewport.getWrapAlignment())
382 wrapMenuItem_actionPerformed(null);
385 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
387 this.overviewMenuItem_actionPerformed(null);
392 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
393 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
394 final String menuLabel = MessageManager
395 .getString("label.copy_format_from");
396 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
397 new ViewSetProvider()
401 public AlignmentPanel[] getAllAlignmentPanels()
404 origview.add(alignPanel);
405 // make an array of all alignment panels except for this one
406 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
407 Arrays.asList(Desktop.getAlignmentPanels(null)));
408 aps.remove(AlignFrame.this.alignPanel);
409 return aps.toArray(new AlignmentPanel[aps.size()]);
411 }, selviews, new ItemListener()
415 public void itemStateChanged(ItemEvent e)
417 if (origview.size() > 0)
419 final AlignmentPanel ap = origview.get(0);
422 * Copy the ViewStyle of the selected panel to 'this one'.
423 * Don't change value of 'scaleProteinAsCdna' unless copying
426 ViewStyleI vs = selviews.get(0).getAlignViewport()
428 boolean fromSplitFrame = selviews.get(0)
429 .getAlignViewport().getCodingComplement() != null;
432 vs.setScaleProteinAsCdna(ap.getAlignViewport()
433 .getViewStyle().isScaleProteinAsCdna());
435 ap.getAlignViewport().setViewStyle(vs);
438 * Also rescale ViewStyle of SplitFrame complement if there is
439 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
440 * the whole ViewStyle (allow cDNA protein to have different
443 AlignViewportI complement = ap.getAlignViewport()
444 .getCodingComplement();
445 if (complement != null && vs.isScaleProteinAsCdna())
447 AlignFrame af = Desktop.getAlignFrameFor(complement);
448 ((SplitFrame) af.getSplitViewContainer())
450 af.setMenusForViewport();
454 ap.setSelected(true);
455 ap.alignFrame.setMenusForViewport();
460 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
461 .indexOf("devel") > -1
462 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
463 .indexOf("test") > -1)
465 formatMenu.add(vsel);
471 * Change the filename and format for the alignment, and enable the 'reload'
472 * button functionality.
479 public void setFileName(String file, String format)
482 setFileFormat(format);
483 reload.setEnabled(true);
487 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
490 void addKeyListener()
492 addKeyListener(new KeyAdapter()
495 public void keyPressed(KeyEvent evt)
497 if (viewport.cursorMode
498 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
499 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
500 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
501 && Character.isDigit(evt.getKeyChar()))
503 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
506 switch (evt.getKeyCode())
509 case 27: // escape key
510 deselectAllSequenceMenuItem_actionPerformed(null);
514 case KeyEvent.VK_DOWN:
515 if (evt.isAltDown() || !viewport.cursorMode)
517 moveSelectedSequences(false);
519 if (viewport.cursorMode)
521 alignPanel.getSeqPanel().moveCursor(0, 1);
526 if (evt.isAltDown() || !viewport.cursorMode)
528 moveSelectedSequences(true);
530 if (viewport.cursorMode)
532 alignPanel.getSeqPanel().moveCursor(0, -1);
537 case KeyEvent.VK_LEFT:
538 if (evt.isAltDown() || !viewport.cursorMode)
540 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
544 alignPanel.getSeqPanel().moveCursor(-1, 0);
549 case KeyEvent.VK_RIGHT:
550 if (evt.isAltDown() || !viewport.cursorMode)
552 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
556 alignPanel.getSeqPanel().moveCursor(1, 0);
560 case KeyEvent.VK_SPACE:
561 if (viewport.cursorMode)
563 alignPanel.getSeqPanel().insertGapAtCursor(
564 evt.isControlDown() || evt.isShiftDown()
569 // case KeyEvent.VK_A:
570 // if (viewport.cursorMode)
572 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
573 // //System.out.println("A");
577 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
578 * System.out.println("closing bracket"); } break;
580 case KeyEvent.VK_DELETE:
581 case KeyEvent.VK_BACK_SPACE:
582 if (!viewport.cursorMode)
584 cut_actionPerformed(null);
588 alignPanel.getSeqPanel().deleteGapAtCursor(
589 evt.isControlDown() || evt.isShiftDown()
596 if (viewport.cursorMode)
598 alignPanel.getSeqPanel().setCursorRow();
602 if (viewport.cursorMode && !evt.isControlDown())
604 alignPanel.getSeqPanel().setCursorColumn();
608 if (viewport.cursorMode)
610 alignPanel.getSeqPanel().setCursorPosition();
614 case KeyEvent.VK_ENTER:
615 case KeyEvent.VK_COMMA:
616 if (viewport.cursorMode)
618 alignPanel.getSeqPanel().setCursorRowAndColumn();
623 if (viewport.cursorMode)
625 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
629 if (viewport.cursorMode)
631 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
636 viewport.cursorMode = !viewport.cursorMode;
637 statusBar.setText(MessageManager.formatMessage(
638 "label.keyboard_editing_mode",
639 new String[] { (viewport.cursorMode ? "on" : "off") }));
640 if (viewport.cursorMode)
642 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
643 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
645 alignPanel.getSeqPanel().seqCanvas.repaint();
651 Help.showHelpWindow();
652 } catch (Exception ex)
654 ex.printStackTrace();
659 boolean toggleSeqs = !evt.isControlDown();
660 boolean toggleCols = !evt.isShiftDown();
661 toggleHiddenRegions(toggleSeqs, toggleCols);
664 case KeyEvent.VK_PAGE_UP:
665 if (viewport.getWrapAlignment())
667 alignPanel.scrollUp(true);
671 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
672 - viewport.endSeq + viewport.startSeq);
675 case KeyEvent.VK_PAGE_DOWN:
676 if (viewport.getWrapAlignment())
678 alignPanel.scrollUp(false);
682 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
683 + viewport.endSeq - viewport.startSeq);
690 public void keyReleased(KeyEvent evt)
692 switch (evt.getKeyCode())
694 case KeyEvent.VK_LEFT:
695 if (evt.isAltDown() || !viewport.cursorMode)
697 viewport.firePropertyChange("alignment", null, viewport
698 .getAlignment().getSequences());
702 case KeyEvent.VK_RIGHT:
703 if (evt.isAltDown() || !viewport.cursorMode)
705 viewport.firePropertyChange("alignment", null, viewport
706 .getAlignment().getSequences());
714 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
716 ap.alignFrame = this;
717 avc = new jalview.controller.AlignViewController(this, viewport,
722 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
724 int aSize = alignPanels.size();
726 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
728 if (aSize == 1 && ap.av.viewName == null)
730 this.getContentPane().add(ap, BorderLayout.CENTER);
736 setInitialTabVisible();
739 expandViews.setEnabled(true);
740 gatherViews.setEnabled(true);
741 tabbedPane.addTab(ap.av.viewName, ap);
743 ap.setVisible(false);
748 if (ap.av.isPadGaps())
750 ap.av.getAlignment().padGaps();
752 ap.av.updateConservation(ap);
753 ap.av.updateConsensus(ap);
754 ap.av.updateStrucConsensus(ap);
758 public void setInitialTabVisible()
760 expandViews.setEnabled(true);
761 gatherViews.setEnabled(true);
762 tabbedPane.setVisible(true);
763 AlignmentPanel first = alignPanels.get(0);
764 tabbedPane.addTab(first.av.viewName, first);
765 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
768 public AlignViewport getViewport()
773 /* Set up intrinsic listeners for dynamically generated GUI bits. */
774 private void addServiceListeners()
776 final java.beans.PropertyChangeListener thisListener;
777 Desktop.instance.addJalviewPropertyChangeListener("services",
778 thisListener = new java.beans.PropertyChangeListener()
781 public void propertyChange(PropertyChangeEvent evt)
783 // // System.out.println("Discoverer property change.");
784 // if (evt.getPropertyName().equals("services"))
786 SwingUtilities.invokeLater(new Runnable()
793 .println("Rebuild WS Menu for service change");
794 BuildWebServiceMenu();
801 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
804 public void internalFrameClosed(
805 javax.swing.event.InternalFrameEvent evt)
807 // System.out.println("deregistering discoverer listener");
808 Desktop.instance.removeJalviewPropertyChangeListener("services",
810 closeMenuItem_actionPerformed(true);
813 // Finally, build the menu once to get current service state
814 new Thread(new Runnable()
819 BuildWebServiceMenu();
825 * Configure menu items that vary according to whether the alignment is
826 * nucleotide or protein
830 public void setGUINucleotide(boolean nucleotide)
832 showTranslation.setVisible(nucleotide);
833 showReverse.setVisible(nucleotide);
834 showReverseComplement.setVisible(nucleotide);
835 conservationMenuItem.setEnabled(!nucleotide);
836 modifyConservation.setEnabled(!nucleotide);
837 showGroupConservation.setEnabled(!nucleotide);
838 rnahelicesColour.setEnabled(nucleotide);
839 purinePyrimidineColour.setEnabled(nucleotide);
840 showComplementMenuItem.setText(MessageManager
841 .getString(nucleotide ? "label.protein" : "label.nucleotide"));
842 setColourSelected(jalview.bin.Cache.getDefault(
843 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
844 : Preferences.DEFAULT_COLOUR_PROT, "None"));
848 * set up menus for the current viewport. This may be called after any
849 * operation that affects the data in the current view (selection changed,
850 * etc) to update the menus to reflect the new state.
853 public void setMenusForViewport()
855 setMenusFromViewport(viewport);
859 * Need to call this method when tabs are selected for multiple views, or when
860 * loading from Jalview2XML.java
865 void setMenusFromViewport(AlignViewport av)
867 padGapsMenuitem.setSelected(av.isPadGaps());
868 colourTextMenuItem.setSelected(av.isShowColourText());
869 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
870 conservationMenuItem.setSelected(av.getConservationSelected());
871 seqLimits.setSelected(av.getShowJVSuffix());
872 idRightAlign.setSelected(av.isRightAlignIds());
873 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
874 renderGapsMenuItem.setSelected(av.isRenderGaps());
875 wrapMenuItem.setSelected(av.getWrapAlignment());
876 scaleAbove.setVisible(av.getWrapAlignment());
877 scaleLeft.setVisible(av.getWrapAlignment());
878 scaleRight.setVisible(av.getWrapAlignment());
879 annotationPanelMenuItem.setState(av.isShowAnnotation());
881 * Show/hide annotations only enabled if annotation panel is shown
883 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
884 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
885 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
886 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
887 viewBoxesMenuItem.setSelected(av.getShowBoxes());
888 viewTextMenuItem.setSelected(av.getShowText());
889 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
890 showGroupConsensus.setSelected(av.isShowGroupConsensus());
891 showGroupConservation.setSelected(av.isShowGroupConservation());
892 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
893 showSequenceLogo.setSelected(av.isShowSequenceLogo());
894 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
896 setColourSelected(ColourSchemeProperty.getColourName(av
897 .getGlobalColourScheme()));
899 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
900 hiddenMarkers.setState(av.getShowHiddenMarkers());
901 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
902 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
903 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
904 autoCalculate.setSelected(av.autoCalculateConsensus);
905 sortByTree.setSelected(av.sortByTree);
906 listenToViewSelections.setSelected(av.followSelection);
907 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
909 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
911 showProducts.setEnabled(canShowProducts());
916 private IProgressIndicator progressBar;
921 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
924 public void setProgressBar(String message, long id)
926 progressBar.setProgressBar(message, id);
930 public void registerHandler(final long id,
931 final IProgressIndicatorHandler handler)
933 progressBar.registerHandler(id, handler);
938 * @return true if any progress bars are still active
941 public boolean operationInProgress()
943 return progressBar.operationInProgress();
947 public void setStatus(String text)
949 statusBar.setText(text);
953 * Added so Castor Mapping file can obtain Jalview Version
955 public String getVersion()
957 return jalview.bin.Cache.getProperty("VERSION");
960 public FeatureRenderer getFeatureRenderer()
962 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
966 public void fetchSequence_actionPerformed(ActionEvent e)
968 new jalview.gui.SequenceFetcher(this);
972 public void addFromFile_actionPerformed(ActionEvent e)
974 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
978 public void reload_actionPerformed(ActionEvent e)
980 if (fileName != null)
982 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
983 // originating file's format
984 // TODO: work out how to recover feature settings for correct view(s) when
986 if (currentFileFormat.equals("Jalview"))
988 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
989 for (int i = 0; i < frames.length; i++)
991 if (frames[i] instanceof AlignFrame && frames[i] != this
992 && ((AlignFrame) frames[i]).fileName != null
993 && ((AlignFrame) frames[i]).fileName.equals(fileName))
997 frames[i].setSelected(true);
998 Desktop.instance.closeAssociatedWindows();
999 } catch (java.beans.PropertyVetoException ex)
1005 Desktop.instance.closeAssociatedWindows();
1007 FileLoader loader = new FileLoader();
1008 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1009 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1013 Rectangle bounds = this.getBounds();
1015 FileLoader loader = new FileLoader();
1016 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1017 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1018 protocol, currentFileFormat);
1020 newframe.setBounds(bounds);
1021 if (featureSettings != null && featureSettings.isShowing())
1023 final Rectangle fspos = featureSettings.frame.getBounds();
1024 // TODO: need a 'show feature settings' function that takes bounds -
1025 // need to refactor Desktop.addFrame
1026 newframe.featureSettings_actionPerformed(null);
1027 final FeatureSettings nfs = newframe.featureSettings;
1028 SwingUtilities.invokeLater(new Runnable()
1033 nfs.frame.setBounds(fspos);
1036 this.featureSettings.close();
1037 this.featureSettings = null;
1039 this.closeMenuItem_actionPerformed(true);
1045 public void addFromText_actionPerformed(ActionEvent e)
1047 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1052 public void addFromURL_actionPerformed(ActionEvent e)
1054 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1058 public void save_actionPerformed(ActionEvent e)
1060 if (fileName == null
1061 || (currentFileFormat == null || !jalview.io.FormatAdapter
1062 .isValidIOFormat(currentFileFormat, true))
1063 || fileName.startsWith("http"))
1065 saveAs_actionPerformed(null);
1069 saveAlignment(fileName, currentFileFormat);
1080 public void saveAs_actionPerformed(ActionEvent e)
1082 JalviewFileChooser chooser = new JalviewFileChooser(
1083 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1084 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1085 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1086 currentFileFormat, false);
1088 chooser.setFileView(new JalviewFileView());
1089 chooser.setDialogTitle(MessageManager
1090 .getString("label.save_alignment_to_file"));
1091 chooser.setToolTipText(MessageManager.getString("action.save"));
1093 int value = chooser.showSaveDialog(this);
1095 if (value == JalviewFileChooser.APPROVE_OPTION)
1097 currentFileFormat = chooser.getSelectedFormat();
1098 while (currentFileFormat == null)
1101 .showInternalMessageDialog(
1104 .getString("label.select_file_format_before_saving"),
1106 .getString("label.file_format_not_specified"),
1107 JOptionPane.WARNING_MESSAGE);
1108 currentFileFormat = chooser.getSelectedFormat();
1109 value = chooser.showSaveDialog(this);
1110 if (value != JalviewFileChooser.APPROVE_OPTION)
1116 fileName = chooser.getSelectedFile().getPath();
1118 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1121 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1122 if (currentFileFormat.indexOf(" ") > -1)
1124 currentFileFormat = currentFileFormat.substring(0,
1125 currentFileFormat.indexOf(" "));
1127 saveAlignment(fileName, currentFileFormat);
1131 public boolean saveAlignment(String file, String format)
1133 boolean success = true;
1135 if (format.equalsIgnoreCase("Jalview"))
1137 String shortName = title;
1139 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1141 shortName = shortName.substring(shortName
1142 .lastIndexOf(java.io.File.separatorChar) + 1);
1145 success = new Jalview2XML().saveAlignment(this, file, shortName);
1147 statusBar.setText(MessageManager.formatMessage(
1148 "label.successfully_saved_to_file_in_format", new Object[] {
1149 fileName, format }));
1154 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1156 warningMessage("Cannot save file " + fileName + " using format "
1157 + format, "Alignment output format not supported");
1158 if (!Jalview.isHeadlessMode())
1160 saveAs_actionPerformed(null);
1165 AlignmentExportData exportData = getAlignmentForExport(format,
1167 if (exportData.getSettings().isCancelled())
1171 FormatAdapter f = new FormatAdapter(alignPanel,
1172 exportData.getSettings());
1173 String output = f.formatSequences(
1175 exportData.getAlignment(), // class cast exceptions will
1176 // occur in the distant future
1177 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1178 f.getCacheSuffixDefault(format),
1179 viewport.getColumnSelection());
1189 java.io.PrintWriter out = new java.io.PrintWriter(
1190 new java.io.FileWriter(file));
1194 this.setTitle(file);
1195 statusBar.setText(MessageManager.formatMessage(
1196 "label.successfully_saved_to_file_in_format",
1197 new Object[] { fileName, format }));
1198 } catch (Exception ex)
1201 ex.printStackTrace();
1208 JOptionPane.showInternalMessageDialog(this, MessageManager
1209 .formatMessage("label.couldnt_save_file",
1210 new Object[] { fileName }), MessageManager
1211 .getString("label.error_saving_file"),
1212 JOptionPane.WARNING_MESSAGE);
1218 private void warningMessage(String warning, String title)
1220 if (new jalview.util.Platform().isHeadless())
1222 System.err.println("Warning: " + title + "\nWarning: " + warning);
1227 JOptionPane.showInternalMessageDialog(this, warning, title,
1228 JOptionPane.WARNING_MESSAGE);
1240 protected void outputText_actionPerformed(ActionEvent e)
1243 AlignmentExportData exportData = getAlignmentForExport(
1244 e.getActionCommand(), viewport, null);
1245 if (exportData.getSettings().isCancelled())
1249 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1250 cap.setForInput(null);
1253 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1254 .formatSequences(e.getActionCommand(),
1255 exportData.getAlignment(),
1256 exportData.getOmitHidden(),
1257 exportData.getStartEndPostions(),
1258 viewport.getColumnSelection()));
1259 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1260 "label.alignment_output_command",
1261 new Object[] { e.getActionCommand() }), 600, 500);
1262 } catch (OutOfMemoryError oom)
1264 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1270 public static AlignmentExportData getAlignmentForExport(
1271 String exportFormat, AlignViewportI viewport,
1272 AlignExportSettingI exportSettings)
1274 AlignmentI alignmentToExport = null;
1275 AlignExportSettingI settings = exportSettings;
1276 String[] omitHidden = null;
1277 int[] alignmentStartEnd = new int[2];
1279 HiddenSequences hiddenSeqs = viewport.getAlignment()
1280 .getHiddenSequences();
1282 alignmentToExport = viewport.getAlignment();
1283 alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
1285 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1286 if (settings == null)
1288 settings = new AlignExportSettings(hasHiddenSeqs,
1289 viewport.hasHiddenColumns(), exportFormat);
1291 // settings.isExportAnnotations();
1293 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1295 omitHidden = viewport.getViewAsString(false);
1298 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1300 alignmentToExport = hiddenSeqs.getFullAlignment();
1304 alignmentToExport = viewport.getAlignment();
1305 alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
1306 .getColumnSelection().getHiddenColumns());
1308 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1309 omitHidden, alignmentStartEnd, settings);
1313 public static int[] getStartEnd(int[] aligmentStartEnd,
1314 List<int[]> hiddenCols)
1316 int startPos = aligmentStartEnd[0];
1317 int endPos = aligmentStartEnd[1];
1319 int[] lowestRange = new int[] { -1, -1 };
1320 int[] higestRange = new int[] { -1, -1 };
1322 for (int[] hiddenCol : hiddenCols)
1324 lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1325 higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1328 if (lowestRange[0] == -1 && lowestRange[1] == -1)
1330 startPos = aligmentStartEnd[0];
1334 startPos = lowestRange[1] + 1;
1337 if (higestRange[0] == -1 && higestRange[1] == -1)
1339 endPos = aligmentStartEnd[1];
1343 endPos = higestRange[0] - 1;
1346 // System.out.println("Export range : " + startPos + " - " + endPos);
1347 return new int[] { startPos, endPos };
1350 public static void main(String[] args)
1352 ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1353 hiddenCols.add(new int[] { 0, 0 });
1354 hiddenCols.add(new int[] { 6, 9 });
1355 hiddenCols.add(new int[] { 11, 12 });
1356 hiddenCols.add(new int[] { 33, 33 });
1357 hiddenCols.add(new int[] { 50, 50 });
1359 int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
1360 // System.out.println("Export range : " + x[0] + " - " + x[1]);
1370 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1372 new HtmlSvgOutput(null, alignPanel);
1376 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1378 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1379 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1382 public void createImageMap(File file, String image)
1384 alignPanel.makePNGImageMap(file, image);
1394 public void createPNG(File f)
1396 alignPanel.makePNG(f);
1406 public void createEPS(File f)
1408 alignPanel.makeEPS(f);
1412 public void createSVG(File f)
1414 alignPanel.makeSVG(f);
1418 public void pageSetup_actionPerformed(ActionEvent e)
1420 PrinterJob printJob = PrinterJob.getPrinterJob();
1421 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1431 public void printMenuItem_actionPerformed(ActionEvent e)
1433 // Putting in a thread avoids Swing painting problems
1434 PrintThread thread = new PrintThread(alignPanel);
1439 public void exportFeatures_actionPerformed(ActionEvent e)
1441 new AnnotationExporter().exportFeatures(alignPanel);
1445 public void exportAnnotations_actionPerformed(ActionEvent e)
1447 new AnnotationExporter().exportAnnotations(alignPanel);
1451 public void associatedData_actionPerformed(ActionEvent e)
1453 // Pick the tree file
1454 JalviewFileChooser chooser = new JalviewFileChooser(
1455 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1456 chooser.setFileView(new JalviewFileView());
1457 chooser.setDialogTitle(MessageManager
1458 .getString("label.load_jalview_annotations"));
1459 chooser.setToolTipText(MessageManager
1460 .getString("label.load_jalview_annotations"));
1462 int value = chooser.showOpenDialog(null);
1464 if (value == JalviewFileChooser.APPROVE_OPTION)
1466 String choice = chooser.getSelectedFile().getPath();
1467 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1468 loadJalviewDataFile(choice, null, null, null);
1474 * Close the current view or all views in the alignment frame. If the frame
1475 * only contains one view then the alignment will be removed from memory.
1477 * @param closeAllTabs
1480 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1482 if (alignPanels != null && alignPanels.size() < 2)
1484 closeAllTabs = true;
1489 if (alignPanels != null)
1493 if (this.isClosed())
1495 // really close all the windows - otherwise wait till
1496 // setClosed(true) is called
1497 for (int i = 0; i < alignPanels.size(); i++)
1499 AlignmentPanel ap = alignPanels.get(i);
1506 closeView(alignPanel);
1513 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1514 * be called recursively, with the frame now in 'closed' state
1516 this.setClosed(true);
1518 } catch (Exception ex)
1520 ex.printStackTrace();
1525 * Close the specified panel and close up tabs appropriately.
1527 * @param panelToClose
1529 public void closeView(AlignmentPanel panelToClose)
1531 int index = tabbedPane.getSelectedIndex();
1532 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1533 alignPanels.remove(panelToClose);
1534 panelToClose.closePanel();
1535 panelToClose = null;
1537 tabbedPane.removeTabAt(closedindex);
1538 tabbedPane.validate();
1540 if (index > closedindex || index == tabbedPane.getTabCount())
1542 // modify currently selected tab index if necessary.
1546 this.tabSelectionChanged(index);
1552 void updateEditMenuBar()
1555 if (viewport.getHistoryList().size() > 0)
1557 undoMenuItem.setEnabled(true);
1558 CommandI command = viewport.getHistoryList().peek();
1559 undoMenuItem.setText(MessageManager.formatMessage(
1560 "label.undo_command",
1561 new Object[] { command.getDescription() }));
1565 undoMenuItem.setEnabled(false);
1566 undoMenuItem.setText(MessageManager.getString("action.undo"));
1569 if (viewport.getRedoList().size() > 0)
1571 redoMenuItem.setEnabled(true);
1573 CommandI command = viewport.getRedoList().peek();
1574 redoMenuItem.setText(MessageManager.formatMessage(
1575 "label.redo_command",
1576 new Object[] { command.getDescription() }));
1580 redoMenuItem.setEnabled(false);
1581 redoMenuItem.setText(MessageManager.getString("action.redo"));
1586 public void addHistoryItem(CommandI command)
1588 if (command.getSize() > 0)
1590 viewport.addToHistoryList(command);
1591 viewport.clearRedoList();
1592 updateEditMenuBar();
1593 viewport.updateHiddenColumns();
1594 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1595 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1596 // viewport.getColumnSelection()
1597 // .getHiddenColumns().size() > 0);
1603 * @return alignment objects for all views
1605 AlignmentI[] getViewAlignments()
1607 if (alignPanels != null)
1609 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1611 for (AlignmentPanel ap : alignPanels)
1613 als[i++] = ap.av.getAlignment();
1617 if (viewport != null)
1619 return new AlignmentI[] { viewport.getAlignment() };
1631 protected void undoMenuItem_actionPerformed(ActionEvent e)
1633 if (viewport.getHistoryList().isEmpty())
1637 CommandI command = viewport.getHistoryList().pop();
1638 viewport.addToRedoList(command);
1639 command.undoCommand(getViewAlignments());
1641 AlignmentViewport originalSource = getOriginatingSource(command);
1642 updateEditMenuBar();
1644 if (originalSource != null)
1646 if (originalSource != viewport)
1649 .warn("Implementation worry: mismatch of viewport origin for undo");
1651 originalSource.updateHiddenColumns();
1652 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1654 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1655 // viewport.getColumnSelection()
1656 // .getHiddenColumns().size() > 0);
1657 originalSource.firePropertyChange("alignment", null, originalSource
1658 .getAlignment().getSequences());
1669 protected void redoMenuItem_actionPerformed(ActionEvent e)
1671 if (viewport.getRedoList().size() < 1)
1676 CommandI command = viewport.getRedoList().pop();
1677 viewport.addToHistoryList(command);
1678 command.doCommand(getViewAlignments());
1680 AlignmentViewport originalSource = getOriginatingSource(command);
1681 updateEditMenuBar();
1683 if (originalSource != null)
1686 if (originalSource != viewport)
1689 .warn("Implementation worry: mismatch of viewport origin for redo");
1691 originalSource.updateHiddenColumns();
1692 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1694 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1695 // viewport.getColumnSelection()
1696 // .getHiddenColumns().size() > 0);
1697 originalSource.firePropertyChange("alignment", null, originalSource
1698 .getAlignment().getSequences());
1702 AlignmentViewport getOriginatingSource(CommandI command)
1704 AlignmentViewport originalSource = null;
1705 // For sequence removal and addition, we need to fire
1706 // the property change event FROM the viewport where the
1707 // original alignment was altered
1708 AlignmentI al = null;
1709 if (command instanceof EditCommand)
1711 EditCommand editCommand = (EditCommand) command;
1712 al = editCommand.getAlignment();
1713 List<Component> comps = PaintRefresher.components.get(viewport
1714 .getSequenceSetId());
1716 for (Component comp : comps)
1718 if (comp instanceof AlignmentPanel)
1720 if (al == ((AlignmentPanel) comp).av.getAlignment())
1722 originalSource = ((AlignmentPanel) comp).av;
1729 if (originalSource == null)
1731 // The original view is closed, we must validate
1732 // the current view against the closed view first
1735 PaintRefresher.validateSequences(al, viewport.getAlignment());
1738 originalSource = viewport;
1741 return originalSource;
1750 public void moveSelectedSequences(boolean up)
1752 SequenceGroup sg = viewport.getSelectionGroup();
1758 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1759 viewport.getHiddenRepSequences(), up);
1760 alignPanel.paintAlignment(true);
1763 synchronized void slideSequences(boolean right, int size)
1765 List<SequenceI> sg = new ArrayList<SequenceI>();
1766 if (viewport.cursorMode)
1768 sg.add(viewport.getAlignment().getSequenceAt(
1769 alignPanel.getSeqPanel().seqCanvas.cursorY));
1771 else if (viewport.getSelectionGroup() != null
1772 && viewport.getSelectionGroup().getSize() != viewport
1773 .getAlignment().getHeight())
1775 sg = viewport.getSelectionGroup().getSequences(
1776 viewport.getHiddenRepSequences());
1784 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1786 for (SequenceI seq : viewport.getAlignment().getSequences())
1788 if (!sg.contains(seq))
1790 invertGroup.add(seq);
1794 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1796 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1797 for (int i = 0; i < invertGroup.size(); i++)
1799 seqs2[i] = invertGroup.get(i);
1802 SlideSequencesCommand ssc;
1805 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1806 size, viewport.getGapCharacter());
1810 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1811 size, viewport.getGapCharacter());
1814 int groupAdjustment = 0;
1815 if (ssc.getGapsInsertedBegin() && right)
1817 if (viewport.cursorMode)
1819 alignPanel.getSeqPanel().moveCursor(size, 0);
1823 groupAdjustment = size;
1826 else if (!ssc.getGapsInsertedBegin() && !right)
1828 if (viewport.cursorMode)
1830 alignPanel.getSeqPanel().moveCursor(-size, 0);
1834 groupAdjustment = -size;
1838 if (groupAdjustment != 0)
1840 viewport.getSelectionGroup().setStartRes(
1841 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1842 viewport.getSelectionGroup().setEndRes(
1843 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1847 * just extend the last slide command if compatible; but not if in
1848 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1850 boolean appendHistoryItem = false;
1851 Deque<CommandI> historyList = viewport.getHistoryList();
1852 boolean inSplitFrame = getSplitViewContainer() != null;
1853 if (!inSplitFrame && historyList != null && historyList.size() > 0
1854 && historyList.peek() instanceof SlideSequencesCommand)
1856 appendHistoryItem = ssc
1857 .appendSlideCommand((SlideSequencesCommand) historyList
1861 if (!appendHistoryItem)
1863 addHistoryItem(ssc);
1876 protected void copy_actionPerformed(ActionEvent e)
1879 if (viewport.getSelectionGroup() == null)
1883 // TODO: preserve the ordering of displayed alignment annotation in any
1884 // internal paste (particularly sequence associated annotation)
1885 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1886 String[] omitHidden = null;
1888 if (viewport.hasHiddenColumns())
1890 omitHidden = viewport.getViewAsString(true);
1893 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1896 StringSelection ss = new StringSelection(output);
1900 jalview.gui.Desktop.internalCopy = true;
1901 // Its really worth setting the clipboard contents
1902 // to empty before setting the large StringSelection!!
1903 Toolkit.getDefaultToolkit().getSystemClipboard()
1904 .setContents(new StringSelection(""), null);
1906 Toolkit.getDefaultToolkit().getSystemClipboard()
1907 .setContents(ss, Desktop.instance);
1908 } catch (OutOfMemoryError er)
1910 new OOMWarning("copying region", er);
1914 ArrayList<int[]> hiddenColumns = null;
1915 if (viewport.hasHiddenColumns())
1917 hiddenColumns = new ArrayList<int[]>();
1918 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1919 .getSelectionGroup().getEndRes();
1920 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1922 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1924 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1925 region[1] - hiddenOffset });
1930 Desktop.jalviewClipboard = new Object[] { seqs,
1931 viewport.getAlignment().getDataset(), hiddenColumns };
1932 statusBar.setText(MessageManager.formatMessage(
1933 "label.copied_sequences_to_clipboard", new Object[] { Integer
1934 .valueOf(seqs.length).toString() }));
1944 protected void pasteNew_actionPerformed(ActionEvent e)
1956 protected void pasteThis_actionPerformed(ActionEvent e)
1962 * Paste contents of Jalview clipboard
1964 * @param newAlignment
1965 * true to paste to a new alignment, otherwise add to this.
1967 void paste(boolean newAlignment)
1969 boolean externalPaste = true;
1972 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1973 Transferable contents = c.getContents(this);
1975 if (contents == null)
1983 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1984 if (str.length() < 1)
1989 format = new IdentifyFile().identify(str, "Paste");
1991 } catch (OutOfMemoryError er)
1993 new OOMWarning("Out of memory pasting sequences!!", er);
1997 SequenceI[] sequences;
1998 boolean annotationAdded = false;
1999 AlignmentI alignment = null;
2001 if (Desktop.jalviewClipboard != null)
2003 // The clipboard was filled from within Jalview, we must use the
2005 // And dataset from the copied alignment
2006 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2007 // be doubly sure that we create *new* sequence objects.
2008 sequences = new SequenceI[newseq.length];
2009 for (int i = 0; i < newseq.length; i++)
2011 sequences[i] = new Sequence(newseq[i]);
2013 alignment = new Alignment(sequences);
2014 externalPaste = false;
2018 // parse the clipboard as an alignment.
2019 alignment = new FormatAdapter().readFile(str, "Paste", format);
2020 sequences = alignment.getSequencesArray();
2024 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2030 if (Desktop.jalviewClipboard != null)
2032 // dataset is inherited
2033 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2037 // new dataset is constructed
2038 alignment.setDataset(null);
2040 alwidth = alignment.getWidth() + 1;
2044 AlignmentI pastedal = alignment; // preserve pasted alignment object
2045 // Add pasted sequences and dataset into existing alignment.
2046 alignment = viewport.getAlignment();
2047 alwidth = alignment.getWidth() + 1;
2048 // decide if we need to import sequences from an existing dataset
2049 boolean importDs = Desktop.jalviewClipboard != null
2050 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2051 // importDs==true instructs us to copy over new dataset sequences from
2052 // an existing alignment
2053 Vector newDs = (importDs) ? new Vector() : null; // used to create
2054 // minimum dataset set
2056 for (int i = 0; i < sequences.length; i++)
2060 newDs.addElement(null);
2062 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2064 if (importDs && ds != null)
2066 if (!newDs.contains(ds))
2068 newDs.setElementAt(ds, i);
2069 ds = new Sequence(ds);
2070 // update with new dataset sequence
2071 sequences[i].setDatasetSequence(ds);
2075 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2080 // copy and derive new dataset sequence
2081 sequences[i] = sequences[i].deriveSequence();
2082 alignment.getDataset().addSequence(
2083 sequences[i].getDatasetSequence());
2084 // TODO: avoid creation of duplicate dataset sequences with a
2085 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2087 alignment.addSequence(sequences[i]); // merges dataset
2091 newDs.clear(); // tidy up
2093 if (alignment.getAlignmentAnnotation() != null)
2095 for (AlignmentAnnotation alan : alignment
2096 .getAlignmentAnnotation())
2098 if (alan.graphGroup > fgroup)
2100 fgroup = alan.graphGroup;
2104 if (pastedal.getAlignmentAnnotation() != null)
2106 // Add any annotation attached to alignment.
2107 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2108 for (int i = 0; i < alann.length; i++)
2110 annotationAdded = true;
2111 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2113 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2114 if (newann.graphGroup > -1)
2116 if (newGraphGroups.size() <= newann.graphGroup
2117 || newGraphGroups.get(newann.graphGroup) == null)
2119 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2121 newGraphGroups.add(q, null);
2123 newGraphGroups.set(newann.graphGroup, new Integer(
2126 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2130 newann.padAnnotation(alwidth);
2131 alignment.addAnnotation(newann);
2141 addHistoryItem(new EditCommand(
2142 MessageManager.getString("label.add_sequences"),
2143 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2145 // Add any annotations attached to sequences
2146 for (int i = 0; i < sequences.length; i++)
2148 if (sequences[i].getAnnotation() != null)
2150 AlignmentAnnotation newann;
2151 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2153 annotationAdded = true;
2154 newann = sequences[i].getAnnotation()[a];
2155 newann.adjustForAlignment();
2156 newann.padAnnotation(alwidth);
2157 if (newann.graphGroup > -1)
2159 if (newann.graphGroup > -1)
2161 if (newGraphGroups.size() <= newann.graphGroup
2162 || newGraphGroups.get(newann.graphGroup) == null)
2164 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2166 newGraphGroups.add(q, null);
2168 newGraphGroups.set(newann.graphGroup, new Integer(
2171 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2175 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2180 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2187 // propagate alignment changed.
2188 viewport.setEndSeq(alignment.getHeight());
2189 if (annotationAdded)
2191 // Duplicate sequence annotation in all views.
2192 AlignmentI[] alview = this.getViewAlignments();
2193 for (int i = 0; i < sequences.length; i++)
2195 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2200 for (int avnum = 0; avnum < alview.length; avnum++)
2202 if (alview[avnum] != alignment)
2204 // duplicate in a view other than the one with input focus
2205 int avwidth = alview[avnum].getWidth() + 1;
2206 // this relies on sann being preserved after we
2207 // modify the sequence's annotation array for each duplication
2208 for (int a = 0; a < sann.length; a++)
2210 AlignmentAnnotation newann = new AlignmentAnnotation(
2212 sequences[i].addAlignmentAnnotation(newann);
2213 newann.padAnnotation(avwidth);
2214 alview[avnum].addAnnotation(newann); // annotation was
2215 // duplicated earlier
2216 // TODO JAL-1145 graphGroups are not updated for sequence
2217 // annotation added to several views. This may cause
2219 alview[avnum].setAnnotationIndex(newann, a);
2224 buildSortByAnnotationScoresMenu();
2226 viewport.firePropertyChange("alignment", null,
2227 alignment.getSequences());
2228 if (alignPanels != null)
2230 for (AlignmentPanel ap : alignPanels)
2232 ap.validateAnnotationDimensions(false);
2237 alignPanel.validateAnnotationDimensions(false);
2243 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2245 String newtitle = new String("Copied sequences");
2247 if (Desktop.jalviewClipboard != null
2248 && Desktop.jalviewClipboard[2] != null)
2250 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2251 for (int[] region : hc)
2253 af.viewport.hideColumns(region[0], region[1]);
2257 // >>>This is a fix for the moment, until a better solution is
2259 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2261 alignPanel.getSeqPanel().seqCanvas
2262 .getFeatureRenderer());
2264 // TODO: maintain provenance of an alignment, rather than just make the
2265 // title a concatenation of operations.
2268 if (title.startsWith("Copied sequences"))
2274 newtitle = newtitle.concat("- from " + title);
2279 newtitle = new String("Pasted sequences");
2282 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2287 } catch (Exception ex)
2289 ex.printStackTrace();
2290 System.out.println("Exception whilst pasting: " + ex);
2291 // could be anything being pasted in here
2297 protected void expand_newalign(ActionEvent e)
2301 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2302 .getAlignment(), -1);
2303 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2305 String newtitle = new String("Flanking alignment");
2307 if (Desktop.jalviewClipboard != null
2308 && Desktop.jalviewClipboard[2] != null)
2310 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2311 for (int region[] : hc)
2313 af.viewport.hideColumns(region[0], region[1]);
2317 // >>>This is a fix for the moment, until a better solution is
2319 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2321 alignPanel.getSeqPanel().seqCanvas
2322 .getFeatureRenderer());
2324 // TODO: maintain provenance of an alignment, rather than just make the
2325 // title a concatenation of operations.
2327 if (title.startsWith("Copied sequences"))
2333 newtitle = newtitle.concat("- from " + title);
2337 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2339 } catch (Exception ex)
2341 ex.printStackTrace();
2342 System.out.println("Exception whilst pasting: " + ex);
2343 // could be anything being pasted in here
2344 } catch (OutOfMemoryError oom)
2346 new OOMWarning("Viewing flanking region of alignment", oom);
2357 protected void cut_actionPerformed(ActionEvent e)
2359 copy_actionPerformed(null);
2360 delete_actionPerformed(null);
2370 protected void delete_actionPerformed(ActionEvent evt)
2373 SequenceGroup sg = viewport.getSelectionGroup();
2380 * If the cut affects all sequences, warn, remove highlighted columns
2382 if (sg.getSize() == viewport.getAlignment().getHeight())
2384 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2385 .getAlignment().getWidth()) ? true : false;
2386 if (isEntireAlignWidth)
2388 int confirm = JOptionPane.showConfirmDialog(this,
2389 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2390 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2391 JOptionPane.OK_CANCEL_OPTION);
2393 if (confirm == JOptionPane.CANCEL_OPTION
2394 || confirm == JOptionPane.CLOSED_OPTION)
2399 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2400 sg.getEndRes() + 1);
2402 SequenceI[] cut = sg.getSequences()
2403 .toArray(new SequenceI[sg.getSize()]);
2405 addHistoryItem(new EditCommand(
2406 MessageManager.getString("label.cut_sequences"), Action.CUT,
2407 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2408 viewport.getAlignment()));
2410 viewport.setSelectionGroup(null);
2411 viewport.sendSelection();
2412 viewport.getAlignment().deleteGroup(sg);
2414 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2416 if (viewport.getAlignment().getHeight() < 1)
2420 this.setClosed(true);
2421 } catch (Exception ex)
2434 protected void deleteGroups_actionPerformed(ActionEvent e)
2436 if (avc.deleteGroups())
2438 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2439 alignPanel.updateAnnotation();
2440 alignPanel.paintAlignment(true);
2451 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2453 SequenceGroup sg = new SequenceGroup();
2455 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2457 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2460 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2461 viewport.setSelectionGroup(sg);
2462 viewport.sendSelection();
2463 alignPanel.paintAlignment(true);
2464 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2474 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2476 if (viewport.cursorMode)
2478 alignPanel.getSeqPanel().keyboardNo1 = null;
2479 alignPanel.getSeqPanel().keyboardNo2 = null;
2481 viewport.setSelectionGroup(null);
2482 viewport.getColumnSelection().clear();
2483 viewport.setSelectionGroup(null);
2484 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2485 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2486 alignPanel.paintAlignment(true);
2487 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2488 viewport.sendSelection();
2498 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2500 SequenceGroup sg = viewport.getSelectionGroup();
2504 selectAllSequenceMenuItem_actionPerformed(null);
2509 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2511 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2514 alignPanel.paintAlignment(true);
2515 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2516 viewport.sendSelection();
2520 public void invertColSel_actionPerformed(ActionEvent e)
2522 viewport.invertColumnSelection();
2523 alignPanel.paintAlignment(true);
2524 viewport.sendSelection();
2534 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2536 trimAlignment(true);
2546 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2548 trimAlignment(false);
2551 void trimAlignment(boolean trimLeft)
2553 ColumnSelection colSel = viewport.getColumnSelection();
2556 if (!colSel.isEmpty())
2560 column = colSel.getMin();
2564 column = colSel.getMax();
2568 if (viewport.getSelectionGroup() != null)
2570 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2571 viewport.getHiddenRepSequences());
2575 seqs = viewport.getAlignment().getSequencesArray();
2578 TrimRegionCommand trimRegion;
2581 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2582 column, viewport.getAlignment());
2583 viewport.setStartRes(0);
2587 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2588 column, viewport.getAlignment());
2591 statusBar.setText(MessageManager.formatMessage(
2592 "label.removed_columns",
2593 new String[] { Integer.valueOf(trimRegion.getSize())
2596 addHistoryItem(trimRegion);
2598 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2600 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2601 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2603 viewport.getAlignment().deleteGroup(sg);
2607 viewport.firePropertyChange("alignment", null, viewport
2608 .getAlignment().getSequences());
2619 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2621 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2624 if (viewport.getSelectionGroup() != null)
2626 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2627 viewport.getHiddenRepSequences());
2628 start = viewport.getSelectionGroup().getStartRes();
2629 end = viewport.getSelectionGroup().getEndRes();
2633 seqs = viewport.getAlignment().getSequencesArray();
2636 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2637 "Remove Gapped Columns", seqs, start, end,
2638 viewport.getAlignment());
2640 addHistoryItem(removeGapCols);
2642 statusBar.setText(MessageManager.formatMessage(
2643 "label.removed_empty_columns",
2644 new Object[] { Integer.valueOf(removeGapCols.getSize())
2647 // This is to maintain viewport position on first residue
2648 // of first sequence
2649 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2650 int startRes = seq.findPosition(viewport.startRes);
2651 // ShiftList shifts;
2652 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2653 // edit.alColumnChanges=shifts.getInverse();
2654 // if (viewport.hasHiddenColumns)
2655 // viewport.getColumnSelection().compensateForEdits(shifts);
2656 viewport.setStartRes(seq.findIndex(startRes) - 1);
2657 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2669 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2671 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2674 if (viewport.getSelectionGroup() != null)
2676 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2677 viewport.getHiddenRepSequences());
2678 start = viewport.getSelectionGroup().getStartRes();
2679 end = viewport.getSelectionGroup().getEndRes();
2683 seqs = viewport.getAlignment().getSequencesArray();
2686 // This is to maintain viewport position on first residue
2687 // of first sequence
2688 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2689 int startRes = seq.findPosition(viewport.startRes);
2691 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2692 viewport.getAlignment()));
2694 viewport.setStartRes(seq.findIndex(startRes) - 1);
2696 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2708 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2710 viewport.setPadGaps(padGapsMenuitem.isSelected());
2711 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2722 public void findMenuItem_actionPerformed(ActionEvent e)
2728 * Create a new view of the current alignment.
2731 public void newView_actionPerformed(ActionEvent e)
2733 newView(null, true);
2737 * Creates and shows a new view of the current alignment.
2740 * title of newly created view; if null, one will be generated
2741 * @param copyAnnotation
2742 * if true then duplicate all annnotation, groups and settings
2743 * @return new alignment panel, already displayed.
2745 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2748 * Create a new AlignmentPanel (with its own, new Viewport)
2750 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2752 if (!copyAnnotation)
2755 * remove all groups and annotation except for the automatic stuff
2757 newap.av.getAlignment().deleteAllGroups();
2758 newap.av.getAlignment().deleteAllAnnotations(false);
2761 newap.av.setGatherViewsHere(false);
2763 if (viewport.viewName == null)
2765 viewport.viewName = MessageManager
2766 .getString("label.view_name_original");
2770 * Views share the same edits undo and redo stacks
2772 newap.av.setHistoryList(viewport.getHistoryList());
2773 newap.av.setRedoList(viewport.getRedoList());
2776 * Views share the same mappings; need to deregister any new mappings
2777 * created by copyAlignPanel, and register the new reference to the shared
2780 newap.av.replaceMappings(viewport.getAlignment());
2782 newap.av.viewName = getNewViewName(viewTitle);
2784 addAlignmentPanel(newap, true);
2785 newap.alignmentChanged();
2787 if (alignPanels.size() == 2)
2789 viewport.setGatherViewsHere(true);
2791 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2796 * Make a new name for the view, ensuring it is unique within the current
2797 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2798 * these now use viewId. Unique view names are still desirable for usability.)
2803 protected String getNewViewName(String viewTitle)
2805 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2806 boolean addFirstIndex = false;
2807 if (viewTitle == null || viewTitle.trim().length() == 0)
2809 viewTitle = MessageManager.getString("action.view");
2810 addFirstIndex = true;
2814 index = 1;// we count from 1 if given a specific name
2816 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2818 List<Component> comps = PaintRefresher.components.get(viewport
2819 .getSequenceSetId());
2821 List<String> existingNames = getExistingViewNames(comps);
2823 while (existingNames.contains(newViewName))
2825 newViewName = viewTitle + " " + (++index);
2831 * Returns a list of distinct view names found in the given list of
2832 * components. View names are held on the viewport of an AlignmentPanel.
2837 protected List<String> getExistingViewNames(List<Component> comps)
2839 List<String> existingNames = new ArrayList<String>();
2840 for (Component comp : comps)
2842 if (comp instanceof AlignmentPanel)
2844 AlignmentPanel ap = (AlignmentPanel) comp;
2845 if (!existingNames.contains(ap.av.viewName))
2847 existingNames.add(ap.av.viewName);
2851 return existingNames;
2855 * Explode tabbed views into separate windows.
2858 public void expandViews_actionPerformed(ActionEvent e)
2860 Desktop.instance.explodeViews(this);
2864 * Gather views in separate windows back into a tabbed presentation.
2867 public void gatherViews_actionPerformed(ActionEvent e)
2869 Desktop.instance.gatherViews(this);
2879 public void font_actionPerformed(ActionEvent e)
2881 new FontChooser(alignPanel);
2891 protected void seqLimit_actionPerformed(ActionEvent e)
2893 viewport.setShowJVSuffix(seqLimits.isSelected());
2895 alignPanel.getIdPanel().getIdCanvas()
2896 .setPreferredSize(alignPanel.calculateIdWidth());
2897 alignPanel.paintAlignment(true);
2901 public void idRightAlign_actionPerformed(ActionEvent e)
2903 viewport.setRightAlignIds(idRightAlign.isSelected());
2904 alignPanel.paintAlignment(true);
2908 public void centreColumnLabels_actionPerformed(ActionEvent e)
2910 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2911 alignPanel.paintAlignment(true);
2917 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2920 protected void followHighlight_actionPerformed()
2923 * Set the 'follow' flag on the Viewport (and scroll to position if now
2926 final boolean state = this.followHighlightMenuItem.getState();
2927 viewport.setFollowHighlight(state);
2930 alignPanel.scrollToPosition(
2931 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2942 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2944 viewport.setColourText(colourTextMenuItem.isSelected());
2945 alignPanel.paintAlignment(true);
2955 public void wrapMenuItem_actionPerformed(ActionEvent e)
2957 scaleAbove.setVisible(wrapMenuItem.isSelected());
2958 scaleLeft.setVisible(wrapMenuItem.isSelected());
2959 scaleRight.setVisible(wrapMenuItem.isSelected());
2960 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2961 alignPanel.updateLayout();
2965 public void showAllSeqs_actionPerformed(ActionEvent e)
2967 viewport.showAllHiddenSeqs();
2971 public void showAllColumns_actionPerformed(ActionEvent e)
2973 viewport.showAllHiddenColumns();
2975 viewport.sendSelection();
2979 public void hideSelSequences_actionPerformed(ActionEvent e)
2981 viewport.hideAllSelectedSeqs();
2982 // alignPanel.paintAlignment(true);
2986 * called by key handler and the hide all/show all menu items
2991 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2994 boolean hide = false;
2995 SequenceGroup sg = viewport.getSelectionGroup();
2996 if (!toggleSeqs && !toggleCols)
2998 // Hide everything by the current selection - this is a hack - we do the
2999 // invert and then hide
3000 // first check that there will be visible columns after the invert.
3001 if ((viewport.getColumnSelection() != null
3002 && viewport.getColumnSelection().getSelected() != null && viewport
3003 .getColumnSelection().getSelected().size() > 0)
3004 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3007 // now invert the sequence set, if required - empty selection implies
3008 // that no hiding is required.
3011 invertSequenceMenuItem_actionPerformed(null);
3012 sg = viewport.getSelectionGroup();
3016 viewport.expandColSelection(sg, true);
3017 // finally invert the column selection and get the new sequence
3019 invertColSel_actionPerformed(null);
3026 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3028 hideSelSequences_actionPerformed(null);
3031 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3034 showAllSeqs_actionPerformed(null);
3040 if (viewport.getColumnSelection().getSelected().size() > 0)
3042 hideSelColumns_actionPerformed(null);
3045 viewport.setSelectionGroup(sg);
3050 showAllColumns_actionPerformed(null);
3059 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3060 * event.ActionEvent)
3063 public void hideAllButSelection_actionPerformed(ActionEvent e)
3065 toggleHiddenRegions(false, false);
3066 viewport.sendSelection();
3073 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3077 public void hideAllSelection_actionPerformed(ActionEvent e)
3079 SequenceGroup sg = viewport.getSelectionGroup();
3080 viewport.expandColSelection(sg, false);
3081 viewport.hideAllSelectedSeqs();
3082 viewport.hideSelectedColumns();
3083 alignPanel.paintAlignment(true);
3084 viewport.sendSelection();
3091 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3095 public void showAllhidden_actionPerformed(ActionEvent e)
3097 viewport.showAllHiddenColumns();
3098 viewport.showAllHiddenSeqs();
3099 alignPanel.paintAlignment(true);
3100 viewport.sendSelection();
3104 public void hideSelColumns_actionPerformed(ActionEvent e)
3106 viewport.hideSelectedColumns();
3107 alignPanel.paintAlignment(true);
3108 viewport.sendSelection();
3112 public void hiddenMarkers_actionPerformed(ActionEvent e)
3114 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3125 protected void scaleAbove_actionPerformed(ActionEvent e)
3127 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3128 alignPanel.paintAlignment(true);
3138 protected void scaleLeft_actionPerformed(ActionEvent e)
3140 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3141 alignPanel.paintAlignment(true);
3151 protected void scaleRight_actionPerformed(ActionEvent e)
3153 viewport.setScaleRightWrapped(scaleRight.isSelected());
3154 alignPanel.paintAlignment(true);
3164 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3166 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3167 alignPanel.paintAlignment(true);
3177 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3179 viewport.setShowText(viewTextMenuItem.isSelected());
3180 alignPanel.paintAlignment(true);
3190 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3192 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3193 alignPanel.paintAlignment(true);
3196 public FeatureSettings featureSettings;
3199 public FeatureSettingsControllerI getFeatureSettingsUI()
3201 return featureSettings;
3205 public void featureSettings_actionPerformed(ActionEvent e)
3207 if (featureSettings != null)
3209 featureSettings.close();
3210 featureSettings = null;
3212 if (!showSeqFeatures.isSelected())
3214 // make sure features are actually displayed
3215 showSeqFeatures.setSelected(true);
3216 showSeqFeatures_actionPerformed(null);
3218 featureSettings = new FeatureSettings(this);
3222 * Set or clear 'Show Sequence Features'
3228 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3230 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3231 alignPanel.paintAlignment(true);
3232 if (alignPanel.getOverviewPanel() != null)
3234 alignPanel.getOverviewPanel().updateOverviewImage();
3239 * Set or clear 'Show Sequence Features'
3245 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3247 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3249 if (viewport.isShowSequenceFeaturesHeight())
3251 // ensure we're actually displaying features
3252 viewport.setShowSequenceFeatures(true);
3253 showSeqFeatures.setSelected(true);
3255 alignPanel.paintAlignment(true);
3256 if (alignPanel.getOverviewPanel() != null)
3258 alignPanel.getOverviewPanel().updateOverviewImage();
3263 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3264 * the annotations panel as a whole.
3266 * The options to show/hide all annotations should be enabled when the panel
3267 * is shown, and disabled when the panel is hidden.
3272 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3274 final boolean setVisible = annotationPanelMenuItem.isSelected();
3275 viewport.setShowAnnotation(setVisible);
3276 this.showAllSeqAnnotations.setEnabled(setVisible);
3277 this.hideAllSeqAnnotations.setEnabled(setVisible);
3278 this.showAllAlAnnotations.setEnabled(setVisible);
3279 this.hideAllAlAnnotations.setEnabled(setVisible);
3280 alignPanel.updateLayout();
3284 public void alignmentProperties()
3286 JEditorPane editPane = new JEditorPane("text/html", "");
3287 editPane.setEditable(false);
3288 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3290 editPane.setText(MessageManager.formatMessage("label.html_content",
3291 new Object[] { contents.toString() }));
3292 JInternalFrame frame = new JInternalFrame();
3293 frame.getContentPane().add(new JScrollPane(editPane));
3295 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3296 "label.alignment_properties", new Object[] { getTitle() }),
3307 public void overviewMenuItem_actionPerformed(ActionEvent e)
3309 if (alignPanel.overviewPanel != null)
3314 JInternalFrame frame = new JInternalFrame();
3315 OverviewPanel overview = new OverviewPanel(alignPanel);
3316 frame.setContentPane(overview);
3317 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3318 "label.overview_params", new Object[] { this.getTitle() }),
3319 frame.getWidth(), frame.getHeight());
3321 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3322 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3325 public void internalFrameClosed(
3326 javax.swing.event.InternalFrameEvent evt)
3328 alignPanel.setOverviewPanel(null);
3332 alignPanel.setOverviewPanel(overview);
3336 public void textColour_actionPerformed(ActionEvent e)
3338 new TextColourChooser().chooseColour(alignPanel, null);
3348 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3360 public void clustalColour_actionPerformed(ActionEvent e)
3362 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3363 viewport.getHiddenRepSequences()));
3373 public void zappoColour_actionPerformed(ActionEvent e)
3375 changeColour(new ZappoColourScheme());
3385 public void taylorColour_actionPerformed(ActionEvent e)
3387 changeColour(new TaylorColourScheme());
3397 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3399 changeColour(new HydrophobicColourScheme());
3409 public void helixColour_actionPerformed(ActionEvent e)
3411 changeColour(new HelixColourScheme());
3421 public void strandColour_actionPerformed(ActionEvent e)
3423 changeColour(new StrandColourScheme());
3433 public void turnColour_actionPerformed(ActionEvent e)
3435 changeColour(new TurnColourScheme());
3445 public void buriedColour_actionPerformed(ActionEvent e)
3447 changeColour(new BuriedColourScheme());
3457 public void nucleotideColour_actionPerformed(ActionEvent e)
3459 changeColour(new NucleotideColourScheme());
3463 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3465 changeColour(new PurinePyrimidineColourScheme());
3469 * public void covariationColour_actionPerformed(ActionEvent e) {
3471 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3475 public void annotationColour_actionPerformed(ActionEvent e)
3477 new AnnotationColourChooser(viewport, alignPanel);
3481 public void annotationColumn_actionPerformed(ActionEvent e)
3483 new AnnotationColumnChooser(viewport, alignPanel);
3487 public void rnahelicesColour_actionPerformed(ActionEvent e)
3489 new RNAHelicesColourChooser(viewport, alignPanel);
3499 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3501 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3511 public void changeColour(ColourSchemeI cs)
3513 // TODO: pull up to controller method
3517 // Make sure viewport is up to date w.r.t. any sliders
3518 if (viewport.getAbovePIDThreshold())
3520 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3522 viewport.setThreshold(threshold);
3525 if (viewport.getConservationSelected())
3527 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3530 if (cs instanceof TCoffeeColourScheme)
3532 tcoffeeColour.setEnabled(true);
3533 tcoffeeColour.setSelected(true);
3537 viewport.setGlobalColourScheme(cs);
3539 alignPanel.paintAlignment(true);
3549 protected void modifyPID_actionPerformed(ActionEvent e)
3551 if (viewport.getAbovePIDThreshold()
3552 && viewport.getGlobalColourScheme() != null)
3554 SliderPanel.setPIDSliderSource(alignPanel,
3555 viewport.getGlobalColourScheme(), "Background");
3556 SliderPanel.showPIDSlider();
3567 protected void modifyConservation_actionPerformed(ActionEvent e)
3569 if (viewport.getConservationSelected()
3570 && viewport.getGlobalColourScheme() != null)
3572 SliderPanel.setConservationSlider(alignPanel,
3573 viewport.getGlobalColourScheme(), "Background");
3574 SliderPanel.showConservationSlider();
3585 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3587 viewport.setConservationSelected(conservationMenuItem.isSelected());
3589 viewport.setAbovePIDThreshold(false);
3590 abovePIDThreshold.setSelected(false);
3592 changeColour(viewport.getGlobalColourScheme());
3594 modifyConservation_actionPerformed(null);
3604 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3606 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3608 conservationMenuItem.setSelected(false);
3609 viewport.setConservationSelected(false);
3611 changeColour(viewport.getGlobalColourScheme());
3613 modifyPID_actionPerformed(null);
3623 public void userDefinedColour_actionPerformed(ActionEvent e)
3625 if (e.getActionCommand().equals(
3626 MessageManager.getString("action.user_defined")))
3628 new UserDefinedColours(alignPanel, null);
3632 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3633 .getUserColourSchemes().get(e.getActionCommand());
3639 public void updateUserColourMenu()
3642 Component[] menuItems = colourMenu.getMenuComponents();
3643 int iSize = menuItems.length;
3644 for (int i = 0; i < iSize; i++)
3646 if (menuItems[i].getName() != null
3647 && menuItems[i].getName().equals("USER_DEFINED"))
3649 colourMenu.remove(menuItems[i]);
3653 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3655 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3656 .getUserColourSchemes().keys();
3658 while (userColours.hasMoreElements())
3660 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3661 userColours.nextElement().toString());
3662 radioItem.setName("USER_DEFINED");
3663 radioItem.addMouseListener(new MouseAdapter()
3666 public void mousePressed(MouseEvent evt)
3668 if (evt.isControlDown()
3669 || SwingUtilities.isRightMouseButton(evt))
3671 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3673 int option = JOptionPane.showInternalConfirmDialog(
3674 jalview.gui.Desktop.desktop,
3676 .getString("label.remove_from_default_list"),
3678 .getString("label.remove_user_defined_colour"),
3679 JOptionPane.YES_NO_OPTION);
3680 if (option == JOptionPane.YES_OPTION)
3682 jalview.gui.UserDefinedColours
3683 .removeColourFromDefaults(radioItem.getText());
3684 colourMenu.remove(radioItem);
3688 radioItem.addActionListener(new ActionListener()
3691 public void actionPerformed(ActionEvent evt)
3693 userDefinedColour_actionPerformed(evt);
3700 radioItem.addActionListener(new ActionListener()
3703 public void actionPerformed(ActionEvent evt)
3705 userDefinedColour_actionPerformed(evt);
3709 colourMenu.insert(radioItem, 15);
3710 colours.add(radioItem);
3722 public void PIDColour_actionPerformed(ActionEvent e)
3724 changeColour(new PIDColourScheme());
3734 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3736 changeColour(new Blosum62ColourScheme());
3746 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3748 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3749 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3750 .getAlignment().getSequenceAt(0), null);
3751 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3752 viewport.getAlignment()));
3753 alignPanel.paintAlignment(true);
3763 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3765 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3766 AlignmentSorter.sortByID(viewport.getAlignment());
3767 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3768 viewport.getAlignment()));
3769 alignPanel.paintAlignment(true);
3779 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3781 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3782 AlignmentSorter.sortByLength(viewport.getAlignment());
3783 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3784 viewport.getAlignment()));
3785 alignPanel.paintAlignment(true);
3795 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3797 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3798 AlignmentSorter.sortByGroup(viewport.getAlignment());
3799 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3800 viewport.getAlignment()));
3802 alignPanel.paintAlignment(true);
3812 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3814 new RedundancyPanel(alignPanel, this);
3824 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3826 if ((viewport.getSelectionGroup() == null)
3827 || (viewport.getSelectionGroup().getSize() < 2))
3829 JOptionPane.showInternalMessageDialog(this, MessageManager
3830 .getString("label.you_must_select_least_two_sequences"),
3831 MessageManager.getString("label.invalid_selection"),
3832 JOptionPane.WARNING_MESSAGE);
3836 JInternalFrame frame = new JInternalFrame();
3837 frame.setContentPane(new PairwiseAlignPanel(viewport));
3838 Desktop.addInternalFrame(frame,
3839 MessageManager.getString("action.pairwise_alignment"), 600,
3851 public void PCAMenuItem_actionPerformed(ActionEvent e)
3853 if (((viewport.getSelectionGroup() != null)
3854 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3855 .getSelectionGroup().getSize() > 0))
3856 || (viewport.getAlignment().getHeight() < 4))
3859 .showInternalMessageDialog(
3862 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3864 .getString("label.sequence_selection_insufficient"),
3865 JOptionPane.WARNING_MESSAGE);
3870 new PCAPanel(alignPanel);
3874 public void autoCalculate_actionPerformed(ActionEvent e)
3876 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3877 if (viewport.autoCalculateConsensus)
3879 viewport.firePropertyChange("alignment", null, viewport
3880 .getAlignment().getSequences());
3885 public void sortByTreeOption_actionPerformed(ActionEvent e)
3887 viewport.sortByTree = sortByTree.isSelected();
3891 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3893 viewport.followSelection = listenToViewSelections.isSelected();
3903 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3905 newTreePanel("AV", "PID", "Average distance tree using PID");
3915 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3917 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3927 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3929 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3939 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3941 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3954 void newTreePanel(String type, String pwType, String title)
3958 if (viewport.getSelectionGroup() != null
3959 && viewport.getSelectionGroup().getSize() > 0)
3961 if (viewport.getSelectionGroup().getSize() < 3)
3967 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3969 .getString("label.not_enough_sequences"),
3970 JOptionPane.WARNING_MESSAGE);
3974 SequenceGroup sg = viewport.getSelectionGroup();
3976 /* Decide if the selection is a column region */
3977 for (SequenceI _s : sg.getSequences())
3979 if (_s.getLength() < sg.getEndRes())
3985 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3987 .getString("label.sequences_selection_not_aligned"),
3988 JOptionPane.WARNING_MESSAGE);
3994 title = title + " on region";
3995 tp = new TreePanel(alignPanel, type, pwType);
3999 // are the visible sequences aligned?
4000 if (!viewport.getAlignment().isAligned(false))
4006 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4008 .getString("label.sequences_not_aligned"),
4009 JOptionPane.WARNING_MESSAGE);
4014 if (viewport.getAlignment().getHeight() < 2)
4019 tp = new TreePanel(alignPanel, type, pwType);
4024 if (viewport.viewName != null)
4026 title += viewport.viewName + " of ";
4029 title += this.title;
4031 Desktop.addInternalFrame(tp, title, 600, 500);
4042 public void addSortByOrderMenuItem(String title,
4043 final AlignmentOrder order)
4045 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4046 "action.by_title_param", new Object[] { title }));
4048 item.addActionListener(new java.awt.event.ActionListener()
4051 public void actionPerformed(ActionEvent e)
4053 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4055 // TODO: JBPNote - have to map order entries to curent SequenceI
4057 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4059 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4062 alignPanel.paintAlignment(true);
4068 * Add a new sort by annotation score menu item
4071 * the menu to add the option to
4073 * the label used to retrieve scores for each sequence on the
4076 public void addSortByAnnotScoreMenuItem(JMenu sort,
4077 final String scoreLabel)
4079 final JMenuItem item = new JMenuItem(scoreLabel);
4081 item.addActionListener(new java.awt.event.ActionListener()
4084 public void actionPerformed(ActionEvent e)
4086 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4087 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4088 viewport.getAlignment());// ,viewport.getSelectionGroup());
4089 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4090 viewport.getAlignment()));
4091 alignPanel.paintAlignment(true);
4097 * last hash for alignment's annotation array - used to minimise cost of
4100 protected int _annotationScoreVectorHash;
4103 * search the alignment and rebuild the sort by annotation score submenu the
4104 * last alignment annotation vector hash is stored to minimize cost of
4105 * rebuilding in subsequence calls.
4109 public void buildSortByAnnotationScoresMenu()
4111 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4116 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4118 sortByAnnotScore.removeAll();
4119 // almost certainly a quicker way to do this - but we keep it simple
4120 Hashtable scoreSorts = new Hashtable();
4121 AlignmentAnnotation aann[];
4122 for (SequenceI sqa : viewport.getAlignment().getSequences())
4124 aann = sqa.getAnnotation();
4125 for (int i = 0; aann != null && i < aann.length; i++)
4127 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4129 scoreSorts.put(aann[i].label, aann[i].label);
4133 Enumeration labels = scoreSorts.keys();
4134 while (labels.hasMoreElements())
4136 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4137 (String) labels.nextElement());
4139 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4142 _annotationScoreVectorHash = viewport.getAlignment()
4143 .getAlignmentAnnotation().hashCode();
4148 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4149 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4150 * call. Listeners are added to remove the menu item when the treePanel is
4151 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4155 * Displayed tree window.
4157 * SortBy menu item title.
4160 public void buildTreeMenu()
4162 calculateTree.removeAll();
4163 // build the calculate menu
4165 for (final String type : new String[] { "NJ", "AV" })
4167 String treecalcnm = MessageManager.getString("label.tree_calc_"
4168 + type.toLowerCase());
4169 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4171 JMenuItem tm = new JMenuItem();
4172 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4173 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4175 String smn = MessageManager.getStringOrReturn(
4176 "label.score_model_", sm.getName());
4177 final String title = MessageManager.formatMessage(
4178 "label.treecalc_title", treecalcnm, smn);
4179 tm.setText(title);//
4180 tm.addActionListener(new java.awt.event.ActionListener()
4183 public void actionPerformed(ActionEvent e)
4185 newTreePanel(type, pwtype, title);
4188 calculateTree.add(tm);
4193 sortByTreeMenu.removeAll();
4195 List<Component> comps = PaintRefresher.components.get(viewport
4196 .getSequenceSetId());
4197 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4198 for (Component comp : comps)
4200 if (comp instanceof TreePanel)
4202 treePanels.add((TreePanel) comp);
4206 if (treePanels.size() < 1)
4208 sortByTreeMenu.setVisible(false);
4212 sortByTreeMenu.setVisible(true);
4214 for (final TreePanel tp : treePanels)
4216 final JMenuItem item = new JMenuItem(tp.getTitle());
4217 item.addActionListener(new java.awt.event.ActionListener()
4220 public void actionPerformed(ActionEvent e)
4222 tp.sortByTree_actionPerformed();
4223 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4228 sortByTreeMenu.add(item);
4232 public boolean sortBy(AlignmentOrder alorder, String undoname)
4234 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4235 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4236 if (undoname != null)
4238 addHistoryItem(new OrderCommand(undoname, oldOrder,
4239 viewport.getAlignment()));
4241 alignPanel.paintAlignment(true);
4246 * Work out whether the whole set of sequences or just the selected set will
4247 * be submitted for multiple alignment.
4250 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4252 // Now, check we have enough sequences
4253 AlignmentView msa = null;
4255 if ((viewport.getSelectionGroup() != null)
4256 && (viewport.getSelectionGroup().getSize() > 1))
4258 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4259 // some common interface!
4261 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4262 * SequenceI[sz = seqs.getSize(false)];
4264 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4265 * seqs.getSequenceAt(i); }
4267 msa = viewport.getAlignmentView(true);
4269 else if (viewport.getSelectionGroup() != null
4270 && viewport.getSelectionGroup().getSize() == 1)
4272 int option = JOptionPane.showConfirmDialog(this,
4273 MessageManager.getString("warn.oneseq_msainput_selection"),
4274 MessageManager.getString("label.invalid_selection"),
4275 JOptionPane.OK_CANCEL_OPTION);
4276 if (option == JOptionPane.OK_OPTION)
4278 msa = viewport.getAlignmentView(false);
4283 msa = viewport.getAlignmentView(false);
4289 * Decides what is submitted to a secondary structure prediction service: the
4290 * first sequence in the alignment, or in the current selection, or, if the
4291 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4292 * region or the whole alignment. (where the first sequence in the set is the
4293 * one that the prediction will be for).
4295 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4297 AlignmentView seqs = null;
4299 if ((viewport.getSelectionGroup() != null)
4300 && (viewport.getSelectionGroup().getSize() > 0))
4302 seqs = viewport.getAlignmentView(true);
4306 seqs = viewport.getAlignmentView(false);
4308 // limit sequences - JBPNote in future - could spawn multiple prediction
4310 // TODO: viewport.getAlignment().isAligned is a global state - the local
4311 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4312 if (!viewport.getAlignment().isAligned(false))
4314 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4315 // TODO: if seqs.getSequences().length>1 then should really have warned
4329 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4331 // Pick the tree file
4332 JalviewFileChooser chooser = new JalviewFileChooser(
4333 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4334 chooser.setFileView(new JalviewFileView());
4335 chooser.setDialogTitle(MessageManager
4336 .getString("label.select_newick_like_tree_file"));
4337 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4339 int value = chooser.showOpenDialog(null);
4341 if (value == JalviewFileChooser.APPROVE_OPTION)
4343 String choice = chooser.getSelectedFile().getPath();
4344 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4345 jalview.io.NewickFile fin = null;
4348 fin = new jalview.io.NewickFile(choice, "File");
4349 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4350 } catch (Exception ex)
4357 .getString("label.problem_reading_tree_file"),
4358 JOptionPane.WARNING_MESSAGE);
4359 ex.printStackTrace();
4361 if (fin != null && fin.hasWarningMessage())
4363 JOptionPane.showMessageDialog(Desktop.desktop, fin
4364 .getWarningMessage(), MessageManager
4365 .getString("label.possible_problem_with_tree_file"),
4366 JOptionPane.WARNING_MESSAGE);
4372 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4374 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4377 public TreePanel ShowNewickTree(NewickFile nf, String title)
4379 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4382 public TreePanel ShowNewickTree(NewickFile nf, String title,
4383 AlignmentView input)
4385 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4388 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4389 int h, int x, int y)
4391 return ShowNewickTree(nf, title, null, w, h, x, y);
4395 * Add a treeviewer for the tree extracted from a newick file object to the
4396 * current alignment view
4403 * Associated alignment input data (or null)
4412 * @return TreePanel handle
4414 public TreePanel ShowNewickTree(NewickFile nf, String title,
4415 AlignmentView input, int w, int h, int x, int y)
4417 TreePanel tp = null;
4423 if (nf.getTree() != null)
4425 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4431 tp.setLocation(x, y);
4434 Desktop.addInternalFrame(tp, title, w, h);
4436 } catch (Exception ex)
4438 ex.printStackTrace();
4444 private boolean buildingMenu = false;
4447 * Generates menu items and listener event actions for web service clients
4450 public void BuildWebServiceMenu()
4452 while (buildingMenu)
4456 System.err.println("Waiting for building menu to finish.");
4458 } catch (Exception e)
4462 final AlignFrame me = this;
4463 buildingMenu = true;
4464 new Thread(new Runnable()
4469 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4472 // System.err.println("Building ws menu again "
4473 // + Thread.currentThread());
4474 // TODO: add support for context dependent disabling of services based
4476 // alignment and current selection
4477 // TODO: add additional serviceHandle parameter to specify abstract
4479 // class independently of AbstractName
4480 // TODO: add in rediscovery GUI function to restart discoverer
4481 // TODO: group services by location as well as function and/or
4483 // object broker mechanism.
4484 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4485 final IProgressIndicator af = me;
4486 final JMenu msawsmenu = new JMenu("Alignment");
4487 final JMenu secstrmenu = new JMenu(
4488 "Secondary Structure Prediction");
4489 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4490 final JMenu analymenu = new JMenu("Analysis");
4491 final JMenu dismenu = new JMenu("Protein Disorder");
4492 // final JMenu msawsmenu = new
4493 // JMenu(MessageManager.getString("label.alignment"));
4494 // final JMenu secstrmenu = new
4495 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4496 // final JMenu seqsrchmenu = new
4497 // JMenu(MessageManager.getString("label.sequence_database_search"));
4498 // final JMenu analymenu = new
4499 // JMenu(MessageManager.getString("label.analysis"));
4500 // final JMenu dismenu = new
4501 // JMenu(MessageManager.getString("label.protein_disorder"));
4502 // JAL-940 - only show secondary structure prediction services from
4503 // the legacy server
4504 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4506 Discoverer.services != null && (Discoverer.services.size() > 0))
4508 // TODO: refactor to allow list of AbstractName/Handler bindings to
4510 // stored or retrieved from elsewhere
4511 // No MSAWS used any more:
4512 // Vector msaws = null; // (Vector)
4513 // Discoverer.services.get("MsaWS");
4514 Vector secstrpr = (Vector) Discoverer.services
4516 if (secstrpr != null)
4518 // Add any secondary structure prediction services
4519 for (int i = 0, j = secstrpr.size(); i < j; i++)
4521 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4523 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4524 .getServiceClient(sh);
4525 int p = secstrmenu.getItemCount();
4526 impl.attachWSMenuEntry(secstrmenu, me);
4527 int q = secstrmenu.getItemCount();
4528 for (int litm = p; litm < q; litm++)
4530 legacyItems.add(secstrmenu.getItem(litm));
4536 // Add all submenus in the order they should appear on the web
4538 wsmenu.add(msawsmenu);
4539 wsmenu.add(secstrmenu);
4540 wsmenu.add(dismenu);
4541 wsmenu.add(analymenu);
4542 // No search services yet
4543 // wsmenu.add(seqsrchmenu);
4545 javax.swing.SwingUtilities.invokeLater(new Runnable()
4552 webService.removeAll();
4553 // first, add discovered services onto the webservices menu
4554 if (wsmenu.size() > 0)
4556 for (int i = 0, j = wsmenu.size(); i < j; i++)
4558 webService.add(wsmenu.get(i));
4563 webService.add(me.webServiceNoServices);
4565 // TODO: move into separate menu builder class.
4566 boolean new_sspred = false;
4567 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4569 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4570 if (jws2servs != null)
4572 if (jws2servs.hasServices())
4574 jws2servs.attachWSMenuEntry(webService, me);
4575 for (Jws2Instance sv : jws2servs.getServices())
4577 if (sv.description.toLowerCase().contains("jpred"))
4579 for (JMenuItem jmi : legacyItems)
4581 jmi.setVisible(false);
4587 if (jws2servs.isRunning())
4589 JMenuItem tm = new JMenuItem(
4590 "Still discovering JABA Services");
4591 tm.setEnabled(false);
4596 build_urlServiceMenu(me.webService);
4597 build_fetchdbmenu(webService);
4598 for (JMenu item : wsmenu)
4600 if (item.getItemCount() == 0)
4602 item.setEnabled(false);
4606 item.setEnabled(true);
4609 } catch (Exception e)
4612 .debug("Exception during web service menu building process.",
4617 } catch (Exception e)
4620 buildingMenu = false;
4627 * construct any groupURL type service menu entries.
4631 private void build_urlServiceMenu(JMenu webService)
4633 // TODO: remove this code when 2.7 is released
4634 // DEBUG - alignmentView
4636 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4637 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4639 * @Override public void actionPerformed(ActionEvent e) {
4640 * jalview.datamodel.AlignmentView
4641 * .testSelectionViews(af.viewport.getAlignment(),
4642 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4644 * }); webService.add(testAlView);
4646 // TODO: refactor to RestClient discoverer and merge menu entries for
4647 // rest-style services with other types of analysis/calculation service
4648 // SHmmr test client - still being implemented.
4649 // DEBUG - alignmentView
4651 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4654 client.attachWSMenuEntry(
4655 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4661 * Searches selected sequences for xRef products and builds the Show
4662 * Cross-References menu (formerly called Show Products)
4664 * @return true if Show Cross-references menu should be enabled.
4666 public boolean canShowProducts()
4668 SequenceI[] selection = viewport.getSequenceSelection();
4669 AlignmentI dataset = viewport.getAlignment().getDataset();
4670 boolean showp = false;
4673 showProducts.removeAll();
4674 final boolean dna = viewport.getAlignment().isNucleotide();
4675 String[] ptypes = (selection == null || selection.length == 0) ? null
4676 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4678 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4681 final AlignFrame af = this;
4682 final String source = ptypes[t];
4683 JMenuItem xtype = new JMenuItem(ptypes[t]);
4684 xtype.addActionListener(new ActionListener()
4688 public void actionPerformed(ActionEvent e)
4690 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4694 showProducts.add(xtype);
4696 showProducts.setVisible(showp);
4697 showProducts.setEnabled(showp);
4698 } catch (Exception e)
4700 jalview.bin.Cache.log
4701 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4708 protected void showProductsFor(final SequenceI[] sel, final boolean dna,
4709 final String source)
4711 Runnable foo = new Runnable()
4717 final long sttime = System.currentTimeMillis();
4718 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4719 "status.searching_for_sequences_from",
4720 new Object[] { source }), sttime);
4724 * 'peer' sequences are any to add to this alignment, for example
4725 * alternative protein products for my protein's gene
4727 List<SequenceI> addedPeers = new ArrayList<SequenceI>();
4728 AlignmentI alignment = AlignFrame.this.getViewport()
4730 Alignment xrefs = CrossRef.findXrefSequences(sel, dna, source,
4731 alignment, addedPeers);
4735 * figure out colour scheme if any to apply to features
4737 ASequenceFetcher sftch = new SequenceFetcher();
4738 List<DbSourceProxy> proxies = sftch.getSourceProxy(source);
4739 FeatureSettingsI featureColourScheme = null;
4740 for (DbSourceProxy proxy : proxies)
4742 FeatureSettingsI preferredColours = proxy
4743 .getFeatureColourScheme();
4744 if (preferredColours != null)
4746 featureColourScheme = preferredColours;
4750 Alignment al = makeCrossReferencesAlignment(
4751 alignment.getDataset(), xrefs);
4754 * Copy dna-to-protein mappings to new alignment
4756 // TODO 1: no mappings are set up for EMBL product
4757 // TODO 2: if they were, should add them to protein alignment, not
4759 // List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4760 // for (AlignedCodonFrame acf : cf)
4762 // al.addCodonFrame(acf);
4764 AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
4766 String newtitle = String.format("%s %s %s",
4767 MessageManager.getString(dna ? "label.proteins"
4768 : "label.nucleotides"), MessageManager
4769 .getString("label.for"), getTitle());
4770 newFrame.setTitle(newtitle);
4772 boolean asSplitFrame = Cache.getDefault(
4773 Preferences.ENABLE_SPLIT_FRAME, true);
4777 * Make a copy of this alignment (sharing the same dataset
4778 * sequences). If we are DNA, drop introns and update mappings
4780 AlignmentI copyAlignment = null;
4781 final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4782 .getSequenceSelection();
4783 final char gapChar = AlignFrame.this.viewport
4785 List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4788 copyAlignment = AlignmentUtils.makeCdsAlignment(
4789 sequenceSelection, cf, gapChar);
4790 al.getCodonFrames().clear();
4791 al.getCodonFrames().addAll(cf);
4795 copyAlignment = new Alignment(new Alignment(
4796 sequenceSelection));
4797 copyAlignment.getCodonFrames().addAll(cf);
4798 copyAlignment.setGapCharacter(gapChar);
4800 StructureSelectionManager ssm = StructureSelectionManager
4801 .getStructureSelectionManager(Desktop.instance);
4802 ssm.registerMappings(cf);
4805 * add in any extra 'peer' sequences discovered
4806 * (e.g. alternative protein products)
4808 for (SequenceI peer : addedPeers)
4810 copyAlignment.addSequence(peer);
4814 * align protein to dna
4818 al.alignAs(copyAlignment);
4822 copyAlignment.alignAs(al);
4825 AlignFrame copyThis = new AlignFrame(copyAlignment,
4826 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4827 copyThis.setTitle(AlignFrame.this.getTitle());
4829 boolean showSequenceFeatures = viewport
4830 .isShowSequenceFeatures();
4831 newFrame.setShowSeqFeatures(showSequenceFeatures);
4832 copyThis.setShowSeqFeatures(showSequenceFeatures);
4833 FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4834 .getFeatureRenderer();
4837 * copy feature rendering settings to split frame
4839 newFrame.alignPanel.getSeqPanel().seqCanvas
4840 .getFeatureRenderer().transferSettings(
4842 copyThis.alignPanel.getSeqPanel().seqCanvas
4843 .getFeatureRenderer().transferSettings(
4847 * apply 'database source' feature configuration
4850 newFrame.getViewport()
4851 .applyFeaturesStyle(featureColourScheme);
4852 copyThis.getViewport()
4853 .applyFeaturesStyle(featureColourScheme);
4855 SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4856 dna ? newFrame : copyThis);
4857 newFrame.setVisible(true);
4858 copyThis.setVisible(true);
4859 String linkedTitle = MessageManager
4860 .getString("label.linked_view_title");
4861 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4866 Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4872 System.err.println("No Sequences generated for xRef type "
4875 } catch (Exception e)
4877 jalview.bin.Cache.log.error(
4878 "Exception when finding crossreferences", e);
4879 } catch (OutOfMemoryError e)
4881 new OOMWarning("whilst fetching crossreferences", e);
4884 jalview.bin.Cache.log.error("Error when finding crossreferences",
4887 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4888 "status.finished_searching_for_sequences_from",
4889 new Object[] { source }), sttime);
4897 protected Alignment makeCrossReferencesAlignment(Alignment dataset,
4900 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4901 for (int s = 0; s < sprods.length; s++)
4903 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4904 if (dataset.getSequences() == null
4905 || !dataset.getSequences().contains(
4906 sprods[s].getDatasetSequence()))
4908 dataset.addSequence(sprods[s].getDatasetSequence());
4910 sprods[s].updatePDBIds();
4912 Alignment al = new Alignment(sprods);
4913 al.setDataset(dataset);
4918 Thread frunner = new Thread(foo);
4922 public boolean canShowTranslationProducts(SequenceI[] selection,
4923 AlignmentI alignment)
4928 return (jalview.analysis.Dna.canTranslate(selection,
4929 viewport.getViewAsVisibleContigs(true)));
4930 } catch (Exception e)
4932 jalview.bin.Cache.log
4933 .warn("canTranslate threw an exception - please report to help@jalview.org",
4940 * Construct and display a new frame containing the translation of this
4941 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4944 public void showTranslation_actionPerformed(ActionEvent e)
4946 AlignmentI al = null;
4949 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4951 al = dna.translateCdna();
4952 } catch (Exception ex)
4954 jalview.bin.Cache.log.error(
4955 "Exception during translation. Please report this !", ex);
4956 final String msg = MessageManager
4957 .getString("label.error_when_translating_sequences_submit_bug_report");
4958 final String errorTitle = MessageManager
4959 .getString("label.implementation_error")
4960 + MessageManager.getString("translation_failed");
4961 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4962 JOptionPane.ERROR_MESSAGE);
4965 if (al == null || al.getHeight() == 0)
4967 final String msg = MessageManager
4968 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4969 final String errorTitle = MessageManager
4970 .getString("label.translation_failed");
4971 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4972 JOptionPane.WARNING_MESSAGE);
4976 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4977 af.setFileFormat(this.currentFileFormat);
4978 final String newTitle = MessageManager.formatMessage(
4979 "label.translation_of_params",
4980 new Object[] { this.getTitle() });
4981 af.setTitle(newTitle);
4982 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4984 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4985 viewport.openSplitFrame(af, new Alignment(seqs));
4989 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4996 * Set the file format
5000 public void setFileFormat(String fileFormat)
5002 this.currentFileFormat = fileFormat;
5006 * Try to load a features file onto the alignment.
5009 * contents or path to retrieve file
5011 * access mode of file (see jalview.io.AlignFile)
5012 * @return true if features file was parsed correctly.
5014 public boolean parseFeaturesFile(String file, String type)
5016 return avc.parseFeaturesFile(file, type,
5017 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
5022 public void refreshFeatureUI(boolean enableIfNecessary)
5024 // note - currently this is only still here rather than in the controller
5025 // because of the featureSettings hard reference that is yet to be
5027 if (enableIfNecessary)
5029 viewport.setShowSequenceFeatures(true);
5030 showSeqFeatures.setSelected(true);
5036 public void dragEnter(DropTargetDragEvent evt)
5041 public void dragExit(DropTargetEvent evt)
5046 public void dragOver(DropTargetDragEvent evt)
5051 public void dropActionChanged(DropTargetDragEvent evt)
5056 public void drop(DropTargetDropEvent evt)
5058 Transferable t = evt.getTransferable();
5059 java.util.List files = null;
5063 DataFlavor uriListFlavor = new DataFlavor(
5064 "text/uri-list;class=java.lang.String");
5065 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5067 // Works on Windows and MacOSX
5068 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5069 files = (java.util.List) t
5070 .getTransferData(DataFlavor.javaFileListFlavor);
5072 else if (t.isDataFlavorSupported(uriListFlavor))
5074 // This is used by Unix drag system
5075 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5076 String data = (String) t.getTransferData(uriListFlavor);
5077 files = new java.util.ArrayList(1);
5078 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5079 data, "\r\n"); st.hasMoreTokens();)
5081 String s = st.nextToken();
5082 if (s.startsWith("#"))
5084 // the line is a comment (as per the RFC 2483)
5088 java.net.URI uri = new java.net.URI(s);
5089 // check to see if we can handle this kind of URI
5090 if (uri.getScheme().toLowerCase().startsWith("http"))
5092 files.add(uri.toString());
5096 // otherwise preserve old behaviour: catch all for file objects
5097 java.io.File file = new java.io.File(uri);
5098 files.add(file.toString());
5102 } catch (Exception e)
5104 e.printStackTrace();
5110 // check to see if any of these files have names matching sequences in
5112 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5113 .getAlignment().getSequencesArray());
5115 * Object[] { String,SequenceI}
5117 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5118 ArrayList<String> filesnotmatched = new ArrayList<String>();
5119 for (int i = 0; i < files.size(); i++)
5121 String file = files.get(i).toString();
5123 String protocol = FormatAdapter.checkProtocol(file);
5124 if (protocol == jalview.io.FormatAdapter.FILE)
5126 File fl = new File(file);
5127 pdbfn = fl.getName();
5129 else if (protocol == jalview.io.FormatAdapter.URL)
5131 URL url = new URL(file);
5132 pdbfn = url.getFile();
5134 if (pdbfn.length() > 0)
5136 // attempt to find a match in the alignment
5137 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5138 int l = 0, c = pdbfn.indexOf(".");
5139 while (mtch == null && c != -1)
5144 } while ((c = pdbfn.indexOf(".", l)) > l);
5147 pdbfn = pdbfn.substring(0, l);
5149 mtch = idm.findAllIdMatches(pdbfn);
5156 type = new IdentifyFile().identify(file, protocol);
5157 } catch (Exception ex)
5163 if (type.equalsIgnoreCase("PDB"))
5165 filesmatched.add(new Object[] { file, protocol, mtch });
5170 // File wasn't named like one of the sequences or wasn't a PDB file.
5171 filesnotmatched.add(file);
5175 if (filesmatched.size() > 0)
5177 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5183 "label.automatically_associate_pdb_files_with_sequences_same_name",
5184 new Object[] { Integer
5190 .getString("label.automatically_associate_pdb_files_by_name"),
5191 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5194 for (Object[] fm : filesmatched)
5196 // try and associate
5197 // TODO: may want to set a standard ID naming formalism for
5198 // associating PDB files which have no IDs.
5199 for (SequenceI toassoc : (SequenceI[]) fm[2])
5201 PDBEntry pe = new AssociatePdbFileWithSeq()
5202 .associatePdbWithSeq((String) fm[0],
5203 (String) fm[1], toassoc, false,
5207 System.err.println("Associated file : "
5208 + ((String) fm[0]) + " with "
5209 + toassoc.getDisplayId(true));
5213 alignPanel.paintAlignment(true);
5217 if (filesnotmatched.size() > 0)
5220 && (Cache.getDefault(
5221 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5227 "label.ignore_unmatched_dropped_files_info",
5228 new Object[] { Integer
5235 .getString("label.ignore_unmatched_dropped_files"),
5236 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5240 for (String fn : filesnotmatched)
5242 loadJalviewDataFile(fn, null, null, null);
5246 } catch (Exception ex)
5248 ex.printStackTrace();
5254 * Attempt to load a "dropped" file or URL string: First by testing whether
5255 * it's an Annotation file, then a JNet file, and finally a features file. If
5256 * all are false then the user may have dropped an alignment file onto this
5260 * either a filename or a URL string.
5262 public void loadJalviewDataFile(String file, String protocol,
5263 String format, SequenceI assocSeq)
5267 if (protocol == null)
5269 protocol = FormatAdapter.checkProtocol(file);
5271 // if the file isn't identified, or not positively identified as some
5272 // other filetype (PFAM is default unidentified alignment file type) then
5273 // try to parse as annotation.
5274 boolean isAnnotation = (format == null || format
5275 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5276 .annotateAlignmentView(viewport, file, protocol) : false;
5280 // first see if its a T-COFFEE score file
5281 TCoffeeScoreFile tcf = null;
5284 tcf = new TCoffeeScoreFile(file, protocol);
5287 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5289 tcoffeeColour.setEnabled(true);
5290 tcoffeeColour.setSelected(true);
5291 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5292 isAnnotation = true;
5294 .setText(MessageManager
5295 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5299 // some problem - if no warning its probable that the ID matching
5300 // process didn't work
5304 tcf.getWarningMessage() == null ? MessageManager
5305 .getString("label.check_file_matches_sequence_ids_alignment")
5306 : tcf.getWarningMessage(),
5308 .getString("label.problem_reading_tcoffee_score_file"),
5309 JOptionPane.WARNING_MESSAGE);
5316 } catch (Exception x)
5319 .debug("Exception when processing data source as T-COFFEE score file",
5325 // try to see if its a JNet 'concise' style annotation file *before*
5327 // try to parse it as a features file
5330 format = new IdentifyFile().identify(file, protocol);
5332 if (format.equalsIgnoreCase("JnetFile"))
5334 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5336 new JnetAnnotationMaker();
5337 JnetAnnotationMaker.add_annotation(predictions,
5338 viewport.getAlignment(), 0, false);
5339 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5340 viewport.getAlignment().setSeqrep(repseq);
5341 ColumnSelection cs = new ColumnSelection();
5342 cs.hideInsertionsFor(repseq);
5343 viewport.setColumnSelection(cs);
5344 isAnnotation = true;
5346 else if (IdentifyFile.FeaturesFile.equals(format))
5348 if (parseFeaturesFile(file, protocol))
5350 alignPanel.paintAlignment(true);
5355 new FileLoader().LoadFile(viewport, file, protocol, format);
5362 alignPanel.adjustAnnotationHeight();
5363 viewport.updateSequenceIdColours();
5364 buildSortByAnnotationScoresMenu();
5365 alignPanel.paintAlignment(true);
5367 } catch (Exception ex)
5369 ex.printStackTrace();
5370 } catch (OutOfMemoryError oom)
5375 } catch (Exception x)
5380 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5381 : "using " + protocol + " from " + file)
5383 + (format != null ? "(parsing as '" + format
5384 + "' file)" : ""), oom, Desktop.desktop);
5389 * Method invoked by the ChangeListener on the tabbed pane, in other words
5390 * when a different tabbed pane is selected by the user or programmatically.
5393 public void tabSelectionChanged(int index)
5397 alignPanel = alignPanels.get(index);
5398 viewport = alignPanel.av;
5399 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5400 setMenusFromViewport(viewport);
5404 * If there is a frame linked to this one in a SplitPane, switch it to the
5405 * same view tab index. No infinite recursion of calls should happen, since
5406 * tabSelectionChanged() should not get invoked on setting the selected
5407 * index to an unchanged value. Guard against setting an invalid index
5408 * before the new view peer tab has been created.
5410 final AlignViewportI peer = viewport.getCodingComplement();
5413 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5414 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5416 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5422 * On right mouse click on view tab, prompt for and set new view name.
5425 public void tabbedPane_mousePressed(MouseEvent e)
5427 if (SwingUtilities.isRightMouseButton(e))
5429 String msg = MessageManager.getString("label.enter_view_name");
5430 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5431 JOptionPane.QUESTION_MESSAGE);
5435 viewport.viewName = reply;
5436 // TODO warn if reply is in getExistingViewNames()?
5437 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5442 public AlignViewport getCurrentView()
5448 * Open the dialog for regex description parsing.
5451 protected void extractScores_actionPerformed(ActionEvent e)
5453 ParseProperties pp = new jalview.analysis.ParseProperties(
5454 viewport.getAlignment());
5455 // TODO: verify regex and introduce GUI dialog for version 2.5
5456 // if (pp.getScoresFromDescription("col", "score column ",
5457 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5459 if (pp.getScoresFromDescription("description column",
5460 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5462 buildSortByAnnotationScoresMenu();
5470 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5474 protected void showDbRefs_actionPerformed(ActionEvent e)
5476 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5482 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5486 protected void showNpFeats_actionPerformed(ActionEvent e)
5488 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5492 * find the viewport amongst the tabs in this alignment frame and close that
5497 public boolean closeView(AlignViewportI av)
5501 this.closeMenuItem_actionPerformed(false);
5504 Component[] comp = tabbedPane.getComponents();
5505 for (int i = 0; comp != null && i < comp.length; i++)
5507 if (comp[i] instanceof AlignmentPanel)
5509 if (((AlignmentPanel) comp[i]).av == av)
5512 closeView((AlignmentPanel) comp[i]);
5520 protected void build_fetchdbmenu(JMenu webService)
5522 // Temporary hack - DBRef Fetcher always top level ws entry.
5523 // TODO We probably want to store a sequence database checklist in
5524 // preferences and have checkboxes.. rather than individual sources selected
5526 final JMenu rfetch = new JMenu(
5527 MessageManager.getString("action.fetch_db_references"));
5528 rfetch.setToolTipText(MessageManager
5529 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5530 webService.add(rfetch);
5532 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5533 MessageManager.getString("option.trim_retrieved_seqs"));
5534 trimrs.setToolTipText(MessageManager
5535 .getString("label.trim_retrieved_sequences"));
5536 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5537 trimrs.addActionListener(new ActionListener()
5540 public void actionPerformed(ActionEvent e)
5542 trimrs.setSelected(trimrs.isSelected());
5543 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5544 Boolean.valueOf(trimrs.isSelected()).toString());
5548 JMenuItem fetchr = new JMenuItem(
5549 MessageManager.getString("label.standard_databases"));
5550 fetchr.setToolTipText(MessageManager
5551 .getString("label.fetch_embl_uniprot"));
5552 fetchr.addActionListener(new ActionListener()
5556 public void actionPerformed(ActionEvent e)
5558 new Thread(new Runnable()
5564 boolean isNuclueotide = alignPanel.alignFrame.getViewport()
5565 .getAlignment().isNucleotide();
5566 new jalview.ws.DBRefFetcher(alignPanel.av
5567 .getSequenceSelection(), alignPanel.alignFrame, null,
5568 alignPanel.alignFrame.featureSettings, isNuclueotide)
5569 .fetchDBRefs(false);
5577 final AlignFrame me = this;
5578 new Thread(new Runnable()
5583 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5584 .getSequenceFetcherSingleton(me);
5585 javax.swing.SwingUtilities.invokeLater(new Runnable()
5590 String[] dbclasses = sf.getOrderedSupportedSources();
5591 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5592 // jalview.util.QuickSort.sort(otherdb, otherdb);
5593 List<DbSourceProxy> otherdb;
5594 JMenu dfetch = new JMenu();
5595 JMenu ifetch = new JMenu();
5596 JMenuItem fetchr = null;
5597 int comp = 0, icomp = 0, mcomp = 15;
5598 String mname = null;
5600 for (String dbclass : dbclasses)
5602 otherdb = sf.getSourceProxy(dbclass);
5603 // add a single entry for this class, or submenu allowing 'fetch
5605 if (otherdb == null || otherdb.size() < 1)
5609 // List<DbSourceProxy> dbs=otherdb;
5610 // otherdb=new ArrayList<DbSourceProxy>();
5611 // for (DbSourceProxy db:dbs)
5613 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5617 mname = "From " + dbclass;
5619 if (otherdb.size() == 1)
5621 final DbSourceProxy[] dassource = otherdb
5622 .toArray(new DbSourceProxy[0]);
5623 DbSourceProxy src = otherdb.get(0);
5624 fetchr = new JMenuItem(src.getDbSource());
5625 fetchr.addActionListener(new ActionListener()
5629 public void actionPerformed(ActionEvent e)
5631 new Thread(new Runnable()
5637 boolean isNuclueotide = alignPanel.alignFrame
5638 .getViewport().getAlignment()
5640 new jalview.ws.DBRefFetcher(alignPanel.av
5641 .getSequenceSelection(),
5642 alignPanel.alignFrame, dassource,
5643 alignPanel.alignFrame.featureSettings,
5644 isNuclueotide).fetchDBRefs(false);
5650 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5651 MessageManager.formatMessage(
5652 "label.fetch_retrieve_from",
5653 new Object[] { src.getDbName() })));
5659 final DbSourceProxy[] dassource = otherdb
5660 .toArray(new DbSourceProxy[0]);
5662 DbSourceProxy src = otherdb.get(0);
5663 fetchr = new JMenuItem(MessageManager.formatMessage(
5664 "label.fetch_all_param",
5665 new Object[] { src.getDbSource() }));
5666 fetchr.addActionListener(new ActionListener()
5669 public void actionPerformed(ActionEvent e)
5671 new Thread(new Runnable()
5677 boolean isNuclueotide = alignPanel.alignFrame
5678 .getViewport().getAlignment()
5680 new jalview.ws.DBRefFetcher(alignPanel.av
5681 .getSequenceSelection(),
5682 alignPanel.alignFrame, dassource,
5683 alignPanel.alignFrame.featureSettings,
5684 isNuclueotide).fetchDBRefs(false);
5690 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5691 MessageManager.formatMessage(
5692 "label.fetch_retrieve_from_all_sources",
5694 Integer.valueOf(otherdb.size())
5695 .toString(), src.getDbSource(),
5696 src.getDbName() })));
5699 // and then build the rest of the individual menus
5700 ifetch = new JMenu(MessageManager.formatMessage(
5701 "label.source_from_db_source",
5702 new Object[] { src.getDbSource() }));
5704 String imname = null;
5706 for (DbSourceProxy sproxy : otherdb)
5708 String dbname = sproxy.getDbName();
5709 String sname = dbname.length() > 5 ? dbname.substring(0,
5710 5) + "..." : dbname;
5711 String msname = dbname.length() > 10 ? dbname.substring(
5712 0, 10) + "..." : dbname;
5715 imname = MessageManager.formatMessage(
5716 "label.from_msname", new Object[] { sname });
5718 fetchr = new JMenuItem(msname);
5719 final DbSourceProxy[] dassrc = { sproxy };
5720 fetchr.addActionListener(new ActionListener()
5724 public void actionPerformed(ActionEvent e)
5726 new Thread(new Runnable()
5732 boolean isNuclueotide = alignPanel.alignFrame
5733 .getViewport().getAlignment()
5735 new jalview.ws.DBRefFetcher(alignPanel.av
5736 .getSequenceSelection(),
5737 alignPanel.alignFrame, dassrc,
5738 alignPanel.alignFrame.featureSettings,
5739 isNuclueotide).fetchDBRefs(false);
5745 fetchr.setToolTipText("<html>"
5746 + MessageManager.formatMessage(
5747 "label.fetch_retrieve_from", new Object[]
5751 if (++icomp >= mcomp || i == (otherdb.size()))
5753 ifetch.setText(MessageManager.formatMessage(
5754 "label.source_to_target", imname, sname));
5756 ifetch = new JMenu();
5764 if (comp >= mcomp || dbi >= (dbclasses.length))
5766 dfetch.setText(MessageManager.formatMessage(
5767 "label.source_to_target", mname, dbclass));
5769 dfetch = new JMenu();
5782 * Left justify the whole alignment.
5785 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5787 AlignmentI al = viewport.getAlignment();
5789 viewport.firePropertyChange("alignment", null, al);
5793 * Right justify the whole alignment.
5796 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5798 AlignmentI al = viewport.getAlignment();
5800 viewport.firePropertyChange("alignment", null, al);
5804 public void setShowSeqFeatures(boolean b)
5806 showSeqFeatures.setSelected(b);
5807 viewport.setShowSequenceFeatures(b);
5814 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5815 * awt.event.ActionEvent)
5818 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5820 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5821 alignPanel.paintAlignment(true);
5828 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5832 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5834 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5835 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5843 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5844 * .event.ActionEvent)
5847 protected void showGroupConservation_actionPerformed(ActionEvent e)
5849 viewport.setShowGroupConservation(showGroupConservation.getState());
5850 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5857 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5858 * .event.ActionEvent)
5861 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5863 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5864 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5871 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5872 * .event.ActionEvent)
5875 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5877 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5878 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5882 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5884 showSequenceLogo.setState(true);
5885 viewport.setShowSequenceLogo(true);
5886 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5887 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5891 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5893 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5900 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5901 * .event.ActionEvent)
5904 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5906 if (avc.makeGroupsFromSelection())
5908 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5909 alignPanel.updateAnnotation();
5910 alignPanel.paintAlignment(true);
5914 public void clearAlignmentSeqRep()
5916 // TODO refactor alignmentseqrep to controller
5917 if (viewport.getAlignment().hasSeqrep())
5919 viewport.getAlignment().setSeqrep(null);
5920 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5921 alignPanel.updateAnnotation();
5922 alignPanel.paintAlignment(true);
5927 protected void createGroup_actionPerformed(ActionEvent e)
5929 if (avc.createGroup())
5931 alignPanel.alignmentChanged();
5936 protected void unGroup_actionPerformed(ActionEvent e)
5940 alignPanel.alignmentChanged();
5945 * make the given alignmentPanel the currently selected tab
5947 * @param alignmentPanel
5949 public void setDisplayedView(AlignmentPanel alignmentPanel)
5951 if (!viewport.getSequenceSetId().equals(
5952 alignmentPanel.av.getSequenceSetId()))
5956 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5958 if (tabbedPane != null
5959 && tabbedPane.getTabCount() > 0
5960 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5961 .getSelectedIndex())
5963 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5968 * Action on selection of menu options to Show or Hide annotations.
5971 * @param forSequences
5972 * update sequence-related annotations
5973 * @param forAlignment
5974 * update non-sequence-related annotations
5977 protected void setAnnotationsVisibility(boolean visible,
5978 boolean forSequences, boolean forAlignment)
5980 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5981 .getAlignmentAnnotation())
5984 * don't display non-positional annotations on an alignment
5986 if (aa.annotations == null)
5990 boolean apply = (aa.sequenceRef == null && forAlignment)
5991 || (aa.sequenceRef != null && forSequences);
5994 aa.visible = visible;
5997 alignPanel.validateAnnotationDimensions(true);
5998 alignPanel.alignmentChanged();
6002 * Store selected annotation sort order for the view and repaint.
6005 protected void sortAnnotations_actionPerformed()
6007 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
6009 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
6010 alignPanel.paintAlignment(true);
6015 * @return alignment panels in this alignment frame
6017 public List<? extends AlignmentViewPanel> getAlignPanels()
6019 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
6023 * Open a new alignment window, with the cDNA associated with this (protein)
6024 * alignment, aligned as is the protein.
6026 protected void viewAsCdna_actionPerformed()
6028 // TODO no longer a menu action - refactor as required
6029 final AlignmentI alignment = getViewport().getAlignment();
6030 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6031 if (mappings == null)
6035 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6036 for (SequenceI aaSeq : alignment.getSequences())
6038 for (AlignedCodonFrame acf : mappings)
6040 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6044 * There is a cDNA mapping for this protein sequence - add to new
6045 * alignment. It will share the same dataset sequence as other mapped
6046 * cDNA (no new mappings need to be created).
6048 final Sequence newSeq = new Sequence(dnaSeq);
6049 newSeq.setDatasetSequence(dnaSeq);
6050 cdnaSeqs.add(newSeq);
6054 if (cdnaSeqs.size() == 0)
6056 // show a warning dialog no mapped cDNA
6059 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6061 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6062 AlignFrame.DEFAULT_HEIGHT);
6063 cdna.alignAs(alignment);
6064 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6066 Desktop.addInternalFrame(alignFrame, newtitle,
6067 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6071 * Set visibility of dna/protein complement view (available when shown in a
6077 protected void showComplement_actionPerformed(boolean show)
6079 SplitContainerI sf = getSplitViewContainer();
6082 sf.setComplementVisible(this, show);
6087 * Generate the reverse (optionally complemented) of the selected sequences,
6088 * and add them to the alignment
6091 protected void showReverse_actionPerformed(boolean complement)
6093 AlignmentI al = null;
6096 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6098 al = dna.reverseCdna(complement);
6099 viewport.addAlignment(al, "");
6100 } catch (Exception ex)
6102 System.err.println(ex.getMessage());
6108 class PrintThread extends Thread
6112 public PrintThread(AlignmentPanel ap)
6117 static PageFormat pf;
6122 PrinterJob printJob = PrinterJob.getPrinterJob();
6126 printJob.setPrintable(ap, pf);
6130 printJob.setPrintable(ap);
6133 if (printJob.printDialog())
6138 } catch (Exception PrintException)
6140 PrintException.printStackTrace();