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.
21 package jalview.appletgui;
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
25 import jalview.analysis.TreeBuilder;
26 import jalview.analysis.scoremodels.PIDModel;
27 import jalview.analysis.scoremodels.ScoreModels;
28 import jalview.api.AlignViewControllerGuiI;
29 import jalview.api.AlignViewControllerI;
30 import jalview.api.AlignViewportI;
31 import jalview.api.FeatureColourI;
32 import jalview.api.FeatureRenderer;
33 import jalview.api.FeatureSettingsControllerI;
34 import jalview.api.SequenceStructureBinding;
35 import jalview.bin.JalviewLite;
36 import jalview.commands.CommandI;
37 import jalview.commands.EditCommand;
38 import jalview.commands.EditCommand.Action;
39 import jalview.commands.OrderCommand;
40 import jalview.commands.RemoveGapColCommand;
41 import jalview.commands.RemoveGapsCommand;
42 import jalview.commands.SlideSequencesCommand;
43 import jalview.commands.TrimRegionCommand;
44 import jalview.datamodel.Alignment;
45 import jalview.datamodel.AlignmentAnnotation;
46 import jalview.datamodel.AlignmentI;
47 import jalview.datamodel.AlignmentOrder;
48 import jalview.datamodel.ColumnSelection;
49 import jalview.datamodel.HiddenColumns;
50 import jalview.datamodel.PDBEntry;
51 import jalview.datamodel.Sequence;
52 import jalview.datamodel.SequenceGroup;
53 import jalview.datamodel.SequenceI;
54 import jalview.io.AnnotationFile;
55 import jalview.io.AppletFormatAdapter;
56 import jalview.io.DataSourceType;
57 import jalview.io.FeaturesFile;
58 import jalview.io.FileFormat;
59 import jalview.io.FileFormatI;
60 import jalview.io.FileFormats;
61 import jalview.io.TCoffeeScoreFile;
62 import jalview.schemes.Blosum62ColourScheme;
63 import jalview.schemes.BuriedColourScheme;
64 import jalview.schemes.ClustalxColourScheme;
65 import jalview.schemes.ColourSchemeI;
66 import jalview.schemes.HelixColourScheme;
67 import jalview.schemes.HydrophobicColourScheme;
68 import jalview.schemes.NucleotideColourScheme;
69 import jalview.schemes.PIDColourScheme;
70 import jalview.schemes.PurinePyrimidineColourScheme;
71 import jalview.schemes.RNAHelicesColour;
72 import jalview.schemes.StrandColourScheme;
73 import jalview.schemes.TCoffeeColourScheme;
74 import jalview.schemes.TaylorColourScheme;
75 import jalview.schemes.TurnColourScheme;
76 import jalview.schemes.ZappoColourScheme;
77 import jalview.structure.StructureSelectionManager;
78 import jalview.structures.models.AAStructureBindingModel;
79 import jalview.util.MappingUtils;
80 import jalview.util.MessageManager;
81 import jalview.viewmodel.AlignmentViewport;
82 import jalview.viewmodel.ViewportRanges;
84 import java.awt.BorderLayout;
85 import java.awt.Canvas;
86 import java.awt.CheckboxMenuItem;
87 import java.awt.Color;
88 import java.awt.FlowLayout;
90 import java.awt.FontMetrics;
91 import java.awt.Frame;
92 import java.awt.Graphics;
93 import java.awt.Label;
95 import java.awt.MenuBar;
96 import java.awt.MenuItem;
97 import java.awt.Panel;
98 import java.awt.event.ActionEvent;
99 import java.awt.event.ActionListener;
100 import java.awt.event.FocusEvent;
101 import java.awt.event.FocusListener;
102 import java.awt.event.ItemEvent;
103 import java.awt.event.ItemListener;
104 import java.awt.event.KeyEvent;
105 import java.awt.event.KeyListener;
106 import java.awt.event.WindowAdapter;
107 import java.awt.event.WindowEvent;
108 import java.io.IOException;
110 import java.net.URLEncoder;
111 import java.util.Arrays;
112 import java.util.Deque;
113 import java.util.HashMap;
114 import java.util.List;
115 import java.util.Map;
116 import java.util.StringTokenizer;
117 import java.util.Vector;
119 import org.jmol.viewer.Viewer;
121 public class AlignFrame extends EmbmenuFrame implements ActionListener,
122 ItemListener, KeyListener, AlignViewControllerGuiI
124 public AlignViewControllerI avc;
126 public AlignmentPanel alignPanel;
128 public AlignViewport viewport;
130 // width and height may be overridden by applet parameters
131 int frameWidth = 700;
133 int frameHeight = 500;
135 String jalviewServletURL;
138 * Flag for showing autocalculated consensus above or below other consensus
141 private boolean showAutoCalculatedAbove;
143 private SequenceAnnotationOrder annotationSortOrder;
146 * Constructor that creates the frame and adds it to the display.
153 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
156 this(al, applet, title, embedded, true);
160 * Constructor that optionally allows the frame to be displayed or only
167 * @param addToDisplay
169 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
170 boolean embedded, boolean addToDisplay)
172 this(al, null, null, applet, title, embedded, addToDisplay);
175 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
176 HiddenColumns hidden, JalviewLite applet,
177 String title, boolean embedded)
179 this(al, hiddenSeqs, hidden, applet, title, embedded, true);
182 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
183 HiddenColumns hidden, JalviewLite applet,
184 String title, boolean embedded, boolean addToDisplay)
188 jalviewServletURL = applet.getParameter("APPLICATION_URL");
194 } catch (Exception ex)
196 ex.printStackTrace();
198 // need to get window geometry before we calculate alignment layout
204 param = applet.getParameter("windowWidth");
207 int width = Integer.parseInt(param);
210 param = applet.getParameter("windowHeight");
213 int height = Integer.parseInt(param);
214 frameHeight = height;
216 } catch (Exception ex)
220 viewport = new AlignViewport(al, applet);
222 if (hiddenSeqs != null && hiddenSeqs.length > 0)
224 viewport.hideSequence(hiddenSeqs);
228 viewport.getAlignment().setHiddenColumns(hidden);
230 viewport.setScaleAboveWrapped(scaleAbove.getState());
232 alignPanel = new AlignmentPanel(this, viewport);
233 avc = new jalview.controller.AlignViewController(this, viewport,
235 viewport.updateConservation(alignPanel);
236 viewport.updateConsensus(alignPanel);
238 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
239 followMouseOverFlag.setState(viewport.isFollowHighlight());
240 showGroupConsensus.setState(viewport.isShowGroupConsensus());
241 showGroupConservation.setState(viewport.isShowGroupConservation());
242 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
243 showSequenceLogo.setState(viewport.isShowSequenceLogo());
244 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
245 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
246 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
247 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
248 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
249 showAlignmentAnnotations.setState(true);
250 showSequenceAnnotations.setState(false);
252 seqLimits.setState(viewport.getShowJVSuffix());
256 String param = applet.getParameter("sortBy");
259 if (param.equalsIgnoreCase("Id"))
261 sortIDMenuItem_actionPerformed();
263 else if (param.equalsIgnoreCase("Pairwise Identity"))
265 sortPairwiseMenuItem_actionPerformed();
267 else if (param.equalsIgnoreCase("Length"))
269 sortLengthMenuItem_actionPerformed();
273 param = applet.getParameter("wrap");
276 if (param.equalsIgnoreCase("true"))
278 wrapMenuItem.setState(true);
279 wrapMenuItem_actionPerformed();
282 param = applet.getParameter("centrecolumnlabels");
285 centreColumnLabelFlag.setState(true);
286 centreColumnLabelFlag_stateChanged();
290 if (viewport.getAlignment().isNucleotide())
292 conservationMenuItem.setEnabled(false);
293 clustalColour.setEnabled(false);
294 BLOSUM62Colour.setEnabled(false);
295 zappoColour.setEnabled(false);
296 taylorColour.setEnabled(false);
297 hydrophobicityColour.setEnabled(false);
298 helixColour.setEnabled(false);
299 strandColour.setEnabled(false);
300 turnColour.setEnabled(false);
301 buriedColour.setEnabled(false);
302 viewport.updateStrucConsensus(alignPanel);
303 if (viewport.getAlignment().hasRNAStructure())
305 RNAHelixColour.setEnabled(true);
309 RNAHelixColour.setEnabled(false);
314 RNAHelixColour.setEnabled(false);
315 purinePyrimidineColour.setEnabled(false);
316 nucleotideColour.setEnabled(false);
318 // Some JVMS send keyevents to Top frame or lowest panel,
319 // Havent worked out why yet. So add to both this frame and seqCanvas for
321 this.addKeyListener(this);
322 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
323 alignPanel.idPanel.idCanvas.addKeyListener(this);
324 alignPanel.scalePanel.addKeyListener(this);
325 alignPanel.annotationPanel.addKeyListener(this);
326 alignPanel.annotationPanelHolder.addKeyListener(this);
327 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
328 alignPanel.alabels.addKeyListener(this);
330 setAnnotationsVisibility();
334 addToDisplay(embedded);
341 public void addToDisplay(boolean embedded)
343 createAlignFrameWindow(embedded);
345 alignPanel.adjustAnnotationHeight();
346 alignPanel.paintAlignment(true);
349 public AlignViewport getAlignViewport()
354 public SeqCanvas getSeqcanvas()
356 return alignPanel.seqPanel.seqCanvas;
360 * Load a features file onto the alignment
363 * file URL, content, or other resolvable path
365 * is protocol for accessing data referred to by file
368 public boolean parseFeaturesFile(String file, DataSourceType type)
370 return parseFeaturesFile(file, type, true);
374 * Load a features file onto the alignment
377 * file URL, content, or other resolvable path
379 * is protocol for accessing data referred to by file
380 * @param autoenabledisplay
381 * when true, display features flag will be automatically enabled if
382 * features are loaded
383 * @return true if data parsed as a features file
385 public boolean parseFeaturesFile(String file, DataSourceType sourceType,
386 boolean autoenabledisplay)
388 boolean featuresFile = false;
391 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
392 .getFeatureRenderer().getFeatureColours();
393 boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
394 "relaxedidmatch", false);
395 featuresFile = new FeaturesFile(file, sourceType).parse(
396 viewport.getAlignment(), colours, true, relaxedIdMatching);
397 } catch (Exception ex)
399 ex.printStackTrace();
404 if (autoenabledisplay)
406 viewport.setShowSequenceFeatures(true);
407 sequenceFeatures.setState(true);
409 if (alignPanel.seqPanel.seqCanvas.fr != null)
411 // update the min/max ranges where necessary
412 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
414 if (viewport.featureSettings != null)
416 viewport.featureSettings.refreshTable();
418 alignPanel.paintAlignment(true);
419 statusBar.setText(MessageManager
420 .getString("label.successfully_added_features_alignment"));
426 public void keyPressed(KeyEvent evt)
428 ViewportRanges ranges = viewport.getRanges();
430 if (viewport.cursorMode
431 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
432 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
433 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
434 && Character.isDigit(evt.getKeyChar()))
436 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
439 switch (evt.getKeyCode())
441 case 27: // escape key
442 deselectAllSequenceMenuItem_actionPerformed();
444 alignPanel.alabels.cancelDrag();
447 if (evt.isControlDown() || evt.isMetaDown())
449 cut_actionPerformed();
453 if (viewport.cursorMode && !evt.isControlDown())
455 alignPanel.seqPanel.setCursorColumn();
457 if (evt.isControlDown() || evt.isMetaDown())
459 copy_actionPerformed();
463 if (evt.isControlDown())
465 paste(evt.isShiftDown());
469 if (evt.isControlDown() || evt.isMetaDown())
471 selectAllSequenceMenuItem_actionPerformed();
474 case KeyEvent.VK_DOWN:
475 if (viewport.cursorMode)
477 alignPanel.seqPanel.moveCursor(0, 1);
481 moveSelectedSequences(false);
486 if (viewport.cursorMode)
488 alignPanel.seqPanel.moveCursor(0, -1);
492 moveSelectedSequences(true);
496 case KeyEvent.VK_LEFT:
497 if (evt.isAltDown() || !viewport.cursorMode)
499 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
503 alignPanel.seqPanel.moveCursor(-1, 0);
507 case KeyEvent.VK_RIGHT:
508 if (evt.isAltDown() || !viewport.cursorMode)
510 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
514 alignPanel.seqPanel.moveCursor(1, 0);
518 case KeyEvent.VK_SPACE:
519 if (viewport.cursorMode)
521 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
522 || evt.isShiftDown() || evt.isAltDown());
526 case KeyEvent.VK_DELETE:
527 case KeyEvent.VK_BACK_SPACE:
528 if (viewport.cursorMode)
530 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
531 || evt.isShiftDown() || evt.isAltDown());
535 cut_actionPerformed();
536 alignPanel.seqPanel.seqCanvas.repaint();
541 if (viewport.cursorMode)
543 alignPanel.seqPanel.setCursorRow();
547 if (viewport.cursorMode)
549 alignPanel.seqPanel.setCursorPosition();
553 case KeyEvent.VK_ENTER:
554 case KeyEvent.VK_COMMA:
555 if (viewport.cursorMode)
557 alignPanel.seqPanel.setCursorRowAndColumn();
562 if (viewport.cursorMode)
564 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
568 if (viewport.cursorMode)
570 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
575 viewport.cursorMode = !viewport.cursorMode;
576 statusBar.setText(MessageManager.formatMessage(
577 "label.keyboard_editing_mode",
578 new String[] { (viewport.cursorMode ? "on" : "off") }));
579 if (viewport.cursorMode)
581 alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
582 alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
587 if (evt.isControlDown())
589 findMenuItem_actionPerformed();
595 boolean toggleSeqs = !evt.isControlDown();
596 boolean toggleCols = !evt.isShiftDown();
597 toggleHiddenRegions(toggleSeqs, toggleCols);
601 case KeyEvent.VK_PAGE_UP:
602 if (viewport.getWrapAlignment())
604 alignPanel.scrollUp(true);
608 alignPanel.setScrollValues(ranges.getStartRes(),
609 2 * ranges.getStartSeq() - ranges.getEndSeq());
613 case KeyEvent.VK_PAGE_DOWN:
614 if (viewport.getWrapAlignment())
616 alignPanel.scrollUp(false);
621 .setScrollValues(ranges.getStartRes(), ranges.getEndSeq());
626 if (evt.isControlDown())
628 undoMenuItem_actionPerformed();
633 if (evt.isControlDown())
635 redoMenuItem_actionPerformed();
640 if (evt.isControlDown())
647 if (evt.isControlDown())
649 trimAlignment(false);
654 if (evt.isControlDown())
656 if (evt.isShiftDown())
658 this.removeAllGapsMenuItem_actionPerformed();
662 removeGappedColumnMenuItem_actionPerformed();
667 if (evt.isControlDown())
671 invertColSel_actionPerformed();
675 invertSequenceMenuItem_actionPerformed();
681 if (evt.isControlDown())
683 if (evt.isShiftDown())
685 this.unGroup_actionPerformed();
689 this.createGroup_actionPerformed();
695 if (evt.isControlDown())
697 this.deleteGroups_actionPerformed();
702 if (evt.isControlDown())
709 alignPanel.paintAlignment(true);
713 * called by key handler and the hide all/show all menu items
718 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
720 boolean hide = false;
721 SequenceGroup sg = viewport.getSelectionGroup();
722 if (!toggleSeqs && !toggleCols)
724 // Hide everything by the current selection - this is a hack - we do the
725 // invert and then hide
726 // first check that there will be visible columns after the invert.
727 if (viewport.hasSelectedColumns()
728 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
731 // now invert the sequence set, if required - empty selection implies
732 // that no hiding is required.
735 invertSequenceMenuItem_actionPerformed();
736 sg = viewport.getSelectionGroup();
740 viewport.expandColSelection(sg, true);
741 // finally invert the column selection and get the new sequence
742 // selection and indicate it should be hidden.
743 invertColSel_actionPerformed();
750 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
753 viewport.hideAllSelectedSeqs();
755 else if (!(toggleCols && viewport.hasSelectedColumns()))
757 viewport.showAllHiddenSeqs();
763 if (viewport.hasSelectedColumns())
765 viewport.hideSelectedColumns();
768 viewport.setSelectionGroup(sg);
773 viewport.showAllHiddenColumns();
775 viewport.sendSelection();
780 public void keyReleased(KeyEvent evt)
785 public void keyTyped(KeyEvent evt)
790 public void itemStateChanged(ItemEvent evt)
792 final Object source = evt.getSource();
793 if (source == displayNonconservedMenuItem)
795 displayNonconservedMenuItem_actionPerformed();
797 else if (source == colourTextMenuItem)
799 colourTextMenuItem_actionPerformed();
801 else if (source == wrapMenuItem)
803 wrapMenuItem_actionPerformed();
805 else if (source == scaleAbove)
807 viewport.setScaleAboveWrapped(scaleAbove.getState());
809 else if (source == scaleLeft)
811 viewport.setScaleLeftWrapped(scaleLeft.getState());
813 else if (source == scaleRight)
815 viewport.setScaleRightWrapped(scaleRight.getState());
817 else if (source == seqLimits)
819 seqLimits_itemStateChanged();
821 else if (source == viewBoxesMenuItem)
823 viewport.setShowBoxes(viewBoxesMenuItem.getState());
825 else if (source == viewTextMenuItem)
827 viewport.setShowText(viewTextMenuItem.getState());
829 else if (source == renderGapsMenuItem)
831 viewport.setRenderGaps(renderGapsMenuItem.getState());
833 else if (source == annotationPanelMenuItem)
835 boolean showAnnotations = annotationPanelMenuItem.getState();
836 showAlignmentAnnotations.setEnabled(showAnnotations);
837 showSequenceAnnotations.setEnabled(showAnnotations);
838 viewport.setShowAnnotation(showAnnotations);
839 alignPanel.setAnnotationVisible(showAnnotations);
841 else if (source == sequenceFeatures)
843 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
844 alignPanel.seqPanel.seqCanvas.repaint();
846 else if (source == showAlignmentAnnotations)
848 setAnnotationsVisibility();
850 else if (source == showSequenceAnnotations)
852 setAnnotationsVisibility();
854 else if (source == sortAnnBySequence)
856 boolean newState = sortAnnBySequence.getState();
857 sortAnnByLabel.setState(false);
858 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
859 : SequenceAnnotationOrder.NONE);
860 setViewportAnnotationOrder();
862 else if (source == sortAnnByLabel)
864 boolean newState = sortAnnByLabel.getState();
865 sortAnnBySequence.setState(false);
866 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
867 : SequenceAnnotationOrder.NONE);
868 setViewportAnnotationOrder();
870 else if (source == showAutoFirst)
872 showAutoLast.setState(!showAutoFirst.getState());
873 setShowAutoCalculatedAbove(showAutoFirst.getState());
874 setViewportAnnotationOrder();
876 else if (source == showAutoLast)
878 showAutoFirst.setState(!showAutoLast.getState());
879 setShowAutoCalculatedAbove(showAutoFirst.getState());
880 setViewportAnnotationOrder();
882 else if (source == conservationMenuItem)
884 conservationMenuItem_actionPerformed();
886 else if (source == abovePIDThreshold)
888 abovePIDThreshold_actionPerformed();
890 else if (source == applyToAllGroups)
892 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
894 else if (source == autoCalculate)
896 viewport.autoCalculateConsensus = autoCalculate.getState();
898 else if (source == sortByTree)
900 viewport.sortByTree = sortByTree.getState();
902 else if (source == this.centreColumnLabelFlag)
904 centreColumnLabelFlag_stateChanged();
906 else if (source == this.followMouseOverFlag)
908 mouseOverFlag_stateChanged();
910 else if (source == showGroupConsensus)
912 showGroupConsensus_actionPerformed();
914 else if (source == showGroupConservation)
916 showGroupConservation_actionPerformed();
918 else if (source == showSequenceLogo)
920 showSequenceLogo_actionPerformed();
922 else if (source == normSequenceLogo)
924 normSequenceLogo_actionPerformed();
926 else if (source == showConsensusHistogram)
928 showConsensusHistogram_actionPerformed();
930 else if (source == applyAutoAnnotationSettings)
932 applyAutoAnnotationSettings_actionPerformed();
934 alignPanel.paintAlignment(true);
938 * Set the visibility state of sequence-related and/or alignment-related
939 * annotations depending on checkbox selections, and repaint.
943 private void setAnnotationsVisibility()
945 boolean showForAlignment = showAlignmentAnnotations.getState();
946 boolean showForSequences = showSequenceAnnotations.getState();
947 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
949 for (AlignmentAnnotation aa : alignPanel.getAlignment()
950 .getAlignmentAnnotation())
952 boolean visible = (aa.sequenceRef == null ? showForAlignment
954 aa.visible = visible;
957 alignPanel.validateAnnotationDimensions(true);
962 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
964 this.annotationSortOrder = order;
968 * Set flags on the viewport that control annotation ordering
970 private void setViewportAnnotationOrder()
972 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
974 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
977 private void setShowAutoCalculatedAbove(boolean showAbove)
979 this.showAutoCalculatedAbove = showAbove;
982 private void mouseOverFlag_stateChanged()
984 viewport.setFollowHighlight(followMouseOverFlag.getState());
985 // TODO: could kick the scrollTo mechanism to reset view for current
989 private void centreColumnLabelFlag_stateChanged()
991 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
992 this.alignPanel.annotationPanel.repaint();
996 public void actionPerformed(ActionEvent evt)
998 viewport.applet.currentAlignFrame = this;
1000 Object source = evt.getSource();
1002 if (source == inputText)
1004 inputText_actionPerformed();
1006 else if (source == loadTree)
1008 loadTree_actionPerformed();
1010 else if (source == loadApplication)
1012 launchFullApplication();
1014 else if (source == loadAnnotations)
1018 else if (source == outputAnnotations)
1020 outputAnnotations(true);
1022 else if (source == outputFeatures)
1024 outputFeatures(true, "Jalview");
1026 else if (source == closeMenuItem)
1028 closeMenuItem_actionPerformed();
1030 else if (source == copy)
1032 copy_actionPerformed();
1034 else if (source == undoMenuItem)
1036 undoMenuItem_actionPerformed();
1038 else if (source == redoMenuItem)
1040 redoMenuItem_actionPerformed();
1042 else if (source == inputText)
1044 inputText_actionPerformed();
1046 else if (source == closeMenuItem)
1048 closeMenuItem_actionPerformed();
1050 else if (source == undoMenuItem)
1052 undoMenuItem_actionPerformed();
1054 else if (source == redoMenuItem)
1056 redoMenuItem_actionPerformed();
1058 else if (source == copy)
1060 copy_actionPerformed();
1062 else if (source == pasteNew)
1064 pasteNew_actionPerformed();
1066 else if (source == pasteThis)
1068 pasteThis_actionPerformed();
1070 else if (source == cut)
1072 cut_actionPerformed();
1074 else if (source == delete)
1076 delete_actionPerformed();
1078 else if (source == createGroup)
1080 createGroup_actionPerformed();
1082 else if (source == unGroup)
1084 unGroup_actionPerformed();
1086 else if (source == grpsFromSelection)
1088 makeGrpsFromSelection_actionPerformed();
1090 else if (source == deleteGroups)
1092 deleteGroups_actionPerformed();
1094 else if (source == selectAllSequenceMenuItem)
1096 selectAllSequenceMenuItem_actionPerformed();
1098 else if (source == deselectAllSequenceMenuItem)
1100 deselectAllSequenceMenuItem_actionPerformed();
1102 else if (source == invertSequenceMenuItem)
1104 invertSequenceMenuItem_actionPerformed();
1105 // uncomment to slave sequence selections in split frame
1106 // viewport.sendSelection();
1108 else if (source == invertColSel)
1110 viewport.invertColumnSelection();
1111 alignPanel.paintAlignment(true);
1112 viewport.sendSelection();
1114 else if (source == remove2LeftMenuItem)
1116 trimAlignment(true);
1118 else if (source == remove2RightMenuItem)
1120 trimAlignment(false);
1122 else if (source == removeGappedColumnMenuItem)
1124 removeGappedColumnMenuItem_actionPerformed();
1126 else if (source == removeAllGapsMenuItem)
1128 removeAllGapsMenuItem_actionPerformed();
1130 else if (source == findMenuItem)
1132 findMenuItem_actionPerformed();
1134 else if (source == font)
1136 new FontChooser(alignPanel);
1138 else if (source == newView)
1142 else if (source == showColumns)
1144 viewport.showAllHiddenColumns();
1145 alignPanel.paintAlignment(true);
1146 viewport.sendSelection();
1148 else if (source == showSeqs)
1150 viewport.showAllHiddenSeqs();
1151 alignPanel.paintAlignment(true);
1152 // uncomment if we want to slave sequence selections in split frame
1153 // viewport.sendSelection();
1155 else if (source == hideColumns)
1157 viewport.hideSelectedColumns();
1158 alignPanel.paintAlignment(true);
1159 viewport.sendSelection();
1161 else if (source == hideSequences
1162 && viewport.getSelectionGroup() != null)
1164 viewport.hideAllSelectedSeqs();
1165 alignPanel.paintAlignment(true);
1166 // uncomment if we want to slave sequence selections in split frame
1167 // viewport.sendSelection();
1169 else if (source == hideAllButSelection)
1171 toggleHiddenRegions(false, false);
1172 alignPanel.paintAlignment(true);
1173 viewport.sendSelection();
1175 else if (source == hideAllSelection)
1177 SequenceGroup sg = viewport.getSelectionGroup();
1178 viewport.expandColSelection(sg, false);
1179 viewport.hideAllSelectedSeqs();
1180 viewport.hideSelectedColumns();
1181 alignPanel.paintAlignment(true);
1182 viewport.sendSelection();
1184 else if (source == showAllHidden)
1186 viewport.showAllHiddenColumns();
1187 viewport.showAllHiddenSeqs();
1188 alignPanel.paintAlignment(true);
1189 viewport.sendSelection();
1191 else if (source == showGroupConsensus)
1193 showGroupConsensus_actionPerformed();
1195 else if (source == showGroupConservation)
1197 showGroupConservation_actionPerformed();
1199 else if (source == showSequenceLogo)
1201 showSequenceLogo_actionPerformed();
1203 else if (source == normSequenceLogo)
1205 normSequenceLogo_actionPerformed();
1207 else if (source == showConsensusHistogram)
1209 showConsensusHistogram_actionPerformed();
1211 else if (source == applyAutoAnnotationSettings)
1213 applyAutoAnnotationSettings_actionPerformed();
1215 else if (source == featureSettings)
1217 new FeatureSettings(alignPanel);
1219 else if (source == alProperties)
1221 StringBuffer contents = new jalview.io.AlignmentProperties(
1222 viewport.getAlignment()).formatAsString();
1223 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1224 cap.setText(contents.toString());
1225 Frame frame = new Frame();
1227 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1228 "label.alignment_properties", new String[] { getTitle() }),
1231 else if (source == overviewMenuItem)
1233 overviewMenuItem_actionPerformed();
1235 else if (source == noColourmenuItem)
1239 else if (source == clustalColour)
1241 abovePIDThreshold.setState(false);
1242 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1244 else if (source == zappoColour)
1246 changeColour(new ZappoColourScheme());
1248 else if (source == taylorColour)
1250 changeColour(new TaylorColourScheme());
1252 else if (source == hydrophobicityColour)
1254 changeColour(new HydrophobicColourScheme());
1256 else if (source == helixColour)
1258 changeColour(new HelixColourScheme());
1260 else if (source == strandColour)
1262 changeColour(new StrandColourScheme());
1264 else if (source == turnColour)
1266 changeColour(new TurnColourScheme());
1268 else if (source == buriedColour)
1270 changeColour(new BuriedColourScheme());
1272 else if (source == nucleotideColour)
1274 changeColour(new NucleotideColourScheme());
1276 else if (source == purinePyrimidineColour)
1278 changeColour(new PurinePyrimidineColourScheme());
1280 // else if (source == RNAInteractionColour)
1282 // changeColour(new RNAInteractionColourScheme());
1284 else if (source == RNAHelixColour)
1286 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1287 // new RNAHelicesColourChooser(viewport, alignPanel);
1289 else if (source == modifyPID)
1291 modifyPID_actionPerformed();
1293 else if (source == modifyConservation)
1295 modifyConservation_actionPerformed();
1297 else if (source == userDefinedColour)
1299 new UserDefinedColours(alignPanel, null);
1301 else if (source == PIDColour)
1303 changeColour(new PIDColourScheme());
1305 else if (source == BLOSUM62Colour)
1307 changeColour(new Blosum62ColourScheme());
1309 else if (source == tcoffeeColour)
1311 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1313 else if (source == annotationColour)
1315 new AnnotationColourChooser(viewport, alignPanel);
1317 else if (source == annotationColumnSelection)
1319 new AnnotationColumnChooser(viewport, alignPanel);
1321 else if (source == sortPairwiseMenuItem)
1323 sortPairwiseMenuItem_actionPerformed();
1325 else if (source == sortIDMenuItem)
1327 sortIDMenuItem_actionPerformed();
1329 else if (source == sortLengthMenuItem)
1331 sortLengthMenuItem_actionPerformed();
1333 else if (source == sortGroupMenuItem)
1335 sortGroupMenuItem_actionPerformed();
1337 else if (source == removeRedundancyMenuItem)
1339 removeRedundancyMenuItem_actionPerformed();
1341 else if (source == pairwiseAlignmentMenuItem)
1343 pairwiseAlignmentMenuItem_actionPerformed();
1345 else if (source == PCAMenuItem)
1347 PCAMenuItem_actionPerformed();
1349 else if (source == averageDistanceTreeMenuItem)
1351 averageDistanceTreeMenuItem_actionPerformed();
1353 else if (source == neighbourTreeMenuItem)
1355 neighbourTreeMenuItem_actionPerformed();
1357 else if (source == njTreeBlosumMenuItem)
1359 njTreeBlosumMenuItem_actionPerformed();
1361 else if (source == avDistanceTreeBlosumMenuItem)
1363 avTreeBlosumMenuItem_actionPerformed();
1365 else if (source == documentation)
1367 documentation_actionPerformed();
1369 else if (source == about)
1371 about_actionPerformed();
1376 public void inputText_actionPerformed()
1378 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1379 Frame frame = new Frame();
1381 jalview.bin.JalviewLite.addFrame(frame,
1382 MessageManager.getString("label.input_cut_paste"), 500, 500);
1385 protected void outputText_actionPerformed(ActionEvent e)
1387 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1388 Frame frame = new Frame();
1390 JalviewLite.addFrame(frame, MessageManager.formatMessage(
1391 "label.alignment_output_command",
1392 new Object[] { e.getActionCommand() }), 600, 500);
1394 FileFormatI fileFormat = FileFormats.getInstance().forName(
1395 e.getActionCommand());
1396 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1397 fileFormat, viewport.getAlignment(),
1398 viewport.getShowJVSuffix()));
1401 public void loadAnnotations()
1403 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1404 cap.setText(MessageManager
1405 .getString("label.paste_features_annotations_Tcoffee_here"));
1406 cap.setAnnotationImport();
1407 Frame frame = new Frame();
1409 jalview.bin.JalviewLite.addFrame(frame,
1410 MessageManager.getString("action.paste_annotations"), 400, 300);
1414 public String outputAnnotations(boolean displayTextbox)
1416 String annotation = new AnnotationFile()
1417 .printAnnotationsForView(viewport);
1421 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1422 Frame frame = new Frame();
1424 jalview.bin.JalviewLite.addFrame(frame,
1425 MessageManager.getString("label.annotations"), 600, 500);
1426 cap.setText(annotation);
1432 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1434 if (alignPanel.getFeatureRenderer() != null
1435 && viewport.getFeaturesDisplayed() != null)
1437 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1443 private List<String> getDisplayedFeatureGroups()
1445 if (alignPanel.getFeatureRenderer() != null
1446 && viewport.getFeaturesDisplayed() != null)
1448 return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
1454 public String outputFeatures(boolean displayTextbox, String format)
1457 FeaturesFile formatter = new FeaturesFile();
1458 if (format.equalsIgnoreCase("Jalview"))
1460 features = formatter.printJalviewFormat(viewport.getAlignment()
1461 .getSequencesArray(), getDisplayedFeatureCols(),
1462 getDisplayedFeatureGroups(), true);
1466 features = formatter.printGffFormat(viewport.getAlignment()
1467 .getSequencesArray(), getDisplayedFeatureCols(),
1468 getDisplayedFeatureGroups(), true);
1473 boolean frimport = false;
1474 if (features == null || features.equals("No Features Visible"))
1476 features = "# No features visible - paste some and import them here.";
1480 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1483 cap.setAnnotationImport();
1485 Frame frame = new Frame();
1487 jalview.bin.JalviewLite.addFrame(frame,
1488 MessageManager.getString("label.features"), 600, 500);
1489 cap.setText(features);
1493 if (features == null)
1502 void launchFullApplication()
1504 StringBuffer url = new StringBuffer(jalviewServletURL);
1506 // allow servlet parameters to be passed in applet parameter
1507 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1509 url.append(firstSep);
1512 + appendProtocol(viewport.applet.getParameter("file")));
1514 if (viewport.applet.getParameter("features") != null)
1516 url.append("&features=");
1517 url.append(appendProtocol(viewport.applet.getParameter("features")));
1520 if (viewport.applet.getParameter("annotations") != null)
1522 url.append("&annotations=");
1523 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1526 if (viewport.applet.getParameter("jnetfile") != null
1527 || viewport.applet.getParameter("jpredfile") != null)
1529 url.append("&annotations=");
1530 url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1531 .getParameter("jnetfile") : viewport.applet
1532 .getParameter("jpredfile")));
1535 if (viewport.applet.getParameter("defaultColour") != null)
1537 url.append("&colour="
1538 + removeWhiteSpace(viewport.applet
1539 .getParameter("defaultColour")));
1542 if (viewport.applet.getParameter("userDefinedColour") != null)
1544 url.append("&colour="
1545 + removeWhiteSpace(viewport.applet
1546 .getParameter("userDefinedColour")));
1548 if (viewport.applet.getParameter("tree") != null)
1551 + appendProtocol(viewport.applet.getParameter("tree")));
1553 if (viewport.applet.getParameter("treeFile") != null)
1556 + appendProtocol(viewport.applet.getParameter("treeFile")));
1559 showURL(url.toString(), "FULL_APP");
1562 String removeWhiteSpace(String colour)
1564 StringBuffer sb = new StringBuffer();
1565 for (int i = 0; i < colour.length(); i++)
1567 if (Character.isWhitespace(colour.charAt(i)))
1573 sb.append(colour.charAt(i));
1577 return sb.toString();
1580 String appendProtocol(String url)
1585 url = URLEncoder.encode(url);
1588 * When we finally deprecate 1.1 compatibility, we can start to use
1589 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1590 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1591 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1592 * ex.printStackTrace(); }
1594 catch (java.net.MalformedURLException ex)
1596 url = viewport.applet.getCodeBase() + url;
1601 public void closeMenuItem_actionPerformed()
1603 PaintRefresher.RemoveComponent(alignPanel);
1604 if (alignPanel.seqPanel != null
1605 && alignPanel.seqPanel.seqCanvas != null)
1607 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1609 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1611 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1614 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1629 void updateEditMenuBar()
1632 if (viewport.getHistoryList().size() > 0)
1634 undoMenuItem.setEnabled(true);
1635 CommandI command = viewport.getHistoryList().peek();
1636 undoMenuItem.setLabel(MessageManager.formatMessage(
1637 "label.undo_command",
1638 new Object[] { command.getDescription() }));
1642 undoMenuItem.setEnabled(false);
1643 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1646 if (viewport.getRedoList().size() > 0)
1648 redoMenuItem.setEnabled(true);
1650 CommandI command = viewport.getRedoList().peek();
1651 redoMenuItem.setLabel(MessageManager.formatMessage(
1652 "label.redo_command",
1653 new Object[] { command.getDescription() }));
1657 redoMenuItem.setEnabled(false);
1658 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1666 public void addHistoryItem(CommandI command)
1668 if (command.getSize() > 0)
1670 viewport.addToHistoryList(command);
1671 viewport.clearRedoList();
1672 updateEditMenuBar();
1673 viewport.updateHiddenColumns();
1678 * TODO: JAL-1104 DOCUMENT ME!
1683 protected void undoMenuItem_actionPerformed()
1685 if (viewport.getHistoryList().isEmpty())
1690 CommandI command = viewport.getHistoryList().pop();
1691 viewport.addToRedoList(command);
1692 command.undoCommand(null);
1694 AlignmentViewport originalSource = getOriginatingSource(command);
1696 if (originalSource != viewport)
1699 .println("Warning: Viewport object mismatch whilst undoing");
1701 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1702 // viewport.getColumnSelection().getHiddenColumns()
1704 updateEditMenuBar();
1705 originalSource.firePropertyChange("alignment", null, originalSource
1706 .getAlignment().getSequences());
1710 * TODO: JAL-1104 DOCUMENT ME!
1715 protected void redoMenuItem_actionPerformed()
1717 if (viewport.getRedoList().isEmpty())
1722 CommandI command = viewport.getRedoList().pop();
1723 viewport.addToHistoryList(command);
1724 command.doCommand(null);
1726 AlignmentViewport originalSource = getOriginatingSource(command);
1728 if (originalSource != viewport)
1731 .println("Warning: Viewport object mismatch whilst re-doing");
1733 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1734 // viewport.getColumnSelection().getHiddenColumns()
1737 updateEditMenuBar();
1738 originalSource.firePropertyChange("alignment", null, originalSource
1739 .getAlignment().getSequences());
1742 AlignmentViewport getOriginatingSource(CommandI command)
1744 AlignmentViewport originalSource = null;
1745 // For sequence removal and addition, we need to fire
1746 // the property change event FROM the viewport where the
1747 // original alignment was altered
1748 AlignmentI al = null;
1749 if (command instanceof EditCommand)
1751 EditCommand editCommand = (EditCommand) command;
1752 al = editCommand.getAlignment();
1753 Vector comps = (Vector) PaintRefresher.components.get(viewport
1754 .getSequenceSetId());
1755 for (int i = 0; i < comps.size(); i++)
1757 if (comps.elementAt(i) instanceof AlignmentPanel)
1759 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1761 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1768 if (originalSource == null)
1770 // The original view is closed, we must validate
1771 // the current view against the closed view first
1774 PaintRefresher.validateSequences(al, viewport.getAlignment());
1777 originalSource = viewport;
1780 return originalSource;
1784 * Move the currently selected sequences up or down one position in the
1789 public void moveSelectedSequences(boolean up)
1791 SequenceGroup sg = viewport.getSelectionGroup();
1796 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1797 up ? null : viewport.getHiddenRepSequences(), up);
1798 alignPanel.paintAlignment(true);
1801 * Also move cDNA/protein complement sequences
1803 AlignViewportI complement = viewport.getCodingComplement();
1804 if (complement != null)
1806 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1807 viewport, complement);
1808 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1809 up ? null : complement.getHiddenRepSequences(), up);
1810 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1814 synchronized void slideSequences(boolean right, int size)
1816 List<SequenceI> sg = new Vector<SequenceI>();
1817 if (viewport.cursorMode)
1819 sg.add(viewport.getAlignment().getSequenceAt(
1820 alignPanel.seqPanel.seqCanvas.cursorY));
1822 else if (viewport.getSelectionGroup() != null
1823 && viewport.getSelectionGroup().getSize() != viewport
1824 .getAlignment().getHeight())
1826 sg = viewport.getSelectionGroup().getSequences(
1827 viewport.getHiddenRepSequences());
1835 Vector<SequenceI> invertGroup = new Vector();
1837 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1839 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1841 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1845 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1847 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1849 for (int i = 0; i < invertGroup.size(); i++)
1851 seqs2[i] = invertGroup.elementAt(i);
1854 SlideSequencesCommand ssc;
1857 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1858 size, viewport.getGapCharacter());
1862 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1863 size, viewport.getGapCharacter());
1866 int groupAdjustment = 0;
1867 if (ssc.getGapsInsertedBegin() && right)
1869 if (viewport.cursorMode)
1871 alignPanel.seqPanel.moveCursor(size, 0);
1875 groupAdjustment = size;
1878 else if (!ssc.getGapsInsertedBegin() && !right)
1880 if (viewport.cursorMode)
1882 alignPanel.seqPanel.moveCursor(-size, 0);
1886 groupAdjustment = -size;
1890 if (groupAdjustment != 0)
1892 viewport.getSelectionGroup().setStartRes(
1893 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1894 viewport.getSelectionGroup().setEndRes(
1895 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1898 boolean appendHistoryItem = false;
1899 Deque<CommandI> historyList = viewport.getHistoryList();
1900 if (historyList != null && historyList.size() > 0
1901 && historyList.peek() instanceof SlideSequencesCommand)
1903 appendHistoryItem = ssc
1904 .appendSlideCommand((SlideSequencesCommand) historyList
1908 if (!appendHistoryItem)
1910 addHistoryItem(ssc);
1916 static StringBuffer copiedSequences;
1918 static Vector copiedHiddenColumns;
1920 protected void copy_actionPerformed()
1922 if (viewport.getSelectionGroup() == null)
1927 SequenceGroup sg = viewport.getSelectionGroup();
1928 copiedSequences = new StringBuffer();
1929 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1930 for (int i = 0; i < sg.getSize(); i++)
1932 SequenceI seq = sg.getSequenceAt(i);
1933 int index = viewport.getAlignment().findIndex(seq);
1934 orderedSeqs.put(index, seq);
1937 int index = 0, startRes, endRes;
1940 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1942 copiedHiddenColumns = new Vector();
1943 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1944 for (int[] region : viewport.getAlignment().getHiddenColumns()
1945 .getHiddenRegions())
1947 copiedHiddenColumns.addElement(new int[] {
1948 region[0] - hiddenOffset, region[1] - hiddenOffset });
1953 copiedHiddenColumns = null;
1956 for (int i = 0; i < sg.getSize(); i++)
1958 SequenceI seq = null;
1962 if (orderedSeqs.containsKey(index))
1964 seq = orderedSeqs.get(index);
1975 // Returns residue following index if gap
1976 startRes = seq.findPosition(sg.getStartRes());
1979 // Need to find the residue preceeding index if gap
1982 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1984 ch = seq.getCharAt(j);
1985 if (!jalview.util.Comparison.isGap((ch)))
1993 endRes += seq.getStart() - 1;
1996 copiedSequences.append(seq.getName()
2002 + seq.getSequenceAsString(sg.getStartRes(),
2003 sg.getEndRes() + 1) + "\n");
2008 protected void pasteNew_actionPerformed()
2013 protected void pasteThis_actionPerformed()
2018 void paste(boolean newAlignment)
2023 if (copiedSequences == null)
2028 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2029 Vector seqs = new Vector();
2030 while (st.hasMoreElements())
2032 String name = st.nextToken();
2033 int start = Integer.parseInt(st.nextToken());
2034 int end = Integer.parseInt(st.nextToken());
2035 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2037 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2038 for (int i = 0; i < seqs.size(); i++)
2040 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2045 String newtitle = MessageManager
2046 .getString("label.copied_sequences");
2047 if (getTitle().startsWith(
2048 MessageManager.getString("label.copied_sequences")))
2050 newtitle = getTitle();
2054 newtitle = newtitle.concat(MessageManager.formatMessage(
2055 "label.from_msname", new String[] { getTitle() }));
2057 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2058 viewport.applet, newtitle, false);
2059 if (copiedHiddenColumns != null)
2061 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2063 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2064 af.viewport.hideColumns(region[0], region[1]);
2068 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2073 addSequences(newSeqs);
2076 } catch (Exception ex)
2078 } // could be anything being pasted in here
2082 void addSequences(SequenceI[] seqs)
2084 for (int i = 0; i < seqs.length; i++)
2086 viewport.getAlignment().addSequence(seqs[i]);
2090 addHistoryItem(new EditCommand(
2091 MessageManager.getString("label.add_sequences"), Action.PASTE,
2092 seqs, 0, viewport.getAlignment().getWidth(),
2093 viewport.getAlignment()));
2095 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2096 viewport.getAlignment().getWidth();
2097 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2102 protected void cut_actionPerformed()
2104 copy_actionPerformed();
2105 delete_actionPerformed();
2108 protected void delete_actionPerformed()
2111 SequenceGroup sg = viewport.getSelectionGroup();
2117 Vector seqs = new Vector();
2119 for (int i = 0; i < sg.getSize(); i++)
2121 seq = sg.getSequenceAt(i);
2122 seqs.addElement(seq);
2126 * If the cut affects all sequences, warn, remove highlighted columns
2128 if (sg.getSize() == viewport.getAlignment().getHeight())
2130 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2131 .getAlignment().getWidth()) ? true : false;
2132 if (isEntireAlignWidth)
2134 String title = MessageManager.getString("label.delete_all");
2135 Panel infoPanel = new Panel();
2136 infoPanel.setLayout(new FlowLayout());
2138 .add(new Label(MessageManager.getString("warn.delete_all")));
2140 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2141 dialog.setMainPanel(infoPanel);
2142 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2143 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2144 dialog.setVisible(true);
2151 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2152 sg.getEndRes() + 1);
2155 SequenceI[] cut = new SequenceI[seqs.size()];
2156 for (int i = 0; i < seqs.size(); i++)
2158 cut[i] = (SequenceI) seqs.elementAt(i);
2162 * //ADD HISTORY ITEM
2164 addHistoryItem(new EditCommand(
2165 MessageManager.getString("label.cut_sequences"), Action.CUT,
2166 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2167 viewport.getAlignment()));
2169 viewport.setSelectionGroup(null);
2170 viewport.getAlignment().deleteGroup(sg);
2172 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2175 if (viewport.getAlignment().getHeight() < 1)
2177 this.setVisible(false);
2179 viewport.sendSelection();
2183 * group consensus toggled
2186 protected void showGroupConsensus_actionPerformed()
2188 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2189 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2194 * group conservation toggled.
2196 protected void showGroupConservation_actionPerformed()
2198 viewport.setShowGroupConservation(showGroupConservation.getState());
2199 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2206 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2207 * .event.ActionEvent)
2209 protected void showConsensusHistogram_actionPerformed()
2211 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2212 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2219 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2220 * .event.ActionEvent)
2222 protected void showSequenceLogo_actionPerformed()
2224 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2225 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2228 protected void normSequenceLogo_actionPerformed()
2230 showSequenceLogo.setState(true);
2231 viewport.setShowSequenceLogo(true);
2232 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2233 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2236 protected void applyAutoAnnotationSettings_actionPerformed()
2238 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2241 protected void makeGrpsFromSelection_actionPerformed()
2243 if (avc.makeGroupsFromSelection())
2245 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2246 alignPanel.updateAnnotation();
2247 alignPanel.paintAlignment(true);
2251 protected void createGroup_actionPerformed()
2256 protected void unGroup_actionPerformed()
2260 alignPanel.alignmentChanged();
2264 protected void deleteGroups_actionPerformed()
2266 if (avc.deleteGroups())
2268 alignPanel.alignmentChanged();
2272 public void selectAllSequenceMenuItem_actionPerformed()
2274 SequenceGroup sg = new SequenceGroup();
2275 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2277 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2279 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2280 viewport.setSelectionGroup(sg);
2281 // JAL-2034 - should delegate to
2282 // alignPanel to decide if overview needs
2284 alignPanel.paintAlignment(false);
2285 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2286 viewport.sendSelection();
2289 public void deselectAllSequenceMenuItem_actionPerformed()
2291 if (viewport.cursorMode)
2293 alignPanel.seqPanel.keyboardNo1 = null;
2294 alignPanel.seqPanel.keyboardNo2 = null;
2296 viewport.setSelectionGroup(null);
2297 viewport.getColumnSelection().clear();
2298 viewport.setSelectionGroup(null);
2299 alignPanel.idPanel.idCanvas.searchResults = null;
2300 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2301 // JAL-2034 - should delegate to
2302 // alignPanel to decide if overview needs
2304 alignPanel.paintAlignment(false);
2305 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2306 viewport.sendSelection();
2309 public void invertSequenceMenuItem_actionPerformed()
2311 SequenceGroup sg = viewport.getSelectionGroup();
2312 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2314 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2317 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2318 viewport.sendSelection();
2321 public void invertColSel_actionPerformed()
2323 viewport.invertColumnSelection();
2324 alignPanel.paintAlignment(true);
2325 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2326 viewport.sendSelection();
2329 void trimAlignment(boolean trimLeft)
2331 AlignmentI al = viewport.getAlignment();
2332 ViewportRanges ranges = viewport.getRanges();
2333 ColumnSelection colSel = viewport.getColumnSelection();
2336 if (!colSel.isEmpty())
2340 column = colSel.getMin();
2344 column = colSel.getMax();
2348 if (viewport.getSelectionGroup() != null)
2350 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2351 viewport.getHiddenRepSequences());
2355 seqs = al.getSequencesArray();
2358 TrimRegionCommand trimRegion;
2361 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2363 ranges.setStartRes(0);
2367 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2371 statusBar.setText(MessageManager.formatMessage(
2372 "label.removed_columns",
2373 new String[] { Integer.valueOf(trimRegion.getSize())
2375 addHistoryItem(trimRegion);
2377 for (SequenceGroup sg : al.getGroups())
2379 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2380 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2386 viewport.firePropertyChange("alignment", null, al.getSequences());
2390 public void removeGappedColumnMenuItem_actionPerformed()
2392 AlignmentI al = viewport.getAlignment();
2393 ViewportRanges ranges = viewport.getRanges();
2395 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2398 if (viewport.getSelectionGroup() != null)
2400 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2401 viewport.getHiddenRepSequences());
2402 start = viewport.getSelectionGroup().getStartRes();
2403 end = viewport.getSelectionGroup().getEndRes();
2407 seqs = viewport.getAlignment().getSequencesArray();
2410 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2411 "Remove Gapped Columns", seqs, start, end,
2412 viewport.getAlignment());
2414 addHistoryItem(removeGapCols);
2416 statusBar.setText(MessageManager.formatMessage(
2417 "label.removed_empty_columns",
2418 new String[] { Integer.valueOf(removeGapCols.getSize())
2421 // This is to maintain viewport position on first residue
2422 // of first sequence
2423 SequenceI seq = al.getSequenceAt(0);
2424 int startRes = seq.findPosition(ranges.getStartRes());
2425 // ShiftList shifts;
2426 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2427 // edit.alColumnChanges=shifts.getInverse();
2428 // if (viewport.hasHiddenColumns)
2429 // viewport.getColumnSelection().compensateForEdits(shifts);
2430 ranges.setStartRes(seq.findIndex(startRes) - 1);
2431 viewport.firePropertyChange("alignment", null, al.getSequences());
2435 public void removeAllGapsMenuItem_actionPerformed()
2437 AlignmentI al = viewport.getAlignment();
2438 ViewportRanges ranges = viewport.getRanges();
2440 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2443 if (viewport.getSelectionGroup() != null)
2445 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2446 viewport.getHiddenRepSequences());
2447 start = viewport.getSelectionGroup().getStartRes();
2448 end = viewport.getSelectionGroup().getEndRes();
2452 seqs = viewport.getAlignment().getSequencesArray();
2455 // This is to maintain viewport position on first residue
2456 // of first sequence
2457 SequenceI seq = al.getSequenceAt(0);
2458 int startRes = seq.findPosition(ranges.getStartRes());
2460 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2463 ranges.setStartRes(seq.findIndex(startRes) - 1);
2465 viewport.firePropertyChange("alignment", null, al.getSequences());
2469 public void findMenuItem_actionPerformed()
2471 new Finder(alignPanel);
2475 * create a new view derived from the current view
2478 * @return frame for the new view
2480 public AlignFrame newView(String viewtitle)
2483 if (viewport.hasHiddenRows())
2485 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2486 .getFullAlignment().getSequencesArray());
2490 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2493 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2495 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2497 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2499 newal.addAnnotation(viewport.getAlignment()
2500 .getAlignmentAnnotation()[i]);
2505 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2507 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2508 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2509 PaintRefresher.Register(newaf.alignPanel,
2510 newaf.alignPanel.av.getSequenceSetId());
2512 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2513 newaf.alignPanel.av.getSequenceSetId());
2514 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2515 newaf.alignPanel.av.getSequenceSetId());
2517 Vector comps = (Vector) PaintRefresher.components.get(viewport
2518 .getSequenceSetId());
2520 for (int i = 0; i < comps.size(); i++)
2522 if (comps.elementAt(i) instanceof AlignmentPanel)
2528 String title = new String(this.getTitle());
2529 if (viewtitle != null)
2531 title = viewtitle + " ( " + title + ")";
2535 if (title.indexOf("(View") > -1)
2537 title = title.substring(0, title.indexOf("(View"));
2539 title += "(View " + viewSize + ")";
2542 newaf.setTitle(title.toString());
2544 newaf.viewport.setHistoryList(viewport.getHistoryList());
2545 newaf.viewport.setRedoList(viewport.getRedoList());
2551 * @return list of feature groups on the view
2553 public String[] getFeatureGroups()
2555 FeatureRenderer fr = null;
2556 if (alignPanel != null
2557 && (fr = alignPanel.getFeatureRenderer()) != null)
2559 List<String> gps = fr.getFeatureGroups();
2560 String[] _gps = gps.toArray(new String[gps.size()]);
2567 * get sequence feature groups that are hidden or shown
2573 public String[] getFeatureGroupsOfState(boolean visible)
2575 FeatureRenderer fr = null;
2576 if (alignPanel != null
2577 && (fr = alignPanel.getFeatureRenderer()) != null)
2579 List<String> gps = fr.getGroups(visible);
2580 String[] _gps = gps.toArray(new String[gps.size()]);
2587 * Change the display state for the given feature groups
2590 * list of group strings
2592 * visible or invisible
2594 public void setFeatureGroupState(String[] groups, boolean state)
2596 FeatureRenderer fr = null;
2597 this.sequenceFeatures.setState(true);
2598 viewport.setShowSequenceFeatures(true);
2599 if (alignPanel != null
2600 && (fr = alignPanel.getFeatureRenderer()) != null)
2603 fr.setGroupVisibility(Arrays.asList(groups), state);
2604 alignPanel.seqPanel.seqCanvas.repaint();
2605 if (alignPanel.overviewPanel != null)
2607 alignPanel.overviewPanel.updateOverviewImage();
2612 public void seqLimits_itemStateChanged()
2614 viewport.setShowJVSuffix(seqLimits.getState());
2615 alignPanel.fontChanged();
2616 alignPanel.paintAlignment(true);
2619 protected void colourTextMenuItem_actionPerformed()
2621 viewport.setColourText(colourTextMenuItem.getState());
2622 alignPanel.paintAlignment(true);
2625 protected void displayNonconservedMenuItem_actionPerformed()
2627 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2628 alignPanel.paintAlignment(true);
2631 protected void wrapMenuItem_actionPerformed()
2633 viewport.setWrapAlignment(wrapMenuItem.getState());
2634 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2635 scaleAbove.setEnabled(wrapMenuItem.getState());
2636 scaleLeft.setEnabled(wrapMenuItem.getState());
2637 scaleRight.setEnabled(wrapMenuItem.getState());
2638 alignPanel.paintAlignment(true);
2641 public void overviewMenuItem_actionPerformed()
2643 if (alignPanel.overviewPanel != null)
2648 Frame frame = new Frame();
2649 OverviewPanel overview = new OverviewPanel(alignPanel);
2650 frame.add(overview);
2651 // +50 must allow for applet frame window
2652 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2653 "label.overview_params", new String[] { this.getTitle() }),
2654 overview.getPreferredSize().width,
2655 overview.getPreferredSize().height + 50);
2658 final AlignmentPanel ap = alignPanel;
2659 frame.addWindowListener(new WindowAdapter()
2662 public void windowClosing(WindowEvent e)
2666 ap.setOverviewPanel(null);
2671 alignPanel.setOverviewPanel(overview);
2676 public void changeColour(ColourSchemeI cs)
2678 viewport.setGlobalColourScheme(cs);
2680 alignPanel.paintAlignment(true);
2683 protected void modifyPID_actionPerformed()
2685 if (viewport.getAbovePIDThreshold()
2686 && viewport.getGlobalColourScheme() != null)
2688 SliderPanel.setPIDSliderSource(alignPanel,
2689 viewport.getResidueShading(), alignPanel.getViewName());
2690 SliderPanel.showPIDSlider();
2694 protected void modifyConservation_actionPerformed()
2696 if (viewport.getConservationSelected()
2697 && viewport.getGlobalColourScheme() != null)
2699 SliderPanel.setConservationSlider(alignPanel,
2700 viewport.getResidueShading(), alignPanel.getViewName());
2701 SliderPanel.showConservationSlider();
2705 protected void conservationMenuItem_actionPerformed()
2707 boolean selected = conservationMenuItem.getState();
2708 modifyConservation.setEnabled(selected);
2709 viewport.setConservationSelected(selected);
2710 viewport.getResidueShading().setConservationApplied(selected);
2712 changeColour(viewport.getGlobalColourScheme());
2716 modifyConservation_actionPerformed();
2720 SliderPanel.hideConservationSlider();
2724 public void abovePIDThreshold_actionPerformed()
2726 boolean selected = abovePIDThreshold.getState();
2727 modifyPID.setEnabled(selected);
2728 viewport.setAbovePIDThreshold(selected);
2731 viewport.getResidueShading().setThreshold(0,
2732 viewport.isIgnoreGapsConsensus());
2735 changeColour(viewport.getGlobalColourScheme());
2739 modifyPID_actionPerformed();
2743 SliderPanel.hidePIDSlider();
2747 public void sortPairwiseMenuItem_actionPerformed()
2749 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2750 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2751 .getAlignment().getSequenceAt(0));
2753 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2754 viewport.getAlignment()));
2755 alignPanel.paintAlignment(true);
2758 public void sortIDMenuItem_actionPerformed()
2760 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2761 AlignmentSorter.sortByID(viewport.getAlignment());
2762 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2763 viewport.getAlignment()));
2764 alignPanel.paintAlignment(true);
2767 public void sortLengthMenuItem_actionPerformed()
2769 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2770 AlignmentSorter.sortByLength(viewport.getAlignment());
2771 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2772 viewport.getAlignment()));
2773 alignPanel.paintAlignment(true);
2776 public void sortGroupMenuItem_actionPerformed()
2778 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2779 AlignmentSorter.sortByGroup(viewport.getAlignment());
2780 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2781 viewport.getAlignment()));
2782 alignPanel.paintAlignment(true);
2786 public void removeRedundancyMenuItem_actionPerformed()
2788 new RedundancyPanel(alignPanel);
2791 public void pairwiseAlignmentMenuItem_actionPerformed()
2793 if (viewport.getSelectionGroup() != null
2794 && viewport.getSelectionGroup().getSize() > 1)
2796 Frame frame = new Frame();
2797 frame.add(new PairwiseAlignPanel(alignPanel));
2798 jalview.bin.JalviewLite.addFrame(frame,
2799 MessageManager.getString("action.pairwise_alignment"), 600,
2804 public void PCAMenuItem_actionPerformed()
2806 // are the sequences aligned?
2807 if (!viewport.getAlignment().isAligned(false))
2810 int Width = viewport.getAlignment().getWidth();
2812 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2814 current = viewport.getAlignment().getSequenceAt(i);
2816 if (current.getLength() < Width)
2818 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2821 alignPanel.paintAlignment(true);
2824 if ((viewport.getSelectionGroup() != null
2825 && viewport.getSelectionGroup().getSize() < 4 && viewport
2826 .getSelectionGroup().getSize() > 0)
2827 || viewport.getAlignment().getHeight() < 4)
2834 new PCAPanel(viewport);
2835 } catch (java.lang.OutOfMemoryError ex)
2841 public void averageDistanceTreeMenuItem_actionPerformed()
2843 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2844 "Average distance tree using PID");
2847 public void neighbourTreeMenuItem_actionPerformed()
2849 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2850 "Neighbour joining tree using PID");
2853 protected void njTreeBlosumMenuItem_actionPerformed()
2855 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance()
2856 .getBlosum62().getName(),
2857 "Neighbour joining tree using BLOSUM62");
2860 protected void avTreeBlosumMenuItem_actionPerformed()
2862 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance()
2863 .getBlosum62().getName(),
2864 "Average distance tree using BLOSUM62");
2867 void newTreePanel(String type, String pwType, String title)
2869 // are the sequences aligned?
2870 if (!viewport.getAlignment().isAligned(false))
2873 int Width = viewport.getAlignment().getWidth();
2875 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2877 current = viewport.getAlignment().getSequenceAt(i);
2879 if (current.getLength() < Width)
2881 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2884 alignPanel.paintAlignment(true);
2888 if ((viewport.getSelectionGroup() != null && viewport
2889 .getSelectionGroup().getSize() > 1)
2890 || (viewport.getAlignment().getHeight() > 1))
2892 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2894 addTreeMenuItem(tp, title);
2896 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2900 void loadTree_actionPerformed()
2902 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2903 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2904 cap.setTreeImport();
2905 Frame frame = new Frame();
2907 jalview.bin.JalviewLite.addFrame(frame,
2908 MessageManager.getString("label.paste_newick_file"), 400, 300);
2911 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2913 TreePanel tp = new TreePanel(alignPanel, treeFile,
2914 MessageManager.getString("label.load_tree_from_file"), tree);
2915 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2916 addTreeMenuItem(tp, treeFile);
2920 * sort the alignment using the given treePanel
2923 * tree used to sort view
2925 * string used for undo event name
2927 public void sortByTree(TreePanel treePanel, String title)
2929 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2931 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2932 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2933 // HistoryItem.SORT));
2934 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2935 "label.order_by_params", new String[] { title }), oldOrder,
2936 viewport.getAlignment()));
2937 alignPanel.paintAlignment(true);
2941 * Do any automatic reordering of the alignment and add the necessary bits to
2942 * the menu structure for the new tree
2947 protected void addTreeMenuItem(final TreePanel treePanel,
2950 final MenuItem item = new MenuItem(title);
2951 sortByTreeMenu.add(item);
2952 item.addActionListener(new java.awt.event.ActionListener()
2955 public void actionPerformed(ActionEvent evt)
2957 sortByTree(treePanel, title); // treePanel.getTitle());
2961 treePanel.addWindowListener(new WindowAdapter()
2964 public void windowOpened(WindowEvent e)
2966 if (viewport.sortByTree)
2968 sortByTree(treePanel, title);
2970 super.windowOpened(e);
2974 public void windowClosing(WindowEvent e)
2976 sortByTreeMenu.remove(item);
2981 public boolean sortBy(AlignmentOrder alorder, String undoname)
2983 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2984 if (viewport.applet.debug)
2986 System.err.println("Sorting " + alorder.getOrder().size()
2987 + " in alignment '" + getTitle() + "'");
2989 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2990 if (undoname != null)
2992 addHistoryItem(new OrderCommand(undoname, oldOrder,
2993 viewport.getAlignment()));
2995 alignPanel.paintAlignment(true);
2999 protected void documentation_actionPerformed()
3001 alignPanel.av.applet.openJalviewHelpUrl();
3004 protected void about_actionPerformed()
3007 class AboutPanel extends Canvas
3013 public AboutPanel(String version, String builddate)
3015 this.version = version;
3016 this.builddate = builddate;
3020 public void paint(Graphics g)
3022 g.setColor(Color.white);
3023 g.fillRect(0, 0, getSize().width, getSize().height);
3024 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3025 FontMetrics fm = g.getFontMetrics();
3026 int fh = fm.getHeight();
3028 g.setColor(Color.black);
3029 // TODO: update this text for each release or centrally store it for
3030 // lite and application
3031 g.setFont(new Font("Helvetica", Font.BOLD, 14));
3032 g.drawString(MessageManager.formatMessage(
3033 "label.jalviewLite_release", new String[] { version }), x,
3035 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3036 g.drawString(MessageManager.formatMessage(
3037 "label.jaview_build_date", new String[] { builddate }), x,
3039 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3040 g.drawString(MessageManager.getString("label.jalview_authors_1"),
3042 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3043 x + 50, y += fh + 8);
3045 MessageManager.getString("label.jalview_dev_managers"), x,
3047 g.drawString(MessageManager
3048 .getString("label.jalview_distribution_lists"), x, y += fh);
3049 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3052 MessageManager.getString("label.jalview_cite_1_authors"),
3055 MessageManager.getString("label.jalview_cite_1_title"), x,
3057 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3062 Frame frame = new Frame();
3063 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3065 jalview.bin.JalviewLite.addFrame(frame,
3066 MessageManager.getString("label.jalview"), 580, 220);
3070 public void showURL(String url, String target)
3072 if (viewport.applet == null)
3074 System.out.println("Not running as applet - no browser available.");
3078 viewport.applet.showURL(url, target);
3082 // ////////////////////////////////////////////////////////////////////////////////
3083 // JBuilder Graphics here
3085 MenuBar alignFrameMenuBar = new MenuBar();
3087 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3089 MenuItem loadApplication = new MenuItem(
3090 MessageManager.getString("label.view_full_application"));
3092 MenuItem loadTree = new MenuItem(
3093 MessageManager.getString("label.load_associated_tree"));
3095 MenuItem loadAnnotations = new MenuItem(
3096 MessageManager.getString("label.load_features_annotations"));
3098 MenuItem outputFeatures = new MenuItem(
3099 MessageManager.getString("label.export_features"));
3101 MenuItem outputAnnotations = new MenuItem(
3102 MessageManager.getString("label.export_annotations"));
3104 MenuItem closeMenuItem = new MenuItem(
3105 MessageManager.getString("action.close"));
3107 MenuItem selectAllSequenceMenuItem = new MenuItem(
3108 MessageManager.getString("action.select_all"));
3110 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3111 MessageManager.getString("action.deselect_all"));
3113 MenuItem invertSequenceMenuItem = new MenuItem(
3114 MessageManager.getString("action.invert_selection"));
3116 MenuItem remove2LeftMenuItem = new MenuItem();
3118 MenuItem remove2RightMenuItem = new MenuItem();
3120 MenuItem removeGappedColumnMenuItem = new MenuItem();
3122 MenuItem removeAllGapsMenuItem = new MenuItem();
3124 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3126 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3128 MenuItem sortPairwiseMenuItem = new MenuItem();
3130 MenuItem sortIDMenuItem = new MenuItem();
3132 MenuItem sortLengthMenuItem = new MenuItem();
3134 MenuItem sortGroupMenuItem = new MenuItem();
3136 MenuItem removeRedundancyMenuItem = new MenuItem();
3138 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3140 MenuItem PCAMenuItem = new MenuItem();
3142 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3144 MenuItem neighbourTreeMenuItem = new MenuItem();
3146 BorderLayout borderLayout1 = new BorderLayout();
3148 public Label statusBar = new Label();
3150 MenuItem clustalColour = new MenuItem();
3152 MenuItem zappoColour = new MenuItem();
3154 MenuItem taylorColour = new MenuItem();
3156 MenuItem hydrophobicityColour = new MenuItem();
3158 MenuItem helixColour = new MenuItem();
3160 MenuItem strandColour = new MenuItem();
3162 MenuItem turnColour = new MenuItem();
3164 MenuItem buriedColour = new MenuItem();
3166 MenuItem purinePyrimidineColour = new MenuItem();
3168 // MenuItem RNAInteractionColour = new MenuItem();
3170 MenuItem RNAHelixColour = new MenuItem();
3172 MenuItem userDefinedColour = new MenuItem();
3174 MenuItem PIDColour = new MenuItem();
3176 MenuItem BLOSUM62Colour = new MenuItem();
3178 MenuItem tcoffeeColour = new MenuItem();
3180 MenuItem njTreeBlosumMenuItem = new MenuItem();
3182 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3184 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3186 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3188 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3190 MenuItem alProperties = new MenuItem(
3191 MessageManager.getString("label.alignment_props"));
3193 MenuItem overviewMenuItem = new MenuItem();
3195 MenuItem undoMenuItem = new MenuItem();
3197 MenuItem redoMenuItem = new MenuItem();
3199 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3201 MenuItem noColourmenuItem = new MenuItem();
3203 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3205 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3207 MenuItem findMenuItem = new MenuItem();
3209 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3211 MenuItem nucleotideColour = new MenuItem();
3213 MenuItem deleteGroups = new MenuItem();
3215 MenuItem grpsFromSelection = new MenuItem();
3217 MenuItem createGroup = new MenuItem();
3219 MenuItem unGroup = new MenuItem();
3221 MenuItem delete = new MenuItem();
3223 MenuItem copy = new MenuItem();
3225 MenuItem cut = new MenuItem();
3227 Menu pasteMenu = new Menu();
3229 MenuItem pasteNew = new MenuItem();
3231 MenuItem pasteThis = new MenuItem();
3233 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3235 MenuItem font = new MenuItem();
3237 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3239 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3241 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3243 MenuItem modifyPID = new MenuItem();
3245 MenuItem modifyConservation = new MenuItem();
3247 CheckboxMenuItem autoCalculate = null;
3249 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3250 "Sort Alignment With New Tree", true);
3252 Menu sortByTreeMenu = new Menu();
3254 MenuItem inputText = new MenuItem();
3256 MenuItem documentation = new MenuItem();
3258 MenuItem about = new MenuItem();
3260 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3262 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3264 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3266 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3268 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3270 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3272 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3274 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3276 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3279 * Initialise menus and other items
3283 private void jbInit() throws Exception
3285 setMenuBar(alignFrameMenuBar);
3288 * Configure File menu items and actions
3291 .setLabel(MessageManager.getString("label.input_from_textbox"));
3292 inputText.addActionListener(this);
3293 Menu outputTextboxMenu = new Menu(
3294 MessageManager.getString("label.out_to_textbox"));
3295 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3297 MenuItem item = new MenuItem(ff);
3299 item.addActionListener(new java.awt.event.ActionListener()
3302 public void actionPerformed(ActionEvent e)
3304 outputText_actionPerformed(e);
3308 outputTextboxMenu.add(item);
3310 closeMenuItem.addActionListener(this);
3311 loadApplication.addActionListener(this);
3312 loadTree.addActionListener(this);
3313 loadAnnotations.addActionListener(this);
3314 outputFeatures.addActionListener(this);
3315 outputAnnotations.addActionListener(this);
3318 * Configure Edit menu items and actions
3320 undoMenuItem.setEnabled(false);
3321 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3322 undoMenuItem.addActionListener(this);
3323 redoMenuItem.setEnabled(false);
3324 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3325 redoMenuItem.addActionListener(this);
3326 copy.setLabel(MessageManager.getString("action.copy"));
3327 copy.addActionListener(this);
3328 cut.setLabel(MessageManager.getString("action.cut"));
3329 cut.addActionListener(this);
3330 delete.setLabel(MessageManager.getString("action.delete"));
3331 delete.addActionListener(this);
3332 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3333 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3334 pasteNew.addActionListener(this);
3335 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3336 pasteThis.addActionListener(this);
3337 remove2LeftMenuItem.setLabel(MessageManager
3338 .getString("action.remove_left"));
3339 remove2LeftMenuItem.addActionListener(this);
3340 remove2RightMenuItem.setLabel(MessageManager
3341 .getString("action.remove_right"));
3342 remove2RightMenuItem.addActionListener(this);
3343 removeGappedColumnMenuItem.setLabel(MessageManager
3344 .getString("action.remove_empty_columns"));
3345 removeGappedColumnMenuItem.addActionListener(this);
3346 removeAllGapsMenuItem.setLabel(MessageManager
3347 .getString("action.remove_all_gaps"));
3348 removeAllGapsMenuItem.addActionListener(this);
3349 removeRedundancyMenuItem.setLabel(MessageManager
3350 .getString("action.remove_redundancy"));
3351 removeRedundancyMenuItem.addActionListener(this);
3354 * Configure Select menu items and actions
3356 findMenuItem.setLabel(MessageManager.getString("action.find"));
3357 findMenuItem.addActionListener(this);
3358 selectAllSequenceMenuItem.addActionListener(this);
3359 deselectAllSequenceMenuItem.addActionListener(this);
3360 invertSequenceMenuItem.setLabel(MessageManager
3361 .getString("action.invert_sequence_selection"));
3362 invertSequenceMenuItem.addActionListener(this);
3363 invertColSel.setLabel(MessageManager
3364 .getString("action.invert_column_selection"));
3365 invertColSel.addActionListener(this);
3366 deleteGroups.setLabel(MessageManager
3367 .getString("action.undefine_groups"));
3368 deleteGroups.addActionListener(this);
3369 grpsFromSelection.setLabel(MessageManager
3370 .getString("action.make_groups_selection"));
3371 grpsFromSelection.addActionListener(this);
3372 createGroup.setLabel(MessageManager.getString("action.create_group"));
3373 createGroup.addActionListener(this);
3374 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3375 unGroup.addActionListener(this);
3377 annotationColumnSelection.setLabel(MessageManager
3378 .getString("action.select_by_annotation"));
3379 annotationColumnSelection.addActionListener(this);
3382 * Configure View menu items and actions
3384 newView.setLabel(MessageManager.getString("action.new_view"));
3385 newView.addActionListener(this);
3386 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3387 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3388 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3389 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3391 .setLabel(MessageManager.getString("label.selected_columns"));
3392 hideSequences.setLabel(MessageManager
3393 .getString("label.selected_sequences"));
3394 hideAllButSelection.setLabel(MessageManager
3395 .getString("label.all_but_selected_region"));
3396 hideAllSelection.setLabel(MessageManager
3397 .getString("label.selected_region"));
3398 showAllHidden.setLabel(MessageManager
3399 .getString("label.all_sequences_columns"));
3400 showColumns.addActionListener(this);
3401 showSeqs.addActionListener(this);
3402 hideColumns.addActionListener(this);
3403 hideSequences.addActionListener(this);
3404 hideAllButSelection.addActionListener(this);
3405 hideAllSelection.addActionListener(this);
3406 showAllHidden.addActionListener(this);
3407 featureSettings.setLabel(MessageManager
3408 .getString("action.feature_settings"));
3409 featureSettings.addActionListener(this);
3410 sequenceFeatures.setLabel(MessageManager
3411 .getString("label.show_sequence_features"));
3412 sequenceFeatures.addItemListener(this);
3413 sequenceFeatures.setState(false);
3414 followMouseOverFlag.setLabel(MessageManager
3415 .getString("label.automatic_scrolling"));
3416 followMouseOverFlag.addItemListener(this);
3417 alProperties.addActionListener(this);
3418 overviewMenuItem.setLabel(MessageManager
3419 .getString("label.overview_window"));
3420 overviewMenuItem.addActionListener(this);
3423 * Configure Annotations menu items and actions
3425 annotationPanelMenuItem.setLabel(MessageManager
3426 .getString("label.show_annotations"));
3427 annotationPanelMenuItem.addItemListener(this);
3428 showGroupConsensus.setLabel(MessageManager
3429 .getString("label.group_consensus"));
3430 showGroupConservation.setLabel(MessageManager
3431 .getString("label.group_conservation"));
3432 showConsensusHistogram.setLabel(MessageManager
3433 .getString("label.show_consensus_histogram"));
3434 showSequenceLogo.setLabel(MessageManager
3435 .getString("label.show_consensus_logo"));
3436 normSequenceLogo.setLabel(MessageManager
3437 .getString("label.norm_consensus_logo"));
3438 applyAutoAnnotationSettings.setLabel(MessageManager
3439 .getString("label.apply_all_groups"));
3440 applyAutoAnnotationSettings.setState(true);
3441 Menu autoAnnMenu = new Menu(
3442 MessageManager.getString("label.autocalculated_annotation"));
3443 showGroupConsensus.addItemListener(this);
3444 showGroupConservation.addItemListener(this);
3445 showConsensusHistogram.addItemListener(this);
3446 showSequenceLogo.addItemListener(this);
3447 normSequenceLogo.addItemListener(this);
3448 applyAutoAnnotationSettings.addItemListener(this);
3449 showAlignmentAnnotations = new CheckboxMenuItem(
3450 MessageManager.getString("label.show_all_al_annotations"));
3451 showSequenceAnnotations = new CheckboxMenuItem(
3452 MessageManager.getString("label.show_all_seq_annotations"));
3453 sortAnnBySequence = new CheckboxMenuItem(
3454 MessageManager.getString("label.sort_annotations_by_sequence"));
3455 sortAnnByLabel = new CheckboxMenuItem(
3456 MessageManager.getString("label.sort_annotations_by_label"));
3457 showAutoFirst = new CheckboxMenuItem(
3458 MessageManager.getString("label.show_first"));
3459 showAutoFirst.setState(false); // pending applet parameter
3460 setShowAutoCalculatedAbove(showAutoFirst.getState());
3461 showAutoLast = new CheckboxMenuItem(
3462 MessageManager.getString("label.show_last"));
3463 showAutoLast.setState(!showAutoFirst.getState());
3464 showAlignmentAnnotations.addItemListener(this);
3465 showSequenceAnnotations.addItemListener(this);
3466 sortAnnBySequence.addItemListener(this);
3467 sortAnnByLabel.addItemListener(this);
3468 showAutoFirst.addItemListener(this);
3469 showAutoLast.addItemListener(this);
3472 * Configure Format menu items and actions
3474 font.setLabel(MessageManager.getString("action.font"));
3475 font.addActionListener(this);
3476 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3477 scaleAbove.setState(true);
3478 scaleAbove.setEnabled(false);
3479 scaleAbove.addItemListener(this);
3480 scaleLeft.setEnabled(false);
3481 scaleLeft.setState(true);
3482 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3483 scaleLeft.addItemListener(this);
3484 scaleRight.setEnabled(false);
3485 scaleRight.setState(true);
3486 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3487 scaleRight.addItemListener(this);
3488 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3489 viewBoxesMenuItem.setState(true);
3490 viewBoxesMenuItem.addItemListener(this);
3491 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3492 viewTextMenuItem.setState(true);
3493 viewTextMenuItem.addItemListener(this);
3494 colourTextMenuItem.setLabel(MessageManager
3495 .getString("label.colour_text"));
3496 colourTextMenuItem.addItemListener(this);
3497 displayNonconservedMenuItem.setLabel(MessageManager
3498 .getString("label.show_non_conserved"));
3499 displayNonconservedMenuItem.addItemListener(this);
3500 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3501 wrapMenuItem.addItemListener(this);
3502 renderGapsMenuItem.setLabel(MessageManager
3503 .getString("action.show_gaps"));
3504 renderGapsMenuItem.setState(true);
3505 renderGapsMenuItem.addItemListener(this);
3506 centreColumnLabelFlag.setLabel(MessageManager
3507 .getString("label.centre_column_labels"));
3508 centreColumnLabelFlag.addItemListener(this);
3509 seqLimits.setState(true);
3510 seqLimits.setLabel(MessageManager
3511 .getString("label.show_sequence_limits"));
3512 seqLimits.addItemListener(this);
3515 * Configure Colour menu items and actions
3517 applyToAllGroups.setLabel(MessageManager
3518 .getString("label.apply_colour_to_all_groups"));
3519 applyToAllGroups.setState(true);
3520 applyToAllGroups.addItemListener(this);
3521 clustalColour.setLabel(MessageManager
3522 .getString("label.colourScheme_clustal"));
3523 clustalColour.addActionListener(this);
3524 zappoColour.setLabel(MessageManager
3525 .getString("label.colourScheme_zappo"));
3526 zappoColour.addActionListener(this);
3527 taylorColour.setLabel(MessageManager
3528 .getString("label.colourScheme_taylor"));
3529 taylorColour.addActionListener(this);
3530 hydrophobicityColour.setLabel(MessageManager
3531 .getString("label.colourScheme_hydrophobic"));
3532 hydrophobicityColour.addActionListener(this);
3533 helixColour.setLabel(MessageManager
3534 .getString("label.colourScheme_helix_propensity"));
3535 helixColour.addActionListener(this);
3536 strandColour.setLabel(MessageManager
3537 .getString("label.colourScheme_strand_propensity"));
3538 strandColour.addActionListener(this);
3539 turnColour.setLabel(MessageManager
3540 .getString("label.colourScheme_turn_propensity"));
3541 turnColour.addActionListener(this);
3542 buriedColour.setLabel(MessageManager
3543 .getString("label.colourScheme_buried_index"));
3544 buriedColour.addActionListener(this);
3545 purinePyrimidineColour.setLabel(MessageManager
3546 .getString("label.colourScheme_purine/pyrimidine"));
3547 purinePyrimidineColour.addActionListener(this);
3548 // RNAInteractionColour.setLabel(MessageManager
3549 // .getString("label.rna_interaction"));
3550 // RNAInteractionColour.addActionListener(this);
3551 RNAHelixColour.setLabel(MessageManager
3552 .getString("label.colourScheme_rna_helices"));
3553 RNAHelixColour.addActionListener(this);
3554 userDefinedColour.setLabel(MessageManager
3555 .getString("action.user_defined"));
3556 userDefinedColour.addActionListener(this);
3557 PIDColour.setLabel(MessageManager
3558 .getString("label.colourScheme_%_identity"));
3559 PIDColour.addActionListener(this);
3560 BLOSUM62Colour.setLabel(MessageManager
3561 .getString("label.colourScheme_blosum62"));
3562 BLOSUM62Colour.addActionListener(this);
3563 tcoffeeColour.setLabel(MessageManager
3564 .getString("label.colourScheme_t-coffee_scores"));
3565 // it will be enabled only if a score file is provided
3566 tcoffeeColour.setEnabled(false);
3567 tcoffeeColour.addActionListener(this);
3568 conservationMenuItem.setLabel(MessageManager
3569 .getString("action.by_conservation"));
3570 conservationMenuItem.addItemListener(this);
3571 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3572 noColourmenuItem.addActionListener(this);
3573 abovePIDThreshold.setLabel(MessageManager
3574 .getString("label.above_identity_threshold"));
3575 abovePIDThreshold.addItemListener(this);
3576 nucleotideColour.setLabel(MessageManager
3577 .getString("label.colourScheme_nucleotide"));
3578 nucleotideColour.addActionListener(this);
3579 modifyPID.setLabel(MessageManager
3580 .getString("label.modify_identity_threshold"));
3581 modifyPID.setEnabled(abovePIDThreshold.getState());
3582 modifyPID.addActionListener(this);
3583 modifyConservation.setLabel(MessageManager
3584 .getString("label.modify_conservation_threshold"));
3585 modifyConservation.setEnabled(conservationMenuItem.getState());
3586 modifyConservation.addActionListener(this);
3587 annotationColour.setLabel(MessageManager
3588 .getString("action.by_annotation"));
3589 annotationColour.addActionListener(this);
3592 * Configure Calculate menu items and actions
3594 sortPairwiseMenuItem.setLabel(MessageManager
3595 .getString("action.by_pairwise_id"));
3596 sortPairwiseMenuItem.addActionListener(this);
3597 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3598 sortIDMenuItem.addActionListener(this);
3599 sortLengthMenuItem.setLabel(MessageManager
3600 .getString("action.by_length"));
3601 sortLengthMenuItem.addActionListener(this);
3602 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3603 sortGroupMenuItem.addActionListener(this);
3604 pairwiseAlignmentMenuItem.setLabel(MessageManager
3605 .getString("action.pairwise_alignment"));
3606 pairwiseAlignmentMenuItem.addActionListener(this);
3607 PCAMenuItem.setLabel(MessageManager
3608 .getString("label.principal_component_analysis"));
3609 PCAMenuItem.addActionListener(this);
3610 autoCalculate = new CheckboxMenuItem(
3611 MessageManager.getString("label.autocalculate_consensus"), true);
3612 averageDistanceTreeMenuItem.setLabel(MessageManager
3613 .getString("label.average_distance_identity"));
3614 averageDistanceTreeMenuItem.addActionListener(this);
3615 neighbourTreeMenuItem.setLabel(MessageManager
3616 .getString("label.neighbour_joining_identity"));
3617 neighbourTreeMenuItem.addActionListener(this);
3618 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3619 .getString("label.average_distance_blosum62"));
3620 avDistanceTreeBlosumMenuItem.addActionListener(this);
3621 njTreeBlosumMenuItem.setLabel(MessageManager
3622 .getString("label.neighbour_blosum62"));
3623 njTreeBlosumMenuItem.addActionListener(this);
3624 sortByTreeMenu.setLabel(MessageManager
3625 .getString("action.by_tree_order"));
3626 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3627 Menu calculateTreeMenu = new Menu(
3628 MessageManager.getString("action.calculate_tree"));
3629 autoCalculate.addItemListener(this);
3630 sortByTree.addItemListener(this);
3633 * Configure Help menu items and actions
3635 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3636 documentation.setLabel(MessageManager.getString("label.documentation"));
3637 documentation.addActionListener(this);
3638 about.setLabel(MessageManager.getString("label.about"));
3639 about.addActionListener(this);
3642 * Add top level menus to frame
3644 alignFrameMenuBar.add(fileMenu);
3645 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3646 alignFrameMenuBar.add(editMenu);
3647 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3648 alignFrameMenuBar.add(selectMenu);
3649 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3650 alignFrameMenuBar.add(viewMenu);
3651 Menu annotationsMenu = new Menu(
3652 MessageManager.getString("action.annotations"));
3653 alignFrameMenuBar.add(annotationsMenu);
3654 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3655 alignFrameMenuBar.add(formatMenu);
3656 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3657 alignFrameMenuBar.add(colourMenu);
3658 Menu calculateMenu = new Menu(
3659 MessageManager.getString("action.calculate"));
3660 alignFrameMenuBar.add(calculateMenu);
3661 alignFrameMenuBar.add(helpMenu);
3666 fileMenu.add(inputText);
3667 fileMenu.add(loadTree);
3668 fileMenu.add(loadAnnotations);
3669 fileMenu.addSeparator();
3670 fileMenu.add(outputTextboxMenu);
3671 fileMenu.add(outputFeatures);
3672 fileMenu.add(outputAnnotations);
3673 if (jalviewServletURL != null)
3675 fileMenu.add(loadApplication);
3677 fileMenu.addSeparator();
3678 fileMenu.add(closeMenuItem);
3683 editMenu.add(undoMenuItem);
3684 editMenu.add(redoMenuItem);
3687 pasteMenu.add(pasteNew);
3688 pasteMenu.add(pasteThis);
3689 editMenu.add(pasteMenu);
3690 editMenu.add(delete);
3691 editMenu.addSeparator();
3692 editMenu.add(remove2LeftMenuItem);
3693 editMenu.add(remove2RightMenuItem);
3694 editMenu.add(removeGappedColumnMenuItem);
3695 editMenu.add(removeAllGapsMenuItem);
3696 editMenu.add(removeRedundancyMenuItem);
3701 selectMenu.add(findMenuItem);
3702 selectMenu.addSeparator();
3703 selectMenu.add(selectAllSequenceMenuItem);
3704 selectMenu.add(deselectAllSequenceMenuItem);
3705 selectMenu.add(invertSequenceMenuItem);
3706 selectMenu.add(invertColSel);
3707 selectMenu.add(createGroup);
3708 selectMenu.add(unGroup);
3709 selectMenu.add(grpsFromSelection);
3710 selectMenu.add(deleteGroups);
3711 selectMenu.add(annotationColumnSelection);
3716 viewMenu.add(newView);
3717 viewMenu.addSeparator();
3718 showMenu.add(showColumns);
3719 showMenu.add(showSeqs);
3720 showMenu.add(showAllHidden);
3721 viewMenu.add(showMenu);
3722 hideMenu.add(hideColumns);
3723 hideMenu.add(hideSequences);
3724 hideMenu.add(hideAllSelection);
3725 hideMenu.add(hideAllButSelection);
3726 viewMenu.add(hideMenu);
3727 viewMenu.addSeparator();
3728 viewMenu.add(followMouseOverFlag);
3729 viewMenu.addSeparator();
3730 viewMenu.add(sequenceFeatures);
3731 viewMenu.add(featureSettings);
3732 viewMenu.addSeparator();
3733 viewMenu.add(alProperties);
3734 viewMenu.addSeparator();
3735 viewMenu.add(overviewMenuItem);
3740 annotationsMenu.add(annotationPanelMenuItem);
3741 annotationsMenu.addSeparator();
3742 annotationsMenu.add(showAlignmentAnnotations);
3743 annotationsMenu.add(showSequenceAnnotations);
3744 annotationsMenu.add(sortAnnBySequence);
3745 annotationsMenu.add(sortAnnByLabel);
3746 annotationsMenu.addSeparator();
3747 autoAnnMenu.add(showAutoFirst);
3748 autoAnnMenu.add(showAutoLast);
3749 autoAnnMenu.addSeparator();
3750 autoAnnMenu.add(applyAutoAnnotationSettings);
3751 autoAnnMenu.add(showConsensusHistogram);
3752 autoAnnMenu.add(showSequenceLogo);
3753 autoAnnMenu.add(normSequenceLogo);
3754 autoAnnMenu.addSeparator();
3755 autoAnnMenu.add(showGroupConservation);
3756 autoAnnMenu.add(showGroupConsensus);
3757 annotationsMenu.add(autoAnnMenu);
3762 formatMenu.add(font);
3763 formatMenu.add(seqLimits);
3764 formatMenu.add(wrapMenuItem);
3765 formatMenu.add(scaleAbove);
3766 formatMenu.add(scaleLeft);
3767 formatMenu.add(scaleRight);
3768 formatMenu.add(viewBoxesMenuItem);
3769 formatMenu.add(viewTextMenuItem);
3770 formatMenu.add(colourTextMenuItem);
3771 formatMenu.add(displayNonconservedMenuItem);
3772 formatMenu.add(renderGapsMenuItem);
3773 formatMenu.add(centreColumnLabelFlag);
3778 colourMenu.add(applyToAllGroups);
3779 colourMenu.addSeparator();
3780 colourMenu.add(noColourmenuItem);
3781 colourMenu.add(clustalColour);
3782 colourMenu.add(BLOSUM62Colour);
3783 colourMenu.add(PIDColour);
3784 colourMenu.add(zappoColour);
3785 colourMenu.add(taylorColour);
3786 colourMenu.add(hydrophobicityColour);
3787 colourMenu.add(helixColour);
3788 colourMenu.add(strandColour);
3789 colourMenu.add(turnColour);
3790 colourMenu.add(buriedColour);
3791 colourMenu.add(nucleotideColour);
3792 colourMenu.add(purinePyrimidineColour);
3793 // colourMenu.add(RNAInteractionColour);
3794 colourMenu.add(tcoffeeColour);
3795 colourMenu.add(userDefinedColour);
3796 colourMenu.addSeparator();
3797 colourMenu.add(conservationMenuItem);
3798 colourMenu.add(modifyConservation);
3799 colourMenu.add(abovePIDThreshold);
3800 colourMenu.add(modifyPID);
3801 colourMenu.add(annotationColour);
3802 colourMenu.add(RNAHelixColour);
3807 sortMenu.add(sortIDMenuItem);
3808 sortMenu.add(sortLengthMenuItem);
3809 sortMenu.add(sortByTreeMenu);
3810 sortMenu.add(sortGroupMenuItem);
3811 sortMenu.add(sortPairwiseMenuItem);
3812 calculateMenu.add(sortMenu);
3813 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3814 calculateTreeMenu.add(neighbourTreeMenuItem);
3815 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3816 calculateTreeMenu.add(njTreeBlosumMenuItem);
3817 calculateMenu.add(calculateTreeMenu);
3818 calculateMenu.addSeparator();
3819 calculateMenu.add(pairwiseAlignmentMenuItem);
3820 calculateMenu.add(PCAMenuItem);
3821 calculateMenu.add(autoCalculate);
3822 calculateMenu.add(sortByTree);
3827 helpMenu.add(documentation);
3828 helpMenu.add(about);
3833 statusBar.setBackground(Color.white);
3834 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3835 statusBar.setText(MessageManager.getString("label.status_bar"));
3836 this.add(statusBar, BorderLayout.SOUTH);
3840 public void setStatus(String string)
3842 statusBar.setText(string);
3845 MenuItem featureSettings = new MenuItem();
3847 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3849 MenuItem annotationColour = new MenuItem();
3851 MenuItem annotationColumnSelection = new MenuItem();
3853 MenuItem invertColSel = new MenuItem();
3855 MenuItem showColumns = new MenuItem();
3857 MenuItem showSeqs = new MenuItem();
3859 MenuItem hideColumns = new MenuItem();
3861 MenuItem hideSequences = new MenuItem();
3863 MenuItem hideAllButSelection = new MenuItem();
3865 MenuItem hideAllSelection = new MenuItem();
3867 MenuItem showAllHidden = new MenuItem();
3869 MenuItem newView = new MenuItem();
3871 private CheckboxMenuItem showAlignmentAnnotations;
3873 private CheckboxMenuItem showSequenceAnnotations;
3875 private CheckboxMenuItem sortAnnBySequence;
3877 private CheckboxMenuItem sortAnnByLabel;
3879 private CheckboxMenuItem showAutoFirst;
3881 private CheckboxMenuItem showAutoLast;
3883 private SplitFrame splitFrame;
3886 * Attach the alignFrame panels after embedding menus, if necessary. This used
3887 * to be called setEmbedded, but is now creates the dropdown menus in a
3888 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3890 * @param reallyEmbedded
3891 * true to attach the view to the applet area on the page rather than
3894 public void createAlignFrameWindow(boolean reallyEmbedded)
3898 embedAlignFrameInApplet(viewport.applet);
3903 // test and embed menu bar if necessary.
3905 if (embedMenuIfNeeded(alignPanel))
3908 * adjust for status bar height too. ? pointless as overridden by layout
3911 alignPanel.setSize(getSize().width,
3912 getSize().height - statusBar.getHeight());
3914 add(statusBar, BorderLayout.SOUTH);
3915 add(alignPanel, BorderLayout.CENTER);
3916 // and register with the applet so it can pass external API calls to us
3917 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3923 * Add the components of this AlignFrame to the applet container.
3927 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3930 // Explicitly build the embedded menu panel for the on-page applet
3932 // view cannot be closed if its actually on the page
3933 fileMenu.remove(closeMenuItem);
3934 fileMenu.remove(3); // Remove Separator
3935 // construct embedded menu, using default font
3936 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3937 // and actually add the components to the applet area
3938 theApplet.setLayout(new BorderLayout());
3939 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3940 theApplet.add(statusBar, BorderLayout.SOUTH);
3941 // TODO should size be left to the layout manager?
3942 alignPanel.setSize(theApplet.getSize().width,
3943 theApplet.getSize().height - embeddedMenu.getHeight()
3944 - statusBar.getHeight());
3945 theApplet.add(alignPanel, BorderLayout.CENTER);
3946 final AlignFrame me = this;
3947 theApplet.addFocusListener(new FocusListener()
3951 public void focusLost(FocusEvent e)
3953 if (theApplet.currentAlignFrame == me)
3955 theApplet.currentAlignFrame = null;
3960 public void focusGained(FocusEvent e)
3962 theApplet.currentAlignFrame = me;
3965 theApplet.validate();
3969 * create a new binding between structures in an existing jmol viewer instance
3970 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3971 * this does not open a new Jmol window, or modify the display of the
3972 * structures in the original jmol window. Note This method doesn't work
3973 * without an additional javascript library to exchange messages between the
3974 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3977 * JmolViewer instance
3978 * @param sequenceIds
3979 * - sequence Ids to search for associations
3981 public SequenceStructureBinding addStructureViewInstance(
3982 Object jmolviewer, String[] sequenceIds)
3984 Viewer viewer = null;
3987 viewer = (Viewer) jmolviewer;
3988 } catch (ClassCastException ex)
3990 System.err.println("Unsupported viewer object :"
3991 + jmolviewer.getClass());
3995 System.err.println("Can't use this object as a structure viewer:"
3996 + jmolviewer.getClass());
3999 SequenceI[] seqs = null;
4000 if (sequenceIds == null || sequenceIds.length == 0)
4002 seqs = viewport.getAlignment().getSequencesArray();
4006 Vector sqi = new Vector();
4007 AlignmentI al = viewport.getAlignment();
4008 for (int sid = 0; sid < sequenceIds.length; sid++)
4010 SequenceI sq = al.findName(sequenceIds[sid]);
4018 seqs = new SequenceI[sqi.size()];
4019 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4021 seqs[sid] = (SequenceI) sqi.elementAt(sid);
4029 AAStructureBindingModel jmv = null;
4030 // TODO: search for a jmv that involves viewer
4032 { // create a new viewer/jalview binding.
4033 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4040 * bind a pdb file to a sequence in the current view
4043 * - sequenceId within the dataset.
4044 * @param pdbEntryString
4045 * - the short name for the PDB file
4047 * - pdb file - either a URL or a valid PDB file.
4048 * @return true if binding was as success TODO: consider making an exception
4049 * structure for indicating when PDB parsing or sequenceId location
4052 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4055 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4056 boolean needtoadd = false;
4057 if (toaddpdb != null)
4059 Vector pdbe = toaddpdb.getAllPDBEntries();
4060 PDBEntry pdbentry = null;
4061 if (pdbe != null && pdbe.size() > 0)
4063 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4065 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4066 if (!pdbentry.getId().equals(pdbEntryString)
4067 && !pdbentry.getFile().equals(pdbFile))
4077 if (pdbentry == null)
4079 pdbentry = new PDBEntry();
4080 pdbentry.setId(pdbEntryString);
4081 pdbentry.setFile(pdbFile);
4082 needtoadd = true; // add this new entry to sequence.
4084 // resolve data source
4085 // TODO: this code should be a refactored to an io package
4086 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4087 pdbFile, FileFormat.PDB);
4088 if (protocol == null)
4094 pdbentry.setProperty("protocol", protocol);
4095 toaddpdb.addPDBId(pdbentry);
4096 alignPanel.getStructureSelectionManager()
4097 .registerPDBEntry(pdbentry);
4103 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4107 Vector sequences = new Vector();
4108 for (int i = 0; i < seqs.length; i++)
4110 if (seqs[i] != null)
4112 sequences.addElement(new Object[] { seqs[i],
4113 (chains != null) ? chains[i] : null });
4116 seqs = new SequenceI[sequences.size()];
4117 chains = new String[sequences.size()];
4118 for (int i = 0, isize = sequences.size(); i < isize; i++)
4120 Object[] oj = (Object[]) sequences.elementAt(i);
4122 seqs[i] = (SequenceI) oj[0];
4123 chains[i] = (String) oj[1];
4126 return new Object[] { seqs, chains };
4130 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4131 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4133 // Scrub any null sequences from the array
4134 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4135 seqs = (SequenceI[]) sqch[0];
4136 chains = (String[]) sqch[1];
4137 if (seqs == null || seqs.length == 0)
4140 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4142 if (protocol == null)
4144 String sourceType = (String) pdb.getProperty("protocol");
4147 protocol = DataSourceType.valueOf(sourceType);
4148 } catch (IllegalArgumentException e)
4152 if (protocol == null)
4154 System.err.println("Couldn't work out protocol to open structure: "
4159 if (applet.useXtrnalSviewer)
4161 // register the association(s) and quit, don't create any windows.
4162 if (StructureSelectionManager.getStructureSelectionManager(applet)
4163 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4165 System.err.println("Failed to map " + pdb.getFile() + " ("
4166 + protocol + ") to any sequences");
4170 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4172 // can only do alignments with Jmol
4173 // find the last jmol window assigned to this alignment
4174 AppletJmol ajm = null, tajm;
4175 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4176 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4178 tajm = (AppletJmol) jmols.elementAt(i);
4179 if (tajm.ap.alignFrame == this)
4188 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4189 // try and add the pdb structure
4194 // otherwise, create a new window
4195 if (applet.jmolAvailable)
4197 new AppletJmol(pdb, seqs, chains, alignPanel,
4199 applet.lastFrameX += 40;
4200 applet.lastFrameY += 40;
4204 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4209 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4210 SequenceI[][] seqs, String[][] chains, String[] protocols)
4212 // TODO Auto-generated method stub
4213 System.err.println("Aligned Structure View: Not yet implemented.");
4217 * modify the current selection, providing the user has not made a selection
4221 * - sequences from this alignment
4223 * - columns to be selected on the alignment
4225 public void select(SequenceGroup sel, ColumnSelection csel,
4226 HiddenColumns hidden)
4228 alignPanel.seqPanel.selection(sel, csel, hidden, null);
4231 public void scrollTo(int row, int column)
4233 alignPanel.seqPanel.scrollTo(row, column);
4236 public void scrollToRow(int row)
4238 alignPanel.seqPanel.scrollToRow(row);
4241 public void scrollToColumn(int column)
4243 alignPanel.seqPanel.scrollToColumn(column);
4247 * @return the alignments unique ID.
4249 public String getSequenceSetId()
4251 return viewport.getSequenceSetId();
4255 * Load the (T-Coffee) score file from the specified url
4258 * File/URL/T-COFFEE score file contents
4259 * @throws IOException
4260 * @return true if alignment was annotated with data from source
4262 public boolean loadScoreFile(String source) throws IOException
4265 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4266 AppletFormatAdapter.checkProtocol(source));
4267 if (!file.isValid())
4269 // TODO: raise dialog for gui
4270 System.err.println("Problems parsing T-Coffee scores: "
4271 + file.getWarningMessage());
4272 System.err.println("Origin was:\n" + source);
4277 * check that the score matrix matches the alignment dimensions
4280 if ((aln = viewport.getAlignment()) != null
4281 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4284 // TODO: raise a dialog box here rather than bomb out.
4286 .println("The scores matrix does not match the alignment dimensions");
4290 // TODO add parameter to indicate if matching should be done
4291 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4293 alignPanel.fontChanged();
4294 tcoffeeColour.setEnabled(true);
4295 // switch to this color
4296 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4301 System.err.println("Problems resolving T-Coffee scores:");
4302 if (file.getWarningMessage() != null)
4304 System.err.println(file.getWarningMessage());
4310 public SplitFrame getSplitFrame()
4312 return this.splitFrame;
4315 public void setSplitFrame(SplitFrame sf)
4317 this.splitFrame = sf;
4320 // may not need this
4322 public void setShowSeqFeatures(boolean b)
4324 // showSeqFeatures.setSelected(b);
4325 viewport.setShowSequenceFeatures(b);
4330 public void setMenusForViewport()
4332 // setMenusFromViewport(viewport);
4337 public void refreshFeatureUI(boolean enableIfNecessary)
4339 if (enableIfNecessary)
4341 sequenceFeatures.setState(true);
4342 alignPanel.av.setShowSequenceFeatures(true);
4347 public FeatureSettingsControllerI getFeatureSettingsUI()
4349 return alignPanel.av.featureSettings;