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.Rectangle;
99 import java.awt.event.ActionEvent;
100 import java.awt.event.ActionListener;
101 import java.awt.event.FocusEvent;
102 import java.awt.event.FocusListener;
103 import java.awt.event.ItemEvent;
104 import java.awt.event.ItemListener;
105 import java.awt.event.KeyEvent;
106 import java.awt.event.KeyListener;
107 import java.awt.event.WindowAdapter;
108 import java.awt.event.WindowEvent;
109 import java.io.IOException;
110 import java.io.UnsupportedEncodingException;
112 import java.net.URLEncoder;
113 import java.util.Arrays;
114 import java.util.Deque;
115 import java.util.HashMap;
116 import java.util.List;
117 import java.util.Map;
118 import java.util.StringTokenizer;
119 import java.util.Vector;
121 import org.jmol.viewer.Viewer;
123 public class AlignFrame extends EmbmenuFrame implements ActionListener,
124 ItemListener, KeyListener, AlignViewControllerGuiI
126 public AlignViewControllerI avc;
128 public AlignmentPanel alignPanel;
130 public AlignViewport viewport;
132 // width and height may be overridden by applet parameters
133 int frameWidth = 700;
135 int frameHeight = 500;
137 String jalviewServletURL;
140 * Flag for showing autocalculated consensus above or below other consensus
143 private boolean showAutoCalculatedAbove;
145 private SequenceAnnotationOrder annotationSortOrder;
148 * Constructor that creates the frame and adds it to the display.
155 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
158 this(al, applet, title, embedded, true);
162 * Constructor that optionally allows the frame to be displayed or only
169 * @param addToDisplay
171 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
172 boolean embedded, boolean addToDisplay)
174 this(al, null, null, applet, title, embedded, addToDisplay);
177 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
178 HiddenColumns hidden, JalviewLite applet, String title,
181 this(al, hiddenSeqs, hidden, applet, title, embedded, true);
184 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
185 HiddenColumns hidden, JalviewLite applet, String title,
186 boolean embedded, boolean addToDisplay)
190 jalviewServletURL = applet.getParameter("APPLICATION_URL");
196 } catch (Exception ex)
198 ex.printStackTrace();
200 // need to get window geometry before we calculate alignment layout
206 param = applet.getParameter("windowWidth");
209 int width = Integer.parseInt(param);
212 param = applet.getParameter("windowHeight");
215 int height = Integer.parseInt(param);
216 frameHeight = height;
218 } catch (Exception ex)
222 viewport = new AlignViewport(al, applet);
224 if (hiddenSeqs != null && hiddenSeqs.length > 0)
226 viewport.hideSequence(hiddenSeqs);
230 viewport.getAlignment().setHiddenColumns(hidden);
232 viewport.setScaleAboveWrapped(scaleAbove.getState());
234 alignPanel = new AlignmentPanel(this, viewport);
235 avc = new jalview.controller.AlignViewController(this, viewport,
237 viewport.updateConservation(alignPanel);
238 viewport.updateConsensus(alignPanel);
239 viewport.initInformationWorker(alignPanel);
241 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
242 followMouseOverFlag.setState(viewport.isFollowHighlight());
243 showGroupConsensus.setState(viewport.isShowGroupConsensus());
244 showGroupConservation.setState(viewport.isShowGroupConservation());
245 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
246 showSequenceLogo.setState(viewport.isShowSequenceLogo());
247 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
248 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
249 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
250 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
251 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
252 showAlignmentAnnotations.setState(true);
253 showSequenceAnnotations.setState(false);
255 seqLimits.setState(viewport.getShowJVSuffix());
259 String param = applet.getParameter("sortBy");
262 if (param.equalsIgnoreCase("Id"))
264 sortIDMenuItem_actionPerformed();
266 else if (param.equalsIgnoreCase("Pairwise Identity"))
268 sortPairwiseMenuItem_actionPerformed();
270 else if (param.equalsIgnoreCase("Length"))
272 sortLengthMenuItem_actionPerformed();
276 param = applet.getParameter("wrap");
279 if (param.equalsIgnoreCase("true"))
281 wrapMenuItem.setState(true);
282 wrapMenuItem_actionPerformed();
285 param = applet.getParameter("centrecolumnlabels");
288 centreColumnLabelFlag.setState(true);
289 centreColumnLabelFlag_stateChanged();
293 if (viewport.getAlignment().isNucleotide())
295 conservationMenuItem.setEnabled(false);
296 clustalColour.setEnabled(false);
297 BLOSUM62Colour.setEnabled(false);
298 zappoColour.setEnabled(false);
299 taylorColour.setEnabled(false);
300 hydrophobicityColour.setEnabled(false);
301 helixColour.setEnabled(false);
302 strandColour.setEnabled(false);
303 turnColour.setEnabled(false);
304 buriedColour.setEnabled(false);
305 viewport.updateStrucConsensus(alignPanel);
306 if (viewport.getAlignment().hasRNAStructure())
308 RNAHelixColour.setEnabled(true);
312 RNAHelixColour.setEnabled(false);
317 RNAHelixColour.setEnabled(false);
318 purinePyrimidineColour.setEnabled(false);
319 nucleotideColour.setEnabled(false);
321 // Some JVMS send keyevents to Top frame or lowest panel,
322 // Havent worked out why yet. So add to both this frame and seqCanvas for
324 this.addKeyListener(this);
325 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
326 alignPanel.idPanel.idCanvas.addKeyListener(this);
327 alignPanel.scalePanel.addKeyListener(this);
328 alignPanel.annotationPanel.addKeyListener(this);
329 alignPanel.annotationPanelHolder.addKeyListener(this);
330 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
331 alignPanel.alabels.addKeyListener(this);
333 setAnnotationsVisibility();
337 addToDisplay(embedded);
344 public void addToDisplay(boolean embedded)
346 createAlignFrameWindow(embedded);
348 alignPanel.adjustAnnotationHeight();
349 alignPanel.paintAlignment(true, true);
352 public AlignViewport getAlignViewport()
357 public SeqCanvas getSeqcanvas()
359 return alignPanel.seqPanel.seqCanvas;
363 * Load a features file onto the alignment
366 * file URL, content, or other resolvable path
368 * is protocol for accessing data referred to by file
371 public boolean parseFeaturesFile(String file, DataSourceType type)
373 return parseFeaturesFile(file, type, true);
377 * Load a features file onto the alignment
380 * file URL, content, or other resolvable path
382 * is protocol for accessing data referred to by file
383 * @param autoenabledisplay
384 * when true, display features flag will be automatically enabled if
385 * features are loaded
386 * @return true if data parsed as a features file
388 public boolean parseFeaturesFile(String file, DataSourceType sourceType,
389 boolean autoenabledisplay)
391 boolean featuresFile = false;
394 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
395 .getFeatureRenderer().getFeatureColours();
396 boolean relaxedIdMatching = viewport.applet
397 .getDefaultParameter("relaxedidmatch", false);
398 featuresFile = new FeaturesFile(file, sourceType).parse(
399 viewport.getAlignment(), colours, true, relaxedIdMatching);
400 } catch (Exception ex)
402 ex.printStackTrace();
407 if (autoenabledisplay)
409 viewport.setShowSequenceFeatures(true);
410 sequenceFeatures.setState(true);
412 if (alignPanel.seqPanel.seqCanvas.fr != null)
414 // update the min/max ranges where necessary
415 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
417 if (viewport.featureSettings != null)
419 viewport.featureSettings.refreshTable();
421 alignPanel.paintAlignment(true, true);
422 setStatus(MessageManager
423 .getString("label.successfully_added_features_alignment"));
429 public void keyPressed(KeyEvent evt)
431 ViewportRanges ranges = viewport.getRanges();
433 if (viewport.cursorMode
434 && ((evt.getKeyCode() >= KeyEvent.VK_0
435 && evt.getKeyCode() <= KeyEvent.VK_9)
436 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
437 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
438 && Character.isDigit(evt.getKeyChar()))
440 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
443 switch (evt.getKeyCode())
445 case 27: // escape key
446 deselectAllSequenceMenuItem_actionPerformed();
448 alignPanel.alabels.cancelDrag();
451 if (evt.isControlDown() || evt.isMetaDown())
453 cut_actionPerformed();
457 if (viewport.cursorMode && !evt.isControlDown())
459 alignPanel.seqPanel.setCursorColumn();
461 if (evt.isControlDown() || evt.isMetaDown())
463 copy_actionPerformed();
467 if (evt.isControlDown())
469 paste(evt.isShiftDown());
473 if (evt.isControlDown() || evt.isMetaDown())
475 selectAllSequenceMenuItem_actionPerformed();
478 case KeyEvent.VK_DOWN:
479 if (viewport.cursorMode)
481 alignPanel.seqPanel.moveCursor(0, 1);
485 moveSelectedSequences(false);
490 if (viewport.cursorMode)
492 alignPanel.seqPanel.moveCursor(0, -1);
496 moveSelectedSequences(true);
500 case KeyEvent.VK_LEFT:
501 if (evt.isAltDown() || !viewport.cursorMode)
503 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
507 alignPanel.seqPanel.moveCursor(-1, 0);
511 case KeyEvent.VK_RIGHT:
512 if (evt.isAltDown() || !viewport.cursorMode)
514 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
518 alignPanel.seqPanel.moveCursor(1, 0);
522 case KeyEvent.VK_SPACE:
523 if (viewport.cursorMode)
525 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
526 || evt.isShiftDown() || evt.isAltDown());
530 case KeyEvent.VK_DELETE:
531 case KeyEvent.VK_BACK_SPACE:
532 if (viewport.cursorMode)
534 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
535 || evt.isShiftDown() || evt.isAltDown());
539 cut_actionPerformed();
540 alignPanel.seqPanel.seqCanvas.repaint();
545 if (viewport.cursorMode)
547 alignPanel.seqPanel.setCursorRow();
551 if (viewport.cursorMode)
553 alignPanel.seqPanel.setCursorPosition();
557 case KeyEvent.VK_ENTER:
558 case KeyEvent.VK_COMMA:
559 if (viewport.cursorMode)
561 alignPanel.seqPanel.setCursorRowAndColumn();
566 if (viewport.cursorMode)
568 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
572 if (viewport.cursorMode)
574 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
579 viewport.cursorMode = !viewport.cursorMode;
580 setStatus(MessageManager
581 .formatMessage("label.keyboard_editing_mode", new String[]
582 { (viewport.cursorMode ? "on" : "off") }));
583 if (viewport.cursorMode)
585 alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
586 alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
591 if (evt.isControlDown())
593 findMenuItem_actionPerformed();
599 boolean toggleSeqs = !evt.isControlDown();
600 boolean toggleCols = !evt.isShiftDown();
601 toggleHiddenRegions(toggleSeqs, toggleCols);
605 case KeyEvent.VK_PAGE_UP:
609 case KeyEvent.VK_PAGE_DOWN:
614 if (evt.isControlDown())
616 undoMenuItem_actionPerformed();
621 if (evt.isControlDown())
623 redoMenuItem_actionPerformed();
628 if (evt.isControlDown())
635 if (evt.isControlDown())
637 trimAlignment(false);
642 if (evt.isControlDown())
644 if (evt.isShiftDown())
646 this.removeAllGapsMenuItem_actionPerformed();
650 removeGappedColumnMenuItem_actionPerformed();
655 if (evt.isControlDown())
659 invertColSel_actionPerformed();
663 invertSequenceMenuItem_actionPerformed();
669 if (evt.isControlDown())
671 if (evt.isShiftDown())
673 this.unGroup_actionPerformed();
677 this.createGroup_actionPerformed();
683 if (evt.isControlDown())
685 this.deleteGroups_actionPerformed();
690 if (evt.isControlDown())
697 // TODO: repaint flags set only if the keystroke warrants it
698 alignPanel.paintAlignment(true, true);
702 * called by key handler and the hide all/show all menu items
707 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
709 boolean hide = false;
710 SequenceGroup sg = viewport.getSelectionGroup();
711 if (!toggleSeqs && !toggleCols)
713 // Hide everything by the current selection - this is a hack - we do the
714 // invert and then hide
715 // first check that there will be visible columns after the invert.
716 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
717 && sg.getStartRes() <= sg.getEndRes()))
719 // now invert the sequence set, if required - empty selection implies
720 // that no hiding is required.
723 invertSequenceMenuItem_actionPerformed();
724 sg = viewport.getSelectionGroup();
728 viewport.expandColSelection(sg, true);
729 // finally invert the column selection and get the new sequence
730 // selection and indicate it should be hidden.
731 invertColSel_actionPerformed();
738 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
741 viewport.hideAllSelectedSeqs();
743 else if (!(toggleCols && viewport.hasSelectedColumns()))
745 viewport.showAllHiddenSeqs();
751 if (viewport.hasSelectedColumns())
753 viewport.hideSelectedColumns();
756 viewport.setSelectionGroup(sg);
761 viewport.showAllHiddenColumns();
763 viewport.sendSelection();
768 public void keyReleased(KeyEvent evt)
773 public void keyTyped(KeyEvent evt)
778 public void itemStateChanged(ItemEvent evt)
780 final Object source = evt.getSource();
781 if (source == displayNonconservedMenuItem)
783 displayNonconservedMenuItem_actionPerformed();
785 else if (source == colourTextMenuItem)
787 colourTextMenuItem_actionPerformed();
789 else if (source == wrapMenuItem)
791 wrapMenuItem_actionPerformed();
793 else if (source == scaleAbove)
795 viewport.setScaleAboveWrapped(scaleAbove.getState());
797 else if (source == scaleLeft)
799 viewport.setScaleLeftWrapped(scaleLeft.getState());
801 else if (source == scaleRight)
803 viewport.setScaleRightWrapped(scaleRight.getState());
805 else if (source == seqLimits)
807 seqLimits_itemStateChanged();
809 else if (source == viewBoxesMenuItem)
811 viewport.setShowBoxes(viewBoxesMenuItem.getState());
813 else if (source == viewTextMenuItem)
815 viewport.setShowText(viewTextMenuItem.getState());
817 else if (source == renderGapsMenuItem)
819 viewport.setRenderGaps(renderGapsMenuItem.getState());
821 else if (source == annotationPanelMenuItem)
823 boolean showAnnotations = annotationPanelMenuItem.getState();
824 showAlignmentAnnotations.setEnabled(showAnnotations);
825 showSequenceAnnotations.setEnabled(showAnnotations);
826 viewport.setShowAnnotation(showAnnotations);
827 alignPanel.setAnnotationVisible(showAnnotations);
829 else if (source == sequenceFeatures)
831 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
832 alignPanel.seqPanel.seqCanvas.repaint();
834 else if (source == showAlignmentAnnotations)
836 setAnnotationsVisibility();
838 else if (source == showSequenceAnnotations)
840 setAnnotationsVisibility();
842 else if (source == sortAnnBySequence)
844 boolean newState = sortAnnBySequence.getState();
845 sortAnnByLabel.setState(false);
846 setAnnotationSortOrder(
847 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
848 : SequenceAnnotationOrder.NONE);
849 setViewportAnnotationOrder();
851 else if (source == sortAnnByLabel)
853 boolean newState = sortAnnByLabel.getState();
854 sortAnnBySequence.setState(false);
855 setAnnotationSortOrder(
856 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
857 : SequenceAnnotationOrder.NONE);
858 setViewportAnnotationOrder();
860 else if (source == showAutoFirst)
862 showAutoLast.setState(!showAutoFirst.getState());
863 setShowAutoCalculatedAbove(showAutoFirst.getState());
864 setViewportAnnotationOrder();
866 else if (source == showAutoLast)
868 showAutoFirst.setState(!showAutoLast.getState());
869 setShowAutoCalculatedAbove(showAutoFirst.getState());
870 setViewportAnnotationOrder();
872 else if (source == conservationMenuItem)
874 conservationMenuItem_actionPerformed();
876 else if (source == abovePIDThreshold)
878 abovePIDThreshold_actionPerformed();
880 else if (source == applyToAllGroups)
882 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
884 else if (source == autoCalculate)
886 viewport.setAutoCalculateConsensusAndConservation(autoCalculate.getState());
888 else if (source == sortByTree)
890 viewport.sortByTree = sortByTree.getState();
892 else if (source == this.centreColumnLabelFlag)
894 centreColumnLabelFlag_stateChanged();
896 else if (source == this.followMouseOverFlag)
898 mouseOverFlag_stateChanged();
900 else if (source == showGroupConsensus)
902 showGroupConsensus_actionPerformed();
904 else if (source == showGroupConservation)
906 showGroupConservation_actionPerformed();
908 else if (source == showSequenceLogo)
910 showSequenceLogo_actionPerformed();
912 else if (source == normSequenceLogo)
914 normSequenceLogo_actionPerformed();
916 else if (source == showConsensusHistogram)
918 showConsensusHistogram_actionPerformed();
920 else if (source == applyAutoAnnotationSettings)
922 applyAutoAnnotationSettings_actionPerformed();
924 // TODO: repaint flags set only if warranted
925 alignPanel.paintAlignment(true, true);
929 * Set the visibility state of sequence-related and/or alignment-related
930 * annotations depending on checkbox selections, and repaint.
934 private void setAnnotationsVisibility()
936 boolean showForAlignment = showAlignmentAnnotations.getState();
937 boolean showForSequences = showSequenceAnnotations.getState();
938 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
940 for (AlignmentAnnotation aa : alignPanel.getAlignment()
941 .getAlignmentAnnotation())
943 boolean visible = (aa.sequenceRef == null ? showForAlignment
945 aa.visible = visible;
948 alignPanel.validateAnnotationDimensions(true);
953 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
955 this.annotationSortOrder = order;
959 * Set flags on the viewport that control annotation ordering
961 private void setViewportAnnotationOrder()
963 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
965 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
968 private void setShowAutoCalculatedAbove(boolean showAbove)
970 this.showAutoCalculatedAbove = showAbove;
973 private void mouseOverFlag_stateChanged()
975 viewport.setFollowHighlight(followMouseOverFlag.getState());
976 // TODO: could kick the scrollTo mechanism to reset view for current
980 private void centreColumnLabelFlag_stateChanged()
982 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
983 this.alignPanel.annotationPanel.repaint();
987 public void actionPerformed(ActionEvent evt)
989 viewport.applet.currentAlignFrame = this;
991 Object source = evt.getSource();
993 if (source == inputText)
995 inputText_actionPerformed();
997 else if (source == loadTree)
999 loadTree_actionPerformed();
1001 else if (source == loadApplication)
1003 launchFullApplication();
1005 else if (source == loadAnnotations)
1009 else if (source == outputAnnotations)
1011 outputAnnotations(true);
1013 else if (source == outputFeatures)
1015 outputFeatures(true, "Jalview");
1017 else if (source == closeMenuItem)
1019 closeMenuItem_actionPerformed();
1021 else if (source == copy)
1023 copy_actionPerformed();
1025 else if (source == undoMenuItem)
1027 undoMenuItem_actionPerformed();
1029 else if (source == redoMenuItem)
1031 redoMenuItem_actionPerformed();
1033 else if (source == inputText)
1035 inputText_actionPerformed();
1037 else if (source == closeMenuItem)
1039 closeMenuItem_actionPerformed();
1041 else if (source == undoMenuItem)
1043 undoMenuItem_actionPerformed();
1045 else if (source == redoMenuItem)
1047 redoMenuItem_actionPerformed();
1049 else if (source == copy)
1051 copy_actionPerformed();
1053 else if (source == pasteNew)
1055 pasteNew_actionPerformed();
1057 else if (source == pasteThis)
1059 pasteThis_actionPerformed();
1061 else if (source == cut)
1063 cut_actionPerformed();
1065 else if (source == delete)
1067 delete_actionPerformed();
1069 else if (source == createGroup)
1071 createGroup_actionPerformed();
1073 else if (source == unGroup)
1075 unGroup_actionPerformed();
1077 else if (source == grpsFromSelection)
1079 makeGrpsFromSelection_actionPerformed();
1081 else if (source == deleteGroups)
1083 deleteGroups_actionPerformed();
1085 else if (source == selectAllSequenceMenuItem)
1087 selectAllSequenceMenuItem_actionPerformed();
1089 else if (source == deselectAllSequenceMenuItem)
1091 deselectAllSequenceMenuItem_actionPerformed();
1093 else if (source == invertSequenceMenuItem)
1095 invertSequenceMenuItem_actionPerformed();
1096 // uncomment to slave sequence selections in split frame
1097 // viewport.sendSelection();
1099 else if (source == invertColSel)
1101 viewport.invertColumnSelection();
1102 alignPanel.paintAlignment(false, false);
1103 viewport.sendSelection();
1105 else if (source == remove2LeftMenuItem)
1107 trimAlignment(true);
1109 else if (source == remove2RightMenuItem)
1111 trimAlignment(false);
1113 else if (source == removeGappedColumnMenuItem)
1115 removeGappedColumnMenuItem_actionPerformed();
1117 else if (source == removeAllGapsMenuItem)
1119 removeAllGapsMenuItem_actionPerformed();
1121 else if (source == findMenuItem)
1123 findMenuItem_actionPerformed();
1125 else if (source == font)
1127 new FontChooser(alignPanel);
1129 else if (source == newView)
1133 else if (source == showColumns)
1135 viewport.showAllHiddenColumns();
1136 alignPanel.paintAlignment(true, true);
1137 viewport.sendSelection();
1139 else if (source == showSeqs)
1141 viewport.showAllHiddenSeqs();
1142 alignPanel.paintAlignment(true, true);
1143 // uncomment if we want to slave sequence selections in split frame
1144 // viewport.sendSelection();
1146 else if (source == hideColumns)
1148 viewport.hideSelectedColumns();
1149 alignPanel.paintAlignment(true, true);
1150 viewport.sendSelection();
1152 else if (source == hideSequences
1153 && viewport.getSelectionGroup() != null)
1155 viewport.hideAllSelectedSeqs();
1156 alignPanel.paintAlignment(true, true);
1157 // uncomment if we want to slave sequence selections in split frame
1158 // viewport.sendSelection();
1160 else if (source == hideAllButSelection)
1162 toggleHiddenRegions(false, false);
1163 alignPanel.paintAlignment(true, true);
1164 viewport.sendSelection();
1166 else if (source == hideAllSelection)
1168 SequenceGroup sg = viewport.getSelectionGroup();
1169 viewport.expandColSelection(sg, false);
1170 viewport.hideAllSelectedSeqs();
1171 viewport.hideSelectedColumns();
1172 alignPanel.paintAlignment(true, true);
1173 viewport.sendSelection();
1175 else if (source == showAllHidden)
1177 viewport.showAllHiddenColumns();
1178 viewport.showAllHiddenSeqs();
1179 alignPanel.paintAlignment(true, true);
1180 viewport.sendSelection();
1182 else if (source == showGroupConsensus)
1184 showGroupConsensus_actionPerformed();
1186 else if (source == showGroupConservation)
1188 showGroupConservation_actionPerformed();
1190 else if (source == showSequenceLogo)
1192 showSequenceLogo_actionPerformed();
1194 else if (source == normSequenceLogo)
1196 normSequenceLogo_actionPerformed();
1198 else if (source == showConsensusHistogram)
1200 showConsensusHistogram_actionPerformed();
1202 else if (source == applyAutoAnnotationSettings)
1204 applyAutoAnnotationSettings_actionPerformed();
1206 else if (source == featureSettings)
1208 showFeatureSettingsUI();
1210 else if (source == alProperties)
1212 StringBuffer contents = new jalview.io.AlignmentProperties(
1213 viewport.getAlignment()).formatAsString();
1214 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1215 cap.setText(contents.toString());
1216 Frame frame = new Frame();
1218 jalview.bin.JalviewLite.addFrame(frame, MessageManager
1219 .formatMessage("label.alignment_properties", new String[]
1220 { getTitle() }), 400, 250);
1222 else if (source == overviewMenuItem)
1224 overviewMenuItem_actionPerformed();
1226 else if (source == noColourmenuItem)
1230 else if (source == clustalColour)
1232 abovePIDThreshold.setState(false);
1233 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1235 else if (source == zappoColour)
1237 changeColour(new ZappoColourScheme());
1239 else if (source == taylorColour)
1241 changeColour(new TaylorColourScheme());
1243 else if (source == hydrophobicityColour)
1245 changeColour(new HydrophobicColourScheme());
1247 else if (source == helixColour)
1249 changeColour(new HelixColourScheme());
1251 else if (source == strandColour)
1253 changeColour(new StrandColourScheme());
1255 else if (source == turnColour)
1257 changeColour(new TurnColourScheme());
1259 else if (source == buriedColour)
1261 changeColour(new BuriedColourScheme());
1263 else if (source == nucleotideColour)
1265 changeColour(new NucleotideColourScheme());
1267 else if (source == purinePyrimidineColour)
1269 changeColour(new PurinePyrimidineColourScheme());
1271 // else if (source == RNAInteractionColour)
1273 // changeColour(new RNAInteractionColourScheme());
1275 else if (source == RNAHelixColour)
1277 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1278 // new RNAHelicesColourChooser(viewport, alignPanel);
1280 else if (source == modifyPID)
1282 modifyPID_actionPerformed();
1284 else if (source == modifyConservation)
1286 modifyConservation_actionPerformed();
1288 else if (source == userDefinedColour)
1290 new UserDefinedColours(alignPanel, null);
1292 else if (source == PIDColour)
1294 changeColour(new PIDColourScheme());
1296 else if (source == BLOSUM62Colour)
1298 changeColour(new Blosum62ColourScheme());
1300 else if (source == tcoffeeColour)
1302 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1304 else if (source == annotationColour)
1306 new AnnotationColourChooser(viewport, alignPanel);
1308 else if (source == annotationColumnSelection)
1310 new AnnotationColumnChooser(viewport, alignPanel);
1312 else if (source == sortPairwiseMenuItem)
1314 sortPairwiseMenuItem_actionPerformed();
1316 else if (source == sortIDMenuItem)
1318 sortIDMenuItem_actionPerformed();
1320 else if (source == sortLengthMenuItem)
1322 sortLengthMenuItem_actionPerformed();
1324 else if (source == sortGroupMenuItem)
1326 sortGroupMenuItem_actionPerformed();
1328 else if (source == sortEValueMenuItem)
1330 sortEValueMenuItem_actionPerformed();
1332 else if (source == sortBitScoreMenuItem)
1334 sortBitScoreMenuItem_actionPerformed();
1336 else if (source == removeRedundancyMenuItem)
1338 removeRedundancyMenuItem_actionPerformed();
1340 else if (source == pairwiseAlignmentMenuItem)
1342 pairwiseAlignmentMenuItem_actionPerformed();
1344 else if (source == PCAMenuItem)
1346 PCAMenuItem_actionPerformed();
1348 else if (source == averageDistanceTreeMenuItem)
1350 averageDistanceTreeMenuItem_actionPerformed();
1352 else if (source == neighbourTreeMenuItem)
1354 neighbourTreeMenuItem_actionPerformed();
1356 else if (source == njTreeBlosumMenuItem)
1358 njTreeBlosumMenuItem_actionPerformed();
1360 else if (source == avDistanceTreeBlosumMenuItem)
1362 avTreeBlosumMenuItem_actionPerformed();
1364 else if (source == documentation)
1366 documentation_actionPerformed();
1368 else if (source == about)
1370 about_actionPerformed();
1375 public void inputText_actionPerformed()
1377 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1378 Frame frame = new Frame();
1380 jalview.bin.JalviewLite.addFrame(frame,
1381 MessageManager.getString("label.input_cut_paste"), 500, 500);
1384 protected void outputText_actionPerformed(ActionEvent e)
1386 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1387 Frame frame = new Frame();
1389 JalviewLite.addFrame(frame, MessageManager
1390 .formatMessage("label.alignment_output_command", new Object[]
1391 { e.getActionCommand() }), 600, 500);
1393 FileFormatI fileFormat = FileFormats.getInstance()
1394 .forName(e.getActionCommand());
1396 new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
1397 viewport.getAlignment(), viewport.getShowJVSuffix()));
1400 public void loadAnnotations()
1402 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1403 cap.setText(MessageManager
1404 .getString("label.paste_features_annotations_Tcoffee_here"));
1405 cap.setAnnotationImport();
1406 Frame frame = new Frame();
1408 jalview.bin.JalviewLite.addFrame(frame,
1409 MessageManager.getString("action.paste_annotations"), 400, 300);
1413 public String outputAnnotations(boolean displayTextbox)
1415 String annotation = new AnnotationFile()
1416 .printAnnotationsForView(viewport);
1420 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1421 Frame frame = new Frame();
1423 jalview.bin.JalviewLite.addFrame(frame,
1424 MessageManager.getString("label.annotations"), 600, 500);
1425 cap.setText(annotation);
1431 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1433 if (alignPanel.getFeatureRenderer() != null
1434 && viewport.getFeaturesDisplayed() != null)
1436 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1442 private List<String> getDisplayedFeatureGroups()
1444 if (alignPanel.getFeatureRenderer() != null
1445 && viewport.getFeaturesDisplayed() != null)
1447 return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
1453 public String outputFeatures(boolean displayTextbox, String format)
1456 FeaturesFile formatter = new FeaturesFile();
1457 if (format.equalsIgnoreCase("Jalview"))
1459 features = formatter.printJalviewFormat(
1460 viewport.getAlignment().getSequencesArray(),
1461 alignPanel.getFeatureRenderer(), true, false);
1465 features = formatter.printGffFormat(viewport.getAlignment()
1466 .getSequencesArray(), alignPanel.getFeatureRenderer(), true,
1472 boolean frimport = false;
1473 if (features == null || features.equals("No Features Visible"))
1475 features = "# No features visible - paste some and import them here.";
1479 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1482 cap.setAnnotationImport();
1484 Frame frame = new Frame();
1486 jalview.bin.JalviewLite.addFrame(frame,
1487 MessageManager.getString("label.features"), 600, 500);
1488 cap.setText(features);
1492 if (features == null)
1501 void launchFullApplication()
1503 StringBuffer url = new StringBuffer(jalviewServletURL);
1505 // allow servlet parameters to be passed in applet parameter
1506 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1508 url.append(firstSep);
1511 "open=" + appendProtocol(viewport.applet.getParameter("file")));
1513 if (viewport.applet.getParameter("features") != null)
1515 url.append("&features=");
1516 url.append(appendProtocol(viewport.applet.getParameter("features")));
1519 if (viewport.applet.getParameter("annotations") != null)
1521 url.append("&annotations=");
1523 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(
1531 viewport.applet.getParameter("jnetfile") != null
1532 ? viewport.applet.getParameter("jnetfile")
1533 : viewport.applet.getParameter("jpredfile")));
1536 if (viewport.applet.getParameter("defaultColour") != null)
1538 url.append("&colour=" + removeWhiteSpace(
1539 viewport.applet.getParameter("defaultColour")));
1542 if (viewport.applet.getParameter("userDefinedColour") != null)
1544 url.append("&colour=" + removeWhiteSpace(
1545 viewport.applet.getParameter("userDefinedColour")));
1547 if (viewport.applet.getParameter("tree") != null)
1550 + appendProtocol(viewport.applet.getParameter("tree")));
1552 if (viewport.applet.getParameter("treeFile") != null)
1555 + appendProtocol(viewport.applet.getParameter("treeFile")));
1558 showURL(url.toString(), "FULL_APP");
1561 String removeWhiteSpace(String colour)
1563 StringBuffer sb = new StringBuffer();
1564 for (int i = 0; i < colour.length(); i++)
1566 if (Character.isWhitespace(colour.charAt(i)))
1572 sb.append(colour.charAt(i));
1576 return sb.toString();
1579 String appendProtocol(String url)
1584 url = URLEncoder.encode(url, "UTF-8");
1587 * When we finally deprecate 1.1 compatibility, we can start to use
1588 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1589 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1590 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1591 * ex.printStackTrace(); }
1593 catch (java.net.MalformedURLException ex)
1595 url = viewport.applet.getCodeBase() + url;
1597 catch (UnsupportedEncodingException ex)
1600 "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
1602 ex.printStackTrace();
1607 public void closeMenuItem_actionPerformed()
1609 PaintRefresher.RemoveComponent(alignPanel);
1610 if (alignPanel.seqPanel != null
1611 && alignPanel.seqPanel.seqCanvas != null)
1613 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1615 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1617 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1620 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1626 if (alignPanel != null && alignPanel.overviewPanel != null)
1628 alignPanel.overviewPanel.dispose();
1637 void updateEditMenuBar()
1640 if (viewport.getHistoryList().size() > 0)
1642 undoMenuItem.setEnabled(true);
1643 CommandI command = viewport.getHistoryList().peek();
1644 undoMenuItem.setLabel(MessageManager
1645 .formatMessage("label.undo_command", new Object[]
1646 { command.getDescription() }));
1650 undoMenuItem.setEnabled(false);
1651 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1654 if (viewport.getRedoList().size() > 0)
1656 redoMenuItem.setEnabled(true);
1658 CommandI command = viewport.getRedoList().peek();
1659 redoMenuItem.setLabel(MessageManager
1660 .formatMessage("label.redo_command", new Object[]
1661 { command.getDescription() }));
1665 redoMenuItem.setEnabled(false);
1666 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1674 public void addHistoryItem(CommandI command)
1676 if (command.getSize() > 0)
1678 viewport.addToHistoryList(command);
1679 viewport.clearRedoList();
1680 updateEditMenuBar();
1681 viewport.updateHiddenColumns();
1686 * TODO: JAL-1104 DOCUMENT ME!
1691 protected void undoMenuItem_actionPerformed()
1693 if (viewport.getHistoryList().isEmpty())
1698 CommandI command = viewport.getHistoryList().pop();
1699 viewport.addToRedoList(command);
1700 command.undoCommand(null);
1702 AlignmentViewport originalSource = getOriginatingSource(command);
1704 if (originalSource != viewport)
1707 .println("Warning: Viewport object mismatch whilst undoing");
1709 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1710 // viewport.getColumnSelection().getHiddenColumns()
1712 updateEditMenuBar();
1713 originalSource.notifyAlignment();
1717 * TODO: JAL-1104 DOCUMENT ME!
1722 protected void redoMenuItem_actionPerformed()
1724 if (viewport.getRedoList().isEmpty())
1729 CommandI command = viewport.getRedoList().pop();
1730 viewport.addToHistoryList(command);
1731 command.doCommand(null);
1733 AlignmentViewport originalSource = getOriginatingSource(command);
1735 if (originalSource != viewport)
1738 .println("Warning: Viewport object mismatch whilst re-doing");
1740 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1741 // viewport.getColumnSelection().getHiddenColumns()
1744 updateEditMenuBar();
1745 originalSource.notifyAlignment();
1748 AlignmentViewport getOriginatingSource(CommandI command)
1750 AlignmentViewport originalSource = null;
1751 // For sequence removal and addition, we need to fire
1752 // the property change event FROM the viewport where the
1753 // original alignment was altered
1754 AlignmentI al = null;
1755 if (command instanceof EditCommand)
1757 EditCommand editCommand = (EditCommand) command;
1758 al = editCommand.getAlignment();
1759 Vector comps = PaintRefresher.components
1760 .get(viewport.getSequenceSetId());
1761 for (int i = 0; i < comps.size(); i++)
1763 if (comps.elementAt(i) instanceof AlignmentPanel)
1765 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1767 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1774 if (originalSource == null)
1776 // The original view is closed, we must validate
1777 // the current view against the closed view first
1780 PaintRefresher.validateSequences(al, viewport.getAlignment());
1783 originalSource = viewport;
1786 return originalSource;
1790 * Move the currently selected sequences up or down one position in the
1795 public void moveSelectedSequences(boolean up)
1797 SequenceGroup sg = viewport.getSelectionGroup();
1802 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1803 up ? null : viewport.getHiddenRepSequences(), up);
1804 alignPanel.paintAlignment(true, false);
1807 * Also move cDNA/protein complement sequences
1809 AlignViewportI complement = viewport.getCodingComplement();
1810 if (complement != null)
1812 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1813 viewport, complement);
1814 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1815 up ? null : complement.getHiddenRepSequences(), up);
1816 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
1821 synchronized void slideSequences(boolean right, int size)
1823 List<SequenceI> sg = new Vector<>();
1824 if (viewport.cursorMode)
1826 sg.add(viewport.getAlignment()
1827 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1829 else if (viewport.getSelectionGroup() != null
1830 && viewport.getSelectionGroup().getSize() != viewport
1831 .getAlignment().getHeight())
1833 sg = viewport.getSelectionGroup()
1834 .getSequences(viewport.getHiddenRepSequences());
1842 Vector<SequenceI> invertGroup = new Vector();
1844 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1846 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1848 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1852 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1854 SequenceI[] seqs2 = invertGroup
1855 .toArray(new SequenceI[invertGroup.size()]);
1856 for (int i = 0; i < invertGroup.size(); i++)
1858 seqs2[i] = invertGroup.elementAt(i);
1861 SlideSequencesCommand ssc;
1864 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1865 viewport.getGapCharacter());
1869 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1870 viewport.getGapCharacter());
1873 int groupAdjustment = 0;
1874 if (ssc.getGapsInsertedBegin() && right)
1876 if (viewport.cursorMode)
1878 alignPanel.seqPanel.moveCursor(size, 0);
1882 groupAdjustment = size;
1885 else if (!ssc.getGapsInsertedBegin() && !right)
1887 if (viewport.cursorMode)
1889 alignPanel.seqPanel.moveCursor(-size, 0);
1893 groupAdjustment = -size;
1897 if (groupAdjustment != 0)
1899 viewport.getSelectionGroup().setStartRes(
1900 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1901 viewport.getSelectionGroup().setEndRes(
1902 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1905 boolean appendHistoryItem = false;
1906 Deque<CommandI> historyList = viewport.getHistoryList();
1907 if (historyList != null && historyList.size() > 0
1908 && historyList.peek() instanceof SlideSequencesCommand)
1910 appendHistoryItem = ssc.appendSlideCommand(
1911 (SlideSequencesCommand) historyList.peek());
1914 if (!appendHistoryItem)
1916 addHistoryItem(ssc);
1922 static StringBuffer copiedSequences;
1924 static HiddenColumns copiedHiddenColumns;
1926 protected void copy_actionPerformed()
1928 if (viewport.getSelectionGroup() == null)
1933 SequenceGroup sg = viewport.getSelectionGroup();
1934 copiedSequences = new StringBuffer();
1935 Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1936 for (int i = 0; i < sg.getSize(); i++)
1938 SequenceI seq = sg.getSequenceAt(i);
1939 int index = viewport.getAlignment().findIndex(seq);
1940 orderedSeqs.put(index, seq);
1943 int index = 0, startRes, endRes;
1946 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1948 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1949 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1951 // create new HiddenColumns object with copy of hidden regions
1952 // between startRes and endRes, offset by startRes
1953 copiedHiddenColumns = new HiddenColumns(
1954 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1955 hiddenCutoff, hiddenOffset);
1959 copiedHiddenColumns = null;
1962 for (int i = 0; i < sg.getSize(); i++)
1964 SequenceI seq = null;
1968 if (orderedSeqs.containsKey(index))
1970 seq = orderedSeqs.get(index);
1981 // Returns residue following index if gap
1982 startRes = seq.findPosition(sg.getStartRes());
1985 // Need to find the residue preceeding index if gap
1988 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1990 ch = seq.getCharAt(j);
1991 if (!jalview.util.Comparison.isGap((ch)))
1999 endRes += seq.getStart() - 1;
2002 copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
2003 + "\t" + seq.getSequenceAsString(sg.getStartRes(),
2010 protected void pasteNew_actionPerformed()
2015 protected void pasteThis_actionPerformed()
2020 void paste(boolean newAlignment)
2024 if (copiedSequences == null)
2029 StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
2031 Vector seqs = new Vector();
2032 while (st.hasMoreElements())
2034 String name = st.nextToken();
2035 int start = Integer.parseInt(st.nextToken());
2036 int end = Integer.parseInt(st.nextToken());
2037 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2039 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2040 for (int i = 0; i < seqs.size(); i++)
2042 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2047 String newtitle = MessageManager
2048 .getString("label.copied_sequences");
2049 if (getTitle().startsWith(
2050 MessageManager.getString("label.copied_sequences")))
2052 newtitle = getTitle();
2056 newtitle = newtitle.concat(MessageManager
2057 .formatMessage("label.from_msname", new String[]
2060 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2061 viewport.applet, newtitle, false);
2062 af.viewport.setHiddenColumns(copiedHiddenColumns);
2064 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2069 addSequences(newSeqs);
2072 } catch (Exception ex)
2074 } // could be anything being pasted in here
2078 void addSequences(SequenceI[] seqs)
2080 for (int i = 0; i < seqs.length; i++)
2082 viewport.getAlignment().addSequence(seqs[i]);
2086 addHistoryItem(new EditCommand(
2087 MessageManager.getString("label.add_sequences"), Action.PASTE,
2088 seqs, 0, viewport.getAlignment().getWidth(),
2089 viewport.getAlignment()));
2091 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
2093 viewport.getAlignment().getWidth();
2094 viewport.notifyAlignment();
2098 protected void cut_actionPerformed()
2100 copy_actionPerformed();
2101 delete_actionPerformed();
2104 protected void delete_actionPerformed()
2107 SequenceGroup sg = viewport.getSelectionGroup();
2113 Vector seqs = new Vector();
2115 for (int i = 0; i < sg.getSize(); i++)
2117 seq = sg.getSequenceAt(i);
2118 seqs.addElement(seq);
2122 * If the cut affects all sequences, warn, remove highlighted columns
2124 if (sg.getSize() == viewport.getAlignment().getHeight())
2126 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2127 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2128 if (isEntireAlignWidth)
2130 String title = MessageManager.getString("label.delete_all");
2131 Panel infoPanel = new Panel();
2132 infoPanel.setLayout(new FlowLayout());
2134 new Label(MessageManager.getString("warn.delete_all")));
2136 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2137 dialog.setMainPanel(infoPanel);
2138 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2139 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2140 dialog.setVisible(true);
2147 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2148 sg.getEndRes() + 1);
2151 SequenceI[] cut = new SequenceI[seqs.size()];
2152 for (int i = 0; i < seqs.size(); i++)
2154 cut[i] = (SequenceI) seqs.elementAt(i);
2158 * //ADD HISTORY ITEM
2160 addHistoryItem(new EditCommand(
2161 MessageManager.getString("label.cut_sequences"), Action.CUT,
2162 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2163 viewport.getAlignment()));
2165 viewport.setSelectionGroup(null);
2166 viewport.getAlignment().deleteGroup(sg);
2168 viewport.notifyAlignment();
2170 if (viewport.getAlignment().getHeight() < 1)
2172 this.setVisible(false);
2174 viewport.sendSelection();
2178 * group consensus toggled
2181 protected void showGroupConsensus_actionPerformed()
2183 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2184 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2189 * group conservation toggled.
2191 protected void showGroupConservation_actionPerformed()
2193 viewport.setShowGroupConservation(showGroupConservation.getState());
2194 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2201 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2202 * .event.ActionEvent)
2204 protected void showConsensusHistogram_actionPerformed()
2206 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2207 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2214 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2215 * .event.ActionEvent)
2217 protected void showSequenceLogo_actionPerformed()
2219 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2220 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2223 protected void normSequenceLogo_actionPerformed()
2225 showSequenceLogo.setState(true);
2226 viewport.setShowSequenceLogo(true);
2227 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2228 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2231 protected void applyAutoAnnotationSettings_actionPerformed()
2233 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2236 protected void makeGrpsFromSelection_actionPerformed()
2238 if (avc.makeGroupsFromSelection())
2240 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2241 alignPanel.updateAnnotation();
2242 alignPanel.paintAlignment(true, true);
2246 protected void createGroup_actionPerformed()
2251 protected void unGroup_actionPerformed()
2255 alignPanel.alignmentChanged();
2259 protected void deleteGroups_actionPerformed()
2261 if (avc.deleteGroups())
2263 alignPanel.alignmentChanged();
2267 public void selectAllSequenceMenuItem_actionPerformed()
2269 SequenceGroup sg = new SequenceGroup();
2270 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2272 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2274 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2275 viewport.setSelectionGroup(sg);
2276 // JAL-2034 - should delegate to
2277 // alignPanel to decide if overview needs
2279 alignPanel.paintAlignment(false, false);
2280 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2281 viewport.sendSelection();
2284 public void deselectAllSequenceMenuItem_actionPerformed()
2286 if (viewport.cursorMode)
2288 alignPanel.seqPanel.keyboardNo1 = null;
2289 alignPanel.seqPanel.keyboardNo2 = null;
2291 viewport.setSelectionGroup(null);
2292 viewport.getColumnSelection().clear();
2293 viewport.setSelectionGroup(null);
2294 alignPanel.idPanel.idCanvas.searchResults = null;
2295 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2296 // JAL-2034 - should delegate to
2297 // alignPanel to decide if overview needs
2299 alignPanel.paintAlignment(false, false);
2300 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2301 viewport.sendSelection();
2304 public void invertSequenceMenuItem_actionPerformed()
2306 SequenceGroup sg = viewport.getSelectionGroup();
2307 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2309 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2312 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2313 viewport.sendSelection();
2316 public void invertColSel_actionPerformed()
2318 viewport.invertColumnSelection();
2319 alignPanel.paintAlignment(true, false);
2320 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2321 viewport.sendSelection();
2324 void trimAlignment(boolean trimLeft)
2326 AlignmentI al = viewport.getAlignment();
2327 ViewportRanges ranges = viewport.getRanges();
2328 ColumnSelection colSel = viewport.getColumnSelection();
2331 if (!colSel.isEmpty())
2335 column = colSel.getMin();
2339 column = colSel.getMax();
2343 if (viewport.getSelectionGroup() != null)
2345 seqs = viewport.getSelectionGroup()
2346 .getSequencesAsArray(viewport.getHiddenRepSequences());
2350 seqs = al.getSequencesArray();
2353 TrimRegionCommand trimRegion;
2356 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2358 ranges.setStartRes(0);
2362 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2366 setStatus(MessageManager
2367 .formatMessage("label.removed_columns", new String[]
2368 { Integer.valueOf(trimRegion.getSize()).toString() }));
2369 addHistoryItem(trimRegion);
2371 for (SequenceGroup sg : al.getGroups())
2373 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2374 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2380 viewport.notifyAlignment();
2384 public void removeGappedColumnMenuItem_actionPerformed()
2386 AlignmentI al = viewport.getAlignment();
2387 ViewportRanges ranges = viewport.getRanges();
2389 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2392 if (viewport.getSelectionGroup() != null)
2394 seqs = viewport.getSelectionGroup()
2395 .getSequencesAsArray(viewport.getHiddenRepSequences());
2396 start = viewport.getSelectionGroup().getStartRes();
2397 end = viewport.getSelectionGroup().getEndRes();
2401 seqs = viewport.getAlignment().getSequencesArray();
2404 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2405 "Remove Gapped Columns", seqs, start, end,
2406 viewport.getAlignment());
2408 addHistoryItem(removeGapCols);
2410 setStatus(MessageManager
2411 .formatMessage("label.removed_empty_columns", new String[]
2412 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2414 // This is to maintain viewport position on first residue
2415 // of first sequence
2416 SequenceI seq = al.getSequenceAt(0);
2417 int startRes = seq.findPosition(ranges.getStartRes());
2418 // ShiftList shifts;
2419 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2420 // edit.alColumnChanges=shifts.getInverse();
2421 // if (viewport.hasHiddenColumns)
2422 // viewport.getColumnSelection().compensateForEdits(shifts);
2423 ranges.setStartRes(seq.findIndex(startRes) - 1);
2424 viewport.notifyAlignment();
2428 public void removeAllGapsMenuItem_actionPerformed()
2430 AlignmentI al = viewport.getAlignment();
2431 ViewportRanges ranges = viewport.getRanges();
2433 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2436 if (viewport.getSelectionGroup() != null)
2438 seqs = viewport.getSelectionGroup()
2439 .getSequencesAsArray(viewport.getHiddenRepSequences());
2440 start = viewport.getSelectionGroup().getStartRes();
2441 end = viewport.getSelectionGroup().getEndRes();
2445 seqs = viewport.getAlignment().getSequencesArray();
2448 // This is to maintain viewport position on first residue
2449 // of first sequence
2450 SequenceI seq = al.getSequenceAt(0);
2451 int startRes = seq.findPosition(ranges.getStartRes());
2454 new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2456 ranges.setStartRes(seq.findIndex(startRes) - 1);
2458 viewport.notifyAlignment();
2462 public void findMenuItem_actionPerformed()
2464 new Finder(alignPanel);
2468 * create a new view derived from the current view
2471 * @return frame for the new view
2473 public AlignFrame newView(String viewtitle)
2476 if (viewport.hasHiddenRows())
2478 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2479 .getFullAlignment().getSequencesArray());
2483 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2486 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2488 for (int i = 0; i < viewport.getAlignment()
2489 .getAlignmentAnnotation().length; i++)
2491 if (!viewport.getAlignment()
2492 .getAlignmentAnnotation()[i].autoCalculated)
2494 newal.addAnnotation(
2495 viewport.getAlignment().getAlignmentAnnotation()[i]);
2500 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2502 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2503 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2504 PaintRefresher.Register(newaf.alignPanel,
2505 newaf.alignPanel.av.getSequenceSetId());
2507 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2508 newaf.alignPanel.av.getSequenceSetId());
2509 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2510 newaf.alignPanel.av.getSequenceSetId());
2512 Vector comps = PaintRefresher.components
2513 .get(viewport.getSequenceSetId());
2515 for (int i = 0; i < comps.size(); i++)
2517 if (comps.elementAt(i) instanceof AlignmentPanel)
2523 String title = new String(this.getTitle());
2524 if (viewtitle != null)
2526 title = viewtitle + " ( " + title + ")";
2530 if (title.indexOf("(View") > -1)
2532 title = title.substring(0, title.indexOf("(View"));
2534 title += "(View " + viewSize + ")";
2537 newaf.setTitle(title.toString());
2539 newaf.viewport.setHistoryList(viewport.getHistoryList());
2540 newaf.viewport.setRedoList(viewport.getRedoList());
2546 * @return list of feature groups on the view
2548 public String[] getFeatureGroups()
2550 FeatureRenderer fr = null;
2551 if (alignPanel != null
2552 && (fr = alignPanel.getFeatureRenderer()) != null)
2554 List<String> gps = fr.getFeatureGroups();
2555 String[] _gps = gps.toArray(new String[gps.size()]);
2562 * get sequence feature groups that are hidden or shown
2568 public String[] getFeatureGroupsOfState(boolean visible)
2570 FeatureRenderer fr = null;
2571 if (alignPanel != null
2572 && (fr = alignPanel.getFeatureRenderer()) != null)
2574 List<String> gps = fr.getGroups(visible);
2575 String[] _gps = gps.toArray(new String[gps.size()]);
2582 * Change the display state for the given feature groups
2585 * list of group strings
2587 * visible or invisible
2589 public void setFeatureGroupState(String[] groups, boolean state)
2591 FeatureRenderer fr = null;
2592 this.sequenceFeatures.setState(true);
2593 viewport.setShowSequenceFeatures(true);
2594 if (alignPanel != null
2595 && (fr = alignPanel.getFeatureRenderer()) != null)
2598 fr.setGroupVisibility(Arrays.asList(groups), state);
2599 alignPanel.seqPanel.seqCanvas.repaint();
2600 if (alignPanel.overviewPanel != null)
2602 alignPanel.overviewPanel.updateOverviewImage();
2607 public void seqLimits_itemStateChanged()
2609 viewport.setShowJVSuffix(seqLimits.getState());
2610 alignPanel.fontChanged();
2611 alignPanel.paintAlignment(true, false);
2614 protected void colourTextMenuItem_actionPerformed()
2616 viewport.setColourText(colourTextMenuItem.getState());
2617 alignPanel.paintAlignment(false, false);
2620 protected void displayNonconservedMenuItem_actionPerformed()
2622 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2623 alignPanel.paintAlignment(false, false);
2626 protected void wrapMenuItem_actionPerformed()
2628 viewport.setWrapAlignment(wrapMenuItem.getState());
2629 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2630 scaleAbove.setEnabled(wrapMenuItem.getState());
2631 scaleLeft.setEnabled(wrapMenuItem.getState());
2632 scaleRight.setEnabled(wrapMenuItem.getState());
2633 alignPanel.paintAlignment(true, false);
2636 public void overviewMenuItem_actionPerformed()
2638 if (alignPanel.overviewPanel != null)
2643 Frame frame = new Frame();
2644 final OverviewPanel overview = new OverviewPanel(alignPanel);
2645 frame.add(overview);
2646 // +50 must allow for applet frame window
2647 jalview.bin.JalviewLite.addFrame(frame, MessageManager
2648 .formatMessage("label.overview_params", new String[]
2649 { this.getTitle() }), overview.getPreferredSize().width,
2650 overview.getPreferredSize().height + 50);
2653 final AlignmentPanel ap = alignPanel;
2654 frame.addWindowListener(new WindowAdapter()
2657 public void windowClosing(WindowEvent e)
2662 ap.setOverviewPanel(null);
2667 alignPanel.setOverviewPanel(overview);
2672 public void changeColour(ColourSchemeI cs)
2674 viewport.setGlobalColourScheme(cs);
2676 alignPanel.paintAlignment(true, true);
2679 protected void modifyPID_actionPerformed()
2681 if (viewport.getAbovePIDThreshold()
2682 && viewport.getGlobalColourScheme() != null)
2684 SliderPanel.setPIDSliderSource(alignPanel,
2685 viewport.getResidueShading(), alignPanel.getViewName());
2686 SliderPanel.showPIDSlider();
2690 protected void modifyConservation_actionPerformed()
2692 if (viewport.getConservationSelected()
2693 && viewport.getGlobalColourScheme() != null)
2695 SliderPanel.setConservationSlider(alignPanel,
2696 viewport.getResidueShading(), alignPanel.getViewName());
2697 SliderPanel.showConservationSlider();
2701 protected void conservationMenuItem_actionPerformed()
2703 boolean selected = conservationMenuItem.getState();
2704 modifyConservation.setEnabled(selected);
2705 viewport.setConservationSelected(selected);
2706 viewport.getResidueShading().setConservationApplied(selected);
2708 changeColour(viewport.getGlobalColourScheme());
2712 modifyConservation_actionPerformed();
2716 SliderPanel.hideConservationSlider();
2720 public void abovePIDThreshold_actionPerformed()
2722 boolean selected = abovePIDThreshold.getState();
2723 modifyPID.setEnabled(selected);
2724 viewport.setAbovePIDThreshold(selected);
2727 viewport.getResidueShading().setThreshold(0,
2728 viewport.isIgnoreGapsConsensus());
2731 changeColour(viewport.getGlobalColourScheme());
2735 modifyPID_actionPerformed();
2739 SliderPanel.hidePIDSlider();
2743 public void sortPairwiseMenuItem_actionPerformed()
2745 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2746 AlignmentSorter.sortByPID(viewport.getAlignment(),
2747 viewport.getAlignment().getSequenceAt(0));
2749 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2750 viewport.getAlignment()));
2751 alignPanel.paintAlignment(true, false);
2754 public void sortIDMenuItem_actionPerformed()
2756 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2757 AlignmentSorter.sortByID(viewport.getAlignment());
2759 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
2760 alignPanel.paintAlignment(true, false);
2763 public void sortLengthMenuItem_actionPerformed()
2765 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2766 AlignmentSorter.sortByLength(viewport.getAlignment());
2767 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2768 viewport.getAlignment()));
2769 alignPanel.paintAlignment(true, false);
2772 public void sortGroupMenuItem_actionPerformed()
2774 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2775 AlignmentSorter.sortByGroup(viewport.getAlignment());
2776 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2777 viewport.getAlignment()));
2778 alignPanel.paintAlignment(true, false);
2782 public void sortEValueMenuItem_actionPerformed()
2784 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2785 AlignmentSorter.sortByEValue(viewport.getAlignment());
2786 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2787 viewport.getAlignment()));
2788 alignPanel.paintAlignment(true, false);
2792 public void sortBitScoreMenuItem_actionPerformed()
2794 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2795 AlignmentSorter.sortByBitScore(viewport.getAlignment());
2796 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2797 viewport.getAlignment()));
2798 alignPanel.paintAlignment(true, false);
2802 public void removeRedundancyMenuItem_actionPerformed()
2804 new RedundancyPanel(alignPanel);
2807 public void pairwiseAlignmentMenuItem_actionPerformed()
2809 if (viewport.getSelectionGroup() != null
2810 && viewport.getSelectionGroup().getSize() > 1)
2812 Frame frame = new Frame();
2813 frame.add(new PairwiseAlignPanel(alignPanel));
2814 jalview.bin.JalviewLite.addFrame(frame,
2815 MessageManager.getString("action.pairwise_alignment"), 600,
2820 public void PCAMenuItem_actionPerformed()
2822 // are the sequences aligned?
2823 if (!viewport.getAlignment().isAligned(false))
2826 int Width = viewport.getAlignment().getWidth();
2828 for (int i = 0; i < viewport.getAlignment().getSequences()
2831 current = viewport.getAlignment().getSequenceAt(i);
2833 if (current.getLength() < Width)
2835 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2838 alignPanel.paintAlignment(false, false);
2841 if ((viewport.getSelectionGroup() != null
2842 && viewport.getSelectionGroup().getSize() < 4
2843 && viewport.getSelectionGroup().getSize() > 0)
2844 || viewport.getAlignment().getHeight() < 4)
2851 new PCAPanel(viewport);
2852 } catch (java.lang.OutOfMemoryError ex)
2858 public void averageDistanceTreeMenuItem_actionPerformed()
2860 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2861 "Average distance tree using PID");
2864 public void neighbourTreeMenuItem_actionPerformed()
2866 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2867 "Neighbour joining tree using PID");
2870 protected void njTreeBlosumMenuItem_actionPerformed()
2872 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2873 ScoreModels.getInstance().getBlosum62().getName(),
2874 "Neighbour joining tree using BLOSUM62");
2877 protected void avTreeBlosumMenuItem_actionPerformed()
2879 newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2880 ScoreModels.getInstance().getBlosum62().getName(),
2881 "Average distance tree using BLOSUM62");
2884 void newTreePanel(String type, String pwType, String title)
2886 // are the sequences aligned?
2887 if (!viewport.getAlignment().isAligned(false))
2890 int Width = viewport.getAlignment().getWidth();
2892 for (int i = 0; i < viewport.getAlignment().getSequences()
2895 current = viewport.getAlignment().getSequenceAt(i);
2897 if (current.getLength() < Width)
2899 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2902 alignPanel.paintAlignment(false, false);
2906 if ((viewport.getSelectionGroup() != null
2907 && viewport.getSelectionGroup().getSize() > 1)
2908 || (viewport.getAlignment().getHeight() > 1))
2910 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2912 addTreeMenuItem(tp, title);
2914 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2918 void loadTree_actionPerformed()
2920 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2921 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2922 cap.setTreeImport();
2923 Frame frame = new Frame();
2925 jalview.bin.JalviewLite.addFrame(frame,
2926 MessageManager.getString("label.paste_newick_file"), 400, 300);
2929 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2931 TreePanel tp = new TreePanel(alignPanel, treeFile,
2932 MessageManager.getString("label.load_tree_from_file"), tree);
2933 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2934 addTreeMenuItem(tp, treeFile);
2938 * sort the alignment using the given treePanel
2941 * tree used to sort view
2943 * string used for undo event name
2945 public void sortByTree(TreePanel treePanel, String title)
2947 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2948 AlignmentSorter.sortByTree(viewport.getAlignment(),
2949 treePanel.getTree());
2950 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2951 // HistoryItem.SORT));
2952 addHistoryItem(new OrderCommand(MessageManager
2953 .formatMessage("label.order_by_params", new String[]
2954 { title }), oldOrder, viewport.getAlignment()));
2955 alignPanel.paintAlignment(true, false);
2959 * Do any automatic reordering of the alignment and add the necessary bits to
2960 * the menu structure for the new tree
2965 protected void addTreeMenuItem(final TreePanel treePanel,
2968 final MenuItem item = new MenuItem(title);
2969 sortByTreeMenu.add(item);
2970 item.addActionListener(new java.awt.event.ActionListener()
2973 public void actionPerformed(ActionEvent evt)
2975 sortByTree(treePanel, title); // treePanel.getTitle());
2979 treePanel.addWindowListener(new WindowAdapter()
2982 public void windowOpened(WindowEvent e)
2984 if (viewport.sortByTree)
2986 sortByTree(treePanel, title);
2988 super.windowOpened(e);
2992 public void windowClosing(WindowEvent e)
2994 sortByTreeMenu.remove(item);
2999 public boolean sortBy(AlignmentOrder alorder, String undoname)
3001 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3002 if (viewport.applet.debug)
3004 System.err.println("Sorting " + alorder.getOrder().size()
3005 + " in alignment '" + getTitle() + "'");
3007 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3008 if (undoname != null)
3010 addHistoryItem(new OrderCommand(undoname, oldOrder,
3011 viewport.getAlignment()));
3013 alignPanel.paintAlignment(true, false);
3017 protected void documentation_actionPerformed()
3019 alignPanel.av.applet.openJalviewHelpUrl();
3022 protected void about_actionPerformed()
3025 class AboutPanel extends Canvas
3031 public AboutPanel(String version, String builddate)
3033 this.version = version;
3034 this.builddate = builddate;
3038 public void paint(Graphics g)
3040 g.setColor(Color.white);
3041 g.fillRect(0, 0, getSize().width, getSize().height);
3042 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3043 FontMetrics fm = g.getFontMetrics();
3044 int fh = fm.getHeight();
3046 g.setColor(Color.black);
3047 // TODO: update this text for each release or centrally store it for
3048 // lite and application
3049 g.setFont(new Font("Helvetica", Font.BOLD, 14));
3050 g.drawString(MessageManager
3051 .formatMessage("label.jalviewLite_release", new String[]
3052 { version }), x, y += fh);
3053 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3054 g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3056 { builddate }), x, y += fh);
3057 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3058 g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3060 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3061 x + 50, y += fh + 8);
3062 g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3064 g.drawString(MessageManager
3065 .getString("label.jalview_distribution_lists"), x, y += fh);
3066 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3069 MessageManager.getString("label.jalview_cite_1_authors"), x,
3071 g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3073 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3078 Frame frame = new Frame();
3079 frame.add(new AboutPanel(JalviewLite.getVersion(),
3080 JalviewLite.getBuildDate()));
3081 jalview.bin.JalviewLite.addFrame(frame,
3082 MessageManager.getString("label.jalview"), 580, 220);
3086 public void showURL(String url, String target)
3088 if (viewport.applet == null)
3090 System.out.println("Not running as applet - no browser available.");
3094 viewport.applet.showURL(url, target);
3098 // ////////////////////////////////////////////////////////////////////////////////
3099 // JBuilder Graphics here
3101 MenuBar alignFrameMenuBar = new MenuBar();
3103 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3105 MenuItem loadApplication = new MenuItem(
3106 MessageManager.getString("label.view_full_application"));
3108 MenuItem loadTree = new MenuItem(
3109 MessageManager.getString("label.load_associated_tree"));
3111 MenuItem loadAnnotations = new MenuItem(
3112 MessageManager.getString("label.load_features_annotations"));
3114 MenuItem outputFeatures = new MenuItem(
3115 MessageManager.getString("label.export_features"));
3117 MenuItem outputAnnotations = new MenuItem(
3118 MessageManager.getString("label.export_annotations"));
3120 MenuItem closeMenuItem = new MenuItem(
3121 MessageManager.getString("action.close"));
3123 MenuItem selectAllSequenceMenuItem = new MenuItem(
3124 MessageManager.getString("action.select_all"));
3126 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3127 MessageManager.getString("action.deselect_all"));
3129 MenuItem invertSequenceMenuItem = new MenuItem(
3130 MessageManager.getString("action.invert_selection"));
3132 MenuItem remove2LeftMenuItem = new MenuItem();
3134 MenuItem remove2RightMenuItem = new MenuItem();
3136 MenuItem removeGappedColumnMenuItem = new MenuItem();
3138 MenuItem removeAllGapsMenuItem = new MenuItem();
3140 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3142 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3144 MenuItem sortPairwiseMenuItem = new MenuItem();
3146 MenuItem sortIDMenuItem = new MenuItem();
3148 MenuItem sortLengthMenuItem = new MenuItem();
3150 MenuItem sortGroupMenuItem = new MenuItem();
3152 MenuItem sortEValueMenuItem = new MenuItem();
3154 MenuItem sortBitScoreMenuItem = new MenuItem();
3156 MenuItem removeRedundancyMenuItem = new MenuItem();
3158 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3160 MenuItem PCAMenuItem = new MenuItem();
3162 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3164 MenuItem neighbourTreeMenuItem = new MenuItem();
3166 BorderLayout borderLayout1 = new BorderLayout();
3168 public Label statusBar = new Label();
3170 MenuItem clustalColour = new MenuItem();
3172 MenuItem zappoColour = new MenuItem();
3174 MenuItem taylorColour = new MenuItem();
3176 MenuItem hydrophobicityColour = new MenuItem();
3178 MenuItem helixColour = new MenuItem();
3180 MenuItem strandColour = new MenuItem();
3182 MenuItem turnColour = new MenuItem();
3184 MenuItem buriedColour = new MenuItem();
3186 MenuItem purinePyrimidineColour = new MenuItem();
3188 // MenuItem RNAInteractionColour = new MenuItem();
3190 MenuItem RNAHelixColour = new MenuItem();
3192 MenuItem userDefinedColour = new MenuItem();
3194 MenuItem PIDColour = new MenuItem();
3196 MenuItem BLOSUM62Colour = new MenuItem();
3198 MenuItem tcoffeeColour = new MenuItem();
3200 MenuItem njTreeBlosumMenuItem = new MenuItem();
3202 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3204 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3206 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3208 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3210 MenuItem alProperties = new MenuItem(
3211 MessageManager.getString("label.alignment_props"));
3213 MenuItem overviewMenuItem = new MenuItem();
3215 MenuItem undoMenuItem = new MenuItem();
3217 MenuItem redoMenuItem = new MenuItem();
3219 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3221 MenuItem noColourmenuItem = new MenuItem();
3223 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3225 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3227 MenuItem findMenuItem = new MenuItem();
3229 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3231 MenuItem nucleotideColour = new MenuItem();
3233 MenuItem deleteGroups = new MenuItem();
3235 MenuItem grpsFromSelection = new MenuItem();
3237 MenuItem createGroup = new MenuItem();
3239 MenuItem unGroup = new MenuItem();
3241 MenuItem delete = new MenuItem();
3243 MenuItem copy = new MenuItem();
3245 MenuItem cut = new MenuItem();
3247 Menu pasteMenu = new Menu();
3249 MenuItem pasteNew = new MenuItem();
3251 MenuItem pasteThis = new MenuItem();
3253 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3255 MenuItem font = new MenuItem();
3257 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3259 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3261 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3263 MenuItem modifyPID = new MenuItem();
3265 MenuItem modifyConservation = new MenuItem();
3267 CheckboxMenuItem autoCalculate = null;
3269 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3270 "Sort Alignment With New Tree", true);
3272 Menu sortByTreeMenu = new Menu();
3274 MenuItem inputText = new MenuItem();
3276 MenuItem documentation = new MenuItem();
3278 MenuItem about = new MenuItem();
3280 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3282 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3284 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3286 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3288 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3290 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3292 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3294 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3296 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3299 * Initialise menus and other items
3303 private void jbInit() throws Exception
3305 setMenuBar(alignFrameMenuBar);
3308 * Configure File menu items and actions
3311 .setLabel(MessageManager.getString("label.input_from_textbox"));
3312 inputText.addActionListener(this);
3313 Menu outputTextboxMenu = new Menu(
3314 MessageManager.getString("label.out_to_textbox"));
3315 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3317 MenuItem item = new MenuItem(ff);
3319 item.addActionListener(new java.awt.event.ActionListener()
3322 public void actionPerformed(ActionEvent e)
3324 outputText_actionPerformed(e);
3328 outputTextboxMenu.add(item);
3330 closeMenuItem.addActionListener(this);
3331 loadApplication.addActionListener(this);
3332 loadTree.addActionListener(this);
3333 loadAnnotations.addActionListener(this);
3334 outputFeatures.addActionListener(this);
3335 outputAnnotations.addActionListener(this);
3338 * Configure Edit menu items and actions
3340 undoMenuItem.setEnabled(false);
3341 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3342 undoMenuItem.addActionListener(this);
3343 redoMenuItem.setEnabled(false);
3344 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3345 redoMenuItem.addActionListener(this);
3346 copy.setLabel(MessageManager.getString("action.copy"));
3347 copy.addActionListener(this);
3348 cut.setLabel(MessageManager.getString("action.cut"));
3349 cut.addActionListener(this);
3350 delete.setLabel(MessageManager.getString("action.delete"));
3351 delete.addActionListener(this);
3352 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3353 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3354 pasteNew.addActionListener(this);
3355 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3356 pasteThis.addActionListener(this);
3358 .setLabel(MessageManager.getString("action.remove_left"));
3359 remove2LeftMenuItem.addActionListener(this);
3360 remove2RightMenuItem
3361 .setLabel(MessageManager.getString("action.remove_right"));
3362 remove2RightMenuItem.addActionListener(this);
3363 removeGappedColumnMenuItem.setLabel(
3364 MessageManager.getString("action.remove_empty_columns"));
3365 removeGappedColumnMenuItem.addActionListener(this);
3366 removeAllGapsMenuItem
3367 .setLabel(MessageManager.getString("action.remove_all_gaps"));
3368 removeAllGapsMenuItem.addActionListener(this);
3369 removeRedundancyMenuItem
3370 .setLabel(MessageManager.getString("action.remove_redundancy"));
3371 removeRedundancyMenuItem.addActionListener(this);
3374 * Configure Select menu items and actions
3376 findMenuItem.setLabel(MessageManager.getString("action.find"));
3377 findMenuItem.addActionListener(this);
3378 selectAllSequenceMenuItem.addActionListener(this);
3379 deselectAllSequenceMenuItem.addActionListener(this);
3380 invertSequenceMenuItem.setLabel(
3381 MessageManager.getString("action.invert_sequence_selection"));
3382 invertSequenceMenuItem.addActionListener(this);
3383 invertColSel.setLabel(
3384 MessageManager.getString("action.invert_column_selection"));
3385 invertColSel.addActionListener(this);
3387 .setLabel(MessageManager.getString("action.undefine_groups"));
3388 deleteGroups.addActionListener(this);
3389 grpsFromSelection.setLabel(
3390 MessageManager.getString("action.make_groups_selection"));
3391 grpsFromSelection.addActionListener(this);
3392 createGroup.setLabel(MessageManager.getString("action.create_group"));
3393 createGroup.addActionListener(this);
3394 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3395 unGroup.addActionListener(this);
3397 annotationColumnSelection.setLabel(
3398 MessageManager.getString("action.select_by_annotation"));
3399 annotationColumnSelection.addActionListener(this);
3402 * Configure View menu items and actions
3404 newView.setLabel(MessageManager.getString("action.new_view"));
3405 newView.addActionListener(this);
3406 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3407 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3408 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3409 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3411 .setLabel(MessageManager.getString("label.selected_columns"));
3413 .setLabel(MessageManager.getString("label.selected_sequences"));
3414 hideAllButSelection.setLabel(
3415 MessageManager.getString("label.all_but_selected_region"));
3417 .setLabel(MessageManager.getString("label.selected_region"));
3418 showAllHidden.setLabel(
3419 MessageManager.getString("label.all_sequences_columns"));
3420 showColumns.addActionListener(this);
3421 showSeqs.addActionListener(this);
3422 hideColumns.addActionListener(this);
3423 hideSequences.addActionListener(this);
3424 hideAllButSelection.addActionListener(this);
3425 hideAllSelection.addActionListener(this);
3426 showAllHidden.addActionListener(this);
3428 .setLabel(MessageManager.getString("action.feature_settings"));
3429 featureSettings.addActionListener(this);
3430 sequenceFeatures.setLabel(
3431 MessageManager.getString("label.show_sequence_features"));
3432 sequenceFeatures.addItemListener(this);
3433 sequenceFeatures.setState(false);
3434 followMouseOverFlag.setLabel(
3435 MessageManager.getString("label.automatic_scrolling"));
3436 followMouseOverFlag.addItemListener(this);
3437 alProperties.addActionListener(this);
3439 .setLabel(MessageManager.getString("label.overview_window"));
3440 overviewMenuItem.addActionListener(this);
3443 * Configure Annotations menu items and actions
3445 annotationPanelMenuItem
3446 .setLabel(MessageManager.getString("label.show_annotations"));
3447 annotationPanelMenuItem.addItemListener(this);
3449 .setLabel(MessageManager.getString("label.group_consensus"));
3450 showGroupConservation
3451 .setLabel(MessageManager.getString("label.group_conservation"));
3452 showConsensusHistogram.setLabel(
3453 MessageManager.getString("label.show_consensus_histogram"));
3454 showSequenceLogo.setLabel(
3455 MessageManager.getString("label.show_consensus_logo"));
3456 normSequenceLogo.setLabel(
3457 MessageManager.getString("label.norm_consensus_logo"));
3458 applyAutoAnnotationSettings
3459 .setLabel(MessageManager.getString("label.apply_all_groups"));
3460 applyAutoAnnotationSettings.setState(true);
3461 Menu autoAnnMenu = new Menu(
3462 MessageManager.getString("label.autocalculated_annotation"));
3463 showGroupConsensus.addItemListener(this);
3464 showGroupConservation.addItemListener(this);
3465 showConsensusHistogram.addItemListener(this);
3466 showSequenceLogo.addItemListener(this);
3467 normSequenceLogo.addItemListener(this);
3468 applyAutoAnnotationSettings.addItemListener(this);
3469 showAlignmentAnnotations = new CheckboxMenuItem(
3470 MessageManager.getString("label.show_all_al_annotations"));
3471 showSequenceAnnotations = new CheckboxMenuItem(
3472 MessageManager.getString("label.show_all_seq_annotations"));
3473 sortAnnBySequence = new CheckboxMenuItem(
3474 MessageManager.getString("label.sort_annotations_by_sequence"));
3475 sortAnnByLabel = new CheckboxMenuItem(
3476 MessageManager.getString("label.sort_annotations_by_label"));
3477 showAutoFirst = new CheckboxMenuItem(
3478 MessageManager.getString("label.show_first"));
3479 showAutoFirst.setState(false); // pending applet parameter
3480 setShowAutoCalculatedAbove(showAutoFirst.getState());
3481 showAutoLast = new CheckboxMenuItem(
3482 MessageManager.getString("label.show_last"));
3483 showAutoLast.setState(!showAutoFirst.getState());
3484 showAlignmentAnnotations.addItemListener(this);
3485 showSequenceAnnotations.addItemListener(this);
3486 sortAnnBySequence.addItemListener(this);
3487 sortAnnByLabel.addItemListener(this);
3488 showAutoFirst.addItemListener(this);
3489 showAutoLast.addItemListener(this);
3492 * Configure Format menu items and actions
3494 font.setLabel(MessageManager.getString("action.font"));
3495 font.addActionListener(this);
3496 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3497 scaleAbove.setState(true);
3498 scaleAbove.setEnabled(false);
3499 scaleAbove.addItemListener(this);
3500 scaleLeft.setEnabled(false);
3501 scaleLeft.setState(true);
3502 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3503 scaleLeft.addItemListener(this);
3504 scaleRight.setEnabled(false);
3505 scaleRight.setState(true);
3506 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3507 scaleRight.addItemListener(this);
3508 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3509 viewBoxesMenuItem.setState(true);
3510 viewBoxesMenuItem.addItemListener(this);
3511 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3512 viewTextMenuItem.setState(true);
3513 viewTextMenuItem.addItemListener(this);
3515 .setLabel(MessageManager.getString("label.colour_text"));
3516 colourTextMenuItem.addItemListener(this);
3517 displayNonconservedMenuItem
3518 .setLabel(MessageManager.getString("label.show_non_conserved"));
3519 displayNonconservedMenuItem.addItemListener(this);
3520 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3521 wrapMenuItem.addItemListener(this);
3523 .setLabel(MessageManager.getString("action.show_gaps"));
3524 renderGapsMenuItem.setState(true);
3525 renderGapsMenuItem.addItemListener(this);
3526 centreColumnLabelFlag.setLabel(
3527 MessageManager.getString("label.centre_column_labels"));
3528 centreColumnLabelFlag.addItemListener(this);
3529 seqLimits.setState(true);
3531 MessageManager.getString("label.show_sequence_limits"));
3532 seqLimits.addItemListener(this);
3535 * Configure Colour menu items and actions
3537 applyToAllGroups.setLabel(
3538 MessageManager.getString("label.apply_colour_to_all_groups"));
3539 applyToAllGroups.setState(true);
3540 applyToAllGroups.addItemListener(this);
3541 clustalColour.setLabel(
3542 MessageManager.getString("label.colourScheme_clustal"));
3543 clustalColour.addActionListener(this);
3545 .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3546 zappoColour.addActionListener(this);
3547 taylorColour.setLabel(
3548 MessageManager.getString("label.colourScheme_taylor"));
3549 taylorColour.addActionListener(this);
3550 hydrophobicityColour.setLabel(
3551 MessageManager.getString("label.colourScheme_hydrophobic"));
3552 hydrophobicityColour.addActionListener(this);
3553 helixColour.setLabel(MessageManager
3554 .getString("label.colourScheme_helix_propensity"));
3555 helixColour.addActionListener(this);
3556 strandColour.setLabel(MessageManager
3557 .getString("label.colourScheme_strand_propensity"));
3558 strandColour.addActionListener(this);
3559 turnColour.setLabel(
3560 MessageManager.getString("label.colourScheme_turn_propensity"));
3561 turnColour.addActionListener(this);
3562 buriedColour.setLabel(
3563 MessageManager.getString("label.colourScheme_buried_index"));
3564 buriedColour.addActionListener(this);
3565 purinePyrimidineColour.setLabel(MessageManager
3566 .getString("label.colourScheme_purine/pyrimidine"));
3567 purinePyrimidineColour.addActionListener(this);
3568 // RNAInteractionColour.setLabel(MessageManager
3569 // .getString("label.rna_interaction"));
3570 // RNAInteractionColour.addActionListener(this);
3571 RNAHelixColour.setLabel(
3572 MessageManager.getString("label.colourScheme_rna_helices"));
3573 RNAHelixColour.addActionListener(this);
3575 .setLabel(MessageManager.getString("action.user_defined"));
3576 userDefinedColour.addActionListener(this);
3578 MessageManager.getString("label.colourScheme_%_identity"));
3579 PIDColour.addActionListener(this);
3580 BLOSUM62Colour.setLabel(
3581 MessageManager.getString("label.colourScheme_blosum62"));
3582 BLOSUM62Colour.addActionListener(this);
3583 tcoffeeColour.setLabel(
3584 MessageManager.getString("label.colourScheme_t-coffee_scores"));
3585 // it will be enabled only if a score file is provided
3586 tcoffeeColour.setEnabled(false);
3587 tcoffeeColour.addActionListener(this);
3588 conservationMenuItem
3589 .setLabel(MessageManager.getString("action.by_conservation"));
3590 conservationMenuItem.addItemListener(this);
3591 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3592 noColourmenuItem.addActionListener(this);
3593 abovePIDThreshold.setLabel(
3594 MessageManager.getString("label.above_identity_threshold"));
3595 abovePIDThreshold.addItemListener(this);
3596 nucleotideColour.setLabel(
3597 MessageManager.getString("label.colourScheme_nucleotide"));
3598 nucleotideColour.addActionListener(this);
3600 MessageManager.getString("label.modify_identity_threshold"));
3601 modifyPID.setEnabled(abovePIDThreshold.getState());
3602 modifyPID.addActionListener(this);
3603 modifyConservation.setLabel(MessageManager
3604 .getString("label.modify_conservation_threshold"));
3605 modifyConservation.setEnabled(conservationMenuItem.getState());
3606 modifyConservation.addActionListener(this);
3608 .setLabel(MessageManager.getString("action.by_annotation"));
3609 annotationColour.addActionListener(this);
3612 * Configure Calculate menu items and actions
3614 sortPairwiseMenuItem
3615 .setLabel(MessageManager.getString("action.by_pairwise_id"));
3616 sortPairwiseMenuItem.addActionListener(this);
3617 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3618 sortIDMenuItem.addActionListener(this);
3620 .setLabel(MessageManager.getString("action.by_length"));
3621 sortLengthMenuItem.addActionListener(this);
3622 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3623 sortGroupMenuItem.addActionListener(this);
3624 pairwiseAlignmentMenuItem.setLabel(
3625 MessageManager.getString("action.pairwise_alignment"));
3626 pairwiseAlignmentMenuItem.addActionListener(this);
3627 PCAMenuItem.setLabel(
3628 MessageManager.getString("label.principal_component_analysis"));
3629 PCAMenuItem.addActionListener(this);
3630 autoCalculate = new CheckboxMenuItem(
3631 MessageManager.getString("label.autocalculate_consensus"),
3633 averageDistanceTreeMenuItem.setLabel(
3634 MessageManager.getString("label.average_distance_identity"));
3635 averageDistanceTreeMenuItem.addActionListener(this);
3636 neighbourTreeMenuItem.setLabel(
3637 MessageManager.getString("label.neighbour_joining_identity"));
3638 neighbourTreeMenuItem.addActionListener(this);
3639 avDistanceTreeBlosumMenuItem.setLabel(
3640 MessageManager.getString("label.average_distance_blosum62"));
3641 avDistanceTreeBlosumMenuItem.addActionListener(this);
3642 njTreeBlosumMenuItem
3643 .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3644 njTreeBlosumMenuItem.addActionListener(this);
3646 .setLabel(MessageManager.getString("action.by_tree_order"));
3647 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3648 Menu calculateTreeMenu = new Menu(
3649 MessageManager.getString("action.calculate_tree"));
3650 autoCalculate.addItemListener(this);
3651 sortByTree.addItemListener(this);
3654 * Configure Help menu items and actions
3656 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3657 documentation.setLabel(MessageManager.getString("label.documentation"));
3658 documentation.addActionListener(this);
3659 about.setLabel(MessageManager.getString("label.about"));
3660 about.addActionListener(this);
3663 * Add top level menus to frame
3665 alignFrameMenuBar.add(fileMenu);
3666 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3667 alignFrameMenuBar.add(editMenu);
3668 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3669 alignFrameMenuBar.add(selectMenu);
3670 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3671 alignFrameMenuBar.add(viewMenu);
3672 Menu annotationsMenu = new Menu(
3673 MessageManager.getString("action.annotations"));
3674 alignFrameMenuBar.add(annotationsMenu);
3675 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3676 alignFrameMenuBar.add(formatMenu);
3677 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3678 alignFrameMenuBar.add(colourMenu);
3679 Menu calculateMenu = new Menu(
3680 MessageManager.getString("action.calculate"));
3681 alignFrameMenuBar.add(calculateMenu);
3682 alignFrameMenuBar.add(helpMenu);
3687 fileMenu.add(inputText);
3688 fileMenu.add(loadTree);
3689 fileMenu.add(loadAnnotations);
3690 fileMenu.addSeparator();
3691 fileMenu.add(outputTextboxMenu);
3692 fileMenu.add(outputFeatures);
3693 fileMenu.add(outputAnnotations);
3694 if (jalviewServletURL != null)
3696 fileMenu.add(loadApplication);
3698 fileMenu.addSeparator();
3699 fileMenu.add(closeMenuItem);
3704 editMenu.add(undoMenuItem);
3705 editMenu.add(redoMenuItem);
3708 pasteMenu.add(pasteNew);
3709 pasteMenu.add(pasteThis);
3710 editMenu.add(pasteMenu);
3711 editMenu.add(delete);
3712 editMenu.addSeparator();
3713 editMenu.add(remove2LeftMenuItem);
3714 editMenu.add(remove2RightMenuItem);
3715 editMenu.add(removeGappedColumnMenuItem);
3716 editMenu.add(removeAllGapsMenuItem);
3717 editMenu.add(removeRedundancyMenuItem);
3722 selectMenu.add(findMenuItem);
3723 selectMenu.addSeparator();
3724 selectMenu.add(selectAllSequenceMenuItem);
3725 selectMenu.add(deselectAllSequenceMenuItem);
3726 selectMenu.add(invertSequenceMenuItem);
3727 selectMenu.add(invertColSel);
3728 selectMenu.add(createGroup);
3729 selectMenu.add(unGroup);
3730 selectMenu.add(grpsFromSelection);
3731 selectMenu.add(deleteGroups);
3732 selectMenu.add(annotationColumnSelection);
3737 viewMenu.add(newView);
3738 viewMenu.addSeparator();
3739 showMenu.add(showColumns);
3740 showMenu.add(showSeqs);
3741 showMenu.add(showAllHidden);
3742 viewMenu.add(showMenu);
3743 hideMenu.add(hideColumns);
3744 hideMenu.add(hideSequences);
3745 hideMenu.add(hideAllSelection);
3746 hideMenu.add(hideAllButSelection);
3747 viewMenu.add(hideMenu);
3748 viewMenu.addSeparator();
3749 viewMenu.add(followMouseOverFlag);
3750 viewMenu.addSeparator();
3751 viewMenu.add(sequenceFeatures);
3752 viewMenu.add(featureSettings);
3753 viewMenu.addSeparator();
3754 viewMenu.add(alProperties);
3755 viewMenu.addSeparator();
3756 viewMenu.add(overviewMenuItem);
3761 annotationsMenu.add(annotationPanelMenuItem);
3762 annotationsMenu.addSeparator();
3763 annotationsMenu.add(showAlignmentAnnotations);
3764 annotationsMenu.add(showSequenceAnnotations);
3765 annotationsMenu.add(sortAnnBySequence);
3766 annotationsMenu.add(sortAnnByLabel);
3767 annotationsMenu.addSeparator();
3768 autoAnnMenu.add(showAutoFirst);
3769 autoAnnMenu.add(showAutoLast);
3770 autoAnnMenu.addSeparator();
3771 autoAnnMenu.add(applyAutoAnnotationSettings);
3772 autoAnnMenu.add(showConsensusHistogram);
3773 autoAnnMenu.add(showSequenceLogo);
3774 autoAnnMenu.add(normSequenceLogo);
3775 autoAnnMenu.addSeparator();
3776 autoAnnMenu.add(showGroupConservation);
3777 autoAnnMenu.add(showGroupConsensus);
3778 annotationsMenu.add(autoAnnMenu);
3783 formatMenu.add(font);
3784 formatMenu.add(seqLimits);
3785 formatMenu.add(wrapMenuItem);
3786 formatMenu.add(scaleAbove);
3787 formatMenu.add(scaleLeft);
3788 formatMenu.add(scaleRight);
3789 formatMenu.add(viewBoxesMenuItem);
3790 formatMenu.add(viewTextMenuItem);
3791 formatMenu.add(colourTextMenuItem);
3792 formatMenu.add(displayNonconservedMenuItem);
3793 formatMenu.add(renderGapsMenuItem);
3794 formatMenu.add(centreColumnLabelFlag);
3799 colourMenu.add(applyToAllGroups);
3800 colourMenu.addSeparator();
3801 colourMenu.add(noColourmenuItem);
3802 colourMenu.add(clustalColour);
3803 colourMenu.add(BLOSUM62Colour);
3804 colourMenu.add(PIDColour);
3805 colourMenu.add(zappoColour);
3806 colourMenu.add(taylorColour);
3807 colourMenu.add(hydrophobicityColour);
3808 colourMenu.add(helixColour);
3809 colourMenu.add(strandColour);
3810 colourMenu.add(turnColour);
3811 colourMenu.add(buriedColour);
3812 colourMenu.add(nucleotideColour);
3813 colourMenu.add(purinePyrimidineColour);
3814 // colourMenu.add(RNAInteractionColour);
3815 colourMenu.add(tcoffeeColour);
3816 colourMenu.add(userDefinedColour);
3817 colourMenu.addSeparator();
3818 colourMenu.add(conservationMenuItem);
3819 colourMenu.add(modifyConservation);
3820 colourMenu.add(abovePIDThreshold);
3821 colourMenu.add(modifyPID);
3822 colourMenu.add(annotationColour);
3823 colourMenu.add(RNAHelixColour);
3828 sortMenu.add(sortIDMenuItem);
3829 sortMenu.add(sortLengthMenuItem);
3830 sortMenu.add(sortByTreeMenu);
3831 sortMenu.add(sortGroupMenuItem);
3832 sortMenu.add(sortPairwiseMenuItem);
3833 calculateMenu.add(sortMenu);
3834 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3835 calculateTreeMenu.add(neighbourTreeMenuItem);
3836 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3837 calculateTreeMenu.add(njTreeBlosumMenuItem);
3838 calculateMenu.add(calculateTreeMenu);
3839 calculateMenu.addSeparator();
3840 calculateMenu.add(pairwiseAlignmentMenuItem);
3841 calculateMenu.add(PCAMenuItem);
3842 calculateMenu.add(autoCalculate);
3843 calculateMenu.add(sortByTree);
3848 helpMenu.add(documentation);
3849 helpMenu.add(about);
3854 statusBar.setBackground(Color.white);
3855 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3856 setStatus(MessageManager.getString("label.status_bar"));
3857 this.add(statusBar, BorderLayout.SOUTH);
3861 public void setStatus(String string)
3863 statusBar.setText(string);
3866 MenuItem featureSettings = new MenuItem();
3868 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3870 MenuItem annotationColour = new MenuItem();
3872 MenuItem annotationColumnSelection = new MenuItem();
3874 MenuItem invertColSel = new MenuItem();
3876 MenuItem showColumns = new MenuItem();
3878 MenuItem showSeqs = new MenuItem();
3880 MenuItem hideColumns = new MenuItem();
3882 MenuItem hideSequences = new MenuItem();
3884 MenuItem hideAllButSelection = new MenuItem();
3886 MenuItem hideAllSelection = new MenuItem();
3888 MenuItem showAllHidden = new MenuItem();
3890 MenuItem newView = new MenuItem();
3892 private CheckboxMenuItem showAlignmentAnnotations;
3894 private CheckboxMenuItem showSequenceAnnotations;
3896 private CheckboxMenuItem sortAnnBySequence;
3898 private CheckboxMenuItem sortAnnByLabel;
3900 private CheckboxMenuItem showAutoFirst;
3902 private CheckboxMenuItem showAutoLast;
3904 private SplitFrame splitFrame;
3907 * Attach the alignFrame panels after embedding menus, if necessary. This used
3908 * to be called setEmbedded, but is now creates the dropdown menus in a
3909 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3911 * @param reallyEmbedded
3912 * true to attach the view to the applet area on the page rather than
3915 public void createAlignFrameWindow(boolean reallyEmbedded)
3919 embedAlignFrameInApplet(viewport.applet);
3924 // test and embed menu bar if necessary.
3926 if (embedMenuIfNeeded(alignPanel))
3929 * adjust for status bar height too. ? pointless as overridden by layout
3932 alignPanel.setSize(getSize().width,
3933 getSize().height - statusBar.getHeight());
3935 add(statusBar, BorderLayout.SOUTH);
3936 add(alignPanel, BorderLayout.CENTER);
3937 // and register with the applet so it can pass external API calls to us
3938 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3944 * Add the components of this AlignFrame to the applet container.
3948 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3951 // Explicitly build the embedded menu panel for the on-page applet
3953 // view cannot be closed if its actually on the page
3954 fileMenu.remove(closeMenuItem);
3955 fileMenu.remove(3); // Remove Separator
3956 // construct embedded menu, using default font
3957 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3958 // and actually add the components to the applet area
3959 theApplet.setLayout(new BorderLayout());
3960 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3961 theApplet.add(statusBar, BorderLayout.SOUTH);
3962 // TODO should size be left to the layout manager?
3963 alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3964 - embeddedMenu.getHeight() - statusBar.getHeight());
3965 theApplet.add(alignPanel, BorderLayout.CENTER);
3966 final AlignFrame me = this;
3967 theApplet.addFocusListener(new FocusListener()
3971 public void focusLost(FocusEvent e)
3973 if (theApplet.currentAlignFrame == me)
3975 theApplet.currentAlignFrame = null;
3980 public void focusGained(FocusEvent e)
3982 theApplet.currentAlignFrame = me;
3985 theApplet.validate();
3989 * create a new binding between structures in an existing jmol viewer instance
3990 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3991 * this does not open a new Jmol window, or modify the display of the
3992 * structures in the original jmol window. Note This method doesn't work
3993 * without an additional javascript library to exchange messages between the
3994 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3997 * JmolViewer instance
3998 * @param sequenceIds
3999 * - sequence Ids to search for associations
4001 public SequenceStructureBinding addStructureViewInstance(
4002 Object jmolviewer, String[] sequenceIds)
4004 Viewer viewer = null;
4007 viewer = (Viewer) jmolviewer;
4008 } catch (ClassCastException ex)
4011 "Unsupported viewer object :" + jmolviewer.getClass());
4015 System.err.println("Can't use this object as a structure viewer:"
4016 + jmolviewer.getClass());
4019 SequenceI[] seqs = null;
4020 if (sequenceIds == null || sequenceIds.length == 0)
4022 seqs = viewport.getAlignment().getSequencesArray();
4026 Vector sqi = new Vector();
4027 AlignmentI al = viewport.getAlignment();
4028 for (int sid = 0; sid < sequenceIds.length; sid++)
4030 SequenceI sq = al.findName(sequenceIds[sid]);
4038 seqs = new SequenceI[sqi.size()];
4039 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4041 seqs[sid] = (SequenceI) sqi.elementAt(sid);
4049 AAStructureBindingModel jmv = null;
4050 // TODO: search for a jmv that involves viewer
4052 { // create a new viewer/jalview binding.
4053 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4060 * bind a pdb file to a sequence in the current view
4063 * - sequenceId within the dataset.
4064 * @param pdbEntryString
4065 * - the short name for the PDB file
4067 * - pdb file - either a URL or a valid PDB file.
4068 * @return true if binding was as success TODO: consider making an exception
4069 * structure for indicating when PDB parsing or sequenceId location
4072 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4075 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4076 boolean needtoadd = false;
4077 if (toaddpdb != null)
4079 Vector pdbe = toaddpdb.getAllPDBEntries();
4080 PDBEntry pdbentry = null;
4081 if (pdbe != null && pdbe.size() > 0)
4083 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4085 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4086 if (!pdbentry.getId().equals(pdbEntryString)
4087 && !pdbentry.getFile().equals(pdbFile))
4097 if (pdbentry == null)
4099 pdbentry = new PDBEntry();
4100 pdbentry.setId(pdbEntryString);
4101 pdbentry.setFile(pdbFile);
4102 needtoadd = true; // add this new entry to sequence.
4104 // resolve data source
4105 // TODO: this code should be a refactored to an io package
4106 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4108 if (protocol == null)
4114 pdbentry.setProperty("protocol", protocol);
4115 toaddpdb.addPDBId(pdbentry);
4116 alignPanel.getStructureSelectionManager()
4117 .registerPDBEntry(pdbentry);
4123 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4127 Vector sequences = new Vector();
4128 for (int i = 0; i < seqs.length; i++)
4130 if (seqs[i] != null)
4133 .addElement(new Object[]
4134 { seqs[i], (chains != null) ? chains[i] : null });
4137 seqs = new SequenceI[sequences.size()];
4138 chains = new String[sequences.size()];
4139 for (int i = 0, isize = sequences.size(); i < isize; i++)
4141 Object[] oj = (Object[]) sequences.elementAt(i);
4143 seqs[i] = (SequenceI) oj[0];
4144 chains[i] = (String) oj[1];
4147 return new Object[] { seqs, chains };
4151 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4152 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4154 // Scrub any null sequences from the array
4155 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4156 seqs = (SequenceI[]) sqch[0];
4157 chains = (String[]) sqch[1];
4158 if (seqs == null || seqs.length == 0)
4161 "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4163 if (protocol == null)
4165 String sourceType = (String) pdb.getProperty("protocol");
4168 protocol = DataSourceType.valueOf(sourceType);
4169 } catch (IllegalArgumentException e)
4173 if (protocol == null)
4175 System.err.println("Couldn't work out protocol to open structure: "
4180 if (applet.useXtrnalSviewer)
4182 // register the association(s) and quit, don't create any windows.
4183 if (StructureSelectionManager.getStructureSelectionManager(applet)
4184 .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
4186 System.err.println("Failed to map " + pdb.getFile() + " ("
4187 + protocol + ") to any sequences");
4191 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4193 // can only do alignments with Jmol
4194 // find the last jmol window assigned to this alignment
4195 AppletJmol ajm = null, tajm;
4196 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4197 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4199 tajm = (AppletJmol) jmols.elementAt(i);
4200 if (tajm.ap.alignFrame == this)
4209 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4210 // try and add the pdb structure
4215 // otherwise, create a new window
4216 if (applet.jmolAvailable)
4218 new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4219 applet.lastFrameX += 40;
4220 applet.lastFrameY += 40;
4224 new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4229 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4230 SequenceI[][] seqs, String[][] chains, String[] protocols)
4232 // TODO Auto-generated method stub
4233 System.err.println("Aligned Structure View: Not yet implemented.");
4237 * modify the current selection, providing the user has not made a selection
4241 * - sequences from this alignment
4243 * - columns to be selected on the alignment
4245 public void select(SequenceGroup sel, ColumnSelection csel,
4246 HiddenColumns hidden)
4248 alignPanel.seqPanel.selection(sel, csel, hidden, null);
4251 public void scrollTo(int row, int column)
4253 alignPanel.seqPanel.scrollTo(row, column);
4256 public void scrollToRow(int row)
4258 alignPanel.seqPanel.scrollToRow(row);
4261 public void scrollToColumn(int column)
4263 alignPanel.seqPanel.scrollToColumn(column);
4267 * @return the alignments unique ID.
4269 public String getSequenceSetId()
4271 return viewport.getSequenceSetId();
4275 * Load the (T-Coffee) score file from the specified url
4278 * File/URL/T-COFFEE score file contents
4279 * @throws IOException
4280 * @return true if alignment was annotated with data from source
4282 public boolean loadScoreFile(String source) throws IOException
4285 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4286 AppletFormatAdapter.checkProtocol(source));
4287 if (!file.isValid())
4289 // TODO: raise dialog for gui
4290 System.err.println("Problems parsing T-Coffee scores: "
4291 + file.getWarningMessage());
4292 System.err.println("Origin was:\n" + source);
4297 * check that the score matrix matches the alignment dimensions
4300 if ((aln = viewport.getAlignment()) != null
4301 && (aln.getHeight() != file.getHeight()
4302 || aln.getWidth() != file.getWidth()))
4304 // TODO: raise a dialog box here rather than bomb out.
4306 "The scores matrix does not match the alignment dimensions");
4310 // TODO add parameter to indicate if matching should be done
4311 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4313 alignPanel.fontChanged();
4314 tcoffeeColour.setEnabled(true);
4315 // switch to this color
4316 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4321 System.err.println("Problems resolving T-Coffee scores:");
4322 if (file.getWarningMessage() != null)
4324 System.err.println(file.getWarningMessage());
4330 public SplitFrame getSplitFrame()
4332 return this.splitFrame;
4335 public void setSplitFrame(SplitFrame sf)
4337 this.splitFrame = sf;
4340 // may not need this
4342 public void setShowSeqFeatures(boolean b)
4344 // showSeqFeatures.setSelected(b);
4345 viewport.setShowSequenceFeatures(b);
4350 public void setMenusForViewport()
4352 // setMenusFromViewport(viewport);
4357 public void refreshFeatureUI(boolean enableIfNecessary)
4359 if (enableIfNecessary)
4361 sequenceFeatures.setState(true);
4362 alignPanel.av.setShowSequenceFeatures(true);
4367 public FeatureSettingsControllerI getFeatureSettingsUI()
4369 return alignPanel.av.featureSettings;
4373 public FeatureSettingsControllerI showFeatureSettingsUI()
4375 return new FeatureSettings(alignPanel);
4378 private Rectangle fs_bounds = null;
4381 public void setFeatureSettingsGeometry(Rectangle bounds)
4387 public Rectangle getFeatureSettingsGeometry()