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.formatMessage("label.keyboard_editing_mode",
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(
1466 viewport.getAlignment().getSequencesArray(),
1467 alignPanel.getFeatureRenderer(), true, false);
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;
1596 } catch (UnsupportedEncodingException ex)
1599 "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
1601 ex.printStackTrace();
1606 public void closeMenuItem_actionPerformed()
1608 PaintRefresher.RemoveComponent(alignPanel);
1609 if (alignPanel.seqPanel != null
1610 && alignPanel.seqPanel.seqCanvas != null)
1612 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1614 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1616 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1619 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1625 if (alignPanel != null && alignPanel.overviewPanel != null)
1627 alignPanel.overviewPanel.dispose();
1636 void updateEditMenuBar()
1639 if (viewport.getHistoryList().size() > 0)
1641 undoMenuItem.setEnabled(true);
1642 CommandI command = viewport.getHistoryList().peek();
1643 undoMenuItem.setLabel(MessageManager
1644 .formatMessage("label.undo_command", new Object[]
1645 { command.getDescription() }));
1649 undoMenuItem.setEnabled(false);
1650 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1653 if (viewport.getRedoList().size() > 0)
1655 redoMenuItem.setEnabled(true);
1657 CommandI command = viewport.getRedoList().peek();
1658 redoMenuItem.setLabel(MessageManager
1659 .formatMessage("label.redo_command", new Object[]
1660 { command.getDescription() }));
1664 redoMenuItem.setEnabled(false);
1665 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1673 public void addHistoryItem(CommandI command)
1675 if (command.getSize() > 0)
1677 viewport.addToHistoryList(command);
1678 viewport.clearRedoList();
1679 updateEditMenuBar();
1680 viewport.updateHiddenColumns();
1685 * TODO: JAL-1104 DOCUMENT ME!
1690 protected void undoMenuItem_actionPerformed()
1692 if (viewport.getHistoryList().isEmpty())
1697 CommandI command = viewport.getHistoryList().pop();
1698 viewport.addToRedoList(command);
1699 command.undoCommand(null);
1701 AlignmentViewport originalSource = getOriginatingSource(command);
1703 if (originalSource != viewport)
1706 .println("Warning: Viewport object mismatch whilst undoing");
1708 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1709 // viewport.getColumnSelection().getHiddenColumns()
1711 updateEditMenuBar();
1712 originalSource.notifyAlignment();
1716 * TODO: JAL-1104 DOCUMENT ME!
1721 protected void redoMenuItem_actionPerformed()
1723 if (viewport.getRedoList().isEmpty())
1728 CommandI command = viewport.getRedoList().pop();
1729 viewport.addToHistoryList(command);
1730 command.doCommand(null);
1732 AlignmentViewport originalSource = getOriginatingSource(command);
1734 if (originalSource != viewport)
1737 .println("Warning: Viewport object mismatch whilst re-doing");
1739 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1740 // viewport.getColumnSelection().getHiddenColumns()
1743 updateEditMenuBar();
1744 originalSource.notifyAlignment();
1747 AlignmentViewport getOriginatingSource(CommandI command)
1749 AlignmentViewport originalSource = null;
1750 // For sequence removal and addition, we need to fire
1751 // the property change event FROM the viewport where the
1752 // original alignment was altered
1753 AlignmentI al = null;
1754 if (command instanceof EditCommand)
1756 EditCommand editCommand = (EditCommand) command;
1757 al = editCommand.getAlignment();
1758 Vector comps = PaintRefresher.components
1759 .get(viewport.getSequenceSetId());
1760 for (int i = 0; i < comps.size(); i++)
1762 if (comps.elementAt(i) instanceof AlignmentPanel)
1764 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1766 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1773 if (originalSource == null)
1775 // The original view is closed, we must validate
1776 // the current view against the closed view first
1779 PaintRefresher.validateSequences(al, viewport.getAlignment());
1782 originalSource = viewport;
1785 return originalSource;
1789 * Move the currently selected sequences up or down one position in the
1794 public void moveSelectedSequences(boolean up)
1796 SequenceGroup sg = viewport.getSelectionGroup();
1801 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1802 up ? null : viewport.getHiddenRepSequences(), up);
1803 alignPanel.paintAlignment(true, false);
1806 * Also move cDNA/protein complement sequences
1808 AlignViewportI complement = viewport.getCodingComplement();
1809 if (complement != null)
1811 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1812 viewport, complement);
1813 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1814 up ? null : complement.getHiddenRepSequences(), up);
1815 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
1820 synchronized void slideSequences(boolean right, int size)
1822 List<SequenceI> sg = new Vector<>();
1823 if (viewport.cursorMode)
1825 sg.add(viewport.getAlignment()
1826 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1828 else if (viewport.getSelectionGroup() != null
1829 && viewport.getSelectionGroup().getSize() != viewport
1830 .getAlignment().getHeight())
1832 sg = viewport.getSelectionGroup()
1833 .getSequences(viewport.getHiddenRepSequences());
1841 Vector<SequenceI> invertGroup = new Vector();
1843 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1845 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1847 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1851 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1853 SequenceI[] seqs2 = invertGroup
1854 .toArray(new SequenceI[invertGroup.size()]);
1855 for (int i = 0; i < invertGroup.size(); i++)
1857 seqs2[i] = invertGroup.elementAt(i);
1860 SlideSequencesCommand ssc;
1863 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1864 viewport.getGapCharacter());
1868 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1869 viewport.getGapCharacter());
1872 int groupAdjustment = 0;
1873 if (ssc.getGapsInsertedBegin() && right)
1875 if (viewport.cursorMode)
1877 alignPanel.seqPanel.moveCursor(size, 0);
1881 groupAdjustment = size;
1884 else if (!ssc.getGapsInsertedBegin() && !right)
1886 if (viewport.cursorMode)
1888 alignPanel.seqPanel.moveCursor(-size, 0);
1892 groupAdjustment = -size;
1896 if (groupAdjustment != 0)
1898 viewport.getSelectionGroup().setStartRes(
1899 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1900 viewport.getSelectionGroup().setEndRes(
1901 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1904 boolean appendHistoryItem = false;
1905 Deque<CommandI> historyList = viewport.getHistoryList();
1906 if (historyList != null && historyList.size() > 0
1907 && historyList.peek() instanceof SlideSequencesCommand)
1909 appendHistoryItem = ssc.appendSlideCommand(
1910 (SlideSequencesCommand) historyList.peek());
1913 if (!appendHistoryItem)
1915 addHistoryItem(ssc);
1921 static StringBuffer copiedSequences;
1923 static HiddenColumns copiedHiddenColumns;
1925 protected void copy_actionPerformed()
1927 if (viewport.getSelectionGroup() == null)
1932 SequenceGroup sg = viewport.getSelectionGroup();
1933 copiedSequences = new StringBuffer();
1934 Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1935 for (int i = 0; i < sg.getSize(); i++)
1937 SequenceI seq = sg.getSequenceAt(i);
1938 int index = viewport.getAlignment().findIndex(seq);
1939 orderedSeqs.put(index, seq);
1942 int index = 0, startRes, endRes;
1945 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1947 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1948 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1950 // create new HiddenColumns object with copy of hidden regions
1951 // between startRes and endRes, offset by startRes
1952 copiedHiddenColumns = new HiddenColumns(
1953 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1954 hiddenCutoff, hiddenOffset);
1958 copiedHiddenColumns = null;
1961 for (int i = 0; i < sg.getSize(); i++)
1963 SequenceI seq = null;
1967 if (orderedSeqs.containsKey(index))
1969 seq = orderedSeqs.get(index);
1980 // Returns residue following index if gap
1981 startRes = seq.findPosition(sg.getStartRes());
1984 // Need to find the residue preceeding index if gap
1987 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1989 ch = seq.getCharAt(j);
1990 if (!jalview.util.Comparison.isGap((ch)))
1998 endRes += seq.getStart() - 1;
2001 copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
2002 + "\t" + seq.getSequenceAsString(sg.getStartRes(),
2009 protected void pasteNew_actionPerformed()
2014 protected void pasteThis_actionPerformed()
2019 void paste(boolean newAlignment)
2023 if (copiedSequences == null)
2028 StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
2030 Vector seqs = new Vector();
2031 while (st.hasMoreElements())
2033 String name = st.nextToken();
2034 int start = Integer.parseInt(st.nextToken());
2035 int end = Integer.parseInt(st.nextToken());
2036 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2038 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2039 for (int i = 0; i < seqs.size(); i++)
2041 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2046 String newtitle = MessageManager
2047 .getString("label.copied_sequences");
2048 if (getTitle().startsWith(
2049 MessageManager.getString("label.copied_sequences")))
2051 newtitle = getTitle();
2055 newtitle = newtitle.concat(MessageManager
2056 .formatMessage("label.from_msname", new String[]
2059 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2060 viewport.applet, newtitle, false);
2061 af.viewport.setHiddenColumns(copiedHiddenColumns);
2063 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2068 addSequences(newSeqs);
2071 } catch (Exception ex)
2073 } // could be anything being pasted in here
2077 void addSequences(SequenceI[] seqs)
2079 for (int i = 0; i < seqs.length; i++)
2081 viewport.getAlignment().addSequence(seqs[i]);
2085 addHistoryItem(new EditCommand(
2086 MessageManager.getString("label.add_sequences"), Action.PASTE,
2087 seqs, 0, viewport.getAlignment().getWidth(),
2088 viewport.getAlignment()));
2090 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
2092 viewport.getAlignment().getWidth();
2093 viewport.notifyAlignment();
2097 protected void cut_actionPerformed()
2099 copy_actionPerformed();
2100 delete_actionPerformed();
2103 protected void delete_actionPerformed()
2106 SequenceGroup sg = viewport.getSelectionGroup();
2112 Vector seqs = new Vector();
2114 for (int i = 0; i < sg.getSize(); i++)
2116 seq = sg.getSequenceAt(i);
2117 seqs.addElement(seq);
2121 * If the cut affects all sequences, warn, remove highlighted columns
2123 if (sg.getSize() == viewport.getAlignment().getHeight())
2125 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2126 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2127 if (isEntireAlignWidth)
2129 String title = MessageManager.getString("label.delete_all");
2130 Panel infoPanel = new Panel();
2131 infoPanel.setLayout(new FlowLayout());
2133 new Label(MessageManager.getString("warn.delete_all")));
2135 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2136 dialog.setMainPanel(infoPanel);
2137 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2138 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2139 dialog.setVisible(true);
2146 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2147 sg.getEndRes() + 1);
2150 SequenceI[] cut = new SequenceI[seqs.size()];
2151 for (int i = 0; i < seqs.size(); i++)
2153 cut[i] = (SequenceI) seqs.elementAt(i);
2157 * //ADD HISTORY ITEM
2159 addHistoryItem(new EditCommand(
2160 MessageManager.getString("label.cut_sequences"), Action.CUT,
2161 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2162 viewport.getAlignment()));
2164 viewport.setSelectionGroup(null);
2165 viewport.getAlignment().deleteGroup(sg);
2167 viewport.notifyAlignment();
2169 if (viewport.getAlignment().getHeight() < 1)
2171 this.setVisible(false);
2173 viewport.sendSelection();
2177 * group consensus toggled
2180 protected void showGroupConsensus_actionPerformed()
2182 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2183 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2188 * group conservation toggled.
2190 protected void showGroupConservation_actionPerformed()
2192 viewport.setShowGroupConservation(showGroupConservation.getState());
2193 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2200 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2201 * .event.ActionEvent)
2203 protected void showConsensusHistogram_actionPerformed()
2205 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2206 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2213 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2214 * .event.ActionEvent)
2216 protected void showSequenceLogo_actionPerformed()
2218 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2219 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2222 protected void normSequenceLogo_actionPerformed()
2224 showSequenceLogo.setState(true);
2225 viewport.setShowSequenceLogo(true);
2226 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2227 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2230 protected void applyAutoAnnotationSettings_actionPerformed()
2232 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2235 protected void makeGrpsFromSelection_actionPerformed()
2237 if (avc.makeGroupsFromSelection())
2239 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2240 alignPanel.updateAnnotation();
2241 alignPanel.paintAlignment(true, true);
2245 protected void createGroup_actionPerformed()
2250 protected void unGroup_actionPerformed()
2254 alignPanel.alignmentChanged();
2258 protected void deleteGroups_actionPerformed()
2260 if (avc.deleteGroups())
2262 alignPanel.alignmentChanged();
2266 public void selectAllSequenceMenuItem_actionPerformed()
2268 SequenceGroup sg = new SequenceGroup();
2269 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2271 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2273 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2274 viewport.setSelectionGroup(sg);
2275 // JAL-2034 - should delegate to
2276 // alignPanel to decide if overview needs
2278 alignPanel.paintAlignment(false, false);
2279 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2280 viewport.sendSelection();
2283 public void deselectAllSequenceMenuItem_actionPerformed()
2285 if (viewport.cursorMode)
2287 alignPanel.seqPanel.keyboardNo1 = null;
2288 alignPanel.seqPanel.keyboardNo2 = null;
2290 viewport.setSelectionGroup(null);
2291 viewport.getColumnSelection().clear();
2292 viewport.setSelectionGroup(null);
2293 alignPanel.idPanel.idCanvas.searchResults = null;
2294 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2295 // JAL-2034 - should delegate to
2296 // alignPanel to decide if overview needs
2298 alignPanel.paintAlignment(false, false);
2299 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2300 viewport.sendSelection();
2303 public void invertSequenceMenuItem_actionPerformed()
2305 SequenceGroup sg = viewport.getSelectionGroup();
2306 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2308 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2311 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2312 viewport.sendSelection();
2315 public void invertColSel_actionPerformed()
2317 viewport.invertColumnSelection();
2318 alignPanel.paintAlignment(true, false);
2319 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2320 viewport.sendSelection();
2323 void trimAlignment(boolean trimLeft)
2325 AlignmentI al = viewport.getAlignment();
2326 ViewportRanges ranges = viewport.getRanges();
2327 ColumnSelection colSel = viewport.getColumnSelection();
2330 if (!colSel.isEmpty())
2334 column = colSel.getMin();
2338 column = colSel.getMax();
2342 if (viewport.getSelectionGroup() != null)
2344 seqs = viewport.getSelectionGroup()
2345 .getSequencesAsArray(viewport.getHiddenRepSequences());
2349 seqs = al.getSequencesArray();
2352 TrimRegionCommand trimRegion;
2355 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2357 ranges.setStartRes(0);
2361 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2365 setStatus(MessageManager.formatMessage("label.removed_columns",
2367 { Integer.valueOf(trimRegion.getSize()).toString() }));
2368 addHistoryItem(trimRegion);
2370 for (SequenceGroup sg : al.getGroups())
2372 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2373 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2379 viewport.notifyAlignment();
2383 public void removeGappedColumnMenuItem_actionPerformed()
2385 AlignmentI al = viewport.getAlignment();
2386 ViewportRanges ranges = viewport.getRanges();
2388 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2391 if (viewport.getSelectionGroup() != null)
2393 seqs = viewport.getSelectionGroup()
2394 .getSequencesAsArray(viewport.getHiddenRepSequences());
2395 start = viewport.getSelectionGroup().getStartRes();
2396 end = viewport.getSelectionGroup().getEndRes();
2400 seqs = viewport.getAlignment().getSequencesArray();
2403 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2404 "Remove Gapped Columns", seqs, start, end,
2405 viewport.getAlignment());
2407 addHistoryItem(removeGapCols);
2409 setStatus(MessageManager.formatMessage("label.removed_empty_columns",
2411 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2413 // This is to maintain viewport position on first residue
2414 // of first sequence
2415 SequenceI seq = al.getSequenceAt(0);
2416 int startRes = seq.findPosition(ranges.getStartRes());
2417 // ShiftList shifts;
2418 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2419 // edit.alColumnChanges=shifts.getInverse();
2420 // if (viewport.hasHiddenColumns)
2421 // viewport.getColumnSelection().compensateForEdits(shifts);
2422 ranges.setStartRes(seq.findIndex(startRes) - 1);
2423 viewport.notifyAlignment();
2427 public void removeAllGapsMenuItem_actionPerformed()
2429 AlignmentI al = viewport.getAlignment();
2430 ViewportRanges ranges = viewport.getRanges();
2432 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2435 if (viewport.getSelectionGroup() != null)
2437 seqs = viewport.getSelectionGroup()
2438 .getSequencesAsArray(viewport.getHiddenRepSequences());
2439 start = viewport.getSelectionGroup().getStartRes();
2440 end = viewport.getSelectionGroup().getEndRes();
2444 seqs = viewport.getAlignment().getSequencesArray();
2447 // This is to maintain viewport position on first residue
2448 // of first sequence
2449 SequenceI seq = al.getSequenceAt(0);
2450 int startRes = seq.findPosition(ranges.getStartRes());
2453 new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2455 ranges.setStartRes(seq.findIndex(startRes) - 1);
2457 viewport.notifyAlignment();
2461 public void findMenuItem_actionPerformed()
2463 new Finder(alignPanel);
2467 * create a new view derived from the current view
2470 * @return frame for the new view
2472 public AlignFrame newView(String viewtitle)
2475 if (viewport.hasHiddenRows())
2477 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2478 .getFullAlignment().getSequencesArray());
2482 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2485 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2487 for (int i = 0; i < viewport.getAlignment()
2488 .getAlignmentAnnotation().length; i++)
2490 if (!viewport.getAlignment()
2491 .getAlignmentAnnotation()[i].autoCalculated)
2493 newal.addAnnotation(
2494 viewport.getAlignment().getAlignmentAnnotation()[i]);
2499 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2501 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2502 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2503 PaintRefresher.Register(newaf.alignPanel,
2504 newaf.alignPanel.av.getSequenceSetId());
2506 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2507 newaf.alignPanel.av.getSequenceSetId());
2508 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2509 newaf.alignPanel.av.getSequenceSetId());
2511 Vector comps = PaintRefresher.components
2512 .get(viewport.getSequenceSetId());
2514 for (int i = 0; i < comps.size(); i++)
2516 if (comps.elementAt(i) instanceof AlignmentPanel)
2522 String title = new String(this.getTitle());
2523 if (viewtitle != null)
2525 title = viewtitle + " ( " + title + ")";
2529 if (title.indexOf("(View") > -1)
2531 title = title.substring(0, title.indexOf("(View"));
2533 title += "(View " + viewSize + ")";
2536 newaf.setTitle(title.toString());
2538 newaf.viewport.setHistoryList(viewport.getHistoryList());
2539 newaf.viewport.setRedoList(viewport.getRedoList());
2545 * @return list of feature groups on the view
2547 public String[] getFeatureGroups()
2549 FeatureRenderer fr = null;
2550 if (alignPanel != null
2551 && (fr = alignPanel.getFeatureRenderer()) != null)
2553 List<String> gps = fr.getFeatureGroups();
2554 String[] _gps = gps.toArray(new String[gps.size()]);
2561 * get sequence feature groups that are hidden or shown
2567 public String[] getFeatureGroupsOfState(boolean visible)
2569 FeatureRenderer fr = null;
2570 if (alignPanel != null
2571 && (fr = alignPanel.getFeatureRenderer()) != null)
2573 List<String> gps = fr.getGroups(visible);
2574 String[] _gps = gps.toArray(new String[gps.size()]);
2581 * Change the display state for the given feature groups
2584 * list of group strings
2586 * visible or invisible
2588 public void setFeatureGroupState(String[] groups, boolean state)
2590 FeatureRenderer fr = null;
2591 this.sequenceFeatures.setState(true);
2592 viewport.setShowSequenceFeatures(true);
2593 if (alignPanel != null
2594 && (fr = alignPanel.getFeatureRenderer()) != null)
2597 fr.setGroupVisibility(Arrays.asList(groups), state);
2598 alignPanel.seqPanel.seqCanvas.repaint();
2599 if (alignPanel.overviewPanel != null)
2601 alignPanel.overviewPanel.updateOverviewImage();
2606 public void seqLimits_itemStateChanged()
2608 viewport.setShowJVSuffix(seqLimits.getState());
2609 alignPanel.fontChanged();
2610 alignPanel.paintAlignment(true, false);
2613 protected void colourTextMenuItem_actionPerformed()
2615 viewport.setColourText(colourTextMenuItem.getState());
2616 alignPanel.paintAlignment(false, false);
2619 protected void displayNonconservedMenuItem_actionPerformed()
2621 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2622 alignPanel.paintAlignment(false, false);
2625 protected void wrapMenuItem_actionPerformed()
2627 viewport.setWrapAlignment(wrapMenuItem.getState());
2628 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2629 scaleAbove.setEnabled(wrapMenuItem.getState());
2630 scaleLeft.setEnabled(wrapMenuItem.getState());
2631 scaleRight.setEnabled(wrapMenuItem.getState());
2632 alignPanel.paintAlignment(true, false);
2635 public void overviewMenuItem_actionPerformed()
2637 if (alignPanel.overviewPanel != null)
2642 Frame frame = new Frame();
2643 final OverviewPanel overview = new OverviewPanel(alignPanel);
2644 frame.add(overview);
2645 // +50 must allow for applet frame window
2646 jalview.bin.JalviewLite.addFrame(frame, MessageManager
2647 .formatMessage("label.overview_params", new String[]
2648 { this.getTitle() }), overview.getPreferredSize().width,
2649 overview.getPreferredSize().height + 50);
2652 final AlignmentPanel ap = alignPanel;
2653 frame.addWindowListener(new WindowAdapter()
2656 public void windowClosing(WindowEvent e)
2661 ap.setOverviewPanel(null);
2666 alignPanel.setOverviewPanel(overview);
2671 public void changeColour(ColourSchemeI cs)
2673 viewport.setGlobalColourScheme(cs);
2675 alignPanel.paintAlignment(true, true);
2678 protected void modifyPID_actionPerformed()
2680 if (viewport.getAbovePIDThreshold()
2681 && viewport.getGlobalColourScheme() != null)
2683 SliderPanel.setPIDSliderSource(alignPanel,
2684 viewport.getResidueShading(), alignPanel.getViewName());
2685 SliderPanel.showPIDSlider();
2689 protected void modifyConservation_actionPerformed()
2691 if (viewport.getConservationSelected()
2692 && viewport.getGlobalColourScheme() != null)
2694 SliderPanel.setConservationSlider(alignPanel,
2695 viewport.getResidueShading(), alignPanel.getViewName());
2696 SliderPanel.showConservationSlider();
2700 protected void conservationMenuItem_actionPerformed()
2702 boolean selected = conservationMenuItem.getState();
2703 modifyConservation.setEnabled(selected);
2704 viewport.setConservationSelected(selected);
2705 viewport.getResidueShading().setConservationApplied(selected);
2707 changeColour(viewport.getGlobalColourScheme());
2711 modifyConservation_actionPerformed();
2715 SliderPanel.hideConservationSlider();
2719 public void abovePIDThreshold_actionPerformed()
2721 boolean selected = abovePIDThreshold.getState();
2722 modifyPID.setEnabled(selected);
2723 viewport.setAbovePIDThreshold(selected);
2726 viewport.getResidueShading().setThreshold(0,
2727 viewport.isIgnoreGapsConsensus());
2730 changeColour(viewport.getGlobalColourScheme());
2734 modifyPID_actionPerformed();
2738 SliderPanel.hidePIDSlider();
2742 public void sortPairwiseMenuItem_actionPerformed()
2744 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2745 AlignmentSorter.sortByPID(viewport.getAlignment(),
2746 viewport.getAlignment().getSequenceAt(0));
2748 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2749 viewport.getAlignment()));
2750 alignPanel.paintAlignment(true, false);
2753 public void sortIDMenuItem_actionPerformed()
2755 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2756 AlignmentSorter.sortByID(viewport.getAlignment());
2758 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
2759 alignPanel.paintAlignment(true, false);
2762 public void sortLengthMenuItem_actionPerformed()
2764 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2765 AlignmentSorter.sortByLength(viewport.getAlignment());
2766 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2767 viewport.getAlignment()));
2768 alignPanel.paintAlignment(true, false);
2771 public void sortGroupMenuItem_actionPerformed()
2773 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2774 AlignmentSorter.sortByGroup(viewport.getAlignment());
2775 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2776 viewport.getAlignment()));
2777 alignPanel.paintAlignment(true, false);
2781 public void sortEValueMenuItem_actionPerformed()
2783 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2784 AlignmentSorter.sortByEValue(viewport.getAlignment());
2785 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2786 viewport.getAlignment()));
2787 alignPanel.paintAlignment(true, false);
2791 public void sortBitScoreMenuItem_actionPerformed()
2793 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2794 AlignmentSorter.sortByBitScore(viewport.getAlignment());
2795 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2796 viewport.getAlignment()));
2797 alignPanel.paintAlignment(true, false);
2801 public void removeRedundancyMenuItem_actionPerformed()
2803 new RedundancyPanel(alignPanel);
2806 public void pairwiseAlignmentMenuItem_actionPerformed()
2808 if (viewport.getSelectionGroup() != null
2809 && viewport.getSelectionGroup().getSize() > 1)
2811 Frame frame = new Frame();
2812 frame.add(new PairwiseAlignPanel(alignPanel));
2813 jalview.bin.JalviewLite.addFrame(frame,
2814 MessageManager.getString("action.pairwise_alignment"), 600,
2819 public void PCAMenuItem_actionPerformed()
2821 // are the sequences aligned?
2822 if (!viewport.getAlignment().isAligned(false))
2825 int Width = viewport.getAlignment().getWidth();
2827 for (int i = 0; i < viewport.getAlignment().getSequences()
2830 current = viewport.getAlignment().getSequenceAt(i);
2832 if (current.getLength() < Width)
2834 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2837 alignPanel.paintAlignment(false, false);
2840 if ((viewport.getSelectionGroup() != null
2841 && viewport.getSelectionGroup().getSize() < 4
2842 && viewport.getSelectionGroup().getSize() > 0)
2843 || viewport.getAlignment().getHeight() < 4)
2850 new PCAPanel(viewport);
2851 } catch (java.lang.OutOfMemoryError ex)
2857 public void averageDistanceTreeMenuItem_actionPerformed()
2859 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2860 "Average distance tree using PID");
2863 public void neighbourTreeMenuItem_actionPerformed()
2865 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2866 "Neighbour joining tree using PID");
2869 protected void njTreeBlosumMenuItem_actionPerformed()
2871 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2872 ScoreModels.getInstance().getBlosum62().getName(),
2873 "Neighbour joining tree using BLOSUM62");
2876 protected void avTreeBlosumMenuItem_actionPerformed()
2878 newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2879 ScoreModels.getInstance().getBlosum62().getName(),
2880 "Average distance tree using BLOSUM62");
2883 void newTreePanel(String type, String pwType, String title)
2885 // are the sequences aligned?
2886 if (!viewport.getAlignment().isAligned(false))
2889 int Width = viewport.getAlignment().getWidth();
2891 for (int i = 0; i < viewport.getAlignment().getSequences()
2894 current = viewport.getAlignment().getSequenceAt(i);
2896 if (current.getLength() < Width)
2898 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2901 alignPanel.paintAlignment(false, false);
2905 if ((viewport.getSelectionGroup() != null
2906 && viewport.getSelectionGroup().getSize() > 1)
2907 || (viewport.getAlignment().getHeight() > 1))
2909 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2911 addTreeMenuItem(tp, title);
2913 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2917 void loadTree_actionPerformed()
2919 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2920 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2921 cap.setTreeImport();
2922 Frame frame = new Frame();
2924 jalview.bin.JalviewLite.addFrame(frame,
2925 MessageManager.getString("label.paste_newick_file"), 400, 300);
2928 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2930 TreePanel tp = new TreePanel(alignPanel, treeFile,
2931 MessageManager.getString("label.load_tree_from_file"), tree);
2932 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2933 addTreeMenuItem(tp, treeFile);
2937 * sort the alignment using the given treePanel
2940 * tree used to sort view
2942 * string used for undo event name
2944 public void sortByTree(TreePanel treePanel, String title)
2946 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2947 AlignmentSorter.sortByTree(viewport.getAlignment(),
2948 treePanel.getTree());
2949 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2950 // HistoryItem.SORT));
2951 addHistoryItem(new OrderCommand(MessageManager
2952 .formatMessage("label.order_by_params", new String[]
2953 { title }), oldOrder, viewport.getAlignment()));
2954 alignPanel.paintAlignment(true, false);
2958 * Do any automatic reordering of the alignment and add the necessary bits to
2959 * the menu structure for the new tree
2964 protected void addTreeMenuItem(final TreePanel treePanel,
2967 final MenuItem item = new MenuItem(title);
2968 sortByTreeMenu.add(item);
2969 item.addActionListener(new java.awt.event.ActionListener()
2972 public void actionPerformed(ActionEvent evt)
2974 sortByTree(treePanel, title); // treePanel.getTitle());
2978 treePanel.addWindowListener(new WindowAdapter()
2981 public void windowOpened(WindowEvent e)
2983 if (viewport.sortByTree)
2985 sortByTree(treePanel, title);
2987 super.windowOpened(e);
2991 public void windowClosing(WindowEvent e)
2993 sortByTreeMenu.remove(item);
2998 public boolean sortBy(AlignmentOrder alorder, String undoname)
3000 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3001 if (viewport.applet.debug)
3003 System.err.println("Sorting " + alorder.getOrder().size()
3004 + " in alignment '" + getTitle() + "'");
3006 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3007 if (undoname != null)
3009 addHistoryItem(new OrderCommand(undoname, oldOrder,
3010 viewport.getAlignment()));
3012 alignPanel.paintAlignment(true, false);
3016 protected void documentation_actionPerformed()
3018 alignPanel.av.applet.openJalviewHelpUrl();
3021 protected void about_actionPerformed()
3024 class AboutPanel extends Canvas
3030 public AboutPanel(String version, String builddate)
3032 this.version = version;
3033 this.builddate = builddate;
3037 public void paint(Graphics g)
3039 g.setColor(Color.white);
3040 g.fillRect(0, 0, getSize().width, getSize().height);
3041 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3042 FontMetrics fm = g.getFontMetrics();
3043 int fh = fm.getHeight();
3045 g.setColor(Color.black);
3046 // TODO: update this text for each release or centrally store it for
3047 // lite and application
3048 g.setFont(new Font("Helvetica", Font.BOLD, 14));
3049 g.drawString(MessageManager
3050 .formatMessage("label.jalviewLite_release", new String[]
3051 { version }), x, y += fh);
3052 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3053 g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3055 { builddate }), x, y += fh);
3056 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3057 g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3059 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3060 x + 50, y += fh + 8);
3061 g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3063 g.drawString(MessageManager
3064 .getString("label.jalview_distribution_lists"), x, y += fh);
3065 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3068 MessageManager.getString("label.jalview_cite_1_authors"), x,
3070 g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3072 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3077 Frame frame = new Frame();
3078 frame.add(new AboutPanel(JalviewLite.getVersion(),
3079 JalviewLite.getBuildDate()));
3080 jalview.bin.JalviewLite.addFrame(frame,
3081 MessageManager.getString("label.jalview"), 580, 220);
3085 public void showURL(String url, String target)
3087 if (viewport.applet == null)
3089 System.out.println("Not running as applet - no browser available.");
3093 viewport.applet.showURL(url, target);
3097 // ////////////////////////////////////////////////////////////////////////////////
3098 // JBuilder Graphics here
3100 MenuBar alignFrameMenuBar = new MenuBar();
3102 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3104 MenuItem loadApplication = new MenuItem(
3105 MessageManager.getString("label.view_full_application"));
3107 MenuItem loadTree = new MenuItem(
3108 MessageManager.getString("label.load_associated_tree"));
3110 MenuItem loadAnnotations = new MenuItem(
3111 MessageManager.getString("label.load_features_annotations"));
3113 MenuItem outputFeatures = new MenuItem(
3114 MessageManager.getString("label.export_features"));
3116 MenuItem outputAnnotations = new MenuItem(
3117 MessageManager.getString("label.export_annotations"));
3119 MenuItem closeMenuItem = new MenuItem(
3120 MessageManager.getString("action.close"));
3122 MenuItem selectAllSequenceMenuItem = new MenuItem(
3123 MessageManager.getString("action.select_all"));
3125 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3126 MessageManager.getString("action.deselect_all"));
3128 MenuItem invertSequenceMenuItem = new MenuItem(
3129 MessageManager.getString("action.invert_selection"));
3131 MenuItem remove2LeftMenuItem = new MenuItem();
3133 MenuItem remove2RightMenuItem = new MenuItem();
3135 MenuItem removeGappedColumnMenuItem = new MenuItem();
3137 MenuItem removeAllGapsMenuItem = new MenuItem();
3139 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3141 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3143 MenuItem sortPairwiseMenuItem = new MenuItem();
3145 MenuItem sortIDMenuItem = new MenuItem();
3147 MenuItem sortLengthMenuItem = new MenuItem();
3149 MenuItem sortGroupMenuItem = new MenuItem();
3151 MenuItem sortEValueMenuItem = new MenuItem();
3153 MenuItem sortBitScoreMenuItem = new MenuItem();
3155 MenuItem removeRedundancyMenuItem = new MenuItem();
3157 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3159 MenuItem PCAMenuItem = new MenuItem();
3161 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3163 MenuItem neighbourTreeMenuItem = new MenuItem();
3165 BorderLayout borderLayout1 = new BorderLayout();
3167 public Label statusBar = new Label();
3169 MenuItem clustalColour = new MenuItem();
3171 MenuItem zappoColour = new MenuItem();
3173 MenuItem taylorColour = new MenuItem();
3175 MenuItem hydrophobicityColour = new MenuItem();
3177 MenuItem helixColour = new MenuItem();
3179 MenuItem strandColour = new MenuItem();
3181 MenuItem turnColour = new MenuItem();
3183 MenuItem buriedColour = new MenuItem();
3185 MenuItem purinePyrimidineColour = new MenuItem();
3187 // MenuItem RNAInteractionColour = new MenuItem();
3189 MenuItem RNAHelixColour = new MenuItem();
3191 MenuItem userDefinedColour = new MenuItem();
3193 MenuItem PIDColour = new MenuItem();
3195 MenuItem BLOSUM62Colour = new MenuItem();
3197 MenuItem tcoffeeColour = new MenuItem();
3199 MenuItem njTreeBlosumMenuItem = new MenuItem();
3201 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3203 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3205 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3207 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3209 MenuItem alProperties = new MenuItem(
3210 MessageManager.getString("label.alignment_props"));
3212 MenuItem overviewMenuItem = new MenuItem();
3214 MenuItem undoMenuItem = new MenuItem();
3216 MenuItem redoMenuItem = new MenuItem();
3218 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3220 MenuItem noColourmenuItem = new MenuItem();
3222 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3224 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3226 MenuItem findMenuItem = new MenuItem();
3228 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3230 MenuItem nucleotideColour = new MenuItem();
3232 MenuItem deleteGroups = new MenuItem();
3234 MenuItem grpsFromSelection = new MenuItem();
3236 MenuItem createGroup = new MenuItem();
3238 MenuItem unGroup = new MenuItem();
3240 MenuItem delete = new MenuItem();
3242 MenuItem copy = new MenuItem();
3244 MenuItem cut = new MenuItem();
3246 Menu pasteMenu = new Menu();
3248 MenuItem pasteNew = new MenuItem();
3250 MenuItem pasteThis = new MenuItem();
3252 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3254 MenuItem font = new MenuItem();
3256 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3258 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3260 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3262 MenuItem modifyPID = new MenuItem();
3264 MenuItem modifyConservation = new MenuItem();
3266 CheckboxMenuItem autoCalculate = null;
3268 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3269 "Sort Alignment With New Tree", true);
3271 Menu sortByTreeMenu = new Menu();
3273 MenuItem inputText = new MenuItem();
3275 MenuItem documentation = new MenuItem();
3277 MenuItem about = new MenuItem();
3279 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3281 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3283 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3285 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3287 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3289 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3291 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3293 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3295 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3298 * Initialise menus and other items
3302 private void jbInit() throws Exception
3304 setMenuBar(alignFrameMenuBar);
3307 * Configure File menu items and actions
3310 .setLabel(MessageManager.getString("label.input_from_textbox"));
3311 inputText.addActionListener(this);
3312 Menu outputTextboxMenu = new Menu(
3313 MessageManager.getString("label.out_to_textbox"));
3314 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3316 MenuItem item = new MenuItem(ff);
3318 item.addActionListener(new java.awt.event.ActionListener()
3321 public void actionPerformed(ActionEvent e)
3323 outputText_actionPerformed(e);
3327 outputTextboxMenu.add(item);
3329 closeMenuItem.addActionListener(this);
3330 loadApplication.addActionListener(this);
3331 loadTree.addActionListener(this);
3332 loadAnnotations.addActionListener(this);
3333 outputFeatures.addActionListener(this);
3334 outputAnnotations.addActionListener(this);
3337 * Configure Edit menu items and actions
3339 undoMenuItem.setEnabled(false);
3340 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3341 undoMenuItem.addActionListener(this);
3342 redoMenuItem.setEnabled(false);
3343 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3344 redoMenuItem.addActionListener(this);
3345 copy.setLabel(MessageManager.getString("action.copy"));
3346 copy.addActionListener(this);
3347 cut.setLabel(MessageManager.getString("action.cut"));
3348 cut.addActionListener(this);
3349 delete.setLabel(MessageManager.getString("action.delete"));
3350 delete.addActionListener(this);
3351 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3352 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3353 pasteNew.addActionListener(this);
3354 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3355 pasteThis.addActionListener(this);
3357 .setLabel(MessageManager.getString("action.remove_left"));
3358 remove2LeftMenuItem.addActionListener(this);
3359 remove2RightMenuItem
3360 .setLabel(MessageManager.getString("action.remove_right"));
3361 remove2RightMenuItem.addActionListener(this);
3362 removeGappedColumnMenuItem.setLabel(
3363 MessageManager.getString("action.remove_empty_columns"));
3364 removeGappedColumnMenuItem.addActionListener(this);
3365 removeAllGapsMenuItem
3366 .setLabel(MessageManager.getString("action.remove_all_gaps"));
3367 removeAllGapsMenuItem.addActionListener(this);
3368 removeRedundancyMenuItem
3369 .setLabel(MessageManager.getString("action.remove_redundancy"));
3370 removeRedundancyMenuItem.addActionListener(this);
3373 * Configure Select menu items and actions
3375 findMenuItem.setLabel(MessageManager.getString("action.find"));
3376 findMenuItem.addActionListener(this);
3377 selectAllSequenceMenuItem.addActionListener(this);
3378 deselectAllSequenceMenuItem.addActionListener(this);
3379 invertSequenceMenuItem.setLabel(
3380 MessageManager.getString("action.invert_sequence_selection"));
3381 invertSequenceMenuItem.addActionListener(this);
3382 invertColSel.setLabel(
3383 MessageManager.getString("action.invert_column_selection"));
3384 invertColSel.addActionListener(this);
3386 .setLabel(MessageManager.getString("action.undefine_groups"));
3387 deleteGroups.addActionListener(this);
3388 grpsFromSelection.setLabel(
3389 MessageManager.getString("action.make_groups_selection"));
3390 grpsFromSelection.addActionListener(this);
3391 createGroup.setLabel(MessageManager.getString("action.create_group"));
3392 createGroup.addActionListener(this);
3393 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3394 unGroup.addActionListener(this);
3396 annotationColumnSelection.setLabel(
3397 MessageManager.getString("action.select_by_annotation"));
3398 annotationColumnSelection.addActionListener(this);
3401 * Configure View menu items and actions
3403 newView.setLabel(MessageManager.getString("action.new_view"));
3404 newView.addActionListener(this);
3405 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3406 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3407 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3408 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3410 .setLabel(MessageManager.getString("label.selected_columns"));
3412 .setLabel(MessageManager.getString("label.selected_sequences"));
3413 hideAllButSelection.setLabel(
3414 MessageManager.getString("label.all_but_selected_region"));
3416 .setLabel(MessageManager.getString("label.selected_region"));
3417 showAllHidden.setLabel(
3418 MessageManager.getString("label.all_sequences_columns"));
3419 showColumns.addActionListener(this);
3420 showSeqs.addActionListener(this);
3421 hideColumns.addActionListener(this);
3422 hideSequences.addActionListener(this);
3423 hideAllButSelection.addActionListener(this);
3424 hideAllSelection.addActionListener(this);
3425 showAllHidden.addActionListener(this);
3427 .setLabel(MessageManager.getString("action.feature_settings"));
3428 featureSettings.addActionListener(this);
3429 sequenceFeatures.setLabel(
3430 MessageManager.getString("label.show_sequence_features"));
3431 sequenceFeatures.addItemListener(this);
3432 sequenceFeatures.setState(false);
3433 followMouseOverFlag.setLabel(
3434 MessageManager.getString("label.automatic_scrolling"));
3435 followMouseOverFlag.addItemListener(this);
3436 alProperties.addActionListener(this);
3438 .setLabel(MessageManager.getString("label.overview_window"));
3439 overviewMenuItem.addActionListener(this);
3442 * Configure Annotations menu items and actions
3444 annotationPanelMenuItem
3445 .setLabel(MessageManager.getString("label.show_annotations"));
3446 annotationPanelMenuItem.addItemListener(this);
3448 .setLabel(MessageManager.getString("label.group_consensus"));
3449 showGroupConservation
3450 .setLabel(MessageManager.getString("label.group_conservation"));
3451 showConsensusHistogram.setLabel(
3452 MessageManager.getString("label.show_consensus_histogram"));
3453 showSequenceLogo.setLabel(
3454 MessageManager.getString("label.show_consensus_logo"));
3455 normSequenceLogo.setLabel(
3456 MessageManager.getString("label.norm_consensus_logo"));
3457 applyAutoAnnotationSettings
3458 .setLabel(MessageManager.getString("label.apply_all_groups"));
3459 applyAutoAnnotationSettings.setState(true);
3460 Menu autoAnnMenu = new Menu(
3461 MessageManager.getString("label.autocalculated_annotation"));
3462 showGroupConsensus.addItemListener(this);
3463 showGroupConservation.addItemListener(this);
3464 showConsensusHistogram.addItemListener(this);
3465 showSequenceLogo.addItemListener(this);
3466 normSequenceLogo.addItemListener(this);
3467 applyAutoAnnotationSettings.addItemListener(this);
3468 showAlignmentAnnotations = new CheckboxMenuItem(
3469 MessageManager.getString("label.show_all_al_annotations"));
3470 showSequenceAnnotations = new CheckboxMenuItem(
3471 MessageManager.getString("label.show_all_seq_annotations"));
3472 sortAnnBySequence = new CheckboxMenuItem(
3473 MessageManager.getString("label.sort_annotations_by_sequence"));
3474 sortAnnByLabel = new CheckboxMenuItem(
3475 MessageManager.getString("label.sort_annotations_by_label"));
3476 showAutoFirst = new CheckboxMenuItem(
3477 MessageManager.getString("label.show_first"));
3478 showAutoFirst.setState(false); // pending applet parameter
3479 setShowAutoCalculatedAbove(showAutoFirst.getState());
3480 showAutoLast = new CheckboxMenuItem(
3481 MessageManager.getString("label.show_last"));
3482 showAutoLast.setState(!showAutoFirst.getState());
3483 showAlignmentAnnotations.addItemListener(this);
3484 showSequenceAnnotations.addItemListener(this);
3485 sortAnnBySequence.addItemListener(this);
3486 sortAnnByLabel.addItemListener(this);
3487 showAutoFirst.addItemListener(this);
3488 showAutoLast.addItemListener(this);
3491 * Configure Format menu items and actions
3493 font.setLabel(MessageManager.getString("action.font"));
3494 font.addActionListener(this);
3495 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3496 scaleAbove.setState(true);
3497 scaleAbove.setEnabled(false);
3498 scaleAbove.addItemListener(this);
3499 scaleLeft.setEnabled(false);
3500 scaleLeft.setState(true);
3501 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3502 scaleLeft.addItemListener(this);
3503 scaleRight.setEnabled(false);
3504 scaleRight.setState(true);
3505 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3506 scaleRight.addItemListener(this);
3507 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3508 viewBoxesMenuItem.setState(true);
3509 viewBoxesMenuItem.addItemListener(this);
3510 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3511 viewTextMenuItem.setState(true);
3512 viewTextMenuItem.addItemListener(this);
3514 .setLabel(MessageManager.getString("label.colour_text"));
3515 colourTextMenuItem.addItemListener(this);
3516 displayNonconservedMenuItem
3517 .setLabel(MessageManager.getString("label.show_non_conserved"));
3518 displayNonconservedMenuItem.addItemListener(this);
3519 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3520 wrapMenuItem.addItemListener(this);
3522 .setLabel(MessageManager.getString("action.show_gaps"));
3523 renderGapsMenuItem.setState(true);
3524 renderGapsMenuItem.addItemListener(this);
3525 centreColumnLabelFlag.setLabel(
3526 MessageManager.getString("label.centre_column_labels"));
3527 centreColumnLabelFlag.addItemListener(this);
3528 seqLimits.setState(true);
3530 MessageManager.getString("label.show_sequence_limits"));
3531 seqLimits.addItemListener(this);
3534 * Configure Colour menu items and actions
3536 applyToAllGroups.setLabel(
3537 MessageManager.getString("label.apply_colour_to_all_groups"));
3538 applyToAllGroups.setState(true);
3539 applyToAllGroups.addItemListener(this);
3540 clustalColour.setLabel(
3541 MessageManager.getString("label.colourScheme_clustal"));
3542 clustalColour.addActionListener(this);
3544 .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3545 zappoColour.addActionListener(this);
3546 taylorColour.setLabel(
3547 MessageManager.getString("label.colourScheme_taylor"));
3548 taylorColour.addActionListener(this);
3549 hydrophobicityColour.setLabel(
3550 MessageManager.getString("label.colourScheme_hydrophobic"));
3551 hydrophobicityColour.addActionListener(this);
3552 helixColour.setLabel(
3553 MessageManager.getString("label.colourScheme_helixpropensity"));
3554 helixColour.addActionListener(this);
3555 strandColour.setLabel(MessageManager
3556 .getString("label.colourScheme_strandpropensity"));
3557 strandColour.addActionListener(this);
3558 turnColour.setLabel(
3559 MessageManager.getString("label.colourScheme_turnpropensity"));
3560 turnColour.addActionListener(this);
3561 buriedColour.setLabel(
3562 MessageManager.getString("label.colourScheme_buriedindex"));
3563 buriedColour.addActionListener(this);
3564 purinePyrimidineColour.setLabel(MessageManager
3565 .getString("label.colourScheme_purine/pyrimidine"));
3566 purinePyrimidineColour.addActionListener(this);
3567 // RNAInteractionColour.setLabel(MessageManager
3568 // .getString("label.rna_interaction"));
3569 // RNAInteractionColour.addActionListener(this);
3570 RNAHelixColour.setLabel(
3571 MessageManager.getString("label.colourScheme_rnahelices"));
3572 RNAHelixColour.addActionListener(this);
3574 .setLabel(MessageManager.getString("action.user_defined"));
3575 userDefinedColour.addActionListener(this);
3577 MessageManager.getString("label.colourScheme_%identity"));
3578 PIDColour.addActionListener(this);
3579 BLOSUM62Colour.setLabel(
3580 MessageManager.getString("label.colourScheme_blosum62"));
3581 BLOSUM62Colour.addActionListener(this);
3582 tcoffeeColour.setLabel(
3583 MessageManager.getString("label.colourScheme_t-coffeescores"));
3584 // it will be enabled only if a score file is provided
3585 tcoffeeColour.setEnabled(false);
3586 tcoffeeColour.addActionListener(this);
3587 conservationMenuItem
3588 .setLabel(MessageManager.getString("action.by_conservation"));
3589 conservationMenuItem.addItemListener(this);
3590 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3591 noColourmenuItem.addActionListener(this);
3592 abovePIDThreshold.setLabel(
3593 MessageManager.getString("label.above_identity_threshold"));
3594 abovePIDThreshold.addItemListener(this);
3595 nucleotideColour.setLabel(
3596 MessageManager.getString("label.colourScheme_nucleotide"));
3597 nucleotideColour.addActionListener(this);
3599 MessageManager.getString("label.modify_identity_threshold"));
3600 modifyPID.setEnabled(abovePIDThreshold.getState());
3601 modifyPID.addActionListener(this);
3602 modifyConservation.setLabel(MessageManager
3603 .getString("label.modify_conservation_threshold"));
3604 modifyConservation.setEnabled(conservationMenuItem.getState());
3605 modifyConservation.addActionListener(this);
3607 .setLabel(MessageManager.getString("action.by_annotation"));
3608 annotationColour.addActionListener(this);
3611 * Configure Calculate menu items and actions
3613 sortPairwiseMenuItem
3614 .setLabel(MessageManager.getString("action.by_pairwise_id"));
3615 sortPairwiseMenuItem.addActionListener(this);
3616 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3617 sortIDMenuItem.addActionListener(this);
3619 .setLabel(MessageManager.getString("action.by_length"));
3620 sortLengthMenuItem.addActionListener(this);
3621 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3622 sortGroupMenuItem.addActionListener(this);
3623 pairwiseAlignmentMenuItem.setLabel(
3624 MessageManager.getString("action.pairwise_alignment"));
3625 pairwiseAlignmentMenuItem.addActionListener(this);
3626 PCAMenuItem.setLabel(
3627 MessageManager.getString("label.principal_component_analysis"));
3628 PCAMenuItem.addActionListener(this);
3629 autoCalculate = new CheckboxMenuItem(
3630 MessageManager.getString("label.autocalculate_consensus"),
3632 averageDistanceTreeMenuItem.setLabel(
3633 MessageManager.getString("label.average_distance_identity"));
3634 averageDistanceTreeMenuItem.addActionListener(this);
3635 neighbourTreeMenuItem.setLabel(
3636 MessageManager.getString("label.neighbour_joining_identity"));
3637 neighbourTreeMenuItem.addActionListener(this);
3638 avDistanceTreeBlosumMenuItem.setLabel(
3639 MessageManager.getString("label.average_distance_blosum62"));
3640 avDistanceTreeBlosumMenuItem.addActionListener(this);
3641 njTreeBlosumMenuItem
3642 .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3643 njTreeBlosumMenuItem.addActionListener(this);
3645 .setLabel(MessageManager.getString("action.by_tree_order"));
3646 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3647 Menu calculateTreeMenu = new Menu(
3648 MessageManager.getString("action.calculate_tree"));
3649 autoCalculate.addItemListener(this);
3650 sortByTree.addItemListener(this);
3653 * Configure Help menu items and actions
3655 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3656 documentation.setLabel(MessageManager.getString("label.documentation"));
3657 documentation.addActionListener(this);
3658 about.setLabel(MessageManager.getString("label.about"));
3659 about.addActionListener(this);
3662 * Add top level menus to frame
3664 alignFrameMenuBar.add(fileMenu);
3665 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3666 alignFrameMenuBar.add(editMenu);
3667 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3668 alignFrameMenuBar.add(selectMenu);
3669 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3670 alignFrameMenuBar.add(viewMenu);
3671 Menu annotationsMenu = new Menu(
3672 MessageManager.getString("action.annotations"));
3673 alignFrameMenuBar.add(annotationsMenu);
3674 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3675 alignFrameMenuBar.add(formatMenu);
3676 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3677 alignFrameMenuBar.add(colourMenu);
3678 Menu calculateMenu = new Menu(
3679 MessageManager.getString("action.calculate"));
3680 alignFrameMenuBar.add(calculateMenu);
3681 alignFrameMenuBar.add(helpMenu);
3686 fileMenu.add(inputText);
3687 fileMenu.add(loadTree);
3688 fileMenu.add(loadAnnotations);
3689 fileMenu.addSeparator();
3690 fileMenu.add(outputTextboxMenu);
3691 fileMenu.add(outputFeatures);
3692 fileMenu.add(outputAnnotations);
3693 if (jalviewServletURL != null)
3695 fileMenu.add(loadApplication);
3697 fileMenu.addSeparator();
3698 fileMenu.add(closeMenuItem);
3703 editMenu.add(undoMenuItem);
3704 editMenu.add(redoMenuItem);
3707 pasteMenu.add(pasteNew);
3708 pasteMenu.add(pasteThis);
3709 editMenu.add(pasteMenu);
3710 editMenu.add(delete);
3711 editMenu.addSeparator();
3712 editMenu.add(remove2LeftMenuItem);
3713 editMenu.add(remove2RightMenuItem);
3714 editMenu.add(removeGappedColumnMenuItem);
3715 editMenu.add(removeAllGapsMenuItem);
3716 editMenu.add(removeRedundancyMenuItem);
3721 selectMenu.add(findMenuItem);
3722 selectMenu.addSeparator();
3723 selectMenu.add(selectAllSequenceMenuItem);
3724 selectMenu.add(deselectAllSequenceMenuItem);
3725 selectMenu.add(invertSequenceMenuItem);
3726 selectMenu.add(invertColSel);
3727 selectMenu.add(createGroup);
3728 selectMenu.add(unGroup);
3729 selectMenu.add(grpsFromSelection);
3730 selectMenu.add(deleteGroups);
3731 selectMenu.add(annotationColumnSelection);
3736 viewMenu.add(newView);
3737 viewMenu.addSeparator();
3738 showMenu.add(showColumns);
3739 showMenu.add(showSeqs);
3740 showMenu.add(showAllHidden);
3741 viewMenu.add(showMenu);
3742 hideMenu.add(hideColumns);
3743 hideMenu.add(hideSequences);
3744 hideMenu.add(hideAllSelection);
3745 hideMenu.add(hideAllButSelection);
3746 viewMenu.add(hideMenu);
3747 viewMenu.addSeparator();
3748 viewMenu.add(followMouseOverFlag);
3749 viewMenu.addSeparator();
3750 viewMenu.add(sequenceFeatures);
3751 viewMenu.add(featureSettings);
3752 viewMenu.addSeparator();
3753 viewMenu.add(alProperties);
3754 viewMenu.addSeparator();
3755 viewMenu.add(overviewMenuItem);
3760 annotationsMenu.add(annotationPanelMenuItem);
3761 annotationsMenu.addSeparator();
3762 annotationsMenu.add(showAlignmentAnnotations);
3763 annotationsMenu.add(showSequenceAnnotations);
3764 annotationsMenu.add(sortAnnBySequence);
3765 annotationsMenu.add(sortAnnByLabel);
3766 annotationsMenu.addSeparator();
3767 autoAnnMenu.add(showAutoFirst);
3768 autoAnnMenu.add(showAutoLast);
3769 autoAnnMenu.addSeparator();
3770 autoAnnMenu.add(applyAutoAnnotationSettings);
3771 autoAnnMenu.add(showConsensusHistogram);
3772 autoAnnMenu.add(showSequenceLogo);
3773 autoAnnMenu.add(normSequenceLogo);
3774 autoAnnMenu.addSeparator();
3775 autoAnnMenu.add(showGroupConservation);
3776 autoAnnMenu.add(showGroupConsensus);
3777 annotationsMenu.add(autoAnnMenu);
3782 formatMenu.add(font);
3783 formatMenu.add(seqLimits);
3784 formatMenu.add(wrapMenuItem);
3785 formatMenu.add(scaleAbove);
3786 formatMenu.add(scaleLeft);
3787 formatMenu.add(scaleRight);
3788 formatMenu.add(viewBoxesMenuItem);
3789 formatMenu.add(viewTextMenuItem);
3790 formatMenu.add(colourTextMenuItem);
3791 formatMenu.add(displayNonconservedMenuItem);
3792 formatMenu.add(renderGapsMenuItem);
3793 formatMenu.add(centreColumnLabelFlag);
3798 colourMenu.add(applyToAllGroups);
3799 colourMenu.addSeparator();
3800 colourMenu.add(noColourmenuItem);
3801 colourMenu.add(clustalColour);
3802 colourMenu.add(BLOSUM62Colour);
3803 colourMenu.add(PIDColour);
3804 colourMenu.add(zappoColour);
3805 colourMenu.add(taylorColour);
3806 colourMenu.add(hydrophobicityColour);
3807 colourMenu.add(helixColour);
3808 colourMenu.add(strandColour);
3809 colourMenu.add(turnColour);
3810 colourMenu.add(buriedColour);
3811 colourMenu.add(nucleotideColour);
3812 colourMenu.add(purinePyrimidineColour);
3813 // colourMenu.add(RNAInteractionColour);
3814 colourMenu.add(tcoffeeColour);
3815 colourMenu.add(userDefinedColour);
3816 colourMenu.addSeparator();
3817 colourMenu.add(conservationMenuItem);
3818 colourMenu.add(modifyConservation);
3819 colourMenu.add(abovePIDThreshold);
3820 colourMenu.add(modifyPID);
3821 colourMenu.add(annotationColour);
3822 colourMenu.add(RNAHelixColour);
3827 sortMenu.add(sortIDMenuItem);
3828 sortMenu.add(sortLengthMenuItem);
3829 sortMenu.add(sortByTreeMenu);
3830 sortMenu.add(sortGroupMenuItem);
3831 sortMenu.add(sortPairwiseMenuItem);
3832 calculateMenu.add(sortMenu);
3833 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3834 calculateTreeMenu.add(neighbourTreeMenuItem);
3835 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3836 calculateTreeMenu.add(njTreeBlosumMenuItem);
3837 calculateMenu.add(calculateTreeMenu);
3838 calculateMenu.addSeparator();
3839 calculateMenu.add(pairwiseAlignmentMenuItem);
3840 calculateMenu.add(PCAMenuItem);
3841 calculateMenu.add(autoCalculate);
3842 calculateMenu.add(sortByTree);
3847 helpMenu.add(documentation);
3848 helpMenu.add(about);
3853 statusBar.setBackground(Color.white);
3854 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3855 setStatus(MessageManager.getString("label.status_bar"));
3856 this.add(statusBar, BorderLayout.SOUTH);
3860 public void setStatus(String string)
3862 statusBar.setText(string);
3865 MenuItem featureSettings = new MenuItem();
3867 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3869 MenuItem annotationColour = new MenuItem();
3871 MenuItem annotationColumnSelection = new MenuItem();
3873 MenuItem invertColSel = new MenuItem();
3875 MenuItem showColumns = new MenuItem();
3877 MenuItem showSeqs = new MenuItem();
3879 MenuItem hideColumns = new MenuItem();
3881 MenuItem hideSequences = new MenuItem();
3883 MenuItem hideAllButSelection = new MenuItem();
3885 MenuItem hideAllSelection = new MenuItem();
3887 MenuItem showAllHidden = new MenuItem();
3889 MenuItem newView = new MenuItem();
3891 private CheckboxMenuItem showAlignmentAnnotations;
3893 private CheckboxMenuItem showSequenceAnnotations;
3895 private CheckboxMenuItem sortAnnBySequence;
3897 private CheckboxMenuItem sortAnnByLabel;
3899 private CheckboxMenuItem showAutoFirst;
3901 private CheckboxMenuItem showAutoLast;
3903 private SplitFrame splitFrame;
3906 * Attach the alignFrame panels after embedding menus, if necessary. This used
3907 * to be called setEmbedded, but is now creates the dropdown menus in a
3908 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3910 * @param reallyEmbedded
3911 * true to attach the view to the applet area on the page rather than
3914 public void createAlignFrameWindow(boolean reallyEmbedded)
3918 embedAlignFrameInApplet(viewport.applet);
3923 // test and embed menu bar if necessary.
3925 if (embedMenuIfNeeded(alignPanel))
3928 * adjust for status bar height too. ? pointless as overridden by layout
3931 alignPanel.setSize(getSize().width,
3932 getSize().height - statusBar.getHeight());
3934 add(statusBar, BorderLayout.SOUTH);
3935 add(alignPanel, BorderLayout.CENTER);
3936 // and register with the applet so it can pass external API calls to us
3937 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3943 * Add the components of this AlignFrame to the applet container.
3947 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3950 // Explicitly build the embedded menu panel for the on-page applet
3952 // view cannot be closed if its actually on the page
3953 fileMenu.remove(closeMenuItem);
3954 fileMenu.remove(3); // Remove Separator
3955 // construct embedded menu, using default font
3956 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3957 // and actually add the components to the applet area
3958 theApplet.setLayout(new BorderLayout());
3959 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3960 theApplet.add(statusBar, BorderLayout.SOUTH);
3961 // TODO should size be left to the layout manager?
3962 alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3963 - embeddedMenu.getHeight() - statusBar.getHeight());
3964 theApplet.add(alignPanel, BorderLayout.CENTER);
3965 final AlignFrame me = this;
3966 theApplet.addFocusListener(new FocusListener()
3970 public void focusLost(FocusEvent e)
3972 if (theApplet.currentAlignFrame == me)
3974 theApplet.currentAlignFrame = null;
3979 public void focusGained(FocusEvent e)
3981 theApplet.currentAlignFrame = me;
3984 theApplet.validate();
3988 * create a new binding between structures in an existing jmol viewer instance
3989 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3990 * this does not open a new Jmol window, or modify the display of the
3991 * structures in the original jmol window. Note This method doesn't work
3992 * without an additional javascript library to exchange messages between the
3993 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3996 * JmolViewer instance
3997 * @param sequenceIds
3998 * - sequence Ids to search for associations
4000 public SequenceStructureBinding addStructureViewInstance(
4001 Object jmolviewer, String[] sequenceIds)
4003 Viewer viewer = null;
4006 viewer = (Viewer) jmolviewer;
4007 } catch (ClassCastException ex)
4010 "Unsupported viewer object :" + jmolviewer.getClass());
4014 System.err.println("Can't use this object as a structure viewer:"
4015 + jmolviewer.getClass());
4018 SequenceI[] seqs = null;
4019 if (sequenceIds == null || sequenceIds.length == 0)
4021 seqs = viewport.getAlignment().getSequencesArray();
4025 Vector sqi = new Vector();
4026 AlignmentI al = viewport.getAlignment();
4027 for (int sid = 0; sid < sequenceIds.length; sid++)
4029 SequenceI sq = al.findName(sequenceIds[sid]);
4037 seqs = new SequenceI[sqi.size()];
4038 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4040 seqs[sid] = (SequenceI) sqi.elementAt(sid);
4048 AAStructureBindingModel jmv = null;
4049 // TODO: search for a jmv that involves viewer
4051 { // create a new viewer/jalview binding.
4052 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4059 * bind a pdb file to a sequence in the current view
4062 * - sequenceId within the dataset.
4063 * @param pdbEntryString
4064 * - the short name for the PDB file
4066 * - pdb file - either a URL or a valid PDB file.
4067 * @return true if binding was as success TODO: consider making an exception
4068 * structure for indicating when PDB parsing or sequenceId location
4071 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4074 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4075 boolean needtoadd = false;
4076 if (toaddpdb != null)
4078 Vector pdbe = toaddpdb.getAllPDBEntries();
4079 PDBEntry pdbentry = null;
4080 if (pdbe != null && pdbe.size() > 0)
4082 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4084 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4085 if (!pdbentry.getId().equals(pdbEntryString)
4086 && !pdbentry.getFile().equals(pdbFile))
4096 if (pdbentry == null)
4098 pdbentry = new PDBEntry();
4099 pdbentry.setId(pdbEntryString);
4100 pdbentry.setFile(pdbFile);
4101 needtoadd = true; // add this new entry to sequence.
4103 // resolve data source
4104 // TODO: this code should be a refactored to an io package
4105 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4107 if (protocol == null)
4113 pdbentry.setProperty("protocol", protocol);
4114 toaddpdb.addPDBId(pdbentry);
4115 alignPanel.getStructureSelectionManager()
4116 .registerPDBEntry(pdbentry);
4122 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4126 Vector sequences = new Vector();
4127 for (int i = 0; i < seqs.length; i++)
4129 if (seqs[i] != null)
4132 .addElement(new Object[]
4133 { seqs[i], (chains != null) ? chains[i] : null });
4136 seqs = new SequenceI[sequences.size()];
4137 chains = new String[sequences.size()];
4138 for (int i = 0, isize = sequences.size(); i < isize; i++)
4140 Object[] oj = (Object[]) sequences.elementAt(i);
4142 seqs[i] = (SequenceI) oj[0];
4143 chains[i] = (String) oj[1];
4146 return new Object[] { seqs, chains };
4150 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4151 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4153 // Scrub any null sequences from the array
4154 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4155 seqs = (SequenceI[]) sqch[0];
4156 chains = (String[]) sqch[1];
4157 if (seqs == null || seqs.length == 0)
4160 "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4162 if (protocol == null)
4164 String sourceType = (String) pdb.getProperty("protocol");
4167 protocol = DataSourceType.valueOf(sourceType);
4168 } catch (IllegalArgumentException e)
4172 if (protocol == null)
4174 System.err.println("Couldn't work out protocol to open structure: "
4179 if (applet.useXtrnalSviewer)
4181 // register the association(s) and quit, don't create any windows.
4182 if (StructureSelectionManager.getStructureSelectionManager(applet)
4183 .setMapping(seqs, chains, pdb.getFile(), protocol,
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()