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 statusBar.setText(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 statusBar.setText(MessageManager
581 .formatMessage("label.keyboard_editing_mode", new String[]
582 { (viewport.cursorMode ? "on" : "off") }));
583 if (viewport.cursorMode)
585 alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
586 alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
591 if (evt.isControlDown())
593 findMenuItem_actionPerformed();
599 boolean toggleSeqs = !evt.isControlDown();
600 boolean toggleCols = !evt.isShiftDown();
601 toggleHiddenRegions(toggleSeqs, toggleCols);
605 case KeyEvent.VK_PAGE_UP:
609 case KeyEvent.VK_PAGE_DOWN:
614 if (evt.isControlDown())
616 undoMenuItem_actionPerformed();
621 if (evt.isControlDown())
623 redoMenuItem_actionPerformed();
628 if (evt.isControlDown())
635 if (evt.isControlDown())
637 trimAlignment(false);
642 if (evt.isControlDown())
644 if (evt.isShiftDown())
646 this.removeAllGapsMenuItem_actionPerformed();
650 removeGappedColumnMenuItem_actionPerformed();
655 if (evt.isControlDown())
659 invertColSel_actionPerformed();
663 invertSequenceMenuItem_actionPerformed();
669 if (evt.isControlDown())
671 if (evt.isShiftDown())
673 this.unGroup_actionPerformed();
677 this.createGroup_actionPerformed();
683 if (evt.isControlDown())
685 this.deleteGroups_actionPerformed();
690 if (evt.isControlDown())
697 // TODO: repaint flags set only if the keystroke warrants it
698 alignPanel.paintAlignment(true, true);
702 * called by key handler and the hide all/show all menu items
707 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
709 boolean hide = false;
710 SequenceGroup sg = viewport.getSelectionGroup();
711 if (!toggleSeqs && !toggleCols)
713 // Hide everything by the current selection - this is a hack - we do the
714 // invert and then hide
715 // first check that there will be visible columns after the invert.
716 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
717 && sg.getStartRes() <= sg.getEndRes()))
719 // now invert the sequence set, if required - empty selection implies
720 // that no hiding is required.
723 invertSequenceMenuItem_actionPerformed();
724 sg = viewport.getSelectionGroup();
728 viewport.expandColSelection(sg, true);
729 // finally invert the column selection and get the new sequence
730 // selection and indicate it should be hidden.
731 invertColSel_actionPerformed();
738 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
741 viewport.hideAllSelectedSeqs();
743 else if (!(toggleCols && viewport.hasSelectedColumns()))
745 viewport.showAllHiddenSeqs();
751 if (viewport.hasSelectedColumns())
753 viewport.hideSelectedColumns();
756 viewport.setSelectionGroup(sg);
761 viewport.showAllHiddenColumns();
763 viewport.sendSelection();
768 public void keyReleased(KeyEvent evt)
773 public void keyTyped(KeyEvent evt)
778 public void itemStateChanged(ItemEvent evt)
780 final Object source = evt.getSource();
781 if (source == displayNonconservedMenuItem)
783 displayNonconservedMenuItem_actionPerformed();
785 else if (source == colourTextMenuItem)
787 colourTextMenuItem_actionPerformed();
789 else if (source == wrapMenuItem)
791 wrapMenuItem_actionPerformed();
793 else if (source == scaleAbove)
795 viewport.setScaleAboveWrapped(scaleAbove.getState());
797 else if (source == scaleLeft)
799 viewport.setScaleLeftWrapped(scaleLeft.getState());
801 else if (source == scaleRight)
803 viewport.setScaleRightWrapped(scaleRight.getState());
805 else if (source == seqLimits)
807 seqLimits_itemStateChanged();
809 else if (source == viewBoxesMenuItem)
811 viewport.setShowBoxes(viewBoxesMenuItem.getState());
813 else if (source == viewTextMenuItem)
815 viewport.setShowText(viewTextMenuItem.getState());
817 else if (source == renderGapsMenuItem)
819 viewport.setRenderGaps(renderGapsMenuItem.getState());
821 else if (source == annotationPanelMenuItem)
823 boolean showAnnotations = annotationPanelMenuItem.getState();
824 showAlignmentAnnotations.setEnabled(showAnnotations);
825 showSequenceAnnotations.setEnabled(showAnnotations);
826 viewport.setShowAnnotation(showAnnotations);
827 alignPanel.setAnnotationVisible(showAnnotations);
829 else if (source == sequenceFeatures)
831 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
832 alignPanel.seqPanel.seqCanvas.repaint();
834 else if (source == showAlignmentAnnotations)
836 setAnnotationsVisibility();
838 else if (source == showSequenceAnnotations)
840 setAnnotationsVisibility();
842 else if (source == sortAnnBySequence)
844 boolean newState = sortAnnBySequence.getState();
845 sortAnnByLabel.setState(false);
846 setAnnotationSortOrder(
847 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
848 : SequenceAnnotationOrder.NONE);
849 setViewportAnnotationOrder();
851 else if (source == sortAnnByLabel)
853 boolean newState = sortAnnByLabel.getState();
854 sortAnnBySequence.setState(false);
855 setAnnotationSortOrder(
856 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
857 : SequenceAnnotationOrder.NONE);
858 setViewportAnnotationOrder();
860 else if (source == showAutoFirst)
862 showAutoLast.setState(!showAutoFirst.getState());
863 setShowAutoCalculatedAbove(showAutoFirst.getState());
864 setViewportAnnotationOrder();
866 else if (source == showAutoLast)
868 showAutoFirst.setState(!showAutoLast.getState());
869 setShowAutoCalculatedAbove(showAutoFirst.getState());
870 setViewportAnnotationOrder();
872 else if (source == conservationMenuItem)
874 conservationMenuItem_actionPerformed();
876 else if (source == abovePIDThreshold)
878 abovePIDThreshold_actionPerformed();
880 else if (source == applyToAllGroups)
882 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
884 else if (source == autoCalculate)
886 viewport.autoCalculateConsensus = autoCalculate.getState();
888 else if (source == sortByTree)
890 viewport.sortByTree = sortByTree.getState();
892 else if (source == this.centreColumnLabelFlag)
894 centreColumnLabelFlag_stateChanged();
896 else if (source == this.followMouseOverFlag)
898 mouseOverFlag_stateChanged();
900 else if (source == showGroupConsensus)
902 showGroupConsensus_actionPerformed();
904 else if (source == showGroupConservation)
906 showGroupConservation_actionPerformed();
908 else if (source == showSequenceLogo)
910 showSequenceLogo_actionPerformed();
912 else if (source == normSequenceLogo)
914 normSequenceLogo_actionPerformed();
916 else if (source == showConsensusHistogram)
918 showConsensusHistogram_actionPerformed();
920 else if (source == applyAutoAnnotationSettings)
922 applyAutoAnnotationSettings_actionPerformed();
924 // TODO: repaint flags set only if warranted
925 alignPanel.paintAlignment(true, true);
929 * Set the visibility state of sequence-related and/or alignment-related
930 * annotations depending on checkbox selections, and repaint.
934 private void setAnnotationsVisibility()
936 boolean showForAlignment = showAlignmentAnnotations.getState();
937 boolean showForSequences = showSequenceAnnotations.getState();
938 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
940 for (AlignmentAnnotation aa : alignPanel.getAlignment()
941 .getAlignmentAnnotation())
943 boolean visible = (aa.sequenceRef == null ? showForAlignment
945 aa.visible = visible;
948 alignPanel.validateAnnotationDimensions(true);
953 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
955 this.annotationSortOrder = order;
959 * Set flags on the viewport that control annotation ordering
961 private void setViewportAnnotationOrder()
963 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
965 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
968 private void setShowAutoCalculatedAbove(boolean showAbove)
970 this.showAutoCalculatedAbove = showAbove;
973 private void mouseOverFlag_stateChanged()
975 viewport.setFollowHighlight(followMouseOverFlag.getState());
976 // TODO: could kick the scrollTo mechanism to reset view for current
980 private void centreColumnLabelFlag_stateChanged()
982 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
983 this.alignPanel.annotationPanel.repaint();
987 public void actionPerformed(ActionEvent evt)
989 viewport.applet.currentAlignFrame = this;
991 Object source = evt.getSource();
993 if (source == inputText)
995 inputText_actionPerformed();
997 else if (source == loadTree)
999 loadTree_actionPerformed();
1001 else if (source == loadApplication)
1003 launchFullApplication();
1005 else if (source == loadAnnotations)
1009 else if (source == outputAnnotations)
1011 outputAnnotations(true);
1013 else if (source == outputFeatures)
1015 outputFeatures(true, "Jalview");
1017 else if (source == closeMenuItem)
1019 closeMenuItem_actionPerformed();
1021 else if (source == copy)
1023 copy_actionPerformed();
1025 else if (source == undoMenuItem)
1027 undoMenuItem_actionPerformed();
1029 else if (source == redoMenuItem)
1031 redoMenuItem_actionPerformed();
1033 else if (source == inputText)
1035 inputText_actionPerformed();
1037 else if (source == closeMenuItem)
1039 closeMenuItem_actionPerformed();
1041 else if (source == undoMenuItem)
1043 undoMenuItem_actionPerformed();
1045 else if (source == redoMenuItem)
1047 redoMenuItem_actionPerformed();
1049 else if (source == copy)
1051 copy_actionPerformed();
1053 else if (source == pasteNew)
1055 pasteNew_actionPerformed();
1057 else if (source == pasteThis)
1059 pasteThis_actionPerformed();
1061 else if (source == cut)
1063 cut_actionPerformed();
1065 else if (source == delete)
1067 delete_actionPerformed();
1069 else if (source == createGroup)
1071 createGroup_actionPerformed();
1073 else if (source == unGroup)
1075 unGroup_actionPerformed();
1077 else if (source == grpsFromSelection)
1079 makeGrpsFromSelection_actionPerformed();
1081 else if (source == deleteGroups)
1083 deleteGroups_actionPerformed();
1085 else if (source == selectAllSequenceMenuItem)
1087 selectAllSequenceMenuItem_actionPerformed();
1089 else if (source == deselectAllSequenceMenuItem)
1091 deselectAllSequenceMenuItem_actionPerformed();
1093 else if (source == invertSequenceMenuItem)
1095 invertSequenceMenuItem_actionPerformed();
1096 // uncomment to slave sequence selections in split frame
1097 // viewport.sendSelection();
1099 else if (source == invertColSel)
1101 viewport.invertColumnSelection();
1102 alignPanel.paintAlignment(false, false);
1103 viewport.sendSelection();
1105 else if (source == remove2LeftMenuItem)
1107 trimAlignment(true);
1109 else if (source == remove2RightMenuItem)
1111 trimAlignment(false);
1113 else if (source == removeGappedColumnMenuItem)
1115 removeGappedColumnMenuItem_actionPerformed();
1117 else if (source == removeAllGapsMenuItem)
1119 removeAllGapsMenuItem_actionPerformed();
1121 else if (source == findMenuItem)
1123 findMenuItem_actionPerformed();
1125 else if (source == font)
1127 new FontChooser(alignPanel);
1129 else if (source == newView)
1133 else if (source == showColumns)
1135 viewport.showAllHiddenColumns();
1136 alignPanel.paintAlignment(true, true);
1137 viewport.sendSelection();
1139 else if (source == showSeqs)
1141 viewport.showAllHiddenSeqs();
1142 alignPanel.paintAlignment(true, true);
1143 // uncomment if we want to slave sequence selections in split frame
1144 // viewport.sendSelection();
1146 else if (source == hideColumns)
1148 viewport.hideSelectedColumns();
1149 alignPanel.paintAlignment(true, true);
1150 viewport.sendSelection();
1152 else if (source == hideSequences
1153 && viewport.getSelectionGroup() != null)
1155 viewport.hideAllSelectedSeqs();
1156 alignPanel.paintAlignment(true, true);
1157 // uncomment if we want to slave sequence selections in split frame
1158 // viewport.sendSelection();
1160 else if (source == hideAllButSelection)
1162 toggleHiddenRegions(false, false);
1163 alignPanel.paintAlignment(true, true);
1164 viewport.sendSelection();
1166 else if (source == hideAllSelection)
1168 SequenceGroup sg = viewport.getSelectionGroup();
1169 viewport.expandColSelection(sg, false);
1170 viewport.hideAllSelectedSeqs();
1171 viewport.hideSelectedColumns();
1172 alignPanel.paintAlignment(true, true);
1173 viewport.sendSelection();
1175 else if (source == showAllHidden)
1177 viewport.showAllHiddenColumns();
1178 viewport.showAllHiddenSeqs();
1179 alignPanel.paintAlignment(true, true);
1180 viewport.sendSelection();
1182 else if (source == showGroupConsensus)
1184 showGroupConsensus_actionPerformed();
1186 else if (source == showGroupConservation)
1188 showGroupConservation_actionPerformed();
1190 else if (source == showSequenceLogo)
1192 showSequenceLogo_actionPerformed();
1194 else if (source == normSequenceLogo)
1196 normSequenceLogo_actionPerformed();
1198 else if (source == showConsensusHistogram)
1200 showConsensusHistogram_actionPerformed();
1202 else if (source == applyAutoAnnotationSettings)
1204 applyAutoAnnotationSettings_actionPerformed();
1206 else if (source == featureSettings)
1208 showFeatureSettingsUI();
1210 else if (source == alProperties)
1212 StringBuffer contents = new jalview.io.AlignmentProperties(
1213 viewport.getAlignment()).formatAsString();
1214 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1215 cap.setText(contents.toString());
1216 Frame frame = new Frame();
1218 jalview.bin.JalviewLite.addFrame(frame, MessageManager
1219 .formatMessage("label.alignment_properties", new String[]
1220 { getTitle() }), 400, 250);
1222 else if (source == overviewMenuItem)
1224 overviewMenuItem_actionPerformed();
1226 else if (source == noColourmenuItem)
1230 else if (source == clustalColour)
1232 abovePIDThreshold.setState(false);
1233 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1235 else if (source == zappoColour)
1237 changeColour(new ZappoColourScheme());
1239 else if (source == taylorColour)
1241 changeColour(new TaylorColourScheme());
1243 else if (source == hydrophobicityColour)
1245 changeColour(new HydrophobicColourScheme());
1247 else if (source == helixColour)
1249 changeColour(new HelixColourScheme());
1251 else if (source == strandColour)
1253 changeColour(new StrandColourScheme());
1255 else if (source == turnColour)
1257 changeColour(new TurnColourScheme());
1259 else if (source == buriedColour)
1261 changeColour(new BuriedColourScheme());
1263 else if (source == nucleotideColour)
1265 changeColour(new NucleotideColourScheme());
1267 else if (source == purinePyrimidineColour)
1269 changeColour(new PurinePyrimidineColourScheme());
1271 // else if (source == RNAInteractionColour)
1273 // changeColour(new RNAInteractionColourScheme());
1275 else if (source == RNAHelixColour)
1277 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1278 // new RNAHelicesColourChooser(viewport, alignPanel);
1280 else if (source == modifyPID)
1282 modifyPID_actionPerformed();
1284 else if (source == modifyConservation)
1286 modifyConservation_actionPerformed();
1288 else if (source == userDefinedColour)
1290 new UserDefinedColours(alignPanel, null);
1292 else if (source == PIDColour)
1294 changeColour(new PIDColourScheme());
1296 else if (source == BLOSUM62Colour)
1298 changeColour(new Blosum62ColourScheme());
1300 else if (source == tcoffeeColour)
1302 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1304 else if (source == annotationColour)
1306 new AnnotationColourChooser(viewport, alignPanel);
1308 else if (source == annotationColumnSelection)
1310 new AnnotationColumnChooser(viewport, alignPanel);
1312 else if (source == sortPairwiseMenuItem)
1314 sortPairwiseMenuItem_actionPerformed();
1316 else if (source == sortIDMenuItem)
1318 sortIDMenuItem_actionPerformed();
1320 else if (source == sortLengthMenuItem)
1322 sortLengthMenuItem_actionPerformed();
1324 else if (source == sortGroupMenuItem)
1326 sortGroupMenuItem_actionPerformed();
1328 else if (source == sortEValueMenuItem)
1330 sortEValueMenuItem_actionPerformed();
1332 else if (source == sortBitScoreMenuItem)
1334 sortBitScoreMenuItem_actionPerformed();
1336 else if (source == removeRedundancyMenuItem)
1338 removeRedundancyMenuItem_actionPerformed();
1340 else if (source == pairwiseAlignmentMenuItem)
1342 pairwiseAlignmentMenuItem_actionPerformed();
1344 else if (source == PCAMenuItem)
1346 PCAMenuItem_actionPerformed();
1348 else if (source == averageDistanceTreeMenuItem)
1350 averageDistanceTreeMenuItem_actionPerformed();
1352 else if (source == neighbourTreeMenuItem)
1354 neighbourTreeMenuItem_actionPerformed();
1356 else if (source == njTreeBlosumMenuItem)
1358 njTreeBlosumMenuItem_actionPerformed();
1360 else if (source == avDistanceTreeBlosumMenuItem)
1362 avTreeBlosumMenuItem_actionPerformed();
1364 else if (source == documentation)
1366 documentation_actionPerformed();
1368 else if (source == about)
1370 about_actionPerformed();
1375 public void inputText_actionPerformed()
1377 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1378 Frame frame = new Frame();
1380 jalview.bin.JalviewLite.addFrame(frame,
1381 MessageManager.getString("label.input_cut_paste"), 500, 500);
1384 protected void outputText_actionPerformed(ActionEvent e)
1386 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1387 Frame frame = new Frame();
1389 JalviewLite.addFrame(frame, MessageManager
1390 .formatMessage("label.alignment_output_command", new Object[]
1391 { e.getActionCommand() }), 600, 500);
1393 FileFormatI fileFormat = FileFormats.getInstance()
1394 .forName(e.getActionCommand());
1396 new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
1397 viewport.getAlignment(), viewport.getShowJVSuffix()));
1400 public void loadAnnotations()
1402 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1403 cap.setText(MessageManager
1404 .getString("label.paste_features_annotations_Tcoffee_here"));
1405 cap.setAnnotationImport();
1406 Frame frame = new Frame();
1408 jalview.bin.JalviewLite.addFrame(frame,
1409 MessageManager.getString("action.paste_annotations"), 400, 300);
1413 public String outputAnnotations(boolean displayTextbox)
1415 String annotation = new AnnotationFile()
1416 .printAnnotationsForView(viewport);
1420 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1421 Frame frame = new Frame();
1423 jalview.bin.JalviewLite.addFrame(frame,
1424 MessageManager.getString("label.annotations"), 600, 500);
1425 cap.setText(annotation);
1431 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1433 if (alignPanel.getFeatureRenderer() != null
1434 && viewport.getFeaturesDisplayed() != null)
1436 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1442 private List<String> getDisplayedFeatureGroups()
1444 if (alignPanel.getFeatureRenderer() != null
1445 && viewport.getFeaturesDisplayed() != null)
1447 return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
1453 public String outputFeatures(boolean displayTextbox, String format)
1456 FeaturesFile formatter = new FeaturesFile();
1457 if (format.equalsIgnoreCase("Jalview"))
1459 features = formatter.printJalviewFormat(
1460 viewport.getAlignment().getSequencesArray(),
1461 alignPanel.getFeatureRenderer(), true, false);
1465 features = formatter.printGffFormat(viewport.getAlignment()
1466 .getSequencesArray(), alignPanel.getFeatureRenderer(), true,
1472 boolean frimport = false;
1473 if (features == null || features.equals("No Features Visible"))
1475 features = "# No features visible - paste some and import them here.";
1479 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1482 cap.setAnnotationImport();
1484 Frame frame = new Frame();
1486 jalview.bin.JalviewLite.addFrame(frame,
1487 MessageManager.getString("label.features"), 600, 500);
1488 cap.setText(features);
1492 if (features == null)
1501 void launchFullApplication()
1503 StringBuffer url = new StringBuffer(jalviewServletURL);
1505 // allow servlet parameters to be passed in applet parameter
1506 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1508 url.append(firstSep);
1511 "open=" + appendProtocol(viewport.applet.getParameter("file")));
1513 if (viewport.applet.getParameter("features") != null)
1515 url.append("&features=");
1516 url.append(appendProtocol(viewport.applet.getParameter("features")));
1519 if (viewport.applet.getParameter("annotations") != null)
1521 url.append("&annotations=");
1523 appendProtocol(viewport.applet.getParameter("annotations")));
1526 if (viewport.applet.getParameter("jnetfile") != null
1527 || viewport.applet.getParameter("jpredfile") != null)
1529 url.append("&annotations=");
1530 url.append(appendProtocol(
1531 viewport.applet.getParameter("jnetfile") != null
1532 ? viewport.applet.getParameter("jnetfile")
1533 : viewport.applet.getParameter("jpredfile")));
1536 if (viewport.applet.getParameter("defaultColour") != null)
1538 url.append("&colour=" + removeWhiteSpace(
1539 viewport.applet.getParameter("defaultColour")));
1542 if (viewport.applet.getParameter("userDefinedColour") != null)
1544 url.append("&colour=" + removeWhiteSpace(
1545 viewport.applet.getParameter("userDefinedColour")));
1547 if (viewport.applet.getParameter("tree") != null)
1550 + appendProtocol(viewport.applet.getParameter("tree")));
1552 if (viewport.applet.getParameter("treeFile") != null)
1555 + appendProtocol(viewport.applet.getParameter("treeFile")));
1558 showURL(url.toString(), "FULL_APP");
1561 String removeWhiteSpace(String colour)
1563 StringBuffer sb = new StringBuffer();
1564 for (int i = 0; i < colour.length(); i++)
1566 if (Character.isWhitespace(colour.charAt(i)))
1572 sb.append(colour.charAt(i));
1576 return sb.toString();
1579 String appendProtocol(String url)
1584 url = URLEncoder.encode(url, "UTF-8");
1587 * When we finally deprecate 1.1 compatibility, we can start to use
1588 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1589 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1590 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1591 * ex.printStackTrace(); }
1593 catch (java.net.MalformedURLException ex)
1595 url = viewport.applet.getCodeBase() + url;
1597 catch (UnsupportedEncodingException ex)
1600 "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
1602 ex.printStackTrace();
1607 public void closeMenuItem_actionPerformed()
1609 PaintRefresher.RemoveComponent(alignPanel);
1610 if (alignPanel.seqPanel != null
1611 && alignPanel.seqPanel.seqCanvas != null)
1613 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1615 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1617 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1620 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1626 if (alignPanel != null && alignPanel.overviewPanel != null)
1628 alignPanel.overviewPanel.dispose();
1637 void updateEditMenuBar()
1640 if (viewport.getHistoryList().size() > 0)
1642 undoMenuItem.setEnabled(true);
1643 CommandI command = viewport.getHistoryList().peek();
1644 undoMenuItem.setLabel(MessageManager
1645 .formatMessage("label.undo_command", new Object[]
1646 { command.getDescription() }));
1650 undoMenuItem.setEnabled(false);
1651 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1654 if (viewport.getRedoList().size() > 0)
1656 redoMenuItem.setEnabled(true);
1658 CommandI command = viewport.getRedoList().peek();
1659 redoMenuItem.setLabel(MessageManager
1660 .formatMessage("label.redo_command", new Object[]
1661 { command.getDescription() }));
1665 redoMenuItem.setEnabled(false);
1666 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1674 public void addHistoryItem(CommandI command)
1676 if (command.getSize() > 0)
1678 viewport.addToHistoryList(command);
1679 viewport.clearRedoList();
1680 updateEditMenuBar();
1681 viewport.updateHiddenColumns();
1686 * TODO: JAL-1104 DOCUMENT ME!
1691 protected void undoMenuItem_actionPerformed()
1693 if (viewport.getHistoryList().isEmpty())
1698 CommandI command = viewport.getHistoryList().pop();
1699 viewport.addToRedoList(command);
1700 command.undoCommand(null);
1702 AlignmentViewport originalSource = getOriginatingSource(command);
1704 if (originalSource != viewport)
1707 .println("Warning: Viewport object mismatch whilst undoing");
1709 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1710 // viewport.getColumnSelection().getHiddenColumns()
1712 updateEditMenuBar();
1713 originalSource.firePropertyChange("alignment", null,
1714 originalSource.getAlignment().getSequences());
1718 * TODO: JAL-1104 DOCUMENT ME!
1723 protected void redoMenuItem_actionPerformed()
1725 if (viewport.getRedoList().isEmpty())
1730 CommandI command = viewport.getRedoList().pop();
1731 viewport.addToHistoryList(command);
1732 command.doCommand(null);
1734 AlignmentViewport originalSource = getOriginatingSource(command);
1736 if (originalSource != viewport)
1739 .println("Warning: Viewport object mismatch whilst re-doing");
1741 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1742 // viewport.getColumnSelection().getHiddenColumns()
1745 updateEditMenuBar();
1746 originalSource.firePropertyChange("alignment", null,
1747 originalSource.getAlignment().getSequences());
1750 AlignmentViewport getOriginatingSource(CommandI command)
1752 AlignmentViewport originalSource = null;
1753 // For sequence removal and addition, we need to fire
1754 // the property change event FROM the viewport where the
1755 // original alignment was altered
1756 AlignmentI al = null;
1757 if (command instanceof EditCommand)
1759 EditCommand editCommand = (EditCommand) command;
1760 al = editCommand.getAlignment();
1761 Vector comps = PaintRefresher.components
1762 .get(viewport.getSequenceSetId());
1763 for (int i = 0; i < comps.size(); i++)
1765 if (comps.elementAt(i) instanceof AlignmentPanel)
1767 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1769 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1776 if (originalSource == null)
1778 // The original view is closed, we must validate
1779 // the current view against the closed view first
1782 PaintRefresher.validateSequences(al, viewport.getAlignment());
1785 originalSource = viewport;
1788 return originalSource;
1792 * Move the currently selected sequences up or down one position in the
1797 public void moveSelectedSequences(boolean up)
1799 SequenceGroup sg = viewport.getSelectionGroup();
1804 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1805 up ? null : viewport.getHiddenRepSequences(), up);
1806 alignPanel.paintAlignment(true, false);
1809 * Also move cDNA/protein complement sequences
1811 AlignViewportI complement = viewport.getCodingComplement();
1812 if (complement != null)
1814 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1815 viewport, complement);
1816 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1817 up ? null : complement.getHiddenRepSequences(), up);
1818 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
1823 synchronized void slideSequences(boolean right, int size)
1825 List<SequenceI> sg = new Vector<>();
1826 if (viewport.cursorMode)
1828 sg.add(viewport.getAlignment()
1829 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1831 else if (viewport.getSelectionGroup() != null
1832 && viewport.getSelectionGroup().getSize() != viewport
1833 .getAlignment().getHeight())
1835 sg = viewport.getSelectionGroup()
1836 .getSequences(viewport.getHiddenRepSequences());
1844 Vector<SequenceI> invertGroup = new Vector();
1846 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1848 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1850 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1854 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1856 SequenceI[] seqs2 = invertGroup
1857 .toArray(new SequenceI[invertGroup.size()]);
1858 for (int i = 0; i < invertGroup.size(); i++)
1860 seqs2[i] = invertGroup.elementAt(i);
1863 SlideSequencesCommand ssc;
1866 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1867 viewport.getGapCharacter());
1871 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1872 viewport.getGapCharacter());
1875 int groupAdjustment = 0;
1876 if (ssc.getGapsInsertedBegin() && right)
1878 if (viewport.cursorMode)
1880 alignPanel.seqPanel.moveCursor(size, 0);
1884 groupAdjustment = size;
1887 else if (!ssc.getGapsInsertedBegin() && !right)
1889 if (viewport.cursorMode)
1891 alignPanel.seqPanel.moveCursor(-size, 0);
1895 groupAdjustment = -size;
1899 if (groupAdjustment != 0)
1901 viewport.getSelectionGroup().setStartRes(
1902 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1903 viewport.getSelectionGroup().setEndRes(
1904 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1907 boolean appendHistoryItem = false;
1908 Deque<CommandI> historyList = viewport.getHistoryList();
1909 if (historyList != null && historyList.size() > 0
1910 && historyList.peek() instanceof SlideSequencesCommand)
1912 appendHistoryItem = ssc.appendSlideCommand(
1913 (SlideSequencesCommand) historyList.peek());
1916 if (!appendHistoryItem)
1918 addHistoryItem(ssc);
1924 static StringBuffer copiedSequences;
1926 static HiddenColumns copiedHiddenColumns;
1928 protected void copy_actionPerformed()
1930 if (viewport.getSelectionGroup() == null)
1935 SequenceGroup sg = viewport.getSelectionGroup();
1936 copiedSequences = new StringBuffer();
1937 Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1938 for (int i = 0; i < sg.getSize(); i++)
1940 SequenceI seq = sg.getSequenceAt(i);
1941 int index = viewport.getAlignment().findIndex(seq);
1942 orderedSeqs.put(index, seq);
1945 int index = 0, startRes, endRes;
1948 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1950 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1951 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1953 // create new HiddenColumns object with copy of hidden regions
1954 // between startRes and endRes, offset by startRes
1955 copiedHiddenColumns = new HiddenColumns(
1956 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1957 hiddenCutoff, hiddenOffset);
1961 copiedHiddenColumns = null;
1964 for (int i = 0; i < sg.getSize(); i++)
1966 SequenceI seq = null;
1970 if (orderedSeqs.containsKey(index))
1972 seq = orderedSeqs.get(index);
1983 // Returns residue following index if gap
1984 startRes = seq.findPosition(sg.getStartRes());
1987 // Need to find the residue preceeding index if gap
1990 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1992 ch = seq.getCharAt(j);
1993 if (!jalview.util.Comparison.isGap((ch)))
2001 endRes += seq.getStart() - 1;
2004 copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
2005 + "\t" + seq.getSequenceAsString(sg.getStartRes(),
2012 protected void pasteNew_actionPerformed()
2017 protected void pasteThis_actionPerformed()
2022 void paste(boolean newAlignment)
2026 if (copiedSequences == null)
2031 StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
2033 Vector seqs = new Vector();
2034 while (st.hasMoreElements())
2036 String name = st.nextToken();
2037 int start = Integer.parseInt(st.nextToken());
2038 int end = Integer.parseInt(st.nextToken());
2039 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2041 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2042 for (int i = 0; i < seqs.size(); i++)
2044 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2049 String newtitle = MessageManager
2050 .getString("label.copied_sequences");
2051 if (getTitle().startsWith(
2052 MessageManager.getString("label.copied_sequences")))
2054 newtitle = getTitle();
2058 newtitle = newtitle.concat(MessageManager
2059 .formatMessage("label.from_msname", new String[]
2062 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2063 viewport.applet, newtitle, false);
2064 af.viewport.setHiddenColumns(copiedHiddenColumns);
2066 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2071 addSequences(newSeqs);
2074 } catch (Exception ex)
2076 } // could be anything being pasted in here
2080 void addSequences(SequenceI[] seqs)
2082 for (int i = 0; i < seqs.length; i++)
2084 viewport.getAlignment().addSequence(seqs[i]);
2088 addHistoryItem(new EditCommand(
2089 MessageManager.getString("label.add_sequences"), Action.PASTE,
2090 seqs, 0, viewport.getAlignment().getWidth(),
2091 viewport.getAlignment()));
2093 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2094 viewport.getAlignment().getWidth();
2095 viewport.firePropertyChange("alignment", null,
2096 viewport.getAlignment().getSequences());
2100 protected void cut_actionPerformed()
2102 copy_actionPerformed();
2103 delete_actionPerformed();
2106 protected void delete_actionPerformed()
2109 SequenceGroup sg = viewport.getSelectionGroup();
2115 Vector seqs = new Vector();
2117 for (int i = 0; i < sg.getSize(); i++)
2119 seq = sg.getSequenceAt(i);
2120 seqs.addElement(seq);
2124 * If the cut affects all sequences, warn, remove highlighted columns
2126 if (sg.getSize() == viewport.getAlignment().getHeight())
2128 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2129 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2130 if (isEntireAlignWidth)
2132 String title = MessageManager.getString("label.delete_all");
2133 Panel infoPanel = new Panel();
2134 infoPanel.setLayout(new FlowLayout());
2136 new Label(MessageManager.getString("warn.delete_all")));
2138 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2139 dialog.setMainPanel(infoPanel);
2140 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2141 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2142 dialog.setVisible(true);
2149 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2150 sg.getEndRes() + 1);
2153 SequenceI[] cut = new SequenceI[seqs.size()];
2154 for (int i = 0; i < seqs.size(); i++)
2156 cut[i] = (SequenceI) seqs.elementAt(i);
2160 * //ADD HISTORY ITEM
2162 addHistoryItem(new EditCommand(
2163 MessageManager.getString("label.cut_sequences"), Action.CUT,
2164 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2165 viewport.getAlignment()));
2167 viewport.setSelectionGroup(null);
2168 viewport.getAlignment().deleteGroup(sg);
2170 viewport.firePropertyChange("alignment", null,
2171 viewport.getAlignment().getSequences());
2173 if (viewport.getAlignment().getHeight() < 1)
2175 this.setVisible(false);
2177 viewport.sendSelection();
2181 * group consensus toggled
2184 protected void showGroupConsensus_actionPerformed()
2186 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2187 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2192 * group conservation toggled.
2194 protected void showGroupConservation_actionPerformed()
2196 viewport.setShowGroupConservation(showGroupConservation.getState());
2197 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2204 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2205 * .event.ActionEvent)
2207 protected void showConsensusHistogram_actionPerformed()
2209 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2210 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2217 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2218 * .event.ActionEvent)
2220 protected void showSequenceLogo_actionPerformed()
2222 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2223 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2226 protected void normSequenceLogo_actionPerformed()
2228 showSequenceLogo.setState(true);
2229 viewport.setShowSequenceLogo(true);
2230 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2231 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2234 protected void applyAutoAnnotationSettings_actionPerformed()
2236 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2239 protected void makeGrpsFromSelection_actionPerformed()
2241 if (avc.makeGroupsFromSelection())
2243 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2244 alignPanel.updateAnnotation();
2245 alignPanel.paintAlignment(true, true);
2249 protected void createGroup_actionPerformed()
2254 protected void unGroup_actionPerformed()
2258 alignPanel.alignmentChanged();
2262 protected void deleteGroups_actionPerformed()
2264 if (avc.deleteGroups())
2266 alignPanel.alignmentChanged();
2270 public void selectAllSequenceMenuItem_actionPerformed()
2272 SequenceGroup sg = new SequenceGroup();
2273 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2275 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2277 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2278 viewport.setSelectionGroup(sg);
2279 // JAL-2034 - should delegate to
2280 // alignPanel to decide if overview needs
2282 alignPanel.paintAlignment(false, false);
2283 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2284 viewport.sendSelection();
2287 public void deselectAllSequenceMenuItem_actionPerformed()
2289 if (viewport.cursorMode)
2291 alignPanel.seqPanel.keyboardNo1 = null;
2292 alignPanel.seqPanel.keyboardNo2 = null;
2294 viewport.setSelectionGroup(null);
2295 viewport.getColumnSelection().clear();
2296 viewport.setSelectionGroup(null);
2297 alignPanel.idPanel.idCanvas.searchResults = null;
2298 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2299 // JAL-2034 - should delegate to
2300 // alignPanel to decide if overview needs
2302 alignPanel.paintAlignment(false, false);
2303 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2304 viewport.sendSelection();
2307 public void invertSequenceMenuItem_actionPerformed()
2309 SequenceGroup sg = viewport.getSelectionGroup();
2310 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2312 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2315 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2316 viewport.sendSelection();
2319 public void invertColSel_actionPerformed()
2321 viewport.invertColumnSelection();
2322 alignPanel.paintAlignment(true, false);
2323 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2324 viewport.sendSelection();
2327 void trimAlignment(boolean trimLeft)
2329 AlignmentI al = viewport.getAlignment();
2330 ViewportRanges ranges = viewport.getRanges();
2331 ColumnSelection colSel = viewport.getColumnSelection();
2334 if (!colSel.isEmpty())
2338 column = colSel.getMin();
2342 column = colSel.getMax();
2346 if (viewport.getSelectionGroup() != null)
2348 seqs = viewport.getSelectionGroup()
2349 .getSequencesAsArray(viewport.getHiddenRepSequences());
2353 seqs = al.getSequencesArray();
2356 TrimRegionCommand trimRegion;
2359 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2361 ranges.setStartRes(0);
2365 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2369 statusBar.setText(MessageManager
2370 .formatMessage("label.removed_columns", new String[]
2371 { Integer.valueOf(trimRegion.getSize()).toString() }));
2372 addHistoryItem(trimRegion);
2374 for (SequenceGroup sg : al.getGroups())
2376 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2377 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2383 viewport.firePropertyChange("alignment", null, al.getSequences());
2387 public void removeGappedColumnMenuItem_actionPerformed()
2389 AlignmentI al = viewport.getAlignment();
2390 ViewportRanges ranges = viewport.getRanges();
2392 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2395 if (viewport.getSelectionGroup() != null)
2397 seqs = viewport.getSelectionGroup()
2398 .getSequencesAsArray(viewport.getHiddenRepSequences());
2399 start = viewport.getSelectionGroup().getStartRes();
2400 end = viewport.getSelectionGroup().getEndRes();
2404 seqs = viewport.getAlignment().getSequencesArray();
2407 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2408 "Remove Gapped Columns", seqs, start, end,
2409 viewport.getAlignment());
2411 addHistoryItem(removeGapCols);
2413 statusBar.setText(MessageManager
2414 .formatMessage("label.removed_empty_columns", new String[]
2415 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2417 // This is to maintain viewport position on first residue
2418 // of first sequence
2419 SequenceI seq = al.getSequenceAt(0);
2420 int startRes = seq.findPosition(ranges.getStartRes());
2421 // ShiftList shifts;
2422 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2423 // edit.alColumnChanges=shifts.getInverse();
2424 // if (viewport.hasHiddenColumns)
2425 // viewport.getColumnSelection().compensateForEdits(shifts);
2426 ranges.setStartRes(seq.findIndex(startRes) - 1);
2427 viewport.firePropertyChange("alignment", null, al.getSequences());
2431 public void removeAllGapsMenuItem_actionPerformed()
2433 AlignmentI al = viewport.getAlignment();
2434 ViewportRanges ranges = viewport.getRanges();
2436 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2439 if (viewport.getSelectionGroup() != null)
2441 seqs = viewport.getSelectionGroup()
2442 .getSequencesAsArray(viewport.getHiddenRepSequences());
2443 start = viewport.getSelectionGroup().getStartRes();
2444 end = viewport.getSelectionGroup().getEndRes();
2448 seqs = viewport.getAlignment().getSequencesArray();
2451 // This is to maintain viewport position on first residue
2452 // of first sequence
2453 SequenceI seq = al.getSequenceAt(0);
2454 int startRes = seq.findPosition(ranges.getStartRes());
2457 new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2459 ranges.setStartRes(seq.findIndex(startRes) - 1);
2461 viewport.firePropertyChange("alignment", null, al.getSequences());
2465 public void findMenuItem_actionPerformed()
2467 new Finder(alignPanel);
2471 * create a new view derived from the current view
2474 * @return frame for the new view
2476 public AlignFrame newView(String viewtitle)
2479 if (viewport.hasHiddenRows())
2481 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2482 .getFullAlignment().getSequencesArray());
2486 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2489 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2491 for (int i = 0; i < viewport.getAlignment()
2492 .getAlignmentAnnotation().length; i++)
2494 if (!viewport.getAlignment()
2495 .getAlignmentAnnotation()[i].autoCalculated)
2497 newal.addAnnotation(
2498 viewport.getAlignment().getAlignmentAnnotation()[i]);
2503 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2505 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2506 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2507 PaintRefresher.Register(newaf.alignPanel,
2508 newaf.alignPanel.av.getSequenceSetId());
2510 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2511 newaf.alignPanel.av.getSequenceSetId());
2512 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2513 newaf.alignPanel.av.getSequenceSetId());
2515 Vector comps = PaintRefresher.components
2516 .get(viewport.getSequenceSetId());
2518 for (int i = 0; i < comps.size(); i++)
2520 if (comps.elementAt(i) instanceof AlignmentPanel)
2526 String title = new String(this.getTitle());
2527 if (viewtitle != null)
2529 title = viewtitle + " ( " + title + ")";
2533 if (title.indexOf("(View") > -1)
2535 title = title.substring(0, title.indexOf("(View"));
2537 title += "(View " + viewSize + ")";
2540 newaf.setTitle(title.toString());
2542 newaf.viewport.setHistoryList(viewport.getHistoryList());
2543 newaf.viewport.setRedoList(viewport.getRedoList());
2549 * @return list of feature groups on the view
2551 public String[] getFeatureGroups()
2553 FeatureRenderer fr = null;
2554 if (alignPanel != null
2555 && (fr = alignPanel.getFeatureRenderer()) != null)
2557 List<String> gps = fr.getFeatureGroups();
2558 String[] _gps = gps.toArray(new String[gps.size()]);
2565 * get sequence feature groups that are hidden or shown
2571 public String[] getFeatureGroupsOfState(boolean visible)
2573 FeatureRenderer fr = null;
2574 if (alignPanel != null
2575 && (fr = alignPanel.getFeatureRenderer()) != null)
2577 List<String> gps = fr.getGroups(visible);
2578 String[] _gps = gps.toArray(new String[gps.size()]);
2585 * Change the display state for the given feature groups
2588 * list of group strings
2590 * visible or invisible
2592 public void setFeatureGroupState(String[] groups, boolean state)
2594 FeatureRenderer fr = null;
2595 this.sequenceFeatures.setState(true);
2596 viewport.setShowSequenceFeatures(true);
2597 if (alignPanel != null
2598 && (fr = alignPanel.getFeatureRenderer()) != null)
2601 fr.setGroupVisibility(Arrays.asList(groups), state);
2602 alignPanel.seqPanel.seqCanvas.repaint();
2603 if (alignPanel.overviewPanel != null)
2605 alignPanel.overviewPanel.updateOverviewImage();
2610 public void seqLimits_itemStateChanged()
2612 viewport.setShowJVSuffix(seqLimits.getState());
2613 alignPanel.fontChanged();
2614 alignPanel.paintAlignment(true, false);
2617 protected void colourTextMenuItem_actionPerformed()
2619 viewport.setColourText(colourTextMenuItem.getState());
2620 alignPanel.paintAlignment(false, false);
2623 protected void displayNonconservedMenuItem_actionPerformed()
2625 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2626 alignPanel.paintAlignment(false, false);
2629 protected void wrapMenuItem_actionPerformed()
2631 viewport.setWrapAlignment(wrapMenuItem.getState());
2632 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2633 scaleAbove.setEnabled(wrapMenuItem.getState());
2634 scaleLeft.setEnabled(wrapMenuItem.getState());
2635 scaleRight.setEnabled(wrapMenuItem.getState());
2636 alignPanel.paintAlignment(true, false);
2639 public void overviewMenuItem_actionPerformed()
2641 if (alignPanel.overviewPanel != null)
2646 Frame frame = new Frame();
2647 final OverviewPanel overview = new OverviewPanel(alignPanel);
2648 frame.add(overview);
2649 // +50 must allow for applet frame window
2650 jalview.bin.JalviewLite.addFrame(frame, MessageManager
2651 .formatMessage("label.overview_params", new String[]
2652 { this.getTitle() }), overview.getPreferredSize().width,
2653 overview.getPreferredSize().height + 50);
2656 final AlignmentPanel ap = alignPanel;
2657 frame.addWindowListener(new WindowAdapter()
2660 public void windowClosing(WindowEvent e)
2665 ap.setOverviewPanel(null);
2670 alignPanel.setOverviewPanel(overview);
2675 public void changeColour(ColourSchemeI cs)
2677 viewport.setGlobalColourScheme(cs);
2679 alignPanel.paintAlignment(true, true);
2682 protected void modifyPID_actionPerformed()
2684 if (viewport.getAbovePIDThreshold()
2685 && viewport.getGlobalColourScheme() != null)
2687 SliderPanel.setPIDSliderSource(alignPanel,
2688 viewport.getResidueShading(), alignPanel.getViewName());
2689 SliderPanel.showPIDSlider();
2693 protected void modifyConservation_actionPerformed()
2695 if (viewport.getConservationSelected()
2696 && viewport.getGlobalColourScheme() != null)
2698 SliderPanel.setConservationSlider(alignPanel,
2699 viewport.getResidueShading(), alignPanel.getViewName());
2700 SliderPanel.showConservationSlider();
2704 protected void conservationMenuItem_actionPerformed()
2706 boolean selected = conservationMenuItem.getState();
2707 modifyConservation.setEnabled(selected);
2708 viewport.setConservationSelected(selected);
2709 viewport.getResidueShading().setConservationApplied(selected);
2711 changeColour(viewport.getGlobalColourScheme());
2715 modifyConservation_actionPerformed();
2719 SliderPanel.hideConservationSlider();
2723 public void abovePIDThreshold_actionPerformed()
2725 boolean selected = abovePIDThreshold.getState();
2726 modifyPID.setEnabled(selected);
2727 viewport.setAbovePIDThreshold(selected);
2730 viewport.getResidueShading().setThreshold(0,
2731 viewport.isIgnoreGapsConsensus());
2734 changeColour(viewport.getGlobalColourScheme());
2738 modifyPID_actionPerformed();
2742 SliderPanel.hidePIDSlider();
2746 public void sortPairwiseMenuItem_actionPerformed()
2748 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2749 AlignmentSorter.sortByPID(viewport.getAlignment(),
2750 viewport.getAlignment().getSequenceAt(0));
2752 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2753 viewport.getAlignment()));
2754 alignPanel.paintAlignment(true, false);
2757 public void sortIDMenuItem_actionPerformed()
2759 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2760 AlignmentSorter.sortByID(viewport.getAlignment());
2762 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
2763 alignPanel.paintAlignment(true, false);
2766 public void sortLengthMenuItem_actionPerformed()
2768 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2769 AlignmentSorter.sortByLength(viewport.getAlignment());
2770 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2771 viewport.getAlignment()));
2772 alignPanel.paintAlignment(true, false);
2775 public void sortGroupMenuItem_actionPerformed()
2777 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2778 AlignmentSorter.sortByGroup(viewport.getAlignment());
2779 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2780 viewport.getAlignment()));
2781 alignPanel.paintAlignment(true, false);
2785 public void sortEValueMenuItem_actionPerformed()
2787 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2788 AlignmentSorter.sortByEValue(viewport.getAlignment());
2789 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2790 viewport.getAlignment()));
2791 alignPanel.paintAlignment(true, false);
2795 public void sortBitScoreMenuItem_actionPerformed()
2797 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2798 AlignmentSorter.sortByBitScore(viewport.getAlignment());
2799 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2800 viewport.getAlignment()));
2801 alignPanel.paintAlignment(true, false);
2805 public void removeRedundancyMenuItem_actionPerformed()
2807 new RedundancyPanel(alignPanel);
2810 public void pairwiseAlignmentMenuItem_actionPerformed()
2812 if (viewport.getSelectionGroup() != null
2813 && viewport.getSelectionGroup().getSize() > 1)
2815 Frame frame = new Frame();
2816 frame.add(new PairwiseAlignPanel(alignPanel));
2817 jalview.bin.JalviewLite.addFrame(frame,
2818 MessageManager.getString("action.pairwise_alignment"), 600,
2823 public void PCAMenuItem_actionPerformed()
2825 // are the sequences aligned?
2826 if (!viewport.getAlignment().isAligned(false))
2829 int Width = viewport.getAlignment().getWidth();
2831 for (int i = 0; i < viewport.getAlignment().getSequences()
2834 current = viewport.getAlignment().getSequenceAt(i);
2836 if (current.getLength() < Width)
2838 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2841 alignPanel.paintAlignment(false, false);
2844 if ((viewport.getSelectionGroup() != null
2845 && viewport.getSelectionGroup().getSize() < 4
2846 && viewport.getSelectionGroup().getSize() > 0)
2847 || viewport.getAlignment().getHeight() < 4)
2854 new PCAPanel(viewport);
2855 } catch (java.lang.OutOfMemoryError ex)
2861 public void averageDistanceTreeMenuItem_actionPerformed()
2863 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2864 "Average distance tree using PID");
2867 public void neighbourTreeMenuItem_actionPerformed()
2869 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2870 "Neighbour joining tree using PID");
2873 protected void njTreeBlosumMenuItem_actionPerformed()
2875 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2876 ScoreModels.getInstance().getBlosum62().getName(),
2877 "Neighbour joining tree using BLOSUM62");
2880 protected void avTreeBlosumMenuItem_actionPerformed()
2882 newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2883 ScoreModels.getInstance().getBlosum62().getName(),
2884 "Average distance tree using BLOSUM62");
2887 void newTreePanel(String type, String pwType, String title)
2889 // are the sequences aligned?
2890 if (!viewport.getAlignment().isAligned(false))
2893 int Width = viewport.getAlignment().getWidth();
2895 for (int i = 0; i < viewport.getAlignment().getSequences()
2898 current = viewport.getAlignment().getSequenceAt(i);
2900 if (current.getLength() < Width)
2902 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2905 alignPanel.paintAlignment(false, false);
2909 if ((viewport.getSelectionGroup() != null
2910 && viewport.getSelectionGroup().getSize() > 1)
2911 || (viewport.getAlignment().getHeight() > 1))
2913 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2915 addTreeMenuItem(tp, title);
2917 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2921 void loadTree_actionPerformed()
2923 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2924 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2925 cap.setTreeImport();
2926 Frame frame = new Frame();
2928 jalview.bin.JalviewLite.addFrame(frame,
2929 MessageManager.getString("label.paste_newick_file"), 400, 300);
2932 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2934 TreePanel tp = new TreePanel(alignPanel, treeFile,
2935 MessageManager.getString("label.load_tree_from_file"), tree);
2936 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2937 addTreeMenuItem(tp, treeFile);
2941 * sort the alignment using the given treePanel
2944 * tree used to sort view
2946 * string used for undo event name
2948 public void sortByTree(TreePanel treePanel, String title)
2950 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2951 AlignmentSorter.sortByTree(viewport.getAlignment(),
2952 treePanel.getTree());
2953 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2954 // HistoryItem.SORT));
2955 addHistoryItem(new OrderCommand(MessageManager
2956 .formatMessage("label.order_by_params", new String[]
2957 { title }), oldOrder, viewport.getAlignment()));
2958 alignPanel.paintAlignment(true, false);
2962 * Do any automatic reordering of the alignment and add the necessary bits to
2963 * the menu structure for the new tree
2968 protected void addTreeMenuItem(final TreePanel treePanel,
2971 final MenuItem item = new MenuItem(title);
2972 sortByTreeMenu.add(item);
2973 item.addActionListener(new java.awt.event.ActionListener()
2976 public void actionPerformed(ActionEvent evt)
2978 sortByTree(treePanel, title); // treePanel.getTitle());
2982 treePanel.addWindowListener(new WindowAdapter()
2985 public void windowOpened(WindowEvent e)
2987 if (viewport.sortByTree)
2989 sortByTree(treePanel, title);
2991 super.windowOpened(e);
2995 public void windowClosing(WindowEvent e)
2997 sortByTreeMenu.remove(item);
3002 public boolean sortBy(AlignmentOrder alorder, String undoname)
3004 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3005 if (viewport.applet.debug)
3007 System.err.println("Sorting " + alorder.getOrder().size()
3008 + " in alignment '" + getTitle() + "'");
3010 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3011 if (undoname != null)
3013 addHistoryItem(new OrderCommand(undoname, oldOrder,
3014 viewport.getAlignment()));
3016 alignPanel.paintAlignment(true, false);
3020 protected void documentation_actionPerformed()
3022 alignPanel.av.applet.openJalviewHelpUrl();
3025 protected void about_actionPerformed()
3028 class AboutPanel extends Canvas
3034 public AboutPanel(String version, String builddate)
3036 this.version = version;
3037 this.builddate = builddate;
3041 public void paint(Graphics g)
3043 g.setColor(Color.white);
3044 g.fillRect(0, 0, getSize().width, getSize().height);
3045 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3046 FontMetrics fm = g.getFontMetrics();
3047 int fh = fm.getHeight();
3049 g.setColor(Color.black);
3050 // TODO: update this text for each release or centrally store it for
3051 // lite and application
3052 g.setFont(new Font("Helvetica", Font.BOLD, 14));
3053 g.drawString(MessageManager
3054 .formatMessage("label.jalviewLite_release", new String[]
3055 { version }), x, y += fh);
3056 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3057 g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3059 { builddate }), x, y += fh);
3060 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3061 g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3063 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3064 x + 50, y += fh + 8);
3065 g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3067 g.drawString(MessageManager
3068 .getString("label.jalview_distribution_lists"), x, y += fh);
3069 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3072 MessageManager.getString("label.jalview_cite_1_authors"), x,
3074 g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3076 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3081 Frame frame = new Frame();
3082 frame.add(new AboutPanel(JalviewLite.getVersion(),
3083 JalviewLite.getBuildDate()));
3084 jalview.bin.JalviewLite.addFrame(frame,
3085 MessageManager.getString("label.jalview"), 580, 220);
3089 public void showURL(String url, String target)
3091 if (viewport.applet == null)
3093 System.out.println("Not running as applet - no browser available.");
3097 viewport.applet.showURL(url, target);
3101 // ////////////////////////////////////////////////////////////////////////////////
3102 // JBuilder Graphics here
3104 MenuBar alignFrameMenuBar = new MenuBar();
3106 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3108 MenuItem loadApplication = new MenuItem(
3109 MessageManager.getString("label.view_full_application"));
3111 MenuItem loadTree = new MenuItem(
3112 MessageManager.getString("label.load_associated_tree"));
3114 MenuItem loadAnnotations = new MenuItem(
3115 MessageManager.getString("label.load_features_annotations"));
3117 MenuItem outputFeatures = new MenuItem(
3118 MessageManager.getString("label.export_features"));
3120 MenuItem outputAnnotations = new MenuItem(
3121 MessageManager.getString("label.export_annotations"));
3123 MenuItem closeMenuItem = new MenuItem(
3124 MessageManager.getString("action.close"));
3126 MenuItem selectAllSequenceMenuItem = new MenuItem(
3127 MessageManager.getString("action.select_all"));
3129 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3130 MessageManager.getString("action.deselect_all"));
3132 MenuItem invertSequenceMenuItem = new MenuItem(
3133 MessageManager.getString("action.invert_selection"));
3135 MenuItem remove2LeftMenuItem = new MenuItem();
3137 MenuItem remove2RightMenuItem = new MenuItem();
3139 MenuItem removeGappedColumnMenuItem = new MenuItem();
3141 MenuItem removeAllGapsMenuItem = new MenuItem();
3143 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3145 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3147 MenuItem sortPairwiseMenuItem = new MenuItem();
3149 MenuItem sortIDMenuItem = new MenuItem();
3151 MenuItem sortLengthMenuItem = new MenuItem();
3153 MenuItem sortGroupMenuItem = new MenuItem();
3155 MenuItem sortEValueMenuItem = new MenuItem();
3157 MenuItem sortBitScoreMenuItem = new MenuItem();
3159 MenuItem removeRedundancyMenuItem = new MenuItem();
3161 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3163 MenuItem PCAMenuItem = new MenuItem();
3165 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3167 MenuItem neighbourTreeMenuItem = new MenuItem();
3169 BorderLayout borderLayout1 = new BorderLayout();
3171 public Label statusBar = new Label();
3173 MenuItem clustalColour = new MenuItem();
3175 MenuItem zappoColour = new MenuItem();
3177 MenuItem taylorColour = new MenuItem();
3179 MenuItem hydrophobicityColour = new MenuItem();
3181 MenuItem helixColour = new MenuItem();
3183 MenuItem strandColour = new MenuItem();
3185 MenuItem turnColour = new MenuItem();
3187 MenuItem buriedColour = new MenuItem();
3189 MenuItem purinePyrimidineColour = new MenuItem();
3191 // MenuItem RNAInteractionColour = new MenuItem();
3193 MenuItem RNAHelixColour = new MenuItem();
3195 MenuItem userDefinedColour = new MenuItem();
3197 MenuItem PIDColour = new MenuItem();
3199 MenuItem BLOSUM62Colour = new MenuItem();
3201 MenuItem tcoffeeColour = new MenuItem();
3203 MenuItem njTreeBlosumMenuItem = new MenuItem();
3205 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3207 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3209 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3211 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3213 MenuItem alProperties = new MenuItem(
3214 MessageManager.getString("label.alignment_props"));
3216 MenuItem overviewMenuItem = new MenuItem();
3218 MenuItem undoMenuItem = new MenuItem();
3220 MenuItem redoMenuItem = new MenuItem();
3222 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3224 MenuItem noColourmenuItem = new MenuItem();
3226 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3228 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3230 MenuItem findMenuItem = new MenuItem();
3232 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3234 MenuItem nucleotideColour = new MenuItem();
3236 MenuItem deleteGroups = new MenuItem();
3238 MenuItem grpsFromSelection = new MenuItem();
3240 MenuItem createGroup = new MenuItem();
3242 MenuItem unGroup = new MenuItem();
3244 MenuItem delete = new MenuItem();
3246 MenuItem copy = new MenuItem();
3248 MenuItem cut = new MenuItem();
3250 Menu pasteMenu = new Menu();
3252 MenuItem pasteNew = new MenuItem();
3254 MenuItem pasteThis = new MenuItem();
3256 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3258 MenuItem font = new MenuItem();
3260 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3262 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3264 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3266 MenuItem modifyPID = new MenuItem();
3268 MenuItem modifyConservation = new MenuItem();
3270 CheckboxMenuItem autoCalculate = null;
3272 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3273 "Sort Alignment With New Tree", true);
3275 Menu sortByTreeMenu = new Menu();
3277 MenuItem inputText = new MenuItem();
3279 MenuItem documentation = new MenuItem();
3281 MenuItem about = new MenuItem();
3283 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3285 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3287 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3289 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3291 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3293 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3295 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3297 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3299 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3302 * Initialise menus and other items
3306 private void jbInit() throws Exception
3308 setMenuBar(alignFrameMenuBar);
3311 * Configure File menu items and actions
3314 .setLabel(MessageManager.getString("label.input_from_textbox"));
3315 inputText.addActionListener(this);
3316 Menu outputTextboxMenu = new Menu(
3317 MessageManager.getString("label.out_to_textbox"));
3318 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3320 MenuItem item = new MenuItem(ff);
3322 item.addActionListener(new java.awt.event.ActionListener()
3325 public void actionPerformed(ActionEvent e)
3327 outputText_actionPerformed(e);
3331 outputTextboxMenu.add(item);
3333 closeMenuItem.addActionListener(this);
3334 loadApplication.addActionListener(this);
3335 loadTree.addActionListener(this);
3336 loadAnnotations.addActionListener(this);
3337 outputFeatures.addActionListener(this);
3338 outputAnnotations.addActionListener(this);
3341 * Configure Edit menu items and actions
3343 undoMenuItem.setEnabled(false);
3344 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3345 undoMenuItem.addActionListener(this);
3346 redoMenuItem.setEnabled(false);
3347 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3348 redoMenuItem.addActionListener(this);
3349 copy.setLabel(MessageManager.getString("action.copy"));
3350 copy.addActionListener(this);
3351 cut.setLabel(MessageManager.getString("action.cut"));
3352 cut.addActionListener(this);
3353 delete.setLabel(MessageManager.getString("action.delete"));
3354 delete.addActionListener(this);
3355 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3356 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3357 pasteNew.addActionListener(this);
3358 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3359 pasteThis.addActionListener(this);
3361 .setLabel(MessageManager.getString("action.remove_left"));
3362 remove2LeftMenuItem.addActionListener(this);
3363 remove2RightMenuItem
3364 .setLabel(MessageManager.getString("action.remove_right"));
3365 remove2RightMenuItem.addActionListener(this);
3366 removeGappedColumnMenuItem.setLabel(
3367 MessageManager.getString("action.remove_empty_columns"));
3368 removeGappedColumnMenuItem.addActionListener(this);
3369 removeAllGapsMenuItem
3370 .setLabel(MessageManager.getString("action.remove_all_gaps"));
3371 removeAllGapsMenuItem.addActionListener(this);
3372 removeRedundancyMenuItem
3373 .setLabel(MessageManager.getString("action.remove_redundancy"));
3374 removeRedundancyMenuItem.addActionListener(this);
3377 * Configure Select menu items and actions
3379 findMenuItem.setLabel(MessageManager.getString("action.find"));
3380 findMenuItem.addActionListener(this);
3381 selectAllSequenceMenuItem.addActionListener(this);
3382 deselectAllSequenceMenuItem.addActionListener(this);
3383 invertSequenceMenuItem.setLabel(
3384 MessageManager.getString("action.invert_sequence_selection"));
3385 invertSequenceMenuItem.addActionListener(this);
3386 invertColSel.setLabel(
3387 MessageManager.getString("action.invert_column_selection"));
3388 invertColSel.addActionListener(this);
3390 .setLabel(MessageManager.getString("action.undefine_groups"));
3391 deleteGroups.addActionListener(this);
3392 grpsFromSelection.setLabel(
3393 MessageManager.getString("action.make_groups_selection"));
3394 grpsFromSelection.addActionListener(this);
3395 createGroup.setLabel(MessageManager.getString("action.create_group"));
3396 createGroup.addActionListener(this);
3397 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3398 unGroup.addActionListener(this);
3400 annotationColumnSelection.setLabel(
3401 MessageManager.getString("action.select_by_annotation"));
3402 annotationColumnSelection.addActionListener(this);
3405 * Configure View menu items and actions
3407 newView.setLabel(MessageManager.getString("action.new_view"));
3408 newView.addActionListener(this);
3409 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3410 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3411 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3412 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3414 .setLabel(MessageManager.getString("label.selected_columns"));
3416 .setLabel(MessageManager.getString("label.selected_sequences"));
3417 hideAllButSelection.setLabel(
3418 MessageManager.getString("label.all_but_selected_region"));
3420 .setLabel(MessageManager.getString("label.selected_region"));
3421 showAllHidden.setLabel(
3422 MessageManager.getString("label.all_sequences_columns"));
3423 showColumns.addActionListener(this);
3424 showSeqs.addActionListener(this);
3425 hideColumns.addActionListener(this);
3426 hideSequences.addActionListener(this);
3427 hideAllButSelection.addActionListener(this);
3428 hideAllSelection.addActionListener(this);
3429 showAllHidden.addActionListener(this);
3431 .setLabel(MessageManager.getString("action.feature_settings"));
3432 featureSettings.addActionListener(this);
3433 sequenceFeatures.setLabel(
3434 MessageManager.getString("label.show_sequence_features"));
3435 sequenceFeatures.addItemListener(this);
3436 sequenceFeatures.setState(false);
3437 followMouseOverFlag.setLabel(
3438 MessageManager.getString("label.automatic_scrolling"));
3439 followMouseOverFlag.addItemListener(this);
3440 alProperties.addActionListener(this);
3442 .setLabel(MessageManager.getString("label.overview_window"));
3443 overviewMenuItem.addActionListener(this);
3446 * Configure Annotations menu items and actions
3448 annotationPanelMenuItem
3449 .setLabel(MessageManager.getString("label.show_annotations"));
3450 annotationPanelMenuItem.addItemListener(this);
3452 .setLabel(MessageManager.getString("label.group_consensus"));
3453 showGroupConservation
3454 .setLabel(MessageManager.getString("label.group_conservation"));
3455 showConsensusHistogram.setLabel(
3456 MessageManager.getString("label.show_consensus_histogram"));
3457 showSequenceLogo.setLabel(
3458 MessageManager.getString("label.show_consensus_logo"));
3459 normSequenceLogo.setLabel(
3460 MessageManager.getString("label.norm_consensus_logo"));
3461 applyAutoAnnotationSettings
3462 .setLabel(MessageManager.getString("label.apply_all_groups"));
3463 applyAutoAnnotationSettings.setState(true);
3464 Menu autoAnnMenu = new Menu(
3465 MessageManager.getString("label.autocalculated_annotation"));
3466 showGroupConsensus.addItemListener(this);
3467 showGroupConservation.addItemListener(this);
3468 showConsensusHistogram.addItemListener(this);
3469 showSequenceLogo.addItemListener(this);
3470 normSequenceLogo.addItemListener(this);
3471 applyAutoAnnotationSettings.addItemListener(this);
3472 showAlignmentAnnotations = new CheckboxMenuItem(
3473 MessageManager.getString("label.show_all_al_annotations"));
3474 showSequenceAnnotations = new CheckboxMenuItem(
3475 MessageManager.getString("label.show_all_seq_annotations"));
3476 sortAnnBySequence = new CheckboxMenuItem(
3477 MessageManager.getString("label.sort_annotations_by_sequence"));
3478 sortAnnByLabel = new CheckboxMenuItem(
3479 MessageManager.getString("label.sort_annotations_by_label"));
3480 showAutoFirst = new CheckboxMenuItem(
3481 MessageManager.getString("label.show_first"));
3482 showAutoFirst.setState(false); // pending applet parameter
3483 setShowAutoCalculatedAbove(showAutoFirst.getState());
3484 showAutoLast = new CheckboxMenuItem(
3485 MessageManager.getString("label.show_last"));
3486 showAutoLast.setState(!showAutoFirst.getState());
3487 showAlignmentAnnotations.addItemListener(this);
3488 showSequenceAnnotations.addItemListener(this);
3489 sortAnnBySequence.addItemListener(this);
3490 sortAnnByLabel.addItemListener(this);
3491 showAutoFirst.addItemListener(this);
3492 showAutoLast.addItemListener(this);
3495 * Configure Format menu items and actions
3497 font.setLabel(MessageManager.getString("action.font"));
3498 font.addActionListener(this);
3499 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3500 scaleAbove.setState(true);
3501 scaleAbove.setEnabled(false);
3502 scaleAbove.addItemListener(this);
3503 scaleLeft.setEnabled(false);
3504 scaleLeft.setState(true);
3505 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3506 scaleLeft.addItemListener(this);
3507 scaleRight.setEnabled(false);
3508 scaleRight.setState(true);
3509 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3510 scaleRight.addItemListener(this);
3511 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3512 viewBoxesMenuItem.setState(true);
3513 viewBoxesMenuItem.addItemListener(this);
3514 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3515 viewTextMenuItem.setState(true);
3516 viewTextMenuItem.addItemListener(this);
3518 .setLabel(MessageManager.getString("label.colour_text"));
3519 colourTextMenuItem.addItemListener(this);
3520 displayNonconservedMenuItem
3521 .setLabel(MessageManager.getString("label.show_non_conserved"));
3522 displayNonconservedMenuItem.addItemListener(this);
3523 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3524 wrapMenuItem.addItemListener(this);
3526 .setLabel(MessageManager.getString("action.show_gaps"));
3527 renderGapsMenuItem.setState(true);
3528 renderGapsMenuItem.addItemListener(this);
3529 centreColumnLabelFlag.setLabel(
3530 MessageManager.getString("label.centre_column_labels"));
3531 centreColumnLabelFlag.addItemListener(this);
3532 seqLimits.setState(true);
3534 MessageManager.getString("label.show_sequence_limits"));
3535 seqLimits.addItemListener(this);
3538 * Configure Colour menu items and actions
3540 applyToAllGroups.setLabel(
3541 MessageManager.getString("label.apply_colour_to_all_groups"));
3542 applyToAllGroups.setState(true);
3543 applyToAllGroups.addItemListener(this);
3544 clustalColour.setLabel(
3545 MessageManager.getString("label.colourScheme_clustal"));
3546 clustalColour.addActionListener(this);
3548 .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3549 zappoColour.addActionListener(this);
3550 taylorColour.setLabel(
3551 MessageManager.getString("label.colourScheme_taylor"));
3552 taylorColour.addActionListener(this);
3553 hydrophobicityColour.setLabel(
3554 MessageManager.getString("label.colourScheme_hydrophobic"));
3555 hydrophobicityColour.addActionListener(this);
3556 helixColour.setLabel(MessageManager
3557 .getString("label.colourScheme_helix_propensity"));
3558 helixColour.addActionListener(this);
3559 strandColour.setLabel(MessageManager
3560 .getString("label.colourScheme_strand_propensity"));
3561 strandColour.addActionListener(this);
3562 turnColour.setLabel(
3563 MessageManager.getString("label.colourScheme_turn_propensity"));
3564 turnColour.addActionListener(this);
3565 buriedColour.setLabel(
3566 MessageManager.getString("label.colourScheme_buried_index"));
3567 buriedColour.addActionListener(this);
3568 purinePyrimidineColour.setLabel(MessageManager
3569 .getString("label.colourScheme_purine/pyrimidine"));
3570 purinePyrimidineColour.addActionListener(this);
3571 // RNAInteractionColour.setLabel(MessageManager
3572 // .getString("label.rna_interaction"));
3573 // RNAInteractionColour.addActionListener(this);
3574 RNAHelixColour.setLabel(
3575 MessageManager.getString("label.colourScheme_rna_helices"));
3576 RNAHelixColour.addActionListener(this);
3578 .setLabel(MessageManager.getString("action.user_defined"));
3579 userDefinedColour.addActionListener(this);
3581 MessageManager.getString("label.colourScheme_%_identity"));
3582 PIDColour.addActionListener(this);
3583 BLOSUM62Colour.setLabel(
3584 MessageManager.getString("label.colourScheme_blosum62"));
3585 BLOSUM62Colour.addActionListener(this);
3586 tcoffeeColour.setLabel(
3587 MessageManager.getString("label.colourScheme_t-coffee_scores"));
3588 // it will be enabled only if a score file is provided
3589 tcoffeeColour.setEnabled(false);
3590 tcoffeeColour.addActionListener(this);
3591 conservationMenuItem
3592 .setLabel(MessageManager.getString("action.by_conservation"));
3593 conservationMenuItem.addItemListener(this);
3594 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3595 noColourmenuItem.addActionListener(this);
3596 abovePIDThreshold.setLabel(
3597 MessageManager.getString("label.above_identity_threshold"));
3598 abovePIDThreshold.addItemListener(this);
3599 nucleotideColour.setLabel(
3600 MessageManager.getString("label.colourScheme_nucleotide"));
3601 nucleotideColour.addActionListener(this);
3603 MessageManager.getString("label.modify_identity_threshold"));
3604 modifyPID.setEnabled(abovePIDThreshold.getState());
3605 modifyPID.addActionListener(this);
3606 modifyConservation.setLabel(MessageManager
3607 .getString("label.modify_conservation_threshold"));
3608 modifyConservation.setEnabled(conservationMenuItem.getState());
3609 modifyConservation.addActionListener(this);
3611 .setLabel(MessageManager.getString("action.by_annotation"));
3612 annotationColour.addActionListener(this);
3615 * Configure Calculate menu items and actions
3617 sortPairwiseMenuItem
3618 .setLabel(MessageManager.getString("action.by_pairwise_id"));
3619 sortPairwiseMenuItem.addActionListener(this);
3620 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3621 sortIDMenuItem.addActionListener(this);
3623 .setLabel(MessageManager.getString("action.by_length"));
3624 sortLengthMenuItem.addActionListener(this);
3625 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3626 sortGroupMenuItem.addActionListener(this);
3627 pairwiseAlignmentMenuItem.setLabel(
3628 MessageManager.getString("action.pairwise_alignment"));
3629 pairwiseAlignmentMenuItem.addActionListener(this);
3630 PCAMenuItem.setLabel(
3631 MessageManager.getString("label.principal_component_analysis"));
3632 PCAMenuItem.addActionListener(this);
3633 autoCalculate = new CheckboxMenuItem(
3634 MessageManager.getString("label.autocalculate_consensus"),
3636 averageDistanceTreeMenuItem.setLabel(
3637 MessageManager.getString("label.average_distance_identity"));
3638 averageDistanceTreeMenuItem.addActionListener(this);
3639 neighbourTreeMenuItem.setLabel(
3640 MessageManager.getString("label.neighbour_joining_identity"));
3641 neighbourTreeMenuItem.addActionListener(this);
3642 avDistanceTreeBlosumMenuItem.setLabel(
3643 MessageManager.getString("label.average_distance_blosum62"));
3644 avDistanceTreeBlosumMenuItem.addActionListener(this);
3645 njTreeBlosumMenuItem
3646 .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3647 njTreeBlosumMenuItem.addActionListener(this);
3649 .setLabel(MessageManager.getString("action.by_tree_order"));
3650 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3651 Menu calculateTreeMenu = new Menu(
3652 MessageManager.getString("action.calculate_tree"));
3653 autoCalculate.addItemListener(this);
3654 sortByTree.addItemListener(this);
3657 * Configure Help menu items and actions
3659 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3660 documentation.setLabel(MessageManager.getString("label.documentation"));
3661 documentation.addActionListener(this);
3662 about.setLabel(MessageManager.getString("label.about"));
3663 about.addActionListener(this);
3666 * Add top level menus to frame
3668 alignFrameMenuBar.add(fileMenu);
3669 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3670 alignFrameMenuBar.add(editMenu);
3671 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3672 alignFrameMenuBar.add(selectMenu);
3673 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3674 alignFrameMenuBar.add(viewMenu);
3675 Menu annotationsMenu = new Menu(
3676 MessageManager.getString("action.annotations"));
3677 alignFrameMenuBar.add(annotationsMenu);
3678 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3679 alignFrameMenuBar.add(formatMenu);
3680 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3681 alignFrameMenuBar.add(colourMenu);
3682 Menu calculateMenu = new Menu(
3683 MessageManager.getString("action.calculate"));
3684 alignFrameMenuBar.add(calculateMenu);
3685 alignFrameMenuBar.add(helpMenu);
3690 fileMenu.add(inputText);
3691 fileMenu.add(loadTree);
3692 fileMenu.add(loadAnnotations);
3693 fileMenu.addSeparator();
3694 fileMenu.add(outputTextboxMenu);
3695 fileMenu.add(outputFeatures);
3696 fileMenu.add(outputAnnotations);
3697 if (jalviewServletURL != null)
3699 fileMenu.add(loadApplication);
3701 fileMenu.addSeparator();
3702 fileMenu.add(closeMenuItem);
3707 editMenu.add(undoMenuItem);
3708 editMenu.add(redoMenuItem);
3711 pasteMenu.add(pasteNew);
3712 pasteMenu.add(pasteThis);
3713 editMenu.add(pasteMenu);
3714 editMenu.add(delete);
3715 editMenu.addSeparator();
3716 editMenu.add(remove2LeftMenuItem);
3717 editMenu.add(remove2RightMenuItem);
3718 editMenu.add(removeGappedColumnMenuItem);
3719 editMenu.add(removeAllGapsMenuItem);
3720 editMenu.add(removeRedundancyMenuItem);
3725 selectMenu.add(findMenuItem);
3726 selectMenu.addSeparator();
3727 selectMenu.add(selectAllSequenceMenuItem);
3728 selectMenu.add(deselectAllSequenceMenuItem);
3729 selectMenu.add(invertSequenceMenuItem);
3730 selectMenu.add(invertColSel);
3731 selectMenu.add(createGroup);
3732 selectMenu.add(unGroup);
3733 selectMenu.add(grpsFromSelection);
3734 selectMenu.add(deleteGroups);
3735 selectMenu.add(annotationColumnSelection);
3740 viewMenu.add(newView);
3741 viewMenu.addSeparator();
3742 showMenu.add(showColumns);
3743 showMenu.add(showSeqs);
3744 showMenu.add(showAllHidden);
3745 viewMenu.add(showMenu);
3746 hideMenu.add(hideColumns);
3747 hideMenu.add(hideSequences);
3748 hideMenu.add(hideAllSelection);
3749 hideMenu.add(hideAllButSelection);
3750 viewMenu.add(hideMenu);
3751 viewMenu.addSeparator();
3752 viewMenu.add(followMouseOverFlag);
3753 viewMenu.addSeparator();
3754 viewMenu.add(sequenceFeatures);
3755 viewMenu.add(featureSettings);
3756 viewMenu.addSeparator();
3757 viewMenu.add(alProperties);
3758 viewMenu.addSeparator();
3759 viewMenu.add(overviewMenuItem);
3764 annotationsMenu.add(annotationPanelMenuItem);
3765 annotationsMenu.addSeparator();
3766 annotationsMenu.add(showAlignmentAnnotations);
3767 annotationsMenu.add(showSequenceAnnotations);
3768 annotationsMenu.add(sortAnnBySequence);
3769 annotationsMenu.add(sortAnnByLabel);
3770 annotationsMenu.addSeparator();
3771 autoAnnMenu.add(showAutoFirst);
3772 autoAnnMenu.add(showAutoLast);
3773 autoAnnMenu.addSeparator();
3774 autoAnnMenu.add(applyAutoAnnotationSettings);
3775 autoAnnMenu.add(showConsensusHistogram);
3776 autoAnnMenu.add(showSequenceLogo);
3777 autoAnnMenu.add(normSequenceLogo);
3778 autoAnnMenu.addSeparator();
3779 autoAnnMenu.add(showGroupConservation);
3780 autoAnnMenu.add(showGroupConsensus);
3781 annotationsMenu.add(autoAnnMenu);
3786 formatMenu.add(font);
3787 formatMenu.add(seqLimits);
3788 formatMenu.add(wrapMenuItem);
3789 formatMenu.add(scaleAbove);
3790 formatMenu.add(scaleLeft);
3791 formatMenu.add(scaleRight);
3792 formatMenu.add(viewBoxesMenuItem);
3793 formatMenu.add(viewTextMenuItem);
3794 formatMenu.add(colourTextMenuItem);
3795 formatMenu.add(displayNonconservedMenuItem);
3796 formatMenu.add(renderGapsMenuItem);
3797 formatMenu.add(centreColumnLabelFlag);
3802 colourMenu.add(applyToAllGroups);
3803 colourMenu.addSeparator();
3804 colourMenu.add(noColourmenuItem);
3805 colourMenu.add(clustalColour);
3806 colourMenu.add(BLOSUM62Colour);
3807 colourMenu.add(PIDColour);
3808 colourMenu.add(zappoColour);
3809 colourMenu.add(taylorColour);
3810 colourMenu.add(hydrophobicityColour);
3811 colourMenu.add(helixColour);
3812 colourMenu.add(strandColour);
3813 colourMenu.add(turnColour);
3814 colourMenu.add(buriedColour);
3815 colourMenu.add(nucleotideColour);
3816 colourMenu.add(purinePyrimidineColour);
3817 // colourMenu.add(RNAInteractionColour);
3818 colourMenu.add(tcoffeeColour);
3819 colourMenu.add(userDefinedColour);
3820 colourMenu.addSeparator();
3821 colourMenu.add(conservationMenuItem);
3822 colourMenu.add(modifyConservation);
3823 colourMenu.add(abovePIDThreshold);
3824 colourMenu.add(modifyPID);
3825 colourMenu.add(annotationColour);
3826 colourMenu.add(RNAHelixColour);
3831 sortMenu.add(sortIDMenuItem);
3832 sortMenu.add(sortLengthMenuItem);
3833 sortMenu.add(sortByTreeMenu);
3834 sortMenu.add(sortGroupMenuItem);
3835 sortMenu.add(sortPairwiseMenuItem);
3836 calculateMenu.add(sortMenu);
3837 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3838 calculateTreeMenu.add(neighbourTreeMenuItem);
3839 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3840 calculateTreeMenu.add(njTreeBlosumMenuItem);
3841 calculateMenu.add(calculateTreeMenu);
3842 calculateMenu.addSeparator();
3843 calculateMenu.add(pairwiseAlignmentMenuItem);
3844 calculateMenu.add(PCAMenuItem);
3845 calculateMenu.add(autoCalculate);
3846 calculateMenu.add(sortByTree);
3851 helpMenu.add(documentation);
3852 helpMenu.add(about);
3857 statusBar.setBackground(Color.white);
3858 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3859 statusBar.setText(MessageManager.getString("label.status_bar"));
3860 this.add(statusBar, BorderLayout.SOUTH);
3864 public void setStatus(String string)
3866 statusBar.setText(string);
3869 MenuItem featureSettings = new MenuItem();
3871 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3873 MenuItem annotationColour = new MenuItem();
3875 MenuItem annotationColumnSelection = new MenuItem();
3877 MenuItem invertColSel = new MenuItem();
3879 MenuItem showColumns = new MenuItem();
3881 MenuItem showSeqs = new MenuItem();
3883 MenuItem hideColumns = new MenuItem();
3885 MenuItem hideSequences = new MenuItem();
3887 MenuItem hideAllButSelection = new MenuItem();
3889 MenuItem hideAllSelection = new MenuItem();
3891 MenuItem showAllHidden = new MenuItem();
3893 MenuItem newView = new MenuItem();
3895 private CheckboxMenuItem showAlignmentAnnotations;
3897 private CheckboxMenuItem showSequenceAnnotations;
3899 private CheckboxMenuItem sortAnnBySequence;
3901 private CheckboxMenuItem sortAnnByLabel;
3903 private CheckboxMenuItem showAutoFirst;
3905 private CheckboxMenuItem showAutoLast;
3907 private SplitFrame splitFrame;
3910 * Attach the alignFrame panels after embedding menus, if necessary. This used
3911 * to be called setEmbedded, but is now creates the dropdown menus in a
3912 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3914 * @param reallyEmbedded
3915 * true to attach the view to the applet area on the page rather than
3918 public void createAlignFrameWindow(boolean reallyEmbedded)
3922 embedAlignFrameInApplet(viewport.applet);
3927 // test and embed menu bar if necessary.
3929 if (embedMenuIfNeeded(alignPanel))
3932 * adjust for status bar height too. ? pointless as overridden by layout
3935 alignPanel.setSize(getSize().width,
3936 getSize().height - statusBar.getHeight());
3938 add(statusBar, BorderLayout.SOUTH);
3939 add(alignPanel, BorderLayout.CENTER);
3940 // and register with the applet so it can pass external API calls to us
3941 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3947 * Add the components of this AlignFrame to the applet container.
3951 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3954 // Explicitly build the embedded menu panel for the on-page applet
3956 // view cannot be closed if its actually on the page
3957 fileMenu.remove(closeMenuItem);
3958 fileMenu.remove(3); // Remove Separator
3959 // construct embedded menu, using default font
3960 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3961 // and actually add the components to the applet area
3962 theApplet.setLayout(new BorderLayout());
3963 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3964 theApplet.add(statusBar, BorderLayout.SOUTH);
3965 // TODO should size be left to the layout manager?
3966 alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3967 - embeddedMenu.getHeight() - statusBar.getHeight());
3968 theApplet.add(alignPanel, BorderLayout.CENTER);
3969 final AlignFrame me = this;
3970 theApplet.addFocusListener(new FocusListener()
3974 public void focusLost(FocusEvent e)
3976 if (theApplet.currentAlignFrame == me)
3978 theApplet.currentAlignFrame = null;
3983 public void focusGained(FocusEvent e)
3985 theApplet.currentAlignFrame = me;
3988 theApplet.validate();
3992 * create a new binding between structures in an existing jmol viewer instance
3993 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3994 * this does not open a new Jmol window, or modify the display of the
3995 * structures in the original jmol window. Note This method doesn't work
3996 * without an additional javascript library to exchange messages between the
3997 * distinct applets. See http://issues.jalview.org/browse/JAL-621
4000 * JmolViewer instance
4001 * @param sequenceIds
4002 * - sequence Ids to search for associations
4004 public SequenceStructureBinding addStructureViewInstance(
4005 Object jmolviewer, String[] sequenceIds)
4007 Viewer viewer = null;
4010 viewer = (Viewer) jmolviewer;
4011 } catch (ClassCastException ex)
4014 "Unsupported viewer object :" + jmolviewer.getClass());
4018 System.err.println("Can't use this object as a structure viewer:"
4019 + jmolviewer.getClass());
4022 SequenceI[] seqs = null;
4023 if (sequenceIds == null || sequenceIds.length == 0)
4025 seqs = viewport.getAlignment().getSequencesArray();
4029 Vector sqi = new Vector();
4030 AlignmentI al = viewport.getAlignment();
4031 for (int sid = 0; sid < sequenceIds.length; sid++)
4033 SequenceI sq = al.findName(sequenceIds[sid]);
4041 seqs = new SequenceI[sqi.size()];
4042 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4044 seqs[sid] = (SequenceI) sqi.elementAt(sid);
4052 AAStructureBindingModel jmv = null;
4053 // TODO: search for a jmv that involves viewer
4055 { // create a new viewer/jalview binding.
4056 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4063 * bind a pdb file to a sequence in the current view
4066 * - sequenceId within the dataset.
4067 * @param pdbEntryString
4068 * - the short name for the PDB file
4070 * - pdb file - either a URL or a valid PDB file.
4071 * @return true if binding was as success TODO: consider making an exception
4072 * structure for indicating when PDB parsing or sequenceId location
4075 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4078 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4079 boolean needtoadd = false;
4080 if (toaddpdb != null)
4082 Vector pdbe = toaddpdb.getAllPDBEntries();
4083 PDBEntry pdbentry = null;
4084 if (pdbe != null && pdbe.size() > 0)
4086 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4088 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4089 if (!pdbentry.getId().equals(pdbEntryString)
4090 && !pdbentry.getFile().equals(pdbFile))
4100 if (pdbentry == null)
4102 pdbentry = new PDBEntry();
4103 pdbentry.setId(pdbEntryString);
4104 pdbentry.setFile(pdbFile);
4105 needtoadd = true; // add this new entry to sequence.
4107 // resolve data source
4108 // TODO: this code should be a refactored to an io package
4109 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4111 if (protocol == null)
4117 pdbentry.setProperty("protocol", protocol);
4118 toaddpdb.addPDBId(pdbentry);
4119 alignPanel.getStructureSelectionManager()
4120 .registerPDBEntry(pdbentry);
4126 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4130 Vector sequences = new Vector();
4131 for (int i = 0; i < seqs.length; i++)
4133 if (seqs[i] != null)
4136 .addElement(new Object[]
4137 { seqs[i], (chains != null) ? chains[i] : null });
4140 seqs = new SequenceI[sequences.size()];
4141 chains = new String[sequences.size()];
4142 for (int i = 0, isize = sequences.size(); i < isize; i++)
4144 Object[] oj = (Object[]) sequences.elementAt(i);
4146 seqs[i] = (SequenceI) oj[0];
4147 chains[i] = (String) oj[1];
4150 return new Object[] { seqs, chains };
4154 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4155 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4157 // Scrub any null sequences from the array
4158 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4159 seqs = (SequenceI[]) sqch[0];
4160 chains = (String[]) sqch[1];
4161 if (seqs == null || seqs.length == 0)
4164 "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4166 if (protocol == null)
4168 String sourceType = (String) pdb.getProperty("protocol");
4171 protocol = DataSourceType.valueOf(sourceType);
4172 } catch (IllegalArgumentException e)
4176 if (protocol == null)
4178 System.err.println("Couldn't work out protocol to open structure: "
4183 if (applet.useXtrnalSviewer)
4185 // register the association(s) and quit, don't create any windows.
4186 if (StructureSelectionManager.getStructureSelectionManager(applet)
4187 .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
4189 System.err.println("Failed to map " + pdb.getFile() + " ("
4190 + protocol + ") to any sequences");
4194 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4196 // can only do alignments with Jmol
4197 // find the last jmol window assigned to this alignment
4198 AppletJmol ajm = null, tajm;
4199 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4200 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4202 tajm = (AppletJmol) jmols.elementAt(i);
4203 if (tajm.ap.alignFrame == this)
4212 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4213 // try and add the pdb structure
4218 // otherwise, create a new window
4219 if (applet.jmolAvailable)
4221 new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4222 applet.lastFrameX += 40;
4223 applet.lastFrameY += 40;
4227 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4232 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4233 SequenceI[][] seqs, String[][] chains, String[] protocols)
4235 // TODO Auto-generated method stub
4236 System.err.println("Aligned Structure View: Not yet implemented.");
4240 * modify the current selection, providing the user has not made a selection
4244 * - sequences from this alignment
4246 * - columns to be selected on the alignment
4248 public void select(SequenceGroup sel, ColumnSelection csel,
4249 HiddenColumns hidden)
4251 alignPanel.seqPanel.selection(sel, csel, hidden, null);
4254 public void scrollTo(int row, int column)
4256 alignPanel.seqPanel.scrollTo(row, column);
4259 public void scrollToRow(int row)
4261 alignPanel.seqPanel.scrollToRow(row);
4264 public void scrollToColumn(int column)
4266 alignPanel.seqPanel.scrollToColumn(column);
4270 * @return the alignments unique ID.
4272 public String getSequenceSetId()
4274 return viewport.getSequenceSetId();
4278 * Load the (T-Coffee) score file from the specified url
4281 * File/URL/T-COFFEE score file contents
4282 * @throws IOException
4283 * @return true if alignment was annotated with data from source
4285 public boolean loadScoreFile(String source) throws IOException
4288 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4289 AppletFormatAdapter.checkProtocol(source));
4290 if (!file.isValid())
4292 // TODO: raise dialog for gui
4293 System.err.println("Problems parsing T-Coffee scores: "
4294 + file.getWarningMessage());
4295 System.err.println("Origin was:\n" + source);
4300 * check that the score matrix matches the alignment dimensions
4303 if ((aln = viewport.getAlignment()) != null
4304 && (aln.getHeight() != file.getHeight()
4305 || aln.getWidth() != file.getWidth()))
4307 // TODO: raise a dialog box here rather than bomb out.
4309 "The scores matrix does not match the alignment dimensions");
4313 // TODO add parameter to indicate if matching should be done
4314 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4316 alignPanel.fontChanged();
4317 tcoffeeColour.setEnabled(true);
4318 // switch to this color
4319 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4324 System.err.println("Problems resolving T-Coffee scores:");
4325 if (file.getWarningMessage() != null)
4327 System.err.println(file.getWarningMessage());
4333 public SplitFrame getSplitFrame()
4335 return this.splitFrame;
4338 public void setSplitFrame(SplitFrame sf)
4340 this.splitFrame = sf;
4343 // may not need this
4345 public void setShowSeqFeatures(boolean b)
4347 // showSeqFeatures.setSelected(b);
4348 viewport.setShowSequenceFeatures(b);
4353 public void setMenusForViewport()
4355 // setMenusFromViewport(viewport);
4360 public void refreshFeatureUI(boolean enableIfNecessary)
4362 if (enableIfNecessary)
4364 sequenceFeatures.setState(true);
4365 alignPanel.av.setShowSequenceFeatures(true);
4370 public FeatureSettingsControllerI getFeatureSettingsUI()
4372 return alignPanel.av.featureSettings;
4376 public FeatureSettingsControllerI showFeatureSettingsUI()
4378 return new FeatureSettings(alignPanel);
4381 private Rectangle fs_bounds = null;
4384 public void setFeatureSettingsGeometry(Rectangle bounds)
4390 public Rectangle getFeatureSettingsGeometry()