2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
25 import jalview.analysis.TreeBuilder;
26 import jalview.analysis.scoremodels.PIDModel;
27 import jalview.analysis.scoremodels.ScoreModels;
28 import jalview.api.AlignViewControllerGuiI;
29 import jalview.api.AlignViewControllerI;
30 import jalview.api.AlignViewportI;
31 import jalview.api.FeatureColourI;
32 import jalview.api.FeatureRenderer;
33 import jalview.api.FeatureSettingsControllerI;
34 import jalview.api.SequenceStructureBinding;
35 import jalview.bin.JalviewLite;
36 import jalview.commands.CommandI;
37 import jalview.commands.EditCommand;
38 import jalview.commands.EditCommand.Action;
39 import jalview.commands.OrderCommand;
40 import jalview.commands.RemoveGapColCommand;
41 import jalview.commands.RemoveGapsCommand;
42 import jalview.commands.SlideSequencesCommand;
43 import jalview.commands.TrimRegionCommand;
44 import jalview.datamodel.Alignment;
45 import jalview.datamodel.AlignmentAnnotation;
46 import jalview.datamodel.AlignmentI;
47 import jalview.datamodel.AlignmentOrder;
48 import jalview.datamodel.ColumnSelection;
49 import jalview.datamodel.HiddenColumns;
50 import jalview.datamodel.PDBEntry;
51 import jalview.datamodel.Sequence;
52 import jalview.datamodel.SequenceGroup;
53 import jalview.datamodel.SequenceI;
54 import jalview.io.AnnotationFile;
55 import jalview.io.AppletFormatAdapter;
56 import jalview.io.DataSourceType;
57 import jalview.io.FeaturesFile;
58 import jalview.io.FileFormat;
59 import jalview.io.FileFormatI;
60 import jalview.io.FileFormats;
61 import jalview.io.TCoffeeScoreFile;
62 import jalview.schemes.Blosum62ColourScheme;
63 import jalview.schemes.BuriedColourScheme;
64 import jalview.schemes.ClustalxColourScheme;
65 import jalview.schemes.ColourSchemeI;
66 import jalview.schemes.HelixColourScheme;
67 import jalview.schemes.HydrophobicColourScheme;
68 import jalview.schemes.NucleotideColourScheme;
69 import jalview.schemes.PIDColourScheme;
70 import jalview.schemes.PurinePyrimidineColourScheme;
71 import jalview.schemes.RNAHelicesColour;
72 import jalview.schemes.StrandColourScheme;
73 import jalview.schemes.TCoffeeColourScheme;
74 import jalview.schemes.TaylorColourScheme;
75 import jalview.schemes.TurnColourScheme;
76 import jalview.schemes.ZappoColourScheme;
77 import jalview.structure.StructureSelectionManager;
78 import jalview.structures.models.AAStructureBindingModel;
79 import jalview.util.MappingUtils;
80 import jalview.util.MessageManager;
81 import jalview.viewmodel.AlignmentViewport;
82 import jalview.viewmodel.ViewportRanges;
84 import java.awt.BorderLayout;
85 import java.awt.Canvas;
86 import java.awt.CheckboxMenuItem;
87 import java.awt.Color;
88 import java.awt.FlowLayout;
90 import java.awt.FontMetrics;
91 import java.awt.Frame;
92 import java.awt.Graphics;
93 import java.awt.Label;
95 import java.awt.MenuBar;
96 import java.awt.MenuItem;
97 import java.awt.Panel;
98 import java.awt.event.ActionEvent;
99 import java.awt.event.ActionListener;
100 import java.awt.event.FocusEvent;
101 import java.awt.event.FocusListener;
102 import java.awt.event.ItemEvent;
103 import java.awt.event.ItemListener;
104 import java.awt.event.KeyEvent;
105 import java.awt.event.KeyListener;
106 import java.awt.event.WindowAdapter;
107 import java.awt.event.WindowEvent;
108 import java.io.IOException;
109 import java.io.UnsupportedEncodingException;
111 import java.net.URLEncoder;
112 import java.util.Arrays;
113 import java.util.Deque;
114 import java.util.HashMap;
115 import java.util.List;
116 import java.util.Map;
117 import java.util.StringTokenizer;
118 import java.util.Vector;
120 import org.jmol.viewer.Viewer;
122 public class AlignFrame extends EmbmenuFrame implements ActionListener,
123 ItemListener, KeyListener, AlignViewControllerGuiI
125 public AlignViewControllerI avc;
127 public AlignmentPanel alignPanel;
129 public AlignViewport viewport;
131 // width and height may be overridden by applet parameters
132 int frameWidth = 700;
134 int frameHeight = 500;
136 String jalviewServletURL;
139 * Flag for showing autocalculated consensus above or below other consensus
142 private boolean showAutoCalculatedAbove;
144 private SequenceAnnotationOrder annotationSortOrder;
147 * Constructor that creates the frame and adds it to the display.
154 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
157 this(al, applet, title, embedded, true);
161 * Constructor that optionally allows the frame to be displayed or only
168 * @param addToDisplay
170 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
171 boolean embedded, boolean addToDisplay)
173 this(al, null, null, applet, title, embedded, addToDisplay);
176 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
177 HiddenColumns hidden, JalviewLite applet, String title,
180 this(al, hiddenSeqs, hidden, applet, title, embedded, true);
183 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
184 HiddenColumns hidden, JalviewLite applet, String title,
185 boolean embedded, boolean addToDisplay)
189 jalviewServletURL = applet.getParameter("APPLICATION_URL");
195 } catch (Exception ex)
197 ex.printStackTrace();
199 // need to get window geometry before we calculate alignment layout
205 param = applet.getParameter("windowWidth");
208 int width = Integer.parseInt(param);
211 param = applet.getParameter("windowHeight");
214 int height = Integer.parseInt(param);
215 frameHeight = height;
217 } catch (Exception ex)
221 viewport = new AlignViewport(al, applet);
223 if (hiddenSeqs != null && hiddenSeqs.length > 0)
225 viewport.hideSequence(hiddenSeqs);
229 viewport.getAlignment().setHiddenColumns(hidden);
231 viewport.setScaleAboveWrapped(scaleAbove.getState());
233 alignPanel = new AlignmentPanel(this, viewport);
234 avc = new jalview.controller.AlignViewController(this, viewport,
236 viewport.updateConservation(alignPanel);
237 viewport.updateConsensus(alignPanel);
238 viewport.initInformationWorker(alignPanel);
240 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
241 followMouseOverFlag.setState(viewport.isFollowHighlight());
242 showGroupConsensus.setState(viewport.isShowGroupConsensus());
243 showGroupConservation.setState(viewport.isShowGroupConservation());
244 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
245 showSequenceLogo.setState(viewport.isShowSequenceLogo());
246 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
247 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
248 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
249 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
250 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
251 showAlignmentAnnotations.setState(true);
252 showSequenceAnnotations.setState(false);
254 seqLimits.setState(viewport.getShowJVSuffix());
258 String param = applet.getParameter("sortBy");
261 if (param.equalsIgnoreCase("Id"))
263 sortIDMenuItem_actionPerformed();
265 else if (param.equalsIgnoreCase("Pairwise Identity"))
267 sortPairwiseMenuItem_actionPerformed();
269 else if (param.equalsIgnoreCase("Length"))
271 sortLengthMenuItem_actionPerformed();
275 param = applet.getParameter("wrap");
278 if (param.equalsIgnoreCase("true"))
280 wrapMenuItem.setState(true);
281 wrapMenuItem_actionPerformed();
284 param = applet.getParameter("centrecolumnlabels");
287 centreColumnLabelFlag.setState(true);
288 centreColumnLabelFlag_stateChanged();
292 if (viewport.getAlignment().isNucleotide())
294 conservationMenuItem.setEnabled(false);
295 clustalColour.setEnabled(false);
296 BLOSUM62Colour.setEnabled(false);
297 zappoColour.setEnabled(false);
298 taylorColour.setEnabled(false);
299 hydrophobicityColour.setEnabled(false);
300 helixColour.setEnabled(false);
301 strandColour.setEnabled(false);
302 turnColour.setEnabled(false);
303 buriedColour.setEnabled(false);
304 viewport.updateStrucConsensus(alignPanel);
305 if (viewport.getAlignment().hasRNAStructure())
307 RNAHelixColour.setEnabled(true);
311 RNAHelixColour.setEnabled(false);
316 RNAHelixColour.setEnabled(false);
317 purinePyrimidineColour.setEnabled(false);
318 nucleotideColour.setEnabled(false);
320 // Some JVMS send keyevents to Top frame or lowest panel,
321 // Havent worked out why yet. So add to both this frame and seqCanvas for
323 this.addKeyListener(this);
324 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
325 alignPanel.idPanel.idCanvas.addKeyListener(this);
326 alignPanel.scalePanel.addKeyListener(this);
327 alignPanel.annotationPanel.addKeyListener(this);
328 alignPanel.annotationPanelHolder.addKeyListener(this);
329 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
330 alignPanel.alabels.addKeyListener(this);
332 setAnnotationsVisibility();
336 addToDisplay(embedded);
343 public void addToDisplay(boolean embedded)
345 createAlignFrameWindow(embedded);
347 alignPanel.adjustAnnotationHeight();
348 alignPanel.paintAlignment(true, true);
351 public AlignViewport getAlignViewport()
356 public SeqCanvas getSeqcanvas()
358 return alignPanel.seqPanel.seqCanvas;
362 * Load a features file onto the alignment
365 * file URL, content, or other resolvable path
367 * is protocol for accessing data referred to by file
370 public boolean parseFeaturesFile(String file, DataSourceType type)
372 return parseFeaturesFile(file, type, true);
376 * Load a features file onto the alignment
379 * file URL, content, or other resolvable path
381 * is protocol for accessing data referred to by file
382 * @param autoenabledisplay
383 * when true, display features flag will be automatically enabled if
384 * features are loaded
385 * @return true if data parsed as a features file
387 public boolean parseFeaturesFile(String file, DataSourceType sourceType,
388 boolean autoenabledisplay)
390 boolean featuresFile = false;
393 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
394 .getFeatureRenderer().getFeatureColours();
395 boolean relaxedIdMatching = viewport.applet
396 .getDefaultParameter("relaxedidmatch", false);
397 featuresFile = new FeaturesFile(file, sourceType).parse(
398 viewport.getAlignment(), colours, true, relaxedIdMatching);
399 } catch (Exception ex)
401 ex.printStackTrace();
406 if (autoenabledisplay)
408 viewport.setShowSequenceFeatures(true);
409 sequenceFeatures.setState(true);
411 if (alignPanel.seqPanel.seqCanvas.fr != null)
413 // update the min/max ranges where necessary
414 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
416 if (viewport.featureSettings != null)
418 viewport.featureSettings.refreshTable();
420 alignPanel.paintAlignment(true, true);
421 statusBar.setText(MessageManager
422 .getString("label.successfully_added_features_alignment"));
428 public void keyPressed(KeyEvent evt)
430 ViewportRanges ranges = viewport.getRanges();
432 if (viewport.cursorMode
433 && ((evt.getKeyCode() >= KeyEvent.VK_0
434 && evt.getKeyCode() <= KeyEvent.VK_9)
435 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
436 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
437 && Character.isDigit(evt.getKeyChar()))
439 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
442 switch (evt.getKeyCode())
444 case 27: // escape key
445 deselectAllSequenceMenuItem_actionPerformed();
447 alignPanel.alabels.cancelDrag();
450 if (evt.isControlDown() || evt.isMetaDown())
452 cut_actionPerformed();
456 if (viewport.cursorMode && !evt.isControlDown())
458 alignPanel.seqPanel.setCursorColumn();
460 if (evt.isControlDown() || evt.isMetaDown())
462 copy_actionPerformed();
466 if (evt.isControlDown())
468 paste(evt.isShiftDown());
472 if (evt.isControlDown() || evt.isMetaDown())
474 selectAllSequenceMenuItem_actionPerformed();
477 case KeyEvent.VK_DOWN:
478 if (viewport.cursorMode)
480 alignPanel.seqPanel.moveCursor(0, 1);
484 moveSelectedSequences(false);
489 if (viewport.cursorMode)
491 alignPanel.seqPanel.moveCursor(0, -1);
495 moveSelectedSequences(true);
499 case KeyEvent.VK_LEFT:
500 if (evt.isAltDown() || !viewport.cursorMode)
502 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
506 alignPanel.seqPanel.moveCursor(-1, 0);
510 case KeyEvent.VK_RIGHT:
511 if (evt.isAltDown() || !viewport.cursorMode)
513 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
517 alignPanel.seqPanel.moveCursor(1, 0);
521 case KeyEvent.VK_SPACE:
522 if (viewport.cursorMode)
524 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
525 || evt.isShiftDown() || evt.isAltDown());
529 case KeyEvent.VK_DELETE:
530 case KeyEvent.VK_BACK_SPACE:
531 if (viewport.cursorMode)
533 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
534 || evt.isShiftDown() || evt.isAltDown());
538 cut_actionPerformed();
539 alignPanel.seqPanel.seqCanvas.repaint();
544 if (viewport.cursorMode)
546 alignPanel.seqPanel.setCursorRow();
550 if (viewport.cursorMode)
552 alignPanel.seqPanel.setCursorPosition();
556 case KeyEvent.VK_ENTER:
557 case KeyEvent.VK_COMMA:
558 if (viewport.cursorMode)
560 alignPanel.seqPanel.setCursorRowAndColumn();
565 if (viewport.cursorMode)
567 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
571 if (viewport.cursorMode)
573 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
578 viewport.cursorMode = !viewport.cursorMode;
579 statusBar.setText(MessageManager
580 .formatMessage("label.keyboard_editing_mode", new String[]
581 { (viewport.cursorMode ? "on" : "off") }));
582 if (viewport.cursorMode)
584 alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
585 alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
590 if (evt.isControlDown())
592 findMenuItem_actionPerformed();
598 boolean toggleSeqs = !evt.isControlDown();
599 boolean toggleCols = !evt.isShiftDown();
600 toggleHiddenRegions(toggleSeqs, toggleCols);
604 case KeyEvent.VK_PAGE_UP:
608 case KeyEvent.VK_PAGE_DOWN:
613 if (evt.isControlDown())
615 undoMenuItem_actionPerformed();
620 if (evt.isControlDown())
622 redoMenuItem_actionPerformed();
627 if (evt.isControlDown())
634 if (evt.isControlDown())
636 trimAlignment(false);
641 if (evt.isControlDown())
643 if (evt.isShiftDown())
645 this.removeAllGapsMenuItem_actionPerformed();
649 removeGappedColumnMenuItem_actionPerformed();
654 if (evt.isControlDown())
658 invertColSel_actionPerformed();
662 invertSequenceMenuItem_actionPerformed();
668 if (evt.isControlDown())
670 if (evt.isShiftDown())
672 this.unGroup_actionPerformed();
676 this.createGroup_actionPerformed();
682 if (evt.isControlDown())
684 this.deleteGroups_actionPerformed();
689 if (evt.isControlDown())
696 // TODO: repaint flags set only if the keystroke warrants it
697 alignPanel.paintAlignment(true, true);
701 * called by key handler and the hide all/show all menu items
706 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
708 boolean hide = false;
709 SequenceGroup sg = viewport.getSelectionGroup();
710 if (!toggleSeqs && !toggleCols)
712 // Hide everything by the current selection - this is a hack - we do the
713 // invert and then hide
714 // first check that there will be visible columns after the invert.
715 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
716 && sg.getStartRes() <= sg.getEndRes()))
718 // now invert the sequence set, if required - empty selection implies
719 // that no hiding is required.
722 invertSequenceMenuItem_actionPerformed();
723 sg = viewport.getSelectionGroup();
727 viewport.expandColSelection(sg, true);
728 // finally invert the column selection and get the new sequence
729 // selection and indicate it should be hidden.
730 invertColSel_actionPerformed();
737 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
740 viewport.hideAllSelectedSeqs();
742 else if (!(toggleCols && viewport.hasSelectedColumns()))
744 viewport.showAllHiddenSeqs();
750 if (viewport.hasSelectedColumns())
752 viewport.hideSelectedColumns();
755 viewport.setSelectionGroup(sg);
760 viewport.showAllHiddenColumns();
762 viewport.sendSelection();
767 public void keyReleased(KeyEvent evt)
772 public void keyTyped(KeyEvent evt)
777 public void itemStateChanged(ItemEvent evt)
779 final Object source = evt.getSource();
780 if (source == displayNonconservedMenuItem)
782 displayNonconservedMenuItem_actionPerformed();
784 else if (source == colourTextMenuItem)
786 colourTextMenuItem_actionPerformed();
788 else if (source == wrapMenuItem)
790 wrapMenuItem_actionPerformed();
792 else if (source == scaleAbove)
794 viewport.setScaleAboveWrapped(scaleAbove.getState());
796 else if (source == scaleLeft)
798 viewport.setScaleLeftWrapped(scaleLeft.getState());
800 else if (source == scaleRight)
802 viewport.setScaleRightWrapped(scaleRight.getState());
804 else if (source == seqLimits)
806 seqLimits_itemStateChanged();
808 else if (source == viewBoxesMenuItem)
810 viewport.setShowBoxes(viewBoxesMenuItem.getState());
812 else if (source == viewTextMenuItem)
814 viewport.setShowText(viewTextMenuItem.getState());
816 else if (source == renderGapsMenuItem)
818 viewport.setRenderGaps(renderGapsMenuItem.getState());
820 else if (source == annotationPanelMenuItem)
822 boolean showAnnotations = annotationPanelMenuItem.getState();
823 showAlignmentAnnotations.setEnabled(showAnnotations);
824 showSequenceAnnotations.setEnabled(showAnnotations);
825 viewport.setShowAnnotation(showAnnotations);
826 alignPanel.setAnnotationVisible(showAnnotations);
828 else if (source == sequenceFeatures)
830 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
831 alignPanel.seqPanel.seqCanvas.repaint();
833 else if (source == showAlignmentAnnotations)
835 setAnnotationsVisibility();
837 else if (source == showSequenceAnnotations)
839 setAnnotationsVisibility();
841 else if (source == sortAnnBySequence)
843 boolean newState = sortAnnBySequence.getState();
844 sortAnnByLabel.setState(false);
845 setAnnotationSortOrder(
846 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
847 : SequenceAnnotationOrder.NONE);
848 setViewportAnnotationOrder();
850 else if (source == sortAnnByLabel)
852 boolean newState = sortAnnByLabel.getState();
853 sortAnnBySequence.setState(false);
854 setAnnotationSortOrder(
855 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
856 : SequenceAnnotationOrder.NONE);
857 setViewportAnnotationOrder();
859 else if (source == showAutoFirst)
861 showAutoLast.setState(!showAutoFirst.getState());
862 setShowAutoCalculatedAbove(showAutoFirst.getState());
863 setViewportAnnotationOrder();
865 else if (source == showAutoLast)
867 showAutoFirst.setState(!showAutoLast.getState());
868 setShowAutoCalculatedAbove(showAutoFirst.getState());
869 setViewportAnnotationOrder();
871 else if (source == conservationMenuItem)
873 conservationMenuItem_actionPerformed();
875 else if (source == abovePIDThreshold)
877 abovePIDThreshold_actionPerformed();
879 else if (source == applyToAllGroups)
881 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
883 else if (source == autoCalculate)
885 viewport.autoCalculateConsensus = autoCalculate.getState();
887 else if (source == sortByTree)
889 viewport.sortByTree = sortByTree.getState();
891 else if (source == this.centreColumnLabelFlag)
893 centreColumnLabelFlag_stateChanged();
895 else if (source == this.followMouseOverFlag)
897 mouseOverFlag_stateChanged();
899 else if (source == showGroupConsensus)
901 showGroupConsensus_actionPerformed();
903 else if (source == showGroupConservation)
905 showGroupConservation_actionPerformed();
907 else if (source == showSequenceLogo)
909 showSequenceLogo_actionPerformed();
911 else if (source == normSequenceLogo)
913 normSequenceLogo_actionPerformed();
915 else if (source == showConsensusHistogram)
917 showConsensusHistogram_actionPerformed();
919 else if (source == applyAutoAnnotationSettings)
921 applyAutoAnnotationSettings_actionPerformed();
923 // TODO: repaint flags set only if warranted
924 alignPanel.paintAlignment(true, true);
928 * Set the visibility state of sequence-related and/or alignment-related
929 * annotations depending on checkbox selections, and repaint.
933 private void setAnnotationsVisibility()
935 boolean showForAlignment = showAlignmentAnnotations.getState();
936 boolean showForSequences = showSequenceAnnotations.getState();
937 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
939 for (AlignmentAnnotation aa : alignPanel.getAlignment()
940 .getAlignmentAnnotation())
942 boolean visible = (aa.sequenceRef == null ? showForAlignment
944 aa.visible = visible;
947 alignPanel.validateAnnotationDimensions(true);
952 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
954 this.annotationSortOrder = order;
958 * Set flags on the viewport that control annotation ordering
960 private void setViewportAnnotationOrder()
962 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
964 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
967 private void setShowAutoCalculatedAbove(boolean showAbove)
969 this.showAutoCalculatedAbove = showAbove;
972 private void mouseOverFlag_stateChanged()
974 viewport.setFollowHighlight(followMouseOverFlag.getState());
975 // TODO: could kick the scrollTo mechanism to reset view for current
979 private void centreColumnLabelFlag_stateChanged()
981 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
982 this.alignPanel.annotationPanel.repaint();
986 public void actionPerformed(ActionEvent evt)
988 viewport.applet.currentAlignFrame = this;
990 Object source = evt.getSource();
992 if (source == inputText)
994 inputText_actionPerformed();
996 else if (source == loadTree)
998 loadTree_actionPerformed();
1000 else if (source == loadApplication)
1002 launchFullApplication();
1004 else if (source == loadAnnotations)
1008 else if (source == outputAnnotations)
1010 outputAnnotations(true);
1012 else if (source == outputFeatures)
1014 outputFeatures(true, "Jalview");
1016 else if (source == closeMenuItem)
1018 closeMenuItem_actionPerformed();
1020 else if (source == copy)
1022 copy_actionPerformed();
1024 else if (source == undoMenuItem)
1026 undoMenuItem_actionPerformed();
1028 else if (source == redoMenuItem)
1030 redoMenuItem_actionPerformed();
1032 else if (source == inputText)
1034 inputText_actionPerformed();
1036 else if (source == closeMenuItem)
1038 closeMenuItem_actionPerformed();
1040 else if (source == undoMenuItem)
1042 undoMenuItem_actionPerformed();
1044 else if (source == redoMenuItem)
1046 redoMenuItem_actionPerformed();
1048 else if (source == copy)
1050 copy_actionPerformed();
1052 else if (source == pasteNew)
1054 pasteNew_actionPerformed();
1056 else if (source == pasteThis)
1058 pasteThis_actionPerformed();
1060 else if (source == cut)
1062 cut_actionPerformed();
1064 else if (source == delete)
1066 delete_actionPerformed();
1068 else if (source == createGroup)
1070 createGroup_actionPerformed();
1072 else if (source == unGroup)
1074 unGroup_actionPerformed();
1076 else if (source == grpsFromSelection)
1078 makeGrpsFromSelection_actionPerformed();
1080 else if (source == deleteGroups)
1082 deleteGroups_actionPerformed();
1084 else if (source == selectAllSequenceMenuItem)
1086 selectAllSequenceMenuItem_actionPerformed();
1088 else if (source == deselectAllSequenceMenuItem)
1090 deselectAllSequenceMenuItem_actionPerformed();
1092 else if (source == invertSequenceMenuItem)
1094 invertSequenceMenuItem_actionPerformed();
1095 // uncomment to slave sequence selections in split frame
1096 // viewport.sendSelection();
1098 else if (source == invertColSel)
1100 viewport.invertColumnSelection();
1101 alignPanel.paintAlignment(false, false);
1102 viewport.sendSelection();
1104 else if (source == remove2LeftMenuItem)
1106 trimAlignment(true);
1108 else if (source == remove2RightMenuItem)
1110 trimAlignment(false);
1112 else if (source == removeGappedColumnMenuItem)
1114 removeGappedColumnMenuItem_actionPerformed();
1116 else if (source == removeAllGapsMenuItem)
1118 removeAllGapsMenuItem_actionPerformed();
1120 else if (source == findMenuItem)
1122 findMenuItem_actionPerformed();
1124 else if (source == font)
1126 new FontChooser(alignPanel);
1128 else if (source == newView)
1132 else if (source == showColumns)
1134 viewport.showAllHiddenColumns();
1135 alignPanel.paintAlignment(true, true);
1136 viewport.sendSelection();
1138 else if (source == showSeqs)
1140 viewport.showAllHiddenSeqs();
1141 alignPanel.paintAlignment(true, true);
1142 // uncomment if we want to slave sequence selections in split frame
1143 // viewport.sendSelection();
1145 else if (source == hideColumns)
1147 viewport.hideSelectedColumns();
1148 alignPanel.paintAlignment(true, true);
1149 viewport.sendSelection();
1151 else if (source == hideSequences
1152 && viewport.getSelectionGroup() != null)
1154 viewport.hideAllSelectedSeqs();
1155 alignPanel.paintAlignment(true, true);
1156 // uncomment if we want to slave sequence selections in split frame
1157 // viewport.sendSelection();
1159 else if (source == hideAllButSelection)
1161 toggleHiddenRegions(false, false);
1162 alignPanel.paintAlignment(true, true);
1163 viewport.sendSelection();
1165 else if (source == hideAllSelection)
1167 SequenceGroup sg = viewport.getSelectionGroup();
1168 viewport.expandColSelection(sg, false);
1169 viewport.hideAllSelectedSeqs();
1170 viewport.hideSelectedColumns();
1171 alignPanel.paintAlignment(true, true);
1172 viewport.sendSelection();
1174 else if (source == showAllHidden)
1176 viewport.showAllHiddenColumns();
1177 viewport.showAllHiddenSeqs();
1178 alignPanel.paintAlignment(true, true);
1179 viewport.sendSelection();
1181 else if (source == showGroupConsensus)
1183 showGroupConsensus_actionPerformed();
1185 else if (source == showGroupConservation)
1187 showGroupConservation_actionPerformed();
1189 else if (source == showSequenceLogo)
1191 showSequenceLogo_actionPerformed();
1193 else if (source == normSequenceLogo)
1195 normSequenceLogo_actionPerformed();
1197 else if (source == showConsensusHistogram)
1199 showConsensusHistogram_actionPerformed();
1201 else if (source == applyAutoAnnotationSettings)
1203 applyAutoAnnotationSettings_actionPerformed();
1205 else if (source == featureSettings)
1207 new FeatureSettings(alignPanel);
1209 else if (source == alProperties)
1211 StringBuffer contents = new jalview.io.AlignmentProperties(
1212 viewport.getAlignment()).formatAsString();
1213 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1214 cap.setText(contents.toString());
1215 Frame frame = new Frame();
1217 jalview.bin.JalviewLite.addFrame(frame, MessageManager
1218 .formatMessage("label.alignment_properties", new String[]
1219 { getTitle() }), 400, 250);
1221 else if (source == overviewMenuItem)
1223 overviewMenuItem_actionPerformed();
1225 else if (source == noColourmenuItem)
1229 else if (source == clustalColour)
1231 abovePIDThreshold.setState(false);
1232 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1234 else if (source == zappoColour)
1236 changeColour(new ZappoColourScheme());
1238 else if (source == taylorColour)
1240 changeColour(new TaylorColourScheme());
1242 else if (source == hydrophobicityColour)
1244 changeColour(new HydrophobicColourScheme());
1246 else if (source == helixColour)
1248 changeColour(new HelixColourScheme());
1250 else if (source == strandColour)
1252 changeColour(new StrandColourScheme());
1254 else if (source == turnColour)
1256 changeColour(new TurnColourScheme());
1258 else if (source == buriedColour)
1260 changeColour(new BuriedColourScheme());
1262 else if (source == nucleotideColour)
1264 changeColour(new NucleotideColourScheme());
1266 else if (source == purinePyrimidineColour)
1268 changeColour(new PurinePyrimidineColourScheme());
1270 // else if (source == RNAInteractionColour)
1272 // changeColour(new RNAInteractionColourScheme());
1274 else if (source == RNAHelixColour)
1276 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1277 // new RNAHelicesColourChooser(viewport, alignPanel);
1279 else if (source == modifyPID)
1281 modifyPID_actionPerformed();
1283 else if (source == modifyConservation)
1285 modifyConservation_actionPerformed();
1287 else if (source == userDefinedColour)
1289 new UserDefinedColours(alignPanel, null);
1291 else if (source == PIDColour)
1293 changeColour(new PIDColourScheme());
1295 else if (source == BLOSUM62Colour)
1297 changeColour(new Blosum62ColourScheme());
1299 else if (source == tcoffeeColour)
1301 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1303 else if (source == annotationColour)
1305 new AnnotationColourChooser(viewport, alignPanel);
1307 else if (source == annotationColumnSelection)
1309 new AnnotationColumnChooser(viewport, alignPanel);
1311 else if (source == sortPairwiseMenuItem)
1313 sortPairwiseMenuItem_actionPerformed();
1315 else if (source == sortIDMenuItem)
1317 sortIDMenuItem_actionPerformed();
1319 else if (source == sortLengthMenuItem)
1321 sortLengthMenuItem_actionPerformed();
1323 else if (source == sortGroupMenuItem)
1325 sortGroupMenuItem_actionPerformed();
1327 else if (source == sortEValueMenuItem)
1329 sortEValueMenuItem_actionPerformed();
1331 else if (source == sortBitScoreMenuItem)
1333 sortBitScoreMenuItem_actionPerformed();
1335 else if (source == removeRedundancyMenuItem)
1337 removeRedundancyMenuItem_actionPerformed();
1339 else if (source == pairwiseAlignmentMenuItem)
1341 pairwiseAlignmentMenuItem_actionPerformed();
1343 else if (source == PCAMenuItem)
1345 PCAMenuItem_actionPerformed();
1347 else if (source == averageDistanceTreeMenuItem)
1349 averageDistanceTreeMenuItem_actionPerformed();
1351 else if (source == neighbourTreeMenuItem)
1353 neighbourTreeMenuItem_actionPerformed();
1355 else if (source == njTreeBlosumMenuItem)
1357 njTreeBlosumMenuItem_actionPerformed();
1359 else if (source == avDistanceTreeBlosumMenuItem)
1361 avTreeBlosumMenuItem_actionPerformed();
1363 else if (source == documentation)
1365 documentation_actionPerformed();
1367 else if (source == about)
1369 about_actionPerformed();
1374 public void inputText_actionPerformed()
1376 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1377 Frame frame = new Frame();
1379 jalview.bin.JalviewLite.addFrame(frame,
1380 MessageManager.getString("label.input_cut_paste"), 500, 500);
1383 protected void outputText_actionPerformed(ActionEvent e)
1385 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1386 Frame frame = new Frame();
1388 JalviewLite.addFrame(frame, MessageManager
1389 .formatMessage("label.alignment_output_command", new Object[]
1390 { e.getActionCommand() }), 600, 500);
1392 FileFormatI fileFormat = FileFormats.getInstance()
1393 .forName(e.getActionCommand());
1395 new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
1396 viewport.getAlignment(), viewport.getShowJVSuffix()));
1399 public void loadAnnotations()
1401 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1402 cap.setText(MessageManager
1403 .getString("label.paste_features_annotations_Tcoffee_here"));
1404 cap.setAnnotationImport();
1405 Frame frame = new Frame();
1407 jalview.bin.JalviewLite.addFrame(frame,
1408 MessageManager.getString("action.paste_annotations"), 400, 300);
1412 public String outputAnnotations(boolean displayTextbox)
1414 String annotation = new AnnotationFile()
1415 .printAnnotationsForView(viewport);
1419 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1420 Frame frame = new Frame();
1422 jalview.bin.JalviewLite.addFrame(frame,
1423 MessageManager.getString("label.annotations"), 600, 500);
1424 cap.setText(annotation);
1430 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1432 if (alignPanel.getFeatureRenderer() != null
1433 && viewport.getFeaturesDisplayed() != null)
1435 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1441 private List<String> getDisplayedFeatureGroups()
1443 if (alignPanel.getFeatureRenderer() != null
1444 && viewport.getFeaturesDisplayed() != null)
1446 return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
1452 public String outputFeatures(boolean displayTextbox, String format)
1455 FeaturesFile formatter = new FeaturesFile();
1456 if (format.equalsIgnoreCase("Jalview"))
1458 features = formatter.printJalviewFormat(
1459 viewport.getAlignment().getSequencesArray(),
1460 alignPanel.getFeatureRenderer(), true, false);
1464 features = formatter.printGffFormat(viewport.getAlignment()
1465 .getSequencesArray(), alignPanel.getFeatureRenderer(), true,
1471 boolean frimport = false;
1472 if (features == null || features.equals("No Features Visible"))
1474 features = "# No features visible - paste some and import them here.";
1478 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1481 cap.setAnnotationImport();
1483 Frame frame = new Frame();
1485 jalview.bin.JalviewLite.addFrame(frame,
1486 MessageManager.getString("label.features"), 600, 500);
1487 cap.setText(features);
1491 if (features == null)
1500 void launchFullApplication()
1502 StringBuffer url = new StringBuffer(jalviewServletURL);
1504 // allow servlet parameters to be passed in applet parameter
1505 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1507 url.append(firstSep);
1510 "open=" + appendProtocol(viewport.applet.getParameter("file")));
1512 if (viewport.applet.getParameter("features") != null)
1514 url.append("&features=");
1515 url.append(appendProtocol(viewport.applet.getParameter("features")));
1518 if (viewport.applet.getParameter("annotations") != null)
1520 url.append("&annotations=");
1522 appendProtocol(viewport.applet.getParameter("annotations")));
1525 if (viewport.applet.getParameter("jnetfile") != null
1526 || viewport.applet.getParameter("jpredfile") != null)
1528 url.append("&annotations=");
1529 url.append(appendProtocol(
1530 viewport.applet.getParameter("jnetfile") != null
1531 ? viewport.applet.getParameter("jnetfile")
1532 : viewport.applet.getParameter("jpredfile")));
1535 if (viewport.applet.getParameter("defaultColour") != null)
1537 url.append("&colour=" + removeWhiteSpace(
1538 viewport.applet.getParameter("defaultColour")));
1541 if (viewport.applet.getParameter("userDefinedColour") != null)
1543 url.append("&colour=" + removeWhiteSpace(
1544 viewport.applet.getParameter("userDefinedColour")));
1546 if (viewport.applet.getParameter("tree") != null)
1549 + appendProtocol(viewport.applet.getParameter("tree")));
1551 if (viewport.applet.getParameter("treeFile") != null)
1554 + appendProtocol(viewport.applet.getParameter("treeFile")));
1557 showURL(url.toString(), "FULL_APP");
1560 String removeWhiteSpace(String colour)
1562 StringBuffer sb = new StringBuffer();
1563 for (int i = 0; i < colour.length(); i++)
1565 if (Character.isWhitespace(colour.charAt(i)))
1571 sb.append(colour.charAt(i));
1575 return sb.toString();
1578 String appendProtocol(String url)
1583 url = URLEncoder.encode(url, "UTF-8");
1586 * When we finally deprecate 1.1 compatibility, we can start to use
1587 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1588 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1589 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1590 * ex.printStackTrace(); }
1592 catch (java.net.MalformedURLException ex)
1594 url = viewport.applet.getCodeBase() + url;
1596 catch (UnsupportedEncodingException ex)
1599 "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
1601 ex.printStackTrace();
1606 public void closeMenuItem_actionPerformed()
1608 PaintRefresher.RemoveComponent(alignPanel);
1609 if (alignPanel.seqPanel != null
1610 && alignPanel.seqPanel.seqCanvas != null)
1612 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1614 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1616 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1619 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1625 if (alignPanel != null && alignPanel.overviewPanel != null)
1627 alignPanel.overviewPanel.dispose();
1636 void updateEditMenuBar()
1639 if (viewport.getHistoryList().size() > 0)
1641 undoMenuItem.setEnabled(true);
1642 CommandI command = viewport.getHistoryList().peek();
1643 undoMenuItem.setLabel(MessageManager
1644 .formatMessage("label.undo_command", new Object[]
1645 { command.getDescription() }));
1649 undoMenuItem.setEnabled(false);
1650 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1653 if (viewport.getRedoList().size() > 0)
1655 redoMenuItem.setEnabled(true);
1657 CommandI command = viewport.getRedoList().peek();
1658 redoMenuItem.setLabel(MessageManager
1659 .formatMessage("label.redo_command", new Object[]
1660 { command.getDescription() }));
1664 redoMenuItem.setEnabled(false);
1665 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1673 public void addHistoryItem(CommandI command)
1675 if (command.getSize() > 0)
1677 viewport.addToHistoryList(command);
1678 viewport.clearRedoList();
1679 updateEditMenuBar();
1680 viewport.updateHiddenColumns();
1685 * TODO: JAL-1104 DOCUMENT ME!
1690 protected void undoMenuItem_actionPerformed()
1692 if (viewport.getHistoryList().isEmpty())
1697 CommandI command = viewport.getHistoryList().pop();
1698 viewport.addToRedoList(command);
1699 command.undoCommand(null);
1701 AlignmentViewport originalSource = getOriginatingSource(command);
1703 if (originalSource != viewport)
1706 .println("Warning: Viewport object mismatch whilst undoing");
1708 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1709 // viewport.getColumnSelection().getHiddenColumns()
1711 updateEditMenuBar();
1712 originalSource.firePropertyChange("alignment", null,
1713 originalSource.getAlignment().getSequences());
1717 * TODO: JAL-1104 DOCUMENT ME!
1722 protected void redoMenuItem_actionPerformed()
1724 if (viewport.getRedoList().isEmpty())
1729 CommandI command = viewport.getRedoList().pop();
1730 viewport.addToHistoryList(command);
1731 command.doCommand(null);
1733 AlignmentViewport originalSource = getOriginatingSource(command);
1735 if (originalSource != viewport)
1738 .println("Warning: Viewport object mismatch whilst re-doing");
1740 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1741 // viewport.getColumnSelection().getHiddenColumns()
1744 updateEditMenuBar();
1745 originalSource.firePropertyChange("alignment", null,
1746 originalSource.getAlignment().getSequences());
1749 AlignmentViewport getOriginatingSource(CommandI command)
1751 AlignmentViewport originalSource = null;
1752 // For sequence removal and addition, we need to fire
1753 // the property change event FROM the viewport where the
1754 // original alignment was altered
1755 AlignmentI al = null;
1756 if (command instanceof EditCommand)
1758 EditCommand editCommand = (EditCommand) command;
1759 al = editCommand.getAlignment();
1760 Vector comps = PaintRefresher.components
1761 .get(viewport.getSequenceSetId());
1762 for (int i = 0; i < comps.size(); i++)
1764 if (comps.elementAt(i) instanceof AlignmentPanel)
1766 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1768 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1775 if (originalSource == null)
1777 // The original view is closed, we must validate
1778 // the current view against the closed view first
1781 PaintRefresher.validateSequences(al, viewport.getAlignment());
1784 originalSource = viewport;
1787 return originalSource;
1791 * Move the currently selected sequences up or down one position in the
1796 public void moveSelectedSequences(boolean up)
1798 SequenceGroup sg = viewport.getSelectionGroup();
1803 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1804 up ? null : viewport.getHiddenRepSequences(), up);
1805 alignPanel.paintAlignment(true, false);
1808 * Also move cDNA/protein complement sequences
1810 AlignViewportI complement = viewport.getCodingComplement();
1811 if (complement != null)
1813 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1814 viewport, complement);
1815 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1816 up ? null : complement.getHiddenRepSequences(), up);
1817 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
1822 synchronized void slideSequences(boolean right, int size)
1824 List<SequenceI> sg = new Vector<>();
1825 if (viewport.cursorMode)
1827 sg.add(viewport.getAlignment()
1828 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1830 else if (viewport.getSelectionGroup() != null
1831 && viewport.getSelectionGroup().getSize() != viewport
1832 .getAlignment().getHeight())
1834 sg = viewport.getSelectionGroup()
1835 .getSequences(viewport.getHiddenRepSequences());
1843 Vector<SequenceI> invertGroup = new Vector();
1845 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1847 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1849 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1853 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1855 SequenceI[] seqs2 = invertGroup
1856 .toArray(new SequenceI[invertGroup.size()]);
1857 for (int i = 0; i < invertGroup.size(); i++)
1859 seqs2[i] = invertGroup.elementAt(i);
1862 SlideSequencesCommand ssc;
1865 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1866 viewport.getGapCharacter());
1870 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1871 viewport.getGapCharacter());
1874 int groupAdjustment = 0;
1875 if (ssc.getGapsInsertedBegin() && right)
1877 if (viewport.cursorMode)
1879 alignPanel.seqPanel.moveCursor(size, 0);
1883 groupAdjustment = size;
1886 else if (!ssc.getGapsInsertedBegin() && !right)
1888 if (viewport.cursorMode)
1890 alignPanel.seqPanel.moveCursor(-size, 0);
1894 groupAdjustment = -size;
1898 if (groupAdjustment != 0)
1900 viewport.getSelectionGroup().setStartRes(
1901 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1902 viewport.getSelectionGroup().setEndRes(
1903 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1906 boolean appendHistoryItem = false;
1907 Deque<CommandI> historyList = viewport.getHistoryList();
1908 if (historyList != null && historyList.size() > 0
1909 && historyList.peek() instanceof SlideSequencesCommand)
1911 appendHistoryItem = ssc.appendSlideCommand(
1912 (SlideSequencesCommand) historyList.peek());
1915 if (!appendHistoryItem)
1917 addHistoryItem(ssc);
1923 static StringBuffer copiedSequences;
1925 static HiddenColumns copiedHiddenColumns;
1927 protected void copy_actionPerformed()
1929 if (viewport.getSelectionGroup() == null)
1934 SequenceGroup sg = viewport.getSelectionGroup();
1935 copiedSequences = new StringBuffer();
1936 Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1937 for (int i = 0; i < sg.getSize(); i++)
1939 SequenceI seq = sg.getSequenceAt(i);
1940 int index = viewport.getAlignment().findIndex(seq);
1941 orderedSeqs.put(index, seq);
1944 int index = 0, startRes, endRes;
1947 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1949 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1950 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1952 // create new HiddenColumns object with copy of hidden regions
1953 // between startRes and endRes, offset by startRes
1954 copiedHiddenColumns = new HiddenColumns(
1955 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1956 hiddenCutoff, hiddenOffset);
1960 copiedHiddenColumns = null;
1963 for (int i = 0; i < sg.getSize(); i++)
1965 SequenceI seq = null;
1969 if (orderedSeqs.containsKey(index))
1971 seq = orderedSeqs.get(index);
1982 // Returns residue following index if gap
1983 startRes = seq.findPosition(sg.getStartRes());
1986 // Need to find the residue preceeding index if gap
1989 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1991 ch = seq.getCharAt(j);
1992 if (!jalview.util.Comparison.isGap((ch)))
2000 endRes += seq.getStart() - 1;
2003 copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
2004 + "\t" + seq.getSequenceAsString(sg.getStartRes(),
2011 protected void pasteNew_actionPerformed()
2016 protected void pasteThis_actionPerformed()
2021 void paste(boolean newAlignment)
2025 if (copiedSequences == null)
2030 StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
2032 Vector seqs = new Vector();
2033 while (st.hasMoreElements())
2035 String name = st.nextToken();
2036 int start = Integer.parseInt(st.nextToken());
2037 int end = Integer.parseInt(st.nextToken());
2038 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2040 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2041 for (int i = 0; i < seqs.size(); i++)
2043 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2048 String newtitle = MessageManager
2049 .getString("label.copied_sequences");
2050 if (getTitle().startsWith(
2051 MessageManager.getString("label.copied_sequences")))
2053 newtitle = getTitle();
2057 newtitle = newtitle.concat(MessageManager
2058 .formatMessage("label.from_msname", new String[]
2061 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2062 viewport.applet, newtitle, false);
2063 af.viewport.setHiddenColumns(copiedHiddenColumns);
2065 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2070 addSequences(newSeqs);
2073 } catch (Exception ex)
2075 } // could be anything being pasted in here
2079 void addSequences(SequenceI[] seqs)
2081 for (int i = 0; i < seqs.length; i++)
2083 viewport.getAlignment().addSequence(seqs[i]);
2087 addHistoryItem(new EditCommand(
2088 MessageManager.getString("label.add_sequences"), Action.PASTE,
2089 seqs, 0, viewport.getAlignment().getWidth(),
2090 viewport.getAlignment()));
2092 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2093 viewport.getAlignment().getWidth();
2094 viewport.firePropertyChange("alignment", null,
2095 viewport.getAlignment().getSequences());
2099 protected void cut_actionPerformed()
2101 copy_actionPerformed();
2102 delete_actionPerformed();
2105 protected void delete_actionPerformed()
2108 SequenceGroup sg = viewport.getSelectionGroup();
2114 Vector seqs = new Vector();
2116 for (int i = 0; i < sg.getSize(); i++)
2118 seq = sg.getSequenceAt(i);
2119 seqs.addElement(seq);
2123 * If the cut affects all sequences, warn, remove highlighted columns
2125 if (sg.getSize() == viewport.getAlignment().getHeight())
2127 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2128 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2129 if (isEntireAlignWidth)
2131 String title = MessageManager.getString("label.delete_all");
2132 Panel infoPanel = new Panel();
2133 infoPanel.setLayout(new FlowLayout());
2135 new Label(MessageManager.getString("warn.delete_all")));
2137 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2138 dialog.setMainPanel(infoPanel);
2139 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2140 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2141 dialog.setVisible(true);
2148 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2149 sg.getEndRes() + 1);
2152 SequenceI[] cut = new SequenceI[seqs.size()];
2153 for (int i = 0; i < seqs.size(); i++)
2155 cut[i] = (SequenceI) seqs.elementAt(i);
2159 * //ADD HISTORY ITEM
2161 addHistoryItem(new EditCommand(
2162 MessageManager.getString("label.cut_sequences"), Action.CUT,
2163 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2164 viewport.getAlignment()));
2166 viewport.setSelectionGroup(null);
2167 viewport.getAlignment().deleteGroup(sg);
2169 viewport.firePropertyChange("alignment", null,
2170 viewport.getAlignment().getSequences());
2172 if (viewport.getAlignment().getHeight() < 1)
2174 this.setVisible(false);
2176 viewport.sendSelection();
2180 * group consensus toggled
2183 protected void showGroupConsensus_actionPerformed()
2185 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2186 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2191 * group conservation toggled.
2193 protected void showGroupConservation_actionPerformed()
2195 viewport.setShowGroupConservation(showGroupConservation.getState());
2196 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2203 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2204 * .event.ActionEvent)
2206 protected void showConsensusHistogram_actionPerformed()
2208 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2209 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2216 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2217 * .event.ActionEvent)
2219 protected void showSequenceLogo_actionPerformed()
2221 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2222 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2225 protected void normSequenceLogo_actionPerformed()
2227 showSequenceLogo.setState(true);
2228 viewport.setShowSequenceLogo(true);
2229 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2230 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2233 protected void applyAutoAnnotationSettings_actionPerformed()
2235 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2238 protected void makeGrpsFromSelection_actionPerformed()
2240 if (avc.makeGroupsFromSelection())
2242 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2243 alignPanel.updateAnnotation();
2244 alignPanel.paintAlignment(true, true);
2248 protected void createGroup_actionPerformed()
2253 protected void unGroup_actionPerformed()
2257 alignPanel.alignmentChanged();
2261 protected void deleteGroups_actionPerformed()
2263 if (avc.deleteGroups())
2265 alignPanel.alignmentChanged();
2269 public void selectAllSequenceMenuItem_actionPerformed()
2271 SequenceGroup sg = new SequenceGroup();
2272 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2274 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2276 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2277 viewport.setSelectionGroup(sg);
2278 // JAL-2034 - should delegate to
2279 // alignPanel to decide if overview needs
2281 alignPanel.paintAlignment(false, false);
2282 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2283 viewport.sendSelection();
2286 public void deselectAllSequenceMenuItem_actionPerformed()
2288 if (viewport.cursorMode)
2290 alignPanel.seqPanel.keyboardNo1 = null;
2291 alignPanel.seqPanel.keyboardNo2 = null;
2293 viewport.setSelectionGroup(null);
2294 viewport.getColumnSelection().clear();
2295 viewport.setSelectionGroup(null);
2296 alignPanel.idPanel.idCanvas.searchResults = null;
2297 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2298 // JAL-2034 - should delegate to
2299 // alignPanel to decide if overview needs
2301 alignPanel.paintAlignment(false, false);
2302 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2303 viewport.sendSelection();
2306 public void invertSequenceMenuItem_actionPerformed()
2308 SequenceGroup sg = viewport.getSelectionGroup();
2309 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2311 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2314 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2315 viewport.sendSelection();
2318 public void invertColSel_actionPerformed()
2320 viewport.invertColumnSelection();
2321 alignPanel.paintAlignment(true, false);
2322 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2323 viewport.sendSelection();
2326 void trimAlignment(boolean trimLeft)
2328 AlignmentI al = viewport.getAlignment();
2329 ViewportRanges ranges = viewport.getRanges();
2330 ColumnSelection colSel = viewport.getColumnSelection();
2333 if (!colSel.isEmpty())
2337 column = colSel.getMin();
2341 column = colSel.getMax();
2345 if (viewport.getSelectionGroup() != null)
2347 seqs = viewport.getSelectionGroup()
2348 .getSequencesAsArray(viewport.getHiddenRepSequences());
2352 seqs = al.getSequencesArray();
2355 TrimRegionCommand trimRegion;
2358 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2360 ranges.setStartRes(0);
2364 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2368 statusBar.setText(MessageManager
2369 .formatMessage("label.removed_columns", new String[]
2370 { Integer.valueOf(trimRegion.getSize()).toString() }));
2371 addHistoryItem(trimRegion);
2373 for (SequenceGroup sg : al.getGroups())
2375 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2376 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2382 viewport.firePropertyChange("alignment", null, al.getSequences());
2386 public void removeGappedColumnMenuItem_actionPerformed()
2388 AlignmentI al = viewport.getAlignment();
2389 ViewportRanges ranges = viewport.getRanges();
2391 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2394 if (viewport.getSelectionGroup() != null)
2396 seqs = viewport.getSelectionGroup()
2397 .getSequencesAsArray(viewport.getHiddenRepSequences());
2398 start = viewport.getSelectionGroup().getStartRes();
2399 end = viewport.getSelectionGroup().getEndRes();
2403 seqs = viewport.getAlignment().getSequencesArray();
2406 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2407 "Remove Gapped Columns", seqs, start, end,
2408 viewport.getAlignment());
2410 addHistoryItem(removeGapCols);
2412 statusBar.setText(MessageManager
2413 .formatMessage("label.removed_empty_columns", new String[]
2414 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2416 // This is to maintain viewport position on first residue
2417 // of first sequence
2418 SequenceI seq = al.getSequenceAt(0);
2419 int startRes = seq.findPosition(ranges.getStartRes());
2420 // ShiftList shifts;
2421 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2422 // edit.alColumnChanges=shifts.getInverse();
2423 // if (viewport.hasHiddenColumns)
2424 // viewport.getColumnSelection().compensateForEdits(shifts);
2425 ranges.setStartRes(seq.findIndex(startRes) - 1);
2426 viewport.firePropertyChange("alignment", null, al.getSequences());
2430 public void removeAllGapsMenuItem_actionPerformed()
2432 AlignmentI al = viewport.getAlignment();
2433 ViewportRanges ranges = viewport.getRanges();
2435 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2438 if (viewport.getSelectionGroup() != null)
2440 seqs = viewport.getSelectionGroup()
2441 .getSequencesAsArray(viewport.getHiddenRepSequences());
2442 start = viewport.getSelectionGroup().getStartRes();
2443 end = viewport.getSelectionGroup().getEndRes();
2447 seqs = viewport.getAlignment().getSequencesArray();
2450 // This is to maintain viewport position on first residue
2451 // of first sequence
2452 SequenceI seq = al.getSequenceAt(0);
2453 int startRes = seq.findPosition(ranges.getStartRes());
2456 new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2458 ranges.setStartRes(seq.findIndex(startRes) - 1);
2460 viewport.firePropertyChange("alignment", null, al.getSequences());
2464 public void findMenuItem_actionPerformed()
2466 new Finder(alignPanel);
2470 * create a new view derived from the current view
2473 * @return frame for the new view
2475 public AlignFrame newView(String viewtitle)
2478 if (viewport.hasHiddenRows())
2480 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2481 .getFullAlignment().getSequencesArray());
2485 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2488 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2490 for (int i = 0; i < viewport.getAlignment()
2491 .getAlignmentAnnotation().length; i++)
2493 if (!viewport.getAlignment()
2494 .getAlignmentAnnotation()[i].autoCalculated)
2496 newal.addAnnotation(
2497 viewport.getAlignment().getAlignmentAnnotation()[i]);
2502 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2504 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2505 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2506 PaintRefresher.Register(newaf.alignPanel,
2507 newaf.alignPanel.av.getSequenceSetId());
2509 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2510 newaf.alignPanel.av.getSequenceSetId());
2511 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2512 newaf.alignPanel.av.getSequenceSetId());
2514 Vector comps = PaintRefresher.components
2515 .get(viewport.getSequenceSetId());
2517 for (int i = 0; i < comps.size(); i++)
2519 if (comps.elementAt(i) instanceof AlignmentPanel)
2525 String title = new String(this.getTitle());
2526 if (viewtitle != null)
2528 title = viewtitle + " ( " + title + ")";
2532 if (title.indexOf("(View") > -1)
2534 title = title.substring(0, title.indexOf("(View"));
2536 title += "(View " + viewSize + ")";
2539 newaf.setTitle(title.toString());
2541 newaf.viewport.setHistoryList(viewport.getHistoryList());
2542 newaf.viewport.setRedoList(viewport.getRedoList());
2548 * @return list of feature groups on the view
2550 public String[] getFeatureGroups()
2552 FeatureRenderer fr = null;
2553 if (alignPanel != null
2554 && (fr = alignPanel.getFeatureRenderer()) != null)
2556 List<String> gps = fr.getFeatureGroups();
2557 String[] _gps = gps.toArray(new String[gps.size()]);
2564 * get sequence feature groups that are hidden or shown
2570 public String[] getFeatureGroupsOfState(boolean visible)
2572 FeatureRenderer fr = null;
2573 if (alignPanel != null
2574 && (fr = alignPanel.getFeatureRenderer()) != null)
2576 List<String> gps = fr.getGroups(visible);
2577 String[] _gps = gps.toArray(new String[gps.size()]);
2584 * Change the display state for the given feature groups
2587 * list of group strings
2589 * visible or invisible
2591 public void setFeatureGroupState(String[] groups, boolean state)
2593 FeatureRenderer fr = null;
2594 this.sequenceFeatures.setState(true);
2595 viewport.setShowSequenceFeatures(true);
2596 if (alignPanel != null
2597 && (fr = alignPanel.getFeatureRenderer()) != null)
2600 fr.setGroupVisibility(Arrays.asList(groups), state);
2601 alignPanel.seqPanel.seqCanvas.repaint();
2602 if (alignPanel.overviewPanel != null)
2604 alignPanel.overviewPanel.updateOverviewImage();
2609 public void seqLimits_itemStateChanged()
2611 viewport.setShowJVSuffix(seqLimits.getState());
2612 alignPanel.fontChanged();
2613 alignPanel.paintAlignment(true, false);
2616 protected void colourTextMenuItem_actionPerformed()
2618 viewport.setColourText(colourTextMenuItem.getState());
2619 alignPanel.paintAlignment(false, false);
2622 protected void displayNonconservedMenuItem_actionPerformed()
2624 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2625 alignPanel.paintAlignment(false, false);
2628 protected void wrapMenuItem_actionPerformed()
2630 viewport.setWrapAlignment(wrapMenuItem.getState());
2631 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2632 scaleAbove.setEnabled(wrapMenuItem.getState());
2633 scaleLeft.setEnabled(wrapMenuItem.getState());
2634 scaleRight.setEnabled(wrapMenuItem.getState());
2635 alignPanel.paintAlignment(true, false);
2638 public void overviewMenuItem_actionPerformed()
2640 if (alignPanel.overviewPanel != null)
2645 Frame frame = new Frame();
2646 final OverviewPanel overview = new OverviewPanel(alignPanel);
2647 frame.add(overview);
2648 // +50 must allow for applet frame window
2649 jalview.bin.JalviewLite.addFrame(frame, MessageManager
2650 .formatMessage("label.overview_params", new String[]
2651 { this.getTitle() }), overview.getPreferredSize().width,
2652 overview.getPreferredSize().height + 50);
2655 final AlignmentPanel ap = alignPanel;
2656 frame.addWindowListener(new WindowAdapter()
2659 public void windowClosing(WindowEvent e)
2664 ap.setOverviewPanel(null);
2669 alignPanel.setOverviewPanel(overview);
2674 public void changeColour(ColourSchemeI cs)
2676 viewport.setGlobalColourScheme(cs);
2678 alignPanel.paintAlignment(true, true);
2681 protected void modifyPID_actionPerformed()
2683 if (viewport.getAbovePIDThreshold()
2684 && viewport.getGlobalColourScheme() != null)
2686 SliderPanel.setPIDSliderSource(alignPanel,
2687 viewport.getResidueShading(), alignPanel.getViewName());
2688 SliderPanel.showPIDSlider();
2692 protected void modifyConservation_actionPerformed()
2694 if (viewport.getConservationSelected()
2695 && viewport.getGlobalColourScheme() != null)
2697 SliderPanel.setConservationSlider(alignPanel,
2698 viewport.getResidueShading(), alignPanel.getViewName());
2699 SliderPanel.showConservationSlider();
2703 protected void conservationMenuItem_actionPerformed()
2705 boolean selected = conservationMenuItem.getState();
2706 modifyConservation.setEnabled(selected);
2707 viewport.setConservationSelected(selected);
2708 viewport.getResidueShading().setConservationApplied(selected);
2710 changeColour(viewport.getGlobalColourScheme());
2714 modifyConservation_actionPerformed();
2718 SliderPanel.hideConservationSlider();
2722 public void abovePIDThreshold_actionPerformed()
2724 boolean selected = abovePIDThreshold.getState();
2725 modifyPID.setEnabled(selected);
2726 viewport.setAbovePIDThreshold(selected);
2729 viewport.getResidueShading().setThreshold(0,
2730 viewport.isIgnoreGapsConsensus());
2733 changeColour(viewport.getGlobalColourScheme());
2737 modifyPID_actionPerformed();
2741 SliderPanel.hidePIDSlider();
2745 public void sortPairwiseMenuItem_actionPerformed()
2747 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2748 AlignmentSorter.sortByPID(viewport.getAlignment(),
2749 viewport.getAlignment().getSequenceAt(0));
2751 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2752 viewport.getAlignment()));
2753 alignPanel.paintAlignment(true, false);
2756 public void sortIDMenuItem_actionPerformed()
2758 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2759 AlignmentSorter.sortByID(viewport.getAlignment());
2761 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
2762 alignPanel.paintAlignment(true, false);
2765 public void sortLengthMenuItem_actionPerformed()
2767 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2768 AlignmentSorter.sortByLength(viewport.getAlignment());
2769 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2770 viewport.getAlignment()));
2771 alignPanel.paintAlignment(true, false);
2774 public void sortGroupMenuItem_actionPerformed()
2776 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2777 AlignmentSorter.sortByGroup(viewport.getAlignment());
2778 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2779 viewport.getAlignment()));
2780 alignPanel.paintAlignment(true, false);
2784 public void sortEValueMenuItem_actionPerformed()
2786 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2787 AlignmentSorter.sortByEValue(viewport.getAlignment());
2788 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2789 viewport.getAlignment()));
2790 alignPanel.paintAlignment(true, false);
2794 public void sortBitScoreMenuItem_actionPerformed()
2796 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2797 AlignmentSorter.sortByBitScore(viewport.getAlignment());
2798 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2799 viewport.getAlignment()));
2800 alignPanel.paintAlignment(true, false);
2804 public void removeRedundancyMenuItem_actionPerformed()
2806 new RedundancyPanel(alignPanel);
2809 public void pairwiseAlignmentMenuItem_actionPerformed()
2811 if (viewport.getSelectionGroup() != null
2812 && viewport.getSelectionGroup().getSize() > 1)
2814 Frame frame = new Frame();
2815 frame.add(new PairwiseAlignPanel(alignPanel));
2816 jalview.bin.JalviewLite.addFrame(frame,
2817 MessageManager.getString("action.pairwise_alignment"), 600,
2822 public void PCAMenuItem_actionPerformed()
2824 // are the sequences aligned?
2825 if (!viewport.getAlignment().isAligned(false))
2828 int Width = viewport.getAlignment().getWidth();
2830 for (int i = 0; i < viewport.getAlignment().getSequences()
2833 current = viewport.getAlignment().getSequenceAt(i);
2835 if (current.getLength() < Width)
2837 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2840 alignPanel.paintAlignment(false, false);
2843 if ((viewport.getSelectionGroup() != null
2844 && viewport.getSelectionGroup().getSize() < 4
2845 && viewport.getSelectionGroup().getSize() > 0)
2846 || viewport.getAlignment().getHeight() < 4)
2853 new PCAPanel(viewport);
2854 } catch (java.lang.OutOfMemoryError ex)
2860 public void averageDistanceTreeMenuItem_actionPerformed()
2862 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2863 "Average distance tree using PID");
2866 public void neighbourTreeMenuItem_actionPerformed()
2868 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2869 "Neighbour joining tree using PID");
2872 protected void njTreeBlosumMenuItem_actionPerformed()
2874 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2875 ScoreModels.getInstance().getBlosum62().getName(),
2876 "Neighbour joining tree using BLOSUM62");
2879 protected void avTreeBlosumMenuItem_actionPerformed()
2881 newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2882 ScoreModels.getInstance().getBlosum62().getName(),
2883 "Average distance tree using BLOSUM62");
2886 void newTreePanel(String type, String pwType, String title)
2888 // are the sequences aligned?
2889 if (!viewport.getAlignment().isAligned(false))
2892 int Width = viewport.getAlignment().getWidth();
2894 for (int i = 0; i < viewport.getAlignment().getSequences()
2897 current = viewport.getAlignment().getSequenceAt(i);
2899 if (current.getLength() < Width)
2901 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2904 alignPanel.paintAlignment(false, false);
2908 if ((viewport.getSelectionGroup() != null
2909 && viewport.getSelectionGroup().getSize() > 1)
2910 || (viewport.getAlignment().getHeight() > 1))
2912 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2914 addTreeMenuItem(tp, title);
2916 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2920 void loadTree_actionPerformed()
2922 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2923 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2924 cap.setTreeImport();
2925 Frame frame = new Frame();
2927 jalview.bin.JalviewLite.addFrame(frame,
2928 MessageManager.getString("label.paste_newick_file"), 400, 300);
2931 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2933 TreePanel tp = new TreePanel(alignPanel, treeFile,
2934 MessageManager.getString("label.load_tree_from_file"), tree);
2935 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2936 addTreeMenuItem(tp, treeFile);
2940 * sort the alignment using the given treePanel
2943 * tree used to sort view
2945 * string used for undo event name
2947 public void sortByTree(TreePanel treePanel, String title)
2949 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2950 AlignmentSorter.sortByTree(viewport.getAlignment(),
2951 treePanel.getTree());
2952 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2953 // HistoryItem.SORT));
2954 addHistoryItem(new OrderCommand(MessageManager
2955 .formatMessage("label.order_by_params", new String[]
2956 { title }), oldOrder, viewport.getAlignment()));
2957 alignPanel.paintAlignment(true, false);
2961 * Do any automatic reordering of the alignment and add the necessary bits to
2962 * the menu structure for the new tree
2967 protected void addTreeMenuItem(final TreePanel treePanel,
2970 final MenuItem item = new MenuItem(title);
2971 sortByTreeMenu.add(item);
2972 item.addActionListener(new java.awt.event.ActionListener()
2975 public void actionPerformed(ActionEvent evt)
2977 sortByTree(treePanel, title); // treePanel.getTitle());
2981 treePanel.addWindowListener(new WindowAdapter()
2984 public void windowOpened(WindowEvent e)
2986 if (viewport.sortByTree)
2988 sortByTree(treePanel, title);
2990 super.windowOpened(e);
2994 public void windowClosing(WindowEvent e)
2996 sortByTreeMenu.remove(item);
3001 public boolean sortBy(AlignmentOrder alorder, String undoname)
3003 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3004 if (viewport.applet.debug)
3006 System.err.println("Sorting " + alorder.getOrder().size()
3007 + " in alignment '" + getTitle() + "'");
3009 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3010 if (undoname != null)
3012 addHistoryItem(new OrderCommand(undoname, oldOrder,
3013 viewport.getAlignment()));
3015 alignPanel.paintAlignment(true, false);
3019 protected void documentation_actionPerformed()
3021 alignPanel.av.applet.openJalviewHelpUrl();
3024 protected void about_actionPerformed()
3027 class AboutPanel extends Canvas
3033 public AboutPanel(String version, String builddate)
3035 this.version = version;
3036 this.builddate = builddate;
3040 public void paint(Graphics g)
3042 g.setColor(Color.white);
3043 g.fillRect(0, 0, getSize().width, getSize().height);
3044 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3045 FontMetrics fm = g.getFontMetrics();
3046 int fh = fm.getHeight();
3048 g.setColor(Color.black);
3049 // TODO: update this text for each release or centrally store it for
3050 // lite and application
3051 g.setFont(new Font("Helvetica", Font.BOLD, 14));
3052 g.drawString(MessageManager
3053 .formatMessage("label.jalviewLite_release", new String[]
3054 { version }), x, y += fh);
3055 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3056 g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3058 { builddate }), x, y += fh);
3059 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3060 g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3062 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3063 x + 50, y += fh + 8);
3064 g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3066 g.drawString(MessageManager
3067 .getString("label.jalview_distribution_lists"), x, y += fh);
3068 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3071 MessageManager.getString("label.jalview_cite_1_authors"), x,
3073 g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3075 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3080 Frame frame = new Frame();
3081 frame.add(new AboutPanel(JalviewLite.getVersion(),
3082 JalviewLite.getBuildDate()));
3083 jalview.bin.JalviewLite.addFrame(frame,
3084 MessageManager.getString("label.jalview"), 580, 220);
3088 public void showURL(String url, String target)
3090 if (viewport.applet == null)
3092 System.out.println("Not running as applet - no browser available.");
3096 viewport.applet.showURL(url, target);
3100 // ////////////////////////////////////////////////////////////////////////////////
3101 // JBuilder Graphics here
3103 MenuBar alignFrameMenuBar = new MenuBar();
3105 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3107 MenuItem loadApplication = new MenuItem(
3108 MessageManager.getString("label.view_full_application"));
3110 MenuItem loadTree = new MenuItem(
3111 MessageManager.getString("label.load_associated_tree"));
3113 MenuItem loadAnnotations = new MenuItem(
3114 MessageManager.getString("label.load_features_annotations"));
3116 MenuItem outputFeatures = new MenuItem(
3117 MessageManager.getString("label.export_features"));
3119 MenuItem outputAnnotations = new MenuItem(
3120 MessageManager.getString("label.export_annotations"));
3122 MenuItem closeMenuItem = new MenuItem(
3123 MessageManager.getString("action.close"));
3125 MenuItem selectAllSequenceMenuItem = new MenuItem(
3126 MessageManager.getString("action.select_all"));
3128 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3129 MessageManager.getString("action.deselect_all"));
3131 MenuItem invertSequenceMenuItem = new MenuItem(
3132 MessageManager.getString("action.invert_selection"));
3134 MenuItem remove2LeftMenuItem = new MenuItem();
3136 MenuItem remove2RightMenuItem = new MenuItem();
3138 MenuItem removeGappedColumnMenuItem = new MenuItem();
3140 MenuItem removeAllGapsMenuItem = new MenuItem();
3142 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3144 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3146 MenuItem sortPairwiseMenuItem = new MenuItem();
3148 MenuItem sortIDMenuItem = new MenuItem();
3150 MenuItem sortLengthMenuItem = new MenuItem();
3152 MenuItem sortGroupMenuItem = new MenuItem();
3154 MenuItem sortEValueMenuItem = new MenuItem();
3156 MenuItem sortBitScoreMenuItem = new MenuItem();
3158 MenuItem removeRedundancyMenuItem = new MenuItem();
3160 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3162 MenuItem PCAMenuItem = new MenuItem();
3164 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3166 MenuItem neighbourTreeMenuItem = new MenuItem();
3168 BorderLayout borderLayout1 = new BorderLayout();
3170 public Label statusBar = new Label();
3172 MenuItem clustalColour = new MenuItem();
3174 MenuItem zappoColour = new MenuItem();
3176 MenuItem taylorColour = new MenuItem();
3178 MenuItem hydrophobicityColour = new MenuItem();
3180 MenuItem helixColour = new MenuItem();
3182 MenuItem strandColour = new MenuItem();
3184 MenuItem turnColour = new MenuItem();
3186 MenuItem buriedColour = new MenuItem();
3188 MenuItem purinePyrimidineColour = new MenuItem();
3190 // MenuItem RNAInteractionColour = new MenuItem();
3192 MenuItem RNAHelixColour = new MenuItem();
3194 MenuItem userDefinedColour = new MenuItem();
3196 MenuItem PIDColour = new MenuItem();
3198 MenuItem BLOSUM62Colour = new MenuItem();
3200 MenuItem tcoffeeColour = new MenuItem();
3202 MenuItem njTreeBlosumMenuItem = new MenuItem();
3204 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3206 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3208 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3210 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3212 MenuItem alProperties = new MenuItem(
3213 MessageManager.getString("label.alignment_props"));
3215 MenuItem overviewMenuItem = new MenuItem();
3217 MenuItem undoMenuItem = new MenuItem();
3219 MenuItem redoMenuItem = new MenuItem();
3221 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3223 MenuItem noColourmenuItem = new MenuItem();
3225 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3227 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3229 MenuItem findMenuItem = new MenuItem();
3231 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3233 MenuItem nucleotideColour = new MenuItem();
3235 MenuItem deleteGroups = new MenuItem();
3237 MenuItem grpsFromSelection = new MenuItem();
3239 MenuItem createGroup = new MenuItem();
3241 MenuItem unGroup = new MenuItem();
3243 MenuItem delete = new MenuItem();
3245 MenuItem copy = new MenuItem();
3247 MenuItem cut = new MenuItem();
3249 Menu pasteMenu = new Menu();
3251 MenuItem pasteNew = new MenuItem();
3253 MenuItem pasteThis = new MenuItem();
3255 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3257 MenuItem font = new MenuItem();
3259 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3261 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3263 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3265 MenuItem modifyPID = new MenuItem();
3267 MenuItem modifyConservation = new MenuItem();
3269 CheckboxMenuItem autoCalculate = null;
3271 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3272 "Sort Alignment With New Tree", true);
3274 Menu sortByTreeMenu = new Menu();
3276 MenuItem inputText = new MenuItem();
3278 MenuItem documentation = new MenuItem();
3280 MenuItem about = new MenuItem();
3282 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3284 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3286 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3288 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3290 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3292 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3294 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3296 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3298 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3301 * Initialise menus and other items
3305 private void jbInit() throws Exception
3307 setMenuBar(alignFrameMenuBar);
3310 * Configure File menu items and actions
3313 .setLabel(MessageManager.getString("label.input_from_textbox"));
3314 inputText.addActionListener(this);
3315 Menu outputTextboxMenu = new Menu(
3316 MessageManager.getString("label.out_to_textbox"));
3317 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3319 MenuItem item = new MenuItem(ff);
3321 item.addActionListener(new java.awt.event.ActionListener()
3324 public void actionPerformed(ActionEvent e)
3326 outputText_actionPerformed(e);
3330 outputTextboxMenu.add(item);
3332 closeMenuItem.addActionListener(this);
3333 loadApplication.addActionListener(this);
3334 loadTree.addActionListener(this);
3335 loadAnnotations.addActionListener(this);
3336 outputFeatures.addActionListener(this);
3337 outputAnnotations.addActionListener(this);
3340 * Configure Edit menu items and actions
3342 undoMenuItem.setEnabled(false);
3343 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3344 undoMenuItem.addActionListener(this);
3345 redoMenuItem.setEnabled(false);
3346 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3347 redoMenuItem.addActionListener(this);
3348 copy.setLabel(MessageManager.getString("action.copy"));
3349 copy.addActionListener(this);
3350 cut.setLabel(MessageManager.getString("action.cut"));
3351 cut.addActionListener(this);
3352 delete.setLabel(MessageManager.getString("action.delete"));
3353 delete.addActionListener(this);
3354 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3355 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3356 pasteNew.addActionListener(this);
3357 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3358 pasteThis.addActionListener(this);
3360 .setLabel(MessageManager.getString("action.remove_left"));
3361 remove2LeftMenuItem.addActionListener(this);
3362 remove2RightMenuItem
3363 .setLabel(MessageManager.getString("action.remove_right"));
3364 remove2RightMenuItem.addActionListener(this);
3365 removeGappedColumnMenuItem.setLabel(
3366 MessageManager.getString("action.remove_empty_columns"));
3367 removeGappedColumnMenuItem.addActionListener(this);
3368 removeAllGapsMenuItem
3369 .setLabel(MessageManager.getString("action.remove_all_gaps"));
3370 removeAllGapsMenuItem.addActionListener(this);
3371 removeRedundancyMenuItem
3372 .setLabel(MessageManager.getString("action.remove_redundancy"));
3373 removeRedundancyMenuItem.addActionListener(this);
3376 * Configure Select menu items and actions
3378 findMenuItem.setLabel(MessageManager.getString("action.find"));
3379 findMenuItem.addActionListener(this);
3380 selectAllSequenceMenuItem.addActionListener(this);
3381 deselectAllSequenceMenuItem.addActionListener(this);
3382 invertSequenceMenuItem.setLabel(
3383 MessageManager.getString("action.invert_sequence_selection"));
3384 invertSequenceMenuItem.addActionListener(this);
3385 invertColSel.setLabel(
3386 MessageManager.getString("action.invert_column_selection"));
3387 invertColSel.addActionListener(this);
3389 .setLabel(MessageManager.getString("action.undefine_groups"));
3390 deleteGroups.addActionListener(this);
3391 grpsFromSelection.setLabel(
3392 MessageManager.getString("action.make_groups_selection"));
3393 grpsFromSelection.addActionListener(this);
3394 createGroup.setLabel(MessageManager.getString("action.create_group"));
3395 createGroup.addActionListener(this);
3396 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3397 unGroup.addActionListener(this);
3399 annotationColumnSelection.setLabel(
3400 MessageManager.getString("action.select_by_annotation"));
3401 annotationColumnSelection.addActionListener(this);
3404 * Configure View menu items and actions
3406 newView.setLabel(MessageManager.getString("action.new_view"));
3407 newView.addActionListener(this);
3408 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3409 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3410 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3411 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3413 .setLabel(MessageManager.getString("label.selected_columns"));
3415 .setLabel(MessageManager.getString("label.selected_sequences"));
3416 hideAllButSelection.setLabel(
3417 MessageManager.getString("label.all_but_selected_region"));
3419 .setLabel(MessageManager.getString("label.selected_region"));
3420 showAllHidden.setLabel(
3421 MessageManager.getString("label.all_sequences_columns"));
3422 showColumns.addActionListener(this);
3423 showSeqs.addActionListener(this);
3424 hideColumns.addActionListener(this);
3425 hideSequences.addActionListener(this);
3426 hideAllButSelection.addActionListener(this);
3427 hideAllSelection.addActionListener(this);
3428 showAllHidden.addActionListener(this);
3430 .setLabel(MessageManager.getString("action.feature_settings"));
3431 featureSettings.addActionListener(this);
3432 sequenceFeatures.setLabel(
3433 MessageManager.getString("label.show_sequence_features"));
3434 sequenceFeatures.addItemListener(this);
3435 sequenceFeatures.setState(false);
3436 followMouseOverFlag.setLabel(
3437 MessageManager.getString("label.automatic_scrolling"));
3438 followMouseOverFlag.addItemListener(this);
3439 alProperties.addActionListener(this);
3441 .setLabel(MessageManager.getString("label.overview_window"));
3442 overviewMenuItem.addActionListener(this);
3445 * Configure Annotations menu items and actions
3447 annotationPanelMenuItem
3448 .setLabel(MessageManager.getString("label.show_annotations"));
3449 annotationPanelMenuItem.addItemListener(this);
3451 .setLabel(MessageManager.getString("label.group_consensus"));
3452 showGroupConservation
3453 .setLabel(MessageManager.getString("label.group_conservation"));
3454 showConsensusHistogram.setLabel(
3455 MessageManager.getString("label.show_consensus_histogram"));
3456 showSequenceLogo.setLabel(
3457 MessageManager.getString("label.show_consensus_logo"));
3458 normSequenceLogo.setLabel(
3459 MessageManager.getString("label.norm_consensus_logo"));
3460 applyAutoAnnotationSettings
3461 .setLabel(MessageManager.getString("label.apply_all_groups"));
3462 applyAutoAnnotationSettings.setState(true);
3463 Menu autoAnnMenu = new Menu(
3464 MessageManager.getString("label.autocalculated_annotation"));
3465 showGroupConsensus.addItemListener(this);
3466 showGroupConservation.addItemListener(this);
3467 showConsensusHistogram.addItemListener(this);
3468 showSequenceLogo.addItemListener(this);
3469 normSequenceLogo.addItemListener(this);
3470 applyAutoAnnotationSettings.addItemListener(this);
3471 showAlignmentAnnotations = new CheckboxMenuItem(
3472 MessageManager.getString("label.show_all_al_annotations"));
3473 showSequenceAnnotations = new CheckboxMenuItem(
3474 MessageManager.getString("label.show_all_seq_annotations"));
3475 sortAnnBySequence = new CheckboxMenuItem(
3476 MessageManager.getString("label.sort_annotations_by_sequence"));
3477 sortAnnByLabel = new CheckboxMenuItem(
3478 MessageManager.getString("label.sort_annotations_by_label"));
3479 showAutoFirst = new CheckboxMenuItem(
3480 MessageManager.getString("label.show_first"));
3481 showAutoFirst.setState(false); // pending applet parameter
3482 setShowAutoCalculatedAbove(showAutoFirst.getState());
3483 showAutoLast = new CheckboxMenuItem(
3484 MessageManager.getString("label.show_last"));
3485 showAutoLast.setState(!showAutoFirst.getState());
3486 showAlignmentAnnotations.addItemListener(this);
3487 showSequenceAnnotations.addItemListener(this);
3488 sortAnnBySequence.addItemListener(this);
3489 sortAnnByLabel.addItemListener(this);
3490 showAutoFirst.addItemListener(this);
3491 showAutoLast.addItemListener(this);
3494 * Configure Format menu items and actions
3496 font.setLabel(MessageManager.getString("action.font"));
3497 font.addActionListener(this);
3498 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3499 scaleAbove.setState(true);
3500 scaleAbove.setEnabled(false);
3501 scaleAbove.addItemListener(this);
3502 scaleLeft.setEnabled(false);
3503 scaleLeft.setState(true);
3504 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3505 scaleLeft.addItemListener(this);
3506 scaleRight.setEnabled(false);
3507 scaleRight.setState(true);
3508 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3509 scaleRight.addItemListener(this);
3510 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3511 viewBoxesMenuItem.setState(true);
3512 viewBoxesMenuItem.addItemListener(this);
3513 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3514 viewTextMenuItem.setState(true);
3515 viewTextMenuItem.addItemListener(this);
3517 .setLabel(MessageManager.getString("label.colour_text"));
3518 colourTextMenuItem.addItemListener(this);
3519 displayNonconservedMenuItem
3520 .setLabel(MessageManager.getString("label.show_non_conserved"));
3521 displayNonconservedMenuItem.addItemListener(this);
3522 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3523 wrapMenuItem.addItemListener(this);
3525 .setLabel(MessageManager.getString("action.show_gaps"));
3526 renderGapsMenuItem.setState(true);
3527 renderGapsMenuItem.addItemListener(this);
3528 centreColumnLabelFlag.setLabel(
3529 MessageManager.getString("label.centre_column_labels"));
3530 centreColumnLabelFlag.addItemListener(this);
3531 seqLimits.setState(true);
3533 MessageManager.getString("label.show_sequence_limits"));
3534 seqLimits.addItemListener(this);
3537 * Configure Colour menu items and actions
3539 applyToAllGroups.setLabel(
3540 MessageManager.getString("label.apply_colour_to_all_groups"));
3541 applyToAllGroups.setState(true);
3542 applyToAllGroups.addItemListener(this);
3543 clustalColour.setLabel(
3544 MessageManager.getString("label.colourScheme_clustal"));
3545 clustalColour.addActionListener(this);
3547 .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3548 zappoColour.addActionListener(this);
3549 taylorColour.setLabel(
3550 MessageManager.getString("label.colourScheme_taylor"));
3551 taylorColour.addActionListener(this);
3552 hydrophobicityColour.setLabel(
3553 MessageManager.getString("label.colourScheme_hydrophobic"));
3554 hydrophobicityColour.addActionListener(this);
3555 helixColour.setLabel(MessageManager
3556 .getString("label.colourScheme_helix_propensity"));
3557 helixColour.addActionListener(this);
3558 strandColour.setLabel(MessageManager
3559 .getString("label.colourScheme_strand_propensity"));
3560 strandColour.addActionListener(this);
3561 turnColour.setLabel(
3562 MessageManager.getString("label.colourScheme_turn_propensity"));
3563 turnColour.addActionListener(this);
3564 buriedColour.setLabel(
3565 MessageManager.getString("label.colourScheme_buried_index"));
3566 buriedColour.addActionListener(this);
3567 purinePyrimidineColour.setLabel(MessageManager
3568 .getString("label.colourScheme_purine/pyrimidine"));
3569 purinePyrimidineColour.addActionListener(this);
3570 // RNAInteractionColour.setLabel(MessageManager
3571 // .getString("label.rna_interaction"));
3572 // RNAInteractionColour.addActionListener(this);
3573 RNAHelixColour.setLabel(
3574 MessageManager.getString("label.colourScheme_rna_helices"));
3575 RNAHelixColour.addActionListener(this);
3577 .setLabel(MessageManager.getString("action.user_defined"));
3578 userDefinedColour.addActionListener(this);
3580 MessageManager.getString("label.colourScheme_%_identity"));
3581 PIDColour.addActionListener(this);
3582 BLOSUM62Colour.setLabel(
3583 MessageManager.getString("label.colourScheme_blosum62"));
3584 BLOSUM62Colour.addActionListener(this);
3585 tcoffeeColour.setLabel(
3586 MessageManager.getString("label.colourScheme_t-coffee_scores"));
3587 // it will be enabled only if a score file is provided
3588 tcoffeeColour.setEnabled(false);
3589 tcoffeeColour.addActionListener(this);
3590 conservationMenuItem
3591 .setLabel(MessageManager.getString("action.by_conservation"));
3592 conservationMenuItem.addItemListener(this);
3593 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3594 noColourmenuItem.addActionListener(this);
3595 abovePIDThreshold.setLabel(
3596 MessageManager.getString("label.above_identity_threshold"));
3597 abovePIDThreshold.addItemListener(this);
3598 nucleotideColour.setLabel(
3599 MessageManager.getString("label.colourScheme_nucleotide"));
3600 nucleotideColour.addActionListener(this);
3602 MessageManager.getString("label.modify_identity_threshold"));
3603 modifyPID.setEnabled(abovePIDThreshold.getState());
3604 modifyPID.addActionListener(this);
3605 modifyConservation.setLabel(MessageManager
3606 .getString("label.modify_conservation_threshold"));
3607 modifyConservation.setEnabled(conservationMenuItem.getState());
3608 modifyConservation.addActionListener(this);
3610 .setLabel(MessageManager.getString("action.by_annotation"));
3611 annotationColour.addActionListener(this);
3614 * Configure Calculate menu items and actions
3616 sortPairwiseMenuItem
3617 .setLabel(MessageManager.getString("action.by_pairwise_id"));
3618 sortPairwiseMenuItem.addActionListener(this);
3619 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3620 sortIDMenuItem.addActionListener(this);
3622 .setLabel(MessageManager.getString("action.by_length"));
3623 sortLengthMenuItem.addActionListener(this);
3624 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3625 sortGroupMenuItem.addActionListener(this);
3626 pairwiseAlignmentMenuItem.setLabel(
3627 MessageManager.getString("action.pairwise_alignment"));
3628 pairwiseAlignmentMenuItem.addActionListener(this);
3629 PCAMenuItem.setLabel(
3630 MessageManager.getString("label.principal_component_analysis"));
3631 PCAMenuItem.addActionListener(this);
3632 autoCalculate = new CheckboxMenuItem(
3633 MessageManager.getString("label.autocalculate_consensus"),
3635 averageDistanceTreeMenuItem.setLabel(
3636 MessageManager.getString("label.average_distance_identity"));
3637 averageDistanceTreeMenuItem.addActionListener(this);
3638 neighbourTreeMenuItem.setLabel(
3639 MessageManager.getString("label.neighbour_joining_identity"));
3640 neighbourTreeMenuItem.addActionListener(this);
3641 avDistanceTreeBlosumMenuItem.setLabel(
3642 MessageManager.getString("label.average_distance_blosum62"));
3643 avDistanceTreeBlosumMenuItem.addActionListener(this);
3644 njTreeBlosumMenuItem
3645 .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3646 njTreeBlosumMenuItem.addActionListener(this);
3648 .setLabel(MessageManager.getString("action.by_tree_order"));
3649 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3650 Menu calculateTreeMenu = new Menu(
3651 MessageManager.getString("action.calculate_tree"));
3652 autoCalculate.addItemListener(this);
3653 sortByTree.addItemListener(this);
3656 * Configure Help menu items and actions
3658 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3659 documentation.setLabel(MessageManager.getString("label.documentation"));
3660 documentation.addActionListener(this);
3661 about.setLabel(MessageManager.getString("label.about"));
3662 about.addActionListener(this);
3665 * Add top level menus to frame
3667 alignFrameMenuBar.add(fileMenu);
3668 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3669 alignFrameMenuBar.add(editMenu);
3670 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3671 alignFrameMenuBar.add(selectMenu);
3672 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3673 alignFrameMenuBar.add(viewMenu);
3674 Menu annotationsMenu = new Menu(
3675 MessageManager.getString("action.annotations"));
3676 alignFrameMenuBar.add(annotationsMenu);
3677 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3678 alignFrameMenuBar.add(formatMenu);
3679 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3680 alignFrameMenuBar.add(colourMenu);
3681 Menu calculateMenu = new Menu(
3682 MessageManager.getString("action.calculate"));
3683 alignFrameMenuBar.add(calculateMenu);
3684 alignFrameMenuBar.add(helpMenu);
3689 fileMenu.add(inputText);
3690 fileMenu.add(loadTree);
3691 fileMenu.add(loadAnnotations);
3692 fileMenu.addSeparator();
3693 fileMenu.add(outputTextboxMenu);
3694 fileMenu.add(outputFeatures);
3695 fileMenu.add(outputAnnotations);
3696 if (jalviewServletURL != null)
3698 fileMenu.add(loadApplication);
3700 fileMenu.addSeparator();
3701 fileMenu.add(closeMenuItem);
3706 editMenu.add(undoMenuItem);
3707 editMenu.add(redoMenuItem);
3710 pasteMenu.add(pasteNew);
3711 pasteMenu.add(pasteThis);
3712 editMenu.add(pasteMenu);
3713 editMenu.add(delete);
3714 editMenu.addSeparator();
3715 editMenu.add(remove2LeftMenuItem);
3716 editMenu.add(remove2RightMenuItem);
3717 editMenu.add(removeGappedColumnMenuItem);
3718 editMenu.add(removeAllGapsMenuItem);
3719 editMenu.add(removeRedundancyMenuItem);
3724 selectMenu.add(findMenuItem);
3725 selectMenu.addSeparator();
3726 selectMenu.add(selectAllSequenceMenuItem);
3727 selectMenu.add(deselectAllSequenceMenuItem);
3728 selectMenu.add(invertSequenceMenuItem);
3729 selectMenu.add(invertColSel);
3730 selectMenu.add(createGroup);
3731 selectMenu.add(unGroup);
3732 selectMenu.add(grpsFromSelection);
3733 selectMenu.add(deleteGroups);
3734 selectMenu.add(annotationColumnSelection);
3739 viewMenu.add(newView);
3740 viewMenu.addSeparator();
3741 showMenu.add(showColumns);
3742 showMenu.add(showSeqs);
3743 showMenu.add(showAllHidden);
3744 viewMenu.add(showMenu);
3745 hideMenu.add(hideColumns);
3746 hideMenu.add(hideSequences);
3747 hideMenu.add(hideAllSelection);
3748 hideMenu.add(hideAllButSelection);
3749 viewMenu.add(hideMenu);
3750 viewMenu.addSeparator();
3751 viewMenu.add(followMouseOverFlag);
3752 viewMenu.addSeparator();
3753 viewMenu.add(sequenceFeatures);
3754 viewMenu.add(featureSettings);
3755 viewMenu.addSeparator();
3756 viewMenu.add(alProperties);
3757 viewMenu.addSeparator();
3758 viewMenu.add(overviewMenuItem);
3763 annotationsMenu.add(annotationPanelMenuItem);
3764 annotationsMenu.addSeparator();
3765 annotationsMenu.add(showAlignmentAnnotations);
3766 annotationsMenu.add(showSequenceAnnotations);
3767 annotationsMenu.add(sortAnnBySequence);
3768 annotationsMenu.add(sortAnnByLabel);
3769 annotationsMenu.addSeparator();
3770 autoAnnMenu.add(showAutoFirst);
3771 autoAnnMenu.add(showAutoLast);
3772 autoAnnMenu.addSeparator();
3773 autoAnnMenu.add(applyAutoAnnotationSettings);
3774 autoAnnMenu.add(showConsensusHistogram);
3775 autoAnnMenu.add(showSequenceLogo);
3776 autoAnnMenu.add(normSequenceLogo);
3777 autoAnnMenu.addSeparator();
3778 autoAnnMenu.add(showGroupConservation);
3779 autoAnnMenu.add(showGroupConsensus);
3780 annotationsMenu.add(autoAnnMenu);
3785 formatMenu.add(font);
3786 formatMenu.add(seqLimits);
3787 formatMenu.add(wrapMenuItem);
3788 formatMenu.add(scaleAbove);
3789 formatMenu.add(scaleLeft);
3790 formatMenu.add(scaleRight);
3791 formatMenu.add(viewBoxesMenuItem);
3792 formatMenu.add(viewTextMenuItem);
3793 formatMenu.add(colourTextMenuItem);
3794 formatMenu.add(displayNonconservedMenuItem);
3795 formatMenu.add(renderGapsMenuItem);
3796 formatMenu.add(centreColumnLabelFlag);
3801 colourMenu.add(applyToAllGroups);
3802 colourMenu.addSeparator();
3803 colourMenu.add(noColourmenuItem);
3804 colourMenu.add(clustalColour);
3805 colourMenu.add(BLOSUM62Colour);
3806 colourMenu.add(PIDColour);
3807 colourMenu.add(zappoColour);
3808 colourMenu.add(taylorColour);
3809 colourMenu.add(hydrophobicityColour);
3810 colourMenu.add(helixColour);
3811 colourMenu.add(strandColour);
3812 colourMenu.add(turnColour);
3813 colourMenu.add(buriedColour);
3814 colourMenu.add(nucleotideColour);
3815 colourMenu.add(purinePyrimidineColour);
3816 // colourMenu.add(RNAInteractionColour);
3817 colourMenu.add(tcoffeeColour);
3818 colourMenu.add(userDefinedColour);
3819 colourMenu.addSeparator();
3820 colourMenu.add(conservationMenuItem);
3821 colourMenu.add(modifyConservation);
3822 colourMenu.add(abovePIDThreshold);
3823 colourMenu.add(modifyPID);
3824 colourMenu.add(annotationColour);
3825 colourMenu.add(RNAHelixColour);
3830 sortMenu.add(sortIDMenuItem);
3831 sortMenu.add(sortLengthMenuItem);
3832 sortMenu.add(sortByTreeMenu);
3833 sortMenu.add(sortGroupMenuItem);
3834 sortMenu.add(sortPairwiseMenuItem);
3835 calculateMenu.add(sortMenu);
3836 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3837 calculateTreeMenu.add(neighbourTreeMenuItem);
3838 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3839 calculateTreeMenu.add(njTreeBlosumMenuItem);
3840 calculateMenu.add(calculateTreeMenu);
3841 calculateMenu.addSeparator();
3842 calculateMenu.add(pairwiseAlignmentMenuItem);
3843 calculateMenu.add(PCAMenuItem);
3844 calculateMenu.add(autoCalculate);
3845 calculateMenu.add(sortByTree);
3850 helpMenu.add(documentation);
3851 helpMenu.add(about);
3856 statusBar.setBackground(Color.white);
3857 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3858 statusBar.setText(MessageManager.getString("label.status_bar"));
3859 this.add(statusBar, BorderLayout.SOUTH);
3863 public void setStatus(String string)
3865 statusBar.setText(string);
3868 MenuItem featureSettings = new MenuItem();
3870 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3872 MenuItem annotationColour = new MenuItem();
3874 MenuItem annotationColumnSelection = new MenuItem();
3876 MenuItem invertColSel = new MenuItem();
3878 MenuItem showColumns = new MenuItem();
3880 MenuItem showSeqs = new MenuItem();
3882 MenuItem hideColumns = new MenuItem();
3884 MenuItem hideSequences = new MenuItem();
3886 MenuItem hideAllButSelection = new MenuItem();
3888 MenuItem hideAllSelection = new MenuItem();
3890 MenuItem showAllHidden = new MenuItem();
3892 MenuItem newView = new MenuItem();
3894 private CheckboxMenuItem showAlignmentAnnotations;
3896 private CheckboxMenuItem showSequenceAnnotations;
3898 private CheckboxMenuItem sortAnnBySequence;
3900 private CheckboxMenuItem sortAnnByLabel;
3902 private CheckboxMenuItem showAutoFirst;
3904 private CheckboxMenuItem showAutoLast;
3906 private SplitFrame splitFrame;
3909 * Attach the alignFrame panels after embedding menus, if necessary. This used
3910 * to be called setEmbedded, but is now creates the dropdown menus in a
3911 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3913 * @param reallyEmbedded
3914 * true to attach the view to the applet area on the page rather than
3917 public void createAlignFrameWindow(boolean reallyEmbedded)
3921 embedAlignFrameInApplet(viewport.applet);
3926 // test and embed menu bar if necessary.
3928 if (embedMenuIfNeeded(alignPanel))
3931 * adjust for status bar height too. ? pointless as overridden by layout
3934 alignPanel.setSize(getSize().width,
3935 getSize().height - statusBar.getHeight());
3937 add(statusBar, BorderLayout.SOUTH);
3938 add(alignPanel, BorderLayout.CENTER);
3939 // and register with the applet so it can pass external API calls to us
3940 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3946 * Add the components of this AlignFrame to the applet container.
3950 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3953 // Explicitly build the embedded menu panel for the on-page applet
3955 // view cannot be closed if its actually on the page
3956 fileMenu.remove(closeMenuItem);
3957 fileMenu.remove(3); // Remove Separator
3958 // construct embedded menu, using default font
3959 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3960 // and actually add the components to the applet area
3961 theApplet.setLayout(new BorderLayout());
3962 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3963 theApplet.add(statusBar, BorderLayout.SOUTH);
3964 // TODO should size be left to the layout manager?
3965 alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3966 - embeddedMenu.getHeight() - statusBar.getHeight());
3967 theApplet.add(alignPanel, BorderLayout.CENTER);
3968 final AlignFrame me = this;
3969 theApplet.addFocusListener(new FocusListener()
3973 public void focusLost(FocusEvent e)
3975 if (theApplet.currentAlignFrame == me)
3977 theApplet.currentAlignFrame = null;
3982 public void focusGained(FocusEvent e)
3984 theApplet.currentAlignFrame = me;
3987 theApplet.validate();
3991 * create a new binding between structures in an existing jmol viewer instance
3992 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3993 * this does not open a new Jmol window, or modify the display of the
3994 * structures in the original jmol window. Note This method doesn't work
3995 * without an additional javascript library to exchange messages between the
3996 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3999 * JmolViewer instance
4000 * @param sequenceIds
4001 * - sequence Ids to search for associations
4003 public SequenceStructureBinding addStructureViewInstance(
4004 Object jmolviewer, String[] sequenceIds)
4006 Viewer viewer = null;
4009 viewer = (Viewer) jmolviewer;
4010 } catch (ClassCastException ex)
4013 "Unsupported viewer object :" + jmolviewer.getClass());
4017 System.err.println("Can't use this object as a structure viewer:"
4018 + jmolviewer.getClass());
4021 SequenceI[] seqs = null;
4022 if (sequenceIds == null || sequenceIds.length == 0)
4024 seqs = viewport.getAlignment().getSequencesArray();
4028 Vector sqi = new Vector();
4029 AlignmentI al = viewport.getAlignment();
4030 for (int sid = 0; sid < sequenceIds.length; sid++)
4032 SequenceI sq = al.findName(sequenceIds[sid]);
4040 seqs = new SequenceI[sqi.size()];
4041 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4043 seqs[sid] = (SequenceI) sqi.elementAt(sid);
4051 AAStructureBindingModel jmv = null;
4052 // TODO: search for a jmv that involves viewer
4054 { // create a new viewer/jalview binding.
4055 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4062 * bind a pdb file to a sequence in the current view
4065 * - sequenceId within the dataset.
4066 * @param pdbEntryString
4067 * - the short name for the PDB file
4069 * - pdb file - either a URL or a valid PDB file.
4070 * @return true if binding was as success TODO: consider making an exception
4071 * structure for indicating when PDB parsing or sequenceId location
4074 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4077 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4078 boolean needtoadd = false;
4079 if (toaddpdb != null)
4081 Vector pdbe = toaddpdb.getAllPDBEntries();
4082 PDBEntry pdbentry = null;
4083 if (pdbe != null && pdbe.size() > 0)
4085 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4087 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4088 if (!pdbentry.getId().equals(pdbEntryString)
4089 && !pdbentry.getFile().equals(pdbFile))
4099 if (pdbentry == null)
4101 pdbentry = new PDBEntry();
4102 pdbentry.setId(pdbEntryString);
4103 pdbentry.setFile(pdbFile);
4104 needtoadd = true; // add this new entry to sequence.
4106 // resolve data source
4107 // TODO: this code should be a refactored to an io package
4108 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4110 if (protocol == null)
4116 pdbentry.setProperty("protocol", protocol);
4117 toaddpdb.addPDBId(pdbentry);
4118 alignPanel.getStructureSelectionManager()
4119 .registerPDBEntry(pdbentry);
4125 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4129 Vector sequences = new Vector();
4130 for (int i = 0; i < seqs.length; i++)
4132 if (seqs[i] != null)
4135 .addElement(new Object[]
4136 { seqs[i], (chains != null) ? chains[i] : null });
4139 seqs = new SequenceI[sequences.size()];
4140 chains = new String[sequences.size()];
4141 for (int i = 0, isize = sequences.size(); i < isize; i++)
4143 Object[] oj = (Object[]) sequences.elementAt(i);
4145 seqs[i] = (SequenceI) oj[0];
4146 chains[i] = (String) oj[1];
4149 return new Object[] { seqs, chains };
4153 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4154 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4156 // Scrub any null sequences from the array
4157 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4158 seqs = (SequenceI[]) sqch[0];
4159 chains = (String[]) sqch[1];
4160 if (seqs == null || seqs.length == 0)
4163 "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4165 if (protocol == null)
4167 String sourceType = (String) pdb.getProperty("protocol");
4170 protocol = DataSourceType.valueOf(sourceType);
4171 } catch (IllegalArgumentException e)
4175 if (protocol == null)
4177 System.err.println("Couldn't work out protocol to open structure: "
4182 if (applet.useXtrnalSviewer)
4184 // register the association(s) and quit, don't create any windows.
4185 if (StructureSelectionManager.getStructureSelectionManager(applet)
4186 .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
4188 System.err.println("Failed to map " + pdb.getFile() + " ("
4189 + protocol + ") to any sequences");
4193 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4195 // can only do alignments with Jmol
4196 // find the last jmol window assigned to this alignment
4197 AppletJmol ajm = null, tajm;
4198 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4199 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4201 tajm = (AppletJmol) jmols.elementAt(i);
4202 if (tajm.ap.alignFrame == this)
4211 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4212 // try and add the pdb structure
4217 // otherwise, create a new window
4218 if (applet.jmolAvailable)
4220 new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4221 applet.lastFrameX += 40;
4222 applet.lastFrameY += 40;
4226 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4231 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4232 SequenceI[][] seqs, String[][] chains, String[] protocols)
4234 // TODO Auto-generated method stub
4235 System.err.println("Aligned Structure View: Not yet implemented.");
4239 * modify the current selection, providing the user has not made a selection
4243 * - sequences from this alignment
4245 * - columns to be selected on the alignment
4247 public void select(SequenceGroup sel, ColumnSelection csel,
4248 HiddenColumns hidden)
4250 alignPanel.seqPanel.selection(sel, csel, hidden, null);
4253 public void scrollTo(int row, int column)
4255 alignPanel.seqPanel.scrollTo(row, column);
4258 public void scrollToRow(int row)
4260 alignPanel.seqPanel.scrollToRow(row);
4263 public void scrollToColumn(int column)
4265 alignPanel.seqPanel.scrollToColumn(column);
4269 * @return the alignments unique ID.
4271 public String getSequenceSetId()
4273 return viewport.getSequenceSetId();
4277 * Load the (T-Coffee) score file from the specified url
4280 * File/URL/T-COFFEE score file contents
4281 * @throws IOException
4282 * @return true if alignment was annotated with data from source
4284 public boolean loadScoreFile(String source) throws IOException
4287 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4288 AppletFormatAdapter.checkProtocol(source));
4289 if (!file.isValid())
4291 // TODO: raise dialog for gui
4292 System.err.println("Problems parsing T-Coffee scores: "
4293 + file.getWarningMessage());
4294 System.err.println("Origin was:\n" + source);
4299 * check that the score matrix matches the alignment dimensions
4302 if ((aln = viewport.getAlignment()) != null
4303 && (aln.getHeight() != file.getHeight()
4304 || aln.getWidth() != file.getWidth()))
4306 // TODO: raise a dialog box here rather than bomb out.
4308 "The scores matrix does not match the alignment dimensions");
4312 // TODO add parameter to indicate if matching should be done
4313 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4315 alignPanel.fontChanged();
4316 tcoffeeColour.setEnabled(true);
4317 // switch to this color
4318 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4323 System.err.println("Problems resolving T-Coffee scores:");
4324 if (file.getWarningMessage() != null)
4326 System.err.println(file.getWarningMessage());
4332 public SplitFrame getSplitFrame()
4334 return this.splitFrame;
4337 public void setSplitFrame(SplitFrame sf)
4339 this.splitFrame = sf;
4342 // may not need this
4344 public void setShowSeqFeatures(boolean b)
4346 // showSeqFeatures.setSelected(b);
4347 viewport.setShowSequenceFeatures(b);
4352 public void setMenusForViewport()
4354 // setMenusFromViewport(viewport);
4359 public void refreshFeatureUI(boolean enableIfNecessary)
4361 if (enableIfNecessary)
4363 sequenceFeatures.setState(true);
4364 alignPanel.av.setShowSequenceFeatures(true);
4369 public FeatureSettingsControllerI getFeatureSettingsUI()
4371 return alignPanel.av.featureSettings;