2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
25 import jalview.analysis.TreeBuilder;
26 import jalview.analysis.scoremodels.PIDModel;
27 import jalview.analysis.scoremodels.ScoreModels;
28 import jalview.api.AlignViewControllerGuiI;
29 import jalview.api.AlignViewControllerI;
30 import jalview.api.AlignViewportI;
31 import jalview.api.FeatureColourI;
32 import jalview.api.FeatureRenderer;
33 import jalview.api.FeatureSettingsControllerI;
34 import jalview.api.SequenceStructureBinding;
35 import jalview.bin.JalviewLite;
36 import jalview.commands.CommandI;
37 import jalview.commands.EditCommand;
38 import jalview.commands.EditCommand.Action;
39 import jalview.commands.OrderCommand;
40 import jalview.commands.RemoveGapColCommand;
41 import jalview.commands.RemoveGapsCommand;
42 import jalview.commands.SlideSequencesCommand;
43 import jalview.commands.TrimRegionCommand;
44 import jalview.datamodel.Alignment;
45 import jalview.datamodel.AlignmentAnnotation;
46 import jalview.datamodel.AlignmentI;
47 import jalview.datamodel.AlignmentOrder;
48 import jalview.datamodel.ColumnSelection;
49 import jalview.datamodel.HiddenColumns;
50 import jalview.datamodel.PDBEntry;
51 import jalview.datamodel.Sequence;
52 import jalview.datamodel.SequenceGroup;
53 import jalview.datamodel.SequenceI;
54 import jalview.io.AnnotationFile;
55 import jalview.io.AppletFormatAdapter;
56 import jalview.io.DataSourceType;
57 import jalview.io.FeaturesFile;
58 import jalview.io.FileFormat;
59 import jalview.io.FileFormatI;
60 import jalview.io.FileFormats;
61 import jalview.io.TCoffeeScoreFile;
62 import jalview.schemes.Blosum62ColourScheme;
63 import jalview.schemes.BuriedColourScheme;
64 import jalview.schemes.ClustalxColourScheme;
65 import jalview.schemes.ColourSchemeI;
66 import jalview.schemes.HelixColourScheme;
67 import jalview.schemes.HydrophobicColourScheme;
68 import jalview.schemes.NucleotideColourScheme;
69 import jalview.schemes.PIDColourScheme;
70 import jalview.schemes.PurinePyrimidineColourScheme;
71 import jalview.schemes.RNAHelicesColour;
72 import jalview.schemes.StrandColourScheme;
73 import jalview.schemes.TCoffeeColourScheme;
74 import jalview.schemes.TaylorColourScheme;
75 import jalview.schemes.TurnColourScheme;
76 import jalview.schemes.ZappoColourScheme;
77 import jalview.structure.StructureSelectionManager;
78 import jalview.structures.models.AAStructureBindingModel;
79 import jalview.util.MappingUtils;
80 import jalview.util.MessageManager;
81 import jalview.viewmodel.AlignmentViewport;
82 import jalview.viewmodel.ViewportRanges;
84 import java.awt.BorderLayout;
85 import java.awt.Canvas;
86 import java.awt.CheckboxMenuItem;
87 import java.awt.Color;
88 import java.awt.FlowLayout;
90 import java.awt.FontMetrics;
91 import java.awt.Frame;
92 import java.awt.Graphics;
93 import java.awt.Label;
95 import java.awt.MenuBar;
96 import java.awt.MenuItem;
97 import java.awt.Panel;
98 import java.awt.Rectangle;
99 import java.awt.event.ActionEvent;
100 import java.awt.event.ActionListener;
101 import java.awt.event.FocusEvent;
102 import java.awt.event.FocusListener;
103 import java.awt.event.ItemEvent;
104 import java.awt.event.ItemListener;
105 import java.awt.event.KeyEvent;
106 import java.awt.event.KeyListener;
107 import java.awt.event.WindowAdapter;
108 import java.awt.event.WindowEvent;
109 import java.io.IOException;
110 import java.io.UnsupportedEncodingException;
112 import java.net.URLEncoder;
113 import java.util.Arrays;
114 import java.util.Deque;
115 import java.util.HashMap;
116 import java.util.List;
117 import java.util.Map;
118 import java.util.StringTokenizer;
119 import java.util.Vector;
121 import org.jmol.viewer.Viewer;
123 public class AlignFrame extends EmbmenuFrame implements ActionListener,
124 ItemListener, KeyListener, AlignViewControllerGuiI
126 public AlignViewControllerI avc;
128 public AlignmentPanel alignPanel;
130 public AlignViewport viewport;
132 // width and height may be overridden by applet parameters
133 int frameWidth = 700;
135 int frameHeight = 500;
137 String jalviewServletURL;
140 * Flag for showing autocalculated consensus above or below other consensus
143 private boolean showAutoCalculatedAbove;
145 private SequenceAnnotationOrder annotationSortOrder;
148 * Constructor that creates the frame and adds it to the display.
155 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
158 this(al, applet, title, embedded, true);
162 * Constructor that optionally allows the frame to be displayed or only
169 * @param addToDisplay
171 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
172 boolean embedded, boolean addToDisplay)
174 this(al, null, null, applet, title, embedded, addToDisplay);
177 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
178 HiddenColumns hidden, JalviewLite applet, String title,
181 this(al, hiddenSeqs, hidden, applet, title, embedded, true);
184 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
185 HiddenColumns hidden, JalviewLite applet, String title,
186 boolean embedded, boolean addToDisplay)
190 jalviewServletURL = applet.getParameter("APPLICATION_URL");
196 } catch (Exception ex)
198 ex.printStackTrace();
200 // need to get window geometry before we calculate alignment layout
206 param = applet.getParameter("windowWidth");
209 int width = Integer.parseInt(param);
212 param = applet.getParameter("windowHeight");
215 int height = Integer.parseInt(param);
216 frameHeight = height;
218 } catch (Exception ex)
222 viewport = new AlignViewport(al, applet);
224 if (hiddenSeqs != null && hiddenSeqs.length > 0)
226 viewport.hideSequence(hiddenSeqs);
230 viewport.getAlignment().setHiddenColumns(hidden);
232 viewport.setScaleAboveWrapped(scaleAbove.getState());
234 alignPanel = new AlignmentPanel(this, viewport);
235 avc = new jalview.controller.AlignViewController(this, viewport,
237 viewport.updateConservation(alignPanel);
238 viewport.updateConsensus(alignPanel);
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 setStatus(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 setStatus(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 showFeatureSettingsUI();
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 == removeRedundancyMenuItem)
1329 removeRedundancyMenuItem_actionPerformed();
1331 else if (source == pairwiseAlignmentMenuItem)
1333 pairwiseAlignmentMenuItem_actionPerformed();
1335 else if (source == PCAMenuItem)
1337 PCAMenuItem_actionPerformed();
1339 else if (source == averageDistanceTreeMenuItem)
1341 averageDistanceTreeMenuItem_actionPerformed();
1343 else if (source == neighbourTreeMenuItem)
1345 neighbourTreeMenuItem_actionPerformed();
1347 else if (source == njTreeBlosumMenuItem)
1349 njTreeBlosumMenuItem_actionPerformed();
1351 else if (source == avDistanceTreeBlosumMenuItem)
1353 avTreeBlosumMenuItem_actionPerformed();
1355 else if (source == documentation)
1357 documentation_actionPerformed();
1359 else if (source == about)
1361 about_actionPerformed();
1366 public void inputText_actionPerformed()
1368 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1369 Frame frame = new Frame();
1371 jalview.bin.JalviewLite.addFrame(frame,
1372 MessageManager.getString("label.input_cut_paste"), 500, 500);
1375 protected void outputText_actionPerformed(ActionEvent e)
1377 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1378 Frame frame = new Frame();
1380 JalviewLite.addFrame(frame, MessageManager
1381 .formatMessage("label.alignment_output_command", new Object[]
1382 { e.getActionCommand() }), 600, 500);
1384 FileFormatI fileFormat = FileFormats.getInstance()
1385 .forName(e.getActionCommand());
1387 new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
1388 viewport.getAlignment(), viewport.getShowJVSuffix()));
1391 public void loadAnnotations()
1393 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1394 cap.setText(MessageManager
1395 .getString("label.paste_features_annotations_Tcoffee_here"));
1396 cap.setAnnotationImport();
1397 Frame frame = new Frame();
1399 jalview.bin.JalviewLite.addFrame(frame,
1400 MessageManager.getString("action.paste_annotations"), 400, 300);
1404 public String outputAnnotations(boolean displayTextbox)
1406 String annotation = new AnnotationFile()
1407 .printAnnotationsForView(viewport);
1411 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1412 Frame frame = new Frame();
1414 jalview.bin.JalviewLite.addFrame(frame,
1415 MessageManager.getString("label.annotations"), 600, 500);
1416 cap.setText(annotation);
1422 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1424 if (alignPanel.getFeatureRenderer() != null
1425 && viewport.getFeaturesDisplayed() != null)
1427 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1433 private List<String> getDisplayedFeatureGroups()
1435 if (alignPanel.getFeatureRenderer() != null
1436 && viewport.getFeaturesDisplayed() != null)
1438 return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
1444 public String outputFeatures(boolean displayTextbox, String format)
1447 FeaturesFile formatter = new FeaturesFile();
1448 if (format.equalsIgnoreCase("Jalview"))
1450 features = formatter.printJalviewFormat(
1451 viewport.getAlignment().getSequencesArray(),
1452 alignPanel.getFeatureRenderer(), true, false);
1456 features = formatter.printGffFormat(viewport.getAlignment()
1457 .getSequencesArray(), alignPanel.getFeatureRenderer(), true,
1463 boolean frimport = false;
1464 if (features == null || features.equals("No Features Visible"))
1466 features = "# No features visible - paste some and import them here.";
1470 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1473 cap.setAnnotationImport();
1475 Frame frame = new Frame();
1477 jalview.bin.JalviewLite.addFrame(frame,
1478 MessageManager.getString("label.features"), 600, 500);
1479 cap.setText(features);
1483 if (features == null)
1492 void launchFullApplication()
1494 StringBuffer url = new StringBuffer(jalviewServletURL);
1496 // allow servlet parameters to be passed in applet parameter
1497 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1499 url.append(firstSep);
1502 "open=" + appendProtocol(viewport.applet.getParameter("file")));
1504 if (viewport.applet.getParameter("features") != null)
1506 url.append("&features=");
1507 url.append(appendProtocol(viewport.applet.getParameter("features")));
1510 if (viewport.applet.getParameter("annotations") != null)
1512 url.append("&annotations=");
1514 appendProtocol(viewport.applet.getParameter("annotations")));
1517 if (viewport.applet.getParameter("jnetfile") != null
1518 || viewport.applet.getParameter("jpredfile") != null)
1520 url.append("&annotations=");
1521 url.append(appendProtocol(
1522 viewport.applet.getParameter("jnetfile") != null
1523 ? viewport.applet.getParameter("jnetfile")
1524 : viewport.applet.getParameter("jpredfile")));
1527 if (viewport.applet.getParameter("defaultColour") != null)
1529 url.append("&colour=" + removeWhiteSpace(
1530 viewport.applet.getParameter("defaultColour")));
1533 if (viewport.applet.getParameter("userDefinedColour") != null)
1535 url.append("&colour=" + removeWhiteSpace(
1536 viewport.applet.getParameter("userDefinedColour")));
1538 if (viewport.applet.getParameter("tree") != null)
1541 + appendProtocol(viewport.applet.getParameter("tree")));
1543 if (viewport.applet.getParameter("treeFile") != null)
1546 + appendProtocol(viewport.applet.getParameter("treeFile")));
1549 showURL(url.toString(), "FULL_APP");
1552 String removeWhiteSpace(String colour)
1554 StringBuffer sb = new StringBuffer();
1555 for (int i = 0; i < colour.length(); i++)
1557 if (Character.isWhitespace(colour.charAt(i)))
1563 sb.append(colour.charAt(i));
1567 return sb.toString();
1570 String appendProtocol(String url)
1575 url = URLEncoder.encode(url, "UTF-8");
1578 * When we finally deprecate 1.1 compatibility, we can start to use
1579 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1580 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1581 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1582 * ex.printStackTrace(); }
1584 catch (java.net.MalformedURLException ex)
1586 url = viewport.applet.getCodeBase() + url;
1588 catch (UnsupportedEncodingException ex)
1591 "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
1593 ex.printStackTrace();
1598 public void closeMenuItem_actionPerformed()
1600 PaintRefresher.RemoveComponent(alignPanel);
1601 if (alignPanel.seqPanel != null
1602 && alignPanel.seqPanel.seqCanvas != null)
1604 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1606 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1608 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1611 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1617 if (alignPanel != null && alignPanel.overviewPanel != null)
1619 alignPanel.overviewPanel.dispose();
1628 void updateEditMenuBar()
1631 if (viewport.getHistoryList().size() > 0)
1633 undoMenuItem.setEnabled(true);
1634 CommandI command = viewport.getHistoryList().peek();
1635 undoMenuItem.setLabel(MessageManager
1636 .formatMessage("label.undo_command", new Object[]
1637 { command.getDescription() }));
1641 undoMenuItem.setEnabled(false);
1642 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1645 if (viewport.getRedoList().size() > 0)
1647 redoMenuItem.setEnabled(true);
1649 CommandI command = viewport.getRedoList().peek();
1650 redoMenuItem.setLabel(MessageManager
1651 .formatMessage("label.redo_command", new Object[]
1652 { command.getDescription() }));
1656 redoMenuItem.setEnabled(false);
1657 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1665 public void addHistoryItem(CommandI command)
1667 if (command.getSize() > 0)
1669 viewport.addToHistoryList(command);
1670 viewport.clearRedoList();
1671 updateEditMenuBar();
1672 viewport.updateHiddenColumns();
1677 * TODO: JAL-1104 DOCUMENT ME!
1682 protected void undoMenuItem_actionPerformed()
1684 if (viewport.getHistoryList().isEmpty())
1689 CommandI command = viewport.getHistoryList().pop();
1690 viewport.addToRedoList(command);
1691 command.undoCommand(null);
1693 AlignmentViewport originalSource = getOriginatingSource(command);
1695 if (originalSource != viewport)
1698 .println("Warning: Viewport object mismatch whilst undoing");
1700 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1701 // viewport.getColumnSelection().getHiddenColumns()
1703 updateEditMenuBar();
1704 originalSource.firePropertyChange("alignment", null,
1705 originalSource.getAlignment().getSequences());
1709 * TODO: JAL-1104 DOCUMENT ME!
1714 protected void redoMenuItem_actionPerformed()
1716 if (viewport.getRedoList().isEmpty())
1721 CommandI command = viewport.getRedoList().pop();
1722 viewport.addToHistoryList(command);
1723 command.doCommand(null);
1725 AlignmentViewport originalSource = getOriginatingSource(command);
1727 if (originalSource != viewport)
1730 .println("Warning: Viewport object mismatch whilst re-doing");
1732 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1733 // viewport.getColumnSelection().getHiddenColumns()
1736 updateEditMenuBar();
1737 originalSource.firePropertyChange("alignment", null,
1738 originalSource.getAlignment().getSequences());
1741 AlignmentViewport getOriginatingSource(CommandI command)
1743 AlignmentViewport originalSource = null;
1744 // For sequence removal and addition, we need to fire
1745 // the property change event FROM the viewport where the
1746 // original alignment was altered
1747 AlignmentI al = null;
1748 if (command instanceof EditCommand)
1750 EditCommand editCommand = (EditCommand) command;
1751 al = editCommand.getAlignment();
1752 Vector comps = PaintRefresher.components
1753 .get(viewport.getSequenceSetId());
1754 for (int i = 0; i < comps.size(); i++)
1756 if (comps.elementAt(i) instanceof AlignmentPanel)
1758 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1760 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1767 if (originalSource == null)
1769 // The original view is closed, we must validate
1770 // the current view against the closed view first
1773 PaintRefresher.validateSequences(al, viewport.getAlignment());
1776 originalSource = viewport;
1779 return originalSource;
1783 * Move the currently selected sequences up or down one position in the
1788 public void moveSelectedSequences(boolean up)
1790 SequenceGroup sg = viewport.getSelectionGroup();
1795 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1796 up ? null : viewport.getHiddenRepSequences(), up);
1797 alignPanel.paintAlignment(true, false);
1800 * Also move cDNA/protein complement sequences
1802 AlignViewportI complement = viewport.getCodingComplement();
1803 if (complement != null)
1805 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1806 viewport, complement);
1807 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1808 up ? null : complement.getHiddenRepSequences(), up);
1809 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
1814 synchronized void slideSequences(boolean right, int size)
1816 List<SequenceI> sg = new Vector<>();
1817 if (viewport.cursorMode)
1819 sg.add(viewport.getAlignment()
1820 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1822 else if (viewport.getSelectionGroup() != null
1823 && viewport.getSelectionGroup().getSize() != viewport
1824 .getAlignment().getHeight())
1826 sg = viewport.getSelectionGroup()
1827 .getSequences(viewport.getHiddenRepSequences());
1835 Vector<SequenceI> invertGroup = new Vector();
1837 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1839 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1841 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1845 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1847 SequenceI[] seqs2 = invertGroup
1848 .toArray(new SequenceI[invertGroup.size()]);
1849 for (int i = 0; i < invertGroup.size(); i++)
1851 seqs2[i] = invertGroup.elementAt(i);
1854 SlideSequencesCommand ssc;
1857 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1858 viewport.getGapCharacter());
1862 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1863 viewport.getGapCharacter());
1866 int groupAdjustment = 0;
1867 if (ssc.getGapsInsertedBegin() && right)
1869 if (viewport.cursorMode)
1871 alignPanel.seqPanel.moveCursor(size, 0);
1875 groupAdjustment = size;
1878 else if (!ssc.getGapsInsertedBegin() && !right)
1880 if (viewport.cursorMode)
1882 alignPanel.seqPanel.moveCursor(-size, 0);
1886 groupAdjustment = -size;
1890 if (groupAdjustment != 0)
1892 viewport.getSelectionGroup().setStartRes(
1893 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1894 viewport.getSelectionGroup().setEndRes(
1895 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1898 boolean appendHistoryItem = false;
1899 Deque<CommandI> historyList = viewport.getHistoryList();
1900 if (historyList != null && historyList.size() > 0
1901 && historyList.peek() instanceof SlideSequencesCommand)
1903 appendHistoryItem = ssc.appendSlideCommand(
1904 (SlideSequencesCommand) historyList.peek());
1907 if (!appendHistoryItem)
1909 addHistoryItem(ssc);
1915 static StringBuffer copiedSequences;
1917 static HiddenColumns copiedHiddenColumns;
1919 protected void copy_actionPerformed()
1921 if (viewport.getSelectionGroup() == null)
1926 SequenceGroup sg = viewport.getSelectionGroup();
1927 copiedSequences = new StringBuffer();
1928 Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1929 for (int i = 0; i < sg.getSize(); i++)
1931 SequenceI seq = sg.getSequenceAt(i);
1932 int index = viewport.getAlignment().findIndex(seq);
1933 orderedSeqs.put(index, seq);
1936 int index = 0, startRes, endRes;
1939 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1941 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1942 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1944 // create new HiddenColumns object with copy of hidden regions
1945 // between startRes and endRes, offset by startRes
1946 copiedHiddenColumns = new HiddenColumns(
1947 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1948 hiddenCutoff, hiddenOffset);
1952 copiedHiddenColumns = null;
1955 for (int i = 0; i < sg.getSize(); i++)
1957 SequenceI seq = null;
1961 if (orderedSeqs.containsKey(index))
1963 seq = orderedSeqs.get(index);
1974 // Returns residue following index if gap
1975 startRes = seq.findPosition(sg.getStartRes());
1978 // Need to find the residue preceeding index if gap
1981 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1983 ch = seq.getCharAt(j);
1984 if (!jalview.util.Comparison.isGap((ch)))
1992 endRes += seq.getStart() - 1;
1995 copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
1996 + "\t" + seq.getSequenceAsString(sg.getStartRes(),
2003 protected void pasteNew_actionPerformed()
2008 protected void pasteThis_actionPerformed()
2013 void paste(boolean newAlignment)
2017 if (copiedSequences == null)
2022 StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
2024 Vector seqs = new Vector();
2025 while (st.hasMoreElements())
2027 String name = st.nextToken();
2028 int start = Integer.parseInt(st.nextToken());
2029 int end = Integer.parseInt(st.nextToken());
2030 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2032 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2033 for (int i = 0; i < seqs.size(); i++)
2035 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2040 String newtitle = MessageManager
2041 .getString("label.copied_sequences");
2042 if (getTitle().startsWith(
2043 MessageManager.getString("label.copied_sequences")))
2045 newtitle = getTitle();
2049 newtitle = newtitle.concat(MessageManager
2050 .formatMessage("label.from_msname", new String[]
2053 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2054 viewport.applet, newtitle, false);
2055 af.viewport.setHiddenColumns(copiedHiddenColumns);
2057 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2062 addSequences(newSeqs);
2065 } catch (Exception ex)
2067 } // could be anything being pasted in here
2071 void addSequences(SequenceI[] seqs)
2073 for (int i = 0; i < seqs.length; i++)
2075 viewport.getAlignment().addSequence(seqs[i]);
2079 addHistoryItem(new EditCommand(
2080 MessageManager.getString("label.add_sequences"), Action.PASTE,
2081 seqs, 0, viewport.getAlignment().getWidth(),
2082 viewport.getAlignment()));
2084 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
2086 viewport.getAlignment().getWidth();
2087 viewport.firePropertyChange("alignment", null,
2088 viewport.getAlignment().getSequences());
2092 protected void cut_actionPerformed()
2094 copy_actionPerformed();
2095 delete_actionPerformed();
2098 protected void delete_actionPerformed()
2101 SequenceGroup sg = viewport.getSelectionGroup();
2107 Vector seqs = new Vector();
2109 for (int i = 0; i < sg.getSize(); i++)
2111 seq = sg.getSequenceAt(i);
2112 seqs.addElement(seq);
2116 * If the cut affects all sequences, warn, remove highlighted columns
2118 if (sg.getSize() == viewport.getAlignment().getHeight())
2120 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2121 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2122 if (isEntireAlignWidth)
2124 String title = MessageManager.getString("label.delete_all");
2125 Panel infoPanel = new Panel();
2126 infoPanel.setLayout(new FlowLayout());
2128 new Label(MessageManager.getString("warn.delete_all")));
2130 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2131 dialog.setMainPanel(infoPanel);
2132 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2133 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2134 dialog.setVisible(true);
2141 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2142 sg.getEndRes() + 1);
2145 SequenceI[] cut = new SequenceI[seqs.size()];
2146 for (int i = 0; i < seqs.size(); i++)
2148 cut[i] = (SequenceI) seqs.elementAt(i);
2152 * //ADD HISTORY ITEM
2154 addHistoryItem(new EditCommand(
2155 MessageManager.getString("label.cut_sequences"), Action.CUT,
2156 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2157 viewport.getAlignment()));
2159 viewport.setSelectionGroup(null);
2160 viewport.getAlignment().deleteGroup(sg);
2162 viewport.firePropertyChange("alignment", null,
2163 viewport.getAlignment().getSequences());
2165 if (viewport.getAlignment().getHeight() < 1)
2167 this.setVisible(false);
2169 viewport.sendSelection();
2173 * group consensus toggled
2176 protected void showGroupConsensus_actionPerformed()
2178 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2179 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2184 * group conservation toggled.
2186 protected void showGroupConservation_actionPerformed()
2188 viewport.setShowGroupConservation(showGroupConservation.getState());
2189 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2196 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2197 * .event.ActionEvent)
2199 protected void showConsensusHistogram_actionPerformed()
2201 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2202 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2209 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2210 * .event.ActionEvent)
2212 protected void showSequenceLogo_actionPerformed()
2214 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2215 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2218 protected void normSequenceLogo_actionPerformed()
2220 showSequenceLogo.setState(true);
2221 viewport.setShowSequenceLogo(true);
2222 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2223 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2226 protected void applyAutoAnnotationSettings_actionPerformed()
2228 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2231 protected void makeGrpsFromSelection_actionPerformed()
2233 if (avc.makeGroupsFromSelection())
2235 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2236 alignPanel.updateAnnotation();
2237 alignPanel.paintAlignment(true, true);
2241 protected void createGroup_actionPerformed()
2246 protected void unGroup_actionPerformed()
2250 alignPanel.alignmentChanged();
2254 protected void deleteGroups_actionPerformed()
2256 if (avc.deleteGroups())
2258 alignPanel.alignmentChanged();
2262 public void selectAllSequenceMenuItem_actionPerformed()
2264 SequenceGroup sg = new SequenceGroup();
2265 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2267 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2269 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2270 viewport.setSelectionGroup(sg);
2271 // JAL-2034 - should delegate to
2272 // alignPanel to decide if overview needs
2274 alignPanel.paintAlignment(false, false);
2275 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2276 viewport.sendSelection();
2279 public void deselectAllSequenceMenuItem_actionPerformed()
2281 if (viewport.cursorMode)
2283 alignPanel.seqPanel.keyboardNo1 = null;
2284 alignPanel.seqPanel.keyboardNo2 = null;
2286 viewport.setSelectionGroup(null);
2287 viewport.getColumnSelection().clear();
2288 viewport.setSelectionGroup(null);
2289 alignPanel.idPanel.idCanvas.searchResults = null;
2290 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2291 // JAL-2034 - should delegate to
2292 // alignPanel to decide if overview needs
2294 alignPanel.paintAlignment(false, false);
2295 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2296 viewport.sendSelection();
2299 public void invertSequenceMenuItem_actionPerformed()
2301 SequenceGroup sg = viewport.getSelectionGroup();
2302 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2304 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2307 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2308 viewport.sendSelection();
2311 public void invertColSel_actionPerformed()
2313 viewport.invertColumnSelection();
2314 alignPanel.paintAlignment(true, false);
2315 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2316 viewport.sendSelection();
2319 void trimAlignment(boolean trimLeft)
2321 AlignmentI al = viewport.getAlignment();
2322 ViewportRanges ranges = viewport.getRanges();
2323 ColumnSelection colSel = viewport.getColumnSelection();
2326 if (!colSel.isEmpty())
2330 column = colSel.getMin();
2334 column = colSel.getMax();
2338 if (viewport.getSelectionGroup() != null)
2340 seqs = viewport.getSelectionGroup()
2341 .getSequencesAsArray(viewport.getHiddenRepSequences());
2345 seqs = al.getSequencesArray();
2348 TrimRegionCommand trimRegion;
2351 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2353 ranges.setStartRes(0);
2357 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2361 setStatus(MessageManager
2362 .formatMessage("label.removed_columns", new String[]
2363 { Integer.valueOf(trimRegion.getSize()).toString() }));
2364 addHistoryItem(trimRegion);
2366 for (SequenceGroup sg : al.getGroups())
2368 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2369 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2375 viewport.firePropertyChange("alignment", null, al.getSequences());
2379 public void removeGappedColumnMenuItem_actionPerformed()
2381 AlignmentI al = viewport.getAlignment();
2382 ViewportRanges ranges = viewport.getRanges();
2384 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2387 if (viewport.getSelectionGroup() != null)
2389 seqs = viewport.getSelectionGroup()
2390 .getSequencesAsArray(viewport.getHiddenRepSequences());
2391 start = viewport.getSelectionGroup().getStartRes();
2392 end = viewport.getSelectionGroup().getEndRes();
2396 seqs = viewport.getAlignment().getSequencesArray();
2399 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2400 "Remove Gapped Columns", seqs, start, end,
2401 viewport.getAlignment());
2403 addHistoryItem(removeGapCols);
2405 setStatus(MessageManager
2406 .formatMessage("label.removed_empty_columns", new String[]
2407 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2409 // This is to maintain viewport position on first residue
2410 // of first sequence
2411 SequenceI seq = al.getSequenceAt(0);
2412 int startRes = seq.findPosition(ranges.getStartRes());
2413 // ShiftList shifts;
2414 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2415 // edit.alColumnChanges=shifts.getInverse();
2416 // if (viewport.hasHiddenColumns)
2417 // viewport.getColumnSelection().compensateForEdits(shifts);
2418 ranges.setStartRes(seq.findIndex(startRes) - 1);
2419 viewport.firePropertyChange("alignment", null, al.getSequences());
2423 public void removeAllGapsMenuItem_actionPerformed()
2425 AlignmentI al = viewport.getAlignment();
2426 ViewportRanges ranges = viewport.getRanges();
2428 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2431 if (viewport.getSelectionGroup() != null)
2433 seqs = viewport.getSelectionGroup()
2434 .getSequencesAsArray(viewport.getHiddenRepSequences());
2435 start = viewport.getSelectionGroup().getStartRes();
2436 end = viewport.getSelectionGroup().getEndRes();
2440 seqs = viewport.getAlignment().getSequencesArray();
2443 // This is to maintain viewport position on first residue
2444 // of first sequence
2445 SequenceI seq = al.getSequenceAt(0);
2446 int startRes = seq.findPosition(ranges.getStartRes());
2449 new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2451 ranges.setStartRes(seq.findIndex(startRes) - 1);
2453 viewport.firePropertyChange("alignment", null, al.getSequences());
2457 public void findMenuItem_actionPerformed()
2459 new Finder(alignPanel);
2463 * create a new view derived from the current view
2466 * @return frame for the new view
2468 public AlignFrame newView(String viewtitle)
2471 if (viewport.hasHiddenRows())
2473 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2474 .getFullAlignment().getSequencesArray());
2478 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2481 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2483 for (int i = 0; i < viewport.getAlignment()
2484 .getAlignmentAnnotation().length; i++)
2486 if (!viewport.getAlignment()
2487 .getAlignmentAnnotation()[i].autoCalculated)
2489 newal.addAnnotation(
2490 viewport.getAlignment().getAlignmentAnnotation()[i]);
2495 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2497 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2498 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2499 PaintRefresher.Register(newaf.alignPanel,
2500 newaf.alignPanel.av.getSequenceSetId());
2502 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2503 newaf.alignPanel.av.getSequenceSetId());
2504 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2505 newaf.alignPanel.av.getSequenceSetId());
2507 Vector comps = PaintRefresher.components
2508 .get(viewport.getSequenceSetId());
2510 for (int i = 0; i < comps.size(); i++)
2512 if (comps.elementAt(i) instanceof AlignmentPanel)
2518 String title = new String(this.getTitle());
2519 if (viewtitle != null)
2521 title = viewtitle + " ( " + title + ")";
2525 if (title.indexOf("(View") > -1)
2527 title = title.substring(0, title.indexOf("(View"));
2529 title += "(View " + viewSize + ")";
2532 newaf.setTitle(title.toString());
2534 newaf.viewport.setHistoryList(viewport.getHistoryList());
2535 newaf.viewport.setRedoList(viewport.getRedoList());
2541 * @return list of feature groups on the view
2543 public String[] getFeatureGroups()
2545 FeatureRenderer fr = null;
2546 if (alignPanel != null
2547 && (fr = alignPanel.getFeatureRenderer()) != null)
2549 List<String> gps = fr.getFeatureGroups();
2550 String[] _gps = gps.toArray(new String[gps.size()]);
2557 * get sequence feature groups that are hidden or shown
2563 public String[] getFeatureGroupsOfState(boolean visible)
2565 FeatureRenderer fr = null;
2566 if (alignPanel != null
2567 && (fr = alignPanel.getFeatureRenderer()) != null)
2569 List<String> gps = fr.getGroups(visible);
2570 String[] _gps = gps.toArray(new String[gps.size()]);
2577 * Change the display state for the given feature groups
2580 * list of group strings
2582 * visible or invisible
2584 public void setFeatureGroupState(String[] groups, boolean state)
2586 FeatureRenderer fr = null;
2587 this.sequenceFeatures.setState(true);
2588 viewport.setShowSequenceFeatures(true);
2589 if (alignPanel != null
2590 && (fr = alignPanel.getFeatureRenderer()) != null)
2593 fr.setGroupVisibility(Arrays.asList(groups), state);
2594 alignPanel.seqPanel.seqCanvas.repaint();
2595 if (alignPanel.overviewPanel != null)
2597 alignPanel.overviewPanel.updateOverviewImage();
2602 public void seqLimits_itemStateChanged()
2604 viewport.setShowJVSuffix(seqLimits.getState());
2605 alignPanel.fontChanged();
2606 alignPanel.paintAlignment(true, false);
2609 protected void colourTextMenuItem_actionPerformed()
2611 viewport.setColourText(colourTextMenuItem.getState());
2612 alignPanel.paintAlignment(false, false);
2615 protected void displayNonconservedMenuItem_actionPerformed()
2617 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2618 alignPanel.paintAlignment(false, false);
2621 protected void wrapMenuItem_actionPerformed()
2623 viewport.setWrapAlignment(wrapMenuItem.getState());
2624 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2625 scaleAbove.setEnabled(wrapMenuItem.getState());
2626 scaleLeft.setEnabled(wrapMenuItem.getState());
2627 scaleRight.setEnabled(wrapMenuItem.getState());
2628 alignPanel.paintAlignment(true, false);
2631 public void overviewMenuItem_actionPerformed()
2633 if (alignPanel.overviewPanel != null)
2638 Frame frame = new Frame();
2639 final OverviewPanel overview = new OverviewPanel(alignPanel);
2640 frame.add(overview);
2641 // +50 must allow for applet frame window
2642 jalview.bin.JalviewLite.addFrame(frame, MessageManager
2643 .formatMessage("label.overview_params", new String[]
2644 { this.getTitle() }), overview.getPreferredSize().width,
2645 overview.getPreferredSize().height + 50);
2648 final AlignmentPanel ap = alignPanel;
2649 frame.addWindowListener(new WindowAdapter()
2652 public void windowClosing(WindowEvent e)
2657 ap.setOverviewPanel(null);
2662 alignPanel.setOverviewPanel(overview);
2667 public void changeColour(ColourSchemeI cs)
2669 viewport.setGlobalColourScheme(cs);
2671 alignPanel.paintAlignment(true, true);
2674 protected void modifyPID_actionPerformed()
2676 if (viewport.getAbovePIDThreshold()
2677 && viewport.getGlobalColourScheme() != null)
2679 SliderPanel.setPIDSliderSource(alignPanel,
2680 viewport.getResidueShading(), alignPanel.getViewName());
2681 SliderPanel.showPIDSlider();
2685 protected void modifyConservation_actionPerformed()
2687 if (viewport.getConservationSelected()
2688 && viewport.getGlobalColourScheme() != null)
2690 SliderPanel.setConservationSlider(alignPanel,
2691 viewport.getResidueShading(), alignPanel.getViewName());
2692 SliderPanel.showConservationSlider();
2696 protected void conservationMenuItem_actionPerformed()
2698 boolean selected = conservationMenuItem.getState();
2699 modifyConservation.setEnabled(selected);
2700 viewport.setConservationSelected(selected);
2701 viewport.getResidueShading().setConservationApplied(selected);
2703 changeColour(viewport.getGlobalColourScheme());
2707 modifyConservation_actionPerformed();
2711 SliderPanel.hideConservationSlider();
2715 public void abovePIDThreshold_actionPerformed()
2717 boolean selected = abovePIDThreshold.getState();
2718 modifyPID.setEnabled(selected);
2719 viewport.setAbovePIDThreshold(selected);
2722 viewport.getResidueShading().setThreshold(0,
2723 viewport.isIgnoreGapsConsensus());
2726 changeColour(viewport.getGlobalColourScheme());
2730 modifyPID_actionPerformed();
2734 SliderPanel.hidePIDSlider();
2738 public void sortPairwiseMenuItem_actionPerformed()
2740 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2741 AlignmentSorter.sortByPID(viewport.getAlignment(),
2742 viewport.getAlignment().getSequenceAt(0));
2744 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2745 viewport.getAlignment()));
2746 alignPanel.paintAlignment(true, false);
2749 public void sortIDMenuItem_actionPerformed()
2751 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2752 AlignmentSorter.sortByID(viewport.getAlignment());
2754 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
2755 alignPanel.paintAlignment(true, false);
2758 public void sortLengthMenuItem_actionPerformed()
2760 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2761 AlignmentSorter.sortByLength(viewport.getAlignment());
2762 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2763 viewport.getAlignment()));
2764 alignPanel.paintAlignment(true, false);
2767 public void sortGroupMenuItem_actionPerformed()
2769 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2770 AlignmentSorter.sortByGroup(viewport.getAlignment());
2771 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2772 viewport.getAlignment()));
2773 alignPanel.paintAlignment(true, false);
2777 public void removeRedundancyMenuItem_actionPerformed()
2779 new RedundancyPanel(alignPanel);
2782 public void pairwiseAlignmentMenuItem_actionPerformed()
2784 if (viewport.getSelectionGroup() != null
2785 && viewport.getSelectionGroup().getSize() > 1)
2787 Frame frame = new Frame();
2788 frame.add(new PairwiseAlignPanel(alignPanel));
2789 jalview.bin.JalviewLite.addFrame(frame,
2790 MessageManager.getString("action.pairwise_alignment"), 600,
2795 public void PCAMenuItem_actionPerformed()
2797 // are the sequences aligned?
2798 if (!viewport.getAlignment().isAligned(false))
2801 int Width = viewport.getAlignment().getWidth();
2803 for (int i = 0; i < viewport.getAlignment().getSequences()
2806 current = viewport.getAlignment().getSequenceAt(i);
2808 if (current.getLength() < Width)
2810 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2813 alignPanel.paintAlignment(false, false);
2816 if ((viewport.getSelectionGroup() != null
2817 && viewport.getSelectionGroup().getSize() < 4
2818 && viewport.getSelectionGroup().getSize() > 0)
2819 || viewport.getAlignment().getHeight() < 4)
2826 new PCAPanel(viewport);
2827 } catch (java.lang.OutOfMemoryError ex)
2833 public void averageDistanceTreeMenuItem_actionPerformed()
2835 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2836 "Average distance tree using PID");
2839 public void neighbourTreeMenuItem_actionPerformed()
2841 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2842 "Neighbour joining tree using PID");
2845 protected void njTreeBlosumMenuItem_actionPerformed()
2847 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2848 ScoreModels.getInstance().getBlosum62().getName(),
2849 "Neighbour joining tree using BLOSUM62");
2852 protected void avTreeBlosumMenuItem_actionPerformed()
2854 newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2855 ScoreModels.getInstance().getBlosum62().getName(),
2856 "Average distance tree using BLOSUM62");
2859 void newTreePanel(String type, String pwType, String title)
2861 // are the sequences aligned?
2862 if (!viewport.getAlignment().isAligned(false))
2865 int Width = viewport.getAlignment().getWidth();
2867 for (int i = 0; i < viewport.getAlignment().getSequences()
2870 current = viewport.getAlignment().getSequenceAt(i);
2872 if (current.getLength() < Width)
2874 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2877 alignPanel.paintAlignment(false, false);
2881 if ((viewport.getSelectionGroup() != null
2882 && viewport.getSelectionGroup().getSize() > 1)
2883 || (viewport.getAlignment().getHeight() > 1))
2885 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2887 addTreeMenuItem(tp, title);
2889 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2893 void loadTree_actionPerformed()
2895 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2896 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2897 cap.setTreeImport();
2898 Frame frame = new Frame();
2900 jalview.bin.JalviewLite.addFrame(frame,
2901 MessageManager.getString("label.paste_newick_file"), 400, 300);
2904 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2906 TreePanel tp = new TreePanel(alignPanel, treeFile,
2907 MessageManager.getString("label.load_tree_from_file"), tree);
2908 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2909 addTreeMenuItem(tp, treeFile);
2913 * sort the alignment using the given treePanel
2916 * tree used to sort view
2918 * string used for undo event name
2920 public void sortByTree(TreePanel treePanel, String title)
2922 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2923 AlignmentSorter.sortByTree(viewport.getAlignment(),
2924 treePanel.getTree());
2925 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2926 // HistoryItem.SORT));
2927 addHistoryItem(new OrderCommand(MessageManager
2928 .formatMessage("label.order_by_params", new String[]
2929 { title }), oldOrder, viewport.getAlignment()));
2930 alignPanel.paintAlignment(true, false);
2934 * Do any automatic reordering of the alignment and add the necessary bits to
2935 * the menu structure for the new tree
2940 protected void addTreeMenuItem(final TreePanel treePanel,
2943 final MenuItem item = new MenuItem(title);
2944 sortByTreeMenu.add(item);
2945 item.addActionListener(new java.awt.event.ActionListener()
2948 public void actionPerformed(ActionEvent evt)
2950 sortByTree(treePanel, title); // treePanel.getTitle());
2954 treePanel.addWindowListener(new WindowAdapter()
2957 public void windowOpened(WindowEvent e)
2959 if (viewport.sortByTree)
2961 sortByTree(treePanel, title);
2963 super.windowOpened(e);
2967 public void windowClosing(WindowEvent e)
2969 sortByTreeMenu.remove(item);
2974 public boolean sortBy(AlignmentOrder alorder, String undoname)
2976 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2977 if (viewport.applet.debug)
2979 System.err.println("Sorting " + alorder.getOrder().size()
2980 + " in alignment '" + getTitle() + "'");
2982 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2983 if (undoname != null)
2985 addHistoryItem(new OrderCommand(undoname, oldOrder,
2986 viewport.getAlignment()));
2988 alignPanel.paintAlignment(true, false);
2992 protected void documentation_actionPerformed()
2994 alignPanel.av.applet.openJalviewHelpUrl();
2997 protected void about_actionPerformed()
3000 class AboutPanel extends Canvas
3006 public AboutPanel(String version, String builddate)
3008 this.version = version;
3009 this.builddate = builddate;
3013 public void paint(Graphics g)
3015 g.setColor(Color.white);
3016 g.fillRect(0, 0, getSize().width, getSize().height);
3017 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3018 FontMetrics fm = g.getFontMetrics();
3019 int fh = fm.getHeight();
3021 g.setColor(Color.black);
3022 // TODO: update this text for each release or centrally store it for
3023 // lite and application
3024 g.setFont(new Font("Helvetica", Font.BOLD, 14));
3025 g.drawString(MessageManager
3026 .formatMessage("label.jalviewLite_release", new String[]
3027 { version }), x, y += fh);
3028 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3029 g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3031 { builddate }), x, y += fh);
3032 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3033 g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3035 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3036 x + 50, y += fh + 8);
3037 g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3039 g.drawString(MessageManager
3040 .getString("label.jalview_distribution_lists"), x, y += fh);
3041 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3044 MessageManager.getString("label.jalview_cite_1_authors"), x,
3046 g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3048 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3053 Frame frame = new Frame();
3054 frame.add(new AboutPanel(JalviewLite.getVersion(),
3055 JalviewLite.getBuildDate()));
3056 jalview.bin.JalviewLite.addFrame(frame,
3057 MessageManager.getString("label.jalview"), 580, 220);
3061 public void showURL(String url, String target)
3063 if (viewport.applet == null)
3065 System.out.println("Not running as applet - no browser available.");
3069 viewport.applet.showURL(url, target);
3073 // ////////////////////////////////////////////////////////////////////////////////
3074 // JBuilder Graphics here
3076 MenuBar alignFrameMenuBar = new MenuBar();
3078 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3080 MenuItem loadApplication = new MenuItem(
3081 MessageManager.getString("label.view_full_application"));
3083 MenuItem loadTree = new MenuItem(
3084 MessageManager.getString("label.load_associated_tree"));
3086 MenuItem loadAnnotations = new MenuItem(
3087 MessageManager.getString("label.load_features_annotations"));
3089 MenuItem outputFeatures = new MenuItem(
3090 MessageManager.getString("label.export_features"));
3092 MenuItem outputAnnotations = new MenuItem(
3093 MessageManager.getString("label.export_annotations"));
3095 MenuItem closeMenuItem = new MenuItem(
3096 MessageManager.getString("action.close"));
3098 MenuItem selectAllSequenceMenuItem = new MenuItem(
3099 MessageManager.getString("action.select_all"));
3101 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3102 MessageManager.getString("action.deselect_all"));
3104 MenuItem invertSequenceMenuItem = new MenuItem(
3105 MessageManager.getString("action.invert_selection"));
3107 MenuItem remove2LeftMenuItem = new MenuItem();
3109 MenuItem remove2RightMenuItem = new MenuItem();
3111 MenuItem removeGappedColumnMenuItem = new MenuItem();
3113 MenuItem removeAllGapsMenuItem = new MenuItem();
3115 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3117 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3119 MenuItem sortPairwiseMenuItem = new MenuItem();
3121 MenuItem sortIDMenuItem = new MenuItem();
3123 MenuItem sortLengthMenuItem = new MenuItem();
3125 MenuItem sortGroupMenuItem = new MenuItem();
3127 MenuItem removeRedundancyMenuItem = new MenuItem();
3129 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3131 MenuItem PCAMenuItem = new MenuItem();
3133 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3135 MenuItem neighbourTreeMenuItem = new MenuItem();
3137 BorderLayout borderLayout1 = new BorderLayout();
3139 public Label statusBar = new Label();
3141 MenuItem clustalColour = new MenuItem();
3143 MenuItem zappoColour = new MenuItem();
3145 MenuItem taylorColour = new MenuItem();
3147 MenuItem hydrophobicityColour = new MenuItem();
3149 MenuItem helixColour = new MenuItem();
3151 MenuItem strandColour = new MenuItem();
3153 MenuItem turnColour = new MenuItem();
3155 MenuItem buriedColour = new MenuItem();
3157 MenuItem purinePyrimidineColour = new MenuItem();
3159 // MenuItem RNAInteractionColour = new MenuItem();
3161 MenuItem RNAHelixColour = new MenuItem();
3163 MenuItem userDefinedColour = new MenuItem();
3165 MenuItem PIDColour = new MenuItem();
3167 MenuItem BLOSUM62Colour = new MenuItem();
3169 MenuItem tcoffeeColour = new MenuItem();
3171 MenuItem njTreeBlosumMenuItem = new MenuItem();
3173 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3175 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3177 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3179 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3181 MenuItem alProperties = new MenuItem(
3182 MessageManager.getString("label.alignment_props"));
3184 MenuItem overviewMenuItem = new MenuItem();
3186 MenuItem undoMenuItem = new MenuItem();
3188 MenuItem redoMenuItem = new MenuItem();
3190 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3192 MenuItem noColourmenuItem = new MenuItem();
3194 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3196 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3198 MenuItem findMenuItem = new MenuItem();
3200 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3202 MenuItem nucleotideColour = new MenuItem();
3204 MenuItem deleteGroups = new MenuItem();
3206 MenuItem grpsFromSelection = new MenuItem();
3208 MenuItem createGroup = new MenuItem();
3210 MenuItem unGroup = new MenuItem();
3212 MenuItem delete = new MenuItem();
3214 MenuItem copy = new MenuItem();
3216 MenuItem cut = new MenuItem();
3218 Menu pasteMenu = new Menu();
3220 MenuItem pasteNew = new MenuItem();
3222 MenuItem pasteThis = new MenuItem();
3224 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3226 MenuItem font = new MenuItem();
3228 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3230 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3232 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3234 MenuItem modifyPID = new MenuItem();
3236 MenuItem modifyConservation = new MenuItem();
3238 CheckboxMenuItem autoCalculate = null;
3240 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3241 "Sort Alignment With New Tree", true);
3243 Menu sortByTreeMenu = new Menu();
3245 MenuItem inputText = new MenuItem();
3247 MenuItem documentation = new MenuItem();
3249 MenuItem about = new MenuItem();
3251 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3253 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3255 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3257 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3259 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3261 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3263 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3265 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3267 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3270 * Initialise menus and other items
3274 private void jbInit() throws Exception
3276 setMenuBar(alignFrameMenuBar);
3279 * Configure File menu items and actions
3282 .setLabel(MessageManager.getString("label.input_from_textbox"));
3283 inputText.addActionListener(this);
3284 Menu outputTextboxMenu = new Menu(
3285 MessageManager.getString("label.out_to_textbox"));
3286 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3288 MenuItem item = new MenuItem(ff);
3290 item.addActionListener(new java.awt.event.ActionListener()
3293 public void actionPerformed(ActionEvent e)
3295 outputText_actionPerformed(e);
3299 outputTextboxMenu.add(item);
3301 closeMenuItem.addActionListener(this);
3302 loadApplication.addActionListener(this);
3303 loadTree.addActionListener(this);
3304 loadAnnotations.addActionListener(this);
3305 outputFeatures.addActionListener(this);
3306 outputAnnotations.addActionListener(this);
3309 * Configure Edit menu items and actions
3311 undoMenuItem.setEnabled(false);
3312 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3313 undoMenuItem.addActionListener(this);
3314 redoMenuItem.setEnabled(false);
3315 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3316 redoMenuItem.addActionListener(this);
3317 copy.setLabel(MessageManager.getString("action.copy"));
3318 copy.addActionListener(this);
3319 cut.setLabel(MessageManager.getString("action.cut"));
3320 cut.addActionListener(this);
3321 delete.setLabel(MessageManager.getString("action.delete"));
3322 delete.addActionListener(this);
3323 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3324 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3325 pasteNew.addActionListener(this);
3326 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3327 pasteThis.addActionListener(this);
3329 .setLabel(MessageManager.getString("action.remove_left"));
3330 remove2LeftMenuItem.addActionListener(this);
3331 remove2RightMenuItem
3332 .setLabel(MessageManager.getString("action.remove_right"));
3333 remove2RightMenuItem.addActionListener(this);
3334 removeGappedColumnMenuItem.setLabel(
3335 MessageManager.getString("action.remove_empty_columns"));
3336 removeGappedColumnMenuItem.addActionListener(this);
3337 removeAllGapsMenuItem
3338 .setLabel(MessageManager.getString("action.remove_all_gaps"));
3339 removeAllGapsMenuItem.addActionListener(this);
3340 removeRedundancyMenuItem
3341 .setLabel(MessageManager.getString("action.remove_redundancy"));
3342 removeRedundancyMenuItem.addActionListener(this);
3345 * Configure Select menu items and actions
3347 findMenuItem.setLabel(MessageManager.getString("action.find"));
3348 findMenuItem.addActionListener(this);
3349 selectAllSequenceMenuItem.addActionListener(this);
3350 deselectAllSequenceMenuItem.addActionListener(this);
3351 invertSequenceMenuItem.setLabel(
3352 MessageManager.getString("action.invert_sequence_selection"));
3353 invertSequenceMenuItem.addActionListener(this);
3354 invertColSel.setLabel(
3355 MessageManager.getString("action.invert_column_selection"));
3356 invertColSel.addActionListener(this);
3358 .setLabel(MessageManager.getString("action.undefine_groups"));
3359 deleteGroups.addActionListener(this);
3360 grpsFromSelection.setLabel(
3361 MessageManager.getString("action.make_groups_selection"));
3362 grpsFromSelection.addActionListener(this);
3363 createGroup.setLabel(MessageManager.getString("action.create_group"));
3364 createGroup.addActionListener(this);
3365 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3366 unGroup.addActionListener(this);
3368 annotationColumnSelection.setLabel(
3369 MessageManager.getString("action.select_by_annotation"));
3370 annotationColumnSelection.addActionListener(this);
3373 * Configure View menu items and actions
3375 newView.setLabel(MessageManager.getString("action.new_view"));
3376 newView.addActionListener(this);
3377 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3378 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3379 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3380 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3382 .setLabel(MessageManager.getString("label.selected_columns"));
3384 .setLabel(MessageManager.getString("label.selected_sequences"));
3385 hideAllButSelection.setLabel(
3386 MessageManager.getString("label.all_but_selected_region"));
3388 .setLabel(MessageManager.getString("label.selected_region"));
3389 showAllHidden.setLabel(
3390 MessageManager.getString("label.all_sequences_columns"));
3391 showColumns.addActionListener(this);
3392 showSeqs.addActionListener(this);
3393 hideColumns.addActionListener(this);
3394 hideSequences.addActionListener(this);
3395 hideAllButSelection.addActionListener(this);
3396 hideAllSelection.addActionListener(this);
3397 showAllHidden.addActionListener(this);
3399 .setLabel(MessageManager.getString("action.feature_settings"));
3400 featureSettings.addActionListener(this);
3401 sequenceFeatures.setLabel(
3402 MessageManager.getString("label.show_sequence_features"));
3403 sequenceFeatures.addItemListener(this);
3404 sequenceFeatures.setState(false);
3405 followMouseOverFlag.setLabel(
3406 MessageManager.getString("label.automatic_scrolling"));
3407 followMouseOverFlag.addItemListener(this);
3408 alProperties.addActionListener(this);
3410 .setLabel(MessageManager.getString("label.overview_window"));
3411 overviewMenuItem.addActionListener(this);
3414 * Configure Annotations menu items and actions
3416 annotationPanelMenuItem
3417 .setLabel(MessageManager.getString("label.show_annotations"));
3418 annotationPanelMenuItem.addItemListener(this);
3420 .setLabel(MessageManager.getString("label.group_consensus"));
3421 showGroupConservation
3422 .setLabel(MessageManager.getString("label.group_conservation"));
3423 showConsensusHistogram.setLabel(
3424 MessageManager.getString("label.show_consensus_histogram"));
3425 showSequenceLogo.setLabel(
3426 MessageManager.getString("label.show_consensus_logo"));
3427 normSequenceLogo.setLabel(
3428 MessageManager.getString("label.norm_consensus_logo"));
3429 applyAutoAnnotationSettings
3430 .setLabel(MessageManager.getString("label.apply_all_groups"));
3431 applyAutoAnnotationSettings.setState(true);
3432 Menu autoAnnMenu = new Menu(
3433 MessageManager.getString("label.autocalculated_annotation"));
3434 showGroupConsensus.addItemListener(this);
3435 showGroupConservation.addItemListener(this);
3436 showConsensusHistogram.addItemListener(this);
3437 showSequenceLogo.addItemListener(this);
3438 normSequenceLogo.addItemListener(this);
3439 applyAutoAnnotationSettings.addItemListener(this);
3440 showAlignmentAnnotations = new CheckboxMenuItem(
3441 MessageManager.getString("label.show_all_al_annotations"));
3442 showSequenceAnnotations = new CheckboxMenuItem(
3443 MessageManager.getString("label.show_all_seq_annotations"));
3444 sortAnnBySequence = new CheckboxMenuItem(
3445 MessageManager.getString("label.sort_annotations_by_sequence"));
3446 sortAnnByLabel = new CheckboxMenuItem(
3447 MessageManager.getString("label.sort_annotations_by_label"));
3448 showAutoFirst = new CheckboxMenuItem(
3449 MessageManager.getString("label.show_first"));
3450 showAutoFirst.setState(false); // pending applet parameter
3451 setShowAutoCalculatedAbove(showAutoFirst.getState());
3452 showAutoLast = new CheckboxMenuItem(
3453 MessageManager.getString("label.show_last"));
3454 showAutoLast.setState(!showAutoFirst.getState());
3455 showAlignmentAnnotations.addItemListener(this);
3456 showSequenceAnnotations.addItemListener(this);
3457 sortAnnBySequence.addItemListener(this);
3458 sortAnnByLabel.addItemListener(this);
3459 showAutoFirst.addItemListener(this);
3460 showAutoLast.addItemListener(this);
3463 * Configure Format menu items and actions
3465 font.setLabel(MessageManager.getString("action.font"));
3466 font.addActionListener(this);
3467 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3468 scaleAbove.setState(true);
3469 scaleAbove.setEnabled(false);
3470 scaleAbove.addItemListener(this);
3471 scaleLeft.setEnabled(false);
3472 scaleLeft.setState(true);
3473 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3474 scaleLeft.addItemListener(this);
3475 scaleRight.setEnabled(false);
3476 scaleRight.setState(true);
3477 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3478 scaleRight.addItemListener(this);
3479 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3480 viewBoxesMenuItem.setState(true);
3481 viewBoxesMenuItem.addItemListener(this);
3482 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3483 viewTextMenuItem.setState(true);
3484 viewTextMenuItem.addItemListener(this);
3486 .setLabel(MessageManager.getString("label.colour_text"));
3487 colourTextMenuItem.addItemListener(this);
3488 displayNonconservedMenuItem
3489 .setLabel(MessageManager.getString("label.show_non_conserved"));
3490 displayNonconservedMenuItem.addItemListener(this);
3491 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3492 wrapMenuItem.addItemListener(this);
3494 .setLabel(MessageManager.getString("action.show_gaps"));
3495 renderGapsMenuItem.setState(true);
3496 renderGapsMenuItem.addItemListener(this);
3497 centreColumnLabelFlag.setLabel(
3498 MessageManager.getString("label.centre_column_labels"));
3499 centreColumnLabelFlag.addItemListener(this);
3500 seqLimits.setState(true);
3502 MessageManager.getString("label.show_sequence_limits"));
3503 seqLimits.addItemListener(this);
3506 * Configure Colour menu items and actions
3508 applyToAllGroups.setLabel(
3509 MessageManager.getString("label.apply_colour_to_all_groups"));
3510 applyToAllGroups.setState(true);
3511 applyToAllGroups.addItemListener(this);
3512 clustalColour.setLabel(
3513 MessageManager.getString("label.colourScheme_clustal"));
3514 clustalColour.addActionListener(this);
3516 .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3517 zappoColour.addActionListener(this);
3518 taylorColour.setLabel(
3519 MessageManager.getString("label.colourScheme_taylor"));
3520 taylorColour.addActionListener(this);
3521 hydrophobicityColour.setLabel(
3522 MessageManager.getString("label.colourScheme_hydrophobic"));
3523 hydrophobicityColour.addActionListener(this);
3524 helixColour.setLabel(MessageManager
3525 .getString("label.colourScheme_helixpropensity"));
3526 helixColour.addActionListener(this);
3527 strandColour.setLabel(MessageManager
3528 .getString("label.colourScheme_strandpropensity"));
3529 strandColour.addActionListener(this);
3530 turnColour.setLabel(
3531 MessageManager.getString("label.colourScheme_turnpropensity"));
3532 turnColour.addActionListener(this);
3533 buriedColour.setLabel(
3534 MessageManager.getString("label.colourScheme_buriedindex"));
3535 buriedColour.addActionListener(this);
3536 purinePyrimidineColour.setLabel(MessageManager
3537 .getString("label.colourScheme_purine/pyrimidine"));
3538 purinePyrimidineColour.addActionListener(this);
3539 // RNAInteractionColour.setLabel(MessageManager
3540 // .getString("label.rna_interaction"));
3541 // RNAInteractionColour.addActionListener(this);
3542 RNAHelixColour.setLabel(
3543 MessageManager.getString("label.colourScheme_rnahelices"));
3544 RNAHelixColour.addActionListener(this);
3546 .setLabel(MessageManager.getString("action.user_defined"));
3547 userDefinedColour.addActionListener(this);
3549 MessageManager.getString("label.colourScheme_%identity"));
3550 PIDColour.addActionListener(this);
3551 BLOSUM62Colour.setLabel(
3552 MessageManager.getString("label.colourScheme_blosum62"));
3553 BLOSUM62Colour.addActionListener(this);
3554 tcoffeeColour.setLabel(
3555 MessageManager.getString("label.colourScheme_t-coffeescores"));
3556 // it will be enabled only if a score file is provided
3557 tcoffeeColour.setEnabled(false);
3558 tcoffeeColour.addActionListener(this);
3559 conservationMenuItem
3560 .setLabel(MessageManager.getString("action.by_conservation"));
3561 conservationMenuItem.addItemListener(this);
3562 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3563 noColourmenuItem.addActionListener(this);
3564 abovePIDThreshold.setLabel(
3565 MessageManager.getString("label.above_identity_threshold"));
3566 abovePIDThreshold.addItemListener(this);
3567 nucleotideColour.setLabel(
3568 MessageManager.getString("label.colourScheme_nucleotide"));
3569 nucleotideColour.addActionListener(this);
3571 MessageManager.getString("label.modify_identity_threshold"));
3572 modifyPID.setEnabled(abovePIDThreshold.getState());
3573 modifyPID.addActionListener(this);
3574 modifyConservation.setLabel(MessageManager
3575 .getString("label.modify_conservation_threshold"));
3576 modifyConservation.setEnabled(conservationMenuItem.getState());
3577 modifyConservation.addActionListener(this);
3579 .setLabel(MessageManager.getString("action.by_annotation"));
3580 annotationColour.addActionListener(this);
3583 * Configure Calculate menu items and actions
3585 sortPairwiseMenuItem
3586 .setLabel(MessageManager.getString("action.by_pairwise_id"));
3587 sortPairwiseMenuItem.addActionListener(this);
3588 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3589 sortIDMenuItem.addActionListener(this);
3591 .setLabel(MessageManager.getString("action.by_length"));
3592 sortLengthMenuItem.addActionListener(this);
3593 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3594 sortGroupMenuItem.addActionListener(this);
3595 pairwiseAlignmentMenuItem.setLabel(
3596 MessageManager.getString("action.pairwise_alignment"));
3597 pairwiseAlignmentMenuItem.addActionListener(this);
3598 PCAMenuItem.setLabel(
3599 MessageManager.getString("label.principal_component_analysis"));
3600 PCAMenuItem.addActionListener(this);
3601 autoCalculate = new CheckboxMenuItem(
3602 MessageManager.getString("label.autocalculate_consensus"),
3604 averageDistanceTreeMenuItem.setLabel(
3605 MessageManager.getString("label.average_distance_identity"));
3606 averageDistanceTreeMenuItem.addActionListener(this);
3607 neighbourTreeMenuItem.setLabel(
3608 MessageManager.getString("label.neighbour_joining_identity"));
3609 neighbourTreeMenuItem.addActionListener(this);
3610 avDistanceTreeBlosumMenuItem.setLabel(
3611 MessageManager.getString("label.average_distance_blosum62"));
3612 avDistanceTreeBlosumMenuItem.addActionListener(this);
3613 njTreeBlosumMenuItem
3614 .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3615 njTreeBlosumMenuItem.addActionListener(this);
3617 .setLabel(MessageManager.getString("action.by_tree_order"));
3618 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3619 Menu calculateTreeMenu = new Menu(
3620 MessageManager.getString("action.calculate_tree"));
3621 autoCalculate.addItemListener(this);
3622 sortByTree.addItemListener(this);
3625 * Configure Help menu items and actions
3627 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3628 documentation.setLabel(MessageManager.getString("label.documentation"));
3629 documentation.addActionListener(this);
3630 about.setLabel(MessageManager.getString("label.about"));
3631 about.addActionListener(this);
3634 * Add top level menus to frame
3636 alignFrameMenuBar.add(fileMenu);
3637 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3638 alignFrameMenuBar.add(editMenu);
3639 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3640 alignFrameMenuBar.add(selectMenu);
3641 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3642 alignFrameMenuBar.add(viewMenu);
3643 Menu annotationsMenu = new Menu(
3644 MessageManager.getString("action.annotations"));
3645 alignFrameMenuBar.add(annotationsMenu);
3646 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3647 alignFrameMenuBar.add(formatMenu);
3648 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3649 alignFrameMenuBar.add(colourMenu);
3650 Menu calculateMenu = new Menu(
3651 MessageManager.getString("action.calculate"));
3652 alignFrameMenuBar.add(calculateMenu);
3653 alignFrameMenuBar.add(helpMenu);
3658 fileMenu.add(inputText);
3659 fileMenu.add(loadTree);
3660 fileMenu.add(loadAnnotations);
3661 fileMenu.addSeparator();
3662 fileMenu.add(outputTextboxMenu);
3663 fileMenu.add(outputFeatures);
3664 fileMenu.add(outputAnnotations);
3665 if (jalviewServletURL != null)
3667 fileMenu.add(loadApplication);
3669 fileMenu.addSeparator();
3670 fileMenu.add(closeMenuItem);
3675 editMenu.add(undoMenuItem);
3676 editMenu.add(redoMenuItem);
3679 pasteMenu.add(pasteNew);
3680 pasteMenu.add(pasteThis);
3681 editMenu.add(pasteMenu);
3682 editMenu.add(delete);
3683 editMenu.addSeparator();
3684 editMenu.add(remove2LeftMenuItem);
3685 editMenu.add(remove2RightMenuItem);
3686 editMenu.add(removeGappedColumnMenuItem);
3687 editMenu.add(removeAllGapsMenuItem);
3688 editMenu.add(removeRedundancyMenuItem);
3693 selectMenu.add(findMenuItem);
3694 selectMenu.addSeparator();
3695 selectMenu.add(selectAllSequenceMenuItem);
3696 selectMenu.add(deselectAllSequenceMenuItem);
3697 selectMenu.add(invertSequenceMenuItem);
3698 selectMenu.add(invertColSel);
3699 selectMenu.add(createGroup);
3700 selectMenu.add(unGroup);
3701 selectMenu.add(grpsFromSelection);
3702 selectMenu.add(deleteGroups);
3703 selectMenu.add(annotationColumnSelection);
3708 viewMenu.add(newView);
3709 viewMenu.addSeparator();
3710 showMenu.add(showColumns);
3711 showMenu.add(showSeqs);
3712 showMenu.add(showAllHidden);
3713 viewMenu.add(showMenu);
3714 hideMenu.add(hideColumns);
3715 hideMenu.add(hideSequences);
3716 hideMenu.add(hideAllSelection);
3717 hideMenu.add(hideAllButSelection);
3718 viewMenu.add(hideMenu);
3719 viewMenu.addSeparator();
3720 viewMenu.add(followMouseOverFlag);
3721 viewMenu.addSeparator();
3722 viewMenu.add(sequenceFeatures);
3723 viewMenu.add(featureSettings);
3724 viewMenu.addSeparator();
3725 viewMenu.add(alProperties);
3726 viewMenu.addSeparator();
3727 viewMenu.add(overviewMenuItem);
3732 annotationsMenu.add(annotationPanelMenuItem);
3733 annotationsMenu.addSeparator();
3734 annotationsMenu.add(showAlignmentAnnotations);
3735 annotationsMenu.add(showSequenceAnnotations);
3736 annotationsMenu.add(sortAnnBySequence);
3737 annotationsMenu.add(sortAnnByLabel);
3738 annotationsMenu.addSeparator();
3739 autoAnnMenu.add(showAutoFirst);
3740 autoAnnMenu.add(showAutoLast);
3741 autoAnnMenu.addSeparator();
3742 autoAnnMenu.add(applyAutoAnnotationSettings);
3743 autoAnnMenu.add(showConsensusHistogram);
3744 autoAnnMenu.add(showSequenceLogo);
3745 autoAnnMenu.add(normSequenceLogo);
3746 autoAnnMenu.addSeparator();
3747 autoAnnMenu.add(showGroupConservation);
3748 autoAnnMenu.add(showGroupConsensus);
3749 annotationsMenu.add(autoAnnMenu);
3754 formatMenu.add(font);
3755 formatMenu.add(seqLimits);
3756 formatMenu.add(wrapMenuItem);
3757 formatMenu.add(scaleAbove);
3758 formatMenu.add(scaleLeft);
3759 formatMenu.add(scaleRight);
3760 formatMenu.add(viewBoxesMenuItem);
3761 formatMenu.add(viewTextMenuItem);
3762 formatMenu.add(colourTextMenuItem);
3763 formatMenu.add(displayNonconservedMenuItem);
3764 formatMenu.add(renderGapsMenuItem);
3765 formatMenu.add(centreColumnLabelFlag);
3770 colourMenu.add(applyToAllGroups);
3771 colourMenu.addSeparator();
3772 colourMenu.add(noColourmenuItem);
3773 colourMenu.add(clustalColour);
3774 colourMenu.add(BLOSUM62Colour);
3775 colourMenu.add(PIDColour);
3776 colourMenu.add(zappoColour);
3777 colourMenu.add(taylorColour);
3778 colourMenu.add(hydrophobicityColour);
3779 colourMenu.add(helixColour);
3780 colourMenu.add(strandColour);
3781 colourMenu.add(turnColour);
3782 colourMenu.add(buriedColour);
3783 colourMenu.add(nucleotideColour);
3784 colourMenu.add(purinePyrimidineColour);
3785 // colourMenu.add(RNAInteractionColour);
3786 colourMenu.add(tcoffeeColour);
3787 colourMenu.add(userDefinedColour);
3788 colourMenu.addSeparator();
3789 colourMenu.add(conservationMenuItem);
3790 colourMenu.add(modifyConservation);
3791 colourMenu.add(abovePIDThreshold);
3792 colourMenu.add(modifyPID);
3793 colourMenu.add(annotationColour);
3794 colourMenu.add(RNAHelixColour);
3799 sortMenu.add(sortIDMenuItem);
3800 sortMenu.add(sortLengthMenuItem);
3801 sortMenu.add(sortByTreeMenu);
3802 sortMenu.add(sortGroupMenuItem);
3803 sortMenu.add(sortPairwiseMenuItem);
3804 calculateMenu.add(sortMenu);
3805 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3806 calculateTreeMenu.add(neighbourTreeMenuItem);
3807 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3808 calculateTreeMenu.add(njTreeBlosumMenuItem);
3809 calculateMenu.add(calculateTreeMenu);
3810 calculateMenu.addSeparator();
3811 calculateMenu.add(pairwiseAlignmentMenuItem);
3812 calculateMenu.add(PCAMenuItem);
3813 calculateMenu.add(autoCalculate);
3814 calculateMenu.add(sortByTree);
3819 helpMenu.add(documentation);
3820 helpMenu.add(about);
3825 statusBar.setBackground(Color.white);
3826 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3827 setStatus(MessageManager.getString("label.status_bar"));
3828 this.add(statusBar, BorderLayout.SOUTH);
3832 public void setStatus(String string)
3834 statusBar.setText(string);
3837 MenuItem featureSettings = new MenuItem();
3839 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3841 MenuItem annotationColour = new MenuItem();
3843 MenuItem annotationColumnSelection = new MenuItem();
3845 MenuItem invertColSel = new MenuItem();
3847 MenuItem showColumns = new MenuItem();
3849 MenuItem showSeqs = new MenuItem();
3851 MenuItem hideColumns = new MenuItem();
3853 MenuItem hideSequences = new MenuItem();
3855 MenuItem hideAllButSelection = new MenuItem();
3857 MenuItem hideAllSelection = new MenuItem();
3859 MenuItem showAllHidden = new MenuItem();
3861 MenuItem newView = new MenuItem();
3863 private CheckboxMenuItem showAlignmentAnnotations;
3865 private CheckboxMenuItem showSequenceAnnotations;
3867 private CheckboxMenuItem sortAnnBySequence;
3869 private CheckboxMenuItem sortAnnByLabel;
3871 private CheckboxMenuItem showAutoFirst;
3873 private CheckboxMenuItem showAutoLast;
3875 private SplitFrame splitFrame;
3878 * Attach the alignFrame panels after embedding menus, if necessary. This used
3879 * to be called setEmbedded, but is now creates the dropdown menus in a
3880 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3882 * @param reallyEmbedded
3883 * true to attach the view to the applet area on the page rather than
3886 public void createAlignFrameWindow(boolean reallyEmbedded)
3890 embedAlignFrameInApplet(viewport.applet);
3895 // test and embed menu bar if necessary.
3897 if (embedMenuIfNeeded(alignPanel))
3900 * adjust for status bar height too. ? pointless as overridden by layout
3903 alignPanel.setSize(getSize().width,
3904 getSize().height - statusBar.getHeight());
3906 add(statusBar, BorderLayout.SOUTH);
3907 add(alignPanel, BorderLayout.CENTER);
3908 // and register with the applet so it can pass external API calls to us
3909 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3915 * Add the components of this AlignFrame to the applet container.
3919 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3922 // Explicitly build the embedded menu panel for the on-page applet
3924 // view cannot be closed if its actually on the page
3925 fileMenu.remove(closeMenuItem);
3926 fileMenu.remove(3); // Remove Separator
3927 // construct embedded menu, using default font
3928 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3929 // and actually add the components to the applet area
3930 theApplet.setLayout(new BorderLayout());
3931 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3932 theApplet.add(statusBar, BorderLayout.SOUTH);
3933 // TODO should size be left to the layout manager?
3934 alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3935 - embeddedMenu.getHeight() - statusBar.getHeight());
3936 theApplet.add(alignPanel, BorderLayout.CENTER);
3937 final AlignFrame me = this;
3938 theApplet.addFocusListener(new FocusListener()
3942 public void focusLost(FocusEvent e)
3944 if (theApplet.currentAlignFrame == me)
3946 theApplet.currentAlignFrame = null;
3951 public void focusGained(FocusEvent e)
3953 theApplet.currentAlignFrame = me;
3956 theApplet.validate();
3960 * create a new binding between structures in an existing jmol viewer instance
3961 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3962 * this does not open a new Jmol window, or modify the display of the
3963 * structures in the original jmol window. Note This method doesn't work
3964 * without an additional javascript library to exchange messages between the
3965 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3968 * JmolViewer instance
3969 * @param sequenceIds
3970 * - sequence Ids to search for associations
3972 public SequenceStructureBinding addStructureViewInstance(
3973 Object jmolviewer, String[] sequenceIds)
3975 Viewer viewer = null;
3978 viewer = (Viewer) jmolviewer;
3979 } catch (ClassCastException ex)
3982 "Unsupported viewer object :" + jmolviewer.getClass());
3986 System.err.println("Can't use this object as a structure viewer:"
3987 + jmolviewer.getClass());
3990 SequenceI[] seqs = null;
3991 if (sequenceIds == null || sequenceIds.length == 0)
3993 seqs = viewport.getAlignment().getSequencesArray();
3997 Vector sqi = new Vector();
3998 AlignmentI al = viewport.getAlignment();
3999 for (int sid = 0; sid < sequenceIds.length; sid++)
4001 SequenceI sq = al.findName(sequenceIds[sid]);
4009 seqs = new SequenceI[sqi.size()];
4010 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4012 seqs[sid] = (SequenceI) sqi.elementAt(sid);
4020 AAStructureBindingModel jmv = null;
4021 // TODO: search for a jmv that involves viewer
4023 { // create a new viewer/jalview binding.
4024 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4031 * bind a pdb file to a sequence in the current view
4034 * - sequenceId within the dataset.
4035 * @param pdbEntryString
4036 * - the short name for the PDB file
4038 * - pdb file - either a URL or a valid PDB file.
4039 * @return true if binding was as success TODO: consider making an exception
4040 * structure for indicating when PDB parsing or sequenceId location
4043 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4046 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4047 boolean needtoadd = false;
4048 if (toaddpdb != null)
4050 Vector pdbe = toaddpdb.getAllPDBEntries();
4051 PDBEntry pdbentry = null;
4052 if (pdbe != null && pdbe.size() > 0)
4054 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4056 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4057 if (!pdbentry.getId().equals(pdbEntryString)
4058 && !pdbentry.getFile().equals(pdbFile))
4068 if (pdbentry == null)
4070 pdbentry = new PDBEntry();
4071 pdbentry.setId(pdbEntryString);
4072 pdbentry.setFile(pdbFile);
4073 needtoadd = true; // add this new entry to sequence.
4075 // resolve data source
4076 // TODO: this code should be a refactored to an io package
4077 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4079 if (protocol == null)
4085 pdbentry.setProperty("protocol", protocol);
4086 toaddpdb.addPDBId(pdbentry);
4087 alignPanel.getStructureSelectionManager()
4088 .registerPDBEntry(pdbentry);
4094 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4098 Vector sequences = new Vector();
4099 for (int i = 0; i < seqs.length; i++)
4101 if (seqs[i] != null)
4104 .addElement(new Object[]
4105 { seqs[i], (chains != null) ? chains[i] : null });
4108 seqs = new SequenceI[sequences.size()];
4109 chains = new String[sequences.size()];
4110 for (int i = 0, isize = sequences.size(); i < isize; i++)
4112 Object[] oj = (Object[]) sequences.elementAt(i);
4114 seqs[i] = (SequenceI) oj[0];
4115 chains[i] = (String) oj[1];
4118 return new Object[] { seqs, chains };
4122 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4123 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4125 // Scrub any null sequences from the array
4126 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4127 seqs = (SequenceI[]) sqch[0];
4128 chains = (String[]) sqch[1];
4129 if (seqs == null || seqs.length == 0)
4132 "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4134 if (protocol == null)
4136 String sourceType = (String) pdb.getProperty("protocol");
4139 protocol = DataSourceType.valueOf(sourceType);
4140 } catch (IllegalArgumentException e)
4144 if (protocol == null)
4146 System.err.println("Couldn't work out protocol to open structure: "
4151 if (applet.useXtrnalSviewer)
4153 // register the association(s) and quit, don't create any windows.
4154 if (StructureSelectionManager.getStructureSelectionManager(applet)
4155 .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
4157 System.err.println("Failed to map " + pdb.getFile() + " ("
4158 + protocol + ") to any sequences");
4162 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4164 // can only do alignments with Jmol
4165 // find the last jmol window assigned to this alignment
4166 AppletJmol ajm = null, tajm;
4167 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4168 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4170 tajm = (AppletJmol) jmols.elementAt(i);
4171 if (tajm.ap.alignFrame == this)
4180 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4181 // try and add the pdb structure
4186 // otherwise, create a new window
4187 if (applet.jmolAvailable)
4189 new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4190 applet.lastFrameX += 40;
4191 applet.lastFrameY += 40;
4195 new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4200 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4201 SequenceI[][] seqs, String[][] chains, String[] protocols)
4203 // TODO Auto-generated method stub
4204 System.err.println("Aligned Structure View: Not yet implemented.");
4208 * modify the current selection, providing the user has not made a selection
4212 * - sequences from this alignment
4214 * - columns to be selected on the alignment
4216 public void select(SequenceGroup sel, ColumnSelection csel,
4217 HiddenColumns hidden)
4219 alignPanel.seqPanel.selection(sel, csel, hidden, null);
4222 public void scrollTo(int row, int column)
4224 alignPanel.seqPanel.scrollTo(row, column);
4227 public void scrollToRow(int row)
4229 alignPanel.seqPanel.scrollToRow(row);
4232 public void scrollToColumn(int column)
4234 alignPanel.seqPanel.scrollToColumn(column);
4238 * @return the alignments unique ID.
4240 public String getSequenceSetId()
4242 return viewport.getSequenceSetId();
4246 * Load the (T-Coffee) score file from the specified url
4249 * File/URL/T-COFFEE score file contents
4250 * @throws IOException
4251 * @return true if alignment was annotated with data from source
4253 public boolean loadScoreFile(String source) throws IOException
4256 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4257 AppletFormatAdapter.checkProtocol(source));
4258 if (!file.isValid())
4260 // TODO: raise dialog for gui
4261 System.err.println("Problems parsing T-Coffee scores: "
4262 + file.getWarningMessage());
4263 System.err.println("Origin was:\n" + source);
4268 * check that the score matrix matches the alignment dimensions
4271 if ((aln = viewport.getAlignment()) != null
4272 && (aln.getHeight() != file.getHeight()
4273 || aln.getWidth() != file.getWidth()))
4275 // TODO: raise a dialog box here rather than bomb out.
4277 "The scores matrix does not match the alignment dimensions");
4281 // TODO add parameter to indicate if matching should be done
4282 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4284 alignPanel.fontChanged();
4285 tcoffeeColour.setEnabled(true);
4286 // switch to this color
4287 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4292 System.err.println("Problems resolving T-Coffee scores:");
4293 if (file.getWarningMessage() != null)
4295 System.err.println(file.getWarningMessage());
4301 public SplitFrame getSplitFrame()
4303 return this.splitFrame;
4306 public void setSplitFrame(SplitFrame sf)
4308 this.splitFrame = sf;
4311 // may not need this
4313 public void setShowSeqFeatures(boolean b)
4315 // showSeqFeatures.setSelected(b);
4316 viewport.setShowSequenceFeatures(b);
4321 public void setMenusForViewport()
4323 // setMenusFromViewport(viewport);
4328 public void refreshFeatureUI(boolean enableIfNecessary)
4330 if (enableIfNecessary)
4332 sequenceFeatures.setState(true);
4333 alignPanel.av.setShowSequenceFeatures(true);
4338 public FeatureSettingsControllerI getFeatureSettingsUI()
4340 return alignPanel.av.featureSettings;
4344 public FeatureSettingsControllerI showFeatureSettingsUI()
4346 return new FeatureSettings(alignPanel);
4349 private Rectangle fs_bounds = null;
4352 public void setFeatureSettingsGeometry(Rectangle bounds)
4358 public Rectangle getFeatureSettingsGeometry()