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.api.AlignViewControllerGuiI;
26 import jalview.api.AlignViewControllerI;
27 import jalview.api.AlignViewportI;
28 import jalview.api.FeatureColourI;
29 import jalview.api.FeatureRenderer;
30 import jalview.api.FeatureSettingsControllerI;
31 import jalview.api.SequenceStructureBinding;
32 import jalview.bin.JalviewLite;
33 import jalview.commands.CommandI;
34 import jalview.commands.EditCommand;
35 import jalview.commands.EditCommand.Action;
36 import jalview.commands.OrderCommand;
37 import jalview.commands.RemoveGapColCommand;
38 import jalview.commands.RemoveGapsCommand;
39 import jalview.commands.SlideSequencesCommand;
40 import jalview.commands.TrimRegionCommand;
41 import jalview.datamodel.Alignment;
42 import jalview.datamodel.AlignmentAnnotation;
43 import jalview.datamodel.AlignmentI;
44 import jalview.datamodel.AlignmentOrder;
45 import jalview.datamodel.ColumnSelection;
46 import jalview.datamodel.PDBEntry;
47 import jalview.datamodel.Sequence;
48 import jalview.datamodel.SequenceGroup;
49 import jalview.datamodel.SequenceI;
50 import jalview.io.AnnotationFile;
51 import jalview.io.AppletFormatAdapter;
52 import jalview.io.FeaturesFile;
53 import jalview.io.TCoffeeScoreFile;
54 import jalview.schemes.Blosum62ColourScheme;
55 import jalview.schemes.BuriedColourScheme;
56 import jalview.schemes.ClustalxColourScheme;
57 import jalview.schemes.ColourSchemeI;
58 import jalview.schemes.HelixColourScheme;
59 import jalview.schemes.HydrophobicColourScheme;
60 import jalview.schemes.NucleotideColourScheme;
61 import jalview.schemes.PIDColourScheme;
62 import jalview.schemes.PurinePyrimidineColourScheme;
63 import jalview.schemes.RNAHelicesColourChooser;
64 import jalview.schemes.StrandColourScheme;
65 import jalview.schemes.TCoffeeColourScheme;
66 import jalview.schemes.TaylorColourScheme;
67 import jalview.schemes.TurnColourScheme;
68 import jalview.schemes.ZappoColourScheme;
69 import jalview.structure.StructureSelectionManager;
70 import jalview.structures.models.AAStructureBindingModel;
71 import jalview.util.MappingUtils;
72 import jalview.util.MessageManager;
73 import jalview.viewmodel.AlignmentViewport;
75 import java.awt.BorderLayout;
76 import java.awt.Canvas;
77 import java.awt.CheckboxMenuItem;
78 import java.awt.Color;
79 import java.awt.FlowLayout;
81 import java.awt.FontMetrics;
82 import java.awt.Frame;
83 import java.awt.Graphics;
84 import java.awt.Label;
86 import java.awt.MenuBar;
87 import java.awt.MenuItem;
88 import java.awt.Panel;
89 import java.awt.event.ActionEvent;
90 import java.awt.event.ActionListener;
91 import java.awt.event.FocusEvent;
92 import java.awt.event.FocusListener;
93 import java.awt.event.ItemEvent;
94 import java.awt.event.ItemListener;
95 import java.awt.event.KeyEvent;
96 import java.awt.event.KeyListener;
97 import java.awt.event.WindowAdapter;
98 import java.awt.event.WindowEvent;
99 import java.io.IOException;
101 import java.net.URLEncoder;
102 import java.util.Arrays;
103 import java.util.Deque;
104 import java.util.HashMap;
105 import java.util.Hashtable;
106 import java.util.List;
107 import java.util.Map;
108 import java.util.StringTokenizer;
109 import java.util.Vector;
111 import org.jmol.viewer.Viewer;
113 public class AlignFrame extends EmbmenuFrame implements ActionListener,
114 ItemListener, KeyListener, AlignViewControllerGuiI
116 public AlignViewControllerI avc;
118 public AlignmentPanel alignPanel;
120 public AlignViewport viewport;
122 // width and height may be overridden by applet parameters
123 int frameWidth = 700;
125 int frameHeight = 500;
127 String jalviewServletURL;
130 * Flag for showing autocalculated consensus above or below other consensus
133 private boolean showAutoCalculatedAbove;
135 private SequenceAnnotationOrder annotationSortOrder;
138 * Constructor that creates the frame and adds it to the display.
145 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
148 this(al, applet, title, embedded, true);
152 * Constructor that optionally allows the frame to be displayed or only
159 * @param addToDisplay
161 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
162 boolean embedded, boolean addToDisplay)
164 this(al, null, null, applet, title, embedded, addToDisplay);
167 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
168 ColumnSelection columnSelection, JalviewLite applet,
169 String title, boolean embedded)
171 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
174 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
175 ColumnSelection columnSelection, JalviewLite applet,
176 String title, boolean embedded, boolean addToDisplay)
180 jalviewServletURL = applet.getParameter("APPLICATION_URL");
186 } catch (Exception ex)
188 ex.printStackTrace();
190 // need to get window geometry before we calculate alignment layout
196 param = applet.getParameter("windowWidth");
199 int width = Integer.parseInt(param);
202 param = applet.getParameter("windowHeight");
205 int height = Integer.parseInt(param);
206 frameHeight = height;
208 } catch (Exception ex)
212 viewport = new AlignViewport(al, applet);
214 if (hiddenSeqs != null && hiddenSeqs.length > 0)
216 viewport.hideSequence(hiddenSeqs);
218 if (columnSelection != null)
220 viewport.setColumnSelection(columnSelection);
222 viewport.setScaleAboveWrapped(scaleAbove.getState());
224 alignPanel = new AlignmentPanel(this, viewport);
225 avc = new jalview.controller.AlignViewController(this, viewport,
227 viewport.updateConservation(alignPanel);
228 viewport.updateConsensus(alignPanel);
230 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
231 followMouseOverFlag.setState(viewport.isFollowHighlight());
232 showGroupConsensus.setState(viewport.isShowGroupConsensus());
233 showGroupConservation.setState(viewport.isShowGroupConservation());
234 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
235 showSequenceLogo.setState(viewport.isShowSequenceLogo());
236 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
237 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
238 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
239 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
240 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
241 showAlignmentAnnotations.setState(true);
242 showSequenceAnnotations.setState(false);
244 seqLimits.setState(viewport.getShowJVSuffix());
248 String param = applet.getParameter("sortBy");
251 if (param.equalsIgnoreCase("Id"))
253 sortIDMenuItem_actionPerformed();
255 else if (param.equalsIgnoreCase("Pairwise Identity"))
257 sortPairwiseMenuItem_actionPerformed();
259 else if (param.equalsIgnoreCase("Length"))
261 sortLengthMenuItem_actionPerformed();
265 param = applet.getParameter("wrap");
268 if (param.equalsIgnoreCase("true"))
270 wrapMenuItem.setState(true);
271 wrapMenuItem_actionPerformed();
274 param = applet.getParameter("centrecolumnlabels");
277 centreColumnLabelFlag.setState(true);
278 centreColumnLabelFlag_stateChanged();
282 if (viewport.getAlignment().isNucleotide())
284 viewport.updateStrucConsensus(alignPanel);
285 if (viewport.getAlignment().hasRNAStructure())
287 RNAHelixColour.setEnabled(true);
291 RNAHelixColour.setEnabled(false);
296 RNAHelixColour.setEnabled(false);
297 purinePyrimidineColour.setEnabled(false);
299 // Some JVMS send keyevents to Top frame or lowest panel,
300 // Havent worked out why yet. So add to both this frame and seqCanvas for
302 this.addKeyListener(this);
303 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
304 alignPanel.idPanel.idCanvas.addKeyListener(this);
305 alignPanel.scalePanel.addKeyListener(this);
306 alignPanel.annotationPanel.addKeyListener(this);
307 alignPanel.annotationPanelHolder.addKeyListener(this);
308 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
309 alignPanel.alabels.addKeyListener(this);
311 setAnnotationsVisibility();
315 addToDisplay(embedded);
322 public void addToDisplay(boolean embedded)
324 createAlignFrameWindow(embedded);
326 alignPanel.adjustAnnotationHeight();
327 alignPanel.paintAlignment(true);
330 public AlignViewport getAlignViewport()
335 public SeqCanvas getSeqcanvas()
337 return alignPanel.seqPanel.seqCanvas;
341 * Load a features file onto the alignment
344 * file URL, content, or other resolvable path
346 * is protocol for accessing data referred to by file
349 public boolean parseFeaturesFile(String file, String type)
351 return parseFeaturesFile(file, type, true);
355 * Load a features file onto the alignment
358 * file URL, content, or other resolvable path
360 * is protocol for accessing data referred to by file
361 * @param autoenabledisplay
362 * when true, display features flag will be automatically enabled if
363 * features are loaded
364 * @return true if data parsed as a features file
366 public boolean parseFeaturesFile(String file, String type,
367 boolean autoenabledisplay)
369 boolean featuresFile = false;
372 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
373 .getFeatureRenderer().getFeatureColours();
374 boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
375 "relaxedidmatch", false);
376 featuresFile = new FeaturesFile(file, type).parse(
377 viewport.getAlignment(), colours, true, relaxedIdMatching);
378 } catch (Exception ex)
380 ex.printStackTrace();
385 if (autoenabledisplay)
387 viewport.setShowSequenceFeatures(true);
388 sequenceFeatures.setState(true);
390 if (alignPanel.seqPanel.seqCanvas.fr != null)
392 // update the min/max ranges where necessary
393 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
395 if (viewport.featureSettings != null)
397 viewport.featureSettings.refreshTable();
399 alignPanel.paintAlignment(true);
400 statusBar.setText(MessageManager
401 .getString("label.successfully_added_features_alignment"));
407 public void keyPressed(KeyEvent evt)
409 if (viewport.cursorMode
410 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
411 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
412 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
413 && Character.isDigit(evt.getKeyChar()))
415 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
418 switch (evt.getKeyCode())
420 case 27: // escape key
421 deselectAllSequenceMenuItem_actionPerformed();
423 alignPanel.alabels.cancelDrag();
426 if (evt.isControlDown() || evt.isMetaDown())
428 cut_actionPerformed();
432 if (viewport.cursorMode && !evt.isControlDown())
434 alignPanel.seqPanel.setCursorColumn();
436 if (evt.isControlDown() || evt.isMetaDown())
438 copy_actionPerformed();
442 if (evt.isControlDown())
444 paste(evt.isShiftDown());
448 if (evt.isControlDown() || evt.isMetaDown())
450 selectAllSequenceMenuItem_actionPerformed();
453 case KeyEvent.VK_DOWN:
454 if (viewport.cursorMode)
456 alignPanel.seqPanel.moveCursor(0, 1);
460 moveSelectedSequences(false);
465 if (viewport.cursorMode)
467 alignPanel.seqPanel.moveCursor(0, -1);
471 moveSelectedSequences(true);
475 case KeyEvent.VK_LEFT:
476 if (evt.isAltDown() || !viewport.cursorMode)
478 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
482 alignPanel.seqPanel.moveCursor(-1, 0);
486 case KeyEvent.VK_RIGHT:
487 if (evt.isAltDown() || !viewport.cursorMode)
489 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
493 alignPanel.seqPanel.moveCursor(1, 0);
497 case KeyEvent.VK_SPACE:
498 if (viewport.cursorMode)
500 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
501 || evt.isShiftDown() || evt.isAltDown());
505 case KeyEvent.VK_DELETE:
506 case KeyEvent.VK_BACK_SPACE:
507 if (viewport.cursorMode)
509 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
510 || evt.isShiftDown() || evt.isAltDown());
514 cut_actionPerformed();
515 alignPanel.seqPanel.seqCanvas.repaint();
520 if (viewport.cursorMode)
522 alignPanel.seqPanel.setCursorRow();
526 if (viewport.cursorMode)
528 alignPanel.seqPanel.setCursorPosition();
532 case KeyEvent.VK_ENTER:
533 case KeyEvent.VK_COMMA:
534 if (viewport.cursorMode)
536 alignPanel.seqPanel.setCursorRowAndColumn();
541 if (viewport.cursorMode)
543 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
547 if (viewport.cursorMode)
549 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
554 viewport.cursorMode = !viewport.cursorMode;
555 statusBar.setText(MessageManager.formatMessage(
556 "label.keyboard_editing_mode",
557 new String[] { (viewport.cursorMode ? "on" : "off") }));
558 if (viewport.cursorMode)
560 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
561 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
566 if (evt.isControlDown())
568 findMenuItem_actionPerformed();
574 boolean toggleSeqs = !evt.isControlDown();
575 boolean toggleCols = !evt.isShiftDown();
576 toggleHiddenRegions(toggleSeqs, toggleCols);
580 case KeyEvent.VK_PAGE_UP:
581 if (viewport.getWrapAlignment())
583 alignPanel.scrollUp(true);
587 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
588 - viewport.endSeq + viewport.startSeq);
592 case KeyEvent.VK_PAGE_DOWN:
593 if (viewport.getWrapAlignment())
595 alignPanel.scrollUp(false);
599 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
600 + viewport.endSeq - viewport.startSeq);
605 if (evt.isControlDown())
607 undoMenuItem_actionPerformed();
612 if (evt.isControlDown())
614 redoMenuItem_actionPerformed();
619 if (evt.isControlDown())
626 if (evt.isControlDown())
628 trimAlignment(false);
633 if (evt.isControlDown())
635 if (evt.isShiftDown())
637 this.removeAllGapsMenuItem_actionPerformed();
641 removeGappedColumnMenuItem_actionPerformed();
646 if (evt.isControlDown())
650 invertColSel_actionPerformed();
654 invertSequenceMenuItem_actionPerformed();
660 if (evt.isControlDown())
662 if (evt.isShiftDown())
664 this.unGroup_actionPerformed();
668 this.createGroup_actionPerformed();
674 if (evt.isControlDown())
676 this.deleteGroups_actionPerformed();
681 if (evt.isControlDown())
688 alignPanel.paintAlignment(true);
692 * called by key handler and the hide all/show all menu items
697 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
699 boolean hide = false;
700 SequenceGroup sg = viewport.getSelectionGroup();
701 if (!toggleSeqs && !toggleCols)
703 // Hide everything by the current selection - this is a hack - we do the
704 // invert and then hide
705 // first check that there will be visible columns after the invert.
706 if ((viewport.getColumnSelection() != null
707 && viewport.getColumnSelection().getSelected() != null && viewport
708 .getColumnSelection().getSelected().size() > 0)
709 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
712 // now invert the sequence set, if required - empty selection implies
713 // that no hiding is required.
716 invertSequenceMenuItem_actionPerformed();
717 sg = viewport.getSelectionGroup();
721 viewport.expandColSelection(sg, true);
722 // finally invert the column selection and get the new sequence
723 // selection and indicate it should be hidden.
724 invertColSel_actionPerformed();
731 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
734 viewport.hideAllSelectedSeqs();
736 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
739 viewport.showAllHiddenSeqs();
745 if (viewport.getColumnSelection().getSelected().size() > 0)
747 viewport.hideSelectedColumns();
750 viewport.setSelectionGroup(sg);
755 viewport.showAllHiddenColumns();
757 viewport.sendSelection();
762 public void keyReleased(KeyEvent evt)
767 public void keyTyped(KeyEvent evt)
772 public void itemStateChanged(ItemEvent evt)
774 final Object source = evt.getSource();
775 if (source == displayNonconservedMenuItem)
777 displayNonconservedMenuItem_actionPerformed();
779 else if (source == colourTextMenuItem)
781 colourTextMenuItem_actionPerformed();
783 else if (source == wrapMenuItem)
785 wrapMenuItem_actionPerformed();
787 else if (source == scaleAbove)
789 viewport.setScaleAboveWrapped(scaleAbove.getState());
791 else if (source == scaleLeft)
793 viewport.setScaleLeftWrapped(scaleLeft.getState());
795 else if (source == scaleRight)
797 viewport.setScaleRightWrapped(scaleRight.getState());
799 else if (source == seqLimits)
801 seqLimits_itemStateChanged();
803 else if (source == viewBoxesMenuItem)
805 viewport.setShowBoxes(viewBoxesMenuItem.getState());
807 else if (source == viewTextMenuItem)
809 viewport.setShowText(viewTextMenuItem.getState());
811 else if (source == renderGapsMenuItem)
813 viewport.setRenderGaps(renderGapsMenuItem.getState());
815 else if (source == annotationPanelMenuItem)
817 boolean showAnnotations = annotationPanelMenuItem.getState();
818 showAlignmentAnnotations.setEnabled(showAnnotations);
819 showSequenceAnnotations.setEnabled(showAnnotations);
820 viewport.setShowAnnotation(showAnnotations);
821 alignPanel.setAnnotationVisible(showAnnotations);
823 else if (source == sequenceFeatures)
825 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
826 alignPanel.seqPanel.seqCanvas.repaint();
828 else if (source == showAlignmentAnnotations)
830 setAnnotationsVisibility();
832 else if (source == showSequenceAnnotations)
834 setAnnotationsVisibility();
836 else if (source == sortAnnBySequence)
838 boolean newState = sortAnnBySequence.getState();
839 sortAnnByLabel.setState(false);
840 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
841 : SequenceAnnotationOrder.NONE);
842 setViewportAnnotationOrder();
844 else if (source == sortAnnByLabel)
846 boolean newState = sortAnnByLabel.getState();
847 sortAnnBySequence.setState(false);
848 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
849 : SequenceAnnotationOrder.NONE);
850 setViewportAnnotationOrder();
852 else if (source == showAutoFirst)
854 showAutoLast.setState(!showAutoFirst.getState());
855 setShowAutoCalculatedAbove(showAutoFirst.getState());
856 setViewportAnnotationOrder();
858 else if (source == showAutoLast)
860 showAutoFirst.setState(!showAutoLast.getState());
861 setShowAutoCalculatedAbove(showAutoFirst.getState());
862 setViewportAnnotationOrder();
864 else if (source == conservationMenuItem)
866 conservationMenuItem_actionPerformed();
868 else if (source == abovePIDThreshold)
870 abovePIDThreshold_actionPerformed();
872 else if (source == applyToAllGroups)
874 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
876 else if (source == autoCalculate)
878 viewport.autoCalculateConsensus = autoCalculate.getState();
880 else if (source == sortByTree)
882 viewport.sortByTree = sortByTree.getState();
884 else if (source == this.centreColumnLabelFlag)
886 centreColumnLabelFlag_stateChanged();
888 else if (source == this.followMouseOverFlag)
890 mouseOverFlag_stateChanged();
892 else if (source == showGroupConsensus)
894 showGroupConsensus_actionPerformed();
896 else if (source == showGroupConservation)
898 showGroupConservation_actionPerformed();
900 else if (source == showSequenceLogo)
902 showSequenceLogo_actionPerformed();
904 else if (source == normSequenceLogo)
906 normSequenceLogo_actionPerformed();
908 else if (source == showConsensusHistogram)
910 showConsensusHistogram_actionPerformed();
912 else if (source == applyAutoAnnotationSettings)
914 applyAutoAnnotationSettings_actionPerformed();
916 alignPanel.paintAlignment(true);
920 * Set the visibility state of sequence-related and/or alignment-related
921 * annotations depending on checkbox selections, and repaint.
925 private void setAnnotationsVisibility()
927 boolean showForAlignment = showAlignmentAnnotations.getState();
928 boolean showForSequences = showSequenceAnnotations.getState();
929 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
931 for (AlignmentAnnotation aa : alignPanel.getAlignment()
932 .getAlignmentAnnotation())
934 boolean visible = (aa.sequenceRef == null ? showForAlignment
936 aa.visible = visible;
939 alignPanel.validateAnnotationDimensions(true);
944 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
946 this.annotationSortOrder = order;
950 * Set flags on the viewport that control annotation ordering
952 private void setViewportAnnotationOrder()
954 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
956 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
959 private void setShowAutoCalculatedAbove(boolean showAbove)
961 this.showAutoCalculatedAbove = showAbove;
964 private void mouseOverFlag_stateChanged()
966 viewport.setFollowHighlight(followMouseOverFlag.getState());
967 // TODO: could kick the scrollTo mechanism to reset view for current
971 private void centreColumnLabelFlag_stateChanged()
973 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
974 this.alignPanel.annotationPanel.repaint();
978 public void actionPerformed(ActionEvent evt)
980 viewport.applet.currentAlignFrame = this;
982 Object source = evt.getSource();
984 if (source == inputText)
986 inputText_actionPerformed();
988 else if (source == loadTree)
990 loadTree_actionPerformed();
992 else if (source == loadApplication)
994 launchFullApplication();
996 else if (source == loadAnnotations)
1000 else if (source == outputAnnotations)
1002 outputAnnotations(true);
1004 else if (source == outputFeatures)
1006 outputFeatures(true, "Jalview");
1008 else if (source == closeMenuItem)
1010 closeMenuItem_actionPerformed();
1012 else if (source == copy)
1014 copy_actionPerformed();
1016 else if (source == undoMenuItem)
1018 undoMenuItem_actionPerformed();
1020 else if (source == redoMenuItem)
1022 redoMenuItem_actionPerformed();
1024 else if (source == inputText)
1026 inputText_actionPerformed();
1028 else if (source == closeMenuItem)
1030 closeMenuItem_actionPerformed();
1032 else if (source == undoMenuItem)
1034 undoMenuItem_actionPerformed();
1036 else if (source == redoMenuItem)
1038 redoMenuItem_actionPerformed();
1040 else if (source == copy)
1042 copy_actionPerformed();
1044 else if (source == pasteNew)
1046 pasteNew_actionPerformed();
1048 else if (source == pasteThis)
1050 pasteThis_actionPerformed();
1052 else if (source == cut)
1054 cut_actionPerformed();
1056 else if (source == delete)
1058 delete_actionPerformed();
1060 else if (source == grpsFromSelection)
1062 makeGrpsFromSelection_actionPerformed();
1064 else if (source == deleteGroups)
1066 deleteGroups_actionPerformed();
1068 else if (source == selectAllSequenceMenuItem)
1070 selectAllSequenceMenuItem_actionPerformed();
1072 else if (source == deselectAllSequenceMenuItem)
1074 deselectAllSequenceMenuItem_actionPerformed();
1076 else if (source == invertSequenceMenuItem)
1078 invertSequenceMenuItem_actionPerformed();
1079 // uncomment to slave sequence selections in split frame
1080 // viewport.sendSelection();
1082 else if (source == invertColSel)
1084 viewport.invertColumnSelection();
1085 alignPanel.paintAlignment(true);
1086 viewport.sendSelection();
1088 else if (source == remove2LeftMenuItem)
1090 trimAlignment(true);
1092 else if (source == remove2RightMenuItem)
1094 trimAlignment(false);
1096 else if (source == removeGappedColumnMenuItem)
1098 removeGappedColumnMenuItem_actionPerformed();
1100 else if (source == removeAllGapsMenuItem)
1102 removeAllGapsMenuItem_actionPerformed();
1104 else if (source == findMenuItem)
1106 findMenuItem_actionPerformed();
1108 else if (source == font)
1110 new FontChooser(alignPanel);
1112 else if (source == newView)
1116 else if (source == showColumns)
1118 viewport.showAllHiddenColumns();
1119 alignPanel.paintAlignment(true);
1120 viewport.sendSelection();
1122 else if (source == showSeqs)
1124 viewport.showAllHiddenSeqs();
1125 alignPanel.paintAlignment(true);
1126 // uncomment if we want to slave sequence selections in split frame
1127 // viewport.sendSelection();
1129 else if (source == hideColumns)
1131 viewport.hideSelectedColumns();
1132 alignPanel.paintAlignment(true);
1133 viewport.sendSelection();
1135 else if (source == hideSequences
1136 && viewport.getSelectionGroup() != null)
1138 viewport.hideAllSelectedSeqs();
1139 alignPanel.paintAlignment(true);
1140 // uncomment if we want to slave sequence selections in split frame
1141 // viewport.sendSelection();
1143 else if (source == hideAllButSelection)
1145 toggleHiddenRegions(false, false);
1146 alignPanel.paintAlignment(true);
1147 viewport.sendSelection();
1149 else if (source == hideAllSelection)
1151 SequenceGroup sg = viewport.getSelectionGroup();
1152 viewport.expandColSelection(sg, false);
1153 viewport.hideAllSelectedSeqs();
1154 viewport.hideSelectedColumns();
1155 alignPanel.paintAlignment(true);
1156 viewport.sendSelection();
1158 else if (source == showAllHidden)
1160 viewport.showAllHiddenColumns();
1161 viewport.showAllHiddenSeqs();
1162 alignPanel.paintAlignment(true);
1163 viewport.sendSelection();
1165 else if (source == showGroupConsensus)
1167 showGroupConsensus_actionPerformed();
1169 else if (source == showGroupConservation)
1171 showGroupConservation_actionPerformed();
1173 else if (source == showSequenceLogo)
1175 showSequenceLogo_actionPerformed();
1177 else if (source == normSequenceLogo)
1179 normSequenceLogo_actionPerformed();
1181 else if (source == showConsensusHistogram)
1183 showConsensusHistogram_actionPerformed();
1185 else if (source == applyAutoAnnotationSettings)
1187 applyAutoAnnotationSettings_actionPerformed();
1189 else if (source == featureSettings)
1191 new FeatureSettings(alignPanel);
1193 else if (source == alProperties)
1195 StringBuffer contents = new jalview.io.AlignmentProperties(
1196 viewport.getAlignment()).formatAsString();
1197 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1198 cap.setText(contents.toString());
1199 Frame frame = new Frame();
1201 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1202 "label.alignment_properties", new String[] { getTitle() }),
1205 else if (source == overviewMenuItem)
1207 overviewMenuItem_actionPerformed();
1209 else if (source == noColourmenuItem)
1213 else if (source == clustalColour)
1215 abovePIDThreshold.setState(false);
1216 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1218 else if (source == zappoColour)
1220 changeColour(new ZappoColourScheme());
1222 else if (source == taylorColour)
1224 changeColour(new TaylorColourScheme());
1226 else if (source == hydrophobicityColour)
1228 changeColour(new HydrophobicColourScheme());
1230 else if (source == helixColour)
1232 changeColour(new HelixColourScheme());
1234 else if (source == strandColour)
1236 changeColour(new StrandColourScheme());
1238 else if (source == turnColour)
1240 changeColour(new TurnColourScheme());
1242 else if (source == buriedColour)
1244 changeColour(new BuriedColourScheme());
1246 else if (source == nucleotideColour)
1248 changeColour(new NucleotideColourScheme());
1250 else if (source == purinePyrimidineColour)
1252 changeColour(new PurinePyrimidineColourScheme());
1254 // else if (source == RNAInteractionColour)
1256 // changeColour(new RNAInteractionColourScheme());
1258 else if (source == RNAHelixColour)
1260 new RNAHelicesColourChooser(viewport, alignPanel);
1262 else if (source == modifyPID)
1264 modifyPID_actionPerformed();
1266 else if (source == modifyConservation)
1268 modifyConservation_actionPerformed();
1270 else if (source == userDefinedColour)
1272 new UserDefinedColours(alignPanel, null);
1274 else if (source == PIDColour)
1276 changeColour(new PIDColourScheme());
1278 else if (source == BLOSUM62Colour)
1280 changeColour(new Blosum62ColourScheme());
1282 else if (source == tcoffeeColour)
1284 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1286 else if (source == annotationColour)
1288 new AnnotationColourChooser(viewport, alignPanel);
1290 else if (source == annotationColumnSelection)
1292 new AnnotationColumnChooser(viewport, alignPanel);
1294 else if (source == sortPairwiseMenuItem)
1296 sortPairwiseMenuItem_actionPerformed();
1298 else if (source == sortIDMenuItem)
1300 sortIDMenuItem_actionPerformed();
1302 else if (source == sortLengthMenuItem)
1304 sortLengthMenuItem_actionPerformed();
1306 else if (source == sortGroupMenuItem)
1308 sortGroupMenuItem_actionPerformed();
1310 else if (source == removeRedundancyMenuItem)
1312 removeRedundancyMenuItem_actionPerformed();
1314 else if (source == pairwiseAlignmentMenuItem)
1316 pairwiseAlignmentMenuItem_actionPerformed();
1318 else if (source == PCAMenuItem)
1320 PCAMenuItem_actionPerformed();
1322 else if (source == averageDistanceTreeMenuItem)
1324 averageDistanceTreeMenuItem_actionPerformed();
1326 else if (source == neighbourTreeMenuItem)
1328 neighbourTreeMenuItem_actionPerformed();
1330 else if (source == njTreeBlosumMenuItem)
1332 njTreeBlosumMenuItem_actionPerformed();
1334 else if (source == avDistanceTreeBlosumMenuItem)
1336 avTreeBlosumMenuItem_actionPerformed();
1338 else if (source == documentation)
1340 documentation_actionPerformed();
1342 else if (source == about)
1344 about_actionPerformed();
1349 public void inputText_actionPerformed()
1351 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1352 Frame frame = new Frame();
1354 jalview.bin.JalviewLite.addFrame(frame,
1355 MessageManager.getString("label.input_cut_paste"), 500, 500);
1358 protected void outputText_actionPerformed(ActionEvent e)
1360 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1361 Frame frame = new Frame();
1363 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1364 "label.alignment_output_command",
1365 new Object[] { e.getActionCommand() }), 600, 500);
1367 FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1368 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1369 e.getActionCommand(), viewport.getAlignment(),
1370 viewport.getShowJVSuffix()));
1373 public void loadAnnotations()
1375 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1376 cap.setText(MessageManager
1377 .getString("label.paste_features_annotations_Tcoffee_here"));
1378 cap.setAnnotationImport();
1379 Frame frame = new Frame();
1381 jalview.bin.JalviewLite.addFrame(frame,
1382 MessageManager.getString("action.paste_annotations"), 400, 300);
1386 public String outputAnnotations(boolean displayTextbox)
1388 String annotation = new AnnotationFile()
1389 .printAnnotationsForView(viewport);
1393 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1394 Frame frame = new Frame();
1396 jalview.bin.JalviewLite.addFrame(frame,
1397 MessageManager.getString("label.annotations"), 600, 500);
1398 cap.setText(annotation);
1404 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1406 if (alignPanel.getFeatureRenderer() != null
1407 && viewport.getFeaturesDisplayed() != null)
1409 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1415 public String outputFeatures(boolean displayTextbox, String format)
1418 FeaturesFile formatter = new FeaturesFile();
1419 if (format.equalsIgnoreCase("Jalview"))
1421 features = formatter.printJalviewFormat(viewport
1422 .getAlignment().getSequencesArray(),
1423 getDisplayedFeatureCols());
1427 features = formatter.printGffFormat(viewport.getAlignment()
1428 .getSequencesArray(), getDisplayedFeatureCols());
1433 boolean frimport = false;
1434 if (features == null || features.equals("No Features Visible"))
1436 features = "# No features visible - paste some and import them here.";
1440 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1443 cap.setAnnotationImport();
1445 Frame frame = new Frame();
1447 jalview.bin.JalviewLite.addFrame(frame,
1448 MessageManager.getString("label.features"), 600, 500);
1449 cap.setText(features);
1453 if (features == null)
1462 void launchFullApplication()
1464 StringBuffer url = new StringBuffer(jalviewServletURL);
1466 // allow servlet parameters to be passed in applet parameter
1467 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1469 url.append(firstSep);
1472 + appendProtocol(viewport.applet.getParameter("file")));
1474 if (viewport.applet.getParameter("features") != null)
1476 url.append("&features=");
1477 url.append(appendProtocol(viewport.applet.getParameter("features")));
1480 if (viewport.applet.getParameter("annotations") != null)
1482 url.append("&annotations=");
1483 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1486 if (viewport.applet.getParameter("jnetfile") != null)
1488 url.append("&annotations=");
1489 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1492 if (viewport.applet.getParameter("defaultColour") != null)
1494 url.append("&colour="
1495 + removeWhiteSpace(viewport.applet
1496 .getParameter("defaultColour")));
1499 if (viewport.applet.getParameter("userDefinedColour") != null)
1501 url.append("&colour="
1502 + removeWhiteSpace(viewport.applet
1503 .getParameter("userDefinedColour")));
1505 if (viewport.applet.getParameter("tree") != null)
1508 + appendProtocol(viewport.applet.getParameter("tree")));
1510 if (viewport.applet.getParameter("treeFile") != null)
1513 + appendProtocol(viewport.applet.getParameter("treeFile")));
1516 showURL(url.toString(), "FULL_APP");
1519 String removeWhiteSpace(String colour)
1521 StringBuffer sb = new StringBuffer();
1522 for (int i = 0; i < colour.length(); i++)
1524 if (Character.isWhitespace(colour.charAt(i)))
1530 sb.append(colour.charAt(i));
1534 return sb.toString();
1537 String appendProtocol(String url)
1542 url = URLEncoder.encode(url);
1545 * When we finally deprecate 1.1 compatibility, we can start to use
1546 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1547 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1548 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1549 * ex.printStackTrace(); }
1551 catch (java.net.MalformedURLException ex)
1553 url = viewport.applet.getCodeBase() + url;
1558 public void closeMenuItem_actionPerformed()
1560 PaintRefresher.RemoveComponent(alignPanel);
1561 if (alignPanel.seqPanel != null
1562 && alignPanel.seqPanel.seqCanvas != null)
1564 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1566 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1568 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1571 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1586 void updateEditMenuBar()
1589 if (viewport.getHistoryList().size() > 0)
1591 undoMenuItem.setEnabled(true);
1592 CommandI command = viewport.getHistoryList().peek();
1593 undoMenuItem.setLabel(MessageManager.formatMessage(
1594 "label.undo_command",
1595 new Object[] { command.getDescription() }));
1599 undoMenuItem.setEnabled(false);
1600 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1603 if (viewport.getRedoList().size() > 0)
1605 redoMenuItem.setEnabled(true);
1607 CommandI command = viewport.getRedoList().peek();
1608 redoMenuItem.setLabel(MessageManager.formatMessage(
1609 "label.redo_command",
1610 new Object[] { command.getDescription() }));
1614 redoMenuItem.setEnabled(false);
1615 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1623 public void addHistoryItem(CommandI command)
1625 if (command.getSize() > 0)
1627 viewport.addToHistoryList(command);
1628 viewport.clearRedoList();
1629 updateEditMenuBar();
1630 viewport.updateHiddenColumns();
1635 * TODO: JAL-1104 DOCUMENT ME!
1640 protected void undoMenuItem_actionPerformed()
1642 if (viewport.getHistoryList().isEmpty())
1647 CommandI command = viewport.getHistoryList().pop();
1648 viewport.addToRedoList(command);
1649 command.undoCommand(null);
1651 AlignmentViewport originalSource = getOriginatingSource(command);
1653 if (originalSource != viewport)
1656 .println("Warning: Viewport object mismatch whilst undoing");
1658 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1659 // viewport.getColumnSelection().getHiddenColumns()
1661 updateEditMenuBar();
1662 originalSource.firePropertyChange("alignment", null, originalSource
1663 .getAlignment().getSequences());
1667 * TODO: JAL-1104 DOCUMENT ME!
1672 protected void redoMenuItem_actionPerformed()
1674 if (viewport.getRedoList().isEmpty())
1679 CommandI command = viewport.getRedoList().pop();
1680 viewport.addToHistoryList(command);
1681 command.doCommand(null);
1683 AlignmentViewport originalSource = getOriginatingSource(command);
1685 if (originalSource != viewport)
1688 .println("Warning: Viewport object mismatch whilst re-doing");
1690 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1691 // viewport.getColumnSelection().getHiddenColumns()
1694 updateEditMenuBar();
1695 originalSource.firePropertyChange("alignment", null, originalSource
1696 .getAlignment().getSequences());
1699 AlignmentViewport getOriginatingSource(CommandI command)
1701 AlignmentViewport originalSource = null;
1702 // For sequence removal and addition, we need to fire
1703 // the property change event FROM the viewport where the
1704 // original alignment was altered
1705 AlignmentI al = null;
1706 if (command instanceof EditCommand)
1708 EditCommand editCommand = (EditCommand) command;
1709 al = editCommand.getAlignment();
1710 Vector comps = (Vector) PaintRefresher.components.get(viewport
1711 .getSequenceSetId());
1712 for (int i = 0; i < comps.size(); i++)
1714 if (comps.elementAt(i) instanceof AlignmentPanel)
1716 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1718 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1725 if (originalSource == null)
1727 // The original view is closed, we must validate
1728 // the current view against the closed view first
1731 PaintRefresher.validateSequences(al, viewport.getAlignment());
1734 originalSource = viewport;
1737 return originalSource;
1741 * Move the currently selected sequences up or down one position in the
1746 public void moveSelectedSequences(boolean up)
1748 SequenceGroup sg = viewport.getSelectionGroup();
1753 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1754 up ? null : viewport.getHiddenRepSequences(), up);
1755 alignPanel.paintAlignment(true);
1758 * Also move cDNA/protein complement sequences
1760 AlignViewportI complement = viewport.getCodingComplement();
1761 if (complement != null)
1763 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1764 viewport, complement);
1765 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1766 up ? null : complement.getHiddenRepSequences(), up);
1767 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1771 synchronized void slideSequences(boolean right, int size)
1773 List<SequenceI> sg = new Vector<SequenceI>();
1774 if (viewport.cursorMode)
1776 sg.add(viewport.getAlignment().getSequenceAt(
1777 alignPanel.seqPanel.seqCanvas.cursorY));
1779 else if (viewport.getSelectionGroup() != null
1780 && viewport.getSelectionGroup().getSize() != viewport
1781 .getAlignment().getHeight())
1783 sg = viewport.getSelectionGroup().getSequences(
1784 viewport.getHiddenRepSequences());
1792 Vector<SequenceI> invertGroup = new Vector();
1794 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1796 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1798 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1802 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1804 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1806 for (int i = 0; i < invertGroup.size(); i++)
1808 seqs2[i] = invertGroup.elementAt(i);
1811 SlideSequencesCommand ssc;
1814 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1815 size, viewport.getGapCharacter());
1819 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1820 size, viewport.getGapCharacter());
1823 int groupAdjustment = 0;
1824 if (ssc.getGapsInsertedBegin() && right)
1826 if (viewport.cursorMode)
1828 alignPanel.seqPanel.moveCursor(size, 0);
1832 groupAdjustment = size;
1835 else if (!ssc.getGapsInsertedBegin() && !right)
1837 if (viewport.cursorMode)
1839 alignPanel.seqPanel.moveCursor(-size, 0);
1843 groupAdjustment = -size;
1847 if (groupAdjustment != 0)
1849 viewport.getSelectionGroup().setStartRes(
1850 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1851 viewport.getSelectionGroup().setEndRes(
1852 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1855 boolean appendHistoryItem = false;
1856 Deque<CommandI> historyList = viewport.getHistoryList();
1857 if (historyList != null && historyList.size() > 0
1858 && historyList.peek() instanceof SlideSequencesCommand)
1860 appendHistoryItem = ssc
1861 .appendSlideCommand((SlideSequencesCommand) historyList
1865 if (!appendHistoryItem)
1867 addHistoryItem(ssc);
1873 static StringBuffer copiedSequences;
1875 static Vector copiedHiddenColumns;
1877 protected void copy_actionPerformed()
1879 if (viewport.getSelectionGroup() == null)
1884 SequenceGroup sg = viewport.getSelectionGroup();
1885 copiedSequences = new StringBuffer();
1886 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1887 for (int i = 0; i < sg.getSize(); i++)
1889 SequenceI seq = sg.getSequenceAt(i);
1890 int index = viewport.getAlignment().findIndex(seq);
1891 orderedSeqs.put(index, seq);
1894 int index = 0, startRes, endRes;
1897 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1899 copiedHiddenColumns = new Vector();
1900 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1901 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1903 copiedHiddenColumns.addElement(new int[] {
1904 region[0] - hiddenOffset, region[1] - hiddenOffset });
1909 copiedHiddenColumns = null;
1912 for (int i = 0; i < sg.getSize(); i++)
1914 SequenceI seq = null;
1918 if (orderedSeqs.containsKey(index))
1920 seq = orderedSeqs.get(index);
1931 // Returns residue following index if gap
1932 startRes = seq.findPosition(sg.getStartRes());
1935 // Need to find the residue preceeding index if gap
1938 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1940 ch = seq.getCharAt(j);
1941 if (!jalview.util.Comparison.isGap((ch)))
1949 endRes += seq.getStart() - 1;
1952 copiedSequences.append(seq.getName()
1958 + seq.getSequenceAsString(sg.getStartRes(),
1959 sg.getEndRes() + 1) + "\n");
1964 protected void pasteNew_actionPerformed()
1969 protected void pasteThis_actionPerformed()
1974 void paste(boolean newAlignment)
1979 if (copiedSequences == null)
1984 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1985 Vector seqs = new Vector();
1986 while (st.hasMoreElements())
1988 String name = st.nextToken();
1989 int start = Integer.parseInt(st.nextToken());
1990 int end = Integer.parseInt(st.nextToken());
1991 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1993 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1994 for (int i = 0; i < seqs.size(); i++)
1996 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2001 String newtitle = MessageManager
2002 .getString("label.copied_sequences");
2003 if (getTitle().startsWith(
2004 MessageManager.getString("label.copied_sequences")))
2006 newtitle = getTitle();
2010 newtitle = newtitle.concat(MessageManager.formatMessage(
2011 "label.from_msname", new String[] { getTitle() }));
2013 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2014 viewport.applet, newtitle, false);
2015 if (copiedHiddenColumns != null)
2017 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2019 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2020 af.viewport.hideColumns(region[0], region[1]);
2024 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2029 addSequences(newSeqs);
2032 } catch (Exception ex)
2034 } // could be anything being pasted in here
2038 void addSequences(SequenceI[] seqs)
2040 for (int i = 0; i < seqs.length; i++)
2042 viewport.getAlignment().addSequence(seqs[i]);
2046 addHistoryItem(new EditCommand(
2047 MessageManager.getString("label.add_sequences"), Action.PASTE,
2048 seqs, 0, viewport.getAlignment().getWidth(),
2049 viewport.getAlignment()));
2051 viewport.setEndSeq(viewport.getAlignment().getHeight());
2052 viewport.getAlignment().getWidth();
2053 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2058 protected void cut_actionPerformed()
2060 copy_actionPerformed();
2061 delete_actionPerformed();
2064 protected void delete_actionPerformed()
2067 SequenceGroup sg = viewport.getSelectionGroup();
2073 Vector seqs = new Vector();
2075 for (int i = 0; i < sg.getSize(); i++)
2077 seq = sg.getSequenceAt(i);
2078 seqs.addElement(seq);
2082 * If the cut affects all sequences, warn, remove highlighted columns
2084 if (sg.getSize() == viewport.getAlignment().getHeight())
2086 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2087 .getAlignment().getWidth()) ? true : false;
2088 if (isEntireAlignWidth)
2090 String title = MessageManager.getString("label.delete_all");
2091 Panel infoPanel = new Panel();
2092 infoPanel.setLayout(new FlowLayout());
2094 .add(new Label(MessageManager.getString("warn.delete_all")));
2096 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2097 dialog.setMainPanel(infoPanel);
2098 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2099 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2100 dialog.setVisible(true);
2107 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2108 sg.getEndRes() + 1);
2111 SequenceI[] cut = new SequenceI[seqs.size()];
2112 for (int i = 0; i < seqs.size(); i++)
2114 cut[i] = (SequenceI) seqs.elementAt(i);
2118 * //ADD HISTORY ITEM
2120 addHistoryItem(new EditCommand(
2121 MessageManager.getString("label.cut_sequences"), Action.CUT,
2122 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2123 viewport.getAlignment()));
2125 viewport.setSelectionGroup(null);
2126 viewport.getAlignment().deleteGroup(sg);
2128 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2131 if (viewport.getAlignment().getHeight() < 1)
2133 this.setVisible(false);
2135 viewport.sendSelection();
2139 * group consensus toggled
2142 protected void showGroupConsensus_actionPerformed()
2144 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2145 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2150 * group conservation toggled.
2152 protected void showGroupConservation_actionPerformed()
2154 viewport.setShowGroupConservation(showGroupConservation.getState());
2155 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2162 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2163 * .event.ActionEvent)
2165 protected void showConsensusHistogram_actionPerformed()
2167 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2168 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2175 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2176 * .event.ActionEvent)
2178 protected void showSequenceLogo_actionPerformed()
2180 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2181 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2184 protected void normSequenceLogo_actionPerformed()
2186 showSequenceLogo.setState(true);
2187 viewport.setShowSequenceLogo(true);
2188 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2189 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2192 protected void applyAutoAnnotationSettings_actionPerformed()
2194 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2197 protected void makeGrpsFromSelection_actionPerformed()
2199 if (avc.makeGroupsFromSelection())
2201 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2202 alignPanel.updateAnnotation();
2203 alignPanel.paintAlignment(true);
2207 protected void createGroup_actionPerformed()
2212 protected void unGroup_actionPerformed()
2216 alignPanel.alignmentChanged();
2220 protected void deleteGroups_actionPerformed()
2222 if (avc.deleteGroups())
2224 alignPanel.alignmentChanged();
2228 public void selectAllSequenceMenuItem_actionPerformed()
2230 SequenceGroup sg = new SequenceGroup();
2231 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2233 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2235 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2236 viewport.setSelectionGroup(sg);
2237 // JAL-2034 - should delegate to
2238 // alignPanel to decide if overview needs
2240 alignPanel.paintAlignment(false);
2241 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2242 viewport.sendSelection();
2245 public void deselectAllSequenceMenuItem_actionPerformed()
2247 if (viewport.cursorMode)
2249 alignPanel.seqPanel.keyboardNo1 = null;
2250 alignPanel.seqPanel.keyboardNo2 = null;
2252 viewport.setSelectionGroup(null);
2253 viewport.getColumnSelection().clear();
2254 viewport.setSelectionGroup(null);
2255 alignPanel.idPanel.idCanvas.searchResults = null;
2256 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2257 // JAL-2034 - should delegate to
2258 // alignPanel to decide if overview needs
2260 alignPanel.paintAlignment(false);
2261 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2262 viewport.sendSelection();
2265 public void invertSequenceMenuItem_actionPerformed()
2267 SequenceGroup sg = viewport.getSelectionGroup();
2268 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2270 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2273 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2274 viewport.sendSelection();
2277 public void invertColSel_actionPerformed()
2279 viewport.invertColumnSelection();
2280 alignPanel.paintAlignment(true);
2281 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2282 viewport.sendSelection();
2285 void trimAlignment(boolean trimLeft)
2287 ColumnSelection colSel = viewport.getColumnSelection();
2290 if (!colSel.isEmpty())
2294 column = colSel.getMin();
2298 column = colSel.getMax();
2302 if (viewport.getSelectionGroup() != null)
2304 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2305 viewport.getHiddenRepSequences());
2309 seqs = viewport.getAlignment().getSequencesArray();
2312 TrimRegionCommand trimRegion;
2315 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2316 column, viewport.getAlignment());
2317 viewport.setStartRes(0);
2321 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2322 column, viewport.getAlignment());
2325 statusBar.setText(MessageManager.formatMessage(
2326 "label.removed_columns",
2327 new String[] { Integer.valueOf(trimRegion.getSize())
2329 addHistoryItem(trimRegion);
2331 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2333 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2334 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2336 viewport.getAlignment().deleteGroup(sg);
2340 viewport.firePropertyChange("alignment", null, viewport
2341 .getAlignment().getSequences());
2345 public void removeGappedColumnMenuItem_actionPerformed()
2347 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2350 if (viewport.getSelectionGroup() != null)
2352 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2353 viewport.getHiddenRepSequences());
2354 start = viewport.getSelectionGroup().getStartRes();
2355 end = viewport.getSelectionGroup().getEndRes();
2359 seqs = viewport.getAlignment().getSequencesArray();
2362 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2363 "Remove Gapped Columns", seqs, start, end,
2364 viewport.getAlignment());
2366 addHistoryItem(removeGapCols);
2368 statusBar.setText(MessageManager.formatMessage(
2369 "label.removed_empty_columns",
2370 new String[] { Integer.valueOf(removeGapCols.getSize())
2373 // This is to maintain viewport position on first residue
2374 // of first sequence
2375 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2376 int startRes = seq.findPosition(viewport.startRes);
2377 // ShiftList shifts;
2378 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2379 // edit.alColumnChanges=shifts.getInverse();
2380 // if (viewport.hasHiddenColumns)
2381 // viewport.getColumnSelection().compensateForEdits(shifts);
2382 viewport.setStartRes(seq.findIndex(startRes) - 1);
2383 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2388 public void removeAllGapsMenuItem_actionPerformed()
2390 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2393 if (viewport.getSelectionGroup() != null)
2395 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2396 viewport.getHiddenRepSequences());
2397 start = viewport.getSelectionGroup().getStartRes();
2398 end = viewport.getSelectionGroup().getEndRes();
2402 seqs = viewport.getAlignment().getSequencesArray();
2405 // This is to maintain viewport position on first residue
2406 // of first sequence
2407 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2408 int startRes = seq.findPosition(viewport.startRes);
2410 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2411 viewport.getAlignment()));
2413 viewport.setStartRes(seq.findIndex(startRes) - 1);
2415 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2420 public void findMenuItem_actionPerformed()
2422 new Finder(alignPanel);
2426 * create a new view derived from the current view
2429 * @return frame for the new view
2431 public AlignFrame newView(String viewtitle)
2434 if (viewport.hasHiddenRows())
2436 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2437 .getFullAlignment().getSequencesArray());
2441 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2444 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2446 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2448 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2450 newal.addAnnotation(viewport.getAlignment()
2451 .getAlignmentAnnotation()[i]);
2456 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2458 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2459 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2460 PaintRefresher.Register(newaf.alignPanel,
2461 newaf.alignPanel.av.getSequenceSetId());
2463 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2464 newaf.alignPanel.av.getSequenceSetId());
2465 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2466 newaf.alignPanel.av.getSequenceSetId());
2468 Vector comps = (Vector) PaintRefresher.components.get(viewport
2469 .getSequenceSetId());
2471 for (int i = 0; i < comps.size(); i++)
2473 if (comps.elementAt(i) instanceof AlignmentPanel)
2479 String title = new String(this.getTitle());
2480 if (viewtitle != null)
2482 title = viewtitle + " ( " + title + ")";
2486 if (title.indexOf("(View") > -1)
2488 title = title.substring(0, title.indexOf("(View"));
2490 title += "(View " + viewSize + ")";
2493 newaf.setTitle(title.toString());
2495 newaf.viewport.setHistoryList(viewport.getHistoryList());
2496 newaf.viewport.setRedoList(viewport.getRedoList());
2502 * @return list of feature groups on the view
2504 public String[] getFeatureGroups()
2506 FeatureRenderer fr = null;
2507 if (alignPanel != null
2508 && (fr = alignPanel.getFeatureRenderer()) != null)
2510 List<String> gps = fr.getFeatureGroups();
2511 String[] _gps = gps.toArray(new String[gps.size()]);
2518 * get sequence feature groups that are hidden or shown
2524 public String[] getFeatureGroupsOfState(boolean visible)
2526 FeatureRenderer fr = null;
2527 if (alignPanel != null
2528 && (fr = alignPanel.getFeatureRenderer()) != null)
2530 List<String> gps = fr.getGroups(visible);
2531 String[] _gps = gps.toArray(new String[gps.size()]);
2538 * Change the display state for the given feature groups
2541 * list of group strings
2543 * visible or invisible
2545 public void setFeatureGroupState(String[] groups, boolean state)
2547 FeatureRenderer fr = null;
2548 this.sequenceFeatures.setState(true);
2549 viewport.setShowSequenceFeatures(true);
2550 if (alignPanel != null
2551 && (fr = alignPanel.getFeatureRenderer()) != null)
2554 fr.setGroupVisibility(Arrays.asList(groups), state);
2555 alignPanel.seqPanel.seqCanvas.repaint();
2556 if (alignPanel.overviewPanel != null)
2558 alignPanel.overviewPanel.updateOverviewImage();
2563 public void seqLimits_itemStateChanged()
2565 viewport.setShowJVSuffix(seqLimits.getState());
2566 alignPanel.fontChanged();
2567 alignPanel.paintAlignment(true);
2570 protected void colourTextMenuItem_actionPerformed()
2572 viewport.setColourText(colourTextMenuItem.getState());
2573 alignPanel.paintAlignment(true);
2576 protected void displayNonconservedMenuItem_actionPerformed()
2578 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2579 alignPanel.paintAlignment(true);
2582 protected void wrapMenuItem_actionPerformed()
2584 viewport.setWrapAlignment(wrapMenuItem.getState());
2585 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2586 scaleAbove.setEnabled(wrapMenuItem.getState());
2587 scaleLeft.setEnabled(wrapMenuItem.getState());
2588 scaleRight.setEnabled(wrapMenuItem.getState());
2589 alignPanel.paintAlignment(true);
2592 public void overviewMenuItem_actionPerformed()
2594 if (alignPanel.overviewPanel != null)
2599 Frame frame = new Frame();
2600 OverviewPanel overview = new OverviewPanel(alignPanel);
2601 frame.add(overview);
2602 // +50 must allow for applet frame window
2603 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2604 "label.overview_params", new String[] { this.getTitle() }),
2605 overview.getPreferredSize().width,
2606 overview.getPreferredSize().height + 50);
2609 final AlignmentPanel ap = alignPanel;
2610 frame.addWindowListener(new WindowAdapter()
2613 public void windowClosing(WindowEvent e)
2617 ap.setOverviewPanel(null);
2622 alignPanel.setOverviewPanel(overview);
2627 public void changeColour(ColourSchemeI cs)
2632 if (viewport.getAbovePIDThreshold())
2634 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2638 if (viewport.getConservationSelected())
2640 cs.setConservationApplied(true);
2641 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2646 cs.setConservationApplied(false);
2649 viewport.setGlobalColourScheme(cs);
2651 alignPanel.paintAlignment(true);
2654 protected void modifyPID_actionPerformed()
2656 if (viewport.getAbovePIDThreshold()
2657 && viewport.getGlobalColourScheme() != null)
2659 SliderPanel.setPIDSliderSource(alignPanel,
2660 viewport.getGlobalColourScheme(), "Background");
2661 SliderPanel.showPIDSlider();
2665 protected void modifyConservation_actionPerformed()
2667 if (viewport.getConservationSelected()
2668 && viewport.getGlobalColourScheme() != null)
2670 SliderPanel.setConservationSlider(alignPanel,
2671 viewport.getGlobalColourScheme(), "Background");
2672 SliderPanel.showConservationSlider();
2676 protected void conservationMenuItem_actionPerformed()
2678 viewport.setConservationSelected(conservationMenuItem.getState());
2680 viewport.setAbovePIDThreshold(false);
2681 abovePIDThreshold.setState(false);
2683 changeColour(viewport.getGlobalColourScheme());
2685 modifyConservation_actionPerformed();
2688 public void abovePIDThreshold_actionPerformed()
2690 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2692 conservationMenuItem.setState(false);
2693 viewport.setConservationSelected(false);
2695 changeColour(viewport.getGlobalColourScheme());
2697 modifyPID_actionPerformed();
2700 public void sortPairwiseMenuItem_actionPerformed()
2702 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2703 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2704 .getAlignment().getSequenceAt(0), null);
2706 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2707 viewport.getAlignment()));
2708 alignPanel.paintAlignment(true);
2711 public void sortIDMenuItem_actionPerformed()
2713 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2714 AlignmentSorter.sortByID(viewport.getAlignment());
2715 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2716 viewport.getAlignment()));
2717 alignPanel.paintAlignment(true);
2720 public void sortLengthMenuItem_actionPerformed()
2722 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2723 AlignmentSorter.sortByLength(viewport.getAlignment());
2724 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2725 viewport.getAlignment()));
2726 alignPanel.paintAlignment(true);
2729 public void sortGroupMenuItem_actionPerformed()
2731 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2732 AlignmentSorter.sortByGroup(viewport.getAlignment());
2733 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2734 viewport.getAlignment()));
2735 alignPanel.paintAlignment(true);
2739 public void removeRedundancyMenuItem_actionPerformed()
2741 new RedundancyPanel(alignPanel);
2744 public void pairwiseAlignmentMenuItem_actionPerformed()
2746 if (viewport.getSelectionGroup() != null
2747 && viewport.getSelectionGroup().getSize() > 1)
2749 Frame frame = new Frame();
2750 frame.add(new PairwiseAlignPanel(alignPanel));
2751 jalview.bin.JalviewLite.addFrame(frame,
2752 MessageManager.getString("action.pairwise_alignment"), 600,
2757 public void PCAMenuItem_actionPerformed()
2759 // are the sequences aligned?
2760 if (!viewport.getAlignment().isAligned(false))
2763 int Width = viewport.getAlignment().getWidth();
2765 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2767 current = viewport.getAlignment().getSequenceAt(i);
2769 if (current.getLength() < Width)
2771 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2774 alignPanel.paintAlignment(true);
2777 if ((viewport.getSelectionGroup() != null
2778 && viewport.getSelectionGroup().getSize() < 4 && viewport
2779 .getSelectionGroup().getSize() > 0)
2780 || viewport.getAlignment().getHeight() < 4)
2787 new PCAPanel(viewport);
2788 } catch (java.lang.OutOfMemoryError ex)
2794 public void averageDistanceTreeMenuItem_actionPerformed()
2796 NewTreePanel("AV", "PID", "Average distance tree using PID");
2799 public void neighbourTreeMenuItem_actionPerformed()
2801 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2804 protected void njTreeBlosumMenuItem_actionPerformed()
2806 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2809 protected void avTreeBlosumMenuItem_actionPerformed()
2811 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2814 void NewTreePanel(String type, String pwType, String title)
2816 // are the sequences aligned?
2817 if (!viewport.getAlignment().isAligned(false))
2820 int Width = viewport.getAlignment().getWidth();
2822 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2824 current = viewport.getAlignment().getSequenceAt(i);
2826 if (current.getLength() < Width)
2828 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2831 alignPanel.paintAlignment(true);
2835 if ((viewport.getSelectionGroup() != null && viewport
2836 .getSelectionGroup().getSize() > 1)
2837 || (viewport.getAlignment().getHeight() > 1))
2839 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2841 addTreeMenuItem(tp, title);
2843 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2847 void loadTree_actionPerformed()
2849 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2850 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2851 cap.setTreeImport();
2852 Frame frame = new Frame();
2854 jalview.bin.JalviewLite.addFrame(frame,
2855 MessageManager.getString("label.paste_newick_file"), 400, 300);
2858 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2860 TreePanel tp = new TreePanel(alignPanel, treeFile,
2861 MessageManager.getString("label.load_tree_from_file"), tree);
2862 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2863 addTreeMenuItem(tp, treeFile);
2867 * sort the alignment using the given treePanel
2870 * tree used to sort view
2872 * string used for undo event name
2874 public void sortByTree(TreePanel treePanel, String title)
2876 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2878 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2879 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2880 // HistoryItem.SORT));
2881 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2882 "label.order_by_params", new String[] { title }), oldOrder,
2883 viewport.getAlignment()));
2884 alignPanel.paintAlignment(true);
2888 * Do any automatic reordering of the alignment and add the necessary bits to
2889 * the menu structure for the new tree
2894 protected void addTreeMenuItem(final TreePanel treePanel,
2897 final MenuItem item = new MenuItem(title);
2898 sortByTreeMenu.add(item);
2899 item.addActionListener(new java.awt.event.ActionListener()
2902 public void actionPerformed(ActionEvent evt)
2904 sortByTree(treePanel, title); // treePanel.getTitle());
2908 treePanel.addWindowListener(new WindowAdapter()
2911 public void windowOpened(WindowEvent e)
2913 if (viewport.sortByTree)
2915 sortByTree(treePanel, title);
2917 super.windowOpened(e);
2921 public void windowClosing(WindowEvent e)
2923 sortByTreeMenu.remove(item);
2928 public boolean sortBy(AlignmentOrder alorder, String undoname)
2930 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2931 if (viewport.applet.debug)
2933 System.err.println("Sorting " + alorder.getOrder().size()
2934 + " in alignment '" + getTitle() + "'");
2936 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2937 if (undoname != null)
2939 addHistoryItem(new OrderCommand(undoname, oldOrder,
2940 viewport.getAlignment()));
2942 alignPanel.paintAlignment(true);
2946 protected void documentation_actionPerformed()
2948 alignPanel.av.applet.openJalviewHelpUrl();
2951 protected void about_actionPerformed()
2954 class AboutPanel extends Canvas
2960 public AboutPanel(String version, String builddate)
2962 this.version = version;
2963 this.builddate = builddate;
2967 public void paint(Graphics g)
2969 g.setColor(Color.white);
2970 g.fillRect(0, 0, getSize().width, getSize().height);
2971 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2972 FontMetrics fm = g.getFontMetrics();
2973 int fh = fm.getHeight();
2975 g.setColor(Color.black);
2976 // TODO: update this text for each release or centrally store it for
2977 // lite and application
2978 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2979 g.drawString(MessageManager.formatMessage(
2980 "label.jalviewLite_release", new String[] { version }), x,
2982 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2983 g.drawString(MessageManager.formatMessage(
2984 "label.jaview_build_date", new String[] { builddate }), x,
2986 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2987 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2989 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2990 x + 50, y += fh + 8);
2992 MessageManager.getString("label.jalview_dev_managers"), x,
2994 g.drawString(MessageManager
2995 .getString("label.jalview_distribution_lists"), x, y += fh);
2996 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2999 MessageManager.getString("label.jalview_cite_1_authors"),
3002 MessageManager.getString("label.jalview_cite_1_title"), x,
3004 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3009 Frame frame = new Frame();
3010 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3012 jalview.bin.JalviewLite.addFrame(frame,
3013 MessageManager.getString("label.jalview"), 580, 220);
3017 public void showURL(String url, String target)
3019 if (viewport.applet == null)
3021 System.out.println("Not running as applet - no browser available.");
3025 viewport.applet.showURL(url, target);
3029 // ////////////////////////////////////////////////////////////////////////////////
3030 // JBuilder Graphics here
3032 MenuBar alignFrameMenuBar = new MenuBar();
3034 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3036 MenuItem loadApplication = new MenuItem(
3037 MessageManager.getString("label.view_full_application"));
3039 MenuItem loadTree = new MenuItem(
3040 MessageManager.getString("label.load_associated_tree"));
3042 MenuItem loadAnnotations = new MenuItem(
3043 MessageManager.getString("label.load_features_annotations"));
3045 MenuItem outputFeatures = new MenuItem(
3046 MessageManager.getString("label.export_features"));
3048 MenuItem outputAnnotations = new MenuItem(
3049 MessageManager.getString("label.export_annotations"));
3051 MenuItem closeMenuItem = new MenuItem(
3052 MessageManager.getString("action.close"));
3054 MenuItem selectAllSequenceMenuItem = new MenuItem(
3055 MessageManager.getString("action.select_all"));
3057 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3058 MessageManager.getString("action.deselect_all"));
3060 MenuItem invertSequenceMenuItem = new MenuItem(
3061 MessageManager.getString("action.invert_selection"));
3063 MenuItem remove2LeftMenuItem = new MenuItem();
3065 MenuItem remove2RightMenuItem = new MenuItem();
3067 MenuItem removeGappedColumnMenuItem = new MenuItem();
3069 MenuItem removeAllGapsMenuItem = new MenuItem();
3071 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3073 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3075 MenuItem sortPairwiseMenuItem = new MenuItem();
3077 MenuItem sortIDMenuItem = new MenuItem();
3079 MenuItem sortLengthMenuItem = new MenuItem();
3081 MenuItem sortGroupMenuItem = new MenuItem();
3083 MenuItem removeRedundancyMenuItem = new MenuItem();
3085 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3087 MenuItem PCAMenuItem = new MenuItem();
3089 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3091 MenuItem neighbourTreeMenuItem = new MenuItem();
3093 BorderLayout borderLayout1 = new BorderLayout();
3095 public Label statusBar = new Label();
3097 MenuItem clustalColour = new MenuItem();
3099 MenuItem zappoColour = new MenuItem();
3101 MenuItem taylorColour = new MenuItem();
3103 MenuItem hydrophobicityColour = new MenuItem();
3105 MenuItem helixColour = new MenuItem();
3107 MenuItem strandColour = new MenuItem();
3109 MenuItem turnColour = new MenuItem();
3111 MenuItem buriedColour = new MenuItem();
3113 MenuItem purinePyrimidineColour = new MenuItem();
3115 // MenuItem RNAInteractionColour = new MenuItem();
3117 MenuItem RNAHelixColour = new MenuItem();
3119 MenuItem userDefinedColour = new MenuItem();
3121 MenuItem PIDColour = new MenuItem();
3123 MenuItem BLOSUM62Colour = new MenuItem();
3125 MenuItem tcoffeeColour = new MenuItem();
3127 MenuItem njTreeBlosumMenuItem = new MenuItem();
3129 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3131 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3133 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3135 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3137 MenuItem alProperties = new MenuItem(
3138 MessageManager.getString("label.alignment_props"));
3140 MenuItem overviewMenuItem = new MenuItem();
3142 MenuItem undoMenuItem = new MenuItem();
3144 MenuItem redoMenuItem = new MenuItem();
3146 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3148 MenuItem noColourmenuItem = new MenuItem();
3150 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3152 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3154 MenuItem findMenuItem = new MenuItem();
3156 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3158 MenuItem nucleotideColour = new MenuItem();
3160 MenuItem deleteGroups = new MenuItem();
3162 MenuItem grpsFromSelection = new MenuItem();
3164 MenuItem createGroup = new MenuItem();
3166 MenuItem unGroup = new MenuItem();
3168 MenuItem delete = new MenuItem();
3170 MenuItem copy = new MenuItem();
3172 MenuItem cut = new MenuItem();
3174 Menu pasteMenu = new Menu();
3176 MenuItem pasteNew = new MenuItem();
3178 MenuItem pasteThis = new MenuItem();
3180 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3182 MenuItem font = new MenuItem();
3184 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3186 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3188 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3190 MenuItem modifyPID = new MenuItem();
3192 MenuItem modifyConservation = new MenuItem();
3194 CheckboxMenuItem autoCalculate = null;
3196 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3197 "Sort Alignment With New Tree", true);
3199 Menu sortByTreeMenu = new Menu();
3201 MenuItem inputText = new MenuItem();
3203 MenuItem documentation = new MenuItem();
3205 MenuItem about = new MenuItem();
3207 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3209 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3211 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3213 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3215 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3217 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3219 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3221 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3223 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3226 * Initialise menus and other items
3230 private void jbInit() throws Exception
3232 setMenuBar(alignFrameMenuBar);
3235 * Configure File menu items and actions
3238 .setLabel(MessageManager.getString("label.input_from_textbox"));
3239 inputText.addActionListener(this);
3240 Menu outputTextboxMenu = new Menu(
3241 MessageManager.getString("label.out_to_textbox"));
3242 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3245 MenuItem item = new MenuItem(
3246 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3248 item.addActionListener(new java.awt.event.ActionListener()
3251 public void actionPerformed(ActionEvent e)
3253 outputText_actionPerformed(e);
3257 outputTextboxMenu.add(item);
3259 closeMenuItem.addActionListener(this);
3260 loadApplication.addActionListener(this);
3261 loadTree.addActionListener(this);
3262 loadAnnotations.addActionListener(this);
3263 outputFeatures.addActionListener(this);
3264 outputAnnotations.addActionListener(this);
3267 * Configure Edit menu items and actions
3269 undoMenuItem.setEnabled(false);
3270 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3271 undoMenuItem.addActionListener(this);
3272 redoMenuItem.setEnabled(false);
3273 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3274 redoMenuItem.addActionListener(this);
3275 copy.setLabel(MessageManager.getString("action.copy"));
3276 copy.addActionListener(this);
3277 cut.setLabel(MessageManager.getString("action.cut"));
3278 cut.addActionListener(this);
3279 delete.setLabel(MessageManager.getString("action.delete"));
3280 delete.addActionListener(this);
3281 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3282 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3283 pasteNew.addActionListener(this);
3284 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3285 pasteThis.addActionListener(this);
3286 remove2LeftMenuItem.setLabel(MessageManager
3287 .getString("action.remove_left"));
3288 remove2LeftMenuItem.addActionListener(this);
3289 remove2RightMenuItem.setLabel(MessageManager
3290 .getString("action.remove_right"));
3291 remove2RightMenuItem.addActionListener(this);
3292 removeGappedColumnMenuItem.setLabel(MessageManager
3293 .getString("action.remove_empty_columns"));
3294 removeGappedColumnMenuItem.addActionListener(this);
3295 removeAllGapsMenuItem.setLabel(MessageManager
3296 .getString("action.remove_all_gaps"));
3297 removeAllGapsMenuItem.addActionListener(this);
3298 removeRedundancyMenuItem.setLabel(MessageManager
3299 .getString("action.remove_redundancy"));
3300 removeRedundancyMenuItem.addActionListener(this);
3303 * Configure Select menu items and actions
3305 findMenuItem.setLabel(MessageManager.getString("action.find"));
3306 findMenuItem.addActionListener(this);
3307 selectAllSequenceMenuItem.addActionListener(this);
3308 deselectAllSequenceMenuItem.addActionListener(this);
3309 invertSequenceMenuItem.setLabel(MessageManager
3310 .getString("action.invert_sequence_selection"));
3311 invertSequenceMenuItem.addActionListener(this);
3312 invertColSel.setLabel(MessageManager
3313 .getString("action.invert_column_selection"));
3314 invertColSel.addActionListener(this);
3315 deleteGroups.setLabel(MessageManager
3316 .getString("action.undefine_groups"));
3317 deleteGroups.addActionListener(this);
3318 grpsFromSelection.setLabel(MessageManager
3319 .getString("action.make_groups_selection"));
3320 grpsFromSelection.addActionListener(this);
3321 createGroup.setLabel(MessageManager.getString("action.create_group"));
3322 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3323 annotationColumnSelection.setLabel(MessageManager
3324 .getString("action.select_by_annotation"));
3325 annotationColumnSelection.addActionListener(this);
3328 * Configure View menu items and actions
3330 newView.setLabel(MessageManager.getString("action.new_view"));
3331 newView.addActionListener(this);
3332 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3333 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3334 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3335 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3337 .setLabel(MessageManager.getString("label.selected_columns"));
3338 hideSequences.setLabel(MessageManager
3339 .getString("label.selected_sequences"));
3340 hideAllButSelection.setLabel(MessageManager
3341 .getString("label.all_but_selected_region"));
3342 hideAllSelection.setLabel(MessageManager
3343 .getString("label.selected_region"));
3344 showAllHidden.setLabel(MessageManager
3345 .getString("label.all_sequences_columns"));
3346 showColumns.addActionListener(this);
3347 showSeqs.addActionListener(this);
3348 hideColumns.addActionListener(this);
3349 hideSequences.addActionListener(this);
3350 hideAllButSelection.addActionListener(this);
3351 hideAllSelection.addActionListener(this);
3352 showAllHidden.addActionListener(this);
3353 featureSettings.setLabel(MessageManager
3354 .getString("action.feature_settings"));
3355 featureSettings.addActionListener(this);
3356 sequenceFeatures.setLabel(MessageManager
3357 .getString("label.show_sequence_features"));
3358 sequenceFeatures.addItemListener(this);
3359 sequenceFeatures.setState(false);
3360 followMouseOverFlag.setLabel(MessageManager
3361 .getString("label.automatic_scrolling"));
3362 followMouseOverFlag.addItemListener(this);
3363 alProperties.addActionListener(this);
3364 overviewMenuItem.setLabel(MessageManager
3365 .getString("label.overview_window"));
3366 overviewMenuItem.addActionListener(this);
3369 * Configure Annotations menu items and actions
3371 annotationPanelMenuItem.setLabel(MessageManager
3372 .getString("label.show_annotations"));
3373 annotationPanelMenuItem.addItemListener(this);
3374 showGroupConsensus.setLabel(MessageManager
3375 .getString("label.group_consensus"));
3376 showGroupConservation.setLabel(MessageManager
3377 .getString("label.group_conservation"));
3378 showConsensusHistogram.setLabel(MessageManager
3379 .getString("label.show_consensus_histogram"));
3380 showSequenceLogo.setLabel(MessageManager
3381 .getString("label.show_consensus_logo"));
3382 normSequenceLogo.setLabel(MessageManager
3383 .getString("label.norm_consensus_logo"));
3384 applyAutoAnnotationSettings.setLabel(MessageManager
3385 .getString("label.apply_all_groups"));
3386 applyAutoAnnotationSettings.setState(true);
3387 Menu autoAnnMenu = new Menu(
3388 MessageManager.getString("label.autocalculated_annotation"));
3389 showGroupConsensus.addItemListener(this);
3390 showGroupConservation.addItemListener(this);
3391 showConsensusHistogram.addItemListener(this);
3392 showSequenceLogo.addItemListener(this);
3393 normSequenceLogo.addItemListener(this);
3394 applyAutoAnnotationSettings.addItemListener(this);
3395 showAlignmentAnnotations = new CheckboxMenuItem(
3396 MessageManager.getString("label.show_all_al_annotations"));
3397 showSequenceAnnotations = new CheckboxMenuItem(
3398 MessageManager.getString("label.show_all_seq_annotations"));
3399 sortAnnBySequence = new CheckboxMenuItem(
3400 MessageManager.getString("label.sort_annotations_by_sequence"));
3401 sortAnnByLabel = new CheckboxMenuItem(
3402 MessageManager.getString("label.sort_annotations_by_label"));
3403 showAutoFirst = new CheckboxMenuItem(
3404 MessageManager.getString("label.show_first"));
3405 showAutoFirst.setState(false); // pending applet parameter
3406 setShowAutoCalculatedAbove(showAutoFirst.getState());
3407 showAutoLast = new CheckboxMenuItem(
3408 MessageManager.getString("label.show_last"));
3409 showAutoLast.setState(!showAutoFirst.getState());
3410 showAlignmentAnnotations.addItemListener(this);
3411 showSequenceAnnotations.addItemListener(this);
3412 sortAnnBySequence.addItemListener(this);
3413 sortAnnByLabel.addItemListener(this);
3414 showAutoFirst.addItemListener(this);
3415 showAutoLast.addItemListener(this);
3418 * Configure Format menu items and actions
3420 font.setLabel(MessageManager.getString("action.font"));
3421 font.addActionListener(this);
3422 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3423 scaleAbove.setState(true);
3424 scaleAbove.setEnabled(false);
3425 scaleAbove.addItemListener(this);
3426 scaleLeft.setEnabled(false);
3427 scaleLeft.setState(true);
3428 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3429 scaleLeft.addItemListener(this);
3430 scaleRight.setEnabled(false);
3431 scaleRight.setState(true);
3432 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3433 scaleRight.addItemListener(this);
3434 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3435 viewBoxesMenuItem.setState(true);
3436 viewBoxesMenuItem.addItemListener(this);
3437 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3438 viewTextMenuItem.setState(true);
3439 viewTextMenuItem.addItemListener(this);
3440 colourTextMenuItem.setLabel(MessageManager
3441 .getString("label.colour_text"));
3442 colourTextMenuItem.addItemListener(this);
3443 displayNonconservedMenuItem.setLabel(MessageManager
3444 .getString("label.show_non_conversed"));
3445 displayNonconservedMenuItem.addItemListener(this);
3446 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3447 wrapMenuItem.addItemListener(this);
3448 renderGapsMenuItem.setLabel(MessageManager
3449 .getString("action.show_gaps"));
3450 renderGapsMenuItem.setState(true);
3451 renderGapsMenuItem.addItemListener(this);
3452 centreColumnLabelFlag.setLabel(MessageManager
3453 .getString("label.centre_column_labels"));
3454 centreColumnLabelFlag.addItemListener(this);
3455 seqLimits.setState(true);
3456 seqLimits.setLabel(MessageManager
3457 .getString("label.show_sequence_limits"));
3458 seqLimits.addItemListener(this);
3461 * Configure Colour menu items and actions
3463 applyToAllGroups.setLabel(MessageManager
3464 .getString("label.apply_colour_to_all_groups"));
3465 applyToAllGroups.setState(true);
3466 applyToAllGroups.addItemListener(this);
3467 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3468 clustalColour.addActionListener(this);
3469 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3470 zappoColour.addActionListener(this);
3471 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3472 taylorColour.addActionListener(this);
3473 hydrophobicityColour.setLabel(MessageManager
3474 .getString("label.hydrophobicity"));
3475 hydrophobicityColour.addActionListener(this);
3477 .setLabel(MessageManager.getString("label.helix_propensity"));
3478 helixColour.addActionListener(this);
3479 strandColour.setLabel(MessageManager
3480 .getString("label.strand_propensity"));
3481 strandColour.addActionListener(this);
3482 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3483 turnColour.addActionListener(this);
3484 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3485 buriedColour.addActionListener(this);
3486 purinePyrimidineColour.setLabel(MessageManager
3487 .getString("label.purine_pyrimidine"));
3488 purinePyrimidineColour.addActionListener(this);
3489 // RNAInteractionColour.setLabel(MessageManager
3490 // .getString("label.rna_interaction"));
3491 // RNAInteractionColour.addActionListener(this);
3492 RNAHelixColour.setLabel(MessageManager
3493 .getString("action.by_rna_helixes"));
3494 RNAHelixColour.addActionListener(this);
3495 userDefinedColour.setLabel(MessageManager
3496 .getString("action.user_defined"));
3497 userDefinedColour.addActionListener(this);
3498 PIDColour.setLabel(MessageManager
3499 .getString("label.percentage_identity"));
3500 PIDColour.addActionListener(this);
3501 BLOSUM62Colour.setLabel(MessageManager
3502 .getString("label.blosum62_score"));
3503 BLOSUM62Colour.addActionListener(this);
3505 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3506 // it will be enabled only if a score file is provided
3507 tcoffeeColour.setEnabled(false);
3508 tcoffeeColour.addActionListener(this);
3509 conservationMenuItem.setLabel(MessageManager
3510 .getString("action.by_conservation"));
3511 conservationMenuItem.addItemListener(this);
3512 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3513 noColourmenuItem.addActionListener(this);
3514 abovePIDThreshold.setLabel(MessageManager
3515 .getString("label.above_identity_threshold"));
3516 abovePIDThreshold.addItemListener(this);
3517 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3518 nucleotideColour.addActionListener(this);
3519 modifyPID.setLabel(MessageManager
3520 .getString("label.modify_identity_thereshold"));
3521 modifyPID.addActionListener(this);
3522 modifyConservation.setLabel(MessageManager
3523 .getString("label.modify_conservation_thereshold"));
3524 modifyConservation.addActionListener(this);
3525 annotationColour.setLabel(MessageManager
3526 .getString("action.by_annotation"));
3527 annotationColour.addActionListener(this);
3530 * Configure Calculate menu items and actions
3532 sortPairwiseMenuItem.setLabel(MessageManager
3533 .getString("action.by_pairwise_id"));
3534 sortPairwiseMenuItem.addActionListener(this);
3535 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3536 sortIDMenuItem.addActionListener(this);
3537 sortLengthMenuItem.setLabel(MessageManager
3538 .getString("action.by_length"));
3539 sortLengthMenuItem.addActionListener(this);
3540 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3541 sortGroupMenuItem.addActionListener(this);
3542 pairwiseAlignmentMenuItem.setLabel(MessageManager
3543 .getString("action.pairwise_alignment"));
3544 pairwiseAlignmentMenuItem.addActionListener(this);
3545 PCAMenuItem.setLabel(MessageManager
3546 .getString("label.principal_component_analysis"));
3547 PCAMenuItem.addActionListener(this);
3548 autoCalculate = new CheckboxMenuItem(
3549 MessageManager.getString("label.autocalculate_consensus"), true);
3550 averageDistanceTreeMenuItem.setLabel(MessageManager
3551 .getString("label.average_distance_identity"));
3552 averageDistanceTreeMenuItem.addActionListener(this);
3553 neighbourTreeMenuItem.setLabel(MessageManager
3554 .getString("label.neighbour_joining_identity"));
3555 neighbourTreeMenuItem.addActionListener(this);
3556 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3557 .getString("label.average_distance_bloslum62"));
3558 avDistanceTreeBlosumMenuItem.addActionListener(this);
3559 njTreeBlosumMenuItem.setLabel(MessageManager
3560 .getString("label.neighbour_blosum62"));
3561 njTreeBlosumMenuItem.addActionListener(this);
3562 sortByTreeMenu.setLabel(MessageManager
3563 .getString("action.by_tree_order"));
3564 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3565 Menu calculateTreeMenu = new Menu(
3566 MessageManager.getString("action.calculate_tree"));
3567 autoCalculate.addItemListener(this);
3568 sortByTree.addItemListener(this);
3571 * Configure Help menu items and actions
3573 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3574 documentation.setLabel(MessageManager.getString("label.documentation"));
3575 documentation.addActionListener(this);
3576 about.setLabel(MessageManager.getString("label.about"));
3577 about.addActionListener(this);
3580 * Add top level menus to frame
3582 alignFrameMenuBar.add(fileMenu);
3583 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3584 alignFrameMenuBar.add(editMenu);
3585 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3586 alignFrameMenuBar.add(selectMenu);
3587 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3588 alignFrameMenuBar.add(viewMenu);
3589 Menu annotationsMenu = new Menu(
3590 MessageManager.getString("action.annotations"));
3591 alignFrameMenuBar.add(annotationsMenu);
3592 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3593 alignFrameMenuBar.add(formatMenu);
3594 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3595 alignFrameMenuBar.add(colourMenu);
3596 Menu calculateMenu = new Menu(
3597 MessageManager.getString("action.calculate"));
3598 alignFrameMenuBar.add(calculateMenu);
3599 alignFrameMenuBar.add(helpMenu);
3604 fileMenu.add(inputText);
3605 fileMenu.add(loadTree);
3606 fileMenu.add(loadAnnotations);
3607 fileMenu.addSeparator();
3608 fileMenu.add(outputTextboxMenu);
3609 fileMenu.add(outputFeatures);
3610 fileMenu.add(outputAnnotations);
3611 if (jalviewServletURL != null)
3613 fileMenu.add(loadApplication);
3615 fileMenu.addSeparator();
3616 fileMenu.add(closeMenuItem);
3621 editMenu.add(undoMenuItem);
3622 editMenu.add(redoMenuItem);
3625 pasteMenu.add(pasteNew);
3626 pasteMenu.add(pasteThis);
3627 editMenu.add(pasteMenu);
3628 editMenu.add(delete);
3629 editMenu.addSeparator();
3630 editMenu.add(remove2LeftMenuItem);
3631 editMenu.add(remove2RightMenuItem);
3632 editMenu.add(removeGappedColumnMenuItem);
3633 editMenu.add(removeAllGapsMenuItem);
3634 editMenu.add(removeRedundancyMenuItem);
3639 selectMenu.add(findMenuItem);
3640 selectMenu.addSeparator();
3641 selectMenu.add(selectAllSequenceMenuItem);
3642 selectMenu.add(deselectAllSequenceMenuItem);
3643 selectMenu.add(invertSequenceMenuItem);
3644 selectMenu.add(invertColSel);
3645 selectMenu.add(createGroup);
3646 selectMenu.add(unGroup);
3647 selectMenu.add(grpsFromSelection);
3648 selectMenu.add(deleteGroups);
3649 selectMenu.add(annotationColumnSelection);
3654 viewMenu.add(newView);
3655 viewMenu.addSeparator();
3656 showMenu.add(showColumns);
3657 showMenu.add(showSeqs);
3658 showMenu.add(showAllHidden);
3659 viewMenu.add(showMenu);
3660 hideMenu.add(hideColumns);
3661 hideMenu.add(hideSequences);
3662 hideMenu.add(hideAllSelection);
3663 hideMenu.add(hideAllButSelection);
3664 viewMenu.add(hideMenu);
3665 viewMenu.addSeparator();
3666 viewMenu.add(followMouseOverFlag);
3667 viewMenu.addSeparator();
3668 viewMenu.add(sequenceFeatures);
3669 viewMenu.add(featureSettings);
3670 viewMenu.addSeparator();
3671 viewMenu.add(alProperties);
3672 viewMenu.addSeparator();
3673 viewMenu.add(overviewMenuItem);
3678 annotationsMenu.add(annotationPanelMenuItem);
3679 annotationsMenu.addSeparator();
3680 annotationsMenu.add(showAlignmentAnnotations);
3681 annotationsMenu.add(showSequenceAnnotations);
3682 annotationsMenu.add(sortAnnBySequence);
3683 annotationsMenu.add(sortAnnByLabel);
3684 annotationsMenu.addSeparator();
3685 autoAnnMenu.add(showAutoFirst);
3686 autoAnnMenu.add(showAutoLast);
3687 autoAnnMenu.addSeparator();
3688 autoAnnMenu.add(applyAutoAnnotationSettings);
3689 autoAnnMenu.add(showConsensusHistogram);
3690 autoAnnMenu.add(showSequenceLogo);
3691 autoAnnMenu.add(normSequenceLogo);
3692 autoAnnMenu.addSeparator();
3693 autoAnnMenu.add(showGroupConservation);
3694 autoAnnMenu.add(showGroupConsensus);
3695 annotationsMenu.add(autoAnnMenu);
3700 formatMenu.add(font);
3701 formatMenu.add(seqLimits);
3702 formatMenu.add(wrapMenuItem);
3703 formatMenu.add(scaleAbove);
3704 formatMenu.add(scaleLeft);
3705 formatMenu.add(scaleRight);
3706 formatMenu.add(viewBoxesMenuItem);
3707 formatMenu.add(viewTextMenuItem);
3708 formatMenu.add(colourTextMenuItem);
3709 formatMenu.add(displayNonconservedMenuItem);
3710 formatMenu.add(renderGapsMenuItem);
3711 formatMenu.add(centreColumnLabelFlag);
3716 colourMenu.add(applyToAllGroups);
3717 colourMenu.addSeparator();
3718 colourMenu.add(noColourmenuItem);
3719 colourMenu.add(clustalColour);
3720 colourMenu.add(BLOSUM62Colour);
3721 colourMenu.add(PIDColour);
3722 colourMenu.add(zappoColour);
3723 colourMenu.add(taylorColour);
3724 colourMenu.add(hydrophobicityColour);
3725 colourMenu.add(helixColour);
3726 colourMenu.add(strandColour);
3727 colourMenu.add(turnColour);
3728 colourMenu.add(buriedColour);
3729 colourMenu.add(nucleotideColour);
3730 colourMenu.add(purinePyrimidineColour);
3731 // colourMenu.add(RNAInteractionColour);
3732 colourMenu.add(tcoffeeColour);
3733 colourMenu.add(userDefinedColour);
3734 colourMenu.addSeparator();
3735 colourMenu.add(conservationMenuItem);
3736 colourMenu.add(modifyConservation);
3737 colourMenu.add(abovePIDThreshold);
3738 colourMenu.add(modifyPID);
3739 colourMenu.add(annotationColour);
3740 colourMenu.add(RNAHelixColour);
3745 sortMenu.add(sortIDMenuItem);
3746 sortMenu.add(sortLengthMenuItem);
3747 sortMenu.add(sortByTreeMenu);
3748 sortMenu.add(sortGroupMenuItem);
3749 sortMenu.add(sortPairwiseMenuItem);
3750 calculateMenu.add(sortMenu);
3751 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3752 calculateTreeMenu.add(neighbourTreeMenuItem);
3753 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3754 calculateTreeMenu.add(njTreeBlosumMenuItem);
3755 calculateMenu.add(calculateTreeMenu);
3756 calculateMenu.addSeparator();
3757 calculateMenu.add(pairwiseAlignmentMenuItem);
3758 calculateMenu.add(PCAMenuItem);
3759 calculateMenu.add(autoCalculate);
3760 calculateMenu.add(sortByTree);
3765 helpMenu.add(documentation);
3766 helpMenu.add(about);
3771 statusBar.setBackground(Color.white);
3772 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3773 statusBar.setText(MessageManager.getString("label.status_bar"));
3774 this.add(statusBar, BorderLayout.SOUTH);
3778 public void setStatus(String string)
3780 statusBar.setText(string);
3783 MenuItem featureSettings = new MenuItem();
3785 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3787 MenuItem annotationColour = new MenuItem();
3789 MenuItem annotationColumnSelection = new MenuItem();
3791 MenuItem invertColSel = new MenuItem();
3793 MenuItem showColumns = new MenuItem();
3795 MenuItem showSeqs = new MenuItem();
3797 MenuItem hideColumns = new MenuItem();
3799 MenuItem hideSequences = new MenuItem();
3801 MenuItem hideAllButSelection = new MenuItem();
3803 MenuItem hideAllSelection = new MenuItem();
3805 MenuItem showAllHidden = new MenuItem();
3807 MenuItem newView = new MenuItem();
3809 private CheckboxMenuItem showAlignmentAnnotations;
3811 private CheckboxMenuItem showSequenceAnnotations;
3813 private CheckboxMenuItem sortAnnBySequence;
3815 private CheckboxMenuItem sortAnnByLabel;
3817 private CheckboxMenuItem showAutoFirst;
3819 private CheckboxMenuItem showAutoLast;
3821 private SplitFrame splitFrame;
3824 * Attach the alignFrame panels after embedding menus, if necessary. This used
3825 * to be called setEmbedded, but is now creates the dropdown menus in a
3826 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3828 * @param reallyEmbedded
3829 * true to attach the view to the applet area on the page rather than
3832 public void createAlignFrameWindow(boolean reallyEmbedded)
3836 embedAlignFrameInApplet(viewport.applet);
3841 // test and embed menu bar if necessary.
3843 if (embedMenuIfNeeded(alignPanel))
3846 * adjust for status bar height too. ? pointless as overridden by layout
3849 alignPanel.setSize(getSize().width,
3850 getSize().height - statusBar.getHeight());
3852 add(statusBar, BorderLayout.SOUTH);
3853 add(alignPanel, BorderLayout.CENTER);
3854 // and register with the applet so it can pass external API calls to us
3855 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3861 * Add the components of this AlignFrame to the applet container.
3865 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3868 // Explicitly build the embedded menu panel for the on-page applet
3870 // view cannot be closed if its actually on the page
3871 fileMenu.remove(closeMenuItem);
3872 fileMenu.remove(3); // Remove Separator
3873 // construct embedded menu, using default font
3874 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3875 // and actually add the components to the applet area
3876 theApplet.setLayout(new BorderLayout());
3877 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3878 theApplet.add(statusBar, BorderLayout.SOUTH);
3879 // TODO should size be left to the layout manager?
3880 alignPanel.setSize(theApplet.getSize().width,
3881 theApplet.getSize().height - embeddedMenu.getHeight()
3882 - statusBar.getHeight());
3883 theApplet.add(alignPanel, BorderLayout.CENTER);
3884 final AlignFrame me = this;
3885 theApplet.addFocusListener(new FocusListener()
3889 public void focusLost(FocusEvent e)
3891 if (theApplet.currentAlignFrame == me)
3893 theApplet.currentAlignFrame = null;
3898 public void focusGained(FocusEvent e)
3900 theApplet.currentAlignFrame = me;
3903 theApplet.validate();
3907 * create a new binding between structures in an existing jmol viewer instance
3908 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3909 * this does not open a new Jmol window, or modify the display of the
3910 * structures in the original jmol window. Note This method doesn't work
3911 * without an additional javascript library to exchange messages between the
3912 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3915 * JmolViewer instance
3916 * @param sequenceIds
3917 * - sequence Ids to search for associations
3919 public SequenceStructureBinding addStructureViewInstance(
3920 Object jmolviewer, String[] sequenceIds)
3922 Viewer viewer = null;
3925 viewer = (Viewer) jmolviewer;
3926 } catch (ClassCastException ex)
3928 System.err.println("Unsupported viewer object :"
3929 + jmolviewer.getClass());
3933 System.err.println("Can't use this object as a structure viewer:"
3934 + jmolviewer.getClass());
3937 SequenceI[] seqs = null;
3938 if (sequenceIds == null || sequenceIds.length == 0)
3940 seqs = viewport.getAlignment().getSequencesArray();
3944 Vector sqi = new Vector();
3945 AlignmentI al = viewport.getAlignment();
3946 for (int sid = 0; sid < sequenceIds.length; sid++)
3948 SequenceI sq = al.findName(sequenceIds[sid]);
3956 seqs = new SequenceI[sqi.size()];
3957 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3959 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3967 AAStructureBindingModel jmv = null;
3968 // TODO: search for a jmv that involves viewer
3970 { // create a new viewer/jalview binding.
3971 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3978 * bind a pdb file to a sequence in the current view
3981 * - sequenceId within the dataset.
3982 * @param pdbEntryString
3983 * - the short name for the PDB file
3985 * - pdb file - either a URL or a valid PDB file.
3986 * @return true if binding was as success TODO: consider making an exception
3987 * structure for indicating when PDB parsing or sequenceId location
3990 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3993 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3994 boolean needtoadd = false;
3995 if (toaddpdb != null)
3997 Vector pdbe = toaddpdb.getAllPDBEntries();
3998 PDBEntry pdbentry = null;
3999 if (pdbe != null && pdbe.size() > 0)
4001 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4003 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4004 if (!pdbentry.getId().equals(pdbEntryString)
4005 && !pdbentry.getFile().equals(pdbFile))
4015 if (pdbentry == null)
4017 pdbentry = new PDBEntry();
4018 pdbentry.setId(pdbEntryString);
4019 pdbentry.setFile(pdbFile);
4020 needtoadd = true; // add this new entry to sequence.
4022 // resolve data source
4023 // TODO: this code should be a refactored to an io package
4024 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4025 if (protocol == null)
4031 // make a note of the access mode and add
4032 if (pdbentry.getProperty() == null)
4034 pdbentry.setProperty(new Hashtable());
4036 pdbentry.getProperty().put("protocol", protocol);
4037 toaddpdb.addPDBId(pdbentry);
4038 alignPanel.getStructureSelectionManager()
4039 .registerPDBEntry(pdbentry);
4045 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4049 Vector sequences = new Vector();
4050 for (int i = 0; i < seqs.length; i++)
4052 if (seqs[i] != null)
4054 sequences.addElement(new Object[] { seqs[i],
4055 (chains != null) ? chains[i] : null });
4058 seqs = new SequenceI[sequences.size()];
4059 chains = new String[sequences.size()];
4060 for (int i = 0, isize = sequences.size(); i < isize; i++)
4062 Object[] oj = (Object[]) sequences.elementAt(i);
4064 seqs[i] = (SequenceI) oj[0];
4065 chains[i] = (String) oj[1];
4068 return new Object[] { seqs, chains };
4072 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4073 SequenceI[] seqs, String[] chains, String protocol)
4075 // Scrub any null sequences from the array
4076 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4077 seqs = (SequenceI[]) sqch[0];
4078 chains = (String[]) sqch[1];
4079 if (seqs == null || seqs.length == 0)
4082 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4084 if (protocol == null || protocol.trim().length() == 0
4085 || protocol.equals("null"))
4087 protocol = (String) pdb.getProperty().get("protocol");
4088 if (protocol == null)
4090 System.err.println("Couldn't work out protocol to open structure: "
4095 if (applet.useXtrnalSviewer)
4097 // register the association(s) and quit, don't create any windows.
4098 if (StructureSelectionManager.getStructureSelectionManager(applet)
4099 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4101 System.err.println("Failed to map " + pdb.getFile() + " ("
4102 + protocol + ") to any sequences");
4106 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4108 // can only do alignments with Jmol
4109 // find the last jmol window assigned to this alignment
4110 jalview.appletgui.AppletJmol ajm = null, tajm;
4111 Vector jmols = applet
4112 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4113 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4115 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4116 if (tajm.ap.alignFrame == this)
4125 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4126 // try and add the pdb structure
4131 // otherwise, create a new window
4132 if (applet.jmolAvailable)
4134 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4136 applet.lastFrameX += 40;
4137 applet.lastFrameY += 40;
4141 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4146 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4147 SequenceI[][] seqs, String[][] chains, String[] protocols)
4149 // TODO Auto-generated method stub
4150 System.err.println("Aligned Structure View: Not yet implemented.");
4154 * modify the current selection, providing the user has not made a selection
4158 * - sequences from this alignment
4160 * - columns to be selected on the alignment
4162 public void select(SequenceGroup sel, ColumnSelection csel)
4164 alignPanel.seqPanel.selection(sel, csel, null);
4167 public void scrollTo(int row, int column)
4169 alignPanel.seqPanel.scrollTo(row, column);
4172 public void scrollToRow(int row)
4174 alignPanel.seqPanel.scrollToRow(row);
4177 public void scrollToColumn(int column)
4179 alignPanel.seqPanel.scrollToColumn(column);
4183 * @return the alignments unique ID.
4185 public String getSequenceSetId()
4187 return viewport.getSequenceSetId();
4191 * Load the (T-Coffee) score file from the specified url
4194 * File/URL/T-COFFEE score file contents
4195 * @throws IOException
4196 * @return true if alignment was annotated with data from source
4198 public boolean loadScoreFile(String source) throws IOException
4201 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4202 AppletFormatAdapter.checkProtocol(source));
4203 if (!file.isValid())
4205 // TODO: raise dialog for gui
4206 System.err.println("Problems parsing T-Coffee scores: "
4207 + file.getWarningMessage());
4208 System.err.println("Origin was:\n" + source);
4213 * check that the score matrix matches the alignment dimensions
4216 if ((aln = viewport.getAlignment()) != null
4217 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4220 // TODO: raise a dialog box here rather than bomb out.
4222 .println("The scores matrix does not match the alignment dimensions");
4226 // TODO add parameter to indicate if matching should be done
4227 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4229 alignPanel.fontChanged();
4230 tcoffeeColour.setEnabled(true);
4231 // switch to this color
4232 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4237 System.err.println("Problems resolving T-Coffee scores:");
4238 if (file.getWarningMessage() != null)
4240 System.err.println(file.getWarningMessage());
4246 public SplitFrame getSplitFrame()
4248 return this.splitFrame;
4251 public void setSplitFrame(SplitFrame sf)
4253 this.splitFrame = sf;
4256 // may not need this
4258 public void setShowSeqFeatures(boolean b)
4260 // showSeqFeatures.setSelected(b);
4261 viewport.setShowSequenceFeatures(b);
4266 public void setMenusForViewport()
4268 // setMenusFromViewport(viewport);
4273 public void refreshFeatureUI(boolean enableIfNecessary)
4275 if (enableIfNecessary)
4277 sequenceFeatures.setState(true);
4278 alignPanel.av.setShowSequenceFeatures(true);
4283 public FeatureSettingsControllerI getFeatureSettingsUI()
4285 return alignPanel.av.featureSettings;