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.hasSelectedColumns()
707 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
710 // now invert the sequence set, if required - empty selection implies
711 // that no hiding is required.
714 invertSequenceMenuItem_actionPerformed();
715 sg = viewport.getSelectionGroup();
719 viewport.expandColSelection(sg, true);
720 // finally invert the column selection and get the new sequence
721 // selection and indicate it should be hidden.
722 invertColSel_actionPerformed();
729 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
732 viewport.hideAllSelectedSeqs();
734 else if (!(toggleCols && viewport.hasSelectedColumns()))
736 viewport.showAllHiddenSeqs();
742 if (viewport.hasSelectedColumns())
744 viewport.hideSelectedColumns();
747 viewport.setSelectionGroup(sg);
752 viewport.showAllHiddenColumns();
754 viewport.sendSelection();
759 public void keyReleased(KeyEvent evt)
764 public void keyTyped(KeyEvent evt)
769 public void itemStateChanged(ItemEvent evt)
771 final Object source = evt.getSource();
772 if (source == displayNonconservedMenuItem)
774 displayNonconservedMenuItem_actionPerformed();
776 else if (source == colourTextMenuItem)
778 colourTextMenuItem_actionPerformed();
780 else if (source == wrapMenuItem)
782 wrapMenuItem_actionPerformed();
784 else if (source == scaleAbove)
786 viewport.setScaleAboveWrapped(scaleAbove.getState());
788 else if (source == scaleLeft)
790 viewport.setScaleLeftWrapped(scaleLeft.getState());
792 else if (source == scaleRight)
794 viewport.setScaleRightWrapped(scaleRight.getState());
796 else if (source == seqLimits)
798 seqLimits_itemStateChanged();
800 else if (source == viewBoxesMenuItem)
802 viewport.setShowBoxes(viewBoxesMenuItem.getState());
804 else if (source == viewTextMenuItem)
806 viewport.setShowText(viewTextMenuItem.getState());
808 else if (source == renderGapsMenuItem)
810 viewport.setRenderGaps(renderGapsMenuItem.getState());
812 else if (source == annotationPanelMenuItem)
814 boolean showAnnotations = annotationPanelMenuItem.getState();
815 showAlignmentAnnotations.setEnabled(showAnnotations);
816 showSequenceAnnotations.setEnabled(showAnnotations);
817 viewport.setShowAnnotation(showAnnotations);
818 alignPanel.setAnnotationVisible(showAnnotations);
820 else if (source == sequenceFeatures)
822 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
823 alignPanel.seqPanel.seqCanvas.repaint();
825 else if (source == showAlignmentAnnotations)
827 setAnnotationsVisibility();
829 else if (source == showSequenceAnnotations)
831 setAnnotationsVisibility();
833 else if (source == sortAnnBySequence)
835 boolean newState = sortAnnBySequence.getState();
836 sortAnnByLabel.setState(false);
837 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
838 : SequenceAnnotationOrder.NONE);
839 setViewportAnnotationOrder();
841 else if (source == sortAnnByLabel)
843 boolean newState = sortAnnByLabel.getState();
844 sortAnnBySequence.setState(false);
845 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
846 : SequenceAnnotationOrder.NONE);
847 setViewportAnnotationOrder();
849 else if (source == showAutoFirst)
851 showAutoLast.setState(!showAutoFirst.getState());
852 setShowAutoCalculatedAbove(showAutoFirst.getState());
853 setViewportAnnotationOrder();
855 else if (source == showAutoLast)
857 showAutoFirst.setState(!showAutoLast.getState());
858 setShowAutoCalculatedAbove(showAutoFirst.getState());
859 setViewportAnnotationOrder();
861 else if (source == conservationMenuItem)
863 conservationMenuItem_actionPerformed();
865 else if (source == abovePIDThreshold)
867 abovePIDThreshold_actionPerformed();
869 else if (source == applyToAllGroups)
871 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
873 else if (source == autoCalculate)
875 viewport.autoCalculateConsensus = autoCalculate.getState();
877 else if (source == sortByTree)
879 viewport.sortByTree = sortByTree.getState();
881 else if (source == this.centreColumnLabelFlag)
883 centreColumnLabelFlag_stateChanged();
885 else if (source == this.followMouseOverFlag)
887 mouseOverFlag_stateChanged();
889 else if (source == showGroupConsensus)
891 showGroupConsensus_actionPerformed();
893 else if (source == showGroupConservation)
895 showGroupConservation_actionPerformed();
897 else if (source == showSequenceLogo)
899 showSequenceLogo_actionPerformed();
901 else if (source == normSequenceLogo)
903 normSequenceLogo_actionPerformed();
905 else if (source == showConsensusHistogram)
907 showConsensusHistogram_actionPerformed();
909 else if (source == applyAutoAnnotationSettings)
911 applyAutoAnnotationSettings_actionPerformed();
913 alignPanel.paintAlignment(true);
917 * Set the visibility state of sequence-related and/or alignment-related
918 * annotations depending on checkbox selections, and repaint.
922 private void setAnnotationsVisibility()
924 boolean showForAlignment = showAlignmentAnnotations.getState();
925 boolean showForSequences = showSequenceAnnotations.getState();
926 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
928 for (AlignmentAnnotation aa : alignPanel.getAlignment()
929 .getAlignmentAnnotation())
931 boolean visible = (aa.sequenceRef == null ? showForAlignment
933 aa.visible = visible;
936 alignPanel.validateAnnotationDimensions(true);
941 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
943 this.annotationSortOrder = order;
947 * Set flags on the viewport that control annotation ordering
949 private void setViewportAnnotationOrder()
951 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
953 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
956 private void setShowAutoCalculatedAbove(boolean showAbove)
958 this.showAutoCalculatedAbove = showAbove;
961 private void mouseOverFlag_stateChanged()
963 viewport.setFollowHighlight(followMouseOverFlag.getState());
964 // TODO: could kick the scrollTo mechanism to reset view for current
968 private void centreColumnLabelFlag_stateChanged()
970 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
971 this.alignPanel.annotationPanel.repaint();
975 public void actionPerformed(ActionEvent evt)
977 viewport.applet.currentAlignFrame = this;
979 Object source = evt.getSource();
981 if (source == inputText)
983 inputText_actionPerformed();
985 else if (source == loadTree)
987 loadTree_actionPerformed();
989 else if (source == loadApplication)
991 launchFullApplication();
993 else if (source == loadAnnotations)
997 else if (source == outputAnnotations)
999 outputAnnotations(true);
1001 else if (source == outputFeatures)
1003 outputFeatures(true, "Jalview");
1005 else if (source == closeMenuItem)
1007 closeMenuItem_actionPerformed();
1009 else if (source == copy)
1011 copy_actionPerformed();
1013 else if (source == undoMenuItem)
1015 undoMenuItem_actionPerformed();
1017 else if (source == redoMenuItem)
1019 redoMenuItem_actionPerformed();
1021 else if (source == inputText)
1023 inputText_actionPerformed();
1025 else if (source == closeMenuItem)
1027 closeMenuItem_actionPerformed();
1029 else if (source == undoMenuItem)
1031 undoMenuItem_actionPerformed();
1033 else if (source == redoMenuItem)
1035 redoMenuItem_actionPerformed();
1037 else if (source == copy)
1039 copy_actionPerformed();
1041 else if (source == pasteNew)
1043 pasteNew_actionPerformed();
1045 else if (source == pasteThis)
1047 pasteThis_actionPerformed();
1049 else if (source == cut)
1051 cut_actionPerformed();
1053 else if (source == delete)
1055 delete_actionPerformed();
1057 else if (source == grpsFromSelection)
1059 makeGrpsFromSelection_actionPerformed();
1061 else if (source == deleteGroups)
1063 deleteGroups_actionPerformed();
1065 else if (source == selectAllSequenceMenuItem)
1067 selectAllSequenceMenuItem_actionPerformed();
1069 else if (source == deselectAllSequenceMenuItem)
1071 deselectAllSequenceMenuItem_actionPerformed();
1073 else if (source == invertSequenceMenuItem)
1075 invertSequenceMenuItem_actionPerformed();
1076 // uncomment to slave sequence selections in split frame
1077 // viewport.sendSelection();
1079 else if (source == invertColSel)
1081 viewport.invertColumnSelection();
1082 alignPanel.paintAlignment(true);
1083 viewport.sendSelection();
1085 else if (source == remove2LeftMenuItem)
1087 trimAlignment(true);
1089 else if (source == remove2RightMenuItem)
1091 trimAlignment(false);
1093 else if (source == removeGappedColumnMenuItem)
1095 removeGappedColumnMenuItem_actionPerformed();
1097 else if (source == removeAllGapsMenuItem)
1099 removeAllGapsMenuItem_actionPerformed();
1101 else if (source == findMenuItem)
1103 findMenuItem_actionPerformed();
1105 else if (source == font)
1107 new FontChooser(alignPanel);
1109 else if (source == newView)
1113 else if (source == showColumns)
1115 viewport.showAllHiddenColumns();
1116 alignPanel.paintAlignment(true);
1117 viewport.sendSelection();
1119 else if (source == showSeqs)
1121 viewport.showAllHiddenSeqs();
1122 alignPanel.paintAlignment(true);
1123 // uncomment if we want to slave sequence selections in split frame
1124 // viewport.sendSelection();
1126 else if (source == hideColumns)
1128 viewport.hideSelectedColumns();
1129 alignPanel.paintAlignment(true);
1130 viewport.sendSelection();
1132 else if (source == hideSequences
1133 && viewport.getSelectionGroup() != null)
1135 viewport.hideAllSelectedSeqs();
1136 alignPanel.paintAlignment(true);
1137 // uncomment if we want to slave sequence selections in split frame
1138 // viewport.sendSelection();
1140 else if (source == hideAllButSelection)
1142 toggleHiddenRegions(false, false);
1143 alignPanel.paintAlignment(true);
1144 viewport.sendSelection();
1146 else if (source == hideAllSelection)
1148 SequenceGroup sg = viewport.getSelectionGroup();
1149 viewport.expandColSelection(sg, false);
1150 viewport.hideAllSelectedSeqs();
1151 viewport.hideSelectedColumns();
1152 alignPanel.paintAlignment(true);
1153 viewport.sendSelection();
1155 else if (source == showAllHidden)
1157 viewport.showAllHiddenColumns();
1158 viewport.showAllHiddenSeqs();
1159 alignPanel.paintAlignment(true);
1160 viewport.sendSelection();
1162 else if (source == showGroupConsensus)
1164 showGroupConsensus_actionPerformed();
1166 else if (source == showGroupConservation)
1168 showGroupConservation_actionPerformed();
1170 else if (source == showSequenceLogo)
1172 showSequenceLogo_actionPerformed();
1174 else if (source == normSequenceLogo)
1176 normSequenceLogo_actionPerformed();
1178 else if (source == showConsensusHistogram)
1180 showConsensusHistogram_actionPerformed();
1182 else if (source == applyAutoAnnotationSettings)
1184 applyAutoAnnotationSettings_actionPerformed();
1186 else if (source == featureSettings)
1188 new FeatureSettings(alignPanel);
1190 else if (source == alProperties)
1192 StringBuffer contents = new jalview.io.AlignmentProperties(
1193 viewport.getAlignment()).formatAsString();
1194 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1195 cap.setText(contents.toString());
1196 Frame frame = new Frame();
1198 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1199 "label.alignment_properties", new String[] { getTitle() }),
1202 else if (source == overviewMenuItem)
1204 overviewMenuItem_actionPerformed();
1206 else if (source == noColourmenuItem)
1210 else if (source == clustalColour)
1212 abovePIDThreshold.setState(false);
1213 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1215 else if (source == zappoColour)
1217 changeColour(new ZappoColourScheme());
1219 else if (source == taylorColour)
1221 changeColour(new TaylorColourScheme());
1223 else if (source == hydrophobicityColour)
1225 changeColour(new HydrophobicColourScheme());
1227 else if (source == helixColour)
1229 changeColour(new HelixColourScheme());
1231 else if (source == strandColour)
1233 changeColour(new StrandColourScheme());
1235 else if (source == turnColour)
1237 changeColour(new TurnColourScheme());
1239 else if (source == buriedColour)
1241 changeColour(new BuriedColourScheme());
1243 else if (source == nucleotideColour)
1245 changeColour(new NucleotideColourScheme());
1247 else if (source == purinePyrimidineColour)
1249 changeColour(new PurinePyrimidineColourScheme());
1251 // else if (source == RNAInteractionColour)
1253 // changeColour(new RNAInteractionColourScheme());
1255 else if (source == RNAHelixColour)
1257 new RNAHelicesColourChooser(viewport, alignPanel);
1259 else if (source == modifyPID)
1261 modifyPID_actionPerformed();
1263 else if (source == modifyConservation)
1265 modifyConservation_actionPerformed();
1267 else if (source == userDefinedColour)
1269 new UserDefinedColours(alignPanel, null);
1271 else if (source == PIDColour)
1273 changeColour(new PIDColourScheme());
1275 else if (source == BLOSUM62Colour)
1277 changeColour(new Blosum62ColourScheme());
1279 else if (source == tcoffeeColour)
1281 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1283 else if (source == annotationColour)
1285 new AnnotationColourChooser(viewport, alignPanel);
1287 else if (source == annotationColumnSelection)
1289 new AnnotationColumnChooser(viewport, alignPanel);
1291 else if (source == sortPairwiseMenuItem)
1293 sortPairwiseMenuItem_actionPerformed();
1295 else if (source == sortIDMenuItem)
1297 sortIDMenuItem_actionPerformed();
1299 else if (source == sortLengthMenuItem)
1301 sortLengthMenuItem_actionPerformed();
1303 else if (source == sortGroupMenuItem)
1305 sortGroupMenuItem_actionPerformed();
1307 else if (source == removeRedundancyMenuItem)
1309 removeRedundancyMenuItem_actionPerformed();
1311 else if (source == pairwiseAlignmentMenuItem)
1313 pairwiseAlignmentMenuItem_actionPerformed();
1315 else if (source == PCAMenuItem)
1317 PCAMenuItem_actionPerformed();
1319 else if (source == averageDistanceTreeMenuItem)
1321 averageDistanceTreeMenuItem_actionPerformed();
1323 else if (source == neighbourTreeMenuItem)
1325 neighbourTreeMenuItem_actionPerformed();
1327 else if (source == njTreeBlosumMenuItem)
1329 njTreeBlosumMenuItem_actionPerformed();
1331 else if (source == avDistanceTreeBlosumMenuItem)
1333 avTreeBlosumMenuItem_actionPerformed();
1335 else if (source == documentation)
1337 documentation_actionPerformed();
1339 else if (source == about)
1341 about_actionPerformed();
1346 public void inputText_actionPerformed()
1348 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1349 Frame frame = new Frame();
1351 jalview.bin.JalviewLite.addFrame(frame,
1352 MessageManager.getString("label.input_cut_paste"), 500, 500);
1355 protected void outputText_actionPerformed(ActionEvent e)
1357 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1358 Frame frame = new Frame();
1360 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1361 "label.alignment_output_command",
1362 new Object[] { e.getActionCommand() }), 600, 500);
1364 FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1365 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1366 e.getActionCommand(), viewport.getAlignment(),
1367 viewport.getShowJVSuffix()));
1370 public void loadAnnotations()
1372 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1373 cap.setText(MessageManager
1374 .getString("label.paste_features_annotations_Tcoffee_here"));
1375 cap.setAnnotationImport();
1376 Frame frame = new Frame();
1378 jalview.bin.JalviewLite.addFrame(frame,
1379 MessageManager.getString("action.paste_annotations"), 400, 300);
1383 public String outputAnnotations(boolean displayTextbox)
1385 String annotation = new AnnotationFile()
1386 .printAnnotationsForView(viewport);
1390 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1391 Frame frame = new Frame();
1393 jalview.bin.JalviewLite.addFrame(frame,
1394 MessageManager.getString("label.annotations"), 600, 500);
1395 cap.setText(annotation);
1401 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1403 if (alignPanel.getFeatureRenderer() != null
1404 && viewport.getFeaturesDisplayed() != null)
1406 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1412 public String outputFeatures(boolean displayTextbox, String format)
1415 FeaturesFile formatter = new FeaturesFile();
1416 if (format.equalsIgnoreCase("Jalview"))
1418 features = formatter.printJalviewFormat(viewport.getAlignment()
1419 .getSequencesArray(), getDisplayedFeatureCols());
1423 features = formatter.printGffFormat(viewport.getAlignment()
1424 .getSequencesArray(), getDisplayedFeatureCols());
1429 boolean frimport = false;
1430 if (features == null || features.equals("No Features Visible"))
1432 features = "# No features visible - paste some and import them here.";
1436 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1439 cap.setAnnotationImport();
1441 Frame frame = new Frame();
1443 jalview.bin.JalviewLite.addFrame(frame,
1444 MessageManager.getString("label.features"), 600, 500);
1445 cap.setText(features);
1449 if (features == null)
1458 void launchFullApplication()
1460 StringBuffer url = new StringBuffer(jalviewServletURL);
1462 // allow servlet parameters to be passed in applet parameter
1463 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1465 url.append(firstSep);
1468 + appendProtocol(viewport.applet.getParameter("file")));
1470 if (viewport.applet.getParameter("features") != null)
1472 url.append("&features=");
1473 url.append(appendProtocol(viewport.applet.getParameter("features")));
1476 if (viewport.applet.getParameter("annotations") != null)
1478 url.append("&annotations=");
1479 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1482 if (viewport.applet.getParameter("jnetfile") != null)
1484 url.append("&annotations=");
1485 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1488 if (viewport.applet.getParameter("defaultColour") != null)
1490 url.append("&colour="
1491 + removeWhiteSpace(viewport.applet
1492 .getParameter("defaultColour")));
1495 if (viewport.applet.getParameter("userDefinedColour") != null)
1497 url.append("&colour="
1498 + removeWhiteSpace(viewport.applet
1499 .getParameter("userDefinedColour")));
1501 if (viewport.applet.getParameter("tree") != null)
1504 + appendProtocol(viewport.applet.getParameter("tree")));
1506 if (viewport.applet.getParameter("treeFile") != null)
1509 + appendProtocol(viewport.applet.getParameter("treeFile")));
1512 showURL(url.toString(), "FULL_APP");
1515 String removeWhiteSpace(String colour)
1517 StringBuffer sb = new StringBuffer();
1518 for (int i = 0; i < colour.length(); i++)
1520 if (Character.isWhitespace(colour.charAt(i)))
1526 sb.append(colour.charAt(i));
1530 return sb.toString();
1533 String appendProtocol(String url)
1538 url = URLEncoder.encode(url);
1541 * When we finally deprecate 1.1 compatibility, we can start to use
1542 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1543 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1544 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1545 * ex.printStackTrace(); }
1547 catch (java.net.MalformedURLException ex)
1549 url = viewport.applet.getCodeBase() + url;
1554 public void closeMenuItem_actionPerformed()
1556 PaintRefresher.RemoveComponent(alignPanel);
1557 if (alignPanel.seqPanel != null
1558 && alignPanel.seqPanel.seqCanvas != null)
1560 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1562 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1564 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1567 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1582 void updateEditMenuBar()
1585 if (viewport.getHistoryList().size() > 0)
1587 undoMenuItem.setEnabled(true);
1588 CommandI command = viewport.getHistoryList().peek();
1589 undoMenuItem.setLabel(MessageManager.formatMessage(
1590 "label.undo_command",
1591 new Object[] { command.getDescription() }));
1595 undoMenuItem.setEnabled(false);
1596 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1599 if (viewport.getRedoList().size() > 0)
1601 redoMenuItem.setEnabled(true);
1603 CommandI command = viewport.getRedoList().peek();
1604 redoMenuItem.setLabel(MessageManager.formatMessage(
1605 "label.redo_command",
1606 new Object[] { command.getDescription() }));
1610 redoMenuItem.setEnabled(false);
1611 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1619 public void addHistoryItem(CommandI command)
1621 if (command.getSize() > 0)
1623 viewport.addToHistoryList(command);
1624 viewport.clearRedoList();
1625 updateEditMenuBar();
1626 viewport.updateHiddenColumns();
1631 * TODO: JAL-1104 DOCUMENT ME!
1636 protected void undoMenuItem_actionPerformed()
1638 if (viewport.getHistoryList().isEmpty())
1643 CommandI command = viewport.getHistoryList().pop();
1644 viewport.addToRedoList(command);
1645 command.undoCommand(null);
1647 AlignmentViewport originalSource = getOriginatingSource(command);
1649 if (originalSource != viewport)
1652 .println("Warning: Viewport object mismatch whilst undoing");
1654 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1655 // viewport.getColumnSelection().getHiddenColumns()
1657 updateEditMenuBar();
1658 originalSource.firePropertyChange("alignment", null, originalSource
1659 .getAlignment().getSequences());
1663 * TODO: JAL-1104 DOCUMENT ME!
1668 protected void redoMenuItem_actionPerformed()
1670 if (viewport.getRedoList().isEmpty())
1675 CommandI command = viewport.getRedoList().pop();
1676 viewport.addToHistoryList(command);
1677 command.doCommand(null);
1679 AlignmentViewport originalSource = getOriginatingSource(command);
1681 if (originalSource != viewport)
1684 .println("Warning: Viewport object mismatch whilst re-doing");
1686 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1687 // viewport.getColumnSelection().getHiddenColumns()
1690 updateEditMenuBar();
1691 originalSource.firePropertyChange("alignment", null, originalSource
1692 .getAlignment().getSequences());
1695 AlignmentViewport getOriginatingSource(CommandI command)
1697 AlignmentViewport originalSource = null;
1698 // For sequence removal and addition, we need to fire
1699 // the property change event FROM the viewport where the
1700 // original alignment was altered
1701 AlignmentI al = null;
1702 if (command instanceof EditCommand)
1704 EditCommand editCommand = (EditCommand) command;
1705 al = editCommand.getAlignment();
1706 Vector comps = (Vector) PaintRefresher.components.get(viewport
1707 .getSequenceSetId());
1708 for (int i = 0; i < comps.size(); i++)
1710 if (comps.elementAt(i) instanceof AlignmentPanel)
1712 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1714 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1721 if (originalSource == null)
1723 // The original view is closed, we must validate
1724 // the current view against the closed view first
1727 PaintRefresher.validateSequences(al, viewport.getAlignment());
1730 originalSource = viewport;
1733 return originalSource;
1737 * Move the currently selected sequences up or down one position in the
1742 public void moveSelectedSequences(boolean up)
1744 SequenceGroup sg = viewport.getSelectionGroup();
1749 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1750 up ? null : viewport.getHiddenRepSequences(), up);
1751 alignPanel.paintAlignment(true);
1754 * Also move cDNA/protein complement sequences
1756 AlignViewportI complement = viewport.getCodingComplement();
1757 if (complement != null)
1759 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1760 viewport, complement);
1761 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1762 up ? null : complement.getHiddenRepSequences(), up);
1763 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1767 synchronized void slideSequences(boolean right, int size)
1769 List<SequenceI> sg = new Vector<SequenceI>();
1770 if (viewport.cursorMode)
1772 sg.add(viewport.getAlignment().getSequenceAt(
1773 alignPanel.seqPanel.seqCanvas.cursorY));
1775 else if (viewport.getSelectionGroup() != null
1776 && viewport.getSelectionGroup().getSize() != viewport
1777 .getAlignment().getHeight())
1779 sg = viewport.getSelectionGroup().getSequences(
1780 viewport.getHiddenRepSequences());
1788 Vector<SequenceI> invertGroup = new Vector();
1790 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1792 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1794 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1798 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1800 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1802 for (int i = 0; i < invertGroup.size(); i++)
1804 seqs2[i] = invertGroup.elementAt(i);
1807 SlideSequencesCommand ssc;
1810 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1811 size, viewport.getGapCharacter());
1815 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1816 size, viewport.getGapCharacter());
1819 int groupAdjustment = 0;
1820 if (ssc.getGapsInsertedBegin() && right)
1822 if (viewport.cursorMode)
1824 alignPanel.seqPanel.moveCursor(size, 0);
1828 groupAdjustment = size;
1831 else if (!ssc.getGapsInsertedBegin() && !right)
1833 if (viewport.cursorMode)
1835 alignPanel.seqPanel.moveCursor(-size, 0);
1839 groupAdjustment = -size;
1843 if (groupAdjustment != 0)
1845 viewport.getSelectionGroup().setStartRes(
1846 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1847 viewport.getSelectionGroup().setEndRes(
1848 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1851 boolean appendHistoryItem = false;
1852 Deque<CommandI> historyList = viewport.getHistoryList();
1853 if (historyList != null && historyList.size() > 0
1854 && historyList.peek() instanceof SlideSequencesCommand)
1856 appendHistoryItem = ssc
1857 .appendSlideCommand((SlideSequencesCommand) historyList
1861 if (!appendHistoryItem)
1863 addHistoryItem(ssc);
1869 static StringBuffer copiedSequences;
1871 static Vector copiedHiddenColumns;
1873 protected void copy_actionPerformed()
1875 if (viewport.getSelectionGroup() == null)
1880 SequenceGroup sg = viewport.getSelectionGroup();
1881 copiedSequences = new StringBuffer();
1882 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1883 for (int i = 0; i < sg.getSize(); i++)
1885 SequenceI seq = sg.getSequenceAt(i);
1886 int index = viewport.getAlignment().findIndex(seq);
1887 orderedSeqs.put(index, seq);
1890 int index = 0, startRes, endRes;
1893 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1895 copiedHiddenColumns = new Vector();
1896 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1897 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1899 copiedHiddenColumns.addElement(new int[] {
1900 region[0] - hiddenOffset, region[1] - hiddenOffset });
1905 copiedHiddenColumns = null;
1908 for (int i = 0; i < sg.getSize(); i++)
1910 SequenceI seq = null;
1914 if (orderedSeqs.containsKey(index))
1916 seq = orderedSeqs.get(index);
1927 // Returns residue following index if gap
1928 startRes = seq.findPosition(sg.getStartRes());
1931 // Need to find the residue preceeding index if gap
1934 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1936 ch = seq.getCharAt(j);
1937 if (!jalview.util.Comparison.isGap((ch)))
1945 endRes += seq.getStart() - 1;
1948 copiedSequences.append(seq.getName()
1954 + seq.getSequenceAsString(sg.getStartRes(),
1955 sg.getEndRes() + 1) + "\n");
1960 protected void pasteNew_actionPerformed()
1965 protected void pasteThis_actionPerformed()
1970 void paste(boolean newAlignment)
1975 if (copiedSequences == null)
1980 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1981 Vector seqs = new Vector();
1982 while (st.hasMoreElements())
1984 String name = st.nextToken();
1985 int start = Integer.parseInt(st.nextToken());
1986 int end = Integer.parseInt(st.nextToken());
1987 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1989 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1990 for (int i = 0; i < seqs.size(); i++)
1992 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1997 String newtitle = MessageManager
1998 .getString("label.copied_sequences");
1999 if (getTitle().startsWith(
2000 MessageManager.getString("label.copied_sequences")))
2002 newtitle = getTitle();
2006 newtitle = newtitle.concat(MessageManager.formatMessage(
2007 "label.from_msname", new String[] { getTitle() }));
2009 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2010 viewport.applet, newtitle, false);
2011 if (copiedHiddenColumns != null)
2013 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2015 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2016 af.viewport.hideColumns(region[0], region[1]);
2020 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2025 addSequences(newSeqs);
2028 } catch (Exception ex)
2030 } // could be anything being pasted in here
2034 void addSequences(SequenceI[] seqs)
2036 for (int i = 0; i < seqs.length; i++)
2038 viewport.getAlignment().addSequence(seqs[i]);
2042 addHistoryItem(new EditCommand(
2043 MessageManager.getString("label.add_sequences"), Action.PASTE,
2044 seqs, 0, viewport.getAlignment().getWidth(),
2045 viewport.getAlignment()));
2047 viewport.setEndSeq(viewport.getAlignment().getHeight());
2048 viewport.getAlignment().getWidth();
2049 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2054 protected void cut_actionPerformed()
2056 copy_actionPerformed();
2057 delete_actionPerformed();
2060 protected void delete_actionPerformed()
2063 SequenceGroup sg = viewport.getSelectionGroup();
2069 Vector seqs = new Vector();
2071 for (int i = 0; i < sg.getSize(); i++)
2073 seq = sg.getSequenceAt(i);
2074 seqs.addElement(seq);
2078 * If the cut affects all sequences, warn, remove highlighted columns
2080 if (sg.getSize() == viewport.getAlignment().getHeight())
2082 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2083 .getAlignment().getWidth()) ? true : false;
2084 if (isEntireAlignWidth)
2086 String title = MessageManager.getString("label.delete_all");
2087 Panel infoPanel = new Panel();
2088 infoPanel.setLayout(new FlowLayout());
2090 .add(new Label(MessageManager.getString("warn.delete_all")));
2092 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2093 dialog.setMainPanel(infoPanel);
2094 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2095 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2096 dialog.setVisible(true);
2103 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2104 sg.getEndRes() + 1);
2107 SequenceI[] cut = new SequenceI[seqs.size()];
2108 for (int i = 0; i < seqs.size(); i++)
2110 cut[i] = (SequenceI) seqs.elementAt(i);
2114 * //ADD HISTORY ITEM
2116 addHistoryItem(new EditCommand(
2117 MessageManager.getString("label.cut_sequences"), Action.CUT,
2118 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2119 viewport.getAlignment()));
2121 viewport.setSelectionGroup(null);
2122 viewport.getAlignment().deleteGroup(sg);
2124 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2127 if (viewport.getAlignment().getHeight() < 1)
2129 this.setVisible(false);
2131 viewport.sendSelection();
2135 * group consensus toggled
2138 protected void showGroupConsensus_actionPerformed()
2140 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2141 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2146 * group conservation toggled.
2148 protected void showGroupConservation_actionPerformed()
2150 viewport.setShowGroupConservation(showGroupConservation.getState());
2151 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2158 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2159 * .event.ActionEvent)
2161 protected void showConsensusHistogram_actionPerformed()
2163 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2164 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2171 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2172 * .event.ActionEvent)
2174 protected void showSequenceLogo_actionPerformed()
2176 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2177 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2180 protected void normSequenceLogo_actionPerformed()
2182 showSequenceLogo.setState(true);
2183 viewport.setShowSequenceLogo(true);
2184 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2185 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2188 protected void applyAutoAnnotationSettings_actionPerformed()
2190 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2193 protected void makeGrpsFromSelection_actionPerformed()
2195 if (avc.makeGroupsFromSelection())
2197 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2198 alignPanel.updateAnnotation();
2199 alignPanel.paintAlignment(true);
2203 protected void createGroup_actionPerformed()
2208 protected void unGroup_actionPerformed()
2212 alignPanel.alignmentChanged();
2216 protected void deleteGroups_actionPerformed()
2218 if (avc.deleteGroups())
2220 alignPanel.alignmentChanged();
2224 public void selectAllSequenceMenuItem_actionPerformed()
2226 SequenceGroup sg = new SequenceGroup();
2227 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2229 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2231 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2232 viewport.setSelectionGroup(sg);
2233 // JAL-2034 - should delegate to
2234 // alignPanel to decide if overview needs
2236 alignPanel.paintAlignment(false);
2237 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2238 viewport.sendSelection();
2241 public void deselectAllSequenceMenuItem_actionPerformed()
2243 if (viewport.cursorMode)
2245 alignPanel.seqPanel.keyboardNo1 = null;
2246 alignPanel.seqPanel.keyboardNo2 = null;
2248 viewport.setSelectionGroup(null);
2249 viewport.getColumnSelection().clear();
2250 viewport.setSelectionGroup(null);
2251 alignPanel.idPanel.idCanvas.searchResults = null;
2252 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2253 // JAL-2034 - should delegate to
2254 // alignPanel to decide if overview needs
2256 alignPanel.paintAlignment(false);
2257 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2258 viewport.sendSelection();
2261 public void invertSequenceMenuItem_actionPerformed()
2263 SequenceGroup sg = viewport.getSelectionGroup();
2264 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2266 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2269 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2270 viewport.sendSelection();
2273 public void invertColSel_actionPerformed()
2275 viewport.invertColumnSelection();
2276 alignPanel.paintAlignment(true);
2277 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2278 viewport.sendSelection();
2281 void trimAlignment(boolean trimLeft)
2283 ColumnSelection colSel = viewport.getColumnSelection();
2286 if (!colSel.isEmpty())
2290 column = colSel.getMin();
2294 column = colSel.getMax();
2298 if (viewport.getSelectionGroup() != null)
2300 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2301 viewport.getHiddenRepSequences());
2305 seqs = viewport.getAlignment().getSequencesArray();
2308 TrimRegionCommand trimRegion;
2311 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2312 column, viewport.getAlignment());
2313 viewport.setStartRes(0);
2317 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2318 column, viewport.getAlignment());
2321 statusBar.setText(MessageManager.formatMessage(
2322 "label.removed_columns",
2323 new String[] { Integer.valueOf(trimRegion.getSize())
2325 addHistoryItem(trimRegion);
2327 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2329 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2330 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2332 viewport.getAlignment().deleteGroup(sg);
2336 viewport.firePropertyChange("alignment", null, viewport
2337 .getAlignment().getSequences());
2341 public void removeGappedColumnMenuItem_actionPerformed()
2343 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2346 if (viewport.getSelectionGroup() != null)
2348 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2349 viewport.getHiddenRepSequences());
2350 start = viewport.getSelectionGroup().getStartRes();
2351 end = viewport.getSelectionGroup().getEndRes();
2355 seqs = viewport.getAlignment().getSequencesArray();
2358 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2359 "Remove Gapped Columns", seqs, start, end,
2360 viewport.getAlignment());
2362 addHistoryItem(removeGapCols);
2364 statusBar.setText(MessageManager.formatMessage(
2365 "label.removed_empty_columns",
2366 new String[] { Integer.valueOf(removeGapCols.getSize())
2369 // This is to maintain viewport position on first residue
2370 // of first sequence
2371 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2372 int startRes = seq.findPosition(viewport.startRes);
2373 // ShiftList shifts;
2374 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2375 // edit.alColumnChanges=shifts.getInverse();
2376 // if (viewport.hasHiddenColumns)
2377 // viewport.getColumnSelection().compensateForEdits(shifts);
2378 viewport.setStartRes(seq.findIndex(startRes) - 1);
2379 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2384 public void removeAllGapsMenuItem_actionPerformed()
2386 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2389 if (viewport.getSelectionGroup() != null)
2391 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2392 viewport.getHiddenRepSequences());
2393 start = viewport.getSelectionGroup().getStartRes();
2394 end = viewport.getSelectionGroup().getEndRes();
2398 seqs = viewport.getAlignment().getSequencesArray();
2401 // This is to maintain viewport position on first residue
2402 // of first sequence
2403 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2404 int startRes = seq.findPosition(viewport.startRes);
2406 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2407 viewport.getAlignment()));
2409 viewport.setStartRes(seq.findIndex(startRes) - 1);
2411 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2416 public void findMenuItem_actionPerformed()
2418 new Finder(alignPanel);
2422 * create a new view derived from the current view
2425 * @return frame for the new view
2427 public AlignFrame newView(String viewtitle)
2430 if (viewport.hasHiddenRows())
2432 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2433 .getFullAlignment().getSequencesArray());
2437 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2440 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2442 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2444 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2446 newal.addAnnotation(viewport.getAlignment()
2447 .getAlignmentAnnotation()[i]);
2452 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2454 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2455 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2456 PaintRefresher.Register(newaf.alignPanel,
2457 newaf.alignPanel.av.getSequenceSetId());
2459 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2460 newaf.alignPanel.av.getSequenceSetId());
2461 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2462 newaf.alignPanel.av.getSequenceSetId());
2464 Vector comps = (Vector) PaintRefresher.components.get(viewport
2465 .getSequenceSetId());
2467 for (int i = 0; i < comps.size(); i++)
2469 if (comps.elementAt(i) instanceof AlignmentPanel)
2475 String title = new String(this.getTitle());
2476 if (viewtitle != null)
2478 title = viewtitle + " ( " + title + ")";
2482 if (title.indexOf("(View") > -1)
2484 title = title.substring(0, title.indexOf("(View"));
2486 title += "(View " + viewSize + ")";
2489 newaf.setTitle(title.toString());
2491 newaf.viewport.setHistoryList(viewport.getHistoryList());
2492 newaf.viewport.setRedoList(viewport.getRedoList());
2498 * @return list of feature groups on the view
2500 public String[] getFeatureGroups()
2502 FeatureRenderer fr = null;
2503 if (alignPanel != null
2504 && (fr = alignPanel.getFeatureRenderer()) != null)
2506 List<String> gps = fr.getFeatureGroups();
2507 String[] _gps = gps.toArray(new String[gps.size()]);
2514 * get sequence feature groups that are hidden or shown
2520 public String[] getFeatureGroupsOfState(boolean visible)
2522 FeatureRenderer fr = null;
2523 if (alignPanel != null
2524 && (fr = alignPanel.getFeatureRenderer()) != null)
2526 List<String> gps = fr.getGroups(visible);
2527 String[] _gps = gps.toArray(new String[gps.size()]);
2534 * Change the display state for the given feature groups
2537 * list of group strings
2539 * visible or invisible
2541 public void setFeatureGroupState(String[] groups, boolean state)
2543 FeatureRenderer fr = null;
2544 this.sequenceFeatures.setState(true);
2545 viewport.setShowSequenceFeatures(true);
2546 if (alignPanel != null
2547 && (fr = alignPanel.getFeatureRenderer()) != null)
2550 fr.setGroupVisibility(Arrays.asList(groups), state);
2551 alignPanel.seqPanel.seqCanvas.repaint();
2552 if (alignPanel.overviewPanel != null)
2554 alignPanel.overviewPanel.updateOverviewImage();
2559 public void seqLimits_itemStateChanged()
2561 viewport.setShowJVSuffix(seqLimits.getState());
2562 alignPanel.fontChanged();
2563 alignPanel.paintAlignment(true);
2566 protected void colourTextMenuItem_actionPerformed()
2568 viewport.setColourText(colourTextMenuItem.getState());
2569 alignPanel.paintAlignment(true);
2572 protected void displayNonconservedMenuItem_actionPerformed()
2574 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2575 alignPanel.paintAlignment(true);
2578 protected void wrapMenuItem_actionPerformed()
2580 viewport.setWrapAlignment(wrapMenuItem.getState());
2581 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2582 scaleAbove.setEnabled(wrapMenuItem.getState());
2583 scaleLeft.setEnabled(wrapMenuItem.getState());
2584 scaleRight.setEnabled(wrapMenuItem.getState());
2585 alignPanel.paintAlignment(true);
2588 public void overviewMenuItem_actionPerformed()
2590 if (alignPanel.overviewPanel != null)
2595 Frame frame = new Frame();
2596 OverviewPanel overview = new OverviewPanel(alignPanel);
2597 frame.add(overview);
2598 // +50 must allow for applet frame window
2599 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2600 "label.overview_params", new String[] { this.getTitle() }),
2601 overview.getPreferredSize().width,
2602 overview.getPreferredSize().height + 50);
2605 final AlignmentPanel ap = alignPanel;
2606 frame.addWindowListener(new WindowAdapter()
2609 public void windowClosing(WindowEvent e)
2613 ap.setOverviewPanel(null);
2618 alignPanel.setOverviewPanel(overview);
2623 public void changeColour(ColourSchemeI cs)
2628 if (viewport.getAbovePIDThreshold())
2630 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2634 if (viewport.getConservationSelected())
2636 cs.setConservationApplied(true);
2637 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2642 cs.setConservationApplied(false);
2645 viewport.setGlobalColourScheme(cs);
2647 alignPanel.paintAlignment(true);
2650 protected void modifyPID_actionPerformed()
2652 if (viewport.getAbovePIDThreshold()
2653 && viewport.getGlobalColourScheme() != null)
2655 SliderPanel.setPIDSliderSource(alignPanel,
2656 viewport.getGlobalColourScheme(), "Background");
2657 SliderPanel.showPIDSlider();
2661 protected void modifyConservation_actionPerformed()
2663 if (viewport.getConservationSelected()
2664 && viewport.getGlobalColourScheme() != null)
2666 SliderPanel.setConservationSlider(alignPanel,
2667 viewport.getGlobalColourScheme(), "Background");
2668 SliderPanel.showConservationSlider();
2672 protected void conservationMenuItem_actionPerformed()
2674 viewport.setConservationSelected(conservationMenuItem.getState());
2676 viewport.setAbovePIDThreshold(false);
2677 abovePIDThreshold.setState(false);
2679 changeColour(viewport.getGlobalColourScheme());
2681 modifyConservation_actionPerformed();
2684 public void abovePIDThreshold_actionPerformed()
2686 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2688 conservationMenuItem.setState(false);
2689 viewport.setConservationSelected(false);
2691 changeColour(viewport.getGlobalColourScheme());
2693 modifyPID_actionPerformed();
2696 public void sortPairwiseMenuItem_actionPerformed()
2698 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2699 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2700 .getAlignment().getSequenceAt(0), null);
2702 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2703 viewport.getAlignment()));
2704 alignPanel.paintAlignment(true);
2707 public void sortIDMenuItem_actionPerformed()
2709 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2710 AlignmentSorter.sortByID(viewport.getAlignment());
2711 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2712 viewport.getAlignment()));
2713 alignPanel.paintAlignment(true);
2716 public void sortLengthMenuItem_actionPerformed()
2718 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2719 AlignmentSorter.sortByLength(viewport.getAlignment());
2720 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2721 viewport.getAlignment()));
2722 alignPanel.paintAlignment(true);
2725 public void sortGroupMenuItem_actionPerformed()
2727 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2728 AlignmentSorter.sortByGroup(viewport.getAlignment());
2729 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2730 viewport.getAlignment()));
2731 alignPanel.paintAlignment(true);
2735 public void removeRedundancyMenuItem_actionPerformed()
2737 new RedundancyPanel(alignPanel);
2740 public void pairwiseAlignmentMenuItem_actionPerformed()
2742 if (viewport.getSelectionGroup() != null
2743 && viewport.getSelectionGroup().getSize() > 1)
2745 Frame frame = new Frame();
2746 frame.add(new PairwiseAlignPanel(alignPanel));
2747 jalview.bin.JalviewLite.addFrame(frame,
2748 MessageManager.getString("action.pairwise_alignment"), 600,
2753 public void PCAMenuItem_actionPerformed()
2755 // are the sequences aligned?
2756 if (!viewport.getAlignment().isAligned(false))
2759 int Width = viewport.getAlignment().getWidth();
2761 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2763 current = viewport.getAlignment().getSequenceAt(i);
2765 if (current.getLength() < Width)
2767 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2770 alignPanel.paintAlignment(true);
2773 if ((viewport.getSelectionGroup() != null
2774 && viewport.getSelectionGroup().getSize() < 4 && viewport
2775 .getSelectionGroup().getSize() > 0)
2776 || viewport.getAlignment().getHeight() < 4)
2783 new PCAPanel(viewport);
2784 } catch (java.lang.OutOfMemoryError ex)
2790 public void averageDistanceTreeMenuItem_actionPerformed()
2792 NewTreePanel("AV", "PID", "Average distance tree using PID");
2795 public void neighbourTreeMenuItem_actionPerformed()
2797 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2800 protected void njTreeBlosumMenuItem_actionPerformed()
2802 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2805 protected void avTreeBlosumMenuItem_actionPerformed()
2807 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2810 void NewTreePanel(String type, String pwType, String title)
2812 // are the sequences aligned?
2813 if (!viewport.getAlignment().isAligned(false))
2816 int Width = viewport.getAlignment().getWidth();
2818 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2820 current = viewport.getAlignment().getSequenceAt(i);
2822 if (current.getLength() < Width)
2824 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2827 alignPanel.paintAlignment(true);
2831 if ((viewport.getSelectionGroup() != null && viewport
2832 .getSelectionGroup().getSize() > 1)
2833 || (viewport.getAlignment().getHeight() > 1))
2835 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2837 addTreeMenuItem(tp, title);
2839 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2843 void loadTree_actionPerformed()
2845 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2846 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2847 cap.setTreeImport();
2848 Frame frame = new Frame();
2850 jalview.bin.JalviewLite.addFrame(frame,
2851 MessageManager.getString("label.paste_newick_file"), 400, 300);
2854 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2856 TreePanel tp = new TreePanel(alignPanel, treeFile,
2857 MessageManager.getString("label.load_tree_from_file"), tree);
2858 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2859 addTreeMenuItem(tp, treeFile);
2863 * sort the alignment using the given treePanel
2866 * tree used to sort view
2868 * string used for undo event name
2870 public void sortByTree(TreePanel treePanel, String title)
2872 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2874 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2875 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2876 // HistoryItem.SORT));
2877 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2878 "label.order_by_params", new String[] { title }), oldOrder,
2879 viewport.getAlignment()));
2880 alignPanel.paintAlignment(true);
2884 * Do any automatic reordering of the alignment and add the necessary bits to
2885 * the menu structure for the new tree
2890 protected void addTreeMenuItem(final TreePanel treePanel,
2893 final MenuItem item = new MenuItem(title);
2894 sortByTreeMenu.add(item);
2895 item.addActionListener(new java.awt.event.ActionListener()
2898 public void actionPerformed(ActionEvent evt)
2900 sortByTree(treePanel, title); // treePanel.getTitle());
2904 treePanel.addWindowListener(new WindowAdapter()
2907 public void windowOpened(WindowEvent e)
2909 if (viewport.sortByTree)
2911 sortByTree(treePanel, title);
2913 super.windowOpened(e);
2917 public void windowClosing(WindowEvent e)
2919 sortByTreeMenu.remove(item);
2924 public boolean sortBy(AlignmentOrder alorder, String undoname)
2926 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2927 if (viewport.applet.debug)
2929 System.err.println("Sorting " + alorder.getOrder().size()
2930 + " in alignment '" + getTitle() + "'");
2932 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2933 if (undoname != null)
2935 addHistoryItem(new OrderCommand(undoname, oldOrder,
2936 viewport.getAlignment()));
2938 alignPanel.paintAlignment(true);
2942 protected void documentation_actionPerformed()
2944 alignPanel.av.applet.openJalviewHelpUrl();
2947 protected void about_actionPerformed()
2950 class AboutPanel extends Canvas
2956 public AboutPanel(String version, String builddate)
2958 this.version = version;
2959 this.builddate = builddate;
2963 public void paint(Graphics g)
2965 g.setColor(Color.white);
2966 g.fillRect(0, 0, getSize().width, getSize().height);
2967 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2968 FontMetrics fm = g.getFontMetrics();
2969 int fh = fm.getHeight();
2971 g.setColor(Color.black);
2972 // TODO: update this text for each release or centrally store it for
2973 // lite and application
2974 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2975 g.drawString(MessageManager.formatMessage(
2976 "label.jalviewLite_release", new String[] { version }), x,
2978 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2979 g.drawString(MessageManager.formatMessage(
2980 "label.jaview_build_date", new String[] { builddate }), x,
2982 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2983 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2985 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2986 x + 50, y += fh + 8);
2988 MessageManager.getString("label.jalview_dev_managers"), x,
2990 g.drawString(MessageManager
2991 .getString("label.jalview_distribution_lists"), x, y += fh);
2992 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2995 MessageManager.getString("label.jalview_cite_1_authors"),
2998 MessageManager.getString("label.jalview_cite_1_title"), x,
3000 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3005 Frame frame = new Frame();
3006 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3008 jalview.bin.JalviewLite.addFrame(frame,
3009 MessageManager.getString("label.jalview"), 580, 220);
3013 public void showURL(String url, String target)
3015 if (viewport.applet == null)
3017 System.out.println("Not running as applet - no browser available.");
3021 viewport.applet.showURL(url, target);
3025 // ////////////////////////////////////////////////////////////////////////////////
3026 // JBuilder Graphics here
3028 MenuBar alignFrameMenuBar = new MenuBar();
3030 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3032 MenuItem loadApplication = new MenuItem(
3033 MessageManager.getString("label.view_full_application"));
3035 MenuItem loadTree = new MenuItem(
3036 MessageManager.getString("label.load_associated_tree"));
3038 MenuItem loadAnnotations = new MenuItem(
3039 MessageManager.getString("label.load_features_annotations"));
3041 MenuItem outputFeatures = new MenuItem(
3042 MessageManager.getString("label.export_features"));
3044 MenuItem outputAnnotations = new MenuItem(
3045 MessageManager.getString("label.export_annotations"));
3047 MenuItem closeMenuItem = new MenuItem(
3048 MessageManager.getString("action.close"));
3050 MenuItem selectAllSequenceMenuItem = new MenuItem(
3051 MessageManager.getString("action.select_all"));
3053 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3054 MessageManager.getString("action.deselect_all"));
3056 MenuItem invertSequenceMenuItem = new MenuItem(
3057 MessageManager.getString("action.invert_selection"));
3059 MenuItem remove2LeftMenuItem = new MenuItem();
3061 MenuItem remove2RightMenuItem = new MenuItem();
3063 MenuItem removeGappedColumnMenuItem = new MenuItem();
3065 MenuItem removeAllGapsMenuItem = new MenuItem();
3067 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3069 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3071 MenuItem sortPairwiseMenuItem = new MenuItem();
3073 MenuItem sortIDMenuItem = new MenuItem();
3075 MenuItem sortLengthMenuItem = new MenuItem();
3077 MenuItem sortGroupMenuItem = new MenuItem();
3079 MenuItem removeRedundancyMenuItem = new MenuItem();
3081 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3083 MenuItem PCAMenuItem = new MenuItem();
3085 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3087 MenuItem neighbourTreeMenuItem = new MenuItem();
3089 BorderLayout borderLayout1 = new BorderLayout();
3091 public Label statusBar = new Label();
3093 MenuItem clustalColour = new MenuItem();
3095 MenuItem zappoColour = new MenuItem();
3097 MenuItem taylorColour = new MenuItem();
3099 MenuItem hydrophobicityColour = new MenuItem();
3101 MenuItem helixColour = new MenuItem();
3103 MenuItem strandColour = new MenuItem();
3105 MenuItem turnColour = new MenuItem();
3107 MenuItem buriedColour = new MenuItem();
3109 MenuItem purinePyrimidineColour = new MenuItem();
3111 // MenuItem RNAInteractionColour = new MenuItem();
3113 MenuItem RNAHelixColour = new MenuItem();
3115 MenuItem userDefinedColour = new MenuItem();
3117 MenuItem PIDColour = new MenuItem();
3119 MenuItem BLOSUM62Colour = new MenuItem();
3121 MenuItem tcoffeeColour = new MenuItem();
3123 MenuItem njTreeBlosumMenuItem = new MenuItem();
3125 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3127 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3129 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3131 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3133 MenuItem alProperties = new MenuItem(
3134 MessageManager.getString("label.alignment_props"));
3136 MenuItem overviewMenuItem = new MenuItem();
3138 MenuItem undoMenuItem = new MenuItem();
3140 MenuItem redoMenuItem = new MenuItem();
3142 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3144 MenuItem noColourmenuItem = new MenuItem();
3146 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3148 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3150 MenuItem findMenuItem = new MenuItem();
3152 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3154 MenuItem nucleotideColour = new MenuItem();
3156 MenuItem deleteGroups = new MenuItem();
3158 MenuItem grpsFromSelection = new MenuItem();
3160 MenuItem createGroup = new MenuItem();
3162 MenuItem unGroup = new MenuItem();
3164 MenuItem delete = new MenuItem();
3166 MenuItem copy = new MenuItem();
3168 MenuItem cut = new MenuItem();
3170 Menu pasteMenu = new Menu();
3172 MenuItem pasteNew = new MenuItem();
3174 MenuItem pasteThis = new MenuItem();
3176 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3178 MenuItem font = new MenuItem();
3180 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3182 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3184 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3186 MenuItem modifyPID = new MenuItem();
3188 MenuItem modifyConservation = new MenuItem();
3190 CheckboxMenuItem autoCalculate = null;
3192 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3193 "Sort Alignment With New Tree", true);
3195 Menu sortByTreeMenu = new Menu();
3197 MenuItem inputText = new MenuItem();
3199 MenuItem documentation = new MenuItem();
3201 MenuItem about = new MenuItem();
3203 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3205 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3207 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3209 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3211 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3213 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3215 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3217 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3219 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3222 * Initialise menus and other items
3226 private void jbInit() throws Exception
3228 setMenuBar(alignFrameMenuBar);
3231 * Configure File menu items and actions
3234 .setLabel(MessageManager.getString("label.input_from_textbox"));
3235 inputText.addActionListener(this);
3236 Menu outputTextboxMenu = new Menu(
3237 MessageManager.getString("label.out_to_textbox"));
3238 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3241 MenuItem item = new MenuItem(
3242 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3244 item.addActionListener(new java.awt.event.ActionListener()
3247 public void actionPerformed(ActionEvent e)
3249 outputText_actionPerformed(e);
3253 outputTextboxMenu.add(item);
3255 closeMenuItem.addActionListener(this);
3256 loadApplication.addActionListener(this);
3257 loadTree.addActionListener(this);
3258 loadAnnotations.addActionListener(this);
3259 outputFeatures.addActionListener(this);
3260 outputAnnotations.addActionListener(this);
3263 * Configure Edit menu items and actions
3265 undoMenuItem.setEnabled(false);
3266 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3267 undoMenuItem.addActionListener(this);
3268 redoMenuItem.setEnabled(false);
3269 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3270 redoMenuItem.addActionListener(this);
3271 copy.setLabel(MessageManager.getString("action.copy"));
3272 copy.addActionListener(this);
3273 cut.setLabel(MessageManager.getString("action.cut"));
3274 cut.addActionListener(this);
3275 delete.setLabel(MessageManager.getString("action.delete"));
3276 delete.addActionListener(this);
3277 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3278 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3279 pasteNew.addActionListener(this);
3280 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3281 pasteThis.addActionListener(this);
3282 remove2LeftMenuItem.setLabel(MessageManager
3283 .getString("action.remove_left"));
3284 remove2LeftMenuItem.addActionListener(this);
3285 remove2RightMenuItem.setLabel(MessageManager
3286 .getString("action.remove_right"));
3287 remove2RightMenuItem.addActionListener(this);
3288 removeGappedColumnMenuItem.setLabel(MessageManager
3289 .getString("action.remove_empty_columns"));
3290 removeGappedColumnMenuItem.addActionListener(this);
3291 removeAllGapsMenuItem.setLabel(MessageManager
3292 .getString("action.remove_all_gaps"));
3293 removeAllGapsMenuItem.addActionListener(this);
3294 removeRedundancyMenuItem.setLabel(MessageManager
3295 .getString("action.remove_redundancy"));
3296 removeRedundancyMenuItem.addActionListener(this);
3299 * Configure Select menu items and actions
3301 findMenuItem.setLabel(MessageManager.getString("action.find"));
3302 findMenuItem.addActionListener(this);
3303 selectAllSequenceMenuItem.addActionListener(this);
3304 deselectAllSequenceMenuItem.addActionListener(this);
3305 invertSequenceMenuItem.setLabel(MessageManager
3306 .getString("action.invert_sequence_selection"));
3307 invertSequenceMenuItem.addActionListener(this);
3308 invertColSel.setLabel(MessageManager
3309 .getString("action.invert_column_selection"));
3310 invertColSel.addActionListener(this);
3311 deleteGroups.setLabel(MessageManager
3312 .getString("action.undefine_groups"));
3313 deleteGroups.addActionListener(this);
3314 grpsFromSelection.setLabel(MessageManager
3315 .getString("action.make_groups_selection"));
3316 grpsFromSelection.addActionListener(this);
3317 createGroup.setLabel(MessageManager.getString("action.create_group"));
3318 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3319 annotationColumnSelection.setLabel(MessageManager
3320 .getString("action.select_by_annotation"));
3321 annotationColumnSelection.addActionListener(this);
3324 * Configure View menu items and actions
3326 newView.setLabel(MessageManager.getString("action.new_view"));
3327 newView.addActionListener(this);
3328 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3329 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3330 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3331 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3333 .setLabel(MessageManager.getString("label.selected_columns"));
3334 hideSequences.setLabel(MessageManager
3335 .getString("label.selected_sequences"));
3336 hideAllButSelection.setLabel(MessageManager
3337 .getString("label.all_but_selected_region"));
3338 hideAllSelection.setLabel(MessageManager
3339 .getString("label.selected_region"));
3340 showAllHidden.setLabel(MessageManager
3341 .getString("label.all_sequences_columns"));
3342 showColumns.addActionListener(this);
3343 showSeqs.addActionListener(this);
3344 hideColumns.addActionListener(this);
3345 hideSequences.addActionListener(this);
3346 hideAllButSelection.addActionListener(this);
3347 hideAllSelection.addActionListener(this);
3348 showAllHidden.addActionListener(this);
3349 featureSettings.setLabel(MessageManager
3350 .getString("action.feature_settings"));
3351 featureSettings.addActionListener(this);
3352 sequenceFeatures.setLabel(MessageManager
3353 .getString("label.show_sequence_features"));
3354 sequenceFeatures.addItemListener(this);
3355 sequenceFeatures.setState(false);
3356 followMouseOverFlag.setLabel(MessageManager
3357 .getString("label.automatic_scrolling"));
3358 followMouseOverFlag.addItemListener(this);
3359 alProperties.addActionListener(this);
3360 overviewMenuItem.setLabel(MessageManager
3361 .getString("label.overview_window"));
3362 overviewMenuItem.addActionListener(this);
3365 * Configure Annotations menu items and actions
3367 annotationPanelMenuItem.setLabel(MessageManager
3368 .getString("label.show_annotations"));
3369 annotationPanelMenuItem.addItemListener(this);
3370 showGroupConsensus.setLabel(MessageManager
3371 .getString("label.group_consensus"));
3372 showGroupConservation.setLabel(MessageManager
3373 .getString("label.group_conservation"));
3374 showConsensusHistogram.setLabel(MessageManager
3375 .getString("label.show_consensus_histogram"));
3376 showSequenceLogo.setLabel(MessageManager
3377 .getString("label.show_consensus_logo"));
3378 normSequenceLogo.setLabel(MessageManager
3379 .getString("label.norm_consensus_logo"));
3380 applyAutoAnnotationSettings.setLabel(MessageManager
3381 .getString("label.apply_all_groups"));
3382 applyAutoAnnotationSettings.setState(true);
3383 Menu autoAnnMenu = new Menu(
3384 MessageManager.getString("label.autocalculated_annotation"));
3385 showGroupConsensus.addItemListener(this);
3386 showGroupConservation.addItemListener(this);
3387 showConsensusHistogram.addItemListener(this);
3388 showSequenceLogo.addItemListener(this);
3389 normSequenceLogo.addItemListener(this);
3390 applyAutoAnnotationSettings.addItemListener(this);
3391 showAlignmentAnnotations = new CheckboxMenuItem(
3392 MessageManager.getString("label.show_all_al_annotations"));
3393 showSequenceAnnotations = new CheckboxMenuItem(
3394 MessageManager.getString("label.show_all_seq_annotations"));
3395 sortAnnBySequence = new CheckboxMenuItem(
3396 MessageManager.getString("label.sort_annotations_by_sequence"));
3397 sortAnnByLabel = new CheckboxMenuItem(
3398 MessageManager.getString("label.sort_annotations_by_label"));
3399 showAutoFirst = new CheckboxMenuItem(
3400 MessageManager.getString("label.show_first"));
3401 showAutoFirst.setState(false); // pending applet parameter
3402 setShowAutoCalculatedAbove(showAutoFirst.getState());
3403 showAutoLast = new CheckboxMenuItem(
3404 MessageManager.getString("label.show_last"));
3405 showAutoLast.setState(!showAutoFirst.getState());
3406 showAlignmentAnnotations.addItemListener(this);
3407 showSequenceAnnotations.addItemListener(this);
3408 sortAnnBySequence.addItemListener(this);
3409 sortAnnByLabel.addItemListener(this);
3410 showAutoFirst.addItemListener(this);
3411 showAutoLast.addItemListener(this);
3414 * Configure Format menu items and actions
3416 font.setLabel(MessageManager.getString("action.font"));
3417 font.addActionListener(this);
3418 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3419 scaleAbove.setState(true);
3420 scaleAbove.setEnabled(false);
3421 scaleAbove.addItemListener(this);
3422 scaleLeft.setEnabled(false);
3423 scaleLeft.setState(true);
3424 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3425 scaleLeft.addItemListener(this);
3426 scaleRight.setEnabled(false);
3427 scaleRight.setState(true);
3428 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3429 scaleRight.addItemListener(this);
3430 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3431 viewBoxesMenuItem.setState(true);
3432 viewBoxesMenuItem.addItemListener(this);
3433 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3434 viewTextMenuItem.setState(true);
3435 viewTextMenuItem.addItemListener(this);
3436 colourTextMenuItem.setLabel(MessageManager
3437 .getString("label.colour_text"));
3438 colourTextMenuItem.addItemListener(this);
3439 displayNonconservedMenuItem.setLabel(MessageManager
3440 .getString("label.show_non_conversed"));
3441 displayNonconservedMenuItem.addItemListener(this);
3442 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3443 wrapMenuItem.addItemListener(this);
3444 renderGapsMenuItem.setLabel(MessageManager
3445 .getString("action.show_gaps"));
3446 renderGapsMenuItem.setState(true);
3447 renderGapsMenuItem.addItemListener(this);
3448 centreColumnLabelFlag.setLabel(MessageManager
3449 .getString("label.centre_column_labels"));
3450 centreColumnLabelFlag.addItemListener(this);
3451 seqLimits.setState(true);
3452 seqLimits.setLabel(MessageManager
3453 .getString("label.show_sequence_limits"));
3454 seqLimits.addItemListener(this);
3457 * Configure Colour menu items and actions
3459 applyToAllGroups.setLabel(MessageManager
3460 .getString("label.apply_colour_to_all_groups"));
3461 applyToAllGroups.setState(true);
3462 applyToAllGroups.addItemListener(this);
3463 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3464 clustalColour.addActionListener(this);
3465 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3466 zappoColour.addActionListener(this);
3467 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3468 taylorColour.addActionListener(this);
3469 hydrophobicityColour.setLabel(MessageManager
3470 .getString("label.hydrophobicity"));
3471 hydrophobicityColour.addActionListener(this);
3473 .setLabel(MessageManager.getString("label.helix_propensity"));
3474 helixColour.addActionListener(this);
3475 strandColour.setLabel(MessageManager
3476 .getString("label.strand_propensity"));
3477 strandColour.addActionListener(this);
3478 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3479 turnColour.addActionListener(this);
3480 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3481 buriedColour.addActionListener(this);
3482 purinePyrimidineColour.setLabel(MessageManager
3483 .getString("label.purine_pyrimidine"));
3484 purinePyrimidineColour.addActionListener(this);
3485 // RNAInteractionColour.setLabel(MessageManager
3486 // .getString("label.rna_interaction"));
3487 // RNAInteractionColour.addActionListener(this);
3488 RNAHelixColour.setLabel(MessageManager
3489 .getString("action.by_rna_helixes"));
3490 RNAHelixColour.addActionListener(this);
3491 userDefinedColour.setLabel(MessageManager
3492 .getString("action.user_defined"));
3493 userDefinedColour.addActionListener(this);
3494 PIDColour.setLabel(MessageManager
3495 .getString("label.percentage_identity"));
3496 PIDColour.addActionListener(this);
3497 BLOSUM62Colour.setLabel(MessageManager
3498 .getString("label.blosum62_score"));
3499 BLOSUM62Colour.addActionListener(this);
3501 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3502 // it will be enabled only if a score file is provided
3503 tcoffeeColour.setEnabled(false);
3504 tcoffeeColour.addActionListener(this);
3505 conservationMenuItem.setLabel(MessageManager
3506 .getString("action.by_conservation"));
3507 conservationMenuItem.addItemListener(this);
3508 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3509 noColourmenuItem.addActionListener(this);
3510 abovePIDThreshold.setLabel(MessageManager
3511 .getString("label.above_identity_threshold"));
3512 abovePIDThreshold.addItemListener(this);
3513 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3514 nucleotideColour.addActionListener(this);
3515 modifyPID.setLabel(MessageManager
3516 .getString("label.modify_identity_threshold"));
3517 modifyPID.addActionListener(this);
3518 modifyConservation.setLabel(MessageManager
3519 .getString("label.modify_conservation_threshold"));
3520 modifyConservation.addActionListener(this);
3521 annotationColour.setLabel(MessageManager
3522 .getString("action.by_annotation"));
3523 annotationColour.addActionListener(this);
3526 * Configure Calculate menu items and actions
3528 sortPairwiseMenuItem.setLabel(MessageManager
3529 .getString("action.by_pairwise_id"));
3530 sortPairwiseMenuItem.addActionListener(this);
3531 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3532 sortIDMenuItem.addActionListener(this);
3533 sortLengthMenuItem.setLabel(MessageManager
3534 .getString("action.by_length"));
3535 sortLengthMenuItem.addActionListener(this);
3536 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3537 sortGroupMenuItem.addActionListener(this);
3538 pairwiseAlignmentMenuItem.setLabel(MessageManager
3539 .getString("action.pairwise_alignment"));
3540 pairwiseAlignmentMenuItem.addActionListener(this);
3541 PCAMenuItem.setLabel(MessageManager
3542 .getString("label.principal_component_analysis"));
3543 PCAMenuItem.addActionListener(this);
3544 autoCalculate = new CheckboxMenuItem(
3545 MessageManager.getString("label.autocalculate_consensus"), true);
3546 averageDistanceTreeMenuItem.setLabel(MessageManager
3547 .getString("label.average_distance_identity"));
3548 averageDistanceTreeMenuItem.addActionListener(this);
3549 neighbourTreeMenuItem.setLabel(MessageManager
3550 .getString("label.neighbour_joining_identity"));
3551 neighbourTreeMenuItem.addActionListener(this);
3552 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3553 .getString("label.average_distance_bloslum62"));
3554 avDistanceTreeBlosumMenuItem.addActionListener(this);
3555 njTreeBlosumMenuItem.setLabel(MessageManager
3556 .getString("label.neighbour_blosum62"));
3557 njTreeBlosumMenuItem.addActionListener(this);
3558 sortByTreeMenu.setLabel(MessageManager
3559 .getString("action.by_tree_order"));
3560 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3561 Menu calculateTreeMenu = new Menu(
3562 MessageManager.getString("action.calculate_tree"));
3563 autoCalculate.addItemListener(this);
3564 sortByTree.addItemListener(this);
3567 * Configure Help menu items and actions
3569 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3570 documentation.setLabel(MessageManager.getString("label.documentation"));
3571 documentation.addActionListener(this);
3572 about.setLabel(MessageManager.getString("label.about"));
3573 about.addActionListener(this);
3576 * Add top level menus to frame
3578 alignFrameMenuBar.add(fileMenu);
3579 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3580 alignFrameMenuBar.add(editMenu);
3581 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3582 alignFrameMenuBar.add(selectMenu);
3583 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3584 alignFrameMenuBar.add(viewMenu);
3585 Menu annotationsMenu = new Menu(
3586 MessageManager.getString("action.annotations"));
3587 alignFrameMenuBar.add(annotationsMenu);
3588 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3589 alignFrameMenuBar.add(formatMenu);
3590 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3591 alignFrameMenuBar.add(colourMenu);
3592 Menu calculateMenu = new Menu(
3593 MessageManager.getString("action.calculate"));
3594 alignFrameMenuBar.add(calculateMenu);
3595 alignFrameMenuBar.add(helpMenu);
3600 fileMenu.add(inputText);
3601 fileMenu.add(loadTree);
3602 fileMenu.add(loadAnnotations);
3603 fileMenu.addSeparator();
3604 fileMenu.add(outputTextboxMenu);
3605 fileMenu.add(outputFeatures);
3606 fileMenu.add(outputAnnotations);
3607 if (jalviewServletURL != null)
3609 fileMenu.add(loadApplication);
3611 fileMenu.addSeparator();
3612 fileMenu.add(closeMenuItem);
3617 editMenu.add(undoMenuItem);
3618 editMenu.add(redoMenuItem);
3621 pasteMenu.add(pasteNew);
3622 pasteMenu.add(pasteThis);
3623 editMenu.add(pasteMenu);
3624 editMenu.add(delete);
3625 editMenu.addSeparator();
3626 editMenu.add(remove2LeftMenuItem);
3627 editMenu.add(remove2RightMenuItem);
3628 editMenu.add(removeGappedColumnMenuItem);
3629 editMenu.add(removeAllGapsMenuItem);
3630 editMenu.add(removeRedundancyMenuItem);
3635 selectMenu.add(findMenuItem);
3636 selectMenu.addSeparator();
3637 selectMenu.add(selectAllSequenceMenuItem);
3638 selectMenu.add(deselectAllSequenceMenuItem);
3639 selectMenu.add(invertSequenceMenuItem);
3640 selectMenu.add(invertColSel);
3641 selectMenu.add(createGroup);
3642 selectMenu.add(unGroup);
3643 selectMenu.add(grpsFromSelection);
3644 selectMenu.add(deleteGroups);
3645 selectMenu.add(annotationColumnSelection);
3650 viewMenu.add(newView);
3651 viewMenu.addSeparator();
3652 showMenu.add(showColumns);
3653 showMenu.add(showSeqs);
3654 showMenu.add(showAllHidden);
3655 viewMenu.add(showMenu);
3656 hideMenu.add(hideColumns);
3657 hideMenu.add(hideSequences);
3658 hideMenu.add(hideAllSelection);
3659 hideMenu.add(hideAllButSelection);
3660 viewMenu.add(hideMenu);
3661 viewMenu.addSeparator();
3662 viewMenu.add(followMouseOverFlag);
3663 viewMenu.addSeparator();
3664 viewMenu.add(sequenceFeatures);
3665 viewMenu.add(featureSettings);
3666 viewMenu.addSeparator();
3667 viewMenu.add(alProperties);
3668 viewMenu.addSeparator();
3669 viewMenu.add(overviewMenuItem);
3674 annotationsMenu.add(annotationPanelMenuItem);
3675 annotationsMenu.addSeparator();
3676 annotationsMenu.add(showAlignmentAnnotations);
3677 annotationsMenu.add(showSequenceAnnotations);
3678 annotationsMenu.add(sortAnnBySequence);
3679 annotationsMenu.add(sortAnnByLabel);
3680 annotationsMenu.addSeparator();
3681 autoAnnMenu.add(showAutoFirst);
3682 autoAnnMenu.add(showAutoLast);
3683 autoAnnMenu.addSeparator();
3684 autoAnnMenu.add(applyAutoAnnotationSettings);
3685 autoAnnMenu.add(showConsensusHistogram);
3686 autoAnnMenu.add(showSequenceLogo);
3687 autoAnnMenu.add(normSequenceLogo);
3688 autoAnnMenu.addSeparator();
3689 autoAnnMenu.add(showGroupConservation);
3690 autoAnnMenu.add(showGroupConsensus);
3691 annotationsMenu.add(autoAnnMenu);
3696 formatMenu.add(font);
3697 formatMenu.add(seqLimits);
3698 formatMenu.add(wrapMenuItem);
3699 formatMenu.add(scaleAbove);
3700 formatMenu.add(scaleLeft);
3701 formatMenu.add(scaleRight);
3702 formatMenu.add(viewBoxesMenuItem);
3703 formatMenu.add(viewTextMenuItem);
3704 formatMenu.add(colourTextMenuItem);
3705 formatMenu.add(displayNonconservedMenuItem);
3706 formatMenu.add(renderGapsMenuItem);
3707 formatMenu.add(centreColumnLabelFlag);
3712 colourMenu.add(applyToAllGroups);
3713 colourMenu.addSeparator();
3714 colourMenu.add(noColourmenuItem);
3715 colourMenu.add(clustalColour);
3716 colourMenu.add(BLOSUM62Colour);
3717 colourMenu.add(PIDColour);
3718 colourMenu.add(zappoColour);
3719 colourMenu.add(taylorColour);
3720 colourMenu.add(hydrophobicityColour);
3721 colourMenu.add(helixColour);
3722 colourMenu.add(strandColour);
3723 colourMenu.add(turnColour);
3724 colourMenu.add(buriedColour);
3725 colourMenu.add(nucleotideColour);
3726 colourMenu.add(purinePyrimidineColour);
3727 // colourMenu.add(RNAInteractionColour);
3728 colourMenu.add(tcoffeeColour);
3729 colourMenu.add(userDefinedColour);
3730 colourMenu.addSeparator();
3731 colourMenu.add(conservationMenuItem);
3732 colourMenu.add(modifyConservation);
3733 colourMenu.add(abovePIDThreshold);
3734 colourMenu.add(modifyPID);
3735 colourMenu.add(annotationColour);
3736 colourMenu.add(RNAHelixColour);
3741 sortMenu.add(sortIDMenuItem);
3742 sortMenu.add(sortLengthMenuItem);
3743 sortMenu.add(sortByTreeMenu);
3744 sortMenu.add(sortGroupMenuItem);
3745 sortMenu.add(sortPairwiseMenuItem);
3746 calculateMenu.add(sortMenu);
3747 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3748 calculateTreeMenu.add(neighbourTreeMenuItem);
3749 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3750 calculateTreeMenu.add(njTreeBlosumMenuItem);
3751 calculateMenu.add(calculateTreeMenu);
3752 calculateMenu.addSeparator();
3753 calculateMenu.add(pairwiseAlignmentMenuItem);
3754 calculateMenu.add(PCAMenuItem);
3755 calculateMenu.add(autoCalculate);
3756 calculateMenu.add(sortByTree);
3761 helpMenu.add(documentation);
3762 helpMenu.add(about);
3767 statusBar.setBackground(Color.white);
3768 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3769 statusBar.setText(MessageManager.getString("label.status_bar"));
3770 this.add(statusBar, BorderLayout.SOUTH);
3774 public void setStatus(String string)
3776 statusBar.setText(string);
3779 MenuItem featureSettings = new MenuItem();
3781 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3783 MenuItem annotationColour = new MenuItem();
3785 MenuItem annotationColumnSelection = new MenuItem();
3787 MenuItem invertColSel = new MenuItem();
3789 MenuItem showColumns = new MenuItem();
3791 MenuItem showSeqs = new MenuItem();
3793 MenuItem hideColumns = new MenuItem();
3795 MenuItem hideSequences = new MenuItem();
3797 MenuItem hideAllButSelection = new MenuItem();
3799 MenuItem hideAllSelection = new MenuItem();
3801 MenuItem showAllHidden = new MenuItem();
3803 MenuItem newView = new MenuItem();
3805 private CheckboxMenuItem showAlignmentAnnotations;
3807 private CheckboxMenuItem showSequenceAnnotations;
3809 private CheckboxMenuItem sortAnnBySequence;
3811 private CheckboxMenuItem sortAnnByLabel;
3813 private CheckboxMenuItem showAutoFirst;
3815 private CheckboxMenuItem showAutoLast;
3817 private SplitFrame splitFrame;
3820 * Attach the alignFrame panels after embedding menus, if necessary. This used
3821 * to be called setEmbedded, but is now creates the dropdown menus in a
3822 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3824 * @param reallyEmbedded
3825 * true to attach the view to the applet area on the page rather than
3828 public void createAlignFrameWindow(boolean reallyEmbedded)
3832 embedAlignFrameInApplet(viewport.applet);
3837 // test and embed menu bar if necessary.
3839 if (embedMenuIfNeeded(alignPanel))
3842 * adjust for status bar height too. ? pointless as overridden by layout
3845 alignPanel.setSize(getSize().width,
3846 getSize().height - statusBar.getHeight());
3848 add(statusBar, BorderLayout.SOUTH);
3849 add(alignPanel, BorderLayout.CENTER);
3850 // and register with the applet so it can pass external API calls to us
3851 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3857 * Add the components of this AlignFrame to the applet container.
3861 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3864 // Explicitly build the embedded menu panel for the on-page applet
3866 // view cannot be closed if its actually on the page
3867 fileMenu.remove(closeMenuItem);
3868 fileMenu.remove(3); // Remove Separator
3869 // construct embedded menu, using default font
3870 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3871 // and actually add the components to the applet area
3872 theApplet.setLayout(new BorderLayout());
3873 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3874 theApplet.add(statusBar, BorderLayout.SOUTH);
3875 // TODO should size be left to the layout manager?
3876 alignPanel.setSize(theApplet.getSize().width,
3877 theApplet.getSize().height - embeddedMenu.getHeight()
3878 - statusBar.getHeight());
3879 theApplet.add(alignPanel, BorderLayout.CENTER);
3880 final AlignFrame me = this;
3881 theApplet.addFocusListener(new FocusListener()
3885 public void focusLost(FocusEvent e)
3887 if (theApplet.currentAlignFrame == me)
3889 theApplet.currentAlignFrame = null;
3894 public void focusGained(FocusEvent e)
3896 theApplet.currentAlignFrame = me;
3899 theApplet.validate();
3903 * create a new binding between structures in an existing jmol viewer instance
3904 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3905 * this does not open a new Jmol window, or modify the display of the
3906 * structures in the original jmol window. Note This method doesn't work
3907 * without an additional javascript library to exchange messages between the
3908 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3911 * JmolViewer instance
3912 * @param sequenceIds
3913 * - sequence Ids to search for associations
3915 public SequenceStructureBinding addStructureViewInstance(
3916 Object jmolviewer, String[] sequenceIds)
3918 Viewer viewer = null;
3921 viewer = (Viewer) jmolviewer;
3922 } catch (ClassCastException ex)
3924 System.err.println("Unsupported viewer object :"
3925 + jmolviewer.getClass());
3929 System.err.println("Can't use this object as a structure viewer:"
3930 + jmolviewer.getClass());
3933 SequenceI[] seqs = null;
3934 if (sequenceIds == null || sequenceIds.length == 0)
3936 seqs = viewport.getAlignment().getSequencesArray();
3940 Vector sqi = new Vector();
3941 AlignmentI al = viewport.getAlignment();
3942 for (int sid = 0; sid < sequenceIds.length; sid++)
3944 SequenceI sq = al.findName(sequenceIds[sid]);
3952 seqs = new SequenceI[sqi.size()];
3953 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3955 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3963 AAStructureBindingModel jmv = null;
3964 // TODO: search for a jmv that involves viewer
3966 { // create a new viewer/jalview binding.
3967 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3974 * bind a pdb file to a sequence in the current view
3977 * - sequenceId within the dataset.
3978 * @param pdbEntryString
3979 * - the short name for the PDB file
3981 * - pdb file - either a URL or a valid PDB file.
3982 * @return true if binding was as success TODO: consider making an exception
3983 * structure for indicating when PDB parsing or sequenceId location
3986 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3989 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3990 boolean needtoadd = false;
3991 if (toaddpdb != null)
3993 Vector pdbe = toaddpdb.getAllPDBEntries();
3994 PDBEntry pdbentry = null;
3995 if (pdbe != null && pdbe.size() > 0)
3997 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3999 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4000 if (!pdbentry.getId().equals(pdbEntryString)
4001 && !pdbentry.getFile().equals(pdbFile))
4011 if (pdbentry == null)
4013 pdbentry = new PDBEntry();
4014 pdbentry.setId(pdbEntryString);
4015 pdbentry.setFile(pdbFile);
4016 needtoadd = true; // add this new entry to sequence.
4018 // resolve data source
4019 // TODO: this code should be a refactored to an io package
4020 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4021 if (protocol == null)
4027 // make a note of the access mode and add
4028 if (pdbentry.getProperty() == null)
4030 pdbentry.setProperty(new Hashtable());
4032 pdbentry.getProperty().put("protocol", protocol);
4033 toaddpdb.addPDBId(pdbentry);
4034 alignPanel.getStructureSelectionManager()
4035 .registerPDBEntry(pdbentry);
4041 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4045 Vector sequences = new Vector();
4046 for (int i = 0; i < seqs.length; i++)
4048 if (seqs[i] != null)
4050 sequences.addElement(new Object[] { seqs[i],
4051 (chains != null) ? chains[i] : null });
4054 seqs = new SequenceI[sequences.size()];
4055 chains = new String[sequences.size()];
4056 for (int i = 0, isize = sequences.size(); i < isize; i++)
4058 Object[] oj = (Object[]) sequences.elementAt(i);
4060 seqs[i] = (SequenceI) oj[0];
4061 chains[i] = (String) oj[1];
4064 return new Object[] { seqs, chains };
4068 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4069 SequenceI[] seqs, String[] chains, String protocol)
4071 // Scrub any null sequences from the array
4072 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4073 seqs = (SequenceI[]) sqch[0];
4074 chains = (String[]) sqch[1];
4075 if (seqs == null || seqs.length == 0)
4078 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4080 if (protocol == null || protocol.trim().length() == 0
4081 || protocol.equals("null"))
4083 protocol = (String) pdb.getProperty().get("protocol");
4084 if (protocol == null)
4086 System.err.println("Couldn't work out protocol to open structure: "
4091 if (applet.useXtrnalSviewer)
4093 // register the association(s) and quit, don't create any windows.
4094 if (StructureSelectionManager.getStructureSelectionManager(applet)
4095 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4097 System.err.println("Failed to map " + pdb.getFile() + " ("
4098 + protocol + ") to any sequences");
4102 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4104 // can only do alignments with Jmol
4105 // find the last jmol window assigned to this alignment
4106 jalview.appletgui.AppletJmol ajm = null, tajm;
4107 Vector jmols = applet
4108 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4109 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4111 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4112 if (tajm.ap.alignFrame == this)
4121 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4122 // try and add the pdb structure
4127 // otherwise, create a new window
4128 if (applet.jmolAvailable)
4130 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4132 applet.lastFrameX += 40;
4133 applet.lastFrameY += 40;
4137 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4142 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4143 SequenceI[][] seqs, String[][] chains, String[] protocols)
4145 // TODO Auto-generated method stub
4146 System.err.println("Aligned Structure View: Not yet implemented.");
4150 * modify the current selection, providing the user has not made a selection
4154 * - sequences from this alignment
4156 * - columns to be selected on the alignment
4158 public void select(SequenceGroup sel, ColumnSelection csel)
4160 alignPanel.seqPanel.selection(sel, csel, null);
4163 public void scrollTo(int row, int column)
4165 alignPanel.seqPanel.scrollTo(row, column);
4168 public void scrollToRow(int row)
4170 alignPanel.seqPanel.scrollToRow(row);
4173 public void scrollToColumn(int column)
4175 alignPanel.seqPanel.scrollToColumn(column);
4179 * @return the alignments unique ID.
4181 public String getSequenceSetId()
4183 return viewport.getSequenceSetId();
4187 * Load the (T-Coffee) score file from the specified url
4190 * File/URL/T-COFFEE score file contents
4191 * @throws IOException
4192 * @return true if alignment was annotated with data from source
4194 public boolean loadScoreFile(String source) throws IOException
4197 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4198 AppletFormatAdapter.checkProtocol(source));
4199 if (!file.isValid())
4201 // TODO: raise dialog for gui
4202 System.err.println("Problems parsing T-Coffee scores: "
4203 + file.getWarningMessage());
4204 System.err.println("Origin was:\n" + source);
4209 * check that the score matrix matches the alignment dimensions
4212 if ((aln = viewport.getAlignment()) != null
4213 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4216 // TODO: raise a dialog box here rather than bomb out.
4218 .println("The scores matrix does not match the alignment dimensions");
4222 // TODO add parameter to indicate if matching should be done
4223 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4225 alignPanel.fontChanged();
4226 tcoffeeColour.setEnabled(true);
4227 // switch to this color
4228 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4233 System.err.println("Problems resolving T-Coffee scores:");
4234 if (file.getWarningMessage() != null)
4236 System.err.println(file.getWarningMessage());
4242 public SplitFrame getSplitFrame()
4244 return this.splitFrame;
4247 public void setSplitFrame(SplitFrame sf)
4249 this.splitFrame = sf;
4252 // may not need this
4254 public void setShowSeqFeatures(boolean b)
4256 // showSeqFeatures.setSelected(b);
4257 viewport.setShowSequenceFeatures(b);
4262 public void setMenusForViewport()
4264 // setMenusFromViewport(viewport);
4269 public void refreshFeatureUI(boolean enableIfNecessary)
4271 if (enableIfNecessary)
4273 sequenceFeatures.setState(true);
4274 alignPanel.av.setShowSequenceFeatures(true);
4279 public FeatureSettingsControllerI getFeatureSettingsUI()
4281 return alignPanel.av.featureSettings;