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.FeatureRenderer;
29 import jalview.api.FeatureSettingsControllerI;
30 import jalview.api.SequenceStructureBinding;
31 import jalview.bin.JalviewLite;
32 import jalview.commands.CommandI;
33 import jalview.commands.EditCommand;
34 import jalview.commands.EditCommand.Action;
35 import jalview.commands.OrderCommand;
36 import jalview.commands.RemoveGapColCommand;
37 import jalview.commands.RemoveGapsCommand;
38 import jalview.commands.SlideSequencesCommand;
39 import jalview.commands.TrimRegionCommand;
40 import jalview.datamodel.Alignment;
41 import jalview.datamodel.AlignmentAnnotation;
42 import jalview.datamodel.AlignmentI;
43 import jalview.datamodel.AlignmentOrder;
44 import jalview.datamodel.ColumnSelection;
45 import jalview.datamodel.PDBEntry;
46 import jalview.datamodel.Sequence;
47 import jalview.datamodel.SequenceGroup;
48 import jalview.datamodel.SequenceI;
49 import jalview.io.AnnotationFile;
50 import jalview.io.AppletFormatAdapter;
51 import jalview.io.FeaturesFile;
52 import jalview.io.TCoffeeScoreFile;
53 import jalview.schemes.Blosum62ColourScheme;
54 import jalview.schemes.BuriedColourScheme;
55 import jalview.schemes.ClustalxColourScheme;
56 import jalview.schemes.ColourSchemeI;
57 import jalview.schemes.HelixColourScheme;
58 import jalview.schemes.HydrophobicColourScheme;
59 import jalview.schemes.NucleotideColourScheme;
60 import jalview.schemes.PIDColourScheme;
61 import jalview.schemes.PurinePyrimidineColourScheme;
62 import jalview.schemes.RNAHelicesColourChooser;
63 import jalview.schemes.StrandColourScheme;
64 import jalview.schemes.TCoffeeColourScheme;
65 import jalview.schemes.TaylorColourScheme;
66 import jalview.schemes.TurnColourScheme;
67 import jalview.schemes.ZappoColourScheme;
68 import jalview.structure.StructureSelectionManager;
69 import jalview.structures.models.AAStructureBindingModel;
70 import jalview.util.MappingUtils;
71 import jalview.util.MessageManager;
72 import jalview.viewmodel.AlignmentViewport;
74 import java.awt.BorderLayout;
75 import java.awt.Canvas;
76 import java.awt.CheckboxMenuItem;
77 import java.awt.Color;
78 import java.awt.FlowLayout;
80 import java.awt.FontMetrics;
81 import java.awt.Frame;
82 import java.awt.Graphics;
83 import java.awt.Label;
85 import java.awt.MenuBar;
86 import java.awt.MenuItem;
87 import java.awt.Panel;
88 import java.awt.event.ActionEvent;
89 import java.awt.event.ActionListener;
90 import java.awt.event.FocusEvent;
91 import java.awt.event.FocusListener;
92 import java.awt.event.ItemEvent;
93 import java.awt.event.ItemListener;
94 import java.awt.event.KeyEvent;
95 import java.awt.event.KeyListener;
96 import java.awt.event.WindowAdapter;
97 import java.awt.event.WindowEvent;
98 import java.io.IOException;
100 import java.net.URLEncoder;
101 import java.util.Arrays;
102 import java.util.Deque;
103 import java.util.HashMap;
104 import java.util.Hashtable;
105 import java.util.List;
106 import java.util.Map;
107 import java.util.StringTokenizer;
108 import java.util.Vector;
110 import org.jmol.viewer.Viewer;
112 public class AlignFrame extends EmbmenuFrame implements ActionListener,
113 ItemListener, KeyListener, AlignViewControllerGuiI
115 public AlignViewControllerI avc;
117 public AlignmentPanel alignPanel;
119 public AlignViewport viewport;
121 // width and height may be overridden by applet parameters
122 int frameWidth = 700;
124 int frameHeight = 500;
126 String jalviewServletURL;
129 * Flag for showing autocalculated consensus above or below other consensus
132 private boolean showAutoCalculatedAbove;
134 private SequenceAnnotationOrder annotationSortOrder;
137 * Constructor that creates the frame and adds it to the display.
144 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
147 this(al, applet, title, embedded, true);
151 * Constructor that optionally allows the frame to be displayed or only
158 * @param addToDisplay
160 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
161 boolean embedded, boolean addToDisplay)
163 this(al, null, null, applet, title, embedded, addToDisplay);
166 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
167 ColumnSelection columnSelection, JalviewLite applet,
168 String title, boolean embedded)
170 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
173 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
174 ColumnSelection columnSelection, JalviewLite applet,
175 String title, boolean embedded, boolean addToDisplay)
179 jalviewServletURL = applet.getParameter("APPLICATION_URL");
185 } catch (Exception ex)
187 ex.printStackTrace();
189 // need to get window geometry before we calculate alignment layout
195 param = applet.getParameter("windowWidth");
198 int width = Integer.parseInt(param);
201 param = applet.getParameter("windowHeight");
204 int height = Integer.parseInt(param);
205 frameHeight = height;
207 } catch (Exception ex)
211 viewport = new AlignViewport(al, applet);
213 if (hiddenSeqs != null && hiddenSeqs.length > 0)
215 viewport.hideSequence(hiddenSeqs);
217 if (columnSelection != null)
219 viewport.setColumnSelection(columnSelection);
222 alignPanel = new AlignmentPanel(this, viewport);
223 avc = new jalview.controller.AlignViewController(this, viewport,
225 viewport.updateConservation(alignPanel);
226 viewport.updateConsensus(alignPanel);
228 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
229 followMouseOverFlag.setState(viewport.isFollowHighlight());
230 showGroupConsensus.setState(viewport.isShowGroupConsensus());
231 showGroupConservation.setState(viewport.isShowGroupConservation());
232 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
233 showSequenceLogo.setState(viewport.isShowSequenceLogo());
234 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
235 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
236 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
237 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
238 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
239 showAlignmentAnnotations.setState(true);
240 showSequenceAnnotations.setState(false);
242 seqLimits.setState(viewport.getShowJVSuffix());
246 String param = applet.getParameter("sortBy");
249 if (param.equalsIgnoreCase("Id"))
251 sortIDMenuItem_actionPerformed();
253 else if (param.equalsIgnoreCase("Pairwise Identity"))
255 sortPairwiseMenuItem_actionPerformed();
257 else if (param.equalsIgnoreCase("Length"))
259 sortLengthMenuItem_actionPerformed();
263 param = applet.getParameter("wrap");
266 if (param.equalsIgnoreCase("true"))
268 wrapMenuItem.setState(true);
269 wrapMenuItem_actionPerformed();
272 param = applet.getParameter("centrecolumnlabels");
275 centreColumnLabelFlag.setState(true);
276 centreColumnLabelFlag_stateChanged();
280 if (viewport.getAlignment().isNucleotide())
282 viewport.updateStrucConsensus(alignPanel);
283 if (viewport.getAlignment().hasRNAStructure())
285 RNAHelixColour.setEnabled(true);
289 RNAHelixColour.setEnabled(false);
294 RNAHelixColour.setEnabled(false);
295 purinePyrimidineColour.setEnabled(false);
297 // Some JVMS send keyevents to Top frame or lowest panel,
298 // Havent worked out why yet. So add to both this frame and seqCanvas for
300 this.addKeyListener(this);
301 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
302 alignPanel.idPanel.idCanvas.addKeyListener(this);
303 alignPanel.scalePanel.addKeyListener(this);
304 alignPanel.annotationPanel.addKeyListener(this);
305 alignPanel.annotationPanelHolder.addKeyListener(this);
306 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
307 alignPanel.alabels.addKeyListener(this);
309 setAnnotationsVisibility();
313 addToDisplay(embedded);
320 public void addToDisplay(boolean embedded)
322 createAlignFrameWindow(embedded);
324 alignPanel.adjustAnnotationHeight();
325 alignPanel.paintAlignment(true);
328 public AlignViewport getAlignViewport()
333 public SeqCanvas getSeqcanvas()
335 return alignPanel.seqPanel.seqCanvas;
339 * Load a features file onto the alignment
342 * file URL, content, or other resolvable path
344 * is protocol for accessing data referred to by file
347 public boolean parseFeaturesFile(String file, String type)
349 return parseFeaturesFile(file, type, true);
353 * Load a features file onto the alignment
356 * file URL, content, or other resolvable path
358 * is protocol for accessing data referred to by file
359 * @param autoenabledisplay
360 * when true, display features flag will be automatically enabled if
361 * features are loaded
362 * @return true if data parsed as a features file
364 public boolean parseFeaturesFile(String file, String type,
365 boolean autoenabledisplay)
367 boolean featuresFile = false;
370 Map<String, Object> colours = alignPanel.seqPanel.seqCanvas
371 .getFeatureRenderer().getFeatureColours();
372 boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
373 "relaxedidmatch", false);
374 featuresFile = new FeaturesFile(file, type).parse(
375 viewport.getAlignment(), colours, true, relaxedIdMatching);
376 } catch (Exception ex)
378 ex.printStackTrace();
383 if (autoenabledisplay)
385 viewport.setShowSequenceFeatures(true);
386 sequenceFeatures.setState(true);
388 if (alignPanel.seqPanel.seqCanvas.fr != null)
390 // update the min/max ranges where necessary
391 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
393 if (viewport.featureSettings != null)
395 viewport.featureSettings.refreshTable();
397 alignPanel.paintAlignment(true);
398 statusBar.setText(MessageManager
399 .getString("label.successfully_added_features_alignment"));
405 public void keyPressed(KeyEvent evt)
407 if (viewport.cursorMode
408 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
409 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
410 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
411 && Character.isDigit(evt.getKeyChar()))
413 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
416 switch (evt.getKeyCode())
418 case 27: // escape key
419 deselectAllSequenceMenuItem_actionPerformed();
421 alignPanel.alabels.cancelDrag();
424 if (evt.isControlDown() || evt.isMetaDown())
426 cut_actionPerformed();
430 if (viewport.cursorMode && !evt.isControlDown())
432 alignPanel.seqPanel.setCursorColumn();
434 if (evt.isControlDown() || evt.isMetaDown())
436 copy_actionPerformed();
440 if (evt.isControlDown())
442 paste(evt.isShiftDown());
446 if (evt.isControlDown() || evt.isMetaDown())
448 selectAllSequenceMenuItem_actionPerformed();
451 case KeyEvent.VK_DOWN:
452 if (viewport.cursorMode)
454 alignPanel.seqPanel.moveCursor(0, 1);
458 moveSelectedSequences(false);
463 if (viewport.cursorMode)
465 alignPanel.seqPanel.moveCursor(0, -1);
469 moveSelectedSequences(true);
473 case KeyEvent.VK_LEFT:
474 if (evt.isAltDown() || !viewport.cursorMode)
476 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
480 alignPanel.seqPanel.moveCursor(-1, 0);
484 case KeyEvent.VK_RIGHT:
485 if (evt.isAltDown() || !viewport.cursorMode)
487 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
491 alignPanel.seqPanel.moveCursor(1, 0);
495 case KeyEvent.VK_SPACE:
496 if (viewport.cursorMode)
498 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
499 || evt.isShiftDown() || evt.isAltDown());
503 case KeyEvent.VK_DELETE:
504 case KeyEvent.VK_BACK_SPACE:
505 if (viewport.cursorMode)
507 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
508 || evt.isShiftDown() || evt.isAltDown());
512 cut_actionPerformed();
513 alignPanel.seqPanel.seqCanvas.repaint();
518 if (viewport.cursorMode)
520 alignPanel.seqPanel.setCursorRow();
524 if (viewport.cursorMode)
526 alignPanel.seqPanel.setCursorPosition();
530 case KeyEvent.VK_ENTER:
531 case KeyEvent.VK_COMMA:
532 if (viewport.cursorMode)
534 alignPanel.seqPanel.setCursorRowAndColumn();
539 if (viewport.cursorMode)
541 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
545 if (viewport.cursorMode)
547 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
552 viewport.cursorMode = !viewport.cursorMode;
553 statusBar.setText(MessageManager.formatMessage(
554 "label.keyboard_editing_mode",
555 new String[] { (viewport.cursorMode ? "on" : "off") }));
556 if (viewport.cursorMode)
558 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
559 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
564 if (evt.isControlDown())
566 findMenuItem_actionPerformed();
572 boolean toggleSeqs = !evt.isControlDown();
573 boolean toggleCols = !evt.isShiftDown();
574 toggleHiddenRegions(toggleSeqs, toggleCols);
578 case KeyEvent.VK_PAGE_UP:
579 if (viewport.getWrapAlignment())
581 alignPanel.scrollUp(true);
585 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
586 - viewport.endSeq + viewport.startSeq);
590 case KeyEvent.VK_PAGE_DOWN:
591 if (viewport.getWrapAlignment())
593 alignPanel.scrollUp(false);
597 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
598 + viewport.endSeq - viewport.startSeq);
603 if (evt.isControlDown())
605 undoMenuItem_actionPerformed();
610 if (evt.isControlDown())
612 redoMenuItem_actionPerformed();
617 if (evt.isControlDown())
624 if (evt.isControlDown())
626 trimAlignment(false);
631 if (evt.isControlDown())
633 if (evt.isShiftDown())
635 this.removeAllGapsMenuItem_actionPerformed();
639 removeGappedColumnMenuItem_actionPerformed();
644 if (evt.isControlDown())
648 invertColSel_actionPerformed();
652 invertSequenceMenuItem_actionPerformed();
658 if (evt.isControlDown())
660 if (evt.isShiftDown())
662 this.unGroup_actionPerformed();
666 this.createGroup_actionPerformed();
672 if (evt.isControlDown())
674 this.deleteGroups_actionPerformed();
679 if (evt.isControlDown())
686 alignPanel.paintAlignment(true);
690 * called by key handler and the hide all/show all menu items
695 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
697 boolean hide = false;
698 SequenceGroup sg = viewport.getSelectionGroup();
699 if (!toggleSeqs && !toggleCols)
701 // Hide everything by the current selection - this is a hack - we do the
702 // invert and then hide
703 // first check that there will be visible columns after the invert.
704 if ((viewport.getColumnSelection() != null
705 && viewport.getColumnSelection().getSelected() != null && viewport
706 .getColumnSelection().getSelected().size() > 0)
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.getColumnSelection().getSelected()
737 viewport.showAllHiddenSeqs();
743 if (viewport.getColumnSelection().getSelected().size() > 0)
745 viewport.hideSelectedColumns();
748 viewport.setSelectionGroup(sg);
753 viewport.showAllHiddenColumns();
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 for (AlignmentAnnotation aa : alignPanel.getAlignment()
927 .getAlignmentAnnotation())
929 boolean visible = (aa.sequenceRef == null ? showForAlignment
931 aa.visible = visible;
933 alignPanel.validateAnnotationDimensions(true);
938 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
940 this.annotationSortOrder = order;
944 * Set flags on the viewport that control annotation ordering
946 private void setViewportAnnotationOrder()
948 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
950 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
953 private void setShowAutoCalculatedAbove(boolean showAbove)
955 this.showAutoCalculatedAbove = showAbove;
958 private void mouseOverFlag_stateChanged()
960 viewport.setFollowHighlight(followMouseOverFlag.getState());
961 // TODO: could kick the scrollTo mechanism to reset view for current
965 private void centreColumnLabelFlag_stateChanged()
967 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
968 this.alignPanel.annotationPanel.repaint();
972 public void actionPerformed(ActionEvent evt)
974 viewport.applet.currentAlignFrame = this;
976 Object source = evt.getSource();
978 if (source == inputText)
980 inputText_actionPerformed();
982 else if (source == loadTree)
984 loadTree_actionPerformed();
986 else if (source == loadApplication)
988 launchFullApplication();
990 else if (source == loadAnnotations)
994 else if (source == outputAnnotations)
996 outputAnnotations(true);
998 else if (source == outputFeatures)
1000 outputFeatures(true, "Jalview");
1002 else if (source == closeMenuItem)
1004 closeMenuItem_actionPerformed();
1006 else if (source == copy)
1008 copy_actionPerformed();
1010 else if (source == undoMenuItem)
1012 undoMenuItem_actionPerformed();
1014 else if (source == redoMenuItem)
1016 redoMenuItem_actionPerformed();
1018 else if (source == inputText)
1020 inputText_actionPerformed();
1022 else if (source == closeMenuItem)
1024 closeMenuItem_actionPerformed();
1026 else if (source == undoMenuItem)
1028 undoMenuItem_actionPerformed();
1030 else if (source == redoMenuItem)
1032 redoMenuItem_actionPerformed();
1034 else if (source == copy)
1036 copy_actionPerformed();
1038 else if (source == pasteNew)
1040 pasteNew_actionPerformed();
1042 else if (source == pasteThis)
1044 pasteThis_actionPerformed();
1046 else if (source == cut)
1048 cut_actionPerformed();
1050 else if (source == delete)
1052 delete_actionPerformed();
1054 else if (source == grpsFromSelection)
1056 makeGrpsFromSelection_actionPerformed();
1058 else if (source == deleteGroups)
1060 deleteGroups_actionPerformed();
1062 else if (source == selectAllSequenceMenuItem)
1064 selectAllSequenceMenuItem_actionPerformed();
1066 else if (source == deselectAllSequenceMenuItem)
1068 deselectAllSequenceMenuItem_actionPerformed();
1070 else if (source == invertSequenceMenuItem)
1072 invertSequenceMenuItem_actionPerformed();
1074 else if (source == invertColSel)
1076 viewport.invertColumnSelection();
1077 alignPanel.paintAlignment(true);
1079 else if (source == remove2LeftMenuItem)
1081 trimAlignment(true);
1083 else if (source == remove2RightMenuItem)
1085 trimAlignment(false);
1087 else if (source == removeGappedColumnMenuItem)
1089 removeGappedColumnMenuItem_actionPerformed();
1091 else if (source == removeAllGapsMenuItem)
1093 removeAllGapsMenuItem_actionPerformed();
1095 else if (source == findMenuItem)
1097 findMenuItem_actionPerformed();
1099 else if (source == font)
1101 new FontChooser(alignPanel);
1103 else if (source == newView)
1107 else if (source == showColumns)
1109 viewport.showAllHiddenColumns();
1110 alignPanel.paintAlignment(true);
1112 else if (source == showSeqs)
1114 viewport.showAllHiddenSeqs();
1115 alignPanel.paintAlignment(true);
1117 else if (source == hideColumns)
1119 viewport.hideSelectedColumns();
1120 alignPanel.paintAlignment(true);
1122 else if (source == hideSequences
1123 && viewport.getSelectionGroup() != null)
1125 viewport.hideAllSelectedSeqs();
1126 alignPanel.paintAlignment(true);
1128 else if (source == hideAllButSelection)
1130 toggleHiddenRegions(false, false);
1131 alignPanel.paintAlignment(true);
1133 else if (source == hideAllSelection)
1135 SequenceGroup sg = viewport.getSelectionGroup();
1136 viewport.expandColSelection(sg, false);
1137 viewport.hideAllSelectedSeqs();
1138 viewport.hideSelectedColumns();
1139 alignPanel.paintAlignment(true);
1141 else if (source == showAllHidden)
1143 viewport.showAllHiddenColumns();
1144 viewport.showAllHiddenSeqs();
1145 alignPanel.paintAlignment(true);
1147 else if (source == showGroupConsensus)
1149 showGroupConsensus_actionPerformed();
1151 else if (source == showGroupConservation)
1153 showGroupConservation_actionPerformed();
1155 else if (source == showSequenceLogo)
1157 showSequenceLogo_actionPerformed();
1159 else if (source == normSequenceLogo)
1161 normSequenceLogo_actionPerformed();
1163 else if (source == showConsensusHistogram)
1165 showConsensusHistogram_actionPerformed();
1167 else if (source == applyAutoAnnotationSettings)
1169 applyAutoAnnotationSettings_actionPerformed();
1171 else if (source == featureSettings)
1173 new FeatureSettings(alignPanel);
1175 else if (source == alProperties)
1177 StringBuffer contents = new jalview.io.AlignmentProperties(
1178 viewport.getAlignment()).formatAsString();
1179 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1180 cap.setText(contents.toString());
1181 Frame frame = new Frame();
1183 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1184 "label.alignment_properties", new String[] { getTitle() }),
1187 else if (source == overviewMenuItem)
1189 overviewMenuItem_actionPerformed();
1191 else if (source == noColourmenuItem)
1195 else if (source == clustalColour)
1197 abovePIDThreshold.setState(false);
1198 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1200 else if (source == zappoColour)
1202 changeColour(new ZappoColourScheme());
1204 else if (source == taylorColour)
1206 changeColour(new TaylorColourScheme());
1208 else if (source == hydrophobicityColour)
1210 changeColour(new HydrophobicColourScheme());
1212 else if (source == helixColour)
1214 changeColour(new HelixColourScheme());
1216 else if (source == strandColour)
1218 changeColour(new StrandColourScheme());
1220 else if (source == turnColour)
1222 changeColour(new TurnColourScheme());
1224 else if (source == buriedColour)
1226 changeColour(new BuriedColourScheme());
1228 else if (source == nucleotideColour)
1230 changeColour(new NucleotideColourScheme());
1232 else if (source == purinePyrimidineColour)
1234 changeColour(new PurinePyrimidineColourScheme());
1236 // else if (source == RNAInteractionColour)
1238 // changeColour(new RNAInteractionColourScheme());
1240 else if (source == RNAHelixColour)
1242 new RNAHelicesColourChooser(viewport, alignPanel);
1244 else if (source == modifyPID)
1246 modifyPID_actionPerformed();
1248 else if (source == modifyConservation)
1250 modifyConservation_actionPerformed();
1252 else if (source == userDefinedColour)
1254 new UserDefinedColours(alignPanel, null);
1256 else if (source == PIDColour)
1258 changeColour(new PIDColourScheme());
1260 else if (source == BLOSUM62Colour)
1262 changeColour(new Blosum62ColourScheme());
1264 else if (source == tcoffeeColour)
1266 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1268 else if (source == annotationColour)
1270 new AnnotationColourChooser(viewport, alignPanel);
1272 else if (source == annotationColumnSelection)
1274 new AnnotationColumnChooser(viewport, alignPanel);
1276 else if (source == sortPairwiseMenuItem)
1278 sortPairwiseMenuItem_actionPerformed();
1280 else if (source == sortIDMenuItem)
1282 sortIDMenuItem_actionPerformed();
1284 else if (source == sortLengthMenuItem)
1286 sortLengthMenuItem_actionPerformed();
1288 else if (source == sortGroupMenuItem)
1290 sortGroupMenuItem_actionPerformed();
1292 else if (source == removeRedundancyMenuItem)
1294 removeRedundancyMenuItem_actionPerformed();
1296 else if (source == pairwiseAlignmentMenuItem)
1298 pairwiseAlignmentMenuItem_actionPerformed();
1300 else if (source == PCAMenuItem)
1302 PCAMenuItem_actionPerformed();
1304 else if (source == averageDistanceTreeMenuItem)
1306 averageDistanceTreeMenuItem_actionPerformed();
1308 else if (source == neighbourTreeMenuItem)
1310 neighbourTreeMenuItem_actionPerformed();
1312 else if (source == njTreeBlosumMenuItem)
1314 njTreeBlosumMenuItem_actionPerformed();
1316 else if (source == avDistanceTreeBlosumMenuItem)
1318 avTreeBlosumMenuItem_actionPerformed();
1320 else if (source == documentation)
1322 documentation_actionPerformed();
1324 else if (source == about)
1326 about_actionPerformed();
1331 public void inputText_actionPerformed()
1333 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1334 Frame frame = new Frame();
1336 jalview.bin.JalviewLite.addFrame(frame,
1337 MessageManager.getString("label.input_cut_paste"), 500, 500);
1340 protected void outputText_actionPerformed(ActionEvent e)
1342 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1343 Frame frame = new Frame();
1345 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1346 "label.alignment_output_command",
1347 new Object[] { e.getActionCommand() }), 600, 500);
1349 FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1350 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1351 e.getActionCommand(), viewport.getAlignment(),
1352 viewport.getShowJVSuffix()));
1355 public void loadAnnotations()
1357 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1358 cap.setText(MessageManager
1359 .getString("label.paste_features_annotations_Tcoffee_here"));
1360 cap.setAnnotationImport();
1361 Frame frame = new Frame();
1363 jalview.bin.JalviewLite.addFrame(frame,
1364 MessageManager.getString("action.paste_annotations"), 400, 300);
1368 public String outputAnnotations(boolean displayTextbox)
1370 String annotation = new AnnotationFile()
1371 .printAnnotationsForView(viewport);
1375 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1376 Frame frame = new Frame();
1378 jalview.bin.JalviewLite.addFrame(frame,
1379 MessageManager.getString("label.annotations"), 600, 500);
1380 cap.setText(annotation);
1386 private Map<String, Object> getDisplayedFeatureCols()
1388 if (alignPanel.getFeatureRenderer() != null
1389 && viewport.getFeaturesDisplayed() != null)
1391 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1397 public String outputFeatures(boolean displayTextbox, String format)
1400 FeaturesFile formatter = new FeaturesFile();
1401 if (format.equalsIgnoreCase("Jalview"))
1403 features = formatter.printJalviewFormat(viewport
1404 .getAlignment().getSequencesArray(),
1405 getDisplayedFeatureCols());
1409 features = formatter.printGffFormat(viewport.getAlignment()
1410 .getSequencesArray(), getDisplayedFeatureCols());
1415 boolean frimport = false;
1416 if (features == null || features.equals("No Features Visible"))
1418 features = "# No features visible - paste some and import them here.";
1422 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1425 cap.setAnnotationImport();
1427 Frame frame = new Frame();
1429 jalview.bin.JalviewLite.addFrame(frame,
1430 MessageManager.getString("label.features"), 600, 500);
1431 cap.setText(features);
1435 if (features == null)
1444 void launchFullApplication()
1446 StringBuffer url = new StringBuffer(jalviewServletURL);
1448 // allow servlet parameters to be passed in applet parameter
1449 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1451 url.append(firstSep);
1454 + appendProtocol(viewport.applet.getParameter("file")));
1456 if (viewport.applet.getParameter("features") != null)
1458 url.append("&features=");
1459 url.append(appendProtocol(viewport.applet.getParameter("features")));
1462 if (viewport.applet.getParameter("annotations") != null)
1464 url.append("&annotations=");
1465 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1468 if (viewport.applet.getParameter("jnetfile") != null)
1470 url.append("&annotations=");
1471 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1474 if (viewport.applet.getParameter("defaultColour") != null)
1476 url.append("&colour="
1477 + removeWhiteSpace(viewport.applet
1478 .getParameter("defaultColour")));
1481 if (viewport.applet.getParameter("userDefinedColour") != null)
1483 url.append("&colour="
1484 + removeWhiteSpace(viewport.applet
1485 .getParameter("userDefinedColour")));
1487 if (viewport.applet.getParameter("tree") != null)
1490 + appendProtocol(viewport.applet.getParameter("tree")));
1492 if (viewport.applet.getParameter("treeFile") != null)
1495 + appendProtocol(viewport.applet.getParameter("treeFile")));
1498 showURL(url.toString(), "FULL_APP");
1501 String removeWhiteSpace(String colour)
1503 StringBuffer sb = new StringBuffer();
1504 for (int i = 0; i < colour.length(); i++)
1506 if (Character.isWhitespace(colour.charAt(i)))
1512 sb.append(colour.charAt(i));
1516 return sb.toString();
1519 String appendProtocol(String url)
1524 url = URLEncoder.encode(url);
1527 * When we finally deprecate 1.1 compatibility, we can start to use
1528 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1529 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1530 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1531 * ex.printStackTrace(); }
1533 catch (java.net.MalformedURLException ex)
1535 url = viewport.applet.getCodeBase() + url;
1540 public void closeMenuItem_actionPerformed()
1542 PaintRefresher.RemoveComponent(alignPanel);
1543 if (alignPanel.seqPanel != null
1544 && alignPanel.seqPanel.seqCanvas != null)
1546 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1548 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1550 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1553 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1568 void updateEditMenuBar()
1571 if (viewport.getHistoryList().size() > 0)
1573 undoMenuItem.setEnabled(true);
1574 CommandI command = viewport.getHistoryList().peek();
1575 undoMenuItem.setLabel(MessageManager.formatMessage(
1576 "label.undo_command",
1577 new Object[] { command.getDescription() }));
1581 undoMenuItem.setEnabled(false);
1582 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1585 if (viewport.getRedoList().size() > 0)
1587 redoMenuItem.setEnabled(true);
1589 CommandI command = viewport.getRedoList().peek();
1590 redoMenuItem.setLabel(MessageManager.formatMessage(
1591 "label.redo_command",
1592 new Object[] { command.getDescription() }));
1596 redoMenuItem.setEnabled(false);
1597 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1605 public void addHistoryItem(CommandI command)
1607 if (command.getSize() > 0)
1609 viewport.addToHistoryList(command);
1610 viewport.clearRedoList();
1611 updateEditMenuBar();
1612 viewport.updateHiddenColumns();
1617 * TODO: JAL-1104 DOCUMENT ME!
1622 protected void undoMenuItem_actionPerformed()
1624 if (viewport.getHistoryList().isEmpty())
1629 CommandI command = viewport.getHistoryList().pop();
1630 viewport.addToRedoList(command);
1631 command.undoCommand(null);
1633 AlignmentViewport originalSource = getOriginatingSource(command);
1635 if (originalSource != viewport)
1638 .println("Warning: Viewport object mismatch whilst undoing");
1640 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1641 // viewport.getColumnSelection().getHiddenColumns()
1643 updateEditMenuBar();
1644 originalSource.firePropertyChange("alignment", null, originalSource
1645 .getAlignment().getSequences());
1649 * TODO: JAL-1104 DOCUMENT ME!
1654 protected void redoMenuItem_actionPerformed()
1656 if (viewport.getRedoList().isEmpty())
1661 CommandI command = viewport.getRedoList().pop();
1662 viewport.addToHistoryList(command);
1663 command.doCommand(null);
1665 AlignmentViewport originalSource = getOriginatingSource(command);
1667 if (originalSource != viewport)
1670 .println("Warning: Viewport object mismatch whilst re-doing");
1672 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1673 // viewport.getColumnSelection().getHiddenColumns()
1676 updateEditMenuBar();
1677 originalSource.firePropertyChange("alignment", null, originalSource
1678 .getAlignment().getSequences());
1681 AlignmentViewport getOriginatingSource(CommandI command)
1683 AlignmentViewport originalSource = null;
1684 // For sequence removal and addition, we need to fire
1685 // the property change event FROM the viewport where the
1686 // original alignment was altered
1687 AlignmentI al = null;
1688 if (command instanceof EditCommand)
1690 EditCommand editCommand = (EditCommand) command;
1691 al = editCommand.getAlignment();
1692 Vector comps = (Vector) PaintRefresher.components.get(viewport
1693 .getSequenceSetId());
1694 for (int i = 0; i < comps.size(); i++)
1696 if (comps.elementAt(i) instanceof AlignmentPanel)
1698 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1700 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1707 if (originalSource == null)
1709 // The original view is closed, we must validate
1710 // the current view against the closed view first
1713 PaintRefresher.validateSequences(al, viewport.getAlignment());
1716 originalSource = viewport;
1719 return originalSource;
1723 * Move the currently selected sequences up or down one position in the
1728 public void moveSelectedSequences(boolean up)
1730 SequenceGroup sg = viewport.getSelectionGroup();
1735 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1736 up ? null : viewport.getHiddenRepSequences(), up);
1737 alignPanel.paintAlignment(true);
1740 * Also move cDNA/protein complement sequences
1742 AlignViewportI complement = viewport.getCodingComplement();
1743 if (complement != null)
1745 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1746 viewport, complement);
1747 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1748 up ? null : complement.getHiddenRepSequences(), up);
1749 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1753 synchronized void slideSequences(boolean right, int size)
1755 List<SequenceI> sg = new Vector<SequenceI>();
1756 if (viewport.cursorMode)
1758 sg.add(viewport.getAlignment().getSequenceAt(
1759 alignPanel.seqPanel.seqCanvas.cursorY));
1761 else if (viewport.getSelectionGroup() != null
1762 && viewport.getSelectionGroup().getSize() != viewport
1763 .getAlignment().getHeight())
1765 sg = viewport.getSelectionGroup().getSequences(
1766 viewport.getHiddenRepSequences());
1774 Vector<SequenceI> invertGroup = new Vector();
1776 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1778 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1780 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1784 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1786 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1788 for (int i = 0; i < invertGroup.size(); i++)
1790 seqs2[i] = invertGroup.elementAt(i);
1793 SlideSequencesCommand ssc;
1796 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1797 size, viewport.getGapCharacter());
1801 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1802 size, viewport.getGapCharacter());
1805 int groupAdjustment = 0;
1806 if (ssc.getGapsInsertedBegin() && right)
1808 if (viewport.cursorMode)
1810 alignPanel.seqPanel.moveCursor(size, 0);
1814 groupAdjustment = size;
1817 else if (!ssc.getGapsInsertedBegin() && !right)
1819 if (viewport.cursorMode)
1821 alignPanel.seqPanel.moveCursor(-size, 0);
1825 groupAdjustment = -size;
1829 if (groupAdjustment != 0)
1831 viewport.getSelectionGroup().setStartRes(
1832 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1833 viewport.getSelectionGroup().setEndRes(
1834 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1837 boolean appendHistoryItem = false;
1838 Deque<CommandI> historyList = viewport.getHistoryList();
1839 if (historyList != null && historyList.size() > 0
1840 && historyList.peek() instanceof SlideSequencesCommand)
1842 appendHistoryItem = ssc
1843 .appendSlideCommand((SlideSequencesCommand) historyList
1847 if (!appendHistoryItem)
1849 addHistoryItem(ssc);
1855 static StringBuffer copiedSequences;
1857 static Vector copiedHiddenColumns;
1859 protected void copy_actionPerformed()
1861 if (viewport.getSelectionGroup() == null)
1866 SequenceGroup sg = viewport.getSelectionGroup();
1867 copiedSequences = new StringBuffer();
1868 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1869 for (int i = 0; i < sg.getSize(); i++)
1871 SequenceI seq = sg.getSequenceAt(i);
1872 int index = viewport.getAlignment().findIndex(seq);
1873 orderedSeqs.put(index, seq);
1876 int index = 0, startRes, endRes;
1879 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1881 copiedHiddenColumns = new Vector();
1882 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1883 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1885 copiedHiddenColumns.addElement(new int[] {
1886 region[0] - hiddenOffset, region[1] - hiddenOffset });
1891 copiedHiddenColumns = null;
1894 for (int i = 0; i < sg.getSize(); i++)
1896 SequenceI seq = null;
1900 if (orderedSeqs.containsKey(index))
1902 seq = orderedSeqs.get(index);
1913 // Returns residue following index if gap
1914 startRes = seq.findPosition(sg.getStartRes());
1917 // Need to find the residue preceeding index if gap
1920 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1922 ch = seq.getCharAt(j);
1923 if (!jalview.util.Comparison.isGap((ch)))
1931 endRes += seq.getStart() - 1;
1934 copiedSequences.append(seq.getName()
1940 + seq.getSequenceAsString(sg.getStartRes(),
1941 sg.getEndRes() + 1) + "\n");
1946 protected void pasteNew_actionPerformed()
1951 protected void pasteThis_actionPerformed()
1956 void paste(boolean newAlignment)
1961 if (copiedSequences == null)
1966 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1967 Vector seqs = new Vector();
1968 while (st.hasMoreElements())
1970 String name = st.nextToken();
1971 int start = Integer.parseInt(st.nextToken());
1972 int end = Integer.parseInt(st.nextToken());
1973 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1975 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1976 for (int i = 0; i < seqs.size(); i++)
1978 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1983 String newtitle = MessageManager
1984 .getString("label.copied_sequences");
1985 if (getTitle().startsWith(
1986 MessageManager.getString("label.copied_sequences")))
1988 newtitle = getTitle();
1992 newtitle = newtitle.concat(MessageManager.formatMessage(
1993 "label.from_msname", new String[] { getTitle() }));
1995 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1996 viewport.applet, newtitle, false);
1997 if (copiedHiddenColumns != null)
1999 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2001 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2002 af.viewport.hideColumns(region[0], region[1]);
2006 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2011 addSequences(newSeqs);
2014 } catch (Exception ex)
2016 } // could be anything being pasted in here
2020 void addSequences(SequenceI[] seqs)
2022 for (int i = 0; i < seqs.length; i++)
2024 viewport.getAlignment().addSequence(seqs[i]);
2028 addHistoryItem(new EditCommand(
2029 MessageManager.getString("label.add_sequences"), Action.PASTE,
2030 seqs, 0, viewport.getAlignment().getWidth(),
2031 viewport.getAlignment()));
2033 viewport.setEndSeq(viewport.getAlignment().getHeight());
2034 viewport.getAlignment().getWidth();
2035 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2040 protected void cut_actionPerformed()
2042 copy_actionPerformed();
2043 delete_actionPerformed();
2046 protected void delete_actionPerformed()
2049 SequenceGroup sg = viewport.getSelectionGroup();
2055 Vector seqs = new Vector();
2057 for (int i = 0; i < sg.getSize(); i++)
2059 seq = sg.getSequenceAt(i);
2060 seqs.addElement(seq);
2064 * If the cut affects all sequences, warn, remove highlighted columns
2066 if (sg.getSize() == viewport.getAlignment().getHeight())
2068 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2069 .getAlignment().getWidth()) ? true : false;
2070 if (isEntireAlignWidth)
2072 String title = MessageManager.getString("label.delete_all");
2073 Panel infoPanel = new Panel();
2074 infoPanel.setLayout(new FlowLayout());
2076 .add(new Label(MessageManager.getString("warn.delete_all")));
2078 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2079 dialog.setMainPanel(infoPanel);
2080 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2081 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2082 dialog.setVisible(true);
2089 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2090 sg.getEndRes() + 1);
2093 SequenceI[] cut = new SequenceI[seqs.size()];
2094 for (int i = 0; i < seqs.size(); i++)
2096 cut[i] = (SequenceI) seqs.elementAt(i);
2100 * //ADD HISTORY ITEM
2102 addHistoryItem(new EditCommand(
2103 MessageManager.getString("label.cut_sequences"), Action.CUT,
2104 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2105 viewport.getAlignment()));
2107 viewport.setSelectionGroup(null);
2108 viewport.getAlignment().deleteGroup(sg);
2110 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2113 if (viewport.getAlignment().getHeight() < 1)
2115 this.setVisible(false);
2117 viewport.sendSelection();
2121 * group consensus toggled
2124 protected void showGroupConsensus_actionPerformed()
2126 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2127 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2132 * group conservation toggled.
2134 protected void showGroupConservation_actionPerformed()
2136 viewport.setShowGroupConservation(showGroupConservation.getState());
2137 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2144 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2145 * .event.ActionEvent)
2147 protected void showConsensusHistogram_actionPerformed()
2149 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2150 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2157 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2158 * .event.ActionEvent)
2160 protected void showSequenceLogo_actionPerformed()
2162 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2163 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2166 protected void normSequenceLogo_actionPerformed()
2168 showSequenceLogo.setState(true);
2169 viewport.setShowSequenceLogo(true);
2170 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2171 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2174 protected void applyAutoAnnotationSettings_actionPerformed()
2176 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2179 protected void makeGrpsFromSelection_actionPerformed()
2181 if (avc.makeGroupsFromSelection())
2183 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2184 alignPanel.updateAnnotation();
2185 alignPanel.paintAlignment(true);
2189 protected void createGroup_actionPerformed()
2194 protected void unGroup_actionPerformed()
2198 alignPanel.alignmentChanged();
2202 protected void deleteGroups_actionPerformed()
2204 if (avc.deleteGroups())
2206 alignPanel.alignmentChanged();
2210 public void selectAllSequenceMenuItem_actionPerformed()
2212 SequenceGroup sg = new SequenceGroup();
2213 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2215 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2217 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2218 viewport.setSelectionGroup(sg);
2219 alignPanel.paintAlignment(true);
2220 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2221 viewport.sendSelection();
2224 public void deselectAllSequenceMenuItem_actionPerformed()
2226 if (viewport.cursorMode)
2228 alignPanel.seqPanel.keyboardNo1 = null;
2229 alignPanel.seqPanel.keyboardNo2 = null;
2231 viewport.setSelectionGroup(null);
2232 viewport.getColumnSelection().clear();
2233 viewport.setSelectionGroup(null);
2234 alignPanel.idPanel.idCanvas.searchResults = null;
2235 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2236 alignPanel.paintAlignment(true);
2237 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2238 viewport.sendSelection();
2241 public void invertSequenceMenuItem_actionPerformed()
2243 SequenceGroup sg = viewport.getSelectionGroup();
2244 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2246 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2249 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2250 viewport.sendSelection();
2253 public void invertColSel_actionPerformed()
2255 viewport.invertColumnSelection();
2256 alignPanel.paintAlignment(true);
2257 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2258 viewport.sendSelection();
2261 void trimAlignment(boolean trimLeft)
2263 ColumnSelection colSel = viewport.getColumnSelection();
2266 if (colSel.size() > 0)
2270 column = colSel.getMin();
2274 column = colSel.getMax();
2278 if (viewport.getSelectionGroup() != null)
2280 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2281 viewport.getHiddenRepSequences());
2285 seqs = viewport.getAlignment().getSequencesArray();
2288 TrimRegionCommand trimRegion;
2291 trimRegion = new TrimRegionCommand("Remove Left",
2292 TrimRegionCommand.TRIM_LEFT, seqs, column,
2293 viewport.getAlignment(), viewport.getColumnSelection(),
2294 viewport.getSelectionGroup());
2295 viewport.setStartRes(0);
2299 trimRegion = new TrimRegionCommand("Remove Right",
2300 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2301 viewport.getAlignment(), viewport.getColumnSelection(),
2302 viewport.getSelectionGroup());
2305 statusBar.setText(MessageManager.formatMessage(
2306 "label.removed_columns",
2307 new String[] { Integer.valueOf(trimRegion.getSize())
2309 addHistoryItem(trimRegion);
2311 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2313 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2314 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2316 viewport.getAlignment().deleteGroup(sg);
2320 viewport.firePropertyChange("alignment", null, viewport
2321 .getAlignment().getSequences());
2325 public void removeGappedColumnMenuItem_actionPerformed()
2327 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2330 if (viewport.getSelectionGroup() != null)
2332 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2333 viewport.getHiddenRepSequences());
2334 start = viewport.getSelectionGroup().getStartRes();
2335 end = viewport.getSelectionGroup().getEndRes();
2339 seqs = viewport.getAlignment().getSequencesArray();
2342 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2343 "Remove Gapped Columns", seqs, start, end,
2344 viewport.getAlignment());
2346 addHistoryItem(removeGapCols);
2348 statusBar.setText(MessageManager.formatMessage(
2349 "label.removed_empty_columns",
2350 new String[] { Integer.valueOf(removeGapCols.getSize())
2353 // This is to maintain viewport position on first residue
2354 // of first sequence
2355 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2356 int startRes = seq.findPosition(viewport.startRes);
2357 // ShiftList shifts;
2358 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2359 // edit.alColumnChanges=shifts.getInverse();
2360 // if (viewport.hasHiddenColumns)
2361 // viewport.getColumnSelection().compensateForEdits(shifts);
2362 viewport.setStartRes(seq.findIndex(startRes) - 1);
2363 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2368 public void removeAllGapsMenuItem_actionPerformed()
2370 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2373 if (viewport.getSelectionGroup() != null)
2375 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2376 viewport.getHiddenRepSequences());
2377 start = viewport.getSelectionGroup().getStartRes();
2378 end = viewport.getSelectionGroup().getEndRes();
2382 seqs = viewport.getAlignment().getSequencesArray();
2385 // This is to maintain viewport position on first residue
2386 // of first sequence
2387 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2388 int startRes = seq.findPosition(viewport.startRes);
2390 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2391 viewport.getAlignment()));
2393 viewport.setStartRes(seq.findIndex(startRes) - 1);
2395 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2400 public void findMenuItem_actionPerformed()
2402 new Finder(alignPanel);
2406 * create a new view derived from the current view
2409 * @return frame for the new view
2411 public AlignFrame newView(String viewtitle)
2414 if (viewport.hasHiddenRows())
2416 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2417 .getFullAlignment().getSequencesArray());
2421 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2424 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2426 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2428 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2430 newal.addAnnotation(viewport.getAlignment()
2431 .getAlignmentAnnotation()[i]);
2436 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2438 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2439 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2440 PaintRefresher.Register(newaf.alignPanel,
2441 newaf.alignPanel.av.getSequenceSetId());
2443 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2444 newaf.alignPanel.av.getSequenceSetId());
2445 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2446 newaf.alignPanel.av.getSequenceSetId());
2448 Vector comps = (Vector) PaintRefresher.components.get(viewport
2449 .getSequenceSetId());
2451 for (int i = 0; i < comps.size(); i++)
2453 if (comps.elementAt(i) instanceof AlignmentPanel)
2459 String title = new String(this.getTitle());
2460 if (viewtitle != null)
2462 title = viewtitle + " ( " + title + ")";
2466 if (title.indexOf("(View") > -1)
2468 title = title.substring(0, title.indexOf("(View"));
2470 title += "(View " + viewSize + ")";
2473 newaf.setTitle(title.toString());
2475 newaf.viewport.setHistoryList(viewport.getHistoryList());
2476 newaf.viewport.setRedoList(viewport.getRedoList());
2482 * @return list of feature groups on the view
2484 public String[] getFeatureGroups()
2486 FeatureRenderer fr = null;
2487 if (alignPanel != null
2488 && (fr = alignPanel.getFeatureRenderer()) != null)
2490 List<String> gps = fr.getFeatureGroups();
2491 String[] _gps = gps.toArray(new String[gps.size()]);
2498 * get sequence feature groups that are hidden or shown
2504 public String[] getFeatureGroupsOfState(boolean visible)
2506 FeatureRenderer fr = null;
2507 if (alignPanel != null
2508 && (fr = alignPanel.getFeatureRenderer()) != null)
2510 List<String> gps = fr.getGroups(visible);
2511 String[] _gps = gps.toArray(new String[gps.size()]);
2518 * Change the display state for the given feature groups
2521 * list of group strings
2523 * visible or invisible
2525 public void setFeatureGroupState(String[] groups, boolean state)
2527 FeatureRenderer fr = null;
2528 this.sequenceFeatures.setState(true);
2529 viewport.setShowSequenceFeatures(true);
2530 if (alignPanel != null
2531 && (fr = alignPanel.getFeatureRenderer()) != null)
2534 fr.setGroupVisibility(Arrays.asList(groups), state);
2535 alignPanel.seqPanel.seqCanvas.repaint();
2536 if (alignPanel.overviewPanel != null)
2538 alignPanel.overviewPanel.updateOverviewImage();
2543 public void seqLimits_itemStateChanged()
2545 viewport.setShowJVSuffix(seqLimits.getState());
2546 alignPanel.fontChanged();
2547 alignPanel.paintAlignment(true);
2550 protected void colourTextMenuItem_actionPerformed()
2552 viewport.setColourText(colourTextMenuItem.getState());
2553 alignPanel.paintAlignment(true);
2556 protected void displayNonconservedMenuItem_actionPerformed()
2558 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2559 alignPanel.paintAlignment(true);
2562 protected void wrapMenuItem_actionPerformed()
2564 viewport.setWrapAlignment(wrapMenuItem.getState());
2565 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2566 scaleAbove.setEnabled(wrapMenuItem.getState());
2567 scaleLeft.setEnabled(wrapMenuItem.getState());
2568 scaleRight.setEnabled(wrapMenuItem.getState());
2569 alignPanel.paintAlignment(true);
2572 public void overviewMenuItem_actionPerformed()
2574 if (alignPanel.overviewPanel != null)
2579 Frame frame = new Frame();
2580 OverviewPanel overview = new OverviewPanel(alignPanel);
2581 frame.add(overview);
2582 // +50 must allow for applet frame window
2583 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2584 "label.overview_params", new String[] { this.getTitle() }),
2585 overview.getPreferredSize().width,
2586 overview.getPreferredSize().height + 50);
2589 final AlignmentPanel ap = alignPanel;
2590 frame.addWindowListener(new WindowAdapter()
2593 public void windowClosing(WindowEvent e)
2597 ap.setOverviewPanel(null);
2602 alignPanel.setOverviewPanel(overview);
2607 public void changeColour(ColourSchemeI cs)
2612 if (viewport.getAbovePIDThreshold())
2614 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2618 if (viewport.getConservationSelected())
2620 cs.setConservationApplied(true);
2621 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2626 cs.setConservationApplied(false);
2629 viewport.setGlobalColourScheme(cs);
2631 alignPanel.paintAlignment(true);
2634 protected void modifyPID_actionPerformed()
2636 if (viewport.getAbovePIDThreshold()
2637 && viewport.getGlobalColourScheme() != null)
2639 SliderPanel.setPIDSliderSource(alignPanel,
2640 viewport.getGlobalColourScheme(), "Background");
2641 SliderPanel.showPIDSlider();
2645 protected void modifyConservation_actionPerformed()
2647 if (viewport.getConservationSelected()
2648 && viewport.getGlobalColourScheme() != null)
2650 SliderPanel.setConservationSlider(alignPanel,
2651 viewport.getGlobalColourScheme(), "Background");
2652 SliderPanel.showConservationSlider();
2656 protected void conservationMenuItem_actionPerformed()
2658 viewport.setConservationSelected(conservationMenuItem.getState());
2660 viewport.setAbovePIDThreshold(false);
2661 abovePIDThreshold.setState(false);
2663 changeColour(viewport.getGlobalColourScheme());
2665 modifyConservation_actionPerformed();
2668 public void abovePIDThreshold_actionPerformed()
2670 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2672 conservationMenuItem.setState(false);
2673 viewport.setConservationSelected(false);
2675 changeColour(viewport.getGlobalColourScheme());
2677 modifyPID_actionPerformed();
2680 public void sortPairwiseMenuItem_actionPerformed()
2682 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2683 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2684 .getAlignment().getSequenceAt(0), null);
2686 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2687 viewport.getAlignment()));
2688 alignPanel.paintAlignment(true);
2691 public void sortIDMenuItem_actionPerformed()
2693 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2694 AlignmentSorter.sortByID(viewport.getAlignment());
2695 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2696 viewport.getAlignment()));
2697 alignPanel.paintAlignment(true);
2700 public void sortLengthMenuItem_actionPerformed()
2702 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2703 AlignmentSorter.sortByLength(viewport.getAlignment());
2704 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2705 viewport.getAlignment()));
2706 alignPanel.paintAlignment(true);
2709 public void sortGroupMenuItem_actionPerformed()
2711 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2712 AlignmentSorter.sortByGroup(viewport.getAlignment());
2713 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2714 viewport.getAlignment()));
2715 alignPanel.paintAlignment(true);
2719 public void removeRedundancyMenuItem_actionPerformed()
2721 new RedundancyPanel(alignPanel);
2724 public void pairwiseAlignmentMenuItem_actionPerformed()
2726 if (viewport.getSelectionGroup() != null
2727 && viewport.getSelectionGroup().getSize() > 1)
2729 Frame frame = new Frame();
2730 frame.add(new PairwiseAlignPanel(alignPanel));
2731 jalview.bin.JalviewLite.addFrame(frame,
2732 MessageManager.getString("action.pairwise_alignment"), 600,
2737 public void PCAMenuItem_actionPerformed()
2739 // are the sequences aligned?
2740 if (!viewport.getAlignment().isAligned(false))
2743 int Width = viewport.getAlignment().getWidth();
2745 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2747 current = viewport.getAlignment().getSequenceAt(i);
2749 if (current.getLength() < Width)
2751 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2754 alignPanel.paintAlignment(true);
2757 if ((viewport.getSelectionGroup() != null
2758 && viewport.getSelectionGroup().getSize() < 4 && viewport
2759 .getSelectionGroup().getSize() > 0)
2760 || viewport.getAlignment().getHeight() < 4)
2767 new PCAPanel(viewport);
2768 } catch (java.lang.OutOfMemoryError ex)
2774 public void averageDistanceTreeMenuItem_actionPerformed()
2776 NewTreePanel("AV", "PID", "Average distance tree using PID");
2779 public void neighbourTreeMenuItem_actionPerformed()
2781 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2784 protected void njTreeBlosumMenuItem_actionPerformed()
2786 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2789 protected void avTreeBlosumMenuItem_actionPerformed()
2791 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2794 void NewTreePanel(String type, String pwType, String title)
2796 // are the sequences aligned?
2797 if (!viewport.getAlignment().isAligned(false))
2800 int Width = viewport.getAlignment().getWidth();
2802 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2804 current = viewport.getAlignment().getSequenceAt(i);
2806 if (current.getLength() < Width)
2808 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2811 alignPanel.paintAlignment(true);
2815 if ((viewport.getSelectionGroup() != null && viewport
2816 .getSelectionGroup().getSize() > 1)
2817 || (viewport.getAlignment().getHeight() > 1))
2819 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2821 addTreeMenuItem(tp, title);
2823 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2827 void loadTree_actionPerformed()
2829 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2830 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2831 cap.setTreeImport();
2832 Frame frame = new Frame();
2834 jalview.bin.JalviewLite.addFrame(frame,
2835 MessageManager.getString("label.paste_newick_file"), 400, 300);
2838 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2840 TreePanel tp = new TreePanel(alignPanel, treeFile,
2841 MessageManager.getString("label.load_tree_from_file"), tree);
2842 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2843 addTreeMenuItem(tp, treeFile);
2847 * sort the alignment using the given treePanel
2850 * tree used to sort view
2852 * string used for undo event name
2854 public void sortByTree(TreePanel treePanel, String title)
2856 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2858 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2859 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2860 // HistoryItem.SORT));
2861 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2862 "label.order_by_params", new String[] { title }), oldOrder,
2863 viewport.getAlignment()));
2864 alignPanel.paintAlignment(true);
2868 * Do any automatic reordering of the alignment and add the necessary bits to
2869 * the menu structure for the new tree
2874 protected void addTreeMenuItem(final TreePanel treePanel,
2877 final MenuItem item = new MenuItem(title);
2878 sortByTreeMenu.add(item);
2879 item.addActionListener(new java.awt.event.ActionListener()
2882 public void actionPerformed(ActionEvent evt)
2884 sortByTree(treePanel, title); // treePanel.getTitle());
2888 treePanel.addWindowListener(new WindowAdapter()
2891 public void windowOpened(WindowEvent e)
2893 if (viewport.sortByTree)
2895 sortByTree(treePanel, title);
2897 super.windowOpened(e);
2901 public void windowClosing(WindowEvent e)
2903 sortByTreeMenu.remove(item);
2908 public boolean sortBy(AlignmentOrder alorder, String undoname)
2910 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2911 if (viewport.applet.debug)
2913 System.err.println("Sorting " + alorder.getOrder().size()
2914 + " in alignment '" + getTitle() + "'");
2916 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2917 if (undoname != null)
2919 addHistoryItem(new OrderCommand(undoname, oldOrder,
2920 viewport.getAlignment()));
2922 alignPanel.paintAlignment(true);
2926 protected void documentation_actionPerformed()
2928 alignPanel.av.applet.openJalviewHelpUrl();
2931 protected void about_actionPerformed()
2934 class AboutPanel extends Canvas
2940 public AboutPanel(String version, String builddate)
2942 this.version = version;
2943 this.builddate = builddate;
2947 public void paint(Graphics g)
2949 g.setColor(Color.white);
2950 g.fillRect(0, 0, getSize().width, getSize().height);
2951 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2952 FontMetrics fm = g.getFontMetrics();
2953 int fh = fm.getHeight();
2955 g.setColor(Color.black);
2956 // TODO: update this text for each release or centrally store it for
2957 // lite and application
2958 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2959 g.drawString(MessageManager.formatMessage(
2960 "label.jalviewLite_release", new String[] { version }), x,
2962 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2963 g.drawString(MessageManager.formatMessage(
2964 "label.jaview_build_date", new String[] { builddate }), x,
2966 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2967 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2969 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2970 x + 50, y += fh + 8);
2972 MessageManager.getString("label.jalview_dev_managers"), x,
2974 g.drawString(MessageManager
2975 .getString("label.jalview_distribution_lists"), x, y += fh);
2976 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2979 MessageManager.getString("label.jalview_cite_1_authors"),
2982 MessageManager.getString("label.jalview_cite_1_title"), x,
2984 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2989 Frame frame = new Frame();
2990 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2992 jalview.bin.JalviewLite.addFrame(frame,
2993 MessageManager.getString("label.jalview"), 580, 220);
2997 public void showURL(String url, String target)
2999 if (viewport.applet == null)
3001 System.out.println("Not running as applet - no browser available.");
3005 viewport.applet.showURL(url, target);
3009 // ////////////////////////////////////////////////////////////////////////////////
3010 // JBuilder Graphics here
3012 MenuBar alignFrameMenuBar = new MenuBar();
3014 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3016 MenuItem loadApplication = new MenuItem(
3017 MessageManager.getString("label.view_full_application"));
3019 MenuItem loadTree = new MenuItem(
3020 MessageManager.getString("label.load_associated_tree"));
3022 MenuItem loadAnnotations = new MenuItem(
3023 MessageManager.getString("label.load_features_annotations"));
3025 MenuItem outputFeatures = new MenuItem(
3026 MessageManager.getString("label.export_features"));
3028 MenuItem outputAnnotations = new MenuItem(
3029 MessageManager.getString("label.export_annotations"));
3031 MenuItem closeMenuItem = new MenuItem(
3032 MessageManager.getString("action.close"));
3034 MenuItem selectAllSequenceMenuItem = new MenuItem(
3035 MessageManager.getString("action.select_all"));
3037 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3038 MessageManager.getString("action.deselect_all"));
3040 MenuItem invertSequenceMenuItem = new MenuItem(
3041 MessageManager.getString("action.invert_selection"));
3043 MenuItem remove2LeftMenuItem = new MenuItem();
3045 MenuItem remove2RightMenuItem = new MenuItem();
3047 MenuItem removeGappedColumnMenuItem = new MenuItem();
3049 MenuItem removeAllGapsMenuItem = new MenuItem();
3051 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3053 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3055 MenuItem sortPairwiseMenuItem = new MenuItem();
3057 MenuItem sortIDMenuItem = new MenuItem();
3059 MenuItem sortLengthMenuItem = new MenuItem();
3061 MenuItem sortGroupMenuItem = new MenuItem();
3063 MenuItem removeRedundancyMenuItem = new MenuItem();
3065 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3067 MenuItem PCAMenuItem = new MenuItem();
3069 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3071 MenuItem neighbourTreeMenuItem = new MenuItem();
3073 BorderLayout borderLayout1 = new BorderLayout();
3075 public Label statusBar = new Label();
3077 MenuItem clustalColour = new MenuItem();
3079 MenuItem zappoColour = new MenuItem();
3081 MenuItem taylorColour = new MenuItem();
3083 MenuItem hydrophobicityColour = new MenuItem();
3085 MenuItem helixColour = new MenuItem();
3087 MenuItem strandColour = new MenuItem();
3089 MenuItem turnColour = new MenuItem();
3091 MenuItem buriedColour = new MenuItem();
3093 MenuItem purinePyrimidineColour = new MenuItem();
3095 // MenuItem RNAInteractionColour = new MenuItem();
3097 MenuItem RNAHelixColour = new MenuItem();
3099 MenuItem userDefinedColour = new MenuItem();
3101 MenuItem PIDColour = new MenuItem();
3103 MenuItem BLOSUM62Colour = new MenuItem();
3105 MenuItem tcoffeeColour = new MenuItem();
3107 MenuItem njTreeBlosumMenuItem = new MenuItem();
3109 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3111 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3113 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3115 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3117 MenuItem alProperties = new MenuItem(
3118 MessageManager.getString("label.alignment_props"));
3120 MenuItem overviewMenuItem = new MenuItem();
3122 MenuItem undoMenuItem = new MenuItem();
3124 MenuItem redoMenuItem = new MenuItem();
3126 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3128 MenuItem noColourmenuItem = new MenuItem();
3130 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3132 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3134 MenuItem findMenuItem = new MenuItem();
3136 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3138 MenuItem nucleotideColour = new MenuItem();
3140 MenuItem deleteGroups = new MenuItem();
3142 MenuItem grpsFromSelection = new MenuItem();
3144 MenuItem createGroup = new MenuItem();
3146 MenuItem unGroup = new MenuItem();
3148 MenuItem delete = new MenuItem();
3150 MenuItem copy = new MenuItem();
3152 MenuItem cut = new MenuItem();
3154 Menu pasteMenu = new Menu();
3156 MenuItem pasteNew = new MenuItem();
3158 MenuItem pasteThis = new MenuItem();
3160 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3162 MenuItem font = new MenuItem();
3164 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3166 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3168 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3170 MenuItem modifyPID = new MenuItem();
3172 MenuItem modifyConservation = new MenuItem();
3174 CheckboxMenuItem autoCalculate = null;
3176 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3177 "Sort Alignment With New Tree", true);
3179 Menu sortByTreeMenu = new Menu();
3181 MenuItem inputText = new MenuItem();
3183 MenuItem documentation = new MenuItem();
3185 MenuItem about = new MenuItem();
3187 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3189 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3191 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3193 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3195 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3197 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3199 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3201 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3203 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3206 * Initialise menus and other items
3210 private void jbInit() throws Exception
3212 setMenuBar(alignFrameMenuBar);
3215 * Configure File menu items and actions
3218 .setLabel(MessageManager.getString("label.input_from_textbox"));
3219 inputText.addActionListener(this);
3220 Menu outputTextboxMenu = new Menu(
3221 MessageManager.getString("label.out_to_textbox"));
3222 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3225 MenuItem item = new MenuItem(
3226 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3228 item.addActionListener(new java.awt.event.ActionListener()
3231 public void actionPerformed(ActionEvent e)
3233 outputText_actionPerformed(e);
3237 outputTextboxMenu.add(item);
3239 closeMenuItem.addActionListener(this);
3240 loadApplication.addActionListener(this);
3241 loadTree.addActionListener(this);
3242 loadAnnotations.addActionListener(this);
3243 outputFeatures.addActionListener(this);
3244 outputAnnotations.addActionListener(this);
3247 * Configure Edit menu items and actions
3249 undoMenuItem.setEnabled(false);
3250 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3251 undoMenuItem.addActionListener(this);
3252 redoMenuItem.setEnabled(false);
3253 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3254 redoMenuItem.addActionListener(this);
3255 copy.setLabel(MessageManager.getString("action.copy"));
3256 copy.addActionListener(this);
3257 cut.setLabel(MessageManager.getString("action.cut"));
3258 cut.addActionListener(this);
3259 delete.setLabel(MessageManager.getString("action.delete"));
3260 delete.addActionListener(this);
3261 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3262 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3263 pasteNew.addActionListener(this);
3264 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3265 pasteThis.addActionListener(this);
3266 remove2LeftMenuItem.setLabel(MessageManager
3267 .getString("action.remove_left"));
3268 remove2LeftMenuItem.addActionListener(this);
3269 remove2RightMenuItem.setLabel(MessageManager
3270 .getString("action.remove_right"));
3271 remove2RightMenuItem.addActionListener(this);
3272 removeGappedColumnMenuItem.setLabel(MessageManager
3273 .getString("action.remove_empty_columns"));
3274 removeGappedColumnMenuItem.addActionListener(this);
3275 removeAllGapsMenuItem.setLabel(MessageManager
3276 .getString("action.remove_all_gaps"));
3277 removeAllGapsMenuItem.addActionListener(this);
3278 removeRedundancyMenuItem.setLabel(MessageManager
3279 .getString("action.remove_redundancy"));
3280 removeRedundancyMenuItem.addActionListener(this);
3283 * Configure Select menu items and actions
3285 findMenuItem.setLabel(MessageManager.getString("action.find"));
3286 findMenuItem.addActionListener(this);
3287 selectAllSequenceMenuItem.addActionListener(this);
3288 deselectAllSequenceMenuItem.addActionListener(this);
3289 invertSequenceMenuItem.setLabel(MessageManager
3290 .getString("action.invert_sequence_selection"));
3291 invertSequenceMenuItem.addActionListener(this);
3292 invertColSel.setLabel(MessageManager
3293 .getString("action.invert_column_selection"));
3294 invertColSel.addActionListener(this);
3295 deleteGroups.setLabel(MessageManager
3296 .getString("action.undefine_groups"));
3297 deleteGroups.addActionListener(this);
3298 grpsFromSelection.setLabel(MessageManager
3299 .getString("action.make_groups_selection"));
3300 grpsFromSelection.addActionListener(this);
3301 createGroup.setLabel(MessageManager.getString("action.create_group"));
3302 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3303 annotationColumnSelection.setLabel(MessageManager
3304 .getString("action.select_by_annotation"));
3305 annotationColumnSelection.addActionListener(this);
3308 * Configure View menu items and actions
3310 newView.setLabel(MessageManager.getString("action.new_view"));
3311 newView.addActionListener(this);
3312 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3313 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3314 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3315 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3317 .setLabel(MessageManager.getString("label.selected_columns"));
3318 hideSequences.setLabel(MessageManager
3319 .getString("label.selected_sequences"));
3320 hideAllButSelection.setLabel(MessageManager
3321 .getString("label.all_but_selected_region"));
3322 hideAllSelection.setLabel(MessageManager
3323 .getString("label.selected_region"));
3324 showAllHidden.setLabel(MessageManager
3325 .getString("label.all_sequences_columns"));
3326 showColumns.addActionListener(this);
3327 showSeqs.addActionListener(this);
3328 hideColumns.addActionListener(this);
3329 hideSequences.addActionListener(this);
3330 hideAllButSelection.addActionListener(this);
3331 hideAllSelection.addActionListener(this);
3332 showAllHidden.addActionListener(this);
3333 featureSettings.setLabel(MessageManager
3334 .getString("action.feature_settings"));
3335 featureSettings.addActionListener(this);
3336 sequenceFeatures.setLabel(MessageManager
3337 .getString("label.show_sequence_features"));
3338 sequenceFeatures.addItemListener(this);
3339 sequenceFeatures.setState(false);
3340 followMouseOverFlag.setLabel(MessageManager
3341 .getString("label.automatic_scrolling"));
3342 followMouseOverFlag.addItemListener(this);
3343 alProperties.addActionListener(this);
3344 overviewMenuItem.setLabel(MessageManager
3345 .getString("label.overview_window"));
3346 overviewMenuItem.addActionListener(this);
3349 * Configure Annotations menu items and actions
3351 annotationPanelMenuItem.setLabel(MessageManager
3352 .getString("label.show_annotations"));
3353 annotationPanelMenuItem.addItemListener(this);
3354 showGroupConsensus.setLabel(MessageManager
3355 .getString("label.group_consensus"));
3356 showGroupConservation.setLabel(MessageManager
3357 .getString("label.group_conservation"));
3358 showConsensusHistogram.setLabel(MessageManager
3359 .getString("label.show_consensus_histogram"));
3360 showSequenceLogo.setLabel(MessageManager
3361 .getString("label.show_consensus_logo"));
3362 normSequenceLogo.setLabel(MessageManager
3363 .getString("label.norm_consensus_logo"));
3364 applyAutoAnnotationSettings.setLabel(MessageManager
3365 .getString("label.apply_all_groups"));
3366 applyAutoAnnotationSettings.setState(true);
3367 Menu autoAnnMenu = new Menu(
3368 MessageManager.getString("label.autocalculated_annotation"));
3369 showGroupConsensus.addItemListener(this);
3370 showGroupConservation.addItemListener(this);
3371 showConsensusHistogram.addItemListener(this);
3372 showSequenceLogo.addItemListener(this);
3373 normSequenceLogo.addItemListener(this);
3374 applyAutoAnnotationSettings.addItemListener(this);
3375 showAlignmentAnnotations = new CheckboxMenuItem(
3376 MessageManager.getString("label.show_all_al_annotations"));
3377 showSequenceAnnotations = new CheckboxMenuItem(
3378 MessageManager.getString("label.show_all_seq_annotations"));
3379 sortAnnBySequence = new CheckboxMenuItem(
3380 MessageManager.getString("label.sort_annotations_by_sequence"));
3381 sortAnnByLabel = new CheckboxMenuItem(
3382 MessageManager.getString("label.sort_annotations_by_label"));
3383 showAutoFirst = new CheckboxMenuItem(
3384 MessageManager.getString("label.show_first"));
3385 showAutoFirst.setState(false); // pending applet parameter
3386 setShowAutoCalculatedAbove(showAutoFirst.getState());
3387 showAutoLast = new CheckboxMenuItem(
3388 MessageManager.getString("label.show_last"));
3389 showAutoLast.setState(!showAutoFirst.getState());
3390 showAlignmentAnnotations.addItemListener(this);
3391 showSequenceAnnotations.addItemListener(this);
3392 sortAnnBySequence.addItemListener(this);
3393 sortAnnByLabel.addItemListener(this);
3394 showAutoFirst.addItemListener(this);
3395 showAutoLast.addItemListener(this);
3398 * Configure Format menu items and actions
3400 font.setLabel(MessageManager.getString("action.font"));
3401 font.addActionListener(this);
3402 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3403 scaleAbove.setState(true);
3404 scaleAbove.setEnabled(false);
3405 scaleAbove.addItemListener(this);
3406 scaleLeft.setEnabled(false);
3407 scaleLeft.setState(true);
3408 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3409 scaleLeft.addItemListener(this);
3410 scaleRight.setEnabled(false);
3411 scaleRight.setState(true);
3412 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3413 scaleRight.addItemListener(this);
3414 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3415 viewBoxesMenuItem.setState(true);
3416 viewBoxesMenuItem.addItemListener(this);
3417 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3418 viewTextMenuItem.setState(true);
3419 viewTextMenuItem.addItemListener(this);
3420 colourTextMenuItem.setLabel(MessageManager
3421 .getString("label.colour_text"));
3422 colourTextMenuItem.addItemListener(this);
3423 displayNonconservedMenuItem.setLabel(MessageManager
3424 .getString("label.show_non_conversed"));
3425 displayNonconservedMenuItem.addItemListener(this);
3426 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3427 wrapMenuItem.addItemListener(this);
3428 renderGapsMenuItem.setLabel(MessageManager
3429 .getString("action.show_gaps"));
3430 renderGapsMenuItem.setState(true);
3431 renderGapsMenuItem.addItemListener(this);
3432 centreColumnLabelFlag.setLabel(MessageManager
3433 .getString("label.centre_column_labels"));
3434 centreColumnLabelFlag.addItemListener(this);
3435 seqLimits.setState(true);
3436 seqLimits.setLabel(MessageManager
3437 .getString("label.show_sequence_limits"));
3438 seqLimits.addItemListener(this);
3441 * Configure Colour menu items and actions
3443 applyToAllGroups.setLabel(MessageManager
3444 .getString("label.apply_colour_to_all_groups"));
3445 applyToAllGroups.setState(true);
3446 applyToAllGroups.addItemListener(this);
3447 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3448 clustalColour.addActionListener(this);
3449 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3450 zappoColour.addActionListener(this);
3451 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3452 taylorColour.addActionListener(this);
3453 hydrophobicityColour.setLabel(MessageManager
3454 .getString("label.hydrophobicity"));
3455 hydrophobicityColour.addActionListener(this);
3457 .setLabel(MessageManager.getString("label.helix_propensity"));
3458 helixColour.addActionListener(this);
3459 strandColour.setLabel(MessageManager
3460 .getString("label.strand_propensity"));
3461 strandColour.addActionListener(this);
3462 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3463 turnColour.addActionListener(this);
3464 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3465 buriedColour.addActionListener(this);
3466 purinePyrimidineColour.setLabel(MessageManager
3467 .getString("label.purine_pyrimidine"));
3468 purinePyrimidineColour.addActionListener(this);
3469 // RNAInteractionColour.setLabel(MessageManager
3470 // .getString("label.rna_interaction"));
3471 // RNAInteractionColour.addActionListener(this);
3472 RNAHelixColour.setLabel(MessageManager
3473 .getString("action.by_rna_helixes"));
3474 RNAHelixColour.addActionListener(this);
3475 userDefinedColour.setLabel(MessageManager
3476 .getString("action.user_defined"));
3477 userDefinedColour.addActionListener(this);
3478 PIDColour.setLabel(MessageManager
3479 .getString("label.percentage_identity"));
3480 PIDColour.addActionListener(this);
3481 BLOSUM62Colour.setLabel(MessageManager
3482 .getString("label.blosum62_score"));
3483 BLOSUM62Colour.addActionListener(this);
3485 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3486 // it will be enabled only if a score file is provided
3487 tcoffeeColour.setEnabled(false);
3488 tcoffeeColour.addActionListener(this);
3489 conservationMenuItem.setLabel(MessageManager
3490 .getString("action.by_conservation"));
3491 conservationMenuItem.addItemListener(this);
3492 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3493 noColourmenuItem.addActionListener(this);
3494 abovePIDThreshold.setLabel(MessageManager
3495 .getString("label.above_identity_threshold"));
3496 abovePIDThreshold.addItemListener(this);
3497 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3498 nucleotideColour.addActionListener(this);
3499 modifyPID.setLabel(MessageManager
3500 .getString("label.modify_identity_thereshold"));
3501 modifyPID.addActionListener(this);
3502 modifyConservation.setLabel(MessageManager
3503 .getString("label.modify_conservation_thereshold"));
3504 modifyConservation.addActionListener(this);
3505 annotationColour.setLabel(MessageManager
3506 .getString("action.by_annotation"));
3507 annotationColour.addActionListener(this);
3510 * Configure Calculate menu items and actions
3512 sortPairwiseMenuItem.setLabel(MessageManager
3513 .getString("action.by_pairwise_id"));
3514 sortPairwiseMenuItem.addActionListener(this);
3515 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3516 sortIDMenuItem.addActionListener(this);
3517 sortLengthMenuItem.setLabel(MessageManager
3518 .getString("action.by_length"));
3519 sortLengthMenuItem.addActionListener(this);
3520 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3521 sortGroupMenuItem.addActionListener(this);
3522 pairwiseAlignmentMenuItem.setLabel(MessageManager
3523 .getString("action.pairwise_alignment"));
3524 pairwiseAlignmentMenuItem.addActionListener(this);
3525 PCAMenuItem.setLabel(MessageManager
3526 .getString("label.principal_component_analysis"));
3527 PCAMenuItem.addActionListener(this);
3528 autoCalculate = new CheckboxMenuItem(
3529 MessageManager.getString("label.autocalculate_consensus"), true);
3530 averageDistanceTreeMenuItem.setLabel(MessageManager
3531 .getString("label.average_distance_identity"));
3532 averageDistanceTreeMenuItem.addActionListener(this);
3533 neighbourTreeMenuItem.setLabel(MessageManager
3534 .getString("label.neighbour_joining_identity"));
3535 neighbourTreeMenuItem.addActionListener(this);
3536 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3537 .getString("label.average_distance_bloslum62"));
3538 avDistanceTreeBlosumMenuItem.addActionListener(this);
3539 njTreeBlosumMenuItem.setLabel(MessageManager
3540 .getString("label.neighbour_blosum62"));
3541 njTreeBlosumMenuItem.addActionListener(this);
3542 sortByTreeMenu.setLabel(MessageManager
3543 .getString("action.by_tree_order"));
3544 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3545 Menu calculateTreeMenu = new Menu(
3546 MessageManager.getString("action.calculate_tree"));
3547 autoCalculate.addItemListener(this);
3548 sortByTree.addItemListener(this);
3551 * Configure Help menu items and actions
3553 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3554 documentation.setLabel(MessageManager.getString("label.documentation"));
3555 documentation.addActionListener(this);
3556 about.setLabel(MessageManager.getString("label.about"));
3557 about.addActionListener(this);
3560 * Add top level menus to frame
3562 alignFrameMenuBar.add(fileMenu);
3563 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3564 alignFrameMenuBar.add(editMenu);
3565 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3566 alignFrameMenuBar.add(selectMenu);
3567 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3568 alignFrameMenuBar.add(viewMenu);
3569 Menu annotationsMenu = new Menu(
3570 MessageManager.getString("action.annotations"));
3571 alignFrameMenuBar.add(annotationsMenu);
3572 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3573 alignFrameMenuBar.add(formatMenu);
3574 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3575 alignFrameMenuBar.add(colourMenu);
3576 Menu calculateMenu = new Menu(
3577 MessageManager.getString("action.calculate"));
3578 alignFrameMenuBar.add(calculateMenu);
3579 alignFrameMenuBar.add(helpMenu);
3584 fileMenu.add(inputText);
3585 fileMenu.add(loadTree);
3586 fileMenu.add(loadAnnotations);
3587 fileMenu.addSeparator();
3588 fileMenu.add(outputTextboxMenu);
3589 fileMenu.add(outputFeatures);
3590 fileMenu.add(outputAnnotations);
3591 if (jalviewServletURL != null)
3593 fileMenu.add(loadApplication);
3595 fileMenu.addSeparator();
3596 fileMenu.add(closeMenuItem);
3601 editMenu.add(undoMenuItem);
3602 editMenu.add(redoMenuItem);
3605 pasteMenu.add(pasteNew);
3606 pasteMenu.add(pasteThis);
3607 editMenu.add(pasteMenu);
3608 editMenu.add(delete);
3609 editMenu.addSeparator();
3610 editMenu.add(remove2LeftMenuItem);
3611 editMenu.add(remove2RightMenuItem);
3612 editMenu.add(removeGappedColumnMenuItem);
3613 editMenu.add(removeAllGapsMenuItem);
3614 editMenu.add(removeRedundancyMenuItem);
3619 selectMenu.add(findMenuItem);
3620 selectMenu.addSeparator();
3621 selectMenu.add(selectAllSequenceMenuItem);
3622 selectMenu.add(deselectAllSequenceMenuItem);
3623 selectMenu.add(invertSequenceMenuItem);
3624 selectMenu.add(invertColSel);
3625 selectMenu.add(createGroup);
3626 selectMenu.add(unGroup);
3627 selectMenu.add(grpsFromSelection);
3628 selectMenu.add(deleteGroups);
3629 selectMenu.add(annotationColumnSelection);
3634 viewMenu.add(newView);
3635 viewMenu.addSeparator();
3636 showMenu.add(showColumns);
3637 showMenu.add(showSeqs);
3638 showMenu.add(showAllHidden);
3639 viewMenu.add(showMenu);
3640 hideMenu.add(hideColumns);
3641 hideMenu.add(hideSequences);
3642 hideMenu.add(hideAllSelection);
3643 hideMenu.add(hideAllButSelection);
3644 viewMenu.add(hideMenu);
3645 viewMenu.addSeparator();
3646 viewMenu.add(followMouseOverFlag);
3647 viewMenu.addSeparator();
3648 viewMenu.add(sequenceFeatures);
3649 viewMenu.add(featureSettings);
3650 viewMenu.addSeparator();
3651 viewMenu.add(alProperties);
3652 viewMenu.addSeparator();
3653 viewMenu.add(overviewMenuItem);
3658 annotationsMenu.add(annotationPanelMenuItem);
3659 annotationsMenu.addSeparator();
3660 annotationsMenu.add(showAlignmentAnnotations);
3661 annotationsMenu.add(showSequenceAnnotations);
3662 annotationsMenu.add(sortAnnBySequence);
3663 annotationsMenu.add(sortAnnByLabel);
3664 annotationsMenu.addSeparator();
3665 autoAnnMenu.add(showAutoFirst);
3666 autoAnnMenu.add(showAutoLast);
3667 autoAnnMenu.addSeparator();
3668 autoAnnMenu.add(applyAutoAnnotationSettings);
3669 autoAnnMenu.add(showConsensusHistogram);
3670 autoAnnMenu.add(showSequenceLogo);
3671 autoAnnMenu.add(normSequenceLogo);
3672 autoAnnMenu.addSeparator();
3673 autoAnnMenu.add(showGroupConservation);
3674 autoAnnMenu.add(showGroupConsensus);
3675 annotationsMenu.add(autoAnnMenu);
3680 formatMenu.add(font);
3681 formatMenu.add(seqLimits);
3682 formatMenu.add(wrapMenuItem);
3683 formatMenu.add(scaleAbove);
3684 formatMenu.add(scaleLeft);
3685 formatMenu.add(scaleRight);
3686 formatMenu.add(viewBoxesMenuItem);
3687 formatMenu.add(viewTextMenuItem);
3688 formatMenu.add(colourTextMenuItem);
3689 formatMenu.add(displayNonconservedMenuItem);
3690 formatMenu.add(renderGapsMenuItem);
3691 formatMenu.add(centreColumnLabelFlag);
3696 colourMenu.add(applyToAllGroups);
3697 colourMenu.addSeparator();
3698 colourMenu.add(noColourmenuItem);
3699 colourMenu.add(clustalColour);
3700 colourMenu.add(BLOSUM62Colour);
3701 colourMenu.add(PIDColour);
3702 colourMenu.add(zappoColour);
3703 colourMenu.add(taylorColour);
3704 colourMenu.add(hydrophobicityColour);
3705 colourMenu.add(helixColour);
3706 colourMenu.add(strandColour);
3707 colourMenu.add(turnColour);
3708 colourMenu.add(buriedColour);
3709 colourMenu.add(nucleotideColour);
3710 colourMenu.add(purinePyrimidineColour);
3711 // colourMenu.add(RNAInteractionColour);
3712 colourMenu.add(tcoffeeColour);
3713 colourMenu.add(userDefinedColour);
3714 colourMenu.addSeparator();
3715 colourMenu.add(conservationMenuItem);
3716 colourMenu.add(modifyConservation);
3717 colourMenu.add(abovePIDThreshold);
3718 colourMenu.add(modifyPID);
3719 colourMenu.add(annotationColour);
3720 colourMenu.add(RNAHelixColour);
3725 sortMenu.add(sortIDMenuItem);
3726 sortMenu.add(sortLengthMenuItem);
3727 sortMenu.add(sortByTreeMenu);
3728 sortMenu.add(sortGroupMenuItem);
3729 sortMenu.add(sortPairwiseMenuItem);
3730 calculateMenu.add(sortMenu);
3731 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3732 calculateTreeMenu.add(neighbourTreeMenuItem);
3733 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3734 calculateTreeMenu.add(njTreeBlosumMenuItem);
3735 calculateMenu.add(calculateTreeMenu);
3736 calculateMenu.addSeparator();
3737 calculateMenu.add(pairwiseAlignmentMenuItem);
3738 calculateMenu.add(PCAMenuItem);
3739 calculateMenu.add(autoCalculate);
3740 calculateMenu.add(sortByTree);
3745 helpMenu.add(documentation);
3746 helpMenu.add(about);
3751 statusBar.setBackground(Color.white);
3752 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3753 statusBar.setText(MessageManager.getString("label.status_bar"));
3754 this.add(statusBar, BorderLayout.SOUTH);
3758 public void setStatus(String string)
3760 statusBar.setText(string);
3763 MenuItem featureSettings = new MenuItem();
3765 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3767 MenuItem annotationColour = new MenuItem();
3769 MenuItem annotationColumnSelection = new MenuItem();
3771 MenuItem invertColSel = new MenuItem();
3773 MenuItem showColumns = new MenuItem();
3775 MenuItem showSeqs = new MenuItem();
3777 MenuItem hideColumns = new MenuItem();
3779 MenuItem hideSequences = new MenuItem();
3781 MenuItem hideAllButSelection = new MenuItem();
3783 MenuItem hideAllSelection = new MenuItem();
3785 MenuItem showAllHidden = new MenuItem();
3787 MenuItem newView = new MenuItem();
3789 private CheckboxMenuItem showAlignmentAnnotations;
3791 private CheckboxMenuItem showSequenceAnnotations;
3793 private CheckboxMenuItem sortAnnBySequence;
3795 private CheckboxMenuItem sortAnnByLabel;
3797 private CheckboxMenuItem showAutoFirst;
3799 private CheckboxMenuItem showAutoLast;
3801 private SplitFrame splitFrame;
3804 * Attach the alignFrame panels after embedding menus, if necessary. This used
3805 * to be called setEmbedded, but is now creates the dropdown menus in a
3806 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3808 * @param reallyEmbedded
3809 * true to attach the view to the applet area on the page rather than
3812 public void createAlignFrameWindow(boolean reallyEmbedded)
3816 embedAlignFrameInApplet(viewport.applet);
3821 // test and embed menu bar if necessary.
3823 if (embedMenuIfNeeded(alignPanel))
3826 * adjust for status bar height too. ? pointless as overridden by layout
3829 alignPanel.setSize(getSize().width,
3830 getSize().height - statusBar.getHeight());
3832 add(statusBar, BorderLayout.SOUTH);
3833 add(alignPanel, BorderLayout.CENTER);
3834 // and register with the applet so it can pass external API calls to us
3835 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3841 * Add the components of this AlignFrame to the applet container.
3845 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3848 // Explicitly build the embedded menu panel for the on-page applet
3850 // view cannot be closed if its actually on the page
3851 fileMenu.remove(closeMenuItem);
3852 fileMenu.remove(3); // Remove Separator
3853 // construct embedded menu, using default font
3854 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3855 // and actually add the components to the applet area
3856 theApplet.setLayout(new BorderLayout());
3857 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3858 theApplet.add(statusBar, BorderLayout.SOUTH);
3859 // TODO should size be left to the layout manager?
3860 alignPanel.setSize(theApplet.getSize().width,
3861 theApplet.getSize().height - embeddedMenu.getHeight()
3862 - statusBar.getHeight());
3863 theApplet.add(alignPanel, BorderLayout.CENTER);
3864 final AlignFrame me = this;
3865 theApplet.addFocusListener(new FocusListener()
3869 public void focusLost(FocusEvent e)
3871 if (theApplet.currentAlignFrame == me)
3873 theApplet.currentAlignFrame = null;
3878 public void focusGained(FocusEvent e)
3880 theApplet.currentAlignFrame = me;
3883 theApplet.validate();
3887 * create a new binding between structures in an existing jmol viewer instance
3888 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3889 * this does not open a new Jmol window, or modify the display of the
3890 * structures in the original jmol window. Note This method doesn't work
3891 * without an additional javascript library to exchange messages between the
3892 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3895 * JmolViewer instance
3896 * @param sequenceIds
3897 * - sequence Ids to search for associations
3899 public SequenceStructureBinding addStructureViewInstance(
3900 Object jmolviewer, String[] sequenceIds)
3902 Viewer viewer = null;
3905 viewer = (Viewer) jmolviewer;
3906 } catch (ClassCastException ex)
3908 System.err.println("Unsupported viewer object :"
3909 + jmolviewer.getClass());
3913 System.err.println("Can't use this object as a structure viewer:"
3914 + jmolviewer.getClass());
3917 SequenceI[] seqs = null;
3918 if (sequenceIds == null || sequenceIds.length == 0)
3920 seqs = viewport.getAlignment().getSequencesArray();
3924 Vector sqi = new Vector();
3925 AlignmentI al = viewport.getAlignment();
3926 for (int sid = 0; sid < sequenceIds.length; sid++)
3928 SequenceI sq = al.findName(sequenceIds[sid]);
3936 seqs = new SequenceI[sqi.size()];
3937 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3939 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3947 AAStructureBindingModel jmv = null;
3948 // TODO: search for a jmv that involves viewer
3950 { // create a new viewer/jalview binding.
3951 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3958 * bind a pdb file to a sequence in the current view
3961 * - sequenceId within the dataset.
3962 * @param pdbEntryString
3963 * - the short name for the PDB file
3965 * - pdb file - either a URL or a valid PDB file.
3966 * @return true if binding was as success TODO: consider making an exception
3967 * structure for indicating when PDB parsing or sequenceId location
3970 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3973 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3974 boolean needtoadd = false;
3975 if (toaddpdb != null)
3977 Vector pdbe = toaddpdb.getAllPDBEntries();
3978 PDBEntry pdbentry = null;
3979 if (pdbe != null && pdbe.size() > 0)
3981 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3983 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3984 if (!pdbentry.getId().equals(pdbEntryString)
3985 && !pdbentry.getFile().equals(pdbFile))
3995 if (pdbentry == null)
3997 pdbentry = new PDBEntry();
3998 pdbentry.setId(pdbEntryString);
3999 pdbentry.setFile(pdbFile);
4000 needtoadd = true; // add this new entry to sequence.
4002 // resolve data source
4003 // TODO: this code should be a refactored to an io package
4004 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4005 if (protocol == null)
4011 // make a note of the access mode and add
4012 if (pdbentry.getProperty() == null)
4014 pdbentry.setProperty(new Hashtable());
4016 pdbentry.getProperty().put("protocol", protocol);
4017 toaddpdb.addPDBId(pdbentry);
4018 alignPanel.getStructureSelectionManager()
4019 .registerPDBEntry(pdbentry);
4025 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4029 Vector sequences = new Vector();
4030 for (int i = 0; i < seqs.length; i++)
4032 if (seqs[i] != null)
4034 sequences.addElement(new Object[] { seqs[i],
4035 (chains != null) ? chains[i] : null });
4038 seqs = new SequenceI[sequences.size()];
4039 chains = new String[sequences.size()];
4040 for (int i = 0, isize = sequences.size(); i < isize; i++)
4042 Object[] oj = (Object[]) sequences.elementAt(i);
4044 seqs[i] = (SequenceI) oj[0];
4045 chains[i] = (String) oj[1];
4048 return new Object[] { seqs, chains };
4052 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4053 SequenceI[] seqs, String[] chains, String protocol)
4055 // Scrub any null sequences from the array
4056 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4057 seqs = (SequenceI[]) sqch[0];
4058 chains = (String[]) sqch[1];
4059 if (seqs == null || seqs.length == 0)
4062 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4064 if (protocol == null || protocol.trim().length() == 0
4065 || protocol.equals("null"))
4067 protocol = (String) pdb.getProperty().get("protocol");
4068 if (protocol == null)
4070 System.err.println("Couldn't work out protocol to open structure: "
4075 if (applet.useXtrnalSviewer)
4077 // register the association(s) and quit, don't create any windows.
4078 if (StructureSelectionManager.getStructureSelectionManager(applet)
4079 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4081 System.err.println("Failed to map " + pdb.getFile() + " ("
4082 + protocol + ") to any sequences");
4086 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4088 // can only do alignments with Jmol
4089 // find the last jmol window assigned to this alignment
4090 jalview.appletgui.AppletJmol ajm = null, tajm;
4091 Vector jmols = applet
4092 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4093 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4095 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4096 if (tajm.ap.alignFrame == this)
4105 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4106 // try and add the pdb structure
4111 // otherwise, create a new window
4112 if (applet.jmolAvailable)
4114 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4116 applet.lastFrameX += 40;
4117 applet.lastFrameY += 40;
4121 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4126 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4127 SequenceI[][] seqs, String[][] chains, String[] protocols)
4129 // TODO Auto-generated method stub
4130 System.err.println("Aligned Structure View: Not yet implemented.");
4134 * modify the current selection, providing the user has not made a selection
4138 * - sequences from this alignment
4140 * - columns to be selected on the alignment
4142 public void select(SequenceGroup sel, ColumnSelection csel)
4144 alignPanel.seqPanel.selection(sel, csel, null);
4147 public void scrollTo(int row, int column)
4149 alignPanel.seqPanel.scrollTo(row, column);
4152 public void scrollToRow(int row)
4154 alignPanel.seqPanel.scrollToRow(row);
4157 public void scrollToColumn(int column)
4159 alignPanel.seqPanel.scrollToColumn(column);
4163 * @return the alignments unique ID.
4165 public String getSequenceSetId()
4167 return viewport.getSequenceSetId();
4171 * Load the (T-Coffee) score file from the specified url
4174 * File/URL/T-COFFEE score file contents
4175 * @throws IOException
4176 * @return true if alignment was annotated with data from source
4178 public boolean loadScoreFile(String source) throws IOException
4181 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4182 AppletFormatAdapter.checkProtocol(source));
4183 if (!file.isValid())
4185 // TODO: raise dialog for gui
4186 System.err.println("Problems parsing T-Coffee scores: "
4187 + file.getWarningMessage());
4188 System.err.println("Origin was:\n" + source);
4193 * check that the score matrix matches the alignment dimensions
4196 if ((aln = viewport.getAlignment()) != null
4197 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4200 // TODO: raise a dialog box here rather than bomb out.
4202 .println("The scores matrix does not match the alignment dimensions");
4206 // TODO add parameter to indicate if matching should be done
4207 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4209 alignPanel.fontChanged();
4210 tcoffeeColour.setEnabled(true);
4211 // switch to this color
4212 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4217 System.err.println("Problems resolving T-Coffee scores:");
4218 if (file.getWarningMessage() != null)
4220 System.err.println(file.getWarningMessage());
4226 public SplitFrame getSplitFrame()
4228 return this.splitFrame;
4231 public void setSplitFrame(SplitFrame sf)
4233 this.splitFrame = sf;
4236 // may not need this
4238 public void setShowSeqFeatures(boolean b)
4240 // showSeqFeatures.setSelected(b);
4241 viewport.setShowSequenceFeatures(b);
4246 public void setMenusForViewport()
4248 // setMenusFromViewport(viewport);
4253 public void refreshFeatureUI(boolean enableIfNecessary)
4255 if (enableIfNecessary)
4257 sequenceFeatures.setState(true);
4258 alignPanel.av.setShowSequenceFeatures(true);
4263 public FeatureSettingsControllerI getFeatureSettingsUI()
4265 return alignPanel.av.featureSettings;