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();
755 viewport.sendSelection();
760 public void keyReleased(KeyEvent evt)
765 public void keyTyped(KeyEvent evt)
770 public void itemStateChanged(ItemEvent evt)
772 final Object source = evt.getSource();
773 if (source == displayNonconservedMenuItem)
775 displayNonconservedMenuItem_actionPerformed();
777 else if (source == colourTextMenuItem)
779 colourTextMenuItem_actionPerformed();
781 else if (source == wrapMenuItem)
783 wrapMenuItem_actionPerformed();
785 else if (source == scaleAbove)
787 viewport.setScaleAboveWrapped(scaleAbove.getState());
789 else if (source == scaleLeft)
791 viewport.setScaleLeftWrapped(scaleLeft.getState());
793 else if (source == scaleRight)
795 viewport.setScaleRightWrapped(scaleRight.getState());
797 else if (source == seqLimits)
799 seqLimits_itemStateChanged();
801 else if (source == viewBoxesMenuItem)
803 viewport.setShowBoxes(viewBoxesMenuItem.getState());
805 else if (source == viewTextMenuItem)
807 viewport.setShowText(viewTextMenuItem.getState());
809 else if (source == renderGapsMenuItem)
811 viewport.setRenderGaps(renderGapsMenuItem.getState());
813 else if (source == annotationPanelMenuItem)
815 boolean showAnnotations = annotationPanelMenuItem.getState();
816 showAlignmentAnnotations.setEnabled(showAnnotations);
817 showSequenceAnnotations.setEnabled(showAnnotations);
818 viewport.setShowAnnotation(showAnnotations);
819 alignPanel.setAnnotationVisible(showAnnotations);
821 else if (source == sequenceFeatures)
823 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
824 alignPanel.seqPanel.seqCanvas.repaint();
826 else if (source == showAlignmentAnnotations)
828 setAnnotationsVisibility();
830 else if (source == showSequenceAnnotations)
832 setAnnotationsVisibility();
834 else if (source == sortAnnBySequence)
836 boolean newState = sortAnnBySequence.getState();
837 sortAnnByLabel.setState(false);
838 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
839 : SequenceAnnotationOrder.NONE);
840 setViewportAnnotationOrder();
842 else if (source == sortAnnByLabel)
844 boolean newState = sortAnnByLabel.getState();
845 sortAnnBySequence.setState(false);
846 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
847 : SequenceAnnotationOrder.NONE);
848 setViewportAnnotationOrder();
850 else if (source == showAutoFirst)
852 showAutoLast.setState(!showAutoFirst.getState());
853 setShowAutoCalculatedAbove(showAutoFirst.getState());
854 setViewportAnnotationOrder();
856 else if (source == showAutoLast)
858 showAutoFirst.setState(!showAutoLast.getState());
859 setShowAutoCalculatedAbove(showAutoFirst.getState());
860 setViewportAnnotationOrder();
862 else if (source == conservationMenuItem)
864 conservationMenuItem_actionPerformed();
866 else if (source == abovePIDThreshold)
868 abovePIDThreshold_actionPerformed();
870 else if (source == applyToAllGroups)
872 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
874 else if (source == autoCalculate)
876 viewport.autoCalculateConsensus = autoCalculate.getState();
878 else if (source == sortByTree)
880 viewport.sortByTree = sortByTree.getState();
882 else if (source == this.centreColumnLabelFlag)
884 centreColumnLabelFlag_stateChanged();
886 else if (source == this.followMouseOverFlag)
888 mouseOverFlag_stateChanged();
890 else if (source == showGroupConsensus)
892 showGroupConsensus_actionPerformed();
894 else if (source == showGroupConservation)
896 showGroupConservation_actionPerformed();
898 else if (source == showSequenceLogo)
900 showSequenceLogo_actionPerformed();
902 else if (source == normSequenceLogo)
904 normSequenceLogo_actionPerformed();
906 else if (source == showConsensusHistogram)
908 showConsensusHistogram_actionPerformed();
910 else if (source == applyAutoAnnotationSettings)
912 applyAutoAnnotationSettings_actionPerformed();
914 alignPanel.paintAlignment(true);
918 * Set the visibility state of sequence-related and/or alignment-related
919 * annotations depending on checkbox selections, and repaint.
923 private void setAnnotationsVisibility()
925 boolean showForAlignment = showAlignmentAnnotations.getState();
926 boolean showForSequences = showSequenceAnnotations.getState();
927 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
929 for (AlignmentAnnotation aa : alignPanel.getAlignment()
930 .getAlignmentAnnotation())
932 boolean visible = (aa.sequenceRef == null ? showForAlignment
934 aa.visible = visible;
937 alignPanel.validateAnnotationDimensions(true);
942 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
944 this.annotationSortOrder = order;
948 * Set flags on the viewport that control annotation ordering
950 private void setViewportAnnotationOrder()
952 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
954 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
957 private void setShowAutoCalculatedAbove(boolean showAbove)
959 this.showAutoCalculatedAbove = showAbove;
962 private void mouseOverFlag_stateChanged()
964 viewport.setFollowHighlight(followMouseOverFlag.getState());
965 // TODO: could kick the scrollTo mechanism to reset view for current
969 private void centreColumnLabelFlag_stateChanged()
971 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
972 this.alignPanel.annotationPanel.repaint();
976 public void actionPerformed(ActionEvent evt)
978 viewport.applet.currentAlignFrame = this;
980 Object source = evt.getSource();
982 if (source == inputText)
984 inputText_actionPerformed();
986 else if (source == loadTree)
988 loadTree_actionPerformed();
990 else if (source == loadApplication)
992 launchFullApplication();
994 else if (source == loadAnnotations)
998 else if (source == outputAnnotations)
1000 outputAnnotations(true);
1002 else if (source == outputFeatures)
1004 outputFeatures(true, "Jalview");
1006 else if (source == closeMenuItem)
1008 closeMenuItem_actionPerformed();
1010 else if (source == copy)
1012 copy_actionPerformed();
1014 else if (source == undoMenuItem)
1016 undoMenuItem_actionPerformed();
1018 else if (source == redoMenuItem)
1020 redoMenuItem_actionPerformed();
1022 else if (source == inputText)
1024 inputText_actionPerformed();
1026 else if (source == closeMenuItem)
1028 closeMenuItem_actionPerformed();
1030 else if (source == undoMenuItem)
1032 undoMenuItem_actionPerformed();
1034 else if (source == redoMenuItem)
1036 redoMenuItem_actionPerformed();
1038 else if (source == copy)
1040 copy_actionPerformed();
1042 else if (source == pasteNew)
1044 pasteNew_actionPerformed();
1046 else if (source == pasteThis)
1048 pasteThis_actionPerformed();
1050 else if (source == cut)
1052 cut_actionPerformed();
1054 else if (source == delete)
1056 delete_actionPerformed();
1058 else if (source == grpsFromSelection)
1060 makeGrpsFromSelection_actionPerformed();
1062 else if (source == deleteGroups)
1064 deleteGroups_actionPerformed();
1066 else if (source == selectAllSequenceMenuItem)
1068 selectAllSequenceMenuItem_actionPerformed();
1070 else if (source == deselectAllSequenceMenuItem)
1072 deselectAllSequenceMenuItem_actionPerformed();
1074 else if (source == invertSequenceMenuItem)
1076 invertSequenceMenuItem_actionPerformed();
1077 // uncomment to slave sequence selections in split frame
1078 // viewport.sendSelection();
1080 else if (source == invertColSel)
1082 viewport.invertColumnSelection();
1083 alignPanel.paintAlignment(true);
1084 viewport.sendSelection();
1086 else if (source == remove2LeftMenuItem)
1088 trimAlignment(true);
1090 else if (source == remove2RightMenuItem)
1092 trimAlignment(false);
1094 else if (source == removeGappedColumnMenuItem)
1096 removeGappedColumnMenuItem_actionPerformed();
1098 else if (source == removeAllGapsMenuItem)
1100 removeAllGapsMenuItem_actionPerformed();
1102 else if (source == findMenuItem)
1104 findMenuItem_actionPerformed();
1106 else if (source == font)
1108 new FontChooser(alignPanel);
1110 else if (source == newView)
1114 else if (source == showColumns)
1116 viewport.showAllHiddenColumns();
1117 alignPanel.paintAlignment(true);
1118 viewport.sendSelection();
1120 else if (source == showSeqs)
1122 viewport.showAllHiddenSeqs();
1123 alignPanel.paintAlignment(true);
1124 // uncomment if we want to slave sequence selections in split frame
1125 // viewport.sendSelection();
1127 else if (source == hideColumns)
1129 viewport.hideSelectedColumns();
1130 alignPanel.paintAlignment(true);
1131 viewport.sendSelection();
1133 else if (source == hideSequences
1134 && viewport.getSelectionGroup() != null)
1136 viewport.hideAllSelectedSeqs();
1137 alignPanel.paintAlignment(true);
1138 // uncomment if we want to slave sequence selections in split frame
1139 // viewport.sendSelection();
1141 else if (source == hideAllButSelection)
1143 toggleHiddenRegions(false, false);
1144 alignPanel.paintAlignment(true);
1145 viewport.sendSelection();
1147 else if (source == hideAllSelection)
1149 SequenceGroup sg = viewport.getSelectionGroup();
1150 viewport.expandColSelection(sg, false);
1151 viewport.hideAllSelectedSeqs();
1152 viewport.hideSelectedColumns();
1153 alignPanel.paintAlignment(true);
1154 viewport.sendSelection();
1156 else if (source == showAllHidden)
1158 viewport.showAllHiddenColumns();
1159 viewport.showAllHiddenSeqs();
1160 alignPanel.paintAlignment(true);
1161 viewport.sendSelection();
1163 else if (source == showGroupConsensus)
1165 showGroupConsensus_actionPerformed();
1167 else if (source == showGroupConservation)
1169 showGroupConservation_actionPerformed();
1171 else if (source == showSequenceLogo)
1173 showSequenceLogo_actionPerformed();
1175 else if (source == normSequenceLogo)
1177 normSequenceLogo_actionPerformed();
1179 else if (source == showConsensusHistogram)
1181 showConsensusHistogram_actionPerformed();
1183 else if (source == applyAutoAnnotationSettings)
1185 applyAutoAnnotationSettings_actionPerformed();
1187 else if (source == featureSettings)
1189 new FeatureSettings(alignPanel);
1191 else if (source == alProperties)
1193 StringBuffer contents = new jalview.io.AlignmentProperties(
1194 viewport.getAlignment()).formatAsString();
1195 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1196 cap.setText(contents.toString());
1197 Frame frame = new Frame();
1199 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1200 "label.alignment_properties", new String[] { getTitle() }),
1203 else if (source == overviewMenuItem)
1205 overviewMenuItem_actionPerformed();
1207 else if (source == noColourmenuItem)
1211 else if (source == clustalColour)
1213 abovePIDThreshold.setState(false);
1214 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1216 else if (source == zappoColour)
1218 changeColour(new ZappoColourScheme());
1220 else if (source == taylorColour)
1222 changeColour(new TaylorColourScheme());
1224 else if (source == hydrophobicityColour)
1226 changeColour(new HydrophobicColourScheme());
1228 else if (source == helixColour)
1230 changeColour(new HelixColourScheme());
1232 else if (source == strandColour)
1234 changeColour(new StrandColourScheme());
1236 else if (source == turnColour)
1238 changeColour(new TurnColourScheme());
1240 else if (source == buriedColour)
1242 changeColour(new BuriedColourScheme());
1244 else if (source == nucleotideColour)
1246 changeColour(new NucleotideColourScheme());
1248 else if (source == purinePyrimidineColour)
1250 changeColour(new PurinePyrimidineColourScheme());
1252 // else if (source == RNAInteractionColour)
1254 // changeColour(new RNAInteractionColourScheme());
1256 else if (source == RNAHelixColour)
1258 new RNAHelicesColourChooser(viewport, alignPanel);
1260 else if (source == modifyPID)
1262 modifyPID_actionPerformed();
1264 else if (source == modifyConservation)
1266 modifyConservation_actionPerformed();
1268 else if (source == userDefinedColour)
1270 new UserDefinedColours(alignPanel, null);
1272 else if (source == PIDColour)
1274 changeColour(new PIDColourScheme());
1276 else if (source == BLOSUM62Colour)
1278 changeColour(new Blosum62ColourScheme());
1280 else if (source == tcoffeeColour)
1282 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1284 else if (source == annotationColour)
1286 new AnnotationColourChooser(viewport, alignPanel);
1288 else if (source == annotationColumnSelection)
1290 new AnnotationColumnChooser(viewport, alignPanel);
1292 else if (source == sortPairwiseMenuItem)
1294 sortPairwiseMenuItem_actionPerformed();
1296 else if (source == sortIDMenuItem)
1298 sortIDMenuItem_actionPerformed();
1300 else if (source == sortLengthMenuItem)
1302 sortLengthMenuItem_actionPerformed();
1304 else if (source == sortGroupMenuItem)
1306 sortGroupMenuItem_actionPerformed();
1308 else if (source == removeRedundancyMenuItem)
1310 removeRedundancyMenuItem_actionPerformed();
1312 else if (source == pairwiseAlignmentMenuItem)
1314 pairwiseAlignmentMenuItem_actionPerformed();
1316 else if (source == PCAMenuItem)
1318 PCAMenuItem_actionPerformed();
1320 else if (source == averageDistanceTreeMenuItem)
1322 averageDistanceTreeMenuItem_actionPerformed();
1324 else if (source == neighbourTreeMenuItem)
1326 neighbourTreeMenuItem_actionPerformed();
1328 else if (source == njTreeBlosumMenuItem)
1330 njTreeBlosumMenuItem_actionPerformed();
1332 else if (source == avDistanceTreeBlosumMenuItem)
1334 avTreeBlosumMenuItem_actionPerformed();
1336 else if (source == documentation)
1338 documentation_actionPerformed();
1340 else if (source == about)
1342 about_actionPerformed();
1347 public void inputText_actionPerformed()
1349 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1350 Frame frame = new Frame();
1352 jalview.bin.JalviewLite.addFrame(frame,
1353 MessageManager.getString("label.input_cut_paste"), 500, 500);
1356 protected void outputText_actionPerformed(ActionEvent e)
1358 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1359 Frame frame = new Frame();
1361 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1362 "label.alignment_output_command",
1363 new Object[] { e.getActionCommand() }), 600, 500);
1365 FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1366 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1367 e.getActionCommand(), viewport.getAlignment(),
1368 viewport.getShowJVSuffix()));
1371 public void loadAnnotations()
1373 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1374 cap.setText(MessageManager
1375 .getString("label.paste_features_annotations_Tcoffee_here"));
1376 cap.setAnnotationImport();
1377 Frame frame = new Frame();
1379 jalview.bin.JalviewLite.addFrame(frame,
1380 MessageManager.getString("action.paste_annotations"), 400, 300);
1384 public String outputAnnotations(boolean displayTextbox)
1386 String annotation = new AnnotationFile()
1387 .printAnnotationsForView(viewport);
1391 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1392 Frame frame = new Frame();
1394 jalview.bin.JalviewLite.addFrame(frame,
1395 MessageManager.getString("label.annotations"), 600, 500);
1396 cap.setText(annotation);
1402 private Map<String, Object> getDisplayedFeatureCols()
1404 if (alignPanel.getFeatureRenderer() != null
1405 && viewport.getFeaturesDisplayed() != null)
1407 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1413 public String outputFeatures(boolean displayTextbox, String format)
1416 FeaturesFile formatter = new FeaturesFile();
1417 if (format.equalsIgnoreCase("Jalview"))
1419 features = formatter.printJalviewFormat(viewport
1420 .getAlignment().getSequencesArray(),
1421 getDisplayedFeatureCols());
1425 features = formatter.printGffFormat(viewport.getAlignment()
1426 .getSequencesArray(), getDisplayedFeatureCols());
1431 boolean frimport = false;
1432 if (features == null || features.equals("No Features Visible"))
1434 features = "# No features visible - paste some and import them here.";
1438 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1441 cap.setAnnotationImport();
1443 Frame frame = new Frame();
1445 jalview.bin.JalviewLite.addFrame(frame,
1446 MessageManager.getString("label.features"), 600, 500);
1447 cap.setText(features);
1451 if (features == null)
1460 void launchFullApplication()
1462 StringBuffer url = new StringBuffer(jalviewServletURL);
1464 // allow servlet parameters to be passed in applet parameter
1465 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1467 url.append(firstSep);
1470 + appendProtocol(viewport.applet.getParameter("file")));
1472 if (viewport.applet.getParameter("features") != null)
1474 url.append("&features=");
1475 url.append(appendProtocol(viewport.applet.getParameter("features")));
1478 if (viewport.applet.getParameter("annotations") != null)
1480 url.append("&annotations=");
1481 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1484 if (viewport.applet.getParameter("jnetfile") != null)
1486 url.append("&annotations=");
1487 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1490 if (viewport.applet.getParameter("defaultColour") != null)
1492 url.append("&colour="
1493 + removeWhiteSpace(viewport.applet
1494 .getParameter("defaultColour")));
1497 if (viewport.applet.getParameter("userDefinedColour") != null)
1499 url.append("&colour="
1500 + removeWhiteSpace(viewport.applet
1501 .getParameter("userDefinedColour")));
1503 if (viewport.applet.getParameter("tree") != null)
1506 + appendProtocol(viewport.applet.getParameter("tree")));
1508 if (viewport.applet.getParameter("treeFile") != null)
1511 + appendProtocol(viewport.applet.getParameter("treeFile")));
1514 showURL(url.toString(), "FULL_APP");
1517 String removeWhiteSpace(String colour)
1519 StringBuffer sb = new StringBuffer();
1520 for (int i = 0; i < colour.length(); i++)
1522 if (Character.isWhitespace(colour.charAt(i)))
1528 sb.append(colour.charAt(i));
1532 return sb.toString();
1535 String appendProtocol(String url)
1540 url = URLEncoder.encode(url);
1543 * When we finally deprecate 1.1 compatibility, we can start to use
1544 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1545 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1546 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1547 * ex.printStackTrace(); }
1549 catch (java.net.MalformedURLException ex)
1551 url = viewport.applet.getCodeBase() + url;
1556 public void closeMenuItem_actionPerformed()
1558 PaintRefresher.RemoveComponent(alignPanel);
1559 if (alignPanel.seqPanel != null
1560 && alignPanel.seqPanel.seqCanvas != null)
1562 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1564 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1566 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1569 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1584 void updateEditMenuBar()
1587 if (viewport.getHistoryList().size() > 0)
1589 undoMenuItem.setEnabled(true);
1590 CommandI command = viewport.getHistoryList().peek();
1591 undoMenuItem.setLabel(MessageManager.formatMessage(
1592 "label.undo_command",
1593 new Object[] { command.getDescription() }));
1597 undoMenuItem.setEnabled(false);
1598 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1601 if (viewport.getRedoList().size() > 0)
1603 redoMenuItem.setEnabled(true);
1605 CommandI command = viewport.getRedoList().peek();
1606 redoMenuItem.setLabel(MessageManager.formatMessage(
1607 "label.redo_command",
1608 new Object[] { command.getDescription() }));
1612 redoMenuItem.setEnabled(false);
1613 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1621 public void addHistoryItem(CommandI command)
1623 if (command.getSize() > 0)
1625 viewport.addToHistoryList(command);
1626 viewport.clearRedoList();
1627 updateEditMenuBar();
1628 viewport.updateHiddenColumns();
1633 * TODO: JAL-1104 DOCUMENT ME!
1638 protected void undoMenuItem_actionPerformed()
1640 if (viewport.getHistoryList().isEmpty())
1645 CommandI command = viewport.getHistoryList().pop();
1646 viewport.addToRedoList(command);
1647 command.undoCommand(null);
1649 AlignmentViewport originalSource = getOriginatingSource(command);
1651 if (originalSource != viewport)
1654 .println("Warning: Viewport object mismatch whilst undoing");
1656 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1657 // viewport.getColumnSelection().getHiddenColumns()
1659 updateEditMenuBar();
1660 originalSource.firePropertyChange("alignment", null, originalSource
1661 .getAlignment().getSequences());
1665 * TODO: JAL-1104 DOCUMENT ME!
1670 protected void redoMenuItem_actionPerformed()
1672 if (viewport.getRedoList().isEmpty())
1677 CommandI command = viewport.getRedoList().pop();
1678 viewport.addToHistoryList(command);
1679 command.doCommand(null);
1681 AlignmentViewport originalSource = getOriginatingSource(command);
1683 if (originalSource != viewport)
1686 .println("Warning: Viewport object mismatch whilst re-doing");
1688 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1689 // viewport.getColumnSelection().getHiddenColumns()
1692 updateEditMenuBar();
1693 originalSource.firePropertyChange("alignment", null, originalSource
1694 .getAlignment().getSequences());
1697 AlignmentViewport getOriginatingSource(CommandI command)
1699 AlignmentViewport originalSource = null;
1700 // For sequence removal and addition, we need to fire
1701 // the property change event FROM the viewport where the
1702 // original alignment was altered
1703 AlignmentI al = null;
1704 if (command instanceof EditCommand)
1706 EditCommand editCommand = (EditCommand) command;
1707 al = editCommand.getAlignment();
1708 Vector comps = (Vector) PaintRefresher.components.get(viewport
1709 .getSequenceSetId());
1710 for (int i = 0; i < comps.size(); i++)
1712 if (comps.elementAt(i) instanceof AlignmentPanel)
1714 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1716 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1723 if (originalSource == null)
1725 // The original view is closed, we must validate
1726 // the current view against the closed view first
1729 PaintRefresher.validateSequences(al, viewport.getAlignment());
1732 originalSource = viewport;
1735 return originalSource;
1739 * Move the currently selected sequences up or down one position in the
1744 public void moveSelectedSequences(boolean up)
1746 SequenceGroup sg = viewport.getSelectionGroup();
1751 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1752 up ? null : viewport.getHiddenRepSequences(), up);
1753 alignPanel.paintAlignment(true);
1756 * Also move cDNA/protein complement sequences
1758 AlignViewportI complement = viewport.getCodingComplement();
1759 if (complement != null)
1761 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1762 viewport, complement);
1763 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1764 up ? null : complement.getHiddenRepSequences(), up);
1765 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1769 synchronized void slideSequences(boolean right, int size)
1771 List<SequenceI> sg = new Vector<SequenceI>();
1772 if (viewport.cursorMode)
1774 sg.add(viewport.getAlignment().getSequenceAt(
1775 alignPanel.seqPanel.seqCanvas.cursorY));
1777 else if (viewport.getSelectionGroup() != null
1778 && viewport.getSelectionGroup().getSize() != viewport
1779 .getAlignment().getHeight())
1781 sg = viewport.getSelectionGroup().getSequences(
1782 viewport.getHiddenRepSequences());
1790 Vector<SequenceI> invertGroup = new Vector();
1792 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1794 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1796 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1800 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1802 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1804 for (int i = 0; i < invertGroup.size(); i++)
1806 seqs2[i] = invertGroup.elementAt(i);
1809 SlideSequencesCommand ssc;
1812 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1813 size, viewport.getGapCharacter());
1817 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1818 size, viewport.getGapCharacter());
1821 int groupAdjustment = 0;
1822 if (ssc.getGapsInsertedBegin() && right)
1824 if (viewport.cursorMode)
1826 alignPanel.seqPanel.moveCursor(size, 0);
1830 groupAdjustment = size;
1833 else if (!ssc.getGapsInsertedBegin() && !right)
1835 if (viewport.cursorMode)
1837 alignPanel.seqPanel.moveCursor(-size, 0);
1841 groupAdjustment = -size;
1845 if (groupAdjustment != 0)
1847 viewport.getSelectionGroup().setStartRes(
1848 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1849 viewport.getSelectionGroup().setEndRes(
1850 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1853 boolean appendHistoryItem = false;
1854 Deque<CommandI> historyList = viewport.getHistoryList();
1855 if (historyList != null && historyList.size() > 0
1856 && historyList.peek() instanceof SlideSequencesCommand)
1858 appendHistoryItem = ssc
1859 .appendSlideCommand((SlideSequencesCommand) historyList
1863 if (!appendHistoryItem)
1865 addHistoryItem(ssc);
1871 static StringBuffer copiedSequences;
1873 static Vector copiedHiddenColumns;
1875 protected void copy_actionPerformed()
1877 if (viewport.getSelectionGroup() == null)
1882 SequenceGroup sg = viewport.getSelectionGroup();
1883 copiedSequences = new StringBuffer();
1884 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1885 for (int i = 0; i < sg.getSize(); i++)
1887 SequenceI seq = sg.getSequenceAt(i);
1888 int index = viewport.getAlignment().findIndex(seq);
1889 orderedSeqs.put(index, seq);
1892 int index = 0, startRes, endRes;
1895 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1897 copiedHiddenColumns = new Vector();
1898 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1899 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1901 copiedHiddenColumns.addElement(new int[] {
1902 region[0] - hiddenOffset, region[1] - hiddenOffset });
1907 copiedHiddenColumns = null;
1910 for (int i = 0; i < sg.getSize(); i++)
1912 SequenceI seq = null;
1916 if (orderedSeqs.containsKey(index))
1918 seq = orderedSeqs.get(index);
1929 // Returns residue following index if gap
1930 startRes = seq.findPosition(sg.getStartRes());
1933 // Need to find the residue preceeding index if gap
1936 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1938 ch = seq.getCharAt(j);
1939 if (!jalview.util.Comparison.isGap((ch)))
1947 endRes += seq.getStart() - 1;
1950 copiedSequences.append(seq.getName()
1956 + seq.getSequenceAsString(sg.getStartRes(),
1957 sg.getEndRes() + 1) + "\n");
1962 protected void pasteNew_actionPerformed()
1967 protected void pasteThis_actionPerformed()
1972 void paste(boolean newAlignment)
1977 if (copiedSequences == null)
1982 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1983 Vector seqs = new Vector();
1984 while (st.hasMoreElements())
1986 String name = st.nextToken();
1987 int start = Integer.parseInt(st.nextToken());
1988 int end = Integer.parseInt(st.nextToken());
1989 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1991 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1992 for (int i = 0; i < seqs.size(); i++)
1994 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1999 String newtitle = MessageManager
2000 .getString("label.copied_sequences");
2001 if (getTitle().startsWith(
2002 MessageManager.getString("label.copied_sequences")))
2004 newtitle = getTitle();
2008 newtitle = newtitle.concat(MessageManager.formatMessage(
2009 "label.from_msname", new String[] { getTitle() }));
2011 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2012 viewport.applet, newtitle, false);
2013 if (copiedHiddenColumns != null)
2015 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2017 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2018 af.viewport.hideColumns(region[0], region[1]);
2022 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2027 addSequences(newSeqs);
2030 } catch (Exception ex)
2032 } // could be anything being pasted in here
2036 void addSequences(SequenceI[] seqs)
2038 for (int i = 0; i < seqs.length; i++)
2040 viewport.getAlignment().addSequence(seqs[i]);
2044 addHistoryItem(new EditCommand(
2045 MessageManager.getString("label.add_sequences"), Action.PASTE,
2046 seqs, 0, viewport.getAlignment().getWidth(),
2047 viewport.getAlignment()));
2049 viewport.setEndSeq(viewport.getAlignment().getHeight());
2050 viewport.getAlignment().getWidth();
2051 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2056 protected void cut_actionPerformed()
2058 copy_actionPerformed();
2059 delete_actionPerformed();
2062 protected void delete_actionPerformed()
2065 SequenceGroup sg = viewport.getSelectionGroup();
2071 Vector seqs = new Vector();
2073 for (int i = 0; i < sg.getSize(); i++)
2075 seq = sg.getSequenceAt(i);
2076 seqs.addElement(seq);
2080 * If the cut affects all sequences, warn, remove highlighted columns
2082 if (sg.getSize() == viewport.getAlignment().getHeight())
2084 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2085 .getAlignment().getWidth()) ? true : false;
2086 if (isEntireAlignWidth)
2088 String title = MessageManager.getString("label.delete_all");
2089 Panel infoPanel = new Panel();
2090 infoPanel.setLayout(new FlowLayout());
2092 .add(new Label(MessageManager.getString("warn.delete_all")));
2094 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2095 dialog.setMainPanel(infoPanel);
2096 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2097 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2098 dialog.setVisible(true);
2105 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2106 sg.getEndRes() + 1);
2109 SequenceI[] cut = new SequenceI[seqs.size()];
2110 for (int i = 0; i < seqs.size(); i++)
2112 cut[i] = (SequenceI) seqs.elementAt(i);
2116 * //ADD HISTORY ITEM
2118 addHistoryItem(new EditCommand(
2119 MessageManager.getString("label.cut_sequences"), Action.CUT,
2120 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2121 viewport.getAlignment()));
2123 viewport.setSelectionGroup(null);
2124 viewport.getAlignment().deleteGroup(sg);
2126 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2129 if (viewport.getAlignment().getHeight() < 1)
2131 this.setVisible(false);
2133 viewport.sendSelection();
2137 * group consensus toggled
2140 protected void showGroupConsensus_actionPerformed()
2142 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2143 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2148 * group conservation toggled.
2150 protected void showGroupConservation_actionPerformed()
2152 viewport.setShowGroupConservation(showGroupConservation.getState());
2153 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2160 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2161 * .event.ActionEvent)
2163 protected void showConsensusHistogram_actionPerformed()
2165 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2166 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2173 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2174 * .event.ActionEvent)
2176 protected void showSequenceLogo_actionPerformed()
2178 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2179 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2182 protected void normSequenceLogo_actionPerformed()
2184 showSequenceLogo.setState(true);
2185 viewport.setShowSequenceLogo(true);
2186 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2187 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2190 protected void applyAutoAnnotationSettings_actionPerformed()
2192 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2195 protected void makeGrpsFromSelection_actionPerformed()
2197 if (avc.makeGroupsFromSelection())
2199 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2200 alignPanel.updateAnnotation();
2201 alignPanel.paintAlignment(true);
2205 protected void createGroup_actionPerformed()
2210 protected void unGroup_actionPerformed()
2214 alignPanel.alignmentChanged();
2218 protected void deleteGroups_actionPerformed()
2220 if (avc.deleteGroups())
2222 alignPanel.alignmentChanged();
2226 public void selectAllSequenceMenuItem_actionPerformed()
2228 SequenceGroup sg = new SequenceGroup();
2229 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2231 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2233 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2234 viewport.setSelectionGroup(sg);
2235 alignPanel.paintAlignment(true);
2236 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2237 viewport.sendSelection();
2240 public void deselectAllSequenceMenuItem_actionPerformed()
2242 if (viewport.cursorMode)
2244 alignPanel.seqPanel.keyboardNo1 = null;
2245 alignPanel.seqPanel.keyboardNo2 = null;
2247 viewport.setSelectionGroup(null);
2248 viewport.getColumnSelection().clear();
2249 viewport.setSelectionGroup(null);
2250 alignPanel.idPanel.idCanvas.searchResults = null;
2251 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2252 alignPanel.paintAlignment(true);
2253 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2254 viewport.sendSelection();
2257 public void invertSequenceMenuItem_actionPerformed()
2259 SequenceGroup sg = viewport.getSelectionGroup();
2260 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2262 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2265 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2266 viewport.sendSelection();
2269 public void invertColSel_actionPerformed()
2271 viewport.invertColumnSelection();
2272 alignPanel.paintAlignment(true);
2273 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2274 viewport.sendSelection();
2277 void trimAlignment(boolean trimLeft)
2279 ColumnSelection colSel = viewport.getColumnSelection();
2282 if (!colSel.isEmpty())
2286 column = colSel.getMin();
2290 column = colSel.getMax();
2294 if (viewport.getSelectionGroup() != null)
2296 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2297 viewport.getHiddenRepSequences());
2301 seqs = viewport.getAlignment().getSequencesArray();
2304 TrimRegionCommand trimRegion;
2307 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2308 column, viewport.getAlignment());
2309 viewport.setStartRes(0);
2313 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2314 column, viewport.getAlignment());
2317 statusBar.setText(MessageManager.formatMessage(
2318 "label.removed_columns",
2319 new String[] { Integer.valueOf(trimRegion.getSize())
2321 addHistoryItem(trimRegion);
2323 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2325 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2326 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2328 viewport.getAlignment().deleteGroup(sg);
2332 viewport.firePropertyChange("alignment", null, viewport
2333 .getAlignment().getSequences());
2337 public void removeGappedColumnMenuItem_actionPerformed()
2339 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2342 if (viewport.getSelectionGroup() != null)
2344 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2345 viewport.getHiddenRepSequences());
2346 start = viewport.getSelectionGroup().getStartRes();
2347 end = viewport.getSelectionGroup().getEndRes();
2351 seqs = viewport.getAlignment().getSequencesArray();
2354 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2355 "Remove Gapped Columns", seqs, start, end,
2356 viewport.getAlignment());
2358 addHistoryItem(removeGapCols);
2360 statusBar.setText(MessageManager.formatMessage(
2361 "label.removed_empty_columns",
2362 new String[] { Integer.valueOf(removeGapCols.getSize())
2365 // This is to maintain viewport position on first residue
2366 // of first sequence
2367 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2368 int startRes = seq.findPosition(viewport.startRes);
2369 // ShiftList shifts;
2370 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2371 // edit.alColumnChanges=shifts.getInverse();
2372 // if (viewport.hasHiddenColumns)
2373 // viewport.getColumnSelection().compensateForEdits(shifts);
2374 viewport.setStartRes(seq.findIndex(startRes) - 1);
2375 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2380 public void removeAllGapsMenuItem_actionPerformed()
2382 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2385 if (viewport.getSelectionGroup() != null)
2387 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2388 viewport.getHiddenRepSequences());
2389 start = viewport.getSelectionGroup().getStartRes();
2390 end = viewport.getSelectionGroup().getEndRes();
2394 seqs = viewport.getAlignment().getSequencesArray();
2397 // This is to maintain viewport position on first residue
2398 // of first sequence
2399 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2400 int startRes = seq.findPosition(viewport.startRes);
2402 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2403 viewport.getAlignment()));
2405 viewport.setStartRes(seq.findIndex(startRes) - 1);
2407 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2412 public void findMenuItem_actionPerformed()
2414 new Finder(alignPanel);
2418 * create a new view derived from the current view
2421 * @return frame for the new view
2423 public AlignFrame newView(String viewtitle)
2426 if (viewport.hasHiddenRows())
2428 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2429 .getFullAlignment().getSequencesArray());
2433 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2436 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2438 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2440 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2442 newal.addAnnotation(viewport.getAlignment()
2443 .getAlignmentAnnotation()[i]);
2448 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2450 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2451 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2452 PaintRefresher.Register(newaf.alignPanel,
2453 newaf.alignPanel.av.getSequenceSetId());
2455 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2456 newaf.alignPanel.av.getSequenceSetId());
2457 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2458 newaf.alignPanel.av.getSequenceSetId());
2460 Vector comps = (Vector) PaintRefresher.components.get(viewport
2461 .getSequenceSetId());
2463 for (int i = 0; i < comps.size(); i++)
2465 if (comps.elementAt(i) instanceof AlignmentPanel)
2471 String title = new String(this.getTitle());
2472 if (viewtitle != null)
2474 title = viewtitle + " ( " + title + ")";
2478 if (title.indexOf("(View") > -1)
2480 title = title.substring(0, title.indexOf("(View"));
2482 title += "(View " + viewSize + ")";
2485 newaf.setTitle(title.toString());
2487 newaf.viewport.setHistoryList(viewport.getHistoryList());
2488 newaf.viewport.setRedoList(viewport.getRedoList());
2494 * @return list of feature groups on the view
2496 public String[] getFeatureGroups()
2498 FeatureRenderer fr = null;
2499 if (alignPanel != null
2500 && (fr = alignPanel.getFeatureRenderer()) != null)
2502 List<String> gps = fr.getFeatureGroups();
2503 String[] _gps = gps.toArray(new String[gps.size()]);
2510 * get sequence feature groups that are hidden or shown
2516 public String[] getFeatureGroupsOfState(boolean visible)
2518 FeatureRenderer fr = null;
2519 if (alignPanel != null
2520 && (fr = alignPanel.getFeatureRenderer()) != null)
2522 List<String> gps = fr.getGroups(visible);
2523 String[] _gps = gps.toArray(new String[gps.size()]);
2530 * Change the display state for the given feature groups
2533 * list of group strings
2535 * visible or invisible
2537 public void setFeatureGroupState(String[] groups, boolean state)
2539 FeatureRenderer fr = null;
2540 this.sequenceFeatures.setState(true);
2541 viewport.setShowSequenceFeatures(true);
2542 if (alignPanel != null
2543 && (fr = alignPanel.getFeatureRenderer()) != null)
2546 fr.setGroupVisibility(Arrays.asList(groups), state);
2547 alignPanel.seqPanel.seqCanvas.repaint();
2548 if (alignPanel.overviewPanel != null)
2550 alignPanel.overviewPanel.updateOverviewImage();
2555 public void seqLimits_itemStateChanged()
2557 viewport.setShowJVSuffix(seqLimits.getState());
2558 alignPanel.fontChanged();
2559 alignPanel.paintAlignment(true);
2562 protected void colourTextMenuItem_actionPerformed()
2564 viewport.setColourText(colourTextMenuItem.getState());
2565 alignPanel.paintAlignment(true);
2568 protected void displayNonconservedMenuItem_actionPerformed()
2570 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2571 alignPanel.paintAlignment(true);
2574 protected void wrapMenuItem_actionPerformed()
2576 viewport.setWrapAlignment(wrapMenuItem.getState());
2577 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2578 scaleAbove.setEnabled(wrapMenuItem.getState());
2579 scaleLeft.setEnabled(wrapMenuItem.getState());
2580 scaleRight.setEnabled(wrapMenuItem.getState());
2581 alignPanel.paintAlignment(true);
2584 public void overviewMenuItem_actionPerformed()
2586 if (alignPanel.overviewPanel != null)
2591 Frame frame = new Frame();
2592 OverviewPanel overview = new OverviewPanel(alignPanel);
2593 frame.add(overview);
2594 // +50 must allow for applet frame window
2595 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2596 "label.overview_params", new String[] { this.getTitle() }),
2597 overview.getPreferredSize().width,
2598 overview.getPreferredSize().height + 50);
2601 final AlignmentPanel ap = alignPanel;
2602 frame.addWindowListener(new WindowAdapter()
2605 public void windowClosing(WindowEvent e)
2609 ap.setOverviewPanel(null);
2614 alignPanel.setOverviewPanel(overview);
2619 public void changeColour(ColourSchemeI cs)
2624 if (viewport.getAbovePIDThreshold())
2626 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2630 if (viewport.getConservationSelected())
2632 cs.setConservationApplied(true);
2633 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2638 cs.setConservationApplied(false);
2641 viewport.setGlobalColourScheme(cs);
2643 alignPanel.paintAlignment(true);
2646 protected void modifyPID_actionPerformed()
2648 if (viewport.getAbovePIDThreshold()
2649 && viewport.getGlobalColourScheme() != null)
2651 SliderPanel.setPIDSliderSource(alignPanel,
2652 viewport.getGlobalColourScheme(), "Background");
2653 SliderPanel.showPIDSlider();
2657 protected void modifyConservation_actionPerformed()
2659 if (viewport.getConservationSelected()
2660 && viewport.getGlobalColourScheme() != null)
2662 SliderPanel.setConservationSlider(alignPanel,
2663 viewport.getGlobalColourScheme(), "Background");
2664 SliderPanel.showConservationSlider();
2668 protected void conservationMenuItem_actionPerformed()
2670 viewport.setConservationSelected(conservationMenuItem.getState());
2672 viewport.setAbovePIDThreshold(false);
2673 abovePIDThreshold.setState(false);
2675 changeColour(viewport.getGlobalColourScheme());
2677 modifyConservation_actionPerformed();
2680 public void abovePIDThreshold_actionPerformed()
2682 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2684 conservationMenuItem.setState(false);
2685 viewport.setConservationSelected(false);
2687 changeColour(viewport.getGlobalColourScheme());
2689 modifyPID_actionPerformed();
2692 public void sortPairwiseMenuItem_actionPerformed()
2694 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2695 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2696 .getAlignment().getSequenceAt(0), null);
2698 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2699 viewport.getAlignment()));
2700 alignPanel.paintAlignment(true);
2703 public void sortIDMenuItem_actionPerformed()
2705 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2706 AlignmentSorter.sortByID(viewport.getAlignment());
2707 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2708 viewport.getAlignment()));
2709 alignPanel.paintAlignment(true);
2712 public void sortLengthMenuItem_actionPerformed()
2714 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2715 AlignmentSorter.sortByLength(viewport.getAlignment());
2716 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2717 viewport.getAlignment()));
2718 alignPanel.paintAlignment(true);
2721 public void sortGroupMenuItem_actionPerformed()
2723 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2724 AlignmentSorter.sortByGroup(viewport.getAlignment());
2725 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2726 viewport.getAlignment()));
2727 alignPanel.paintAlignment(true);
2731 public void removeRedundancyMenuItem_actionPerformed()
2733 new RedundancyPanel(alignPanel);
2736 public void pairwiseAlignmentMenuItem_actionPerformed()
2738 if (viewport.getSelectionGroup() != null
2739 && viewport.getSelectionGroup().getSize() > 1)
2741 Frame frame = new Frame();
2742 frame.add(new PairwiseAlignPanel(alignPanel));
2743 jalview.bin.JalviewLite.addFrame(frame,
2744 MessageManager.getString("action.pairwise_alignment"), 600,
2749 public void PCAMenuItem_actionPerformed()
2751 // are the sequences aligned?
2752 if (!viewport.getAlignment().isAligned(false))
2755 int Width = viewport.getAlignment().getWidth();
2757 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2759 current = viewport.getAlignment().getSequenceAt(i);
2761 if (current.getLength() < Width)
2763 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2766 alignPanel.paintAlignment(true);
2769 if ((viewport.getSelectionGroup() != null
2770 && viewport.getSelectionGroup().getSize() < 4 && viewport
2771 .getSelectionGroup().getSize() > 0)
2772 || viewport.getAlignment().getHeight() < 4)
2779 new PCAPanel(viewport);
2780 } catch (java.lang.OutOfMemoryError ex)
2786 public void averageDistanceTreeMenuItem_actionPerformed()
2788 NewTreePanel("AV", "PID", "Average distance tree using PID");
2791 public void neighbourTreeMenuItem_actionPerformed()
2793 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2796 protected void njTreeBlosumMenuItem_actionPerformed()
2798 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2801 protected void avTreeBlosumMenuItem_actionPerformed()
2803 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2806 void NewTreePanel(String type, String pwType, String title)
2808 // are the sequences aligned?
2809 if (!viewport.getAlignment().isAligned(false))
2812 int Width = viewport.getAlignment().getWidth();
2814 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2816 current = viewport.getAlignment().getSequenceAt(i);
2818 if (current.getLength() < Width)
2820 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2823 alignPanel.paintAlignment(true);
2827 if ((viewport.getSelectionGroup() != null && viewport
2828 .getSelectionGroup().getSize() > 1)
2829 || (viewport.getAlignment().getHeight() > 1))
2831 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2833 addTreeMenuItem(tp, title);
2835 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2839 void loadTree_actionPerformed()
2841 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2842 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2843 cap.setTreeImport();
2844 Frame frame = new Frame();
2846 jalview.bin.JalviewLite.addFrame(frame,
2847 MessageManager.getString("label.paste_newick_file"), 400, 300);
2850 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2852 TreePanel tp = new TreePanel(alignPanel, treeFile,
2853 MessageManager.getString("label.load_tree_from_file"), tree);
2854 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2855 addTreeMenuItem(tp, treeFile);
2859 * sort the alignment using the given treePanel
2862 * tree used to sort view
2864 * string used for undo event name
2866 public void sortByTree(TreePanel treePanel, String title)
2868 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2870 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2871 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2872 // HistoryItem.SORT));
2873 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2874 "label.order_by_params", new String[] { title }), oldOrder,
2875 viewport.getAlignment()));
2876 alignPanel.paintAlignment(true);
2880 * Do any automatic reordering of the alignment and add the necessary bits to
2881 * the menu structure for the new tree
2886 protected void addTreeMenuItem(final TreePanel treePanel,
2889 final MenuItem item = new MenuItem(title);
2890 sortByTreeMenu.add(item);
2891 item.addActionListener(new java.awt.event.ActionListener()
2894 public void actionPerformed(ActionEvent evt)
2896 sortByTree(treePanel, title); // treePanel.getTitle());
2900 treePanel.addWindowListener(new WindowAdapter()
2903 public void windowOpened(WindowEvent e)
2905 if (viewport.sortByTree)
2907 sortByTree(treePanel, title);
2909 super.windowOpened(e);
2913 public void windowClosing(WindowEvent e)
2915 sortByTreeMenu.remove(item);
2920 public boolean sortBy(AlignmentOrder alorder, String undoname)
2922 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2923 if (viewport.applet.debug)
2925 System.err.println("Sorting " + alorder.getOrder().size()
2926 + " in alignment '" + getTitle() + "'");
2928 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2929 if (undoname != null)
2931 addHistoryItem(new OrderCommand(undoname, oldOrder,
2932 viewport.getAlignment()));
2934 alignPanel.paintAlignment(true);
2938 protected void documentation_actionPerformed()
2940 alignPanel.av.applet.openJalviewHelpUrl();
2943 protected void about_actionPerformed()
2946 class AboutPanel extends Canvas
2952 public AboutPanel(String version, String builddate)
2954 this.version = version;
2955 this.builddate = builddate;
2959 public void paint(Graphics g)
2961 g.setColor(Color.white);
2962 g.fillRect(0, 0, getSize().width, getSize().height);
2963 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2964 FontMetrics fm = g.getFontMetrics();
2965 int fh = fm.getHeight();
2967 g.setColor(Color.black);
2968 // TODO: update this text for each release or centrally store it for
2969 // lite and application
2970 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2971 g.drawString(MessageManager.formatMessage(
2972 "label.jalviewLite_release", new String[] { version }), x,
2974 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2975 g.drawString(MessageManager.formatMessage(
2976 "label.jaview_build_date", new String[] { builddate }), x,
2978 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2979 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2981 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2982 x + 50, y += fh + 8);
2984 MessageManager.getString("label.jalview_dev_managers"), x,
2986 g.drawString(MessageManager
2987 .getString("label.jalview_distribution_lists"), x, y += fh);
2988 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2991 MessageManager.getString("label.jalview_cite_1_authors"),
2994 MessageManager.getString("label.jalview_cite_1_title"), x,
2996 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3001 Frame frame = new Frame();
3002 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3004 jalview.bin.JalviewLite.addFrame(frame,
3005 MessageManager.getString("label.jalview"), 580, 220);
3009 public void showURL(String url, String target)
3011 if (viewport.applet == null)
3013 System.out.println("Not running as applet - no browser available.");
3017 viewport.applet.showURL(url, target);
3021 // ////////////////////////////////////////////////////////////////////////////////
3022 // JBuilder Graphics here
3024 MenuBar alignFrameMenuBar = new MenuBar();
3026 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3028 MenuItem loadApplication = new MenuItem(
3029 MessageManager.getString("label.view_full_application"));
3031 MenuItem loadTree = new MenuItem(
3032 MessageManager.getString("label.load_associated_tree"));
3034 MenuItem loadAnnotations = new MenuItem(
3035 MessageManager.getString("label.load_features_annotations"));
3037 MenuItem outputFeatures = new MenuItem(
3038 MessageManager.getString("label.export_features"));
3040 MenuItem outputAnnotations = new MenuItem(
3041 MessageManager.getString("label.export_annotations"));
3043 MenuItem closeMenuItem = new MenuItem(
3044 MessageManager.getString("action.close"));
3046 MenuItem selectAllSequenceMenuItem = new MenuItem(
3047 MessageManager.getString("action.select_all"));
3049 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3050 MessageManager.getString("action.deselect_all"));
3052 MenuItem invertSequenceMenuItem = new MenuItem(
3053 MessageManager.getString("action.invert_selection"));
3055 MenuItem remove2LeftMenuItem = new MenuItem();
3057 MenuItem remove2RightMenuItem = new MenuItem();
3059 MenuItem removeGappedColumnMenuItem = new MenuItem();
3061 MenuItem removeAllGapsMenuItem = new MenuItem();
3063 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3065 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3067 MenuItem sortPairwiseMenuItem = new MenuItem();
3069 MenuItem sortIDMenuItem = new MenuItem();
3071 MenuItem sortLengthMenuItem = new MenuItem();
3073 MenuItem sortGroupMenuItem = new MenuItem();
3075 MenuItem removeRedundancyMenuItem = new MenuItem();
3077 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3079 MenuItem PCAMenuItem = new MenuItem();
3081 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3083 MenuItem neighbourTreeMenuItem = new MenuItem();
3085 BorderLayout borderLayout1 = new BorderLayout();
3087 public Label statusBar = new Label();
3089 MenuItem clustalColour = new MenuItem();
3091 MenuItem zappoColour = new MenuItem();
3093 MenuItem taylorColour = new MenuItem();
3095 MenuItem hydrophobicityColour = new MenuItem();
3097 MenuItem helixColour = new MenuItem();
3099 MenuItem strandColour = new MenuItem();
3101 MenuItem turnColour = new MenuItem();
3103 MenuItem buriedColour = new MenuItem();
3105 MenuItem purinePyrimidineColour = new MenuItem();
3107 // MenuItem RNAInteractionColour = new MenuItem();
3109 MenuItem RNAHelixColour = new MenuItem();
3111 MenuItem userDefinedColour = new MenuItem();
3113 MenuItem PIDColour = new MenuItem();
3115 MenuItem BLOSUM62Colour = new MenuItem();
3117 MenuItem tcoffeeColour = new MenuItem();
3119 MenuItem njTreeBlosumMenuItem = new MenuItem();
3121 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3123 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3125 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3127 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3129 MenuItem alProperties = new MenuItem(
3130 MessageManager.getString("label.alignment_props"));
3132 MenuItem overviewMenuItem = new MenuItem();
3134 MenuItem undoMenuItem = new MenuItem();
3136 MenuItem redoMenuItem = new MenuItem();
3138 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3140 MenuItem noColourmenuItem = new MenuItem();
3142 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3144 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3146 MenuItem findMenuItem = new MenuItem();
3148 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3150 MenuItem nucleotideColour = new MenuItem();
3152 MenuItem deleteGroups = new MenuItem();
3154 MenuItem grpsFromSelection = new MenuItem();
3156 MenuItem createGroup = new MenuItem();
3158 MenuItem unGroup = new MenuItem();
3160 MenuItem delete = new MenuItem();
3162 MenuItem copy = new MenuItem();
3164 MenuItem cut = new MenuItem();
3166 Menu pasteMenu = new Menu();
3168 MenuItem pasteNew = new MenuItem();
3170 MenuItem pasteThis = new MenuItem();
3172 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3174 MenuItem font = new MenuItem();
3176 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3178 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3180 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3182 MenuItem modifyPID = new MenuItem();
3184 MenuItem modifyConservation = new MenuItem();
3186 CheckboxMenuItem autoCalculate = null;
3188 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3189 "Sort Alignment With New Tree", true);
3191 Menu sortByTreeMenu = new Menu();
3193 MenuItem inputText = new MenuItem();
3195 MenuItem documentation = new MenuItem();
3197 MenuItem about = new MenuItem();
3199 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3201 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3203 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3205 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3207 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3209 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3211 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3213 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3215 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3218 * Initialise menus and other items
3222 private void jbInit() throws Exception
3224 setMenuBar(alignFrameMenuBar);
3227 * Configure File menu items and actions
3230 .setLabel(MessageManager.getString("label.input_from_textbox"));
3231 inputText.addActionListener(this);
3232 Menu outputTextboxMenu = new Menu(
3233 MessageManager.getString("label.out_to_textbox"));
3234 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3237 MenuItem item = new MenuItem(
3238 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3240 item.addActionListener(new java.awt.event.ActionListener()
3243 public void actionPerformed(ActionEvent e)
3245 outputText_actionPerformed(e);
3249 outputTextboxMenu.add(item);
3251 closeMenuItem.addActionListener(this);
3252 loadApplication.addActionListener(this);
3253 loadTree.addActionListener(this);
3254 loadAnnotations.addActionListener(this);
3255 outputFeatures.addActionListener(this);
3256 outputAnnotations.addActionListener(this);
3259 * Configure Edit menu items and actions
3261 undoMenuItem.setEnabled(false);
3262 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3263 undoMenuItem.addActionListener(this);
3264 redoMenuItem.setEnabled(false);
3265 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3266 redoMenuItem.addActionListener(this);
3267 copy.setLabel(MessageManager.getString("action.copy"));
3268 copy.addActionListener(this);
3269 cut.setLabel(MessageManager.getString("action.cut"));
3270 cut.addActionListener(this);
3271 delete.setLabel(MessageManager.getString("action.delete"));
3272 delete.addActionListener(this);
3273 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3274 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3275 pasteNew.addActionListener(this);
3276 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3277 pasteThis.addActionListener(this);
3278 remove2LeftMenuItem.setLabel(MessageManager
3279 .getString("action.remove_left"));
3280 remove2LeftMenuItem.addActionListener(this);
3281 remove2RightMenuItem.setLabel(MessageManager
3282 .getString("action.remove_right"));
3283 remove2RightMenuItem.addActionListener(this);
3284 removeGappedColumnMenuItem.setLabel(MessageManager
3285 .getString("action.remove_empty_columns"));
3286 removeGappedColumnMenuItem.addActionListener(this);
3287 removeAllGapsMenuItem.setLabel(MessageManager
3288 .getString("action.remove_all_gaps"));
3289 removeAllGapsMenuItem.addActionListener(this);
3290 removeRedundancyMenuItem.setLabel(MessageManager
3291 .getString("action.remove_redundancy"));
3292 removeRedundancyMenuItem.addActionListener(this);
3295 * Configure Select menu items and actions
3297 findMenuItem.setLabel(MessageManager.getString("action.find"));
3298 findMenuItem.addActionListener(this);
3299 selectAllSequenceMenuItem.addActionListener(this);
3300 deselectAllSequenceMenuItem.addActionListener(this);
3301 invertSequenceMenuItem.setLabel(MessageManager
3302 .getString("action.invert_sequence_selection"));
3303 invertSequenceMenuItem.addActionListener(this);
3304 invertColSel.setLabel(MessageManager
3305 .getString("action.invert_column_selection"));
3306 invertColSel.addActionListener(this);
3307 deleteGroups.setLabel(MessageManager
3308 .getString("action.undefine_groups"));
3309 deleteGroups.addActionListener(this);
3310 grpsFromSelection.setLabel(MessageManager
3311 .getString("action.make_groups_selection"));
3312 grpsFromSelection.addActionListener(this);
3313 createGroup.setLabel(MessageManager.getString("action.create_group"));
3314 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3315 annotationColumnSelection.setLabel(MessageManager
3316 .getString("action.select_by_annotation"));
3317 annotationColumnSelection.addActionListener(this);
3320 * Configure View menu items and actions
3322 newView.setLabel(MessageManager.getString("action.new_view"));
3323 newView.addActionListener(this);
3324 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3325 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3326 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3327 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3329 .setLabel(MessageManager.getString("label.selected_columns"));
3330 hideSequences.setLabel(MessageManager
3331 .getString("label.selected_sequences"));
3332 hideAllButSelection.setLabel(MessageManager
3333 .getString("label.all_but_selected_region"));
3334 hideAllSelection.setLabel(MessageManager
3335 .getString("label.selected_region"));
3336 showAllHidden.setLabel(MessageManager
3337 .getString("label.all_sequences_columns"));
3338 showColumns.addActionListener(this);
3339 showSeqs.addActionListener(this);
3340 hideColumns.addActionListener(this);
3341 hideSequences.addActionListener(this);
3342 hideAllButSelection.addActionListener(this);
3343 hideAllSelection.addActionListener(this);
3344 showAllHidden.addActionListener(this);
3345 featureSettings.setLabel(MessageManager
3346 .getString("action.feature_settings"));
3347 featureSettings.addActionListener(this);
3348 sequenceFeatures.setLabel(MessageManager
3349 .getString("label.show_sequence_features"));
3350 sequenceFeatures.addItemListener(this);
3351 sequenceFeatures.setState(false);
3352 followMouseOverFlag.setLabel(MessageManager
3353 .getString("label.automatic_scrolling"));
3354 followMouseOverFlag.addItemListener(this);
3355 alProperties.addActionListener(this);
3356 overviewMenuItem.setLabel(MessageManager
3357 .getString("label.overview_window"));
3358 overviewMenuItem.addActionListener(this);
3361 * Configure Annotations menu items and actions
3363 annotationPanelMenuItem.setLabel(MessageManager
3364 .getString("label.show_annotations"));
3365 annotationPanelMenuItem.addItemListener(this);
3366 showGroupConsensus.setLabel(MessageManager
3367 .getString("label.group_consensus"));
3368 showGroupConservation.setLabel(MessageManager
3369 .getString("label.group_conservation"));
3370 showConsensusHistogram.setLabel(MessageManager
3371 .getString("label.show_consensus_histogram"));
3372 showSequenceLogo.setLabel(MessageManager
3373 .getString("label.show_consensus_logo"));
3374 normSequenceLogo.setLabel(MessageManager
3375 .getString("label.norm_consensus_logo"));
3376 applyAutoAnnotationSettings.setLabel(MessageManager
3377 .getString("label.apply_all_groups"));
3378 applyAutoAnnotationSettings.setState(true);
3379 Menu autoAnnMenu = new Menu(
3380 MessageManager.getString("label.autocalculated_annotation"));
3381 showGroupConsensus.addItemListener(this);
3382 showGroupConservation.addItemListener(this);
3383 showConsensusHistogram.addItemListener(this);
3384 showSequenceLogo.addItemListener(this);
3385 normSequenceLogo.addItemListener(this);
3386 applyAutoAnnotationSettings.addItemListener(this);
3387 showAlignmentAnnotations = new CheckboxMenuItem(
3388 MessageManager.getString("label.show_all_al_annotations"));
3389 showSequenceAnnotations = new CheckboxMenuItem(
3390 MessageManager.getString("label.show_all_seq_annotations"));
3391 sortAnnBySequence = new CheckboxMenuItem(
3392 MessageManager.getString("label.sort_annotations_by_sequence"));
3393 sortAnnByLabel = new CheckboxMenuItem(
3394 MessageManager.getString("label.sort_annotations_by_label"));
3395 showAutoFirst = new CheckboxMenuItem(
3396 MessageManager.getString("label.show_first"));
3397 showAutoFirst.setState(false); // pending applet parameter
3398 setShowAutoCalculatedAbove(showAutoFirst.getState());
3399 showAutoLast = new CheckboxMenuItem(
3400 MessageManager.getString("label.show_last"));
3401 showAutoLast.setState(!showAutoFirst.getState());
3402 showAlignmentAnnotations.addItemListener(this);
3403 showSequenceAnnotations.addItemListener(this);
3404 sortAnnBySequence.addItemListener(this);
3405 sortAnnByLabel.addItemListener(this);
3406 showAutoFirst.addItemListener(this);
3407 showAutoLast.addItemListener(this);
3410 * Configure Format menu items and actions
3412 font.setLabel(MessageManager.getString("action.font"));
3413 font.addActionListener(this);
3414 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3415 scaleAbove.setState(true);
3416 scaleAbove.setEnabled(false);
3417 scaleAbove.addItemListener(this);
3418 scaleLeft.setEnabled(false);
3419 scaleLeft.setState(true);
3420 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3421 scaleLeft.addItemListener(this);
3422 scaleRight.setEnabled(false);
3423 scaleRight.setState(true);
3424 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3425 scaleRight.addItemListener(this);
3426 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3427 viewBoxesMenuItem.setState(true);
3428 viewBoxesMenuItem.addItemListener(this);
3429 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3430 viewTextMenuItem.setState(true);
3431 viewTextMenuItem.addItemListener(this);
3432 colourTextMenuItem.setLabel(MessageManager
3433 .getString("label.colour_text"));
3434 colourTextMenuItem.addItemListener(this);
3435 displayNonconservedMenuItem.setLabel(MessageManager
3436 .getString("label.show_non_conversed"));
3437 displayNonconservedMenuItem.addItemListener(this);
3438 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3439 wrapMenuItem.addItemListener(this);
3440 renderGapsMenuItem.setLabel(MessageManager
3441 .getString("action.show_gaps"));
3442 renderGapsMenuItem.setState(true);
3443 renderGapsMenuItem.addItemListener(this);
3444 centreColumnLabelFlag.setLabel(MessageManager
3445 .getString("label.centre_column_labels"));
3446 centreColumnLabelFlag.addItemListener(this);
3447 seqLimits.setState(true);
3448 seqLimits.setLabel(MessageManager
3449 .getString("label.show_sequence_limits"));
3450 seqLimits.addItemListener(this);
3453 * Configure Colour menu items and actions
3455 applyToAllGroups.setLabel(MessageManager
3456 .getString("label.apply_colour_to_all_groups"));
3457 applyToAllGroups.setState(true);
3458 applyToAllGroups.addItemListener(this);
3459 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3460 clustalColour.addActionListener(this);
3461 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3462 zappoColour.addActionListener(this);
3463 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3464 taylorColour.addActionListener(this);
3465 hydrophobicityColour.setLabel(MessageManager
3466 .getString("label.hydrophobicity"));
3467 hydrophobicityColour.addActionListener(this);
3469 .setLabel(MessageManager.getString("label.helix_propensity"));
3470 helixColour.addActionListener(this);
3471 strandColour.setLabel(MessageManager
3472 .getString("label.strand_propensity"));
3473 strandColour.addActionListener(this);
3474 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3475 turnColour.addActionListener(this);
3476 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3477 buriedColour.addActionListener(this);
3478 purinePyrimidineColour.setLabel(MessageManager
3479 .getString("label.purine_pyrimidine"));
3480 purinePyrimidineColour.addActionListener(this);
3481 // RNAInteractionColour.setLabel(MessageManager
3482 // .getString("label.rna_interaction"));
3483 // RNAInteractionColour.addActionListener(this);
3484 RNAHelixColour.setLabel(MessageManager
3485 .getString("action.by_rna_helixes"));
3486 RNAHelixColour.addActionListener(this);
3487 userDefinedColour.setLabel(MessageManager
3488 .getString("action.user_defined"));
3489 userDefinedColour.addActionListener(this);
3490 PIDColour.setLabel(MessageManager
3491 .getString("label.percentage_identity"));
3492 PIDColour.addActionListener(this);
3493 BLOSUM62Colour.setLabel(MessageManager
3494 .getString("label.blosum62_score"));
3495 BLOSUM62Colour.addActionListener(this);
3497 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3498 // it will be enabled only if a score file is provided
3499 tcoffeeColour.setEnabled(false);
3500 tcoffeeColour.addActionListener(this);
3501 conservationMenuItem.setLabel(MessageManager
3502 .getString("action.by_conservation"));
3503 conservationMenuItem.addItemListener(this);
3504 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3505 noColourmenuItem.addActionListener(this);
3506 abovePIDThreshold.setLabel(MessageManager
3507 .getString("label.above_identity_threshold"));
3508 abovePIDThreshold.addItemListener(this);
3509 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3510 nucleotideColour.addActionListener(this);
3511 modifyPID.setLabel(MessageManager
3512 .getString("label.modify_identity_thereshold"));
3513 modifyPID.addActionListener(this);
3514 modifyConservation.setLabel(MessageManager
3515 .getString("label.modify_conservation_thereshold"));
3516 modifyConservation.addActionListener(this);
3517 annotationColour.setLabel(MessageManager
3518 .getString("action.by_annotation"));
3519 annotationColour.addActionListener(this);
3522 * Configure Calculate menu items and actions
3524 sortPairwiseMenuItem.setLabel(MessageManager
3525 .getString("action.by_pairwise_id"));
3526 sortPairwiseMenuItem.addActionListener(this);
3527 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3528 sortIDMenuItem.addActionListener(this);
3529 sortLengthMenuItem.setLabel(MessageManager
3530 .getString("action.by_length"));
3531 sortLengthMenuItem.addActionListener(this);
3532 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3533 sortGroupMenuItem.addActionListener(this);
3534 pairwiseAlignmentMenuItem.setLabel(MessageManager
3535 .getString("action.pairwise_alignment"));
3536 pairwiseAlignmentMenuItem.addActionListener(this);
3537 PCAMenuItem.setLabel(MessageManager
3538 .getString("label.principal_component_analysis"));
3539 PCAMenuItem.addActionListener(this);
3540 autoCalculate = new CheckboxMenuItem(
3541 MessageManager.getString("label.autocalculate_consensus"), true);
3542 averageDistanceTreeMenuItem.setLabel(MessageManager
3543 .getString("label.average_distance_identity"));
3544 averageDistanceTreeMenuItem.addActionListener(this);
3545 neighbourTreeMenuItem.setLabel(MessageManager
3546 .getString("label.neighbour_joining_identity"));
3547 neighbourTreeMenuItem.addActionListener(this);
3548 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3549 .getString("label.average_distance_bloslum62"));
3550 avDistanceTreeBlosumMenuItem.addActionListener(this);
3551 njTreeBlosumMenuItem.setLabel(MessageManager
3552 .getString("label.neighbour_blosum62"));
3553 njTreeBlosumMenuItem.addActionListener(this);
3554 sortByTreeMenu.setLabel(MessageManager
3555 .getString("action.by_tree_order"));
3556 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3557 Menu calculateTreeMenu = new Menu(
3558 MessageManager.getString("action.calculate_tree"));
3559 autoCalculate.addItemListener(this);
3560 sortByTree.addItemListener(this);
3563 * Configure Help menu items and actions
3565 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3566 documentation.setLabel(MessageManager.getString("label.documentation"));
3567 documentation.addActionListener(this);
3568 about.setLabel(MessageManager.getString("label.about"));
3569 about.addActionListener(this);
3572 * Add top level menus to frame
3574 alignFrameMenuBar.add(fileMenu);
3575 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3576 alignFrameMenuBar.add(editMenu);
3577 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3578 alignFrameMenuBar.add(selectMenu);
3579 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3580 alignFrameMenuBar.add(viewMenu);
3581 Menu annotationsMenu = new Menu(
3582 MessageManager.getString("action.annotations"));
3583 alignFrameMenuBar.add(annotationsMenu);
3584 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3585 alignFrameMenuBar.add(formatMenu);
3586 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3587 alignFrameMenuBar.add(colourMenu);
3588 Menu calculateMenu = new Menu(
3589 MessageManager.getString("action.calculate"));
3590 alignFrameMenuBar.add(calculateMenu);
3591 alignFrameMenuBar.add(helpMenu);
3596 fileMenu.add(inputText);
3597 fileMenu.add(loadTree);
3598 fileMenu.add(loadAnnotations);
3599 fileMenu.addSeparator();
3600 fileMenu.add(outputTextboxMenu);
3601 fileMenu.add(outputFeatures);
3602 fileMenu.add(outputAnnotations);
3603 if (jalviewServletURL != null)
3605 fileMenu.add(loadApplication);
3607 fileMenu.addSeparator();
3608 fileMenu.add(closeMenuItem);
3613 editMenu.add(undoMenuItem);
3614 editMenu.add(redoMenuItem);
3617 pasteMenu.add(pasteNew);
3618 pasteMenu.add(pasteThis);
3619 editMenu.add(pasteMenu);
3620 editMenu.add(delete);
3621 editMenu.addSeparator();
3622 editMenu.add(remove2LeftMenuItem);
3623 editMenu.add(remove2RightMenuItem);
3624 editMenu.add(removeGappedColumnMenuItem);
3625 editMenu.add(removeAllGapsMenuItem);
3626 editMenu.add(removeRedundancyMenuItem);
3631 selectMenu.add(findMenuItem);
3632 selectMenu.addSeparator();
3633 selectMenu.add(selectAllSequenceMenuItem);
3634 selectMenu.add(deselectAllSequenceMenuItem);
3635 selectMenu.add(invertSequenceMenuItem);
3636 selectMenu.add(invertColSel);
3637 selectMenu.add(createGroup);
3638 selectMenu.add(unGroup);
3639 selectMenu.add(grpsFromSelection);
3640 selectMenu.add(deleteGroups);
3641 selectMenu.add(annotationColumnSelection);
3646 viewMenu.add(newView);
3647 viewMenu.addSeparator();
3648 showMenu.add(showColumns);
3649 showMenu.add(showSeqs);
3650 showMenu.add(showAllHidden);
3651 viewMenu.add(showMenu);
3652 hideMenu.add(hideColumns);
3653 hideMenu.add(hideSequences);
3654 hideMenu.add(hideAllSelection);
3655 hideMenu.add(hideAllButSelection);
3656 viewMenu.add(hideMenu);
3657 viewMenu.addSeparator();
3658 viewMenu.add(followMouseOverFlag);
3659 viewMenu.addSeparator();
3660 viewMenu.add(sequenceFeatures);
3661 viewMenu.add(featureSettings);
3662 viewMenu.addSeparator();
3663 viewMenu.add(alProperties);
3664 viewMenu.addSeparator();
3665 viewMenu.add(overviewMenuItem);
3670 annotationsMenu.add(annotationPanelMenuItem);
3671 annotationsMenu.addSeparator();
3672 annotationsMenu.add(showAlignmentAnnotations);
3673 annotationsMenu.add(showSequenceAnnotations);
3674 annotationsMenu.add(sortAnnBySequence);
3675 annotationsMenu.add(sortAnnByLabel);
3676 annotationsMenu.addSeparator();
3677 autoAnnMenu.add(showAutoFirst);
3678 autoAnnMenu.add(showAutoLast);
3679 autoAnnMenu.addSeparator();
3680 autoAnnMenu.add(applyAutoAnnotationSettings);
3681 autoAnnMenu.add(showConsensusHistogram);
3682 autoAnnMenu.add(showSequenceLogo);
3683 autoAnnMenu.add(normSequenceLogo);
3684 autoAnnMenu.addSeparator();
3685 autoAnnMenu.add(showGroupConservation);
3686 autoAnnMenu.add(showGroupConsensus);
3687 annotationsMenu.add(autoAnnMenu);
3692 formatMenu.add(font);
3693 formatMenu.add(seqLimits);
3694 formatMenu.add(wrapMenuItem);
3695 formatMenu.add(scaleAbove);
3696 formatMenu.add(scaleLeft);
3697 formatMenu.add(scaleRight);
3698 formatMenu.add(viewBoxesMenuItem);
3699 formatMenu.add(viewTextMenuItem);
3700 formatMenu.add(colourTextMenuItem);
3701 formatMenu.add(displayNonconservedMenuItem);
3702 formatMenu.add(renderGapsMenuItem);
3703 formatMenu.add(centreColumnLabelFlag);
3708 colourMenu.add(applyToAllGroups);
3709 colourMenu.addSeparator();
3710 colourMenu.add(noColourmenuItem);
3711 colourMenu.add(clustalColour);
3712 colourMenu.add(BLOSUM62Colour);
3713 colourMenu.add(PIDColour);
3714 colourMenu.add(zappoColour);
3715 colourMenu.add(taylorColour);
3716 colourMenu.add(hydrophobicityColour);
3717 colourMenu.add(helixColour);
3718 colourMenu.add(strandColour);
3719 colourMenu.add(turnColour);
3720 colourMenu.add(buriedColour);
3721 colourMenu.add(nucleotideColour);
3722 colourMenu.add(purinePyrimidineColour);
3723 // colourMenu.add(RNAInteractionColour);
3724 colourMenu.add(tcoffeeColour);
3725 colourMenu.add(userDefinedColour);
3726 colourMenu.addSeparator();
3727 colourMenu.add(conservationMenuItem);
3728 colourMenu.add(modifyConservation);
3729 colourMenu.add(abovePIDThreshold);
3730 colourMenu.add(modifyPID);
3731 colourMenu.add(annotationColour);
3732 colourMenu.add(RNAHelixColour);
3737 sortMenu.add(sortIDMenuItem);
3738 sortMenu.add(sortLengthMenuItem);
3739 sortMenu.add(sortByTreeMenu);
3740 sortMenu.add(sortGroupMenuItem);
3741 sortMenu.add(sortPairwiseMenuItem);
3742 calculateMenu.add(sortMenu);
3743 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3744 calculateTreeMenu.add(neighbourTreeMenuItem);
3745 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3746 calculateTreeMenu.add(njTreeBlosumMenuItem);
3747 calculateMenu.add(calculateTreeMenu);
3748 calculateMenu.addSeparator();
3749 calculateMenu.add(pairwiseAlignmentMenuItem);
3750 calculateMenu.add(PCAMenuItem);
3751 calculateMenu.add(autoCalculate);
3752 calculateMenu.add(sortByTree);
3757 helpMenu.add(documentation);
3758 helpMenu.add(about);
3763 statusBar.setBackground(Color.white);
3764 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3765 statusBar.setText(MessageManager.getString("label.status_bar"));
3766 this.add(statusBar, BorderLayout.SOUTH);
3770 public void setStatus(String string)
3772 statusBar.setText(string);
3775 MenuItem featureSettings = new MenuItem();
3777 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3779 MenuItem annotationColour = new MenuItem();
3781 MenuItem annotationColumnSelection = new MenuItem();
3783 MenuItem invertColSel = new MenuItem();
3785 MenuItem showColumns = new MenuItem();
3787 MenuItem showSeqs = new MenuItem();
3789 MenuItem hideColumns = new MenuItem();
3791 MenuItem hideSequences = new MenuItem();
3793 MenuItem hideAllButSelection = new MenuItem();
3795 MenuItem hideAllSelection = new MenuItem();
3797 MenuItem showAllHidden = new MenuItem();
3799 MenuItem newView = new MenuItem();
3801 private CheckboxMenuItem showAlignmentAnnotations;
3803 private CheckboxMenuItem showSequenceAnnotations;
3805 private CheckboxMenuItem sortAnnBySequence;
3807 private CheckboxMenuItem sortAnnByLabel;
3809 private CheckboxMenuItem showAutoFirst;
3811 private CheckboxMenuItem showAutoLast;
3813 private SplitFrame splitFrame;
3816 * Attach the alignFrame panels after embedding menus, if necessary. This used
3817 * to be called setEmbedded, but is now creates the dropdown menus in a
3818 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3820 * @param reallyEmbedded
3821 * true to attach the view to the applet area on the page rather than
3824 public void createAlignFrameWindow(boolean reallyEmbedded)
3828 embedAlignFrameInApplet(viewport.applet);
3833 // test and embed menu bar if necessary.
3835 if (embedMenuIfNeeded(alignPanel))
3838 * adjust for status bar height too. ? pointless as overridden by layout
3841 alignPanel.setSize(getSize().width,
3842 getSize().height - statusBar.getHeight());
3844 add(statusBar, BorderLayout.SOUTH);
3845 add(alignPanel, BorderLayout.CENTER);
3846 // and register with the applet so it can pass external API calls to us
3847 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3853 * Add the components of this AlignFrame to the applet container.
3857 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3860 // Explicitly build the embedded menu panel for the on-page applet
3862 // view cannot be closed if its actually on the page
3863 fileMenu.remove(closeMenuItem);
3864 fileMenu.remove(3); // Remove Separator
3865 // construct embedded menu, using default font
3866 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3867 // and actually add the components to the applet area
3868 theApplet.setLayout(new BorderLayout());
3869 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3870 theApplet.add(statusBar, BorderLayout.SOUTH);
3871 // TODO should size be left to the layout manager?
3872 alignPanel.setSize(theApplet.getSize().width,
3873 theApplet.getSize().height - embeddedMenu.getHeight()
3874 - statusBar.getHeight());
3875 theApplet.add(alignPanel, BorderLayout.CENTER);
3876 final AlignFrame me = this;
3877 theApplet.addFocusListener(new FocusListener()
3881 public void focusLost(FocusEvent e)
3883 if (theApplet.currentAlignFrame == me)
3885 theApplet.currentAlignFrame = null;
3890 public void focusGained(FocusEvent e)
3892 theApplet.currentAlignFrame = me;
3895 theApplet.validate();
3899 * create a new binding between structures in an existing jmol viewer instance
3900 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3901 * this does not open a new Jmol window, or modify the display of the
3902 * structures in the original jmol window. Note This method doesn't work
3903 * without an additional javascript library to exchange messages between the
3904 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3907 * JmolViewer instance
3908 * @param sequenceIds
3909 * - sequence Ids to search for associations
3911 public SequenceStructureBinding addStructureViewInstance(
3912 Object jmolviewer, String[] sequenceIds)
3914 Viewer viewer = null;
3917 viewer = (Viewer) jmolviewer;
3918 } catch (ClassCastException ex)
3920 System.err.println("Unsupported viewer object :"
3921 + jmolviewer.getClass());
3925 System.err.println("Can't use this object as a structure viewer:"
3926 + jmolviewer.getClass());
3929 SequenceI[] seqs = null;
3930 if (sequenceIds == null || sequenceIds.length == 0)
3932 seqs = viewport.getAlignment().getSequencesArray();
3936 Vector sqi = new Vector();
3937 AlignmentI al = viewport.getAlignment();
3938 for (int sid = 0; sid < sequenceIds.length; sid++)
3940 SequenceI sq = al.findName(sequenceIds[sid]);
3948 seqs = new SequenceI[sqi.size()];
3949 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3951 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3959 AAStructureBindingModel jmv = null;
3960 // TODO: search for a jmv that involves viewer
3962 { // create a new viewer/jalview binding.
3963 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3970 * bind a pdb file to a sequence in the current view
3973 * - sequenceId within the dataset.
3974 * @param pdbEntryString
3975 * - the short name for the PDB file
3977 * - pdb file - either a URL or a valid PDB file.
3978 * @return true if binding was as success TODO: consider making an exception
3979 * structure for indicating when PDB parsing or sequenceId location
3982 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3985 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3986 boolean needtoadd = false;
3987 if (toaddpdb != null)
3989 Vector pdbe = toaddpdb.getAllPDBEntries();
3990 PDBEntry pdbentry = null;
3991 if (pdbe != null && pdbe.size() > 0)
3993 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3995 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3996 if (!pdbentry.getId().equals(pdbEntryString)
3997 && !pdbentry.getFile().equals(pdbFile))
4007 if (pdbentry == null)
4009 pdbentry = new PDBEntry();
4010 pdbentry.setId(pdbEntryString);
4011 pdbentry.setFile(pdbFile);
4012 needtoadd = true; // add this new entry to sequence.
4014 // resolve data source
4015 // TODO: this code should be a refactored to an io package
4016 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4017 if (protocol == null)
4023 // make a note of the access mode and add
4024 if (pdbentry.getProperty() == null)
4026 pdbentry.setProperty(new Hashtable());
4028 pdbentry.getProperty().put("protocol", protocol);
4029 toaddpdb.addPDBId(pdbentry);
4030 alignPanel.getStructureSelectionManager()
4031 .registerPDBEntry(pdbentry);
4037 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4041 Vector sequences = new Vector();
4042 for (int i = 0; i < seqs.length; i++)
4044 if (seqs[i] != null)
4046 sequences.addElement(new Object[] { seqs[i],
4047 (chains != null) ? chains[i] : null });
4050 seqs = new SequenceI[sequences.size()];
4051 chains = new String[sequences.size()];
4052 for (int i = 0, isize = sequences.size(); i < isize; i++)
4054 Object[] oj = (Object[]) sequences.elementAt(i);
4056 seqs[i] = (SequenceI) oj[0];
4057 chains[i] = (String) oj[1];
4060 return new Object[] { seqs, chains };
4064 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4065 SequenceI[] seqs, String[] chains, String protocol)
4067 // Scrub any null sequences from the array
4068 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4069 seqs = (SequenceI[]) sqch[0];
4070 chains = (String[]) sqch[1];
4071 if (seqs == null || seqs.length == 0)
4074 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4076 if (protocol == null || protocol.trim().length() == 0
4077 || protocol.equals("null"))
4079 protocol = (String) pdb.getProperty().get("protocol");
4080 if (protocol == null)
4082 System.err.println("Couldn't work out protocol to open structure: "
4087 if (applet.useXtrnalSviewer)
4089 // register the association(s) and quit, don't create any windows.
4090 if (StructureSelectionManager.getStructureSelectionManager(applet)
4091 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4093 System.err.println("Failed to map " + pdb.getFile() + " ("
4094 + protocol + ") to any sequences");
4098 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4100 // can only do alignments with Jmol
4101 // find the last jmol window assigned to this alignment
4102 jalview.appletgui.AppletJmol ajm = null, tajm;
4103 Vector jmols = applet
4104 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4105 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4107 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4108 if (tajm.ap.alignFrame == this)
4117 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4118 // try and add the pdb structure
4123 // otherwise, create a new window
4124 if (applet.jmolAvailable)
4126 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4128 applet.lastFrameX += 40;
4129 applet.lastFrameY += 40;
4133 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4138 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4139 SequenceI[][] seqs, String[][] chains, String[] protocols)
4141 // TODO Auto-generated method stub
4142 System.err.println("Aligned Structure View: Not yet implemented.");
4146 * modify the current selection, providing the user has not made a selection
4150 * - sequences from this alignment
4152 * - columns to be selected on the alignment
4154 public void select(SequenceGroup sel, ColumnSelection csel)
4156 alignPanel.seqPanel.selection(sel, csel, null);
4159 public void scrollTo(int row, int column)
4161 alignPanel.seqPanel.scrollTo(row, column);
4164 public void scrollToRow(int row)
4166 alignPanel.seqPanel.scrollToRow(row);
4169 public void scrollToColumn(int column)
4171 alignPanel.seqPanel.scrollToColumn(column);
4175 * @return the alignments unique ID.
4177 public String getSequenceSetId()
4179 return viewport.getSequenceSetId();
4183 * Load the (T-Coffee) score file from the specified url
4186 * File/URL/T-COFFEE score file contents
4187 * @throws IOException
4188 * @return true if alignment was annotated with data from source
4190 public boolean loadScoreFile(String source) throws IOException
4193 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4194 AppletFormatAdapter.checkProtocol(source));
4195 if (!file.isValid())
4197 // TODO: raise dialog for gui
4198 System.err.println("Problems parsing T-Coffee scores: "
4199 + file.getWarningMessage());
4200 System.err.println("Origin was:\n" + source);
4205 * check that the score matrix matches the alignment dimensions
4208 if ((aln = viewport.getAlignment()) != null
4209 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4212 // TODO: raise a dialog box here rather than bomb out.
4214 .println("The scores matrix does not match the alignment dimensions");
4218 // TODO add parameter to indicate if matching should be done
4219 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4221 alignPanel.fontChanged();
4222 tcoffeeColour.setEnabled(true);
4223 // switch to this color
4224 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4229 System.err.println("Problems resolving T-Coffee scores:");
4230 if (file.getWarningMessage() != null)
4232 System.err.println(file.getWarningMessage());
4238 public SplitFrame getSplitFrame()
4240 return this.splitFrame;
4243 public void setSplitFrame(SplitFrame sf)
4245 this.splitFrame = sf;
4248 // may not need this
4250 public void setShowSeqFeatures(boolean b)
4252 // showSeqFeatures.setSelected(b);
4253 viewport.setShowSequenceFeatures(b);
4258 public void setMenusForViewport()
4260 // setMenusFromViewport(viewport);
4265 public void refreshFeatureUI(boolean enableIfNecessary)
4267 if (enableIfNecessary)
4269 sequenceFeatures.setState(true);
4270 alignPanel.av.setShowSequenceFeatures(true);
4275 public FeatureSettingsControllerI getFeatureSettingsUI()
4277 return alignPanel.av.featureSettings;